Daily Papers

Foundation models have progressed from learning and reasoning over existing knowledge, to increasingly learning through action, tool use, and outcome feedback. We argue that the next frontier is a further transition: from solving and acting within problems specified by humans to participating in the process by which new problems, representations, explanations, and knowledge are created. We refer to this capability as Discovery Intelligence. We formulate Discovery Foundation Models (DFMs) as general-purpose model systems for open-ended discovery. A DFM operates over a revisable research state and supports seven coupled capabilities spanning problem discovery, formulation, representation construction, hypothesis formation, intervention, evidence-grounded revision, and continual discovery improvement. We instantiate this framework with Zetema, which couples explicit research-state dynamics, verification and experimental gating, external grounding, and cross-task Discovery Skill evolution. We further ground the framework with GALILEO, a real therapeutic-discovery system in which Dry-Lab reasoning, robotic and hands-on Wet-Lab experimentation, external biological evidence, and iterative hypothesis and design revision form a closed physical discovery loop. We then formulate a unified approach to capability formation and process-centered evaluation, enabling discovery behavior to be trained, improved, and measured beyond final-answer performance. Together, these components establish discovery as a learnable, executable, and evaluable capability of foundation-model systems. We view this shift as a broader progression in intelligence scaling: from learning over existing knowledge, to learning from action outcomes, and ultimately to participating in the construction, testing, and revision of the structures through which new knowledge is discovered. Code: https://github.com/Gen-Verse/DFM-Plans

Causal discovery aims to uncover causal structures from data and is fundamental to scientific reasoning and intervention-based decision making. Its evaluation relies heavily on structural causal models (SCMs), which specify a causal graph together with the mechanisms that generate data, yet existing studies differ substantially in graph families, mechanisms, and evaluation protocols. The emergence of causal discovery foundation models (CDFMs) further complicates evaluation: performance may reflect not only causal discovery ability, but also overlap between pretraining environments and test SCMs, making results on fixed synthetic benchmarks difficult to interpret. We introduce CausalArena, a unified and evolvable benchmark for causal discovery under a common protocol. Synthetic SCMs supply controlled breadth over structures and mechanisms; semantic operational SCMs provide human-auditable, semantically grounded environments beyond standard synthetic generators; and formula-grounded SCMs test discovery under explicit scientific mechanisms. Public real-world datasets provide an additional external-validity check. Experiments across classical, neural, and pretrained methods reveal substantial ranking shifts across SCM families and protocols, showing that strong performance in one benchmark regime does not reliably transfer to others. These results highlight benchmark diversity and pretraining--evaluation overlap as central challenges for evaluating causal discovery in the foundation model era.

Causal discovery aims to recover directed causal relations from observational and interventional data, providing a basis for mechanistic understanding and reliable decision-making. Causal discovery foundation models (CDFMs) seek to amortize this problem by mapping a dataset directly to a causal graph in a single forward pass, avoiding per-dataset testing, search, or optimization. However, existing CDFMs remain limited, often failing to consistently match strong classical methods, and we find that a key bottleneck is how causal pretraining tasks are constructed. Based on this observation, we propose TabCausal, a data-driven CDFM trained with broad causal pretraining over diverse graph priors, structural mechanisms, noise models, dimensions, sample sizes, and intervention regimes. A dynamic task construction strategy composes these causal environments into varied discovery tasks, enabling more transferable structural learning from observational and mixed-interventional data. On large-scale synthetic benchmarks, TabCausal achieves better macro-averaged performance than a diverse set of causal discovery baselines. To further bridge abstract synthetic generators and realistic causal reasoning scenarios, we introduce a protocol-guided and LLM-audited semantic causal environment benchmark, where domain-grounded SCMs generate interpretable observational and interventional datasets for out-of-distribution analysis. Across both synthetic and semantic environments, TabCausal demonstrates robust structure recovery, especially under interventional evidence, highlighting broad causal pretraining as a key ingredient for transferable amortized causal discovery.

The vision of a broadly capable and goal-directed agent, such as an Internet-browsing agent in the digital world and a household humanoid in the physical world, has rapidly advanced, thanks to the generalization capability of foundation models. Such a generalist agent needs to have a large and diverse skill repertoire, such as finding directions between two travel locations and buying specific items from the Internet. If each skill needs to be specified manually through a fixed set of human-annotated instructions, the agent's skill repertoire will necessarily be limited due to the quantity and diversity of human-annotated instructions. In this work, we address this challenge by proposing Proposer-Agent-Evaluator, an effective learning system that enables foundation model agents to autonomously discover and practice skills in the wild. At the heart of PAE is a context-aware task proposer that autonomously proposes tasks for the agent to practice with context information of the environment such as user demos or even just the name of the website itself for Internet-browsing agents. Then, the agent policy attempts those tasks with thoughts and actual grounded operations in the real world with resulting trajectories evaluated by an autonomous VLM-based success evaluator. The success evaluation serves as the reward signal for the agent to refine its policies through RL. We validate PAE on challenging vision-based web navigation, using both real-world and self-hosted websites from WebVoyager and WebArena.To the best of our knowledge, this work represents the first effective learning system to apply autonomous task proposal with RL for agents that generalizes real-world human-annotated benchmarks with SOTA performances. Our open-source checkpoints and code can be found in https://yanqval.github.io/PAE/

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.

Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose a new DL algorithm, Iterative Codebook Feature Learning~(ICFL), and combine it with a pre-processing step that uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

Text-based foundation models have become an important part of scientific discovery, with molecular foundation models accelerating advancements in material science and molecular design.However, existing models are constrained by closed-vocabulary tokenizers that capture only a fraction of molecular space. In this work, we systematically evaluate 34 tokenizers, including 19 chemistry-specific ones, and reveal significant gaps in their coverage of the SMILES molecular representation. To assess the impact of tokenizer choice, we introduce n-gram language models as a low-cost proxy and validate their effectiveness by pretraining and finetuning 18 RoBERTa-style encoders for molecular property prediction. To overcome the limitations of existing tokenizers, we propose two new tokenizers -- Smirk and Smirk-GPE -- with full coverage of the OpenSMILES specification. The proposed tokenizers systematically integrate nuclear, electronic, and geometric degrees of freedom; facilitating applications in pharmacology, agriculture, biology, and energy storage. Our results highlight the need for open-vocabulary modeling and chemically diverse benchmarks in cheminformatics.

We address the challenging task of 3D object segmentation in complex scene point clouds without relying on any scene-level human annotations during training. Existing methods are typically constrained to identifying simple objects, primarily due to insufficient object priors in the learning process. In this paper, we present FoundObj, a novel framework featuring a superpoint-based object discovery agent that incrementally merges suitable neighboring superpoints, guided by our innovative semantic and geometric reward modules. These modules synergistically leverage semantic and geometric priors from self-supervised 2D/3D foundation models, providing complementary feedback to the object discovery agent and enabling robust identification of multi-class objects through reinforcement learning. Extensive experiments on diverse benchmarks demonstrate that our approach consistently outperforms existing baselines. Notably, our method exhibits strong generalization in zero-shot and long-tail scenarios, underscoring its potential for scalable, label-free 3D object segmentation.

Foundation models are premised on the idea that sequence prediction can uncover deeper domain understanding, much like how Kepler's predictions of planetary motion later led to the discovery of Newtonian mechanics. However, evaluating whether these models truly capture deeper structure remains a challenge. We develop a technique for evaluating foundation models that examines how they adapt to synthetic datasets generated from some postulated world model. Our technique measures whether the foundation model's inductive bias aligns with the world model, and so we refer to it as an inductive bias probe. Across multiple domains, we find that foundation models can excel at their training tasks yet fail to develop inductive biases towards the underlying world model when adapted to new tasks. We particularly find that foundation models trained on orbital trajectories consistently fail to apply Newtonian mechanics when adapted to new physics tasks. Further analysis reveals that these models behave as if they develop task-specific heuristics that fail to generalize.

Matched molecular pairs (MMPs) capture the local chemical edits that medicinal chemists routinely use to design analogs, but existing ML approaches either operate at the whole-molecule level with limited edit controllability or learn MMP-style edits from restricted settings and small models. We propose a variable-to-variable formulation of analog generation and train a foundation model on large-scale MMP transformations (MMPTs) to generate diverse variables conditioned on an input variable. To enable practical control, we develop prompting mechanisms that let the users specify preferred transformation patterns during generation. We further introduce MMPT-RAG, a retrieval-augmented framework that uses external reference analogs as contextual guidance to steer generation and generalize from project-specific series. Experiments on general chemical corpora and patent-specific datasets demonstrate improved diversity, novelty, and controllability, and show that our method recovers realistic analog structures in practical discovery scenarios.

Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently complex and interconnected processes and are further constrained by limited observational data in many environmental applications. Foundation models, which leverages large-scale pre-training and universal representations of complex and heterogeneous data, offer transformative opportunities for capturing spatiotemporal dynamics and dependencies in environmental processes, and facilitate adaptation to a broad range of applications. This survey presents a comprehensive overview of foundation model applications in environmental science, highlighting advancements in common environmental use cases including forward prediction, data generation, data assimilation, downscaling, inverse modeling, model ensembling, and decision-making across domains. We also detail the process of developing these models, covering data collection, architecture design, training, tuning, and evaluation. Through discussions on these emerging methods as well as their future opportunities, we aim to promote interdisciplinary collaboration that accelerates advancements in machine learning for driving scientific discovery in addressing critical environmental challenges.

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Perceiving visual scenes as objects and background -- like humans do -- Object-Centric Learning (OCL) aggregates image or video feature maps into object-level feature vectors, termed slots. OCL's self-supervision of reconstructing the input from these aggregated slots struggles with complex object textures, thus Vision Foundation Model (VFM) representations are used as the aggregation input and reconstruction target. However, existing methods leverage VFM representations in diverse ways and often fail to fully exploit their potential. In response, we propose a clean architecture -- Vector-Quantized VFMs for OCL (VQ-VFM-OCL, or VVO) -- that unifies mainstream OCL methods. The key to our unification is simple yet effective, just shared quantizing the same VFM representation as the reconstruction target. Through mathematical modeling and statistical verification, we further analyze why VFM representations facilitate OCL aggregation and how their shared quantization as reconstruction targets strengthens OCL supervision. Experiments show that across different VFMs, aggregators and decoders, our VVO consistently outperforms baselines in object discovery and recognition, as well as downstream visual prediction and reasoning. The source code is available in supplemental files.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Causal discovery from observational tabular data remains fundamentally challenging, primarily due to the heterogeneity of underlying causal mechanisms and the high-dimensional combinatorial search space of Directed Acyclic Graphs (DAGs). In this paper, we propose DAG-FM, a novel foundation model architecture that amortizes causal discovery. Unlike direct matrix prediction, DAG-FM decomposes the causal discovery process into two auto-regressive stages using two specialized Transformer-based sub-modules: a leaf-node predictor and a parent-node predictor. To effectively model complex row-column interactions, we adopt a robust tabular interaction block to output feature-wise representations. Crucially, to handle diverse and unknown Functional Causal Model (FCM) assumptions in real-world scenarios, we introduce Mixture-of-Leaf-Experts (MoLE), allowing the model to dynamically route and adapt to identifiable mechanism families. Through an iterative inference algorithm, DAG-FM seamlessly extracts causal orderings and constructs valid DAGs. Extensive experiments demonstrate that DAG-FM achieves state-of-the-art performance on both synthetic benchmarks and complex real-world datasets, significantly outperforming traditional classical algorithms and recent foundation models in both accuracy and scalability.

Causal discovery, the process of recovering underlying causal structures from observational data, is a fundamental pursuit across scientific disciplines. Over the past decades, numerous algorithms have been developed to tackle this challenge through workflows tailored to the specific causal mechanisms underlying each type of dataset, demonstrating effectiveness across a wide range of applications. However, as the volume and heterogeneity of real-world data continue to grow, this dataset-specific approach inevitably leads to a fragmented, test-driven paradigm that struggles to scale to the demands of modern scientific discovery. To address this, we formulate the Causal Discovery Foundation Model (CDFM) as a unified, general-purpose framework for zero-shot structural inference. To ensure reliable generalization across unknown domains, we first investigate the theoretical boundaries of causal identifiability, revealing the indispensable role of causal prior mechanisms in this process. Building on these insights, we formulate a principled variational framework that treats unknown causal mechanisms as latent variables and mathematically decomposes the intractable marginal likelihood into distinct, tractable learning modules. The variational decomposition provides a conceptual design principle for the architecture design of CDFM, while comprehensive causal knowledge guides the large-scale synthesis of our pretraining data. By pretraining on a massive, highly diverse space of synthetic structural causal models, CDFM successfully internalizes complex statistical asymmetries. Extensive experiments demonstrate that CDFM consistently outperforms traditional algorithms, driving a paradigm shift toward a general-purpose causal discovery foundation model.

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genome. As GFMs scale up and reshape the landscape of AI-driven genomics, the field faces an urgent need for rigorous and reproducible evaluation. We present OmniGenBench, a modular benchmarking platform designed to unify the data, model, benchmarking, and interpretability layers across GFMs. OmniGenBench enables standardized, one-command evaluation of any GFM across five benchmark suites, with seamless integration of over 31 open-source models. Through automated pipelines and community-extensible features, the platform addresses critical reproducibility challenges, including data transparency, model interoperability, benchmark fragmentation, and black-box interpretability. OmniGenBench aims to serve as foundational infrastructure for reproducible genomic AI research, accelerating trustworthy discovery and collaborative innovation in the era of genome-scale modeling.

