Daily Papers

Visual events are a composition of temporal actions involving actors spatially interacting with objects. When developing computer vision models that can reason about compositional spatio-temporal events, we need benchmarks that can analyze progress and uncover shortcomings. Existing video question answering benchmarks are useful, but they often conflate multiple sources of error into one accuracy metric and have strong biases that models can exploit, making it difficult to pinpoint model weaknesses. We present Action Genome Question Answering (AGQA), a new benchmark for compositional spatio-temporal reasoning. AGQA contains 192M unbalanced question answer pairs for 9.6K videos. We also provide a balanced subset of 3.9M question answer pairs, 3 orders of magnitude larger than existing benchmarks, that minimizes bias by balancing the answer distributions and types of question structures. Although human evaluators marked 86.02% of our question-answer pairs as correct, the best model achieves only 47.74% accuracy. In addition, AGQA introduces multiple training/test splits to test for various reasoning abilities, including generalization to novel compositions, to indirect references, and to more compositional steps. Using AGQA, we evaluate modern visual reasoning systems, demonstrating that the best models barely perform better than non-visual baselines exploiting linguistic biases and that none of the existing models generalize to novel compositions unseen during training.

Spatio-Temporal Scene Graphs (STSGs) provide a concise and expressive representation of dynamic scenes by modeling objects and their evolving relationships over time. However, real-world visual relationships often exhibit a long-tailed distribution, causing existing methods for tasks like Video Scene Graph Generation (VidSGG) and Scene Graph Anticipation (SGA) to produce biased scene graphs. To this end, we propose ImparTail, a novel training framework that leverages loss masking and curriculum learning to mitigate bias in the generation and anticipation of spatio-temporal scene graphs. Unlike prior methods that add extra architectural components to learn unbiased estimators, we propose an impartial training objective that reduces the dominance of head classes during learning and focuses on underrepresented tail relationships. Our curriculum-driven mask generation strategy further empowers the model to adaptively adjust its bias mitigation strategy over time, enabling more balanced and robust estimations. To thoroughly assess performance under various distribution shifts, we also introduce two new tasks Robust Spatio-Temporal Scene Graph Generation and Robust Scene Graph Anticipation offering a challenging benchmark for evaluating the resilience of STSG models. Extensive experiments on the Action Genome dataset demonstrate the superior unbiased performance and robustness of our method compared to existing baselines.

Spatio-temporal scene graphs represent interactions in a video by decomposing scenes into individual objects and their pair-wise temporal relationships. Long-term anticipation of the fine-grained pair-wise relationships between objects is a challenging problem. To this end, we introduce the task of Scene Graph Anticipation (SGA). We adapt state-of-the-art scene graph generation methods as baselines to anticipate future pair-wise relationships between objects and propose a novel approach SceneSayer. In SceneSayer, we leverage object-centric representations of relationships to reason about the observed video frames and model the evolution of relationships between objects. We take a continuous time perspective and model the latent dynamics of the evolution of object interactions using concepts of NeuralODE and NeuralSDE, respectively. We infer representations of future relationships by solving an Ordinary Differential Equation and a Stochastic Differential Equation, respectively. Extensive experimentation on the Action Genome dataset validates the efficacy of the proposed methods.

Video scene graph generation (VidSGG) aims to capture objects and their evolving relationships in videos. This requires accounting for both the persistence of object identities and abrupt changes in relationships. Existing methods aggregate information across frames to exploit temporal context, but an emphasis on consistency can obscure these changes. As a result, a model may retain its previous prediction even after the underlying relation has changed. We refer to this failure mode as relational semantic inertia. To address this issue, we propose Relation-Transition-Aware Transformer (RTAformer), a one-stage framework that separately models entity persistence and relation changes. It injects calibrated differences between adjacent-frame relation queries to guide predicate updates, while cross-frame instance alignment during training helps reduce cross-frame representational drift. Experiments on Action Genome show improvements in recall and mean recall over existing methods, with ablation studies supporting the contributions of the proposed components and comparisons using matched backbones showing larger gains on relation-transition frames than on non-transition frames.

Dynamic Scene Graph Generation (DSGG) focuses on identifying visual relationships within the spatial-temporal domain of videos. Conventional approaches often employ multi-stage pipelines, which typically consist of object detection, temporal association, and multi-relation classification. However, these methods exhibit inherent limitations due to the separation of multiple stages, and independent optimization of these sub-problems may yield sub-optimal solutions. To remedy these limitations, we propose a one-stage end-to-end framework, termed OED, which streamlines the DSGG pipeline. This framework reformulates the task as a set prediction problem and leverages pair-wise features to represent each subject-object pair within the scene graph. Moreover, another challenge of DSGG is capturing temporal dependencies, we introduce a Progressively Refined Module (PRM) for aggregating temporal context without the constraints of additional trackers or handcrafted trajectories, enabling end-to-end optimization of the network. Extensive experiments conducted on the Action Genome benchmark demonstrate the effectiveness of our design. The code and models are available at https://github.com/guanw-pku/OED.

Dynamic scene graphs (DSGs) capture spatio-temporal interactions across videos as langlesubject, predicate, objectrangle triplets, and underpin downstream tasks such as video captioning, video question answering, and action analysis. However, end-to-end dynamic scene graph generation (DSGG) methods are closed-set: they recognize only objects and predicates from a fixed training vocabulary and struggle with the long-tailed distribution of rare concepts, severely limiting their real-world applicability. Existing open-vocabulary models typically inherit pretrained large language models, resulting in multi-stage training and inference with substantial cost. We introduce OvDSGG, the first end-to-end framework for open-vocabulary DSGG. OvDSGG builds on top of an open-vocabulary Spatial Backbone and a Temporal Backbone; we further propose a Triplet Feature Extraction Module that bridges them, and a Visual-Language Alignment Module that preserves open-vocabulary recognition by learning an adaptive decision boundary in the joint visual-language feature space, without expensive knowledge distillation in existing methods. We further introduce a rigorous open-vocabulary DSGG benchmark adapted from Action Genome, with disjoint Base/Novel splits for both objects and predicates. OvDSGG significantly outperforms open-vocabulary baselines across all metrics, with zero-shot Recall@K scores 10.0--20.4 percentage point higher than the next-best baseline, while on closed-set DSGG remaining competitive with state-of-the-art models. Code and benchmark are publicly available at https://github.com/jhelsby/OvDSGG/.

Dynamic Scene Graph Generation (DSGG) aims to create a scene graph for each video frame by detecting objects and predicting their relationships. Weakly Supervised DSGG (WS-DSGG) reduces annotation workload by using an unlocalized scene graph from a single frame per video for training. Existing WS-DSGG methods depend on an off-the-shelf external object detector to generate pseudo labels for subsequent DSGG training. However, detectors trained on static, object-centric images struggle in dynamic, relation-aware scenarios required for DSGG, leading to inaccurate localization and low-confidence proposals. To address the challenges posed by external object detectors in WS-DSGG, we propose a Temporal-enhanced Relation-aware Knowledge Transferring (TRKT) method, which leverages knowledge to enhance detection in relation-aware dynamic scenarios. TRKT is built on two key components:(1)Relation-aware knowledge mining: we first employ object and relation class decoders that generate category-specific attention maps to highlight both object regions and interactive areas. Then we propose an Inter-frame Attention Augmentation strategy that exploits optical flow for neighboring frames to enhance the attention maps, making them motion-aware and robust to motion blur. This step yields relation- and motion-aware knowledge mining for WS-DSGG. (2) we introduce a Dual-stream Fusion Module that integrates category-specific attention maps into external detections to refine object localization and boost confidence scores for object proposals. Extensive experiments demonstrate that TRKT achieves state-of-the-art performance on Action Genome dataset. Our code is avaliable at https://github.com/XZPKU/TRKT.git.

Spatio-temporal scene graphs provide a principled representation for modeling evolving object interactions, yet existing methods remain fundamentally frame-centric: they reason only about currently visible objects, discard entities upon occlusion, and operate in 2D. To address this, we first introduce ActionGenome4D, a dataset that upgrades Action Genome videos into 4D scenes via feed-forward 3D reconstruction, world-frame oriented bounding boxes for every object involved in actions, and dense relationship annotations including for objects that are temporarily unobserved due to occlusion or camera motion. Building on this data, we formalize World Scene Graph Generation (WSGG), the task of constructing a world scene graph at each timestamp that encompasses all interacting objects in the scene, both observed and unobserved. We then propose three complementary methods, each exploring a different inductive bias for reasoning about unobserved objects: PWG (Persistent World Graph), which implements object permanence via a zero-order feature buffer; MWAE (Masked World Auto-Encoder), which reframes unobserved-object reasoning as masked completion with cross-view associative retrieval; and 4DST (4D Scene Transformer), which replaces the static buffer with differentiable per-object temporal attention enriched by 3D motion and camera-pose features. We further design and evaluate the performance of strong open-source Vision-Language Models on the WSGG task via a suite of Graph RAG-based approaches, establishing baselines for unlocalized relationship prediction. WSGG thus advances video scene understanding toward world-centric, temporally persistent, and interpretable scene reasoning.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

The task of Grammatical Error Correction (GEC) has received remarkable attention with wide applications in Natural Language Processing (NLP) in recent years. While one of the key principles of GEC is to keep the correct parts unchanged and avoid over-correction, previous sequence-to-sequence (seq2seq) models generate results from scratch, which are not guaranteed to follow the original sentence structure and may suffer from the over-correction problem. In the meantime, the recently proposed sequence tagging models can overcome the over-correction problem by only generating edit operations, but are conditioned on human designed language-specific tagging labels. In this paper, we combine the pros and alleviate the cons of both models by proposing a novel Sequence-to-Action~(S2A) module. The S2A module jointly takes the source and target sentences as input, and is able to automatically generate a token-level action sequence before predicting each token, where each action is generated from three choices named SKIP, COPY and GENerate. Then the actions are fused with the basic seq2seq framework to provide final predictions. We conduct experiments on the benchmark datasets of both English and Chinese GEC tasks. Our model consistently outperforms the seq2seq baselines, while being able to significantly alleviate the over-correction problem as well as holding better generality and diversity in the generation results compared to the sequence tagging models.

The genome holds the blueprint that governs the biological properties of the cell. Consequently, advancing our knowledge of genomic function is crucial both for a broader understanding of biology and for continued biomedical advances. The success of large language models on natural language and protein sequences has motivated similar efforts on genomic data. However, standard genomic language models (gLMs) often require extremely large computational resources and still fall behind traditional methods on some downstream tasks. Recently, MSA-based pretraining has been proposed as an efficient alternative, but existing models are limited to short input contexts, restricting their use to short-range tasks, such as variant effect prediction. In this work, we present RAGenome, the first retrieval-based gLM that scales pretraining to longer contexts (100times longer than existing MSA-based gLMs), allowing it to capture both across-species evolutionary relationships and within-species longer-range interactions. Trained on whole-genome alignments from 100 vertebrates, RAGenome substantially improves the long-range capabilities of MSA-based gLMs, raising gene finding performance from 0.45 to 0.60, while remaining competitive on purely evolutionary-based tasks like prioritizing pathogenic variants. RAGenome provides competitive gLM performance at a fraction of the training cost, unifying evolutionary modeling and long-range capabilities within a single, flexible, scalable framework. Code is available at https://github.com/PanosAntoniadis/RAGenome.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

AI co-scientists could accelerate computational research, but over a long-running study the workflow also has to stay inspectable, resumable and reproducible, which requires persistent computational state and provenance. Here we present OpenAI4S, an open-source scientific research agent built around the principle of Code as Action, Science as Sessions. OpenAI4S combines a persistent computing runtime with research-session management: orchestration is handled through structured tool calls, while scientific actions are represented as complete code cells executed in persistent Python and R kernels. An append-only Action Ledger, per-cell execution records, versioned artifacts, environment records, and workspace checkpoints preserve how results were produced and support session recovery, branching, and extension. Configurable sandboxing, permission controls, and code and trajectory screening provide complementary safeguards. We evaluate OpenAI4S on 36 research scenarios spanning retrosynthesis, molecular dynamics, protein binder design, protein mutation, catalyst screening, and mineral spectroscopy, measuring scientific task accuracy, workflow completeness, and reproducibility of the resulting repositories. OpenAI4S achieves an overall score of 7.83, compared with 5.7--6.4 for a general-purpose coding harness evaluated with three frontier models, with the largest gains on long-horizon and computation-intensive workflows. These results suggest that integrating persistent execution with session-level provenance can improve the reliability of AI-assisted scientific workflows. Environment specification and full rerunnability remain weak for every evaluated system, ours included, so reproducibility is still an open problem for scientific agents. The system is available under the MIT license at https://github.com/PKU-YuanGroup/OpenAI4S{github.com/PKU-YuanGroup/OpenAI4S}.

