Daily Papers

Fine-grained visual understanding requires distinguishing subtle differences in local attributes and spatial relations, yet remains challenging for existing vision-language models. Unified multimodal models (UMMs) offer a new opportunity through generation pathways that preserve rich visual information complementary to understanding. However, existing generation-assisted understanding methods mainly rely on generative supervision or explicit generation and have not systematically explored direct use of native generation-side representations. To address this gap, we systematically analyze what generation-side representations offer for fine-grained understanding, finding that they are more sensitive to fine-grained semantic changes, capture task-relevant changes missed by understanding-side representations, and depend on correct spatial organization for this advantage. Guided by these findings, we design GAFU, a post-training framework that unlocks native generation-side information for fine-grained understanding. It compresses generation-side visual representations into compact \(G\) tokens that preserve fine-grained visual details, enabling task-conditioned retrieval by the understanding pathway. Experiments show that GAFU consistently outperforms SFT baselines trained on the same data across diverse visual understanding tasks and UMM architectures, with maximum relative improvements of 20.00\%, 17.94\%, and 8.62\% on VStar-Bench, OmniSpatial, and VSR-Bench, respectively. Overall, GAFU converts complementary information from the generation pathway into gains in fine-grained visual understanding, providing an effective path toward synergy between generation and understanding in UMMs.

Unified multimodal models (UMMs) jointly support visual understanding and image generation, yet information flow between these two capabilities remains largely asymmetric: understanding representations routinely condition generation, whereas generative representations are rarely reused for multimodal reasoning. In this work, we investigate whether intermediate representations from a UMM's native diffusion branch can enhance spatial reasoning without compromising general multimodal understanding. We propose DiFuse, which selectively incorporates intermediate diffusion representations into the understanding pathway of UMMs. Through systematic layer-wise analysis, we identify which diffusion representations are most informative and where they can be integrated with minimal interference to semantic processing. Guided by these findings, DiFuse spatially aligns diffusion features with visual tokens and injects them into selected multimodal decoder layers via residual fusion. Extensive experiments on UniWorld-V1 show that, DiFuse consistently improves spatial reasoning over a matched SFT baseline while maintaining broadly comparable performance on general multimodal benchmarks. Further analyses show that these gains depend critically on the choice of diffusion representations, injection positions, and the preservation of spatial correspondence between diffusion features and visual tokens. Results on OmniGen2 further demonstrate the transferability of DiFuse across unified multimodal architectures. Overall, our findings show that native diffusion representations can provide complementary spatial cues for multimodal reasoning when selectively integrated in a structure-preserving manner.

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.

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines.

An oft-cited open problem of federated learning is the existence of data heterogeneity at the clients. One pathway to understanding the drastic accuracy drop in federated learning is by scrutinizing the behavior of the clients' deep models on data with different levels of "difficulty", which has been left unaddressed. In this paper, we investigate a different and rarely studied dimension of FL: ordered learning. Specifically, we aim to investigate how ordered learning principles can contribute to alleviating the heterogeneity effects in FL. We present theoretical analysis and conduct extensive empirical studies on the efficacy of orderings spanning three kinds of learning: curriculum, anti-curriculum, and random curriculum. We find that curriculum learning largely alleviates non-IIDness. Interestingly, the more disparate the data distributions across clients the more they benefit from ordered learning. We provide analysis explaining this phenomenon, specifically indicating how curriculum training appears to make the objective landscape progressively less convex, suggesting fast converging iterations at the beginning of the training procedure. We derive quantitative results of convergence for both convex and nonconvex objectives by modeling the curriculum training on federated devices as local SGD with locally biased stochastic gradients. Also, inspired by ordered learning, we propose a novel client selection technique that benefits from the real-world disparity in the clients. Our proposed approach to client selection has a synergic effect when applied together with ordered learning in FL.

In recent years, rapid advances in Multimodal Large Language Models (MLLMs) have increasingly stimulated research on ancient Chinese scripts. As the evolution of written characters constitutes a fundamental pathway for understanding cultural transformation and historical continuity, how MLLMs can be systematically leveraged to support and advance text evolution analysis remains an open and largely underexplored problem. To bridge this gap, we construct a comprehensive benchmark comprising 11 tasks and over 130,000 instances, specifically designed to evaluate the capability of MLLMs in analyzing the evolution of ancient Chinese scripts. We conduct extensive evaluations across multiple widely used MLLMs and observe that, while existing models demonstrate a limited ability in glyph-level comparison, their performance on core tasks-such as character recognition and evolutionary reasoning-remains substantially constrained. Motivated by these findings, we propose a glyph-driven fine-tuning framework (GEVO) that explicitly encourages models to capture evolutionary consistency in glyph transformations and enhances their understanding of text evolution. Experimental results show that even models at the 2B scale achieve consistent and comprehensive performance improvements across all evaluated tasks. To facilitate future research, we publicly release both the benchmark and the trained modelshttps://github.com/songruiecho/GEVO.

We present Lance, a lightweight native unified model supporting multimodal understanding, generation, and editing for both images and videos. Rather than relying on model capacity scaling or text-image-dominant designs, Lance explores a practical paradigm for unified multimodal modeling via collaborative multi-task training. It is grounded in two core principles: unified context modeling and decoupled capability pathways. Specifically, Lance is trained from scratch and employs a dual-stream mixture-of-experts architecture on shared interleaved multimodal sequences, enabling joint context learning while decoupling the pathways for understanding and generation. We further introduce modality-aware rotary positional encoding to mitigate interference among heterogeneous visual tokens and boost cross-task alignment. During training, Lance adopts a staged multi-task training paradigm with capability-oriented objectives and adaptive data scheduling to strengthen both semantic comprehension and visual generation performance. Experimental results demonstrate that Lance substantially outperforms existing open-source unified models in image and video generation, while retaining strong multimodal understanding capabilities. The homepage is available at https://lance-project.github.io.

Anthropomorphism, or the attribution of human traits to technology, is an automatic and unconscious response that occurs even in those with advanced technical expertise. In this position paper, we analyze hundreds of thousands of research articles to present empirical evidence of the prevalence and growth of anthropomorphic terminology in research on large language models (LLMs). We argue for challenging the deeper assumptions reflected in this terminology -- which, though often useful, may inadvertently constrain LLM development -- and broadening beyond them to open new pathways for understanding and improving LLMs. Specifically, we identify and examine five anthropomorphic assumptions that shape research across the LLM development lifecycle. For each assumption (e.g., that LLMs must use natural language for reasoning, or that they should be evaluated on benchmarks originally meant for humans), we demonstrate empirical, non-anthropomorphic alternatives that remain under-explored yet offer promising directions for LLM research and development.