Recent advancements in foundation models have enhanced AI systems' capabilities in autonomous tool usage and reasoning. However, their ability in location or map-based reasoning - which improves daily life by optimizing navigation, facilitating resource discovery, and streamlining logistics - has not been systematically studied. To bridge this gap, we introduce MapEval, a benchmark designed to assess diverse and complex map-based user queries with geo-spatial reasoning. MapEval features three task types (textual, API-based, and visual) that require collecting world information via map tools, processing heterogeneous geo-spatial contexts (e.g., named entities, travel distances, user reviews or ratings, images), and compositional reasoning, which all state-of-the-art foundation models find challenging. Comprising 700 unique multiple-choice questions about locations across 180 cities and 54 countries, MapEval evaluates foundation models' ability to handle spatial relationships, map infographics, travel planning, and navigation challenges. Using MapEval, we conducted a comprehensive evaluation of 28 prominent foundation models. While no single model excelled across all tasks, Claude-3.5-Sonnet, GPT-4o, and Gemini-1.5-Pro achieved competitive performance overall. However, substantial performance gaps emerged, particularly in MapEval, where agents with Claude-3.5-Sonnet outperformed GPT-4o and Gemini-1.5-Pro by 16% and 21%, respectively, and the gaps became even more amplified when compared to open-source LLMs. Our detailed analyses provide insights into the strengths and weaknesses of current models, though all models still fall short of human performance by more than 20% on average, struggling with complex map images and rigorous geo-spatial reasoning. This gap highlights MapEval's critical role in advancing general-purpose foundation models with stronger geo-spatial understanding.

Foundation models, pre-trained on a large amount of data have demonstrated impressive zero-shot capabilities in various downstream tasks. However, in object detection and instance segmentation, two fundamental computer vision tasks heavily reliant on extensive human annotations, foundation models such as SAM and DINO struggle to achieve satisfactory performance. In this study, we reveal that the devil is in the object boundary, i.e., these foundation models fail to discern boundaries between individual objects. For the first time, we probe that CLIP, which has never accessed any instance-level annotations, can provide a highly beneficial and strong instance-level boundary prior in the clustering results of its particular intermediate layer. Following this surprising observation, we propose Zip which Zips up CLip and SAM in a novel classification-first-then-discovery pipeline, enabling annotation-free, complex-scene-capable, open-vocabulary object detection and instance segmentation. Our Zip significantly boosts SAM's mask AP on COCO dataset by 12.5% and establishes state-of-the-art performance in various settings, including training-free, self-training, and label-efficient finetuning. Furthermore, annotation-free Zip even achieves comparable performance to the best-performing open-vocabulary object detecters using base annotations. Code is released at https://github.com/ChengShiest/Zip-Your-CLIP

Weakly supervised semantic segmentation aims to achieve pixel-level predictions using image-level labels. Existing methods typically entangle semantic recognition and object localization, which often leads models to focus exclusively on sparse discriminative regions. Although foundation models show immense potential, many approaches still follow the tightly coupled optimization paradigm, struggling to effectively alleviate pseudo-label noise and often relying on time-consuming multi-stage retraining or unstable end-to-end joint optimization. To address the above challenges, we present ModuSeg, a training-free weakly supervised semantic segmentation framework centered on explicitly decoupling object discovery and semantic assignment. Specifically, we integrate a general mask proposer to extract geometric proposals with reliable boundaries, while leveraging semantic foundation models to construct an offline feature bank, transforming segmentation into a non-parametric feature retrieval process. Furthermore, we propose semantic boundary purification and soft-masked feature aggregation strategies to effectively mitigate boundary ambiguity and quantization errors, thereby extracting high-quality category prototypes. Extensive experiments demonstrate that the proposed decoupled architecture better preserves fine boundaries without parameter fine-tuning and achieves highly competitive performance on standard benchmark datasets. Code is available at https://github.com/Autumnair007/ModuSeg.

Toward recursive self-improvement, we investigate LLM agents autonomously designing foundation models beyond standard Transformers. We introduce a dual-framework approach: AIRA-Compose for high-level architecture search, and AIRA-Design for low-level mechanistic implementation. AIRA-Compose uses 11 agents to explore fundamental computational primitives under a 24-hour budget. Agents evaluate million-parameter candidates, extrapolating top designs to 350M, 1B, and 3B scales. This yields 14 architectures across two families: AIRAformers (Transformer-based) and AIRAhybrids (Transformer-Mamba). Pre-trained at 1B scale, these consistently outperform Llama 3.2 and Composer-found baselines. On downstream tasks, AIRAformer-D and AIRAhybrid-D improve accuracy by 2.4% and 3.8% over Llama 3.2. Furthermore, AIRA-Compose finds models with highly efficient scaling frontiers: AIRAformer-C scales 54% and 71% faster than Llama 3.2 and Composer's best Transformer, while AIRAhybrid-C outscales Nemotron-2 by 23% and Composer's best hybrid by 37%. AIRA-Design tasks 20 agents with writing novel attention mechanisms for long-range dependencies and high-performing training scripts. On the Long Range Arena benchmark, agent-designed architectures reach within 2.3% and 2.6% of human state-of-the-art on document matching and text classification. On the Autoresearch benchmark, Greedy Opus 4.5 achieves 0.968 validation bits-per-byte under a fixed time budget, surpassing the published minimum. Together, these frameworks show AI agents can autonomously discover architectures and algorithmic optimizations matching or surpassing hand-designed baselines. This establishes a powerful paradigm for discovering next-generation foundation models, marking a clear step toward recursive self-improvement.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

The rapid development of pretrained foundation models has enabled more general image segmentation. Multimodal large language models (MLLMs) have been widely explored for image segmentation with complex queries that require high-level reasoning. Despite promising progress, existing methods are often constrained by limited training data and the gap between MLLMs and mask generation modules. To better transfer MLLMs' perception and reasoning ability to complex reasoning-based segmentation tasks, we propose a two-stage framework Rea2Seg for mask generation and selection. Specifically, the framework first identifies potential regions as candidate masks based on the attention maps of a segmentation MLLM. It then employs an MLLM to reason over the question and candidate masks and assign scores to each mask. The final segmentation result is obtained by reranking the candidates and selecting the highest-scoring mask, reformulating image segmentation as candidate discovery followed by discriminative mask selection. We also notice that a large portion of questions in existing benchmarks focus on commonsense reasoning, and these questions usually do not fully require joint visual observation and reasoning. To address this issue, we introduce a new benchmark called ReasonSeg-SGDR that comprehensively evaluates a model's perception, grounding, and reasoning abilities across multiple dimensions, including discriminative recognition, spatial reasoning, geometric reasoning, and multi-step reasoning, with fine-grained mask generation. In addition, we collect training data to enhance MLLMs' ability to jointly understand multimodal queries and candidate masks, and to assign scores through reasoning. Experimental results on the proposed benchmark and ReasonSeg demonstrate the effectiveness of the unified mask generation and selection framework.

The rapid advancement of large language models (LLMs) and multimodal foundation models has sparked growing interest in their potential for scientific research. However, scientific intelligence encompasses a broad spectrum of abilities ranging from understanding fundamental knowledge to conducting creative discovery, and existing benchmarks remain fragmented. Most focus on narrow tasks and fail to reflect the hierarchical and multi-disciplinary nature of real scientific inquiry. We introduce HiSciBench, a hierarchical benchmark designed to evaluate foundation models across five levels that mirror the complete scientific workflow: Scientific Literacy (L1), Literature Parsing (L2), Literature-based Question Answering (L3), Literature Review Generation (L4), and Scientific Discovery (L5). HiSciBench contains 8,735 carefully curated instances spanning six major scientific disciplines, including mathematics, physics, chemistry, biology, geography, and astronomy, and supports multimodal inputs including text, equations, figures, and tables, as well as cross-lingual evaluation. Unlike prior benchmarks that assess isolated abilities, HiSciBench provides an integrated, dependency-aware framework that enables detailed diagnosis of model capabilities across different stages of scientific reasoning. Comprehensive evaluations of leading models, including GPT-5, DeepSeek-R1, and several multimodal systems, reveal substantial performance gaps: while models achieve up to 69\% accuracy on basic literacy tasks, performance declines sharply to 25\% on discovery-level challenges. HiSciBench establishes a new standard for evaluating scientific Intelligence and offers actionable insights for developing models that are not only more capable but also more reliable. The benchmark will be publicly released to facilitate future research.

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at https://github.com/Eurekashen/MolSpectLLM{https://github.com/Eurekashen/MolSpectLLM}.

Chemical pretrained models, sometimes referred to as foundation models, are receiving considerable interest for drug discovery applications. The general chemical knowledge extracted from self-supervised training has the potential to improve predictions for critical drug discovery endpoints, including on-target potency and ADMET properties. Multi-task learning has previously been successfully leveraged to improve predictive models. Here, we show that enabling multitasking in finetuning of chemical pretrained graph neural network models such as Kinetic GROVER Multi-Task (KERMT), an enhanced version of the GROVER model, and Knowledge-guided Pre-training of Graph Transformer (KGPT) significantly improves performance over non-pretrained graph neural network models. Surprisingly, we find that the performance improvement from finetuning KERMT in a multitask manner is most significant at larger data sizes. Additionally, we publish two multitask ADMET data splits to enable more accurate benchmarking of multitask deep learning methods for drug property prediction. Finally, we provide an accelerated implementation of the KERMT model on GitHub, unlocking large-scale pretraining, finetuning, and inference in industrial drug discovery workflows.

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Current AI-assisted skin image diagnosis has achieved dermatologist-level performance in classifying skin cancer, driven by rapid advancements in deep learning architectures. However, unlike traditional vision tasks, skin images in general present unique challenges due to the limited availability of well-annotated datasets, complex variations in conditions, and the necessity for detailed interpretations to ensure patient safety. Previous segmentation methods have sought to reduce image noise and enhance diagnostic performance, but these techniques require fine-grained, pixel-level ground truth masks for training. In contrast, with the rise of foundation models, the Segment Anything Model (SAM) has been introduced to facilitate promptable segmentation, enabling the automation of the segmentation process with simple yet effective prompts. Efforts applying SAM predominantly focus on dermatoscopy images, which present more easily identifiable lesion boundaries than clinical photos taken with smartphones. This limitation constrains the practicality of these approaches to real-world applications. To overcome the challenges posed by noisy clinical photos acquired via non-standardized protocols and to improve diagnostic accessibility, we propose a novel Cross-Attentive Fusion framework for interpretable skin lesion diagnosis. Our method leverages SAM to generate visual concepts for skin diseases using prompts, integrating local visual concepts with global image features to enhance model performance. Extensive evaluation on two skin disease datasets demonstrates our proposed method's effectiveness on lesion diagnosis and interpretability.

Deploying learned robot manipulation policies in industrial settings requires rigorous pre-deployment validation, yet exhaustive testing across high-dimensional parameter spaces is intractable. We present ROBOGATE, a deployment risk management framework that combines physics-based simulation with a two-stage adaptive sampling strategy to efficiently discover failure boundaries in the operational parameter space. Stage 1 employs Latin Hypercube Sampling (LHS) across an 8-dimensional parameter space to establish a coarse failure landscape from 20,000 uniformly distributed experiments. Stage 2 applies boundary-focused sampling that concentrates 10,000 additional experiments in the 30-70% success rate transition zone, enabling precise failure boundary mapping. Using NVIDIA Isaac Sim with Newton physics, we evaluate a scripted pick-and-place controller on two robot embodiments -- Franka Panda (7-DOF) and UR5e (6-DOF) -- across 30,000 total experiments. Our logistic regression risk model achieves an AUC of 0.780 on the combined dataset (vs. 0.754 for Stage 1 alone), identifies a closed-form failure boundary equation, and reveals four universal danger zones affecting both robot platforms. We further demonstrate the framework on VLA (Vision-Language-Action) model evaluation, where Octo-Small achieves 0.0% success rate on 68 adversarial scenarios versus 100% for the scripted baseline -- a 100-point gap that underscores the challenge of deploying foundation models in industrial settings. ROBOGATE is open-source and runs on a single GPU workstation.

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

We introduceGraphGPT, a novel self-supervised generative pre-trained model for graph learning based on the Graph Eulerian Transformer (GET). First, we propose GET, which combines a standard transformer encoder or decoder architecture with an innovative graph-to-sequence transformation method. This method converts graphs or sampled subgraphs into sequences of tokens representing nodes, edges, and attributes in a reversible manner using Eulerian paths. We pre-train GET using either of the two self-supervised tasks: next-token prediction (NTP) and scheduled masked-token prediction (SMTP). The pre-trained model is then fine-tuned for downstream tasks such as graph-, edge-, and node-level prediction. Despite its simplicity, GraphGPT achieves performance comparable to or surpassing state-of-the-art methods on multiple large-scale Open Graph Benchmark (OGB) datasets. It demonstrates exceptional results on the molecular property prediction dataset PCQM4Mv2 and the protein-protein interaction dataset ogbl-ppa. Notably, generative pre-training enables scaling GraphGPT to 2 billion parameters while maintaining performance gains - a breakthrough that overcomes the scalability limitations of traditional Graph Neural Networks (GNNs) and prior graph transformers (GTs). To advance research in graph foundation models and facilitate scientific discovery in chemistry, materials science, and related fields, we will release the source code (https://github.com/alibaba/graph-gpt) and pre-trained checkpoints.