Despite rapid progress in LLM agents, performance on long-horizon, tool-using tasks remains fragile. To better understand this fragility, we ask a simple question: do all actions contribute equally to failure? Analyzing execution traces on τ-Bench (Airline/Retail) and SWE-Bench Verified, we decompose trajectories into mutating (environment-changing) vs.\ non-mutating steps and formalize decisive deviations, earliest action, level divergences that flip success to failure. A logistic regression reveals that each additional deviation in a mutating action reduces the odds of success by upto 92% on Airline and upto 96% on Retail for SoTA models. In contrast, deviations in non-mutating actions have little to no effect. Errors also grow with context length as agents drift from role and act on stale constraints. Motivated by these observations, we introduce , a model-agnostic, gradient-free, test-time safeguard that (i) adds mutation-gated verification, (ii) injects Targeted Reflection before mutating steps, and (iii) performs block-based context cleaning. delivers consistent gains, e.g., Qwen3-Thinking: +28\% relative on Airline, +11\% on Retail, and +7\% on SWE-Bench Verified; Claude: +9\%/+7\%. We further identify ceiling effects in τ-Bench, where annotation errors and underspecified tasks artificially cap model performance. To address this, we release τ-Bench Verified, which restores benchmark headroom through targeted revisions. Our results argue for action-level analysis, targeted safeguards, and reliable evaluations as prerequisites for robust multi-turn agents.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

Discrete biological sequence optimization often requires goal-directed, parser-valid edits to an existing protein or molecule. Diffusion models support iterative refinement but do not expose a controllable discrete-edit interface, while autoregressive LLMs can be myopic when planning constrained edits over multiple steps. We introduce STRIDE (Sequence Trajectory Refinement via Iterative Discrete Editing), a post-training framework that trains an LLM to emit executable INSERT/DELETE/REPLACE trajectories for variable-length refinement. STRIDE first learns Levenshtein-aligned shortest-edit demonstrations, then uses supervised fine-tuning and group-based policy optimization to align trajectories with task rewards while preserving coherent editing. On an oracle-based full-action protein stress test, STRIDE raises success over Vanilla SFT from 42% to 89% and novelty among unique improvements from 47% to 97%. On instruction-conditioned molecular editing, the GSPO-aligned variant improves strict success, controllability, and SMILES validity over the SFT-only STRIDE model (code: https://github.com/daiheng-zhang/STRIDE).

Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature". While effective at capturing local syntax, these generative paradigms prioritize token-level reconstruction over high-level functional context. We introduce JEPA-DNA, a model-agnostic continual training framework that integrates a Joint-Embedding Predictive Architecture (JEPA) with traditional generative objectives. By supervising global sequence embeddings in a latent space, JEPA-DNA forces models to predict the functional representations of masked genomic segments, shifting the learning signal from token recovery to semantic alignment. We evaluate JEPA-DNA on 17 diverse genomic benchmark tasks, demonstrating consistent gains in linear probing and zero-shot performance regardless of the underlying GFM architecture or generative objective. Our framework establishes a new state-of-the-art for GFMs, surpassing the best existing models by bridging generative precision with latent semantic grounding. Through extensive ablation studies, we further characterize the synergistic interplay between generative and latent objectives. Our code is publicly available at https://github.com/NVIDIA-Digital-Bio/JEPA-DNA.

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.

Recent advancements in machine learning have significantly improved the identification of disease-associated genes from gene expression datasets. However, these processes often require extensive expertise and manual effort, limiting their scalability. Large Language Model (LLM)-based agents have shown promise in automating these tasks due to their increasing problem-solving abilities. To support the evaluation and development of such methods, we introduce GenoTEX, a benchmark dataset for the automated analysis of gene expression data. GenoTEX provides annotated code and results for solving a wide range of gene identification problems, encompassing dataset selection, preprocessing, and statistical analysis, in a pipeline that follows computational genomics standards. The benchmark includes expert-curated annotations from bioinformaticians to ensure accuracy and reliability. To provide baselines for these tasks, we present GenoAgent, a team of LLM-based agents that adopt a multi-step programming workflow with flexible self-correction, to collaboratively analyze gene expression datasets. Our experiments demonstrate the potential of LLM-based methods in analyzing genomic data, while error analysis highlights the challenges and areas for future improvement. We propose GenoTEX as a promising resource for benchmarking and enhancing automated methods for gene expression data analysis. The benchmark is available at https://github.com/Liu-Hy/GenoTex.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Long-range dependencies are critical for understanding genomic structure and function, yet most conventional methods struggle with them. Widely adopted transformer-based models, while excelling at short-context tasks, are limited by the attention module's quadratic computational complexity and inability to extrapolate to sequences longer than those seen in training. In this work, we explore State Space Models (SSMs) as a promising alternative by benchmarking two SSM-inspired architectures, Caduceus and Hawk, on long-range genomics modeling tasks under conditions parallel to a 50M parameter transformer baseline. We discover that SSMs match transformer performance and exhibit impressive zero-shot extrapolation across multiple tasks, handling contexts 10 to 100 times longer than those seen during training, indicating more generalizable representations better suited for modeling the long and complex human genome. Moreover, we demonstrate that these models can efficiently process sequences of 1M tokens on a single GPU, allowing for modeling entire genomic regions at once, even in labs with limited compute. Our findings establish SSMs as efficient and scalable for long-context genomic analysis.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

Scaling generalist vision-language-action (VLA) policies is severely bottlenecked by the inherent heterogeneity of embodied data, which spans diverse robot morphologies, camera configurations, and low-level action spaces. Existing paradigms typically address this mismatch through explicit action retargeting, human-to-robot video synthesis, or dataset-specific adaptation branches, fundamentally hindering the joint learning of a unified policy. We introduce UCAG-P, a camera-centric unified action formulation that structurally aligns heterogeneous embodied datasets into a shared geometric action space. Rather than treating robot-specific commands as the shared policy target, UCAG-P represents manipulation through camera-observable anchor motion in image and camera-frame coordinates, treating robot arms, humanoids, and human hands as different embodiments of a common action schema. A geometry-conditioned action translator combines predicted motion with target-embodiment kinematics to produce executable controls. The resulting decoupled architecture allows a shared VLA policy to learn transferable manipulation geometry while retaining embodiment-specific controllability. UCAG-P is trained on 4.03K hours of robot and simulation data and 2.34K hours of human demonstrations. A single checkpoint reaches 98.3% on LIBERO, 88.7% and 89.2% on RoboTwin Easy and Hard, 82.0% zero-shot on LIBERO-Plus, and 62.0% on RoboCasa GR-1, without benchmark-specific fine-tuning.

The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an investigation of intelligent monitoring systems as a means of tackling the issue of the reproducibility crisis. Specifically, we first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. This dataset comprises fine-grained hierarchical annotations intended for the purpose of studying activity understanding in BioLab. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings. Finally, we provide a thorough experimental evaluation of contemporary video understanding models and highlight their limitations in this specialized domain to identify potential avenues for future research. We hope ProBio with associated benchmarks may garner increased focus on modern AI techniques in the realm of molecular biology.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Existing action quality assessment (AQA) datasets and methods rely primarily on visual inputs such as RGB and pose, overlooking physiological dynamics such as muscle mechanics and often modeling actions as monolithic patterns. These limitations hinder fine-grained, biomechanically grounded feedback. We introduce MyoMechanix, a multimodal ecosystem for weight-loaded actions that aligns motion with muscle activity. Expert-annotated, it contains 7,500+ samples of 20 actions from 38 subjects, with synchronized multiview RGB video, 3D pose, sEMG, and additional physiological signals, forming the largest multimodal AQA benchmark to date. We further construct the Fitness Knowledge Graph (FKG), which organizes expert annotations into structured relationships among actions, phases, key steps, errors, and corrective feedback, enabling compositional scoring and interpretable assessment. Building on these representations, we develop CUBIST (Compositional Ontological Reasoning Engine), which performs decomposition-analysis-recomposition for fine-grained error attribution and feedback generation. We also establish MyoMechanix-AQA, MyoMechanix-VideoQA, and a novel MyoMechanix-Video2EMG task. Experiments show that multimodal sensing and structured representations improve performance, interpretability, and error attribution, with CUBIST achieving state-of-the-art results; VideoQA enhances language-grounded action understanding; and Video2EMG suggests video-based alternatives to costly EMG sensing. MyoMechanix advances skilled activity understanding toward biomechanically grounded, multimodal, and compositional reasoning for Physical AI applications in fitness, rehabilitation, healthcare, and machine learning. Project page: https://haoyin116.github.io/MyoMechanix/

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

Large language models are increasingly expected to execute complex workflows whose success depends on maintaining interdependent constraints and producing artifacts that satisfy strict end-to-end verification. Yet successful execution experience is typically lost after a single run, forcing subsequent models to rediscover strategies and failure modes from scratch. We study whether such experience can instead be externalized and reused through EvoMap, where verifier-confirmed execution trajectories are consolidated into structured Gene. To evaluate this setting, we introduce the Long-Workflow Benchmark (LongWoF-Bench), comprising 778 machine-verifiable tasks across code generation, agent-environment synthesis, mathematical reasoning, and rule following. On the 252 tasks with verifier-confirmed Opus trajectories, evolved EvoMap Gene outperform Skill across all seven evaluated models by 8.7-15.5 percentage points, with the gains extending to consumer models from different model families. In contrast, reference-distilled Gene do not exhibit the same advantage, indicating that compact representation alone is insufficient and that Gene utility is closely associated with verified experience provenance. For Claude Opus, Gene reuse also completes 39 more tasks than Skill while reducing solve-time token consumption by 9.9%. Together, these results show that verified execution experience can be retained and shared as a reusable external resource, enabling models to improve long-workflow completion without repeatedly paying the full cost of experience discovery.

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models consistently outperform random baselines and can exploit local sequence signals such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Clinical decision-making requires nuanced reasoning over heterogeneous evidence and traceable justifications. While recent LLM multi-agent systems (MAS) show promise, they largely optimise for outcome accuracy while overlooking process-grounded reasoning aligned with clinical standards. One critical real-world case of this is gene-disease validity curation, where experts must determine whether a gene is causally implicated in a disease by synthesising diverse biomedical evidence. We introduce an agent-as-tool reinforcement learning framework for this task with two objectives: (i) process-level supervision to ensure reasoning follows valid clinical pathways, and (ii) efficient coordination via a hierarchical multi-agent system. Our evaluation on the ClinGen dataset shows that with outcome-only rewards, MAS with a GRPO-trained Qwen3-4B supervisor agent substantially improves final outcome accuracy from 0.195 with a base model supervisor to 0.732, but results in poor process alignment (0.392 F1). Conversely, with process + outcome rewards, MAS with GRPO-trained supervisor achieves higher outcome accuracy (0.750) while significantly improving process fidelity to 0.520 F1. Our code is available at https://github.com/chaeeunlee-io/GeneDiseaseCurationAgents.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

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.

Assembly101 is a new procedural activity dataset featuring 4321 videos of people assembling and disassembling 101 "take-apart" toy vehicles. Participants work without fixed instructions, and the sequences feature rich and natural variations in action ordering, mistakes, and corrections. Assembly101 is the first multi-view action dataset, with simultaneous static (8) and egocentric (4) recordings. Sequences are annotated with more than 100K coarse and 1M fine-grained action segments, and 18M 3D hand poses. We benchmark on three action understanding tasks: recognition, anticipation and temporal segmentation. Additionally, we propose a novel task of detecting mistakes. The unique recording format and rich set of annotations allow us to investigate generalization to new toys, cross-view transfer, long-tailed distributions, and pose vs. appearance. We envision that Assembly101 will serve as a new challenge to investigate various activity understanding problems.