Spatial understanding of the physical world from 2D visual inputs hinges on two complementary forms of geometric knowledge: holistic 3D structural perception and fine-grained metric scale estimation. Existing multimodal large language models (MLLMs) typically address only one facet, ingesting either depth maps or point clouds as additional model inputs, which incurs substantial computational overhead and inherits the generalization limitations of upstream prediction models. We propose GAMSI, a dual-pathway Geometry-Aware MLLM for Spatial Intelligence that takes only RGB images as input while internalizing both forms of geometric prior within a unified autoregressive backbone. Specifically, we introduce Metric-Structure Decoupled Queries (MSDQ) which employ two groups of learnable queries to respectively extract dense metric signals and sparse structural cues from the shared visual context, with a task-decoupled attention mask further preventing the two pathways from contaminating each other. Building on this, an Expert-Guided Visual Grounding (EVG) module projects the aggregated cues back to frame-level visual features and aligns them with vision foundation models, which serve purely as training-time supervision, rather than as model inputs. We further build a multi-task spatial instruction-tuning dataset (MTS) comprising 152{,}776 samples spanning 13 task types and three visual modalities, consolidated from six public datasets. Trained with a two-stage curriculum, GAMSI achieves state-of-the-art performance on seven spatial intelligence benchmarks.

Scientific figures and tables encode essential experimental evidence, yet remain difficult for digital libraries and multimodal AI systems to retrieve and interpret. The ALD/E-ImageMiner benchmark and ICDAR 2026 Competition on Information Extraction from Atomic Layer Deposition/Etching Scientific Figures provide 1,951 figures from 205 publications, expert-annotated for classification, data table extraction, summarization, and visual question answering. In these companion proceedings, we present a forward-looking perspective on how the benchmark can guide future scientific-image challenges. We examine how its tasks probe capabilities from visual and quantitative reading to domain-grounded reasoning and evidential justification, and how Bloom-informed question design can support deeper scientific understanding. We propose "scientific conceptual understanding from images" as a long-term benchmark objective, with future directions including broader domains and figure types, contextual and cross-document synthesis, hypothesis evaluation, provenance, uncertainty, counterfactual grounding, and open-ended multimodal research. This perspective connects the ICDAR 2026 challenge to a broader agenda for machine-actionable scientific visual knowledge and verifiable multimodal scientific AI.

AI explanations are often mentioned as a way to improve human-AI decision-making, but empirical studies have not found consistent evidence of explanations' effectiveness and, on the contrary, suggest that they can increase overreliance when the AI system is wrong. While many factors may affect reliance on AI support, one important factor is how decision-makers reconcile their own intuition -- beliefs or heuristics, based on prior knowledge, experience, or pattern recognition, used to make judgments -- with the information provided by the AI system to determine when to override AI predictions. We conduct a think-aloud, mixed-methods study with two explanation types (feature- and example-based) for two prediction tasks to explore how decision-makers' intuition affects their use of AI predictions and explanations, and ultimately their choice of when to rely on AI. Our results identify three types of intuition involved in reasoning about AI predictions and explanations: intuition about the task outcome, features, and AI limitations. Building on these, we summarize three observed pathways for decision-makers to apply their own intuition and override AI predictions. We use these pathways to explain why (1) the feature-based explanations we used did not improve participants' decision outcomes and increased their overreliance on AI, and (2) the example-based explanations we used improved decision-makers' performance over feature-based explanations and helped achieve complementary human-AI performance. Overall, our work identifies directions for further development of AI decision-support systems and explanation methods that help decision-makers effectively apply their intuition to achieve appropriate reliance on AI.

In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storms), and their implications for cancer are discussed. Genomic alterations spur cancer genome evolution. Thus, the relationship between cancer clonal evolution and cancer stems cells is commented. The key question in cancer biology concerns how these genomic alterations support cancer development and metastasis in the context of biological functioning. Thus far, efforts such as pathway analysis have improved the understanding of the functional contributions of genetic mutations and DNA copy number variations to cancer development, progression and metastasis. However, the known pathways correspond to a small fraction, plausibly 5-10%, of somatic mutations and genes with an altered copy number. To develop a comprehensive understanding of the function of these genomic alterations in cancer, an integrative network framework is proposed and discussed. Finally, the challenges and the directions of studying cancer omic data using an integrative network approach are commented.

Large language models have been shown to achieve remarkable performance across a variety of natural language tasks using few-shot learning, which drastically reduces the number of task-specific training examples needed to adapt the model to a particular application. To further our understanding of the impact of scale on few-shot learning, we trained a 540-billion parameter, densely activated, Transformer language model, which we call Pathways Language Model PaLM. We trained PaLM on 6144 TPU v4 chips using Pathways, a new ML system which enables highly efficient training across multiple TPU Pods. We demonstrate continued benefits of scaling by achieving state-of-the-art few-shot learning results on hundreds of language understanding and generation benchmarks. On a number of these tasks, PaLM 540B achieves breakthrough performance, outperforming the finetuned state-of-the-art on a suite of multi-step reasoning tasks, and outperforming average human performance on the recently released BIG-bench benchmark. A significant number of BIG-bench tasks showed discontinuous improvements from model scale, meaning that performance steeply increased as we scaled to our largest model. PaLM also has strong capabilities in multilingual tasks and source code generation, which we demonstrate on a wide array of benchmarks. We additionally provide a comprehensive analysis on bias and toxicity, and study the extent of training data memorization with respect to model scale. Finally, we discuss the ethical considerations related to large language models and discuss potential mitigation strategies.

Recent advancements in Large Multimodal Models (LMMs) have greatly enhanced their proficiency in 2D visual understanding tasks, enabling them to effectively process and understand images and videos. However, the development of LMMs with 3D-awareness for 3D scene understanding has been hindered by the lack of large-scale 3D vision-language datasets and powerful 3D encoders. In this paper, we introduce a simple yet effective framework called LLaVA-3D. Leveraging the strong 2D understanding priors from LLaVA, our LLaVA-3D efficiently adapts LLaVA for 3D scene understanding without compromising 2D understanding capabilities. To achieve this, we employ a simple yet effective representation, 3D Patch, which connects 2D CLIP patch features with their corresponding positions in 3D space. By integrating the 3D Patches into 2D LMMs and employing joint 2D and 3D vision-language instruction tuning, we establish a unified architecture for both 2D image understanding and 3D scene understanding. Experimental results show that LLaVA-3D converges 3.5x faster than existing 3D LMMs when trained on 3D vision-language datasets. Moreover, LLaVA-3D not only achieves state-of-the-art performance across various 3D tasks but also maintains comparable 2D image understanding and vision-language conversation capabilities with LLaVA.

Visual-Language Models (VLMs) have become a powerful tool for bridging the gap between visual and linguistic understanding. However, the conventional learning approaches for VLMs often suffer from limitations, such as the high resource requirements of collecting and training image-text paired data. Recent research has suggested that language understanding plays a crucial role in the performance of VLMs, potentially indicating that text-only training could be a viable approach. In this work, we investigate the feasibility of enhancing fine-grained visual understanding in VLMs through text-only training. Inspired by how humans develop visual concept understanding, where rich textual descriptions can guide visual recognition, we hypothesize that VLMs can also benefit from leveraging text-based representations to improve their visual recognition abilities. We conduct comprehensive experiments on two distinct domains: fine-grained species classification and cultural visual understanding tasks. Our findings demonstrate that text-only training can be comparable to conventional image-text training while significantly reducing computational costs. This suggests a more efficient and cost-effective pathway for advancing VLM capabilities, particularly valuable in resource-constrained environments.