Object-centric learning (OCL) seeks to learn representations that only encode an object, isolated from other objects or background cues in a scene. This approach underpins various aims, including out-of-distribution (OOD) generalization, sample-efficient composition, and modeling of structured environments. Most research has focused on developing unsupervised mechanisms that separate objects into discrete slots in the representation space, evaluated using unsupervised object discovery. However, with recent sample-efficient segmentation models, we can separate objects in the pixel space and encode them independently. This achieves remarkable zero-shot performance on OOD object discovery benchmarks, is scalable to foundation models, and can handle a variable number of slots out-of-the-box. Hence, the goal of OCL methods to obtain object-centric representations has been largely achieved. Despite this progress, a key question remains: How does the ability to separate objects within a scene contribute to broader OCL objectives, such as OOD generalization? We address this by investigating the OOD generalization challenge caused by spurious background cues through the lens of OCL. We propose a novel, training-free probe called Object-Centric Classification with Applied Masks (OCCAM), demonstrating that segmentation-based encoding of individual objects significantly outperforms slot-based OCL methods. However, challenges in real-world applications remain. We provide the toolbox for the OCL community to use scalable object-centric representations, and focus on practical applications and fundamental questions, such as understanding object perception in human cognition. Our code is available https://github.com/AlexanderRubinstein/OCCAM{here}.

Light curves describe temporal variations in the brightness of celestial objects. Learning robust representations of light curves is essential for large-scale automatic discovery in the dynamic universe, but existing time-series foundation models often struggle with the uneven sampling, complex noise, and wide range of physical timescales that characterize astronomical observations. We propose a domain-informed representation learning framework for irregular astronomical time series with Joint-Embedding predictive architecture (JEPA), combining semantics-preserving views, uncertainty-aware tokenization, and multi-view self-distillation. The encoders are trained with multi-view self-distillation using LeJEPA regularization on the LEAVES dataset and evaluated on the StarEmbed classification benchmark. On StarEmbed, our model outperforms hand-crafted features on 15 of 16 classification metrics. In few-shot linear probing, it achieves macro-F1 scores of 42.56 pm 7.21 with one sample per class and 63.58 pm 1.20 with 100 samples per class, consistently improving over hand-crafted features. Beyond variable-star classification, the learned representation supports similarity search, parameter estimation, and photometric zero-point drift detection. We further evaluate cross-domain adaptation on 12 heterogeneous irregular time-series datasets from PYRREGULAR, where the adapted variant matches or exceeds previous state-of-the-art performance on 5 datasets, compared with at most 3 wins by any single prior baseline. These results demonstrate that domain-informed multi-view self-distillation is an effective strategy for learning representations of irregular time series, while also highlighting that successful time-series representation learning requires domain-specific inductive biases rather than a universally optimal architecture.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

Causal discovery for both cross-sectional and temporal data has traditionally followed a dataset-specific paradigm, where a new model is fitted for each individual dataset. Such an approach limits the potential of multi-dataset pretraining. The concept of large causal models (LCMs) envisions a class of pre-trained neural architectures specifically designed for temporal causal discovery. Prior approaches are constrained to small variable counts, degrade with larger inputs, and rely heavily on synthetic data, limiting generalization. We propose a principled framework for LCMs, combining diverse synthetic generators with realistic time-series datasets, allowing learning at scale. Extensive experiments on synthetic, semi-synthetic and realistic benchmarks show that LCMs scale effectively to higher variable counts and deeper architectures while maintaining strong performance. Trained models achieve competitive or superior accuracy compared to classical and neural baselines, particularly in out-of-distribution settings, while enabling fast, single-pass inference. Results demonstrate LCMs as a promising foundation-model paradigm for temporal causal discovery. Experiments and model weights are available at https://github.com/kougioulis/LCM-paper/.

We introduce Arrow, a foundation model for zero-shot causal discovery on observational tabular data. Arrow factorizes a directed acyclic graph into an undirected skeleton and a topological order, guaranteeing acyclicity by construction. Given a new dataset, it uses a transformer-based architecture to contextualize variables within and across observations, then predicts skeleton edge probabilities and node order scores that together define a graph. Arrow is trained in a supervised fashion on synthetic datasets with ground-truth graphs, using an end-to-end differentiable directed edge composite likelihood induced by the skeleton-order factorization. The training distribution spans diverse graph families, functional forms, noise models, and dataset shapes. Across in- and out-of-distribution synthetic, semi-synthetic, and real datasets, Arrow matches or outperforms existing causal discovery methods at substantially lower inference cost than competitive alternatives. Our results demonstrate that large-scale pretraining on diverse synthetic data can yield zero-shot causal discovery models that are fast, accurate, and reusable on new datasets.

Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds. However, the computational burden to develop and deploy state-of-the-art models continuously increases, limiting their scalability. Most large-scale models are unimodal in nature and overlook the potential to leverage complementary molecular data modalities. To address these shortcomings, this paper introduces the Graph-Language Alignment for Chemical Inference and Exploration using Representations (GLACIER) model, a student-teacher framework that integrates molecular graphs, SMILES strings, and physicochemical descriptors to learn rich molecular embeddings. Our framework consists of three stages: (1) we pretrain three student encoders on 100,000 drug-like molecules: a message-passing neural network for molecular graphs, a transformer-based encoder for SMILES strings, and a multilayer perceptron for physicochemical descriptors, (2) we fuse these student modalities using a novel Finsler geometry-aware module, and (3) distill complementary knowledge from large teacher models, including MiniMol and MolFormer, into a single lightweight model via contrastive learning. We demonstrate that GLACIER is a robust framework that delivers high predictive performance and computational efficiency in complex molecular property prediction tasks. Our code is publicly available at https://github.com/eemokey/glacier.

Discovering functional crystalline materials entails navigating an immense combinatorial design space. While recent advances in generative artificial intelligence have enabled the sampling of chemically plausible compositions and structures, a fundamental challenge remains: the objective misalignment between likelihood-based sampling in generative modelling and targeted focus on underexplored regions where novel compounds reside. Here, we introduce a reinforcement learning framework that guides latent denoising diffusion models toward diverse and novel, yet thermodynamically viable crystalline compounds. Our approach integrates group relative policy optimisation with verifiable, multi-objective rewards that jointly balance creativity, stability, and diversity. Beyond de novo generation, we demonstrate enhanced property-guided design that preserves chemical validity, while targeting desired functional properties. This approach establishes a modular foundation for controllable AI-driven inverse design that addresses the novelty-validity trade-off across scientific discovery applications of generative models.

Molecular generation is a central challenge in drug discovery, requiring models that explore vast chemical space while satisfying diverse design constraints. We present Molexar, a unified multimodal molecular foundation model built on Fragment-SELFIES, a robust, fragment-aware molecular language with validity-preserving decoding and explicit fragment structure. A pretrained autoregressive decoder learns the Fragment-SELFIES syntax and molecular distribution; supervised fine-tuning (SFT) then trains the same decoder on condition-molecule pairs spanning scalar molecular properties, pharmacophore fingerprints, protein sequences, and binding pockets, injecting each condition by in-place replacement of value-token embeddings so that all generation modes share one autoregressive path. Molexar achieves strong efficiency at a small parameter count while matching or exceeding larger models. The pretrained model reaches 100% validity and high drug-likeness in unconditional and fragment-constrained generation; the SFT model follows single- and multi-property instructions and remains competitive on target-conditioned generation on the CrossDocked2020 test set. On MolGenBench, Molexar further generates molecules with favorable safety and potency. These results establish Molexar as a practical unified foundation for computational chemistry and drug-design workflows.

Physical understanding and reasoning depend on forming compact and generalizable representations of the world. While modern vision-language models can recognize and explain diverse physical events, they often lack explicit representations of the underlying mechanisms-such as object states, physical parameters, and governing dynamics-needed for reliably reasoning how the world evolves and responds to interventions. In this work, we introduce Code-as-World, a paradigm that represents physical worlds through executable world representations. By expressing physical composition, dynamic evolution, and visual appearance as executable code, Code-as-World provides a compact, quantitatively grounded, and controllable abstraction of the physical world. To construct such representations from multimodal observations, such as natural-language descriptions or real-world videos, we develop an agentic discovery loop inspired by abductive reasoning, where an agent proposes, executes, renders, verifies, and iteratively refines executable world hypotheses. As a concrete application, we use verified executable worlds to provide scalable physical supervision for training vision-language models on quantitative physical reasoning. Experiments show that Code-as-World-VL achieves state-of-the-art performance on QuantiPhy and surpasses leading proprietary models, highlighting the potential of executable world representations as a scalable foundation for physical intelligence.

Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical space. Yet, the lack of standardized evaluation frameworks makes it challenging to evaluate, compare, and further develop these ML models meaningfully. In this work, we introduce LeMat-GenBench, a unified benchmark for generative models of crystalline materials, supported by a set of evaluation metrics designed to better inform model development and downstream applications. We release both an open-source evaluation suite and a public leaderboard on Hugging Face, and benchmark 12 recent generative models. Results reveal that an increase in stability leads to a decrease in novelty and diversity on average, with no model excelling across all dimensions. Altogether, LeMat-GenBench establishes a reproducible and extensible foundation for fair model comparison and aims to guide the development of more reliable, discovery-oriented generative models for crystalline materials.

*Automated circuit discovery* is a central tool in mechanistic interpretability for identifying the internal components of neural networks responsible for specific behaviors. While prior methods have made significant progress, they typically depend on heuristics or approximations and do not offer provable guarantees over continuous input domains for the resulting circuits. In this work, we leverage recent advances in neural network verification to propose a suite of automated algorithms that yield circuits with *provable guarantees*. We focus on three types of guarantees: (1) *input domain robustness*, ensuring the circuit agrees with the model across a continuous input region; (2) *robust patching*, certifying circuit alignment under continuous patching perturbations; and (3) *minimality*, formalizing and capturing a wide array of various notions of succinctness. Interestingly, we uncover a diverse set of novel theoretical connections among these three families of guarantees, with critical implications for the convergence of our algorithms. Finally, we conduct experiments with state-of-the-art verifiers on various vision models, showing that our algorithms yield circuits with substantially stronger robustness guarantees than standard circuit discovery methods, establishing a principled foundation for provable circuit discovery.

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.

Large language models (LLMs) have revolutionized automated code generation, yet the evaluation of their real-world effectiveness remains limited by static benchmarks and simplistic metrics. We present ProxyWar, a novel framework that systematically assesses code generation quality by embedding LLM-generated agents within diverse, competitive game environments. Unlike existing approaches, ProxyWar evaluates not only functional correctness but also the operational characteristics of generated programs, combining automated testing, iterative code repair, and multi-agent tournaments to provide a holistic view of program behavior. Applied to a range of state-of-the-art coders and games, our approach uncovers notable discrepancies between benchmark scores and actual performance in dynamic settings, revealing overlooked limitations and opportunities for improvement. These findings highlight the need for richer, competition-based evaluation of code generation. Looking forward, ProxyWar lays a foundation for research into LLM-driven algorithm discovery, adaptive problem solving, and the study of practical efficiency and robustness, including the potential for models to outperform hand-crafted agents. The project is available at https://github.com/xinke-wang/ProxyWar.

Bumblebee is a foundation model for particle physics discovery, inspired by BERT. By removing positional encodings and embedding particle 4-vectors, Bumblebee captures both generator- and reconstruction-level information while ensuring sequence-order invariance. Pre-trained on a masked task, it improves dileptonic top quark reconstruction resolution by 10-20% and excels in downstream tasks, including toponium discrimination (AUROC 0.877) and initial state classification (AUROC 0.625). The flexibility of Bumblebee makes it suitable for a wide range of particle physics applications, especially the discovery of new particles.

We introduce FragAtlas-62M, a specialized foundation model trained on the largest fragment dataset to date. Built on the complete ZINC-22 fragment subset comprising over 62 million molecules, it achieves unprecedented coverage of fragment chemical space. Our GPT-2 based model (42.7M parameters) generates 99.90% chemically valid fragments. Validation across 12 descriptors and three fingerprint methods shows generated fragments closely match the training distribution (all effect sizes < 0.4). The model retains 53.6% of known ZINC fragments while producing 22% novel structures with practical relevance. We release FragAtlas-62M with training code, preprocessed data, documentation, and model weights to accelerate adoption.

Foundation models for materials modeling are advancing quickly, but their training remains expensive, often placing state-of-the-art methods out of reach for many research groups. We introduce Nequix, a compact E(3)-equivariant potential that pairs a simplified NequIP design with modern training practices, including equivariant root-mean-square layer normalization and the Muon optimizer, to retain accuracy while substantially reducing compute requirements. Built in JAX, Nequix has 700K parameters and was trained in 500 A100-GPU hours. On the Matbench-Discovery and MDR Phonon benchmarks, Nequix ranks third overall while requiring less than one quarter of the training cost of most other methods, and it delivers an order-of-magnitude faster inference speed than the current top-ranked model. We release model weights and fully reproducible codebase at https://github.com/atomicarchitects/nequix

Scientific discovery increasingly requires AI systems that can reason over scientific evidence of heterogeneous modalities, interact with scientific tools and environments, and sustain progress across long task horizons. We present Intern-S2-Preview, a series of scientific agentic foundation models designed to support multimodal scientific understanding, reasoning, generation, and long-horizon tasks. The training pipeline begins with scientific multimodal pre-training over rendered scientific documents, interleaved image-text data, and diverse scientific corpora. Starting from the pretrained checkpoint, we apply a unified post-training pipeline consisting of supervised fine-tuning, scalable multi-task reinforcement learning (RL), black- and white-box agentic RL, and on-policy distillation. This pipeline is supported by practical techniques that improve rollout and training stability and efficiency, including partial rollout with off-policy correction, adaptive length regularization, online speculative decoding, robust multi-task optimization, and trace-aware experience assembly for agentic tasks. At the architecture level, Intern-S2-Preview-397B extends time series modelling from efficient long-sequence understanding to numerical forecasting, while Memory Decoder is studied as a separate memory-augmented path for rapid scientific specialization without modifying the frozen 397B backbone. Evaluations across scientific, multimodal, agentic, and general-purpose benchmarks show that Intern-S2-Preview-397B achieves competitive or leading results in multiple settings. The time series modules improve scientific signal understanding and forecasting on SciTS, while the separate Intern-MemDec-4B extension improves the Biology-Instructions average score from 56.92 to 60.32 without modifying the frozen 397B backbone.