Action models are essential for enabling autonomous agents to perform complex tasks. However, training large action models remains challenging due to the diversity of agent environments and the complexity of agentic data. Despite growing interest, existing infrastructure provides limited support for scalable, agent-specific fine-tuning. We present ActionStudio, a lightweight and extensible data and training framework designed for large action models. ActionStudio unifies heterogeneous agent trajectories through a standardized format, supports diverse training paradigms including LoRA, full fine-tuning, and distributed setups, and integrates robust preprocessing and verification tools. We validate its effectiveness across both public and realistic industry benchmarks, demonstrating strong performance and practical scalability. We open-sourced code and data at https://github.com/SalesforceAIResearch/xLAM to facilitate research in the community.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

The choice of action spaces is a critical yet unresolved challenge in developing capable, end-to-end trainable agents. This paper first presents a large-scale, systematic comparison of prominent abstracted action spaces and tokenizers for Vision-Language-Action (VLA) or hierarchical agent models in the open-ended Minecraft. Our analysis reveals that no single action space is universally optimal; instead, the most effective abstraction is highly task-dependent, creating a dilemma for building generalist agents. To resolve this, we introduce Chain of Action (CoA), a novel framework that unifies high-level planning and low-level control within a single, monolithic VLA model. CoA treats an abstracted action not as a command for a separate policy, but as an intermediate reasoning step--akin to a chain of thought--that guides the generation of the final, executable action. Furthermore, we demonstrate that an All-in-One agent trained on a diverse mixture of action spaces using the CoA paradigm learns a more robust and generalizable policy. This unified agent achieves a new state-of-the-art, improving the overall task success rate over strong, specialized baselines. To foster reproducible research, we release the OpenHA (Open Hierarchical Agents) suite, which includes our comprehensive benchmark of over 800 distinct tasks, curated datasets, source code, and all pretrained model checkpoints at https://github.com/CraftJarvis/OpenHA

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.

Forward latent world models predict how actions change a scene, but recover actions for a desired change only through expensive test-time search. We introduce INTACT (INtent-To-ACTion), an end-to-end JEPA that turns action-labeled, reward-free trajectories into a deployable intent-to-action interface. Each transition supplies physical intent z_{t+1}-z_t, while a future goal supplies deployment intent sg(z_g)-z_t. The architecture is isomorphic between the local and goal motion-intent backbone-input graphs through an identical four-slot grammar and shared parameters, and between supported local and goal motion-intent families through action-law semantics induced by the same predictor rather than pointwise latent equality. INTACT also provides intact transfer from RGB evidence to action-effective latent intent coordinates and from intent families to their corresponding action-law families. Asymmetric endpoint gradients ground physical successors and fix future goals as anchors, joining representation learning and control without pointwise latent matching or globally linear dynamics. The resulting coordinates support a robust distributional action law: its conditional mean serves directly as a search-free policy, while sampling remains available for diversity or optional verification. On the four official LeWM tasks, one-epoch, zero-search models reach 85.78\%, 100.00\%, 97.67\%, and 97.89\% success. Optional local CEM centered on the Direct plan reaches 96.86\% macro success using 384 instead of 9,000 candidate sequences, reducing sampling by 23.44times while improving pure CEM by 16.00 points. One shared four-task encoder reaches 89.39\% E5 Direct macro and improves every task over jointly trained LeWM, while predicted--expert action-family kNN tracks Direct success at r=0.954. Direct inference takes 2.9--5.5 ms.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face limitations due to restricted access to domain-specific databases. GeneGPT is the current state-of-the-art system that enhances LLMs by utilizing specialized API calls, though it is constrained by rigid API dependencies and limited adaptability. We replicate GeneGPT and propose GenomAgent, a multi-agent framework that efficiently coordinates specialized agents for complex genomics queries. Evaluated on nine tasks from the GeneTuring benchmark, GenomAgent outperforms GeneGPT by 12% on average, and its flexible architecture extends beyond genomics to various scientific domains needing expert knowledge extraction.

Building general-purpose embodied agents across diverse hardware remains a central challenge in robotics, often framed as the ''one-brain, many-forms'' paradigm. Progress is hindered by fragmented data, inconsistent representations, and misaligned training objectives. We present ABot-M0, a framework that builds a systematic data curation pipeline while jointly optimizing model architecture and training strategies, enabling end-to-end transformation of heterogeneous raw data into unified, efficient representations. From six public datasets, we clean, standardize, and balance samples to construct UniACT-dataset, a large-scale dataset with over 6 million trajectories and 9,500 hours of data, covering diverse robot morphologies and task scenarios. Unified pre-training improves knowledge transfer and generalization across platforms and tasks, supporting general-purpose embodied intelligence. To improve action prediction efficiency and stability, we propose the Action Manifold Hypothesis: effective robot actions lie not in the full high-dimensional space but on a low-dimensional, smooth manifold governed by physical laws and task constraints. Based on this, we introduce Action Manifold Learning (AML), which uses a DiT backbone to predict clean, continuous action sequences directly. This shifts learning from denoising to projection onto feasible manifolds, improving decoding speed and policy stability. ABot-M0 supports modular perception via a dual-stream mechanism that integrates VLM semantics with geometric priors and multi-view inputs from plug-and-play 3D modules such as VGGT and Qwen-Image-Edit, enhancing spatial understanding without modifying the backbone and mitigating standard VLM limitations in 3D reasoning. Experiments show components operate independently with additive benefits. We will release all code and pipelines for reproducibility and future research.

Unlocking deep, interpretable biological reasoning from complex genomic data is a major AI challenge hindering scientific discovery. Current DNA foundation models, despite strong sequence representation, struggle with multi-step reasoning and lack inherent transparent, biologically intuitive explanations. We introduce BioReason, a pioneering architecture that, for the first time, deeply integrates a DNA foundation model with a Large Language Model (LLM). This novel connection enables the LLM to directly process and reason with genomic information as a fundamental input, fostering a new form of multimodal biological understanding. BioReason's sophisticated multi-step reasoning is developed through supervised fine-tuning and targeted reinforcement learning, guiding the system to generate logical, biologically coherent deductions. On biological reasoning benchmarks including KEGG-based disease pathway prediction - where accuracy improves from 88% to 97% - and variant effect prediction, BioReason demonstrates an average 15% performance gain over strong single-modality baselines. BioReason reasons over unseen biological entities and articulates decision-making through interpretable, step-by-step biological traces, offering a transformative approach for AI in biology that enables deeper mechanistic insights and accelerates testable hypothesis generation from genomic data. Data, code, and checkpoints are publicly available at https://github.com/bowang-lab/BioReason

Vision-language-action (VLA) models have advanced rapidly across backbones, training recipes, and data scale, yet the action decoder, which converts the backbone's hidden state into a continuous control signal, has barely changed and remains a single-point predictor across the majority of current VLAs. Whether implemented via autoregressive token bins, L1 regression, or flow-matching denoising, the resulting decoder treats the action space as unstructured, leaving the geometric proximity of neighboring actions unexploited during training. To advance this, we introduce ActionMap, a voxel heatmap action head that drops into an existing VLA in place of its native action decoder. For each new action, the head predicts a voxel heatmap over the action space, where each voxel directly stores the probability of the corresponding action. Across LIBERO simulation and real-world Franka manipulation, our heatmap head surpasses two architecturally distinct backbones at matched training steps (e.g., +8.2% over OpenVLA-OFT's L1 regression head on the LIBERO four-suite average), converges at comparable or faster rates on both backbones, and remains markedly more data-efficient at low training data. The cross-backbone consistency indicates that action representation is a real lever for VLA performance, distinct from further backbone or recipe scaling. Project Page: https://showlab.github.io/ActionMap/.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject to several limitations common in LLMs such as hallucinations. In response, we present GeneAgent, a first-of-its-kind language agent featuring self-verification capability. It autonomously interacts with various biological databases and leverages relevant domain knowledge to improve accuracy and reduce hallucination occurrences. Benchmarking on 1,106 gene sets from different sources, GeneAgent consistently outperforms standard GPT-4 by a significant margin. Moreover, a detailed manual review confirms the effectiveness of the self-verification module in minimizing hallucinations and generating more reliable analytical narratives. To demonstrate its practical utility, we apply GeneAgent to seven novel gene sets derived from mouse B2905 melanoma cell lines, with expert evaluations showing that GeneAgent offers novel insights into gene functions and subsequently expedites knowledge discovery.

Imitation learning has emerged as a powerful paradigm for learning visuomotor policies, but its generalisation and stability are limited by the scale and quality of demonstration data needed. A promising direction is to leverage more abundant but heterogeneous data sources, which differ in action space and often lack action labels altogether. Existing co-training approaches that combine heterogeneous data sources rely on heuristic and hand-engineered alignment techniques. In contrast, we argue that action representations should be grounded in prediction: actions that produce the same effect on the environment should share the same representation, regardless of their sources. To this end, we instantiate this principle by using a grounded latent-action world model (GLAM), a pair of generative models with a shared latent action space across data sources that is grounded by predicting future observations consistently across sources. This latent action space is used to train downstream behavioural cloning (BC) policies which map observations to latent actions and decode them back to robot actions, providing a paradigm for learning from heterogeneous data. Empirically, we demonstrate that GLAM successfully learns an aligned latent action space that facilitates action transfer across data sources with and without action labels. Across five manipulation tasks in simulation and in the real world, GLAM-aligned policies significantly outperform BC baselines and prior latent-action methods, achieving an average of +48% improvement in task success rate with the same data-scarce setting. Videos and code are available at https://viccccciv.github.io/glam/.

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse DNA elements, potentially enabling various genomic prediction, interpretation and design tasks. Despite their potential, existing benchmarks do not adequately assess the capabilities of DNALMs on key downstream applications involving an important class of non-coding DNA elements critical for regulating gene activity. In this study, we introduce DART-Eval, a suite of representative benchmarks specifically focused on regulatory DNA to evaluate model performance across zero-shot, probed, and fine-tuned scenarios against contemporary ab initio models as baselines. Our benchmarks target biologically meaningful downstream tasks such as functional sequence feature discovery, predicting cell-type specific regulatory activity, and counterfactual prediction of the impacts of genetic variants. We find that current DNALMs exhibit inconsistent performance and do not offer compelling gains over alternative baseline models for most tasks, while requiring significantly more computational resources. We discuss potentially promising modeling, data curation, and evaluation strategies for the next generation of DNALMs. Our code is available at https://github.com/kundajelab/DART-Eval.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Large Action Models (LAMs) extend large language models by enabling autonomous decision-making and tool execution, making them promising for automating scientific workflows. However, scientific workflows impose strict requirements on reproducibility, auditability, and deterministic execution, which are not satisfied by generic LLM-based agents. Unconstrained action generation can lead to silent state changes, non-deterministic executions, and irreproducible experimental results, limiting the applicability of LAMs in scientific settings. In this paper, we propose R-LAM, a reproducibility-constrained framework for applying Large Action Models to scientific workflow automation. R-LAM introduces structured action schemas, deterministic execution policies, and explicit provenance tracking to ensure that every action and intermediate artifact is auditable and replayable. The framework supports failure-aware execution loops and controlled workflow forking, enabling iterative experimentation without compromising reproducibility. We implement R-LAM as a lightweight Python framework and release it as an open-source PyPI package to facilitate reproducible research. An experimental evaluation of representative scientific workflows demonstrates that R-LAM improves reproducibility success rates and execution reliability compared to unconstrained LLM-based agents, while retaining adaptive control over workflow execution.

Autonomous agents such as Claude Code and Codex now operate for hours or even days. Understanding their runtime behavior has become critical for downstream tasks such as diagnosing inefficiencies, fixing bugs, and ensuring better oversight. A primary way to gain this understanding is analyzing the reasoning trajectories and execution traces these agents generate. Yet such data remains in unstructured natural-language form, making it difficult for humans to interpret at scale. We introduce ACT*ONOMY (a combination of Action and Taxonomy), a taxonomy for describing and analyzing agent behavior at runtime. ACT*ONOMY has two components: (1) the taxonomy itself, developed through Grounded Theory and structured as a three-level hierarchy of 10 actions, 46 subactions, and 120 leaf categories; and (2) an open repository that hosts the living taxonomy, provides an automated analysis pipeline that applies it to agent trajectories analysis, and defines an extension protocol for customization and growth. Our experiments show that ACTONOMY can compare behavioral profiles across agents and characterize a single agent's behavior across diverse trajectories, surfacing patterns indicative of failure modes. By providing a shared vocabulary, ACT*ONOMY helps researchers, agent designers, and end users interpret agent behavior more consistently, enabling better oversight and control.