Existing large audio-language models perceive the world as "mono"-a single stream of audio that ignores the critical spatial dimension ("where") required for universal audio scene analysis (ASA). To bridge this gap, we first introduce a hierarchical framework for audio scene analysis. Guided by this framework, we introduce a system that enables large audio-language models (LALMs) to understand and reason about the complex acoustic world. Our system endows LALMs with universal spatial understanding through four key innovations: (1) A scalable simulation pipeline that synthesizes high-quality First-Order-Ambisonics(FOA) data; (2) A unified model framework that integrates universal spatial encoding with a dense hybrid projection mechanism to bridge the modality gap; (3) A progressive training curriculum that evolves from representation alignment to reinforcement learning-based reasoning; and (4) A comprehensive benchmark for audio scene analysis (ASA) designed to rigorously evaluate atomic perception, relational integration, and cognitive reasoning capabilities, on which our model demonstrates comparatively strong capability for spatial understanding. Our work provides a clear pathway for leveraging the powerful reasoning abilities of LALMs towards holistic ASA, advancing from "mono" semantic recognition to spatial intelligence.

Simulating ecohydrological processes is essential for understanding complex environmental systems and guiding sustainable management amid accelerating climate change and human pressures. Process-based models provide physical realism but can suffer from structural rigidity, high computational costs, and complex calibration, while machine learning (ML) methods are efficient and flexible yet often lack interpretability and transferability. We propose a unified three-phase framework that integrates process-based models with ML and progressively embeds them into artificial intelligence (AI) through knowledge distillation. Phase I, behavioral distillation, enhances process models via surrogate learning and model simplification to capture key dynamics at lower computational cost. Phase II, structural distillation, reformulates process equations as modular components within a graph neural network (GNN), enabling multiscale representation and seamless integration with ML models. Phase III, cognitive distillation, embeds expert reasoning and adaptive decision-making into intelligent modeling agents using the Eyes-Brain-Hands-Mouth architecture. Demonstrations for the Samish watershed highlight the framework's applicability to ecohydrological modeling, showing that it can reproduce process-based model outputs, improve predictive accuracy, and support scenario-based decision-making. The framework offers a scalable and transferable pathway toward next-generation intelligent ecohydrological modeling systems, with the potential extension to other process-based domains.

Video emotion understanding is commonly studied as an offline classification problem, where the complete video segment is available before prediction. Real-time interaction, however, requires emotion decisions from incomplete and evolving evidence. This paper studies streaming video emotion understanding as a reliability-aware decision process over evolving emotion beliefs. In this setting, a single confident prefix prediction can still be unreliable when the underlying belief trajectory is unstable or repeatedly switches across emotion classes. We propose TRACE, a trajectory-aware reliability framework that forms low-latency emotion beliefs from streaming audio prefixes, estimates reliability from confidence, entropy, stability, and class-switching patterns, and selectively invokes contextual belief reinterpretation with visual, textual, and neighboring-utterance evidence. TRACE keeps stable cases in the low-latency online pathway while allocating stronger multimodal reasoning to uncertain cases that remain ambiguous. Experiments on StreamMER, MELD, and MER2024 show that TRACE improves the accuracy-cost trade-off, retaining most full-context gains while reducing unnecessary contextual reasoning.

Despite superior reasoning prowess demonstrated by Large Language Models (LLMs) with Chain-of-Thought (CoT) prompting, a lack of understanding prevails around the internal mechanisms of the models that facilitate CoT generation. This work investigates the neural sub-structures within LLMs that manifest CoT reasoning from a mechanistic point of view. From an analysis of Llama-2 7B applied to multistep reasoning over fictional ontologies, we demonstrate that LLMs deploy multiple parallel pathways of answer generation for step-by-step reasoning. These parallel pathways provide sequential answers from the input question context as well as the generated CoT. We observe a functional rift in the middle layers of the LLM. Token representations in the initial half remain strongly biased towards the pretraining prior, with the in-context prior taking over in the later half. This internal phase shift manifests in different functional components: attention heads that write the answer token appear in the later half, attention heads that move information along ontological relationships appear in the initial half, and so on. To the best of our knowledge, this is the first attempt towards mechanistic investigation of CoT reasoning in LLMs.

How can we imbue robots with the ability to manipulate objects precisely but also to reason about them in terms of abstract concepts? Recent works in manipulation have shown that end-to-end networks can learn dexterous skills that require precise spatial reasoning, but these methods often fail to generalize to new goals or quickly learn transferable concepts across tasks. In parallel, there has been great progress in learning generalizable semantic representations for vision and language by training on large-scale internet data, however these representations lack the spatial understanding necessary for fine-grained manipulation. To this end, we propose a framework that combines the best of both worlds: a two-stream architecture with semantic and spatial pathways for vision-based manipulation. Specifically, we present CLIPort, a language-conditioned imitation-learning agent that combines the broad semantic understanding (what) of CLIP [1] with the spatial precision (where) of Transporter [2]. Our end-to-end framework is capable of solving a variety of language-specified tabletop tasks from packing unseen objects to folding cloths, all without any explicit representations of object poses, instance segmentations, memory, symbolic states, or syntactic structures. Experiments in simulated and real-world settings show that our approach is data efficient in few-shot settings and generalizes effectively to seen and unseen semantic concepts. We even learn one multi-task policy for 10 simulated and 9 real-world tasks that is better or comparable to single-task policies.

In-context machine translation (MT) with large language models (LLMs) is a promising approach for low-resource MT, as it can readily take advantage of linguistic resources such as grammar books and dictionaries. Such resources are usually selectively integrated into the prompt so that LLMs can directly perform translation without any specific training, via their in-context learning capability (ICL). However, the relative importance of each type of resource e.g., dictionary, grammar book, and retrieved parallel examples, is not entirely clear. To address this gap, this study systematically investigates how each resource and its quality affects the translation performance, with the Manchu language as our case study. To remove any prior knowledge of Manchu encoded in the LLM parameters and single out the effect of ICL, we also experiment with an encrypted version of Manchu texts. Our results indicate that high-quality dictionaries and good parallel examples are very helpful, while grammars hardly help. In a follow-up study, we showcase a promising application of in-context MT: parallel data augmentation as a way to bootstrap the conventional MT model. When monolingual data abound, generating synthetic parallel data through in-context MT offers a pathway to mitigate data scarcity and build effective and efficient low-resource neural MT systems.