Scientific foundation models hold great promise for advancing nuclear and particle physics by improving analysis precision and accelerating discovery. Yet, progress in this field is often limited by the lack of openly available large scale datasets, as well as standardized evaluation tasks and metrics. Furthermore, the specialized knowledge and software typically required to process particle physics data pose significant barriers to interdisciplinary collaboration with the broader machine learning community. This work introduces a large, openly accessible dataset of 10 million simulated proton-proton collisions, designed to support self-supervised training of foundation models. To facilitate ease of use, the dataset is provided in a common NumPy format. In addition, it includes 70,000 labeled examples spanning three well defined downstream tasks: track finding, particle identification, and noise tagging, to enable systematic evaluation of the foundation model's adaptability. The simulated data are generated using the Pythia Monte Carlo event generator at a center of mass energy of sqrt(s) = 200 GeV and processed with Geant4 to include realistic detector conditions and signal emulation in the sPHENIX Time Projection Chamber at the Relativistic Heavy Ion Collider, located at Brookhaven National Laboratory. This dataset resource establishes a common ground for interdisciplinary research, enabling machine learning scientists and physicists alike to explore scaling behaviors, assess transferability, and accelerate progress toward foundation models in nuclear and high energy physics. The complete simulation and reconstruction chain is reproducible with the sPHENIX software stack. All data and code locations are provided under Data Accessibility.

Biomedical image analysis is fundamental for biomedical discovery in cell biology, pathology, radiology, and many other biomedical domains. Holistic image analysis comprises interdependent subtasks such as segmentation, detection, and recognition of relevant objects. Here, we propose BiomedParse, a biomedical foundation model for imaging parsing that can jointly conduct segmentation, detection, and recognition for 82 object types across 9 imaging modalities. Through joint learning, we can improve accuracy for individual tasks and enable novel applications such as segmenting all relevant objects in an image through a text prompt, rather than requiring users to laboriously specify the bounding box for each object. We leveraged readily available natural-language labels or descriptions accompanying those datasets and use GPT-4 to harmonize the noisy, unstructured text information with established biomedical object ontologies. We created a large dataset comprising over six million triples of image, segmentation mask, and textual description. On image segmentation, we showed that BiomedParse is broadly applicable, outperforming state-of-the-art methods on 102,855 test image-mask-label triples across 9 imaging modalities (everything). On object detection, which aims to locate a specific object of interest, BiomedParse again attained state-of-the-art performance, especially on objects with irregular shapes (everywhere). On object recognition, which aims to identify all objects in a given image along with their semantic types, we showed that BiomedParse can simultaneously segment and label all biomedical objects in an image (all at once). In summary, BiomedParse is an all-in-one tool for biomedical image analysis by jointly solving segmentation, detection, and recognition for all major biomedical image modalities, paving the path for efficient and accurate image-based biomedical discovery.

Scientific discovery is increasingly shifting from isolated disciplines to multi-domain reasoning, and AI for science faces a similar transition. Existing systems are either specialised for individual domains or unify scientific data mainly through text tokenisation and prompt-based interfaces, limiting their ability to handle diverse scientific inputs, produce modality-native outputs, and support joint understanding, reasoning, and generation across scientific domains. We introduce MKB, a unified scientific multimodal model for both understanding and generation, built around a shared Transformer backbone and modality-tailored encoders, adapters, and decoders. MKB covers six scientific branches, including DNA, RNA, proteins, small molecules, earth science, and medical images, and supports native outputs such as biological sequences, molecular strings, meteorological fields, and segmentation masks. Training follows a two-stage modality-then-language curriculum: Stage 1 aligns modality-specific components with the frozen backbone, and Stage 2 consolidates them with the language backbone using mixed scientific and general corpora. Experiments show that MKB achieves competitive scientific understanding across biological and molecular benchmarks, produces high-fidelity native outputs for weather forecasting, biological generation, and medical-image segmentation, and largely retains the general capabilities of its Qwen3-VL backbone. These results demonstrate the feasibility of the proposed paradigm, suggesting that shared-backbone models with modality-tailored components can provide a promising foundation for future cross-domain scientific multimodal exploration. The model and code are publicly available at https://github.com/Shanghai-Academy-of-AI-For-Science/MKB and https://huggingface.co/sais-org/MKB.

In recent years, foundation models (FMs) such as large language models (LLMs) and latent diffusion models (LDMs) have profoundly impacted diverse sectors, including music. This comprehensive review examines state-of-the-art (SOTA) pre-trained models and foundation models in music, spanning from representation learning, generative learning and multimodal learning. We first contextualise the significance of music in various industries and trace the evolution of AI in music. By delineating the modalities targeted by foundation models, we discover many of the music representations are underexplored in FM development. Then, emphasis is placed on the lack of versatility of previous methods on diverse music applications, along with the potential of FMs in music understanding, generation and medical application. By comprehensively exploring the details of the model pre-training paradigm, architectural choices, tokenisation, finetuning methodologies and controllability, we emphasise the important topics that should have been well explored, like instruction tuning and in-context learning, scaling law and emergent ability, as well as long-sequence modelling etc. A dedicated section presents insights into music agents, accompanied by a thorough analysis of datasets and evaluations essential for pre-training and downstream tasks. Finally, by underscoring the vital importance of ethical considerations, we advocate that following research on FM for music should focus more on such issues as interpretability, transparency, human responsibility, and copyright issues. The paper offers insights into future challenges and trends on FMs for music, aiming to shape the trajectory of human-AI collaboration in the music realm.

Recent Multimodal Large Language Models (MLLMs) exhibit impressive abilities to perceive images and follow open-ended instructions. The capabilities of MLLMs depend on two crucial factors: the model architecture to facilitate the feature alignment of visual modules and large language models; the multimodal instruction tuning datasets for human instruction following. (i) For the model architecture, most existing models introduce an external bridge module to connect vision encoders with language models, which needs an additional feature-alignment pre-training. In this work, we discover that compact pre-trained vision language models can inherently serve as ``out-of-the-box'' bridges between vision and language. Based on this, we propose Muffin framework, which directly employs pre-trained vision-language models to act as providers of visual signals. (ii) For the multimodal instruction tuning datasets, existing methods omit the complementary relationship between different datasets and simply mix datasets from different tasks. Instead, we propose UniMM-Chat dataset which explores the complementarities of datasets to generate 1.1M high-quality and diverse multimodal instructions. We merge information describing the same image from diverse datasets and transforms it into more knowledge-intensive conversation data. Experimental results demonstrate the effectiveness of the Muffin framework and UniMM-Chat dataset. Muffin achieves state-of-the-art performance on a wide range of vision-language tasks, significantly surpassing state-of-the-art models like LLaVA and InstructBLIP. Our model and dataset are all accessible at https://github.com/thunlp/muffin.

Bioassay activity prediction is often data-limited because drug-discovery datasets rely on time-consuming and expensive wet-lab experiments for data generation and evaluation. This challenge has inspired recent research into molecular foundation models (MFMs), which aim to encode general-purpose chemical knowledge into molecular representations that generalize well in data-constrained scenarios. This paper presents Monroe, a new MFM with several innovations over the existing state of the art: increased scale allowing pre-training on over 81 million molecules from the PM6 quantum chemistry dataset; improved graph representation of stereochemistry; improved training losses including conformer denoising and embedding decorrelation; improved multi-task learning; and the use of a prior-data-fitted model (TabPFN) for downstream in-context prediction. Our evaluations use a principled pairwise comparison framework that measures statistically significant performance differences. Across established Polaris benchmarks, Monroe matches or exceeds existing MFMs, while on activity cliff benchmarks, designed to assess utility for molecular discovery, it achieves significant improvements over prior methods. Finally, ablation and transfer experiments show that PFN-based downstream predictors also substantially improve two leading existing models, MiniMol and CheMeleon, yielding new state-of-the-art variants we call MiniMol_PFN and CheMeleon_PFN, suggesting that our downstream adaptation strategy generalizes beyond Monroe. Source code is at github.com/blazejba/monroe.

Accurately predicting the three-dimensional structures of protein-ligand complexes remains a fundamental challenge in computational drug discovery that limits the pace and success of therapeutic design. Deep learning methods have recently shown strong potential as structural prediction tools, achieving promising accuracy across diverse biomolecular systems. However, their performance and utility are constrained by scarce experimental data, inefficient architectures, physically invalid poses, and the limited ability to exploit auxiliary information available at inference. To address these issues, we introduce Pearl (Placing Every Atom in the Right Location), a foundation model for protein-ligand cofolding at scale. Pearl addresses these challenges with three key innovations: (1) training recipes that include large-scale synthetic data to overcome data scarcity; (2) architectures that incorporate an SO(3)-equivariant diffusion module to inherently respect 3D rotational symmetries, improving generalization and sample efficiency, and (3) controllable inference, including a generalized multi-chain templating system supporting both protein and non-polymeric components as well as dual unconditional/conditional modes. Pearl establishes a new state-of-the-art performance in protein-ligand cofolding. On the key metric of generating accurate (RMSD < 2 Å) and physically valid poses, Pearl surpasses AlphaFold 3 and other open source baselines on the public Runs N' Poses and PoseBusters benchmarks, delivering 14.5% and 14.2% improvements, respectively, over the next best model. In the pocket-conditional cofolding regime, Pearl delivers 3.6times improvement on a proprietary set of challenging, real-world drug targets at the more rigorous RMSD < 1 Å threshold. Finally, we demonstrate that model performance correlates directly with synthetic dataset size used in training.

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CRYOFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

While deep learning is transforming data analysis in high-energy physics, computational challenges limit its potential. We address these challenges in the context of collider physics by introducing EveNet, an event-level foundation model pretrained on 500 million simulated collision events using a hybrid objective of self-supervised learning and physics-informed supervision. By leveraging a shared particle-cloud representation, EveNet outperforms state-of-the-art baselines across diverse tasks, including searches for heavy resonances and exotic Higgs decays, and demonstrates exceptional data efficiency in low-statistics regimes. Crucially, we validate the transferability of the model to experimental data by rediscovering the Υ meson in CMS Open Data and show its capacity for precision physics through the robust extraction of quantum correlation observables stable against systematic uncertainties. These results indicate that EveNet can successfully encode the fundamental physical structure of particle interactions, which offers a unified and resource-efficient framework to accelerate discovery at current and future colliders.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

Computational pathology foundation models (CPathFMs) have emerged as a powerful approach for analyzing histopathological data, leveraging self-supervised learning to extract robust feature representations from unlabeled whole-slide images. These models, categorized into uni-modal and multi-modal frameworks, have demonstrated promise in automating complex pathology tasks such as segmentation, classification, and biomarker discovery. However, the development of CPathFMs presents significant challenges, such as limited data accessibility, high variability across datasets, the necessity for domain-specific adaptation, and the lack of standardized evaluation benchmarks. This survey provides a comprehensive review of CPathFMs in computational pathology, focusing on datasets, adaptation strategies, and evaluation tasks. We analyze key techniques, such as contrastive learning and multi-modal integration, and highlight existing gaps in current research. Finally, we explore future directions from four perspectives for advancing CPathFMs. This survey serves as a valuable resource for researchers, clinicians, and AI practitioners, guiding the advancement of CPathFMs toward robust and clinically applicable AI-driven pathology solutions.

Foundation models use large datasets to build an effective representation of data that can be deployed on diverse downstream tasks. Previous research developed the OmniLearn foundation model for jet physics, using unique properties of particle physics, and showed that it could significantly advance discovery potential across collider experiments. This paper introduces a major upgrade, resulting in the OmniLearned framework. This framework has three new elements: (1) updates to the model architecture and training, (2) using over one billion jets used for training, and (3) providing well-documented software for accessing all datasets and models. We demonstrate OmniLearned with three representative tasks: top-quark jet tagging with the community Delphes-based benchmark dataset, b-tagging with ATLAS full simulation, and anomaly detection with CMS experimental data. In each case, OmniLearned is the state of the art, further expanding the discovery potential of past, current, and future collider experiments.