Vision-language-action (VLA) models show strong potential for end-to-end autonomous driving by leveraging world knowledge and understanding to excel in long-tail scenarios. However, current VLAs have two limitations: 1) Degeneration into vision-action (VA) models. For low latency, regression/flow-based methods directly generate actions but underuse VLM understanding, causing unsafe, unexplainable actions. 2) Autoregressive high latency. Autoregressive methods sequentially generate chain-of-thought (CoT) and action tokens, fully leveraging VLM understanding, but high latency hinders deployment. To enable low-latency deployment while using CoT to assist action generation, we propose AUGUstus, an Autonomous-driving VLA model with Unified Generation and Understanding. We unify diffusion-based action generation and autoregressive CoT understanding in one model, where understanding only serves generation. Joint CoT supervision preserves VLM spatial understanding in shared representation for safer, more accurate trajectories. AUGUstus-mode orders action generation before CoT, so CoT supervises reliable actions during training while inference needs only action output, enabling low latency. AUGUstus-GRPO, a unified GRPO algorithm, jointly optimizes action and CoT, improving action performance. Experiments show AUGUstus achieves 94.6 PDMS on NAVSIMv1 and 90.7 EPDMS on NAVSIMv2, SOTA planning without scorer module. On nuScenes, it achieves average L2 error 0.27 m and average collision rate 0.05%, best among compared methods. To validate AUGUstus practicality, we train on in-house data with 512 NVIDIA H800 GPUs for ~2 days, evaluate on an internal 1,000 km dataset, and preliminarily deploy on a real vehicle, achieving 12 Hz operation. Project page: https://augustus-ad.github.io

Vision-language-action (VLA) models have shown promise as generalist robotic policies by jointly leveraging visual, linguistic, and proprioceptive modalities to generate action trajectories. While recent benchmarks have advanced VLA research in domestic tasks, professional science-oriented domains remain underexplored. We introduce AutoBio, a simulation framework and benchmark designed to evaluate robotic automation in biology laboratory environments--an application domain that combines structured protocols with demanding precision and multimodal interaction. AutoBio extends existing simulation capabilities through a pipeline for digitizing real-world laboratory instruments, specialized physics plugins for mechanisms ubiquitous in laboratory workflows, and a rendering stack that support dynamic instrument interfaces and transparent materials through physically based rendering. Our benchmark comprises biologically grounded tasks spanning three difficulty levels, enabling standardized evaluation of language-guided robotic manipulation in experimental protocols. We provide infrastructure for demonstration generation and seamless integration with VLA models. Baseline evaluations with two SOTA VLA models reveal significant gaps in precision manipulation, visual reasoning, and instruction following in scientific workflows. By releasing AutoBio, we aim to catalyze research on generalist robotic systems for complex, high-precision, and multimodal professional environments. The simulator and benchmark are publicly available to facilitate reproducible research.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic semantics, leading to wasted computation on low-information background and preventing understanding-driven compression for long contexts. Here, we present OpticalDNA, a vision-based framework that reframes genomic modeling as Optical Character Recognition (OCR)-style document understanding. OpticalDNA renders DNA into structured visual layouts and trains an OCR-capable vision--language model with a visual DNA encoder and a document decoder, where the encoder produces compact, reconstructible visual tokens for high-fidelity compression. Building on this representation, OpticalDNA defines prompt-conditioned objectives over core genomic primitives-reading, region grounding, subsequence retrieval, and masked span completion-thereby learning layout-aware DNA representations that retain fine-grained genomic information under a reduced effective token budget. Across diverse genomic benchmarks, OpticalDNA consistently outperforms recent baselines; on sequences up to 450k bases, it achieves the best overall performance with nearly 20times fewer effective tokens, and surpasses models with up to 985times more activated parameters while tuning only 256k trainable parameters.

Large Language Model (LLM) agents, capable of performing a broad range of actions, such as invoking tools and controlling robots, show great potential in tackling real-world challenges. LLM agents are typically prompted to produce actions by generating JSON or text in a pre-defined format, which is usually limited by constrained action space (e.g., the scope of pre-defined tools) and restricted flexibility (e.g., inability to compose multiple tools). This work proposes to use executable Python code to consolidate LLM agents' actions into a unified action space (CodeAct). Integrated with a Python interpreter, CodeAct can execute code actions and dynamically revise prior actions or emit new actions upon new observations through multi-turn interactions. Our extensive analysis of 17 LLMs on API-Bank and a newly curated benchmark shows that CodeAct outperforms widely used alternatives (up to 20% higher success rate). The encouraging performance of CodeAct motivates us to build an open-source LLM agent that interacts with environments by executing interpretable code and collaborates with users using natural language. To this end, we collect an instruction-tuning dataset CodeActInstruct that consists of 7k multi-turn interactions using CodeAct. We show that it can be used with existing data to improve models in agent-oriented tasks without compromising their general capability. CodeActAgent, finetuned from Llama2 and Mistral, is integrated with Python interpreter and uniquely tailored to perform sophisticated tasks (e.g., model training) using existing libraries and autonomously self-debug.

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major objective in biology is to understand biological sequences. Genomic Language Models (gLMs), which are LLMs trained on DNA sequences, have the potential to significantly advance our understanding of genomes and how DNA elements at various scales interact to give rise to complex functions. To showcase this potential, we highlight key applications of gLMs, including functional constraint prediction, sequence design, and transfer learning. Despite notable recent progress, however, developing effective and efficient gLMs presents numerous challenges, especially for species with large, complex genomes. Here, we discuss major considerations for developing and evaluating gLMs.

Large language model (LLM) agents are increasingly capable of automating components of machine learning development, yet existing biomedical benchmarks mainly focus on question answering, reasoning, and tool usage, or evaluate only narrow aspects of biomedical ML coding. We present BioXArena, a biomedical machine learning benchmark designed to evaluate whether agents can generate task-specific model training pipelines for heterogeneous and multi-modal biomedical datasets. BioXArena contains 76 end-to-end tasks across 9 domains, including sequence modeling, single-cell analysis, structural biology, network biology, chemical biology, perturbation dynamics, phenotype-disease modeling, biomedical imaging, and text-integrated learning. Each task is curated from primary biomedical sources into a unified evaluation framework with hidden labels, held-out graders, and biology-aware metrics normalized to a 0 to 1 scale. Agents are required to write executable code, train predictive models, and generate submissions for private test samples. Most tasks involve multiple input modalities, including tabular data, images, natural language, molecular sequences, omics matrices, and protein structures. We evaluate 11 agent configurations in a standardized 2-hour single-GPU environment. MLEvolve with Gemini-3.1-Pro achieves the highest average score of 0.666, followed by GPT-5.4 with 0.636, while no single agent consistently dominates across all domains. We additionally perform extensive ablation studies, robustness evaluations, scaling analyses, cost analyses, and failure-mode investigations to better understand how model backbones, agent scaffolds, inference budgets, and biomedical domains influence BioML coding performance. We will publicly release all benchmark tasks, graders, execution runners, leaderboard results, and agent trajectories.

Public viral genome resources such as the National Center for Biotechnology Information (NCBI) Virus database are central to outbreak response, evolutionary analysis, vaccine design, and genomic surveillance. Yet many high-value retrieval workflows remain optimized for interactive use rather than deterministic, reproducible programmatic interfaces. This creates a challenge for Large Language Model (LLM)-based scientific agents, where errors in metadata interpretation, filtering logic, or retrieval can propagate into incorrect datasets. To evaluate agentic viral data retrieval, we built VirBench, a manually curated benchmark of 120 queries spanning diverse pathogens, taxonomic levels, and metadata filters. When autonomous AI systems, including Biomni, Claude, GPT, and Edison Analysis, were tasked with these queries without a dedicated retrieval layer, performance varied widely: mean accuracy ranged from 16.9% for Claude Sonnet 4 to 91.3% for GPT-5.5, with newer frontier models showing progress but residual errors remaining consequential. To address this, we built gget virus, a deterministic query framework that formalizes NCBI Virus-style filtering as a reproducible programmatic system. By staging retrieval, applying metadata constraints before sequence download, and retrieving structured GenBank records, gget virus reduces data transfer by more than 98% for high-volume queries while preserving exact-match semantics. Instructing autonomous AI systems to use gget virus increased accuracy to at least 90.0% across all evaluated systems and up to 99.7% for GPT-5.5, improved response stability to 0.92-1.00, reduced error magnitude, and generally decreased runtime and tool calls. Together, this work establishes deterministic data access as critical infrastructure for reliable agentic science and provides a reproducible retrieval layer for robust human- and AI-driven viral genomics workflows.

Large language models (LLMs) have demonstrated strong capabilities in biological reasoning; however, genomic disease inference remains largely dependent on memorized gene-disease associations rather than understanding biological pathways. This shortcut learning undermines robustness and generalization, and breaks down when molecular identifiers are unavailable. We present GenoMorph, a multimodal genomic reasoning framework that shifts disease prediction from associative gene-disease mapping toward pathway-grounded reasoning. GenoMorph couples a frozen DNA foundation model with question-conditioned cross-attention fusion, self-adaptive latent reasoning (LatentSp), a residual reasoning gate for iterative genomic evidence reinjection, and rejection sampling fine-tuning regularized by hierarchical optimal transport (OT). Rather than learning direct gene-disease mappings, GenoMorph aligns genomic sequence representations with latent pathway dynamics, enabling reasoning trajectories that follow molecular interactions before producing disease predictions. LatentSp dynamically allocates computation according to reasoning confidence, reducing unnecessary reasoning steps and improving inference efficiency. We further construct an anonymized benchmark from the Kyoto Encyclopedia of Genes and Genomes (KEGG), replacing every gene and molecular identifier with anonymous symbols while preserving sequences and pathway topology, thereby removing memorization shortcuts. GenoMorph raises the weighted F1 from 0.7863 (BioReason) to 0.9412, and rejection sampling fine-tuning with self-adaptive latent reasoning pushes it to 0.9725 while cutting latency nearly 60%. On the anonymized benchmark it reaches 0.9465 F1, substantially outperforming prior systems and confirming that accurate disease prediction can arise from pathway reasoning rather than memorized gene-disease associations.

World models have emerged as promising neural simulators for autonomous driving, with the potential to supplement scarce real-world data and enable closed-loop evaluations. However, current research primarily evaluates these models based on visual realism or downstream task performance, with limited focus on fidelity to specific action instructions - a crucial property for generating targeted simulation scenes. Although some studies address action fidelity, their evaluations rely on closed-source mechanisms, limiting reproducibility. To address this gap, we develop an open-access evaluation framework, ACT-Bench, for quantifying action fidelity, along with a baseline world model, Terra. Our benchmarking framework includes a large-scale dataset pairing short context videos from nuScenes with corresponding future trajectory data, which provides conditional input for generating future video frames and enables evaluation of action fidelity for executed motions. Furthermore, Terra is trained on multiple large-scale trajectory-annotated datasets to enhance action fidelity. Leveraging this framework, we demonstrate that the state-of-the-art model does not fully adhere to given instructions, while Terra achieves improved action fidelity. All components of our benchmark framework will be made publicly available to support future research.

Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biological foundation models, specifically nucleotide foundation models (NFMs), the field lacks a unified standard for viral genomics to facilitate community development and enforce biosecurity constraints. To address this, we introduce ViroBench, the first comprehensive and large-scale benchmark specifically designed for NFMs in viral settings. ViroBench evaluates models across two critical dimensions: biological understanding and latent biosecurity risk, covering 18 diverse scenarios within 4 task types. Extensive evaluation of 66 NFMs across diverse architectures yields three critical conclusions. Firstly, NFMs exhibit a performance degradation in biological understanding under phylogenetic and temporal shifts, indicating weak extrapolation capabilities. Secondly, generation tasks reveal a decoupling between statistical likelihood and biological functional validity, posing latent biosecurity risks. Thirdly, controlled ablation studies reveal that taxonomic diversity in pretraining data outweighs parameter scale. Specifically, a lightweight baseline trained on diverse data achieves a 67.5% performance gain over its original model. Overall, ViroBench provides interpretable, diagnostic evaluations and a reproducible measurement framework for future research on viral nucleotide foundation models. The datasets and code are publicly available at https://github.com/QIANJINYDX/ViroBench.