Safety-aligned large language models (LLMs) remain vulnerable to jailbreaks and can over-refuse benign requests. Understanding these failures requires distinguishing harmfulness recognition from the computation that writes refusal. We reframe this as a pathway question and make it measurable on residual-stream updates in decoder-only Transformers, separating the harmfulness information a module update exposes from the change it produces in readable refusal evidence. Across 18 Base-Instruct pairs spanning Qwen, Llama, and Gemma, harmfulness is decoded more readily from attention updates, particularly in early layers, whereas MLP updates contribute more strongly to harm-selective refusal writing in aligned models. Post-training strengthens MLP refusal writing in all 18 pairs without systematically improving harmfulness decodability, while positive MLP writing becomes more concentrated in deeper layers after post-training. Across six reasoning-enabled models, harmfulness remains decodable during reasoning while strong refusal writing concentrates at answer onset, a pattern that persists with reasoning disabled. Causal interventions further support this pathway: resetting downstream MLP updates to their clean values substantially reduces the refusal shift caused by upstream attention interventions. Building on these findings, we introduce Sentinel, which combines an attention-derived perception score P with an MLP-derived decision score D. Their joint profiles characterize jailbreaks and over-refusals, and conditional routing with both signals achieves a lower aggregate error rate than single-signal routing and evaluated fixed reminders across eight models.

Recent advancements in Large Language Models (LLMs) have sparked widespread concerns about their safety. Recent work demonstrates that safety alignment of LLMs can be easily removed by fine-tuning with a few adversarially chosen instruction-following examples, i.e., fine-tuning attacks. We take a further step to understand fine-tuning attacks in multilingual LLMs. We first discover cross-lingual generalization of fine-tuning attacks: using a few adversarially chosen instruction-following examples in one language, multilingual LLMs can also be easily compromised (e.g., multilingual LLMs fail to refuse harmful prompts in other languages). Motivated by this finding, we hypothesize that safety-related information is language-agnostic and propose a new method termed Safety Information Localization (SIL) to identify the safety-related information in the model parameter space. Through SIL, we validate this hypothesis and find that only changing 20% of weight parameters in fine-tuning attacks can break safety alignment across all languages. Furthermore, we provide evidence to the alternative pathways hypothesis for why freezing safety-related parameters does not prevent fine-tuning attacks, and we demonstrate that our attack vector can still jailbreak LLMs adapted to new languages.

Long video understanding is essential for human-like intelligence, enabling coherent perception and reasoning over extended temporal contexts. While the emerging thinking-with-frames paradigm, which alternates between global temporal reasoning and local frame examination, has advanced the reasoning capabilities of video multi-modal large language models (MLLMs), it suffers from a significant efficiency bottleneck due to the progressively growing and redundant multi-modal context. To address this, we propose SpecTemp, a reinforcement learning-based Speculative Temporal reasoning framework that decouples temporal perception from reasoning via a cooperative dual-model design. In SpecTemp, a lightweight draft MLLM rapidly explores and proposes salient frames from densely sampled temporal regions, while a powerful target MLLM focuses on temporal reasoning and verifies the draft's proposals, iteratively refining its attention until convergence. This design mirrors the collaborative pathways of the human brain, balancing efficiency with accuracy. To support training, we construct the SpecTemp-80K dataset, featuring synchronized dual-level annotations for coarse evidence spans and fine-grained frame-level evidence. Experiments across multiple video understanding benchmarks demonstrate that SpecTemp not only maintains competitive accuracy but also significantly accelerates inference compared with existing thinking-with-frames methods.

In this work, we introduce Wallaroo, a simple autoregressive baseline that leverages next-token prediction to unify multi-modal understanding, image generation, and editing at the same time. Moreover, Wallaroo supports multi-resolution image input and output, as well as bilingual support for both Chinese and English. We decouple the visual encoding into separate pathways and apply a four-stage training strategy to reshape the model's capabilities. Experiments are conducted on various benchmarks where Wallaroo produces competitive performance or exceeds other unified models, suggesting the great potential of autoregressive models in unifying multi-modality understanding and generation. Our code is available at https://github.com/JiePKU/Wallaroo.

Machine unlearning is becoming essential for building trustworthy and compliant language models. Yet unlearning success varies considerably across individual samples: some are reliably erased, while others persist despite the same procedure. We argue that this disparity is not only a data-side phenomenon, but also reflects model-internal mechanisms that encode and protect memorized information. We study this problem from a mechanistic perspective based on model circuits--structured interaction pathways that govern how predictions are formed. We propose Circuit-guided Unlearning Difficulty (CUD), a {\em pre-unlearning} metric that assigns each sample a continuous difficulty score using circuit-level signals. Extensive experiments demonstrate that CUD reliably separates intrinsically easy and hard samples, and remains stable across unlearning methods. We identify key circuit-level patterns that reveal a mechanistic signature of difficulty: easy-to-unlearn samples are associated with shorter, shallower interactions concentrated in earlier-to-intermediate parts of the original model, whereas hard samples rely on longer and deeper pathways closer to late-stage computation. Compared to existing qualitative studies, CUD takes a first step toward a principled, fine-grained, and interpretable analysis of unlearning difficulty; and motivates the development of unlearning methods grounded in model mechanisms.

Humans can effortlessly localize the direction of a sound source and integrate it with visual cues for reasoning, yet this remains challenging for embodied agents. In particular, it is still unclear how to effectively evaluate and model spatial audio understanding in embodied settings. To address this gap, we introduce OmniEchoBench, a unified benchmark for spatial audio-visual perception and audio-vision-language navigation. OmniEchoBench comprises six tasks over 197 real-world spatial audio-visual scenes, 2,972 question-answer pairs, and 900 navigation samples with first-order ambisonics (FOA) audio collected from 30 real-world environments. To enable scalable training supervision, we develop a controllable rendering pipeline for spatial audio. It preserves geometric consistency among sound sources, visual observations, and agent trajectories. Building on this, we propose OmniEcho, a spatially aware omni-modal model. It introduces an FOA spatial encoder alongside a pretrained semantic audio pathway. Extensive experiments show that OmniEcho achieves state-of-the-art performance on spatial audio-visual perception. For our sound-guided navigation, OmniEcho reaches a performance level close to that of traditional vision-language navigation. These results demonstrate that spatial audio can serve as a valuable signal for embodied scene reasoning and navigation, while also highlighting fine-grained spatial localization and distance estimation as important open challenges.

Context faithfulness is essential for reliable reasoning in context-dependent scenarios. However, large language models often struggle to ground their outputs in the provided context, resulting in irrelevant responses. Inspired by the emergent expert specialization observed in mixture-of-experts architectures, this work investigates whether certain experts exhibit specialization in context utilization, offering a potential pathway toward targeted optimization for improved context faithfulness. To explore this, we propose Router Lens, a method that accurately identifies context-faithful experts. Our analysis reveals that these experts progressively amplify attention to relevant contextual information, thereby enhancing context grounding. Building on this insight, we introduce Context-faithful Expert Fine-Tuning (CEFT), a lightweight optimization approach that selectively fine-tunes context-faithful experts. Experiments across a wide range of benchmarks and models demonstrate that CEFT matches or surpasses the performance of full fine-tuning while being significantly more efficient.