Rigorous and reproducible evaluation is critical for assessing the state of the art and for guiding scientific advances in Artificial Intelligence. Evaluation is challenging in practice due to several reasons, including benchmark saturation, lack of transparency in methods used for measurement, development challenges in extracting measurements for generative tasks, and, more generally, the extensive number of capabilities required for a well-rounded comparison across models. We make three contributions to alleviate the above challenges. First, we present Eureka, an open-source framework for standardizing evaluations of large foundation models beyond single-score reporting and rankings. Second, we introduce Eureka-Bench as an extensible collection of benchmarks testing capabilities that (i) are still challenging for state-of-the-art models and (ii) represent fundamental but overlooked language and multimodal capabilities. The inherent space for improvement in non-saturated benchmarks enables us to discover meaningful differences between models at a capability level. Third, using Eureka, we conduct an analysis of 12 state-of-the-art models, providing in-depth insights into failure understanding and model comparison, which can be leveraged to plan targeted improvements. In contrast to recent trends in reports and leaderboards showing absolute rankings and claims for one model or another to be the best, our analysis shows that there is no such best model. Different models have different strengths, but there are models that appear more often than others as best performers for some capabilities. Despite the recent improvements, current models still struggle with several fundamental capabilities including detailed image understanding, benefiting from multimodal input when available rather than fully relying on language, factuality and grounding for information retrieval, and over refusals.

Recent text and image foundation models are incredibly impressive, and these models are attracting an ever-increasing portion of research resources. In this position piece we aim to shift the ML research community's priorities ever so slightly to a different modality: tabular data. Tabular data is the dominant modality in many fields, yet it is given hardly any research attention and significantly lags behind in terms of scale and power. We believe the time is now to start developing tabular foundation models, or what we coin a Large Tabular Model (LTM). LTMs could revolutionise the way science and ML use tabular data: not as single datasets that are analyzed in a vacuum, but contextualized with respect to related datasets. The potential impact is far-reaching: from few-shot tabular models to automating data science; from out-of-distribution synthetic data to empowering multidisciplinary scientific discovery. We intend to excite reflections on the modalities we study, and convince some researchers to study large tabular models.

Foundation models and self-supervised learning (SSL) have become central to modern AI, yet research in this area remains hindered by complex codebases, redundant re-implementations, and the heavy engineering burden of scaling experiments. We present stable-pretraining, a modular, extensible, and performance-optimized library built on top of PyTorch, Lightning, Hugging Face, and TorchMetrics. Unlike prior toolkits focused narrowly on reproducing state-of-the-art results, stable-pretraining is designed for flexibility and iteration speed: it unifies essential SSL utilities--including probes, collapse detection metrics, augmentation pipelines, and extensible evaluation routines--within a coherent and reliable framework. A central design principle is logging everything, enabling fine-grained visibility into training dynamics that makes debugging, monitoring, and reproducibility seamless. We validate the library by demonstrating its ability to generate new research insights with minimal overhead, including depthwise representation probing and the analysis of CLIP degradation under synthetic data finetuning. By lowering barriers to entry while remaining scalable to large experiments, stable-pretraining aims to accelerate discovery and expand the possibilities of foundation model research.

Addressing critical global challenges, from food security and disaster risk to disease outbreaks and socio-economic vulnerability, demands high-fidelity geospatial modeling. However, building predictive planetary models remains bottlenecked by a fragmented data ecosystem, requiring manual data retrieval, multimodal data curation and fusion along with iterative model selection. We present the Planetary Prediction Engine (PPE), an autonomous AI system that executes this end-to-end workflow directly from natural-language queries. PPE synthesizes multimodal datasets on the fly, retrieving spatiotemporally relevant covariates across open-web and Earth observation platforms (Data Commons, Google Earth Engine) and fusing them with geospatial foundation model embeddings (PDFM, AlphaEarth). Simultaneously, it searches over task-tailored model architecture families with automated overfitting guards. Across diverse tasks, geographies, and scientific domains, PPE consistently outperforms state-of-the-art or manually tuned expert baselines. For US spatial regression, PPE improves mean R^2 across 21 CDC health indicators (76.8% vs. 60.0%), FEMA national risk indices (64.9% vs. 60.0%), and the Social Vulnerability Index (66.2% vs. 58.6%). For spatial downscaling in data-scarce settings, PPE integrates localized proxies to double baseline accuracy in Nigerian food security indicators (R^2 of 66.1% vs. 31.5%). For epidemiological nowcasting of the 2026 DRC Bundibugyo Ebola outbreak, PPE achieves a Recall@10 of 83.3% (identifying 15 of 18 newly invaded health zones across five weekly forecasts), a +10.3 percentage-point improvement over the public state-of-the-art modeling (~73%). By combining autonomous multimodal planetary data discovery with targeted model optimization, PPE lowers the technical barrier to planetary-scale analytics, enabling rapid, customized, expert-level deployment.

Foundation models have revolutionized natural language processing through a ``train once, deploy anywhere'' paradigm, where a single pre-trained model adapts to countless downstream tasks without retraining. Access to a Physics Foundation Model (PFM) would be transformative -- democratizing access to high-fidelity simulations, accelerating scientific discovery, and eliminating the need for specialized solver development. Yet current physics-aware machine learning approaches remain fundamentally limited to single, narrow domains and require retraining for each new system. We present the General Physics Transformer (GPhyT), trained on 1.8 TB of diverse simulation data, that demonstrates foundation model capabilities are achievable for physics. Our key insight is that transformers can learn to infer governing dynamics from context, enabling a single model to simulate fluid-solid interactions, shock waves, thermal convection, and multi-phase dynamics without being told the underlying equations. GPhyT achieves three critical breakthroughs: (1) superior performance across multiple physics domains, outperforming specialized architectures by up to 29x, (2) zero-shot generalization to entirely unseen physical systems through in-context learning, and (3) stable long-term predictions through 50-timestep rollouts. By establishing that a single model can learn generalizable physical principles from data alone, this work opens the path toward a universal PFM that could transform computational science and engineering.

Although Large Language Models (LLMs) and Large Multimodal Models (LMMs) exhibit impressive skills in various domains, their ability for mathematical reasoning within visual contexts has not been formally examined. Equipping LLMs and LMMs with this capability is vital for general-purpose AI assistants and showcases promising potential in education, data analysis, and scientific discovery. To bridge this gap, we present MathVista, a benchmark designed to amalgamate challenges from diverse mathematical and visual tasks. We first taxonomize the key task types, reasoning skills, and visual contexts from the literature to guide our selection from 28 existing math-focused and visual question answering datasets. Then, we construct three new datasets, IQTest, FunctionQA, and PaperQA, to accommodate for missing types of visual contexts. The problems featured often require deep visual understanding beyond OCR or image captioning, and compositional reasoning with rich domain-specific tools, thus posing a notable challenge to existing models. We conduct a comprehensive evaluation of 11 prominent open-source and proprietary foundation models (LLMs, LLMs augmented with tools, and LMMs), and early experiments with GPT-4V. The best-performing model, Multimodal Bard, achieves only 58% of human performance (34.8% vs 60.3%), indicating ample room for further improvement. Given this significant gap, MathVista fuels future research in the development of general-purpose AI agents capable of tackling mathematically intensive and visually rich real-world tasks. Preliminary tests show that MathVista also presents challenges to GPT-4V, underscoring the benchmark's importance. The project is available at https://mathvista.github.io/.

The rapid evolution of Multi-modality Large Language Models (MLLMs) has catalyzed a shift in computer vision from specialized models to general-purpose foundation models. Nevertheless, there is still an inadequacy in assessing the abilities of MLLMs on low-level visual perception and understanding. To address this gap, we present Q-Bench, a holistic benchmark crafted to systematically evaluate potential abilities of MLLMs on three realms: low-level visual perception, low-level visual description, and overall visual quality assessment. a) To evaluate the low-level perception ability, we construct the LLVisionQA dataset, consisting of 2,990 diverse-sourced images, each equipped with a human-asked question focusing on its low-level attributes. We then measure the correctness of MLLMs on answering these questions. b) To examine the description ability of MLLMs on low-level information, we propose the LLDescribe dataset consisting of long expert-labelled golden low-level text descriptions on 499 images, and a GPT-involved comparison pipeline between outputs of MLLMs and the golden descriptions. c) Besides these two tasks, we further measure their visual quality assessment ability to align with human opinion scores. Specifically, we design a softmax-based strategy that enables MLLMs to predict quantifiable quality scores, and evaluate them on various existing image quality assessment (IQA) datasets. Our evaluation across the three abilities confirms that MLLMs possess preliminary low-level visual skills. However, these skills are still unstable and relatively imprecise, indicating the need for specific enhancements on MLLMs towards these abilities. We hope that our benchmark can encourage the research community to delve deeper to discover and enhance these untapped potentials of MLLMs. Project Page: https://vqassessment.github.io/Q-Bench.

Time series reasoning is crucial to decision-making in diverse domains, including finance, energy usage, traffic, weather, and scientific discovery. While existing time series foundation models (TSFMs) can capture low-level dynamic patterns and provide accurate forecasting, further analysis usually requires additional background knowledge and sophisticated reasoning, which are lacking in most TSFMs but can be achieved through large language models (LLMs). On the other hand, without expensive post-training, LLMs often struggle with the numerical understanding of time series data. Although it is intuitive to integrate the two types of models, developing effective training recipes that align the two modalities for reasoning tasks is still an open challenge. To this end, we propose TS-Reasoner that aligns the latent representations of TSFMs with the textual inputs of LLMs for downstream understanding/reasoning tasks. Specifically, we propose a simple yet effective method to curate diverse, synthetic pairs of time series and textual captions for alignment training. We then develop a two-stage training recipe that applies instruction finetuning after the alignment pretraining. Unlike existing works that train an LLM to take time series as inputs, we leverage a pretrained TSFM and freeze it during training. Extensive experiments on several benchmarks demonstrate that TS-Reasoner not only outperforms a wide range of prevailing LLMs, Vision Language Models (VLMs), and Time Series LLMs, but also achieves this with remarkable data efficiency, e.g., using less than half the training data.

The prediction of crystal properties is essential for understanding structure-property relationships and accelerating the discovery of functional materials. However, conventional approaches relying on experimental measurements or density functional theory (DFT) calculations are often resource-intensive, limiting their scalability. Machine learning (ML) models offer a promising alternative by learning complex structure-property relationships from data, enabling faster predictions. Yet, existing ML models often rely on labeled data, adopt representations that poorly capture essential structural characteristics, and lack integration with physical principles--factors that limit their generalizability and interpretability. Here, we introduce CLOUD (Crystal Language mOdel for Unified and Differentiable materials modeling), a transformer-based framework trained on a novel Symmetry-Consistent Ordered Parameter Encoding (SCOPE) that encodes crystal symmetry, Wyckoff positions, and composition in a compact, coordinate-free string representation. Pre-trained on over six million crystal structures, CLOUD is fine-tuned on multiple downstream tasks and achieves competitive performance in predicting a wide range of material properties, demonstrating strong scaling performance. Furthermore, as proof of concept of differentiable materials modeling, CLOUD is applied to predict the phonon internal energy and heat capacity, which integrates the Debye model to preserve thermodynamic consistency. The CLOUD-DEBYE framework enforces thermodynamic consistency and enables temperature-dependent property prediction without requiring additional data. These results demonstrate the potential of CLOUD as a scalable and physics-informed foundation model for crystalline materials, unifying symmetry-consistent representations with physically grounded learning for property prediction and materials discovery.

The rapid advancement of foundation modelslarge-scale neural networks trained on diverse, extensive datasetshas revolutionized artificial intelligence, enabling unprecedented advancements across domains such as natural language processing, computer vision, and scientific discovery. However, the substantial parameter count of these models, often reaching billions or trillions, poses significant challenges in adapting them to specific downstream tasks. Low-Rank Adaptation (LoRA) has emerged as a highly promising approach for mitigating these challenges, offering a parameter-efficient mechanism to fine-tune foundation models with minimal computational overhead. This survey provides the first comprehensive review of LoRA techniques beyond large Language Models to general foundation models, including recent techniques foundations, emerging frontiers and applications of low-rank adaptation across multiple domains. Finally, this survey discusses key challenges and future research directions in theoretical understanding, scalability, and robustness. This survey serves as a valuable resource for researchers and practitioners working with efficient foundation model adaptation.

Self-supervised image backbones can be used to address complex 2D tasks (e.g., semantic segmentation, object discovery) very efficiently and with little or no downstream supervision. Ideally, 3D backbones for lidar should be able to inherit these properties after distillation of these powerful 2D features. The most recent methods for image-to-lidar distillation on autonomous driving data show promising results, obtained thanks to distillation methods that keep improving. Yet, we still notice a large performance gap when measuring the quality of distilled and fully supervised features by linear probing. In this work, instead of focusing only on the distillation method, we study the effect of three pillars for distillation: the 3D backbone, the pretrained 2D backbones, and the pretraining dataset. In particular, thanks to our scalable distillation method named ScaLR, we show that scaling the 2D and 3D backbones and pretraining on diverse datasets leads to a substantial improvement of the feature quality. This allows us to significantly reduce the gap between the quality of distilled and fully-supervised 3D features, and to improve the robustness of the pretrained backbones to domain gaps and perturbations.