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains underexplored. This paper follows the guidance of the central dogma to redesign both the data and model pipeline and offers a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions between coding and non-coding regions through masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive experiments show that Life-Code achieves state-of-the-art results on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

With the increasing awareness of health and the growing desire for aesthetic physique, fitness has become a prevailing trend. However, the potential risks associated with fitness training, especially with weight-loaded fitness actions, cannot be overlooked. Action Quality Assessment (AQA), a technology that quantifies the quality of human action and provides feedback, holds the potential to assist fitness enthusiasts of varying skill levels in achieving better training outcomes. Nevertheless, current AQA methodologies and datasets are limited to single-view competitive sports scenarios and RGB modality and lack professional assessment and guidance of fitness actions. To address this gap, we propose the FLEX dataset, the first multi-modal, multi-action, large-scale dataset that incorporates surface electromyography (sEMG) signals into AQA. FLEX utilizes high-precision MoCap to collect 20 different weight-loaded actions performed by 38 subjects across 3 different skill levels for 10 repetitions each, containing 5 different views of the RGB video, 3D pose, sEMG, and physiological information. Additionally, FLEX incorporates knowledge graphs into AQA, constructing annotation rules in the form of penalty functions that map weight-loaded actions, action keysteps, error types, and feedback. We conducted various baseline methodologies on FLEX, demonstrating that multimodal data, multiview data, and fine-grained annotations significantly enhance model performance. FLEX not only advances AQA methodologies and datasets towards multi-modal and multi-action scenarios but also fosters the integration of artificial intelligence within the fitness domain. Dataset and code are available at https://haoyin116.github.io/FLEX_Dataset.

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Continual learning in robotics seeks systems that can constantly adapt to changing environments and tasks, mirroring human adaptability. A key challenge is refining dynamics models, essential for planning and control, while addressing issues such as safe adaptation, catastrophic forgetting, outlier management, data efficiency, and balancing exploration with exploitation -- all within task and onboard resource constraints. Towards this goal, we introduce a generative framework leveraging flow matching for online robot dynamics model alignment. Rather than executing actions based on a misaligned model, our approach refines planned actions to better match with those the robot would take if its model was well aligned. We find that by transforming the actions themselves rather than exploring with a misaligned model -- as is traditionally done -- the robot collects informative data more efficiently, thereby accelerating learning. Moreover, we validate that the method can handle an evolving and possibly imperfect model while reducing, if desired, the dependency on replay buffers or legacy model snapshots. We validate our approach using two platforms: an unmanned ground vehicle and a quadrotor. The results highlight the method's adaptability and efficiency, with a record 34.2\% higher task success rate, demonstrating its potential towards enabling continual robot learning. Code: https://github.com/AlejandroMllo/action_flow_matching.

Tool-using agents make consequential changes to external state, yet correct outcomes do not guarantee that their actions were supported by evidence established beforehand. We study where this evidence-to-action chain breaks as agents move from deciding whether to act to executing single actions and dependent workflows. Across ten model-harness configurations, strong static action assessment can coexist with much weaker interactive execution. Failures often begin before execution: agents stop with incomplete investigation or act before required evidence is established. Once required evidence is obtained, single-action execution is usually reliable, while multi-action workflows additionally expose unresolved prerequisites and incomplete execution. For this analysis, we introduce SafeActBench, comprising 656 cases across six operational domains and five protocols that progress from static action judgment and investigated non-action to single- and multi-action workflows. A provenance-bound Evidence Ledger and deterministic trajectory evaluator track what information was established, when actions occurred, and whether downstream dependencies were satisfied. These results show that failures arise not only from missing information, but also from how agents use established evidence when deciding and executing actions.

We introduce UbiPhysio, a milestone framework that delivers fine-grained action description and feedback in natural language to support people's daily functioning, fitness, and rehabilitation activities. This expert-like capability assists users in properly executing actions and maintaining engagement in remote fitness and rehabilitation programs. Specifically, the proposed UbiPhysio framework comprises a fine-grained action descriptor and a knowledge retrieval-enhanced feedback module. The action descriptor translates action data, represented by a set of biomechanical movement features we designed based on clinical priors, into textual descriptions of action types and potential movement patterns. Building on physiotherapeutic domain knowledge, the feedback module provides clear and engaging expert feedback. We evaluated UbiPhysio's performance through extensive experiments with data from 104 diverse participants, collected in a home-like setting during 25 types of everyday activities and exercises. We assessed the quality of the language output under different tuning strategies using standard benchmarks. We conducted a user study to gather insights from clinical physiotherapists and potential users about our framework. Our initial tests show promise for deploying UbiPhysio in real-life settings without specialized devices.

Vision-language-action (VLA) models increasingly rely on diffusion- or flow-matching-based action heads to generate continuous robot actions. These action heads typically process the denoising trajectory in a largely uniform manner. However, we observe that the conditioning focus naturally shifts across denoising stages: early stages combine language instructions and visual observations to establish a coarse action trajectory, whereas later stages place greater emphasis on current visual observations for action alignment. Based on this insight, we introduce StairVLA, a stage-aware hierarchical action generation framework that uses partially denoised actions as a natural interface between coarse long-horizon action generation and local refinement. A high-level VLA performs early denoising to produce a reusable long-horizon partially denoised action trajectory, while a lightweight refiner operates at a higher frequency to refine local action chunks using the latest observations. This design amortizes expensive high-level VLA computation while preserving frequent closed-loop correction. On LIBERO, our GR00T-style instantiation improves average success from 96.5% to 97.8% while reducing amortized inference latency from 115.0 ms to 44.2 ms per action chunk. More broadly, across two VLA backbones, simulation benchmarks, and real-robot tasks, StairVLA consistently reduces inference cost while maintaining strong task performance.

Large discrete action spaces (LDAS) remain a central challenge in reinforcement learning. Existing solution approaches can handle unstructured LDAS with up to a few million actions. However, many real-world applications in logistics, production, and transportation systems have combinatorial action spaces, whose size grows well beyond millions of actions, even on small instances. Fortunately, such action spaces exhibit structure, e.g., equally spaced discrete resource units. With this work, we focus on handling structured LDAS (SLDAS) with sizes that cannot be handled by current benchmarks: we propose Dynamic Neighborhood Construction (DNC), a novel exploitation paradigm for SLDAS. We present a scalable neighborhood exploration heuristic that utilizes this paradigm and efficiently explores the discrete neighborhood around the continuous proxy action in structured action spaces with up to 10^{73} actions. We demonstrate the performance of our method by benchmarking it against three state-of-the-art approaches designed for large discrete action spaces across two distinct environments. Our results show that DNC matches or outperforms state-of-the-art approaches while being computationally more efficient. Furthermore, our method scales to action spaces that so far remained computationally intractable for existing methodologies.

State-of-the-art physical AI models generate a chunk of actions per inference through diffusion or flow matching, iteratively refining an initial noise sample into an action trajectory. Because this inference process is inherently stochastic, committing to a single trajectory per round is brittle, and this brittleness compounds across the many sequential rounds that comprise a complete episode. We introduce KeyStone, an inference-time self-consistency method for diffusion-based action generation that draws K candidate action chunks in parallel from a shared model context, clusters them in continuous action space, and returns the medoid of the largest cluster -- no additional model required. Two properties make this practical. First, the compact nature of action trajectories makes diffusion inference memory-bandwidth bound, leaving spare compute capacity to run K chains in parallel with no additional wall-clock latency. Second, unlike token or pixel spaces where distance carries no semantic meaning and selection requires a learned judge, action chunks are geometrically structured such that Euclidean distance directly reflects physical similarity, making selection principled and judge-free. Across diverse vision-language-action models (VLAs) and world-action models (WAMs), KeyStone improves task success rates by up to 13.3\% over single-trajectory sampling with negligible latency overhead, while having on par accuracy with model-based selectors at no training cost. We open source KeyStone at https://github.com/dywsjtu/keystone.

This study focuses on a novel task in text-to-image (T2I) generation, namely action customization. The objective of this task is to learn the co-existing action from limited data and generalize it to unseen humans or even animals. Experimental results show that existing subject-driven customization methods fail to learn the representative characteristics of actions and struggle in decoupling actions from context features, including appearance. To overcome the preference for low-level features and the entanglement of high-level features, we propose an inversion-based method Action-Disentangled Identifier (ADI) to learn action-specific identifiers from the exemplar images. ADI first expands the semantic conditioning space by introducing layer-wise identifier tokens, thereby increasing the representational richness while distributing the inversion across different features. Then, to block the inversion of action-agnostic features, ADI extracts the gradient invariance from the constructed sample triples and masks the updates of irrelevant channels. To comprehensively evaluate the task, we present an ActionBench that includes a variety of actions, each accompanied by meticulously selected samples. Both quantitative and qualitative results show that our ADI outperforms existing baselines in action-customized T2I generation. Our project page is at https://adi-t2i.github.io/ADI.

A generalist robotic policy needs both semantic understanding for task planning and the ability to interact with the environment through predictive capabilities. To tackle this, we present MM-ACT, a unified Vision-Language-Action (VLA) model that integrates text, image, and action in shared token space and performs generation across all three modalities. MM-ACT adopts a re-mask parallel decoding strategy for text and image generation, and employs a one-step parallel decoding strategy for action generation to improve efficiency. We introduce Context-Shared Multimodal Learning, a unified training paradigm that supervises generation in all three modalities from a shared context, enhancing action generation through cross-modal learning. Experiments were conducted on the LIBERO simulation and Franka real-robot setups as well as RoboTwin2.0 to assess in-domain and out-of-domain performances respectively. Our approach achieves a success rate of 96.3% on LIBERO, 72.0% across three tasks of real Franka, and 52.38% across eight bimanual tasks of RoboTwin2.0 with an additional gain of 9.25% from cross-modal learning. We release our codes, models and data at https://github.com/HHYHRHY/MM-ACT.

Understanding the underlying linguistic rules of plant genomes remains a fundamental challenge in computational biology. Recent advances including AgroNT and PDLLMs have made notable progress although, they suffer from excessive parameter size and limited ability to model the bidirectional nature of DNA strands respectively. To address these limitations, we propose PlantBiMoE, a lightweight and expressive plant genome language model that integrates bidirectional Mamba and a Sparse Mixture-of-Experts (SparseMoE) framework. The bidirectional Mamba enables the model to effectively capture structural dependencies across both the forward and reverse DNA strands, while SparseMoE significantly reduces the number of active parameters, improving computational efficiency without sacrificing modeling capacity. We evaluated and tested our model on the Modified Plants Genome Benchmark (MPGB), an enhanced genomic benchmark, which consolidates 31 datasets across 11 representative tasks, with input sequence lengths ranging from 50 to 6,000 bp. Experimental results demonstrate that PlantBiMoE achieves the best performance on 20 out of 31 datasets and the average best when comparing with existing models. In summary, all above results demonstrate that our model can effectively represent plant genomic sequences, serving as a robust computational tool for diverse genomic tasks, while making substantive contributions to plant genomics, gene editing, and synthetic biology. The code is available at: https://github.com/HUST-Keep-Lin/PlantBiMoE

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

Generative recommendation (GR) is an emerging paradigm where user actions are tokenized into discrete token patterns and autoregressively generated as predictions. However, existing GR models tokenize each action independently, assigning the same fixed tokens to identical actions across all sequences without considering contextual relationships. This lack of context-awareness can lead to suboptimal performance, as the same action may hold different meanings depending on its surrounding context. To address this issue, we propose ActionPiece to explicitly incorporate context when tokenizing action sequences. In ActionPiece, each action is represented as a set of item features, which serve as the initial tokens. Given the action sequence corpora, we construct the vocabulary by merging feature patterns as new tokens, based on their co-occurrence frequency both within individual sets and across adjacent sets. Considering the unordered nature of feature sets, we further introduce set permutation regularization, which produces multiple segmentations of action sequences with the same semantics. Experiments on public datasets demonstrate that ActionPiece consistently outperforms existing action tokenization methods, improving NDCG@10 by 6.00% to 12.82%.