Large Language Models (LLMs) often rely on long chain-of-thought (CoT) reasoning to solve complex tasks. While effective, these trajectories are frequently inefficient, leading to high latency from excessive token generation, or unstable reasoning that alternates between underthinking (shallow, inconsistent steps) and overthinking (repetitive, verbose reasoning). In this work, we study the structure of reasoning trajectories and uncover specialized attention heads that correlate with distinct cognitive behaviors such as verification and backtracking. By lightly intervening on these heads at inference time, we can steer the model away from inefficient modes. Building on this insight, we propose CREST, a training-free method for Cognitive REasoning Steering at Test-time. CREST has two components: (1) an offline calibration step that identifies cognitive heads and derives head-specific steering vectors, and (2) an inference-time procedure that rotates hidden representations to suppress components along those vectors. CREST adaptively suppresses unproductive reasoning behaviors, yielding both higher accuracy and lower computational cost. Across diverse reasoning benchmarks and models, CREST improves accuracy by up to 17.5% while reducing token usage by 37.6%, offering a simple and effective pathway to faster, more reliable LLM reasoning.

Multimodal large language models (MLLMs) have recently shown strong performance in visual understanding, yet they often lack temporal awareness, particularly in egocentric settings where reasoning depends on the correct ordering and evolution of events. This deficiency stems in part from training objectives that fail to explicitly reward temporal reasoning and instead rely on frame-level spatial shortcuts. To address this limitation, we propose Temporal Global Policy Optimization (TGPO), a reinforcement learning with verifiable rewards (RLVR) algorithm designed to incentivize temporal awareness in MLLMs. TGPO contrasts model outputs generated from temporally ordered versus shuffled video frames to derive calibrated, globally normalized reward signals that explicitly favor temporally coherent reasoning. Integrated with GRPO and GSPO, TGPO supports cold-start RL training and effectively suppresses spatial shortcut behaviors learned by existing MLLMs. Experiments across five egocentric video benchmarks demonstrate that TGPO consistently improves temporal grounding and causal coherence, outperforming prior RL-based video reasoning approaches. Our results suggest that TGPO offers a simple and scalable pathway toward temporally robust MLLMs for egocentric video understanding.

While Vision-Language Models (VLMs) have advanced highlevel reasoning in autonomous driving, their ability to ground this reasoning in the underlying physics of ego-motion remains poorly understood. We introduce EgoDyn-Bench, a diagnostic benchmark for evaluating the semantic ego-motion understanding of vision-centric foundation models. By mapping continuous vehicle kinematics to discrete motion concepts via a deterministic oracle, we decouple a model's internal physical logic from its visual perception. Our large-scale empirical audit spanning 20 + models, including closed-source MLLMs, open-source VLMs across multiple scales, and specialized VLAs, identifies a significant Perception Bottleneck: while models exhibit logical physical concepts, they consistently fail to accurately align them with visual observations, frequently underperforming classical non-learned geometric baselines. This failure persists across model scales and domain-specific training, indicating a structural deficit in how current architectures couple visual perception with physical reasoning. We demonstrate that providing explicit trajectory encodings substantially restores physical consistency across all evaluated models, revealing a functional disentanglement between vision and language: egomotion logic is derived almost exclusively from the language modality, while visual observations contribute negligible additional signal. This structural finding provides a standardized diagnostic framework and a practical pathway toward physically aligned embodied AI. Keywords: Ego-motion - Physical Reasoning - Foundation Models

Benign fine-tuning severely weakens the safety alignment of large language models (LLMs), so we study why refusal behavior is so fragile. While prior work often attributes this failure to gradient conflict, we propose a fundamentally different Fisher-geometric explanation: safety Fisher is low-rank, and alignment makes the safety geometry flatter while preserving an output-routing pathway. After 100 benign fine-tuning examples, this pathway is selectively re-sharpened in output-side MLP modules, explaining the asymmetric fragility: safety can collapse to high attack success rates, while general utility degrades mildly. The routing view also explains why few safety examples can restore refusal behavior, indicating that internal safety-relevant representations are preserved. Finally, we show that LoRA and ASAM mitigate early collapse by suppressing output-side sharpness, but their protection weakens at larger fine-tuning scales. Overall, safety failure is best understood as a disruption of a low-rank output-routing mechanism

Large Language Models (LLMs) have shown to be capable of various tasks, yet their capability in interpreting and reasoning over tabular data remains an underexplored area. In this context, this study investigates from three core perspectives: the robustness of LLMs to structural perturbations in tables, the comparative analysis of textual and symbolic reasoning on tables, and the potential of boosting model performance through the aggregation of multiple reasoning pathways. We discover that structural variance of tables presenting the same content reveals a notable performance decline, particularly in symbolic reasoning tasks. This prompts the proposal of a method for table structure normalization. Moreover, textual reasoning slightly edges out symbolic reasoning, and a detailed error analysis reveals that each exhibits different strengths depending on the specific tasks. Notably, the aggregation of textual and symbolic reasoning pathways, bolstered by a mix self-consistency mechanism, resulted in achieving SOTA performance, with an accuracy of 73.6% on WIKITABLEQUESTIONS, representing a substantial advancement over previous existing table processing paradigms of LLMs.

Multimodal generative models have made significant strides in image editing, demonstrating impressive performance on a variety of static tasks. However, their proficiency typically does not extend to complex scenarios requiring dynamic reasoning, leaving them ill-equipped to model the coherent, intermediate logical pathways that constitute a multi-step evolution from an initial state to a final one. This capacity is crucial for unlocking a deeper level of procedural and causal understanding in visual manipulation. To systematically measure this critical limitation, we introduce InEdit-Bench, the first evaluation benchmark dedicated to reasoning over intermediate pathways in image editing. InEdit-Bench comprises meticulously annotated test cases covering four fundamental task categories: state transition, dynamic process, temporal sequence, and scientific simulation. Additionally, to enable fine-grained evaluation, we propose a set of assessment criteria to evaluate the logical coherence and visual naturalness of the generated pathways, as well as the model's fidelity to specified path constraints. Our comprehensive evaluation of 14 representative image editing models on InEdit-Bench reveals significant and widespread shortcomings in this domain. By providing a standardized and challenging benchmark, we aim for InEdit-Bench to catalyze research and steer development towards more dynamic, reason-aware, and intelligent multimodal generative models.

Recent works augment Vision-Language Models with geometry features from pretrained 3D models, expecting that the geometric signal will boost spatial reasoning. However, we find that simply fusing geometry features and training on standard spatial QA yields only marginal improvements on high-level multi-hop tasks. We attribute this gap to a training-signal problem: standard spatial QA can be largely answered from visual features and language priors, so the geometry pathway receives weak gradients and fails to integrate with the visual features. To provide a training signal that requires geometry, we propose novel-view semantic rendering as an auxiliary training task that requires the model to predict the semantic layout of an unobserved viewpoint, inspired by humans' ability to mentally simulate novel viewpoints during spatial reasoning. This task encourages joint use of both pathways: geometry provides pose-dependent visibility, while vision provides semantic content. Our auxiliary task yields consistent improvements over the geometry-augmented baseline across all three benchmarks (up to +1.6 on VSI-Bench, +2.2 on ReVSI, +2.9 on our 3D-Point-QA dataset) and our full model surpasses prior open-source methods on VSI-Bench and on ReVSI. Project page: https://yuqunw.github.io/Render2Reason/.