In this work, we provide DZEN, a dataset of parallel Dzongkha and English test questions for Bhutanese middle and high school students. The over 5K questions in our collection span a variety of scientific topics and include factual, application, and reasoning-based questions. We use our parallel dataset to test a number of Large Language Models (LLMs) and find a significant performance difference between the models in English and Dzongkha. We also look at different prompting strategies and discover that Chain-of-Thought (CoT) prompting works well for reasoning questions but less well for factual ones. We also find that adding English translations enhances the precision of Dzongkha question responses. Our results point to exciting avenues for further study to improve LLM performance in Dzongkha and, more generally, in low-resource languages. We release the dataset at: https://github.com/kraritt/llm_dzongkha_evaluation.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

Object navigation (ObjectNav) requires an agent to navigate through unseen environments to find queried objects. Many previous methods attempted to solve this task by relying on supervised or reinforcement learning, where they are trained on limited household datasets with close-set objects. However, two key challenges are unsolved: understanding free-form natural language instructions that demand open-set objects, and generalizing to new environments in a zero-shot manner. Aiming to solve the two challenges, in this paper, we propose OpenFMNav, an Open-set Foundation Model based framework for zero-shot object Navigation. We first unleash the reasoning abilities of large language models (LLMs) to extract proposed objects from natural language instructions that meet the user's demand. We then leverage the generalizability of large vision language models (VLMs) to actively discover and detect candidate objects from the scene, building a Versatile Semantic Score Map (VSSM). Then, by conducting common sense reasoning on VSSM, our method can perform effective language-guided exploration and exploitation of the scene and finally reach the goal. By leveraging the reasoning and generalizing abilities of foundation models, our method can understand free-form human instructions and perform effective open-set zero-shot navigation in diverse environments. Extensive experiments on the HM3D ObjectNav benchmark show that our method surpasses all the strong baselines on all metrics, proving our method's effectiveness. Furthermore, we perform real robot demonstrations to validate our method's open-set-ness and generalizability to real-world environments.

Traditional AI methods often rely on task-specific model designs and training, which constrain both the scalability of model size and generalization across different tasks. Here, we introduce ChemFM, a large foundation model specifically developed for chemicals. By conducting a series of scaling experiments, we identify UniChem as the informative molecular database for pre-training the foundation model. ChemFM comprises 3 billion parameters and is pre-trained on 178 million molecules using self-supervised causal language modeling to extract generalizable molecular representations. This model can be adapted to diverse downstream chemical applications using either full-parameter or parameter-efficient fine-tuning methods. ChemFM consistently outperforms state-of-the-art task-specific AI models across all tested tasks. Notably, it achieves up to 67.48% performance improvement across 34 property prediction benchmarks, up to 33.80% reduction in mean average deviation between conditioned and actual properties of generated molecules in conditional molecular generation tasks, and up to 3.7% top-1 accuracy improvement across 4 reaction prediction datasets. Moreover, ChemFM demonstrates its superior performance in predicting antibiotic activity and cytotoxicity, highlighting its potential to advance the discovery of novel antibiotics. Furthermore, we demonstrate that, as a foundation model, ChemFM exhibits strong data efficiency, requiring significantly fewer labeled training samples to achieve state-of-the-art performance. We anticipate that ChemFM will significantly advance chemistry research by providing a foundation model capable of effectively generalizing across a broad range of tasks with minimal additional training.

The discovery of novel Ionic Liquids (ILs) is hindered by critical challenges in property prediction, including limited data, poor model accuracy, and fragmented workflows. Leveraging the power of Large Language Models (LLMs), we introduce AIonopedia, to the best of our knowledge, the first LLM agent for IL discovery. Powered by an LLM-augmented multimodal domain foundation model for ILs, AIonopedia enables accurate property predictions and incorporates a hierarchical search architecture for molecular screening and design. Trained and evaluated on a newly curated and comprehensive IL dataset, our model delivers superior performance. Complementing these results, evaluations on literature-reported systems indicate that the agent can perform effective IL modification. Moving beyond offline tests, the practical efficacy was further confirmed through real-world wet-lab validation, in which the agent demonstrated exceptional generalization capabilities on challenging out-of-distribution tasks, underscoring its ability to accelerate real-world IL discovery.

Ask a pretrained biomedical language model whether "cortisol 28 ug/dL" and "stock-market volatility" are related, and it returns a cosine similarity of 0.83 on a scale where 1.0 means identical. The two share no mechanism. This is not a corner case: every off-the-shelf biomedical encoder we tested (BioBERT, PubMedBERT, BioM-ELECTRA) scores unrelated cross-domain pairs between 0.76 and 0.92 when the answer should be near zero. Accuracy on cross-domain discrimination is 0%. Retrieval systems survive this, because a language model downstream filters the noise. A Large Behavioural Model (LBM), a foundation model whose subject is a person rather than a sentence, does not: it reasons over a graph of a user's life and treats embedding proximity as evidence that two events are causally linked. False proximity writes a false causal edge, and everything downstream inherits the error. Here, embedding geometry is not a tuning knob; it is correctness. We report the fix. A contrastive pass over 72,034 pairs raises PubMedBERT BIOSSES correlation from 0.633 to 0.828 and within-vs-across-domain separation from 1.05x to 1.63x. A second pass, BODHI, mines hard negatives from edges absent in a biomedical knowledge graph and lifts separation to 2.30x and the discrimination gap to +0.392, at a 4.5% BIOSSES cost. On an Intel Xeon 6737P with AMX, OpenVINO cuts single-query latency from 1367 ms to 10 ms (133x) and reaches 555 sentences/sec. One finding contradicts standard advice: FP16 beats INT8 on this silicon at every serving batch size, and we explain why. The same model on a no-AMX Ice Lake instance runs 13-27x slower. We release the benchmark suite, training corpora, the BODHI generator, and the OpenVINO scripts.

Spatial proteomics technologies have transformed our understanding of complex tissue architectures by enabling simultaneous analysis of multiple molecular markers and their spatial organization. The high dimensionality of these data, varying marker combinations across experiments and heterogeneous study designs pose unique challenges for computational analysis. Here, we present Virtual Tissues (VirTues), a foundation model framework for biological tissues that operates across the molecular, cellular and tissue scale. VirTues introduces innovations in transformer architecture design, including a novel tokenization scheme that captures both spatial and marker dimensions, and attention mechanisms that scale to high-dimensional multiplex data while maintaining interpretability. Trained on diverse cancer and non-cancer tissue datasets, VirTues demonstrates strong generalization capabilities without task-specific fine-tuning, enabling cross-study analysis and novel marker integration. As a generalist model, VirTues outperforms existing approaches across clinical diagnostics, biological discovery and patient case retrieval tasks, while providing insights into tissue function and disease mechanisms.

Can Large Language Models (LLMs) understand and reason about quantum operators? Despite their remarkable capabilities in mathematics and symbolic reasoning, LLMs remain inherently blind to quantum representations such as unitary matrices. In this work, we take a step toward bridging this gap by introducing an approach that maps unitary operators into the latent space of an LLM, enabling unified modeling over quantum and linguistic inputs. We instantiate this idea on Clifford+T circuit synthesis over a Pauli rotation gate set, where our model achieves results competitive with state-of-the-art methods and scales consistently with training data, with no signs of saturation. Our approach further enables language-conditioned synthesis, allowing gate constraints unseen during training to be specified directly in natural language. This work suggests a path toward quantum--aware foundation models that can natively interpret and reason about quantum operations, which could have broader implications reaching across quantum compilation and algorithm discovery.

Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery. Here, we introduce Open Drug Discovery Engine (OpenDDE), an open-source, all-atom biomolecular foundation model that uses co-folding as the entry point to a scalable AI-driven drug discovery engine. Rather than treating structure prediction as an isolated endpoint, OpenDDE is designed as a shared structural reasoning layer for modeling sequence-structure-function relationships across biomolecular complexes, enabling complex structure prediction today while providing a foundation for de novo design, affinity estimation, structure-conditioned optimization, and more. OpenDDE integrates advances in all-atom architecture, atomic latent reasoning, inference optimization, and large-scale data processing to achieve IsoDDE-level co-folding accuracy within a reproducible and openly accessible framework. We also identify two scaling-law directions for co-folding models, revealing practical routes for continued improvement through data, model, inference, and training scaling. By releasing training code, inference pipelines, checkpoints, and benchmarks, OpenDDE aims to democratize access to frontier biomolecular intelligence, accelerate global collaboration, and lay an open foundation for next-generation drug discovery systems that can move from predicting molecular structures toward designing, scoring, and optimizing therapeutic candidates for human health.

Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and behaviour. Moreover, these hidden features can be directly manipulated to steer model behaviour. However, it remains an open question whether this phenomenon is unique to models trained on inherently structured data (ie. language, images) or if it is a general property of foundation models. In this work, we investigate the internal representations of a large physics-focused foundation model. Inspired by recent work identifying single directions in activation space for complex behaviours in LLMs, we extract activation vectors from the model during forward passes over simulation datasets for different physical regimes. We then compute "delta" representations between the two regimes. These delta tensors act as concept directions in activation space, encoding specific physical features. By injecting these concept directions back into the model during inference, we can steer its predictions, demonstrating causal control over physical behaviours, such as inducing or removing some particular physical feature from a simulation. These results suggest that scientific foundation models learn generalised representations of physical principles. They do not merely rely on superficial correlations and patterns in the simulations. Our findings open new avenues for understanding and controlling scientific foundation models and has implications for AI-enabled scientific discovery.

Apollo did not reach the Moon merely because its engineers could solve difficult equations. It succeeded by turning a distant ambition into a mission architecture of explicit objectives, simulation, verification, and repeated correction. AI now faces a similar transition: frontier models can solve difficult tasks once the problem, tools, and success criteria are specified, yet consequential real-world challenges rarely arrive in an executable or verifiable form. We introduce Apodex Discovery, a framework for building and evaluating discoverative AI through the heavy-duty solver, a system comprising a foundation model, harness, tools, and control policies that pursues extended, stateful, verifiable investigations. It has three core components. First, a problem-scouting process surveyed 561 industries across 16 sectors, assembled 423 high-value real-world problems, and selected 20 for the initial release. Second, a common environment-task-episode abstraction provides data, tools, constraints, feedback, trajectory recording, and verification of intermediate artifacts and final submissions. Third, HDS6 evaluates Tools, Repair, Alternatives, Coherence, Evidence, and Scope independently of final-task success. In AAV capsid design, Apodex surpassed the published state of the art by 7% across viability, tropism, structure prediction, and generative design. In drug repurposing and reformulation, a task-specific biomedical environment improved the mean normalized prediction score of GPT-5.5 and GPT-5.6-sol by 2.5 and 7.6 points over the same closed-book backbone. Controlled ablations show that the fixed TRACES episode interface enables attribution of performance differences to specific solver components. Apodex Discovery moves AI evaluation beyond predefined benchmarks toward verifiable investigations aimed at genuine discovery.

Differentially private (DP) synthetic data, which closely resembles the original private data while maintaining strong privacy guarantees, has become a key tool for unlocking the value of private data without compromising privacy. Recently, Private Evolution (PE) has emerged as a promising method for generating DP synthetic data. Unlike other training-based approaches, PE only requires access to inference APIs from foundation models, enabling it to harness the power of state-of-the-art (SoTA) models. However, a suitable foundation model for a specific private data domain is not always available. In this paper, we discover that the PE framework is sufficiently general to allow APIs beyond foundation models. In particular, we demonstrate that many SoTA data synthesizers that do not rely on neural networks--such as computer graphics-based image generators, which we refer to as simulators--can be effectively integrated into PE. This insight significantly broadens PE's applicability and unlocks the potential of powerful simulators for DP data synthesis. We explore this approach, named Sim-PE, in the context of image synthesis. Across four diverse simulators, Sim-PE performs well, improving the downstream classification accuracy of PE by up to 3x, reducing FID by up to 80%, and offering much greater efficiency. We also show that simulators and foundation models can be easily leveraged together within PE to achieve further improvements. The code is open-sourced in the Private Evolution Python library: https://github.com/microsoft/DPSDA.

Finding scientifically interesting phenomena through slow, manual labeling campaigns severely limits our ability to explore the billions of galaxy images produced by telescopes. In this work, we develop a pipeline to create a semantic search engine from completely unlabeled image data. Our method leverages Vision-Language Models (VLMs) to generate descriptions for galaxy images, then contrastively aligns a pre-trained multimodal astronomy foundation model with these embedded descriptions to produce searchable embeddings at scale. We find that current VLMs provide descriptions that are sufficiently informative to train a semantic search model that outperforms direct image similarity search. Our model, AION-Search, achieves state-of-the-art zero-shot performance on finding rare phenomena despite training on randomly selected images with no deliberate curation for rare cases. Furthermore, we introduce a VLM-based re-ranking method that nearly doubles the recall for our most challenging targets in the top-100 results. For the first time, AION-Search enables flexible semantic search scalable to 140 million galaxy images, enabling discovery from previously infeasible searches. More broadly, our work provides an approach for making large, unlabeled scientific image archives semantically searchable, expanding data exploration capabilities in fields from Earth observation to microscopy. The code, data, and app are publicly available at https://github.com/NolanKoblischke/AION-Search

Artificial Intelligence (AI) algorithms frequently learn creative and unexpected solutions, surprising even expert researchers who develop and study them. They often astonish practitioners by discovering unanticipated behavior, exploiting loopholes in reward signals, or spontaneously uncovering previously unknown scientific phenomena. However, accounts of such unconventional behavior across machine learning are seldom formally documented. This work presents 26 curated firsthand anecdotes from various machine learning subfields representing the work of over 100 researchers. These anecdotes showcase the capability of modern AI systems to circumvent human-imposed design limitations and discover unexpected solutions to the tasks we train them on. Furthermore, these accounts are particularly important for the safety of future AI systems. They illustrate the fundamental challenge of aligning models with human values without diminishing their creativity, so they can make surprising discoveries without producing surprising, potentially harmful outcomes. The paper first details AI achieving superhuman success through reinforcement learning across many challenging domains. However, reward-driven optimization can fail when the model learns to hack an underspecified reward or unarticulated constraint. We then present case studies suggesting that harnessing internet-scale foundation models (FMs) has not resolved these fundamental challenges and, in fact, can supercharge them. Nevertheless, we argue that these same learning dynamics can be harnessed to accelerate scientific discovery. Finally, we hope this work provides a consolidated resource to inform future research and demonstrates that the tendency toward unexpected behaviors is commonplace in modern AI, highlighting the need to anticipate and manage AI's capacity for innovative, yet unpredictable, solutions. (abstract abridged)

Artificial intelligence is transforming computational materials science, improving the prediction of material properties, and accelerating the discovery of novel materials. Recently, publicly available material data repositories have grown rapidly. This growth encompasses not only more materials, but also a greater variety and quantity of their associated properties. Existing machine learning efforts in materials science focus primarily on single-modality tasks, i.e., relationships between materials and a single physical property, thus not taking advantage of the rich and multimodal set of material properties. Here, we introduce Multimodal Learning for Materials (MultiMat), which enables self-supervised multi-modality training of foundation models for materials. We demonstrate our framework's potential using data from the Materials Project database on multiple axes: (i) MultiMat achieves state-of-the-art performance for challenging material property prediction tasks; (ii) MultiMat enables novel and accurate material discovery via latent space similarity, enabling screening for stable materials with desired properties; and (iii) MultiMat encodes interpretable emergent features that may provide novel scientific insights.