Vision-Language-Action (VLA) models leveraging the native autoregressive paradigm of Vision-Language Models (VLMs) have demonstrated superior instruction-following and training efficiency. Central to this paradigm is action tokenization, yet its design has primarily focused on reconstruction fidelity, failing to address its direct impact on VLA optimization. Consequently, the fundamental question of what makes for good action tokenizers remains unanswered. In this paper, we bridge this gap by establishing design principles specifically from the perspective of VLA optimization. We identify a set of best practices based on information-theoretic insights, including maximized temporal token overlap, minimized vocabulary redundancy, enhanced multimodal mutual information, and token independence. Guided by these principles, we introduce ActionCodec, a high-performance action tokenizer that significantly enhances both training efficiency and VLA performance across diverse simulation and real-world benchmarks. Notably, on LIBERO, a SmolVLM2-2.2B fine-tuned with ActionCodec achieves a 95.5\% success rate without any robotics pre-training. With advanced architectural enhancements, this reaches 97.4\%, representing a new SOTA for VLA models without robotics pre-training. We believe our established design principles, alongside the released model, will provide a clear roadmap for the community to develop more effective action tokenizers.

LeWorldModel trains a latent world model with a prediction loss and a single anti-collapse regulariser, and reports approximately 87% of goals reached on TwoRoom, its simplest diagnostic environment. We reproduce that result by independent reimplementation on roughly $25 of rented compute, with all evaluation on one laptop CPU. We reach 94.0% at the repository's evaluation goal offset, against 84.0% for the authors' own released checkpoint measured under our protocol on identical episodes, and we reproduce the reported representation result directly (position probe Pearson r = 0.9988 against a reported 0.996). Reaching that point required four conventions that determine the outcome and appear in no released configuration file: dense action gathering across a frameskip block, a programmatically-set action-encoder width, ImageNet pixel normalisation, and action z-scoring. A reproducer following the released configurations alone obtains a model whose predictor cannot converge. The evaluation protocol is itself contested by the released material. The paper's appendix and the repository's configuration specify different goal offsets and step budgets; on the authors' own weights these yield 14.0% and 84.0%, and only the configuration's values reproduce the reported figure. On fifty identical episodes, changing nothing but how the goal is constructed moves that checkpoint from 84.0% to 8.0%. Two findings generalise. One-step prediction accuracy does not predict long-horizon planning success: across three checkpoints spanning a sevenfold range in prediction error, including the authors' own, it orders short-horizon success monotonically and fails to order long-horizon success at all. And a batch normalisation layer inflated our reported validation loss by up to a factor of 300, concealing a training loss that was flat throughout.

Vision-Language-Action (VLA) models can turn multimodal context into robot actions, but their action decoders are still trained largely by behavior cloning. This supervises which motor command was demonstrated while leaving implicit the local objective served by the behavior under the instruction. Future-based supervision enriches action learning with frames, latent observations, trajectories, or motion representations, but these signals capture particular realizations of what may happen rather than the shared semantic objective of the forthcoming behavior. We propose Intention Distillation (INDI), which distills behavior-level intent into the action decoder. During training, a frozen teacher VLM interprets a demonstrated segment from the current observation, instruction, coarse action summary, and corresponding execution video. From its standard inputs, the deployed VLA recovers the resulting multimodal intent representation at an intermediate decoder layer and uses it to organize action prediction together with representations of how the behavior unfolds and what it achieves. On SimplerEnv-Bridge, INDI improves GR00T-N1.7 from 64.3% to 84.7%, and on RoboCasa Kitchen it improves the controlled GR00T-N1.7 baseline from 64.1% to 70.3%, with consistent gains on π_{0.5} across both benchmarks. In real-world tasks, INDI improves average success from 62.0% to 68.7%, with gains of up to 12.0 pp on longer-horizon tasks. Further analyses show that the recovered latent is used by the decoder, captures behavior objective and execution progress, and organizes downstream predictions in an objective-dependent manner. These results show that action decoders benefit from explicitly modeling the semantic objective of the behavior they generate.

Teaching robots to autonomously complete everyday tasks remains a challenge. Imitation Learning (IL) is a powerful approach that imbues robots with skills via demonstrations, but is limited by the labor-intensive process of collecting teleoperated robot data. Human videos offer a scalable alternative, but it remains difficult to directly train IL policies from them due to the lack of robot action labels. To address this, we propose to represent actions as short-horizon 2D trajectories on an image. These actions, or motion tracks, capture the predicted direction of motion for either human hands or robot end-effectors. We instantiate an IL policy called Motion Track Policy (MT-pi) which receives image observations and outputs motion tracks as actions. By leveraging this unified, cross-embodiment action space, MT-pi completes tasks with high success given just minutes of human video and limited additional robot demonstrations. At test time, we predict motion tracks from two camera views, recovering 6DoF trajectories via multi-view synthesis. MT-pi achieves an average success rate of 86.5% across 4 real-world tasks, outperforming state-of-the-art IL baselines which do not leverage human data or our action space by 40%, and generalizes to scenarios seen only in human videos. Code and videos are available on our website https://portal-cornell.github.io/motion_track_policy/.

Action supervision in vision-language-action (VLA) models is often treated as a downstream objective for learning action prediction. In this paper, we study it instead as a force that shapes inherited multimodal representations. We show that this shaping has a dual effect: it is necessary for forming action-compatible representations, but when action supervision is applied too directly to the inherited multimodal pathway, it can also destabilize representations that support language-side processing and object grounding. To address this tension, we introduce Action QFormer, a query-based action-facing interface that uses instruction-conditioned queries to reorganize inherited multimodal information into action-facing representations before downstream action generation. In zero-shot sim-to-real navigation, Action QFormer improves average closed-loop task success from 18.8% to 56.3%, raises fixed-instruction action-generation correctness from 22.5% to 75.5%, and nearly eliminates out-of-distribution instruction generations. Further analyses show that Action QFormer changes how action supervision shapes inherited multimodal representations, reducing broad upstream rewriting while preserving targeted and sometimes constructive action-supervised adaptation. These results suggest that improving VLA performance requires not only stronger pretrained backbones, but also better ways of selecting and organizing inherited multimodal information while controlling how it is shaped under action supervision.

Power grid operation is becoming more complex due to the increase in generation of renewable energy. The recent series of Learning To Run a Power Network (L2RPN) competitions have encouraged the use of artificial agents to assist human dispatchers in operating power grids. However, the combinatorial nature of the action space poses a challenge to both conventional optimizers and learned controllers. Action space factorization, which breaks down decision-making into smaller sub-tasks, is one approach to tackle the curse of dimensionality. In this study, we propose a centrally coordinated multi-agent (CCMA) architecture for action space factorization. In this approach, regional agents propose actions and subsequently a coordinating agent selects the final action. We investigate several implementations of the CCMA architecture, and benchmark in different experimental settings against various L2RPN baseline approaches. The CCMA architecture exhibits higher sample efficiency and superior final performance than the baseline approaches. The results suggest high potential of the CCMA approach for further application in higher-dimensional L2RPN as well as real-world power grid settings.

We introduce Paper2Agent, an automated framework that converts research papers into AI agents. Paper2Agent transforms research output from passive artifacts into active systems that can accelerate downstream use, adoption, and discovery. Conventional research papers require readers to invest substantial effort to understand and adapt a paper's code, data, and methods to their own work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by automatically converting a paper into an AI agent that acts as a knowledgeable research assistant. It systematically analyzes the paper and the associated codebase using multiple agents to construct a Model Context Protocol (MCP) server, then iteratively generates and runs tests to refine and robustify the resulting MCP. These paper MCPs can then be flexibly connected to a chat agent (e.g. Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the original paper. We demonstrate Paper2Agent's effectiveness in creating reliable and capable paper agents through in-depth case studies. Paper2Agent created an agent that leverages AlphaGenome to interpret genomic variants and agents based on ScanPy and TISSUE to carry out single-cell and spatial transcriptomics analyses. We validate that these paper agents can reproduce the original paper's results and can correctly carry out novel user queries. By turning static papers into dynamic, interactive AI agents, Paper2Agent introduces a new paradigm for knowledge dissemination and a foundation for the collaborative ecosystem of AI co-scientists.

Our goal is to synthesize 3D human motions given textual inputs describing simultaneous actions, for example 'waving hand' while 'walking' at the same time. We refer to generating such simultaneous movements as performing 'spatial compositions'. In contrast to temporal compositions that seek to transition from one action to another, spatial compositing requires understanding which body parts are involved in which action, to be able to move them simultaneously. Motivated by the observation that the correspondence between actions and body parts is encoded in powerful language models, we extract this knowledge by prompting GPT-3 with text such as "what are the body parts involved in the action <action name>?", while also providing the parts list and few-shot examples. Given this action-part mapping, we combine body parts from two motions together and establish the first automated method to spatially compose two actions. However, training data with compositional actions is always limited by the combinatorics. Hence, we further create synthetic data with this approach, and use it to train a new state-of-the-art text-to-motion generation model, called SINC ("SImultaneous actioN Compositions for 3D human motions"). In our experiments, that training with such GPT-guided synthetic data improves spatial composition generation over baselines. Our code is publicly available at https://sinc.is.tue.mpg.de/.

Inferring physical actions from visual observations is a fundamental capability for advancing machine intelligence in the physical world. Achieving this requires large-scale, open-vocabulary video action datasets that span broad domains. We introduce Action100M, a large-scale dataset constructed from 1.2M Internet instructional videos (14.6 years of duration), yielding O(100 million) temporally localized segments with open-vocabulary action supervision and rich captions. Action100M is generated by a fully automated pipeline that (i) performs hierarchical temporal segmentation using V-JEPA 2 embeddings, (ii) produces multi-level frame and segment captions organized as a Tree-of-Captions, and (iii) aggregates evidence with a reasoning model (GPT-OSS-120B) under a multi-round Self-Refine procedure to output structured annotations (brief/detailed action, actor, brief/detailed caption). Training VL-JEPA on Action100M demonstrates consistent data-scaling improvements and strong zero-shot performance across diverse action recognition benchmarks, establishing Action100M as a new foundation for scalable research in video understanding and world modeling.

In robotic visuomotor policy learning, diffusion-based models have achieved significant success in improving the accuracy of action trajectory generation compared to traditional autoregressive models. However, they suffer from inefficiency due to multiple denoising steps and limited flexibility from complex constraints. In this paper, we introduce Coarse-to-Fine AutoRegressive Policy (CARP), a novel paradigm for visuomotor policy learning that redefines the autoregressive action generation process as a coarse-to-fine, next-scale approach. CARP decouples action generation into two stages: first, an action autoencoder learns multi-scale representations of the entire action sequence; then, a GPT-style transformer refines the sequence prediction through a coarse-to-fine autoregressive process. This straightforward and intuitive approach produces highly accurate and smooth actions, matching or even surpassing the performance of diffusion-based policies while maintaining efficiency on par with autoregressive policies. We conduct extensive evaluations across diverse settings, including single-task and multi-task scenarios on state-based and image-based simulation benchmarks, as well as real-world tasks. CARP achieves competitive success rates, with up to a 10% improvement, and delivers 10x faster inference compared to state-of-the-art policies, establishing a high-performance, efficient, and flexible paradigm for action generation in robotic tasks.

This report presents TAP-JEPA, our runner-up submission to the EPIC-KITCHENS-100 (EK-100) Action Anticipation Challenge at EgoVis 2026. The task is to anticipate the next verb, noun, and verb-noun action from an egocentric clip that ends before the target action begins. Instead of fine-tuning a large video backbone, TAP-JEPA builds a compact anticipation model on frozen V-JEPA 2.1 features: a ViT-G/384 encoder extracts visible pre-action tokens, the pre-trained latent predictor estimates near-future tokens from the observed context, and both token groups are fused by attentive probes with task-specific queries for verbs, nouns, and action pairs. For the final submission, we expand supervised training with the official training split and most of the validation split, reserving a small subset for sanity checks and qualitative inspection, and adopt a two-stage score fusion that first averages eight independently initialized probe replicas within each epoch and then merges candidates from epochs 12-20 with field-dependent weights. On the official open-testing leaderboard, our sunshinesky entry achieves 27.91 percent overall action Mean Top-5 Recall (MT5R), ranking second and only 0.04 percentage points behind the top score.