Vision-Language Models (VLMs) have demonstrated remarkable performance across a variety of real-world tasks. However, existing VLMs typically process visual information by serializing images, a method that diverges significantly from the parallel nature of human vision. Moreover, their opaque internal mechanisms hinder both deeper understanding and architectural innovation. Inspired by the dual-stream hypothesis of human vision, which distinguishes the "what" and "where" pathways, we deconstruct the visual processing in VLMs into object recognition and spatial perception for separate study. For object recognition, we convert images into text token maps and find that the model's perception of image content unfolds as a two-stage process from shallow to deep layers, beginning with attribute recognition and culminating in semantic disambiguation. For spatial perception, we theoretically derive and empirically verify the geometric structure underlying the positional representation in VLMs. Based on these findings, we introduce an instruction-agnostic token compression algorithm based on a plug-and-play visual decoder to improve decoding efficiency, and a RoPE scaling technique to enhance spatial reasoning. Through rigorous experiments, our work validates these analyses, offering a deeper understanding of VLM internals and providing clear principles for designing more capable future architectures.

AI companion chatbots are increasingly popular with teens. While these interactions are entertaining, they also risk overuse that can potentially disrupt offline daily life. We examined how adolescents describe reliance on AI companions, mapping their experiences onto behavioral addiction frameworks and exploring pathways to disengagement, by analyzing 318 Reddit posts made by users who self-disclosed as 13-17 years old on the Character.AI subreddit. We found teens often begin using chatbots for support or creative play, but these activities can deepen into strong attachments marked by conflict, withdrawal, tolerance, relapse, and mood regulation. Reported consequences include sleep loss, academic decline, and strained real-world connections. Disengagement commonly arises when teens recognize harm, re-engage with offline life, or encounter restrictive platform changes. We highlight specific risks of character-based companion chatbots based on teens' perspectives and introduce a design framework (CARE) for guidance for safer systems and setting directions for future teen-centered research.

Vision-Language Models (VLMs) combine visual perception with the general capabilities, such as reasoning, of Large Language Models (LLMs). However, the mechanisms by which these two abilities can be combined and contribute remain poorly understood. In this work, we explore to compose perception and reasoning through model merging that connects parameters of different models. Unlike previous works that often focus on merging models of the same kind, we propose merging models across modalities, enabling the incorporation of the reasoning capabilities of LLMs into VLMs. Through extensive experiments, we demonstrate that model merging offers a successful pathway to transfer reasoning abilities from LLMs to VLMs in a training-free manner. Moreover, we utilize the merged models to understand the internal mechanism of perception and reasoning and how merging affects it. We find that perception capabilities are predominantly encoded in the early layers of the model, whereas reasoning is largely facilitated by the middle-to-late layers. After merging, we observe that all layers begin to contribute to reasoning, whereas the distribution of perception abilities across layers remains largely unchanged. These observations shed light on the potential of model merging as a tool for multimodal integration and interpretation.

Complex tables with multi-level headers, merged cells and heterogeneous layouts pose persistent challenges for LLMs in both understanding and reasoning. Existing approaches typically rely on table linearization or normalized grid modeling. However, these representations struggle to explicitly capture hierarchical structures and cross-dimensional dependencies, which can lead to misalignment between structural semantics and textual representations for non-standard tables. To address this issue, we propose an Orthogonal Hierarchical Decomposition (OHD) framework that constructs structure-preserving input representations of complex tables for LLMs. OHD introduces an Orthogonal Tree Induction (OTI) method based on spatial--semantic co-constraints, which decomposes irregular tables into a column tree and a row tree to capture vertical and horizontal hierarchical dependencies, respectively. Building on this representation, we design a dual-pathway association protocol to symmetrically reconstruct semantic lineage of each cell, and incorporate an LLM as a semantic arbitrator to align multi-level semantic information. We evaluate OHD framework on two complex table question answering benchmarks, AITQA and HiTab. Experimental results show that OHD consistently outperforms existing representation paradigms across multiple evaluation metrics.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

In this paper, we introduce Janus, an autoregressive framework that unifies multimodal understanding and generation. Prior research often relies on a single visual encoder for both tasks, such as Chameleon. However, due to the differing levels of information granularity required by multimodal understanding and generation, this approach can lead to suboptimal performance, particularly in multimodal understanding. To address this issue, we decouple visual encoding into separate pathways, while still leveraging a single, unified transformer architecture for processing. The decoupling not only alleviates the conflict between the visual encoder's roles in understanding and generation, but also enhances the framework's flexibility. For instance, both the multimodal understanding and generation components can independently select their most suitable encoding methods. Experiments show that Janus surpasses previous unified model and matches or exceeds the performance of task-specific models. The simplicity, high flexibility, and effectiveness of Janus make it a strong candidate for next-generation unified multimodal models.

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions.To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm. To guarantee robust scalability, we establish a predictive scaling law and reveal the progressive emergence of structural understanding via loss perspective, culminating in a strong 1.7-billion model. Building on this foundation, we devise a multiple sequence alignment (MSA)-based in-context learning strategy to unify protein design into a general framework, where AMix-1 recognizes deep evolutionary signals among MSAs and consistently generates structurally and functionally coherent proteins. This framework enables the successful design of a dramatically improved AmeR variant with an up to 50times activity increase over its wild type. Pushing the boundaries of protein engineering, we further empower AMix-1 with an evolutionary test-time scaling algorithm for in silico directed evolution that delivers substantial, scalable performance gains as verification budgets are intensified, laying the groundwork for next-generation lab-in-the-loop protein design.

The National Comprehensive Cancer Network (NCCN) provides evidence-based guidelines for cancer treatment. Translating complex patient presentations into guideline-compliant treatment recommendations is time-intensive, requires specialized expertise, and is prone to error. Advances in large language model (LLM) capabilities promise to reduce the time required to generate treatment recommendations and improve accuracy. We present an LLM agent-based approach to automatically generate guideline-concordant treatment trajectories for patients with non-small cell lung cancer (NSCLC). Our contributions are threefold. First, we construct a novel longitudinal dataset of 121 cases of NSCLC patients that includes clinical encounters, diagnostic results, and medical histories, each expertly annotated with the corresponding NCCN guideline trajectories by board-certified oncologists. Second, we demonstrate that existing LLMs possess domain-specific knowledge that enables high-quality proxy benchmark generation for both model development and evaluation, achieving strong correlation (Spearman coefficient r=0.88, RMSE = 0.08) with expert-annotated benchmarks. Third, we develop a hybrid approach combining expensive human annotations with model consistency information to create both the agent framework that predicts the relevant guidelines for a patient, as well as a meta-classifier that verifies prediction accuracy with calibrated confidence scores for treatment recommendations (AUROC=0.800), a critical capability for communicating the accuracy of outputs, custom-tailoring tradeoffs in performance, and supporting regulatory compliance. This work establishes a framework for clinically viable LLM-based guideline adherence systems that balance accuracy, interpretability, and regulatory requirements while reducing annotation costs, providing a scalable pathway toward automated clinical decision support.