Computational materials discovery is limited by the high cost of first-principles calculations. Machine learning (ML) potentials that predict energies from crystal structures are promising, but existing methods face computational bottlenecks. Steerable graph neural networks (GNNs) encode geometry with spherical harmonics, respecting atomic symmetries -- permutation, rotation, and translation -- for physically realistic predictions. Yet maintaining equivariance is difficult: activation functions must be modified, and each layer must handle multiple data types for different harmonic orders. We present Facet, a GNN architecture for efficient ML potentials, developed through systematic analysis of steerable GNNs. Our innovations include replacing expensive multi-layer perceptrons (MLPs) for interatomic distances with splines, which match performance while cutting computational and memory demands. We also introduce a general-purpose equivariant layer that mixes node information via spherical grid projection followed by standard MLPs -- faster than tensor products and more expressive than linear or gate layers. On the MPTrj dataset, Facet matches leading models with far fewer parameters and under 10% of their training compute. On a crystal relaxation task, it runs twice as fast as MACE models. We further show SevenNet-0's parameters can be reduced by over 25% with no accuracy loss. These techniques enable more than 10x faster training of large-scale foundation models for ML potentials, potentially reshaping computational materials discovery.

Visual foundation models provide strong perceptual features for robotics, but their dense representations lack explicit object-level structure, limiting robustness and contractility in manipulation tasks. We propose STORM (Slot-based Task-aware Object-centric Representation for robotic Manipulation), a lightweight object-centric adaptation module that augments frozen visual foundation models with a small set of semantic-aware slots for robotic manipulation. Rather than retraining large backbones, STORM employs a multi-phase training strategy: object-centric slots are first stabilized through visual--semantic pretraining using language embeddings, then jointly adapted with a downstream manipulation policy. This staged learning prevents degenerate slot formation and preserves semantic consistency while aligning perception with task objectives. Experiments on object discovery benchmarks and simulated manipulation tasks show that STORM improves generalization to visual distractors, and control performance compared to directly using frozen foundation model features or training object-centric representations end-to-end. Our results highlight multi-phase adaptation as an efficient mechanism for transforming generic foundation model features into task-aware object-centric representations for robotic control.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

The goal of object-centric representation learning is to decompose visual scenes into a structured representation that isolates the entities. Recent successes have shown that object-centric representation learning can be scaled to real-world scenes by utilizing pre-trained self-supervised features. However, so far, object-centric methods have mostly been applied in-distribution, with models trained and evaluated on the same dataset. This is in contrast to the wider trend in machine learning towards general-purpose models directly applicable to unseen data and tasks. Thus, in this work, we study current object-centric methods through the lens of zero-shot generalization by introducing a benchmark comprising eight different synthetic and real-world datasets. We analyze the factors influencing zero-shot performance and find that training on diverse real-world images improves transferability to unseen scenarios. Furthermore, inspired by the success of task-specific fine-tuning in foundation models, we introduce a novel fine-tuning strategy to adapt pre-trained vision encoders for the task of object discovery. We find that the proposed approach results in state-of-the-art performance for unsupervised object discovery, exhibiting strong zero-shot transfer to unseen datasets.

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Scientific artifacts such as models and datasets are foundations for research. With the rapid growth of platforms like HuggingFace, researchers now have access to a large number of artifacts. Yet, a key challenge remains: how can we automatically discover the state-of-the-art (SOTA) model for a given dataset by fully leveraging existing artifacts? We formalize this task as automatic SOTA discovery by modeling HuggingFace as an artifact graph, where nodes are models/datasets and edges represent evaluations. We propose ArtifactLinker, a two-stage framework: (1) ranking promising unobserved model--dataset links using Graph Neural Networks (GNNs) or graph-augmented Large Language Models (LLMs), and (2) verifying top-ranked links via coding experiments with LLM-based agents. We further introduce a benchmark named ArtifactBench with 14,053 artifacts and 51,337 relations to evaluate the performance of both stages. Results show that (1) graph structures between existing artifacts are effective for missing link prediction; (2) end-to-end ranking and verification with ArtifactLinker help discover potential SOTA results and research insights.

The transition from monolithic language models to modular, skill-equipped agents marks a defining shift in how large language models (LLMs) are deployed in practice. Rather than encoding all procedural knowledge within model weights, agent skills -- composable packages of instructions, code, and resources that agents load on demand -- enable dynamic capability extension without retraining. It is formalized in a paradigm of progressive disclosure, portable skill definitions, and integration with the Model Context Protocol (MCP). This survey provides a comprehensive treatment of the agent skills landscape, as it has rapidly evolved during the last few months. We organize the field along four axes: (i) architectural foundations, examining the SKILL.md specification, progressive context loading, and the complementary roles of skills and MCP; (ii) skill acquisition, covering reinforcement learning with skill libraries, autonomous skill discovery (SEAgent), and compositional skill synthesis; (iii) deployment at scale, including the computer-use agent (CUA) stack, GUI grounding advances, and benchmark progress on OSWorld and SWE-bench; and (iv) security, where recent empirical analyses reveal that 26.1% of community-contributed skills contain vulnerabilities, motivating our proposed Skill Trust and Lifecycle Governance Framework -- a four-tier, gate-based permission model that maps skill provenance to graduated deployment capabilities. We identify seven open challenges -- from cross-platform skill portability to capability-based permission models -- and propose a research agenda for realizing trustworthy, self-improving skill ecosystems. Unlike prior surveys that broadly cover LLM agents or tool use, this work focuses specifically on the emerging skill abstraction layer and its implications for the next generation of agentic systems. Project repo: https://github.com/scienceaix/agentskills

Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful static representations, but they do not explicitly model the distribution of cellular states for generative simulation. Here, we introduce Lingshu-Cell, a masked discrete diffusion model that learns transcriptomic state distributions and supports conditional simulation under perturbation. By operating directly in a discrete token space that is compatible with the sparse, non-sequential nature of single-cell transcriptomic data, Lingshu-Cell captures complex transcriptome-wide expression dependencies across approximately 18,000 genes without relying on prior gene selection, such as filtering by high variability or ranking by expression level. Across diverse tissues and species, Lingshu-Cell accurately reproduces transcriptomic distributions, marker-gene expression patterns and cell-subtype proportions, demonstrating its ability to capture complex cellular heterogeneity. Moreover, by jointly embedding cell type or donor identity with perturbation, Lingshu-Cell can predict whole-transcriptome expression changes for novel combinations of identity and perturbation. It achieves leading performance on the Virtual Cell Challenge H1 genetic perturbation benchmark and in predicting cytokine-induced responses in human PBMCs. Together, these results establish Lingshu-Cell as a flexible cellular world model for in silico simulation of cell states and perturbation responses, laying the foundation for a new paradigm in biological discovery and perturbation screening.

As foundational models reshape scientific discovery, a bottleneck persists in dynamical system reconstruction (DSR): the ability to learn across system hierarchies. Many meta-learning approaches have been applied successfully to single systems, but falter when confronted with sparse, loosely related datasets requiring multiple hierarchies to be learned. Mixture of Experts (MoE) offers a natural paradigm to address these challenges. Despite their potential, we demonstrate that naive MoEs are inadequate for the nuanced demands of hierarchical DSR, largely due to their gradient descent-based gating update mechanism which leads to slow updates and conflicted routing during training. To overcome this limitation, we introduce MixER: Mixture of Expert Reconstructors, a novel sparse top-1 MoE layer employing a custom gating update algorithm based on K-means and least squares. Extensive experiments validate MixER's capabilities, demonstrating efficient training and scalability to systems of up to ten parametric ordinary differential equations. However, our layer underperforms state-of-the-art meta-learners in high-data regimes, particularly when each expert is constrained to process only a fraction of a dataset composed of highly related data points. Further analysis with synthetic and neuroscientific time series suggests that the quality of the contextual representations generated by MixER is closely linked to the presence of hierarchical structure in the data.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

Foundation models have revolutionized language modeling, while whether this success is replicated in scientific computing remains unexplored. We present OmniArch, the first prototype aiming at solving multi-scale and multi-physics scientific computing problems with physical alignment. We addressed all three challenges with one unified architecture. Its pre-training stage contains a Fourier Encoder-decoder fading out the disharmony across separated dimensions and a Transformer backbone integrating quantities through temporal dynamics, and the novel PDE-Aligner performs physics-informed fine-tuning under flexible conditions. As far as we know, we first conduct 1D-2D-3D united pre-training on the PDEBench, and it sets not only new performance benchmarks for 1D, 2D, and 3D PDEs but also demonstrates exceptional adaptability to new physics via in-context and zero-shot learning approaches, which supports realistic engineering applications and foresight physics discovery.

Purpose: This study introduces the first adaptation of RETFound for joint optic disc (OD) and optic cup (OC) segmentation. RETFound is a well-known foundation model developed for fundus camera and optical coherence tomography images, which has shown promising performance in disease diagnosis. Methods: We propose FunduSegmenter, a model integrating a series of novel modules with RETFound, including a Pre-adapter, a Decoder, a Post-adapter, skip connections with Convolutional Block Attention Module and a Vision Transformer block adapter. The model is evaluated on a proprietary dataset, GoDARTS, and four public datasets, IDRiD, Drishti-GS, RIM-ONE-r3, and REFUGE, through internal verification, external verification and domain generalization experiments. Results: An average Dice similarity coefficient of 90.51% was achieved in internal verification, which outperformed all baselines, some substantially (nnU-Net: 82.91%; DUNet: 89.17%; TransUNet: 87.91%). In all external verification experiments, the average results were about 3% higher than those of the best baseline, and our model was also competitive in domain generalization. Conclusions: This study explored the potential of the latent general representations learned by RETFound for OD and OC segmentation in fundus camera images. Our FunduSegmenter generally outperformed state-of-the-art baseline methods. The proposed modules are general and can be extended to fine-tuning other foundation models. Translational Relevance: The model shows strong stability and generalization on both in-distribution and out-of-distribution data, providing stable OD and OC segmentation. This is an essential step for many automated tasks, from setting the accurate retinal coordinate to biomarker discovery. The code and trained weights are available at: https://github.com/JusticeZzy/FunduSegmenter.

Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range electrostatic effects. We present a new electrostatic foundation model for molecular chemistry that extends the MACE architecture with explicit treatment of long-range interactions and electrostatic induction. Our approach combines local many-body geometric features with a non-self-consistent field formalism that updates learnable charge and spin densities through polarisable iterations to model induction, followed by global charge equilibration via learnable Fukui functions to control total charge and total spin. This design enables an accurate and physical description of systems with varying charge and spin states while maintaining computational efficiency. Trained on the OMol25 dataset of 100 million hybrid DFT calculations, our models achieve chemical accuracy across diverse benchmarks, with accuracy competitive with hybrid DFT on thermochemistry, reaction barriers, conformational energies, and transition metal complexes. Notably, we demonstrate that the inclusion of long-range electrostatics leads to a large improvement in the description of non-covalent interactions and supramolecular complexes over non-electrostatic models, including sub-kcal/mol prediction of molecular crystal formation energy in the X23-DMC dataset and a fourfold improvement over short-ranged models on protein-ligand interactions. The model's ability to handle variable charge and spin states, respond to external fields, provide interpretable spin-resolved charge densities, and maintain accuracy from small molecules to protein-ligand complexes positions it as a versatile tool for computational molecular chemistry and drug discovery.