In this paper, we introduce GUIDE, a novel dataset tailored for the advancement of Multimodal Large Language Model (MLLM) applications, particularly focusing on Robotic Process Automation (RPA) use cases. Our dataset encompasses diverse data from various websites including Apollo(62.67\%), Gmail(3.43\%), Calendar(10.98\%) and Canva(22.92\%). Each data entry includes an image, a task description, the last action taken, CoT and the next action to be performed along with grounding information of where the action needs to be executed. The data is collected using our in-house advanced annotation tool NEXTAG (Next Action Grounding and Annotation Tool). The data is adapted for multiple OS, browsers and display types. It is collected by multiple annotators to capture the variation of design and the way person uses a website. Through this dataset, we aim to facilitate research and development in the realm of LLMs for graphical user interfaces, particularly in tasks related to RPA. The dataset's multi-platform nature and coverage of diverse websites enable the exploration of cross-interface capabilities in automation tasks. We believe that our dataset will serve as a valuable resource for advancing the capabilities of multi-platform LLMs in practical applications, fostering innovation in the field of automation and natural language understanding. Using GUIDE, we build V-Zen, the first RPA model to automate multiple websites using our in-House Automation tool AUTONODE

We introduce NitroGen, a vision-action foundation model for generalist gaming agents that is trained on 40,000 hours of gameplay videos across more than 1,000 games. We incorporate three key ingredients: 1) an internet-scale video-action dataset constructed by automatically extracting player actions from publicly available gameplay videos, 2) a multi-game benchmark environment that can measure cross-game generalization, and 3) a unified vision-action model trained with large-scale behavior cloning. NitroGen exhibits strong competence across diverse domains, including combat encounters in 3D action games, high-precision control in 2D platformers, and exploration in procedurally generated worlds. It transfers effectively to unseen games, achieving up to 52% relative improvement in task success rates over models trained from scratch. We release the dataset, evaluation suite, and model weights to advance research on generalist embodied agents.

Modern scientific ecosystems are rich in procedural knowledge across repositories, APIs, scripts, notebooks, documentation, databases, and papers, yet much of this knowledge remains fragmented across heterogeneous artifacts that agents cannot readily operationalize. This gap between abundant scientific know-how and usable agent capabilities is a key bottleneck for building effective scientific agents. We present SkillFoundry, a self-evolving framework that converts such resources into validated agent skills, reusable packages that encode task scope, inputs and outputs, execution steps, environment assumptions, provenance, and tests. SkillFoundry organizes a target domain as a domain knowledge tree, mines resources from high-value branches, extracts operational contracts, compiles them into executable skill packages, and then iteratively expands, repairs, merges, or prunes the resulting library through a closed-loop validation process. SkillFoundry produces a substantially novel and internally valid skill library, with 71.1\% of mined skills differing from existing skill libraries such as SkillHub and SkillSMP. We demonstrate that these mined skills improve coding agent performance on five of the six MoSciBench datasets. We further show that SkillFoundry can design new task-specific skills on demand for concrete scientific objectives, and that the resulting skills substantially improve performance on two challenging genomics tasks: cell type annotation and the scDRS workflow. Together, these results show that automatically mined skills improve agent performance on benchmarks and domain-specific tasks, expand coverage beyond hand-crafted skill libraries, and provide a practical foundation for more capable scientific agents.

Language-guided human motion synthesis has been a challenging task due to the inherent complexity and diversity of human behaviors. Previous methods face limitations in generalization to novel actions, often resulting in unrealistic or incoherent motion sequences. In this paper, we propose ATOM (ATomic mOtion Modeling) to mitigate this problem, by decomposing actions into atomic actions, and employing a curriculum learning strategy to learn atomic action composition. First, we disentangle complex human motions into a set of atomic actions during learning, and then assemble novel actions using the learned atomic actions, which offers better adaptability to new actions. Moreover, we introduce a curriculum learning training strategy that leverages masked motion modeling with a gradual increase in the mask ratio, and thus facilitates atomic action assembly. This approach mitigates the overfitting problem commonly encountered in previous methods while enforcing the model to learn better motion representations. We demonstrate the effectiveness of ATOM through extensive experiments, including text-to-motion and action-to-motion synthesis tasks. We further illustrate its superiority in synthesizing plausible and coherent text-guided human motion sequences.

In recent years, there has been a trend in the field of Reinforcement Learning (RL) towards large action models trained offline on large-scale datasets via sequence modeling. Existing models are primarily based on the Transformer architecture, which result in powerful agents. However, due to slow inference times, Transformer-based approaches are impractical for real-time applications, such as robotics. Recently, modern recurrent architectures, such as xLSTM and Mamba, have been proposed that exhibit parallelization benefits during training similar to the Transformer architecture while offering fast inference. In this work, we study the aptitude of these modern recurrent architectures for large action models. Consequently, we propose a Large Recurrent Action Model (LRAM) with an xLSTM at its core that comes with linear-time inference complexity and natural sequence length extrapolation abilities. Experiments on 432 tasks from 6 domains show that LRAM compares favorably to Transformers in terms of performance and speed.

Scaling action-controllable world models is limited by the scarcity of action labels. While latent action learning promises to extract control interfaces from unlabeled video, learned latents often fail to transfer across contexts: they entangle scene-specific cues and lack a shared coordinate system. This occurs because standard objectives operate only within each clip, providing no mechanism to align action semantics across contexts. Our key insight is that although actions are unobserved, their semantic effects are observable and can serve as a shared reference. We introduce SeqΔ-REPA, a sequence-level control-effect alignment objective that anchors integrated latent action to temporal feature differences from a frozen, self-supervised video encoder. Building on this, we present Olaf-World, a pipeline that pretrains action-conditioned video world models from large-scale passive video. Extensive experiments demonstrate that our method learns a more structured latent action space, leading to stronger zero-shot action transfer and more data-efficient adaptation to new control interfaces than state-of-the-art baselines.

Vision-Language-Action (VLA) models have emerged as a promising approach for generalizable robotic manipulations. In particular, flow matching-based VLA models have shown remarkable success due to their capability to generate precise and smooth action sequences and capture multimodal distributions. However, the iterative denoising process in the action head acts as a major computational bottleneck, posing a critical challenge for real-time deployment. To address this challenge, we propose ActionCache, a plug-and-play external cache that opportunistically reuses past intermediate actions to warm-start generations from the vicinity of target actions, thereby drastically reducing the inference latency. Specifically, ActionCache stores the intermediate actions with compact multimodal keys, which enables retrieval from similar past contexts across different episodes or even different tasks. Experimental results in simulation and real-world environments demonstrate that ActionCache maintains high task success rates in a low-latency regime, achieving inference acceleration of up to 11.75times and 34.43times for representative flow-based VLA models, π_{0.5} and GR00T-N1.6, respectively.

Assessing action quality is both imperative and challenging due to its significant impact on the quality of AI-generated videos, further complicated by the inherently ambiguous nature of actions within AI-generated video (AIGV). Current action quality assessment (AQA) algorithms predominantly focus on actions from real specific scenarios and are pre-trained with normative action features, thus rendering them inapplicable in AIGVs. To address these problems, we construct GAIA, a Generic AI-generated Action dataset, by conducting a large-scale subjective evaluation from a novel causal reasoning-based perspective, resulting in 971,244 ratings among 9,180 video-action pairs. Based on GAIA, we evaluate a suite of popular text-to-video (T2V) models on their ability to generate visually rational actions, revealing their pros and cons on different categories of actions. We also extend GAIA as a testbed to benchmark the AQA capacity of existing automatic evaluation methods. Results show that traditional AQA methods, action-related metrics in recent T2V benchmarks, and mainstream video quality methods perform poorly with an average SRCC of 0.454, 0.191, and 0.519, respectively, indicating a sizable gap between current models and human action perception patterns in AIGVs. Our findings underscore the significance of action quality as a unique perspective for studying AIGVs and can catalyze progress towards methods with enhanced capacities for AQA in AIGVs.

Language model agents increasingly automate post-training, but when given the full training stack they converge on supervised fine-tuning and spend most effort revising training data. Existing systems give the agent one kind of control, selecting rows from a fixed pool or calling a generator, whereas a human data engineer adjusts proportions, prunes, repairs, replaces and synthesizes the data. We design a data action space for these changes and ask whether an automated system can make the full range rather than one of them, and what structure that requires. We first run this loop with a single agent, and it reaches only one action, adjusting category proportions, while its context fills with execution output and is discarded mid-search. We therefore introduce AutoSFT, a multi-agent system where a meta agent separates execution from analysis, gathers proposals from independent angles, and calls a synthesis subagent for capabilities the pool cannot cover, with the model, the trainer, and the budget fixed within each comparison. Adding each component in turn helps: the executor halves context loss, the analysis subagents lift the best IFEval by +6.5, and synthesis adds +3.4 IFEval and +2.9 IFBench. The same loop transfers to code, where analysis adds +3.7 MBPP+ over a single agent that does not improve. Every result comes from runs that retrain from the base model each round, so each component's effect is individually attributable. Our findings suggest that automating SFT data research depends more on covering diverse data actions than on a stronger single action.

Based on their superior comprehension and reasoning capabilities, Large Language Model (LLM) driven agent frameworks have achieved significant success in numerous complex reasoning tasks. ReAct-like agents can solve various intricate problems step-by-step through progressive planning and tool calls, iteratively optimizing new steps based on environmental feedback. However, as the planning capabilities of LLMs improve, the actions invoked by tool calls in ReAct-like frameworks often misalign with complex planning and challenging data organization. Code Action addresses these issues while also introducing the challenges of a more complex action space and more difficult action organization. To leverage Code Action and tackle the challenges of its complexity, this paper proposes Policy and Action Dual-Control Agent (PoAct) for generalized applications. The aim is to achieve higher-quality code actions and more accurate reasoning paths by dynamically switching reasoning policies and modifying the action space. Experimental results on the Agent Benchmark for both legal and generic scenarios demonstrate the superior reasoning capabilities and reduced token consumption of our approach in complex tasks. On the LegalAgentBench, our method shows a 20 percent improvement over the baseline while requiring fewer tokens. We conducted experiments and analyses on the GPT-4o and GLM-4 series models, demonstrating the significant potential and scalability of our approach to solve complex problems.

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Vision-Language-Action (VLA) models commonly generate robot actions token by token through Large Language Model (LLM) decoders, causing inference latency to grow with action sequence length and limiting closed-loop control frequency. We present Goal-Conditioned Vision-Predictor-Action (VPA), which replaces autoregressive decoders with a lightweight latent control loop. A shared vision encoder and a frozen text encoder embed observations, goal images, and instructions; a neuro-symbolic selector chooses a discrete skill; a Joint-Embedding Predictive Architecture (JEPA) predictor forecasts the next latent state; and a flow-matching solver generates an entire action chunk in a few integration steps, so that sequential network evaluations per decision step do not depend on the action horizon. We analyze inference complexity, regularization against representation collapse, and conditions under which latent sub-goal thresholding limits error accumulation across task phases. As an initial proof of concept, we evaluated VPA on the LIBERO-10 suite. The trainable model has under 20M parameters (checkpoint under 75 MB, excluding a frozen 63.4M-parameter CLIP text encoder); a decision step of a single-camera reference configuration takes 10-14 ms on an Apple M4; and trained only on LIBERO-10 demonstrations in under three hours on a single GPU, a two-camera policy succeeded in 40.0% of 200 evaluation episodes. These preliminary results from a single training run suggest the approach is workable. Code and weights are available at https://github.com/ylee-sling/Vision-Predictor-Action and https://huggingface.co/ylee-sling/vpa-libero10, and archived at https://doi.org/10.5281/zenodo.22960920.

Self-improving coding agents that iteratively rewrite their own source code have demonstrated impressive performance on coding tasks. However, existing solutions generally derive self-modification from a single failure trajectory at a time, overlooking rich comparative signals available in the agent's expanding archive of past attempts. According to Mendelian principles of controlled inheritance, we introduce Mendel Gödel Machine (MGM). In addition to the general single-trajectory clonal mutation, MGM includes two new types of self-modification that better utilizes evidences accumulated: the reaction-norm mutation edits an agent based on its trajectories on multiple tasks simultaneously, and the cross-lineage hybridization edits an agent using the trajectory of a reference agent from another lineage on the same task. Under an additive fitness landscape model, we prove theoretically and demonstrate via controlled surrogate simulation that the new strategies facilitate a faster and better convergence over single-trajectory baselines. Experiments on SWE-bench and Polyglot confirm MGM's consistent improvement in performance, efficiency, and generalizability.