The deployment of Multimodal Large Language Models (MLLMs) in agriculture is currently stalled by a critical trade-off: the existing literature lacks the large-scale agricultural datasets required for robust model development and evaluation, while current state-of-the-art models lack the verified domain expertise necessary to reason across diverse taxonomies. To address these challenges, we propose the Vision-to-Verified-Knowledge (V2VK) pipeline, a novel generative AI-driven annotation framework that integrates visual captioning with web-augmented scientific retrieval to autonomously generate the AgriMM benchmark, effectively eliminating biological hallucinations by grounding training data in verified phytopathological literature. The AgriMM benchmark contains over 3,000 agricultural classes and more than 607k VQAs spanning multiple tasks, including fine-grained plant species identification, plant disease symptom recognition, crop counting, and ripeness assessment. Leveraging this verifiable data, we present AgriChat, a specialized MLLM that presents broad knowledge across thousands of agricultural classes and provides detailed agricultural assessments with extensive explanations. Extensive evaluation across diverse tasks, datasets, and evaluation conditions reveals both the capabilities and limitations of current agricultural MLLMs, while demonstrating AgriChat's superior performance over other open-source models, including internal and external benchmarks. The results validate that preserving visual detail combined with web-verified knowledge constitutes a reliable pathway toward robust and trustworthy agricultural AI. The code and dataset are publicly available at https://github.com/boudiafA/AgriChat .

Long video understanding is a key challenge that plagues the advancement of Multimodal Large language Models (MLLMs). In this paper, we study this problem from the perspective of visual memory mechanism, and proposed a novel and training-free approach, termed Flexible Memory (FlexMem). In principle, FlexMem aims to mimic human behavior of video watching, i.e., continually watching video content and recalling the most relevant memory fragments to answer the question. In this way, FlexMem can help MLLMs achieve video understanding of infinite lengths, unlike previous methods that process all video information at once and have input upper-limit. Concretely, FlexMem first consider the visual KV caches as the memory sources, and realize the effective memory transfer and writing via a dual-pathway compression design. Afterwards, FlexMem also explores different memory reading strategies for the diverse video understanding tasks, including the popular streaming one. To validate FlexMem, we apply it to two popular video-MLLMs, and conduct extensive experiments on five long video and one streaming video task. The experimental results show that on a single 3090 GPU, our FlexMem can achieve obvious improvements than existing efficient video understanding methods and process more than 1k frames, which also helps the base MLLMs achieve comparable or even better performance than SOTA MLLMs on some benchmarks, e.g. , GPT-4o and Gemini-1.5 Pro.

Vision-language models (VLMs) are powerful general-purpose reasoners, yet converting them into robot control policies (VLAs) is surprisingly difficult. The root cause is a two-fold gap: VLMs are trained on internet-scale images with language-understanding objectives, while VLAs must perceive robot scenes and predict motor actions. Fine-tuning a VLM directly on robot action data forces the model to cross both gaps at once -- the learning curve is steep and the rich generalizations learned during pretraining tend to degrade rather than transfer. We argue that this gap can be bridged gradually with the right intermediate data. We introduce embodied trajectory-coupled (ETC) data -- vision-language supervision derived from the same robot scenes and trajectories used for action learning. Because ETC data shares the visual context of robot operation while retaining familiar language-understanding objectives, it provides a natural stepping stone between VLM pretraining and VLA fine-tuning. Building on this, we design a three-stage training recipe. Distribution Bridging first adapts the VLM to embodied visual-language semantics. Objective Bridging then gradually shifts the model toward action prediction while preserving the acquired representations. Retentive Adaptation finally specializes the policy to the target deployment domain. We further show that mixing task-relevant out-of-distribution ETC data with a small amount of action data enables the model to generalize to novel visual-language conditions without requiring additional robot demonstrations. Simulation and real-robot experiments confirm that this gradual bridging strategy is the key to transferring VLM generalization into robust, deployable robot policies.

Training acceleration methods for diffusion transformers, such as REPA and dispersive regularization, are commonly explained by additional supervision, spatial-structure priors, or improved feature geometry. We revisit this view and uncover a striking internal change: the AdaLN-Zero residual gate α, which directly controls how conditioned updates enter the residual stream, is substantially reorganized by these methods. This observation motivates our hypothesis that acceleration arises, at least in part, from reshaping the residual gating pathway rather than solely from the feature structures explicitly imposed by auxiliary objectives. Supporting this view, accelerated models are markedly more sensitive to perturbations of α, and their gate geometry reflects semantic relationships among classes. We further introduce the normalized participation ratio (nPR) to characterize the channel-wise organization of the gates and find that, across REPA teachers, projector architectures, and radial-objective targets, broader gate participation accompanies better generation quality. Guided by this insight, we propose a simple teacher-free radial objective that promotes broader gate participation through feature-norm regularization, without pairwise feature comparisons. On ImageNet 256times256 with SiT-B/2, our method improves FID over dispersive loss while increasing mean gate participation over timesteps and classes, further supporting the link between gate organization and training acceleration. Our results identify residual-gate reorganization as a measurable axis of diffusion training acceleration and suggest a simple direction for further acceleration.

Chart understanding presents a critical test to the reasoning capabilities of Vision-Language Models (VLMs). Prior approaches face critical limitations: some rely on external tools, making them brittle and constrained by a predefined toolkit, while others fine-tune specialist models that often adopt a single reasoning strategy, such as text-based chain-of-thought (CoT). The intermediate steps of text-based reasoning are difficult to verify, which complicates the use of reinforcement-learning signals that reward factual accuracy. To address this, we propose a Code-as-Thought (CaT) approach to represent the visual information of a chart in a verifiable, symbolic format. Our key insight is that this strategy must be adaptive: a fixed, code-only implementation consistently fails on complex charts where symbolic representation is unsuitable. This finding leads us to introduce Visual Programmability: a learnable property that determines if a chart-question pair is better solved with code or direct visual analysis. We implement this concept in an adaptive framework where a VLM learns to choose between the CaT pathway and a direct visual reasoning pathway. The selection policy of the model is trained with reinforcement learning using a novel dual-reward system. This system combines a data-accuracy reward to ground the model in facts and prevent numerical hallucination, with a decision reward that teaches the model when to use each strategy, preventing it from defaulting to a single reasoning mode. Experiments demonstrate strong and robust performance across diverse chart-understanding benchmarks. Our work shows that VLMs can be taught not only to reason but also how to reason, dynamically selecting the optimal reasoning pathway for each task.