Object detection is integral to a bevy of real-world applications, from robotics to medical image analysis. To be used reliably in such applications, models must be capable of handling unexpected - or novel - objects. The open world object detection (OWD) paradigm addresses this challenge by enabling models to detect unknown objects and learn discovered ones incrementally. However, OWD method development is hindered due to the stringent benchmark and task definitions. These definitions effectively prohibit foundation models. Here, we aim to relax these definitions and investigate the utilization of pre-trained foundation models in OWD. First, we show that existing benchmarks are insufficient in evaluating methods that utilize foundation models, as even naive integration methods nearly saturate these benchmarks. This result motivated us to curate a new and challenging benchmark for these models. Therefore, we introduce a new benchmark that includes five real-world application-driven datasets, including challenging domains such as aerial and surgical images, and establish baselines. We exploit the inherent connection between classes in application-driven datasets and introduce a novel method, Foundation Object detection Model for the Open world, or FOMO, which identifies unknown objects based on their shared attributes with the base known objects. FOMO has ~3x unknown object mAP compared to baselines on our benchmark. However, our results indicate a significant place for improvement - suggesting a great research opportunity in further scaling object detection methods to real-world domains. Our code and benchmark are available at https://orrzohar.github.io/projects/fomo/.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

Go-Explore is a powerful family of algorithms designed to solve hard-exploration problems, built on the principle of archiving discovered states, and iteratively returning to and exploring from the most promising states. This approach has led to superhuman performance across a wide variety of challenging problems including Atari games and robotic control, but requires manually designing heuristics to guide exploration, which is time-consuming and infeasible in general. To resolve this, we propose Intelligent Go-Explore (IGE) which greatly extends the scope of the original Go-Explore by replacing these heuristics with the intelligence and internalized human notions of interestingness captured by giant foundation models (FMs). This provides IGE with a human-like ability to instinctively identify how interesting or promising any new state is (e.g. discovering new objects, locations, or behaviors), even in complex environments where heuristics are hard to define. Moreover, IGE offers the exciting and previously impossible opportunity to recognize and capitalize on serendipitous discoveries that cannot be predicted ahead of time. We evaluate IGE on a range of language-based tasks that require search and exploration. In Game of 24, a multistep mathematical reasoning problem, IGE reaches 100% success rate 70.8% faster than the best classic graph search baseline. Next, in BabyAI-Text, a challenging partially observable gridworld, IGE exceeds the previous SOTA with orders of magnitude fewer online samples. Finally, in TextWorld, we show the unique ability of IGE to succeed in settings requiring long-horizon exploration where prior SOTA FM agents like Reflexion completely fail. Overall, IGE combines the tremendous strengths of FMs and the powerful Go-Explore algorithm, opening up a new frontier of research into creating more generally capable agents with impressive exploration capabilities.

The massive and large-scale design of foundational semiconductor integrated circuits (ICs) is crucial to sustaining the advancement of many emerging and future technologies, such as generative AI, 5G/6G, and quantum computing. Excitingly, recent studies have shown the great capabilities of foundational models in expediting the design of digital ICs. Yet, applying generative AI techniques to accelerate the design of analog ICs remains a significant challenge due to critical domain-specific issues, such as the lack of a comprehensive dataset and effective representation methods for analog circuits. This paper proposes, AnalogGenie, a textbf{Gen}erattextbf{i}ve textbf{e}ngine for automatic design/discovery of textbf{Analog} circuit topologies--the most challenging and creative task in the conventional manual design flow of analog ICs. AnalogGenie addresses two key gaps in the field: building a foundational comprehensive dataset of analog circuit topology and developing a scalable sequence-based graph representation universal to analog circuits. Experimental results show the remarkable generation performance of AnalogGenie in broadening the variety of analog ICs, increasing the number of devices within a single design, and discovering unseen circuit topologies far beyond any prior arts. Our work paves the way to transform the longstanding time-consuming manual design flow of analog ICs to an automatic and massive manner powered by generative AI. Our source code is available at https://github.com/xz-group/AnalogGenie.

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

Foundation Models are neural networks that are capable of simultaneously solving many problems. Large Language Foundation Models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new Foundation Model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet Foundation Models beyond proof-of-principle studies and into the toolkit of practitioners.

Deep learning foundation models are revolutionizing many facets of science by leveraging vast amounts of data to learn general-purpose representations that can be adapted to tackle diverse downstream tasks. Foundation models hold the promise to also transform our ability to model our planet and its subsystems by exploiting the vast expanse of Earth system data. Here we introduce Aurora, a large-scale foundation model of the atmosphere trained on over a million hours of diverse weather and climate data. Aurora leverages the strengths of the foundation modelling approach to produce operational forecasts for a wide variety of atmospheric prediction problems, including those with limited training data, heterogeneous variables, and extreme events. In under a minute, Aurora produces 5-day global air pollution predictions and 10-day high-resolution weather forecasts that outperform state-of-the-art classical simulation tools and the best specialized deep learning models. Taken together, these results indicate that foundation models can transform environmental forecasting.

Foundation models pretrained on diverse data at scale have demonstrated extraordinary capabilities in a wide range of vision and language tasks. When such models are deployed in real world environments, they inevitably interface with other entities and agents. For example, language models are often used to interact with human beings through dialogue, and visual perception models are used to autonomously navigate neighborhood streets. In response to these developments, new paradigms are emerging for training foundation models to interact with other agents and perform long-term reasoning. These paradigms leverage the existence of ever-larger datasets curated for multimodal, multitask, and generalist interaction. Research at the intersection of foundation models and decision making holds tremendous promise for creating powerful new systems that can interact effectively across a diverse range of applications such as dialogue, autonomous driving, healthcare, education, and robotics. In this manuscript, we examine the scope of foundation models for decision making, and provide conceptual tools and technical background for understanding the problem space and exploring new research directions. We review recent approaches that ground foundation models in practical decision making applications through a variety of methods such as prompting, conditional generative modeling, planning, optimal control, and reinforcement learning, and discuss common challenges and open problems in the field.

Following its success for vision and text, the "foundation model" (FM) paradigm -- pretraining large models on massive data, then fine-tuning on target tasks -- has rapidly expanded to domains in the sciences, engineering, healthcare, and beyond. Has this achieved what the original FMs accomplished, i.e. the supplanting of traditional supervised learning in their domains? To answer we look at three modalities -- genomics, satellite imaging, and time series -- with multiple recent FMs and compare them to a standard supervised learning workflow: model development, hyperparameter tuning, and training, all using only data from the target task. Across these three specialized domains, we find that it is consistently possible to train simple supervised models -- no more complicated than a lightly modified wide ResNet or UNet -- that match or even outperform the latest foundation models. Our work demonstrates that the benefits of large-scale pretraining have yet to be realized in many specialized areas, reinforces the need to compare new FMs to strong, well-tuned baselines, and introduces two new, easy-to-use, open-source, and automated workflows for doing so.

Materials discovery and development are critical for addressing global challenges. Yet, the exponential growth in materials science literature comprising vast amounts of textual data has created significant bottlenecks in knowledge extraction, synthesis, and scientific reasoning. Large Language Models (LLMs) offer unprecedented opportunities to accelerate materials research through automated analysis and prediction. Still, their effective deployment requires domain-specific adaptation for understanding and solving domain-relevant tasks. Here, we present LLaMat, a family of foundational models for materials science developed through continued pretraining of LLaMA models on an extensive corpus of materials literature and crystallographic data. Through systematic evaluation, we demonstrate that LLaMat excels in materials-specific NLP and structured information extraction while maintaining general linguistic capabilities. The specialized LLaMat-CIF variant demonstrates unprecedented capabilities in crystal structure generation, predicting stable crystals with high coverage across the periodic table. Intriguingly, despite LLaMA-3's superior performance in comparison to LLaMA-2, we observe that LLaMat-2 demonstrates unexpectedly enhanced domain-specific performance across diverse materials science tasks, including structured information extraction from text and tables, more particularly in crystal structure generation, a potential adaptation rigidity in overtrained LLMs. Altogether, the present work demonstrates the effectiveness of domain adaptation towards developing practically deployable LLM copilots for materials research. Beyond materials science, our findings reveal important considerations for domain adaptation of LLMs, such as model selection, training methodology, and domain-specific performance, which may influence the development of specialized scientific AI systems.

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

Foundation models have enabled rapid progress across many specialized domains by leveraging large-scale pre-training on unlabeled data, demonstrating strong generalization to a variety of downstream tasks. While such models have gained significant attention in fields like Earth Observation, their application to Mars science remains limited. A key enabler of progress in other domains has been the availability of standardized benchmarks that support systematic evaluation. In contrast, Mars science lacks such benchmarks and standardized evaluation frameworks, which have limited progress toward developing foundation models for Martian tasks. To address this gap, we introduce Mars-Bench, the first benchmark designed to systematically evaluate models across a broad range of Mars-related tasks using both orbital and surface imagery. Mars-Bench comprises 20 datasets spanning classification, segmentation, and object detection, focused on key geologic features such as craters, cones, boulders, and frost. We provide standardized, ready-to-use datasets and baseline evaluations using models pre-trained on natural images, Earth satellite data, and state-of-the-art vision-language models. Results from all analyses suggest that Mars-specific foundation models may offer advantages over general-domain counterparts, motivating further exploration of domain-adapted pre-training. Mars-Bench aims to establish a standardized foundation for developing and comparing machine learning models for Mars science. Our data, models, and code are available at: https://mars-bench.github.io/.

Gastrointestinal (GI) endoscopy is essential in identifying GI tract abnormalities in order to detect diseases in their early stages and improve patient outcomes. Although deep learning has shown success in supporting GI diagnostics and decision-making, these models require curated datasets with labels that are expensive to acquire. Foundation models offer a promising solution by learning general-purpose representations, which can be finetuned for specific tasks, overcoming data scarcity. Developing foundation models for medical imaging holds significant potential, but the sensitive and protected nature of medical data presents unique challenges. Foundation model training typically requires extensive datasets, and while hospitals generate large volumes of data, privacy restrictions prevent direct data sharing, making foundation model training infeasible in most scenarios. In this work, we propose a FL framework for training foundation models for gastroendoscopy imaging, enabling data to remain within local hospital environments while contributing to a shared model. We explore several established FL algorithms, assessing their suitability for training foundation models without relying on task-specific labels, conducting experiments in both homogeneous and heterogeneous settings. We evaluate the trained foundation model on three critical downstream tasks--classification, detection, and segmentation--and demonstrate that it achieves improved performance across all tasks, highlighting the effectiveness of our approach in a federated, privacy-preserving setting.

Foundation models (FMs), large deep learning models pre-trained on vast, unlabeled datasets, exhibit powerful capabilities in understanding complex patterns and generating sophisticated outputs. However, they often struggle to adapt to specific tasks. Reinforcement learning (RL), which allows agents to learn through interaction and feedback, offers a compelling solution. Integrating RL with FMs enables these models to achieve desired outcomes and excel at particular tasks. Additionally, RL can be enhanced by leveraging the reasoning and generalization capabilities of FMs. This synergy is revolutionizing various fields, including robotics. FMs, rich in knowledge and generalization, provide robots with valuable information, while RL facilitates learning and adaptation through real-world interactions. This survey paper comprehensively explores this exciting intersection, examining how these paradigms can be integrated to advance robotic intelligence. We analyze the use of foundation models as action planners, the development of robotics-specific foundation models, and the mutual benefits of combining FMs with RL. Furthermore, we present a taxonomy of integration approaches, including large language models, vision-language models, diffusion models, and transformer-based RL models. We also explore how RL can utilize world representations learned from FMs to enhance robotic task execution. Our survey aims to synthesize current research and highlight key challenges in robotic reasoning and control, particularly in the context of integrating FMs and RL--two rapidly evolving technologies. By doing so, we seek to spark future research and emphasize critical areas that require further investigation to enhance robotics. We provide an updated collection of papers based on our taxonomy, accessible on our open-source project website at: https://github.com/clmoro/Robotics-RL-FMs-Integration.

We survey applications of pretrained foundation models in robotics. Traditional deep learning models in robotics are trained on small datasets tailored for specific tasks, which limits their adaptability across diverse applications. In contrast, foundation models pretrained on internet-scale data appear to have superior generalization capabilities, and in some instances display an emergent ability to find zero-shot solutions to problems that are not present in the training data. Foundation models may hold the potential to enhance various components of the robot autonomy stack, from perception to decision-making and control. For example, large language models can generate code or provide common sense reasoning, while vision-language models enable open-vocabulary visual recognition. However, significant open research challenges remain, particularly around the scarcity of robot-relevant training data, safety guarantees and uncertainty quantification, and real-time execution. In this survey, we study recent papers that have used or built foundation models to solve robotics problems. We explore how foundation models contribute to improving robot capabilities in the domains of perception, decision-making, and control. We discuss the challenges hindering the adoption of foundation models in robot autonomy and provide opportunities and potential pathways for future advancements. The GitHub project corresponding to this paper (Preliminary release. We are committed to further enhancing and updating this work to ensure its quality and relevance) can be found here: https://github.com/robotics-survey/Awesome-Robotics-Foundation-Models

Ensuring equitable Artificial Intelligence (AI) in healthcare demands systems that make unbiased decisions across all demographic groups, bridging technical innovation with ethical principles. Foundation Models (FMs), trained on vast datasets through self-supervised learning, enable efficient adaptation across medical imaging tasks while reducing dependency on labeled data. These models demonstrate potential for enhancing fairness, though significant challenges remain in achieving consistent performance across demographic groups. Our review indicates that effective bias mitigation in FMs requires systematic interventions throughout all stages of development. While previous approaches focused primarily on model-level bias mitigation, our analysis reveals that fairness in FMs requires integrated interventions throughout the development pipeline, from data documentation to deployment protocols. This comprehensive framework advances current knowledge by demonstrating how systematic bias mitigation, combined with policy engagement, can effectively address both technical and institutional barriers to equitable AI in healthcare. The development of equitable FMs represents a critical step toward democratizing advanced healthcare technologies, particularly for underserved populations and regions with limited medical infrastructure and computational resources.