DNA foundation models have become transformative tools in bioinformatics and healthcare applications. Trained on vast genomic datasets, these models can be used to generate sequence embeddings, dense vector representations that capture complex genomic information. These embeddings are increasingly being shared via Embeddings-as-a-Service (EaaS) frameworks to facilitate downstream tasks, while supposedly protecting the privacy of the underlying raw sequences. However, as this practice becomes more prevalent, the security of these representations is being called into question. This study evaluates the resilience of DNA foundation models to model inversion attacks, whereby adversaries attempt to reconstruct sensitive training data from model outputs. In our study, the model's output for reconstructing the DNA sequence is a zero-shot embedding, which is then fed to a decoder. We evaluated the privacy of three DNA foundation models: DNABERT-2, Evo 2, and Nucleotide Transformer v2 (NTv2). Our results show that per-token embeddings allow near-perfect sequence reconstruction across all models. For mean-pooled embeddings, reconstruction quality degrades as sequence length increases, though it remains substantially above random baselines. Evo 2 and NTv2 prove to be most vulnerable, especially for shorter sequences with reconstruction similarities > 90%, while DNABERT-2's BPE tokenization provides the greatest resilience. We found that the correlation between embedding similarity and sequence similarity was a key predictor of reconstruction success. Our findings emphasize the urgent need for privacy-aware design in genomic foundation models prior to their widespread deployment in EaaS settings. Training code, model weights and evaluation pipeline are released on: https://github.com/not-a-feature/DNA-Embedding-Inversion.

Scientific discovery is often slowed by the manual development of computational tools needed to analyze complex experimental data. Building such tools is costly and time-consuming because scientists must iteratively review literature, test modeling and scientific assumptions against empirical data, and implement these insights into efficient software. Large language models (LLMs) have demonstrated strong capabilities in synthesizing literature, reasoning with empirical data, and generating domain-specific code, offering new opportunities to accelerate computational method development. Existing LLM-based systems either focus on performing scientific analyses using existing computational methods or on developing computational methods or models for general machine learning without effectively integrating the often unstructured knowledge specific to scientific domains. Here, we introduce TusoAI , an agentic AI system that takes a scientific task description with an evaluation function and autonomously develops and optimizes computational methods for the application. TusoAI integrates domain knowledge into a knowledge tree representation and performs iterative, domain-specific optimization and model diagnosis, improving performance over a pool of candidate solutions. We conducted comprehensive benchmark evaluations demonstrating that TusoAI outperforms state-of-the-art expert methods, MLE agents, and scientific AI agents across diverse tasks, such as single-cell RNA-seq data denoising and satellite-based earth monitoring. Applying TusoAI to two key open problems in genetics improved existing computational methods and uncovered novel biology, including 9 new associations between autoimmune diseases and T cell subtypes and 7 previously unreported links between disease variants linked to their target genes. Our code is publicly available at https://github.com/Alistair-Turcan/TusoAI.

AI for scientific discovery is entering an agentic era, where protein-engineering systems are expected to prioritize future wet-lab experiments rather than merely fit static measurements. We introduce TadA-Bench, a million-variant wet-lab replay benchmark from 31 TadA directed-evolution rounds for future-round discovery toward agentic protein engineering. TadA-Bench preserves the campaign chronology and defines a fixed-data replay task: given earlier experimental rounds, models rank variants that appear only in later rounds. It provides aligned DNA, RNA, and protein views, and uses Seq2Graph, a graph-based label-unification pipeline, to reconcile noisy enrichment measurements into consistent cross-round activity labels. Random-split controls show strong interpolation, but future-round ranking and finite-budget candidate selection are much weaker. Controlled analyses suggest that evolutionary coverage is more informative than local data density, positioning TadA-Bench as a reproducible wet-lab replay substrate for future-round discovery toward agentic protein engineering; the data and code are released on Hugging Face and GitHub.

Revision-capable generation is appealing because it can insert or revise earlier content, but many non-autoregressive and edit-based approaches obtain this flexibility through repeated sequence-level computation. We propose Reviser, a decoder-only Transformer that generates a response as a sequence of cursor-relative actions on a mutable canvas. At each step, Reviser predicts exactly one action token: INSERT(token), MOVE(Δ), or STOP, and is autoregressive over edit-history actions rather than final text order. This design enables genuinely non-monotonic generation while preserving a simple next-action interface. On a continuation benchmark, Reviser is strongly preferred to SEDD and MDLM in our arena evaluations, and trajectory statistics confirm that the model performs frequent backward moves and mid-canvas insertions rather than merely emulating end-append decoding. Against size-matched autoregressive baselines, Reviser is competitive at both the 100M and 300M scales. Under our shared FLOPs convention, Reviser also requires substantially less inference compute than representative multi-pass refinement and diffusion-style baselines.

Hit-like molecular generation with therapeutic potential is essential for target-specific drug discovery. However, the field lacks heterogeneous data and unified frameworks for integrating diverse molecular representations. To bridge this gap, we introduce TextOmics, a pioneering benchmark that establishes one-to-one correspondences between omics expressions and molecular textual descriptions. TextOmics provides a heterogeneous dataset that facilitates molecular generation through representations alignment. Built upon this foundation, we propose ToDi, a generative framework that jointly conditions on omics expressions and molecular textual descriptions to produce biologically relevant, chemically valid, hit-like molecules. ToDi leverages two encoders (OmicsEn and TextEn) to capture multi-level biological and semantic associations, and develops conditional diffusion (DiffGen) for controllable generation. Extensive experiments confirm the effectiveness of TextOmics and demonstrate ToDi outperforms existing state-of-the-art approaches, while also showcasing remarkable potential in zero-shot therapeutic molecular generation. Sources are available at: https://github.com/hala-ToDi.

Vision-language-action models (VLAs) have recently advanced robotic manipulation, yet the effects of different robot-data pre-training paradigms remain difficult to compare because existing models often differ in architecture, data, action space, and evaluation protocol. We present VLAFlow (Vision-Language-Action Flow), a unified flow-matching framework for controlled comparison of VLA training objectives. Using a heterogeneous robot corpus, OXEMix, containing approximately 5,000 hours of data from DROID, OpenX-Embodiment, OpenX-Augmented, and RoboCOIN, we evaluate four paradigms under the same pi0-style architecture, shared VLM backbone, action expert, and 14-dimensional action space: action-only modeling (MindPI), language-supervised co-training (MindLPI), future latent alignment (MindWPI), and their combination (MindLWPI). Experiments on LIBERO, LIBERO-Plus, and SimplerEnv show that action-only pre-training is sensitive to heterogeneous data. In contrast, language supervision helps preserve vision-language generalization, while future latent alignment improves state-transition and action-outcome modeling. By combining both signals, MindLWPI achieves the most stable overall transfer performance across benchmarks. These results suggest a meta-action space view: language and future latent representations provide complementary intermediate constraints that make heterogeneous action supervision smoother and more transferable.

Agentic AI systems increasingly act through heterogeneous runtimes: local coding hooks, SDK tools, browser automation, managed-agent traces, API gateways, and workflow engines. A single operational act such as publishing code, changing identity state, moving money, or exporting data may therefore be represented by many incompatible runtime records. This makes a basic governance question difficult to answer: what action was actually approved, what evidence binds the approval to execution, and can an independent verifier reproduce the same action identity later? This paper presents Canonical Action Verification and Attestation (CAVA), a runtime-semantics layer for converting heterogeneous agent activity into canonical runtime action objects. CAVA is positioned below Proof-Carrying Agent Actions (PCAA): PCAA defines the deployer-owned route-review-prove governance process, while CAVA defines the stable action object that process governs. The paper formalizes canonical action identity, semantic pattern detection, approval binding, receipt integrity, runtime-portable projection, and optional attestation substrates. We study a reference implementation through a 96-seed, 384-variant benchmark covering semantic equivalence, semantic separation, wrapper bypass, false-positive control, approval binding, receipt reproducibility, attestation tamper detection, runtime portability, semantic pattern detection, policy degradation, and Azure deployment drills. The contribution is a systems formulation of action-level canonicalization and policy-addressable semantic patterns as a necessary substrate for deployer-side AI governance.

Standard behavior cloning supervises actions without explicitly constraining the future representation paired with each demonstrated action chunk. We introduce JEPA Policy, a diffusion-free framework that uses the action chunk and its observed future representation as paired training targets. Action and future-representation tokens interact in a shared Transformer and are refined through two forward passes. Future prediction can therefore shape the representation used to generate actions. Dual-branch and gradient-routing controls attribute the gain to this shared topology rather than to an auxiliary prediction head alone. Across nine simulated tasks, JEPA Policy improves mean success over the action-only MIP baseline and outperforms Diffusion Policy under the evaluated configurations, while adding 0.29 ms to MIP's model latency. A five-task, 630-episode physical-robot study produces the same pooled ranking. Further audits find no complete representation collapse under action supervision and identify a task-conditioned failure-ranking signal in future-prediction error. These results support paired future-representation supervision as a practical approach to low-latency visuomotor imitation without iterative generative sampling.

The advancement of large Vision-Language-Action (VLA) models has significantly improved robotic manipulation in terms of language-guided task execution and generalization to unseen scenarios. While existing VLAs adapted from pretrained large Vision-Language-Models (VLM) have demonstrated promising generalizability, their task performance is still unsatisfactory as indicated by the low tasks success rates in different environments. In this paper, we present a new advanced VLA architecture derived from VLM. Unlike previous works that directly repurpose VLM for action prediction by simple action quantization, we propose a omponentized VLA architecture that has a specialized action module conditioned on VLM output. We systematically study the design of the action module and demonstrates the strong performance enhancement with diffusion action transformers for action sequence modeling, as well as their favorable scaling behaviors. We also conduct comprehensive experiments and ablation studies to evaluate the efficacy of our models with varied designs. The evaluation on 5 robot embodiments in simulation and real work shows that our model not only significantly surpasses existing VLAs in task performance and but also exhibits remarkable adaptation to new robots and generalization to unseen objects and backgrounds. It exceeds the average success rates of OpenVLA which has similar model size (7B) with ours by over 35% in simulated evaluation and 55% in real robot experiments. It also outperforms the large RT-2-X model (55B) by 18% absolute success rates in simulation. Code and models can be found on our project page (https://cogact.github.io/).

Recent years, multimodal models have made remarkable strides and pave the way for intelligent browser use agents. However, when solving tasks on real world webpages in multi-turn, long-horizon trajectories, current agents still suffer from disordered action sequencing and excessive trial and error during execution. This paper introduces Recon-Act, a self-evolving multi-agent framework grounded in Reconnaissance-Action behavioral paradigm. The system comprises a Reconnaissance Team and an Action Team: the former conducts comparative analysis and tool generation, while the latter handles intent decomposition, tool orchestration, and execution. By contrasting the erroneous trajectories with successful ones, the Reconnaissance Team infers remedies, and abstracts them into a unified notion of generalized tools, either expressed as hints or as rule-based codes, and register to the tool archive in real time. The Action Team reinference the process empowered with these targeting tools, thus establishing a closed-loop training pipeline of data-tools-action-feedback. Following the 6 level implementation roadmap proposed in this work, we have currently reached Level 3 (with limited human-in-the-loop intervention). Leveraging generalized tools obtained through reconnaissance, Recon-Act substantially improves adaptability to unseen websites and solvability on long-horizon tasks, and achieves state-of-the-art performance on the challenging VisualWebArena dataset.

The study of complex human interactions and group activities has become a focal point in human-centric computer vision. However, progress in related tasks is often hindered by the challenges of obtaining large-scale labeled datasets from real-world scenarios. To address the limitation, we introduce M3Act, a synthetic data generator for multi-view multi-group multi-person human atomic actions and group activities. Powered by Unity Engine, M3Act features multiple semantic groups, highly diverse and photorealistic images, and a comprehensive set of annotations, which facilitates the learning of human-centered tasks across single-person, multi-person, and multi-group conditions. We demonstrate the advantages of M3Act across three core experiments. The results suggest our synthetic dataset can significantly improve the performance of several downstream methods and replace real-world datasets to reduce cost. Notably, M3Act improves the state-of-the-art MOTRv2 on DanceTrack dataset, leading to a hop on the leaderboard from 10th to 2nd place. Moreover, M3Act opens new research for controllable 3D group activity generation. We define multiple metrics and propose a competitive baseline for the novel task. Our code and data are available at our project page: http://cjerry1243.github.io/M3Act.