Image degradation from blur, noise, compression, and poor illumination severely undermines multimodal understanding in real-world settings. Unified multimodal models that combine understanding and generation within a single architecture are a natural fit for this challenge, as their generative pathway can model the fine-grained visual structure that degradation destroys. Yet these models fail to leverage their own generative capacity on degraded inputs. We trace this disconnect to two compounding factors: existing training regimes never ask the model to invoke generation during reasoning, and the standard decode-reencode pathway does not support effective joint optimization. We present CLEAR, a framework that connects the two capabilities through three progressive steps: (1) supervised fine-tuning on a degradation-aware dataset to establish the generate-then-answer reasoning pattern; (2) a Latent Representation Bridge that replaces the decode-reencode detour with a direct, optimizable connection between generation and reasoning; (3) Interleaved GRPO, a reinforcement learning method that jointly optimizes text reasoning and visual generation under answer-correctness rewards. We construct MMD-Bench, covering three degradation severity levels across six standard multimodal benchmarks. Experiments show that CLEAR substantially improves robustness on degraded inputs while preserving clean-image performance. Our analysis further reveals that removing pixel-level reconstruction supervision leads to intermediate visual states with higher perceptual quality, suggesting that task-driven optimization and visual quality are naturally aligned.

While Multimodal Large Language Models (MLLMs) have achieved remarkable progress, visual understanding and generation are typically treated as divergent objectives. Existing unified frameworks often rely on discrete visual tokenization or diffusion objectives whose generative targets differ from the continuous representations consumed by visual understanding models, making direct transfer to enhance existing pretrained MLLMs non-trivial. In this work, we present GAS, a generation-guided training framework that reinterprets visual generation as auxiliary supervision for representation learning. Concretely, GAS adapts Next Embedding Prediction (NEP) as a cross-modal generation paradigm within a decoupled Mixture-of-Transformers (MoT) architecture. By maintaining a shared lower trunk and parallel upper layers, GAS lets generation losses enrich the shared visual pathway with finer spatial precision and stronger visual retention while shielding the upper understanding layers from direct generation gradients. To maximize this synergy, we further construct highly correlated generation tasks that demand deep cognitive grounding rather than generic synthesis alone. Across model scales and training stages, GAS improves aggregate multimodal understanding, with its most reliable gains on perception and spatial comprehension. Crucially, because the auxiliary generation branch is discarded after training, these gains incur zero inference overhead. Extensive controlled comparisons and representation-level analyses further clarify when and why generation-guided training benefits understanding, and demonstrate the feasibility of generation-guided training as a practical route to stronger multimodal understanding.

Audio-visual understanding remains challenging because models must jointly interpret spoken content, visual events, and their temporal relationships. Existing omni models typically introduce dedicated audio encoders and rely on expensive audio-video-text training, tightly coupling omni capability to specific VLM backbones and potentially weakening their existing visual and reasoning abilities. This raises three questions: whether native omni training is necessary for every new VLM, whether speech-centric omni capability can be added while preserving the original backbone, and where richer acoustic representations remain essential. We introduce Training-Free Omni (TFO), a plug-and-play framework that converts a frozen VLM into a speech-centric omni model without architectural modification, or multimodal re-alignment. TFO uses Whisper to extract confidence-filtered, timestamped transcripts and routes them through the VLM's existing language interface, while leaving its visual pathway unchanged. Across matched comparisons with native omni models on 56 benchmarks and 21 languages, TFO is competitive on audio-visual understanding, improves average audio-only performance across all five model settings, and achieves substantial multilingual speech gains. Freezing the VLM also generally preserves stronger image/video understanding, visual grounding, coding, mathematical reasoning, and medical question answering than the corresponding native omni checkpoints. These results show that strong speech-centric omni understanding can often be obtained through modular audio-to-language routing rather than costly backbone-specific training.

Video understanding is shifting from the offline paradigm -- taking a fully recorded video as input and producing a single answer after it ends -- toward real-time interaction, in which the model perceives new frames while still replying, revises its answer as new evidence appears, and remains silent when there is nothing to say. We present MOSS-Video-Preview to validate this paradigm. Our central claim is that perception must not be blocked by generation; its natural realization is a two-channel architecture. We argue that a cross-attention backbone is better suited to real-time vision-language fusion than the prevailing decoder-only design: visual features enter through a side channel rather than joining the autoregressive sequence, so perception and generation run on separate, non-blocking pathways -- reducing the frequency of visual processing and exposing a clean channel-wise interface for independent compression. We complement this with a data synthesis pipeline that converts dense captions into real-time understanding QA whose answers are revised to match what the model has perceived so far, and we specialize an offline model on these data to elicit real-time behavior. Our model trails the strong Qwen2.5-VL-7B baseline overall -- a gap we attribute primarily to data and scale rather than the architecture -- yet attains competitive offline video and multimodal understanding, remains robust on the spatial and fine-grained temporal reasoning central to real-time use, and acquires behaviors that offline models lack: continuous perception, answer revision, and timely silence. On a single H200 with 256 frames per video, it achieves about a 5x speedup in time to first token and 2.7x higher decoding throughput, with negligible degradation in offline ability. Our study of paradigm, architecture, and data outlines a viable path toward real-time video understanding.

Large audio-language models (LALMs) have achieved strong performance in general audio understanding, yet most are designed for monaural input and discard the inter-channel cues essential for spatial perception. In contrast, existing spatial audio-language models are purpose-built for spatial tasks and fail to capitalize on the general understanding capabilities of monaural LALMs. We present MiDashengLM-Spatial, the first open-source end-to-end unified audio-language model, to our knowledge, which supports both general audio understanding and spatial awareness within a single architecture. It extends MiDashengLM with a spatial audio encoder, Spatial-Dasheng, integrated through a hierarchical semantic-to-spatial conditioning module that injects intermediate semantic representations into the spatial branch at multiple depths while preserving the original semantic pathway. To provide spatial audio-language supervision at scale, we develop a data synthesis pipeline that renders diverse spatial acoustic scenes with scene-level spatial descriptions and question-answer pairs. Experiments show that Spatial-Dasheng achieves strong performance on sound event localization and detection in real-world scenes, and that MiDashengLM-Spatial substantially outperforms existing LALMs on spatial understanding and reasoning benchmarks. Meanwhile, it remains competitive with state-of-the-art 8B-scale LALMs on diverse monaural benchmarks, demonstrating that spatial awareness can be acquired without compromising general audio understanding. The source code and model checkpoint are available at https://github.com/xiaomi-research/midashenglm-spatial and https://huggingface.co/mispeech/midashenglm-spatial.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Video Large Language Models (VLMs) have achieved remarkable results on a variety of vision language tasks, yet their practical use is limited by the "needle in a haystack" problem: the massive number of visual tokens produced from raw video frames exhausts the model's context window. Existing solutions alleviate this issue by selecting a sparse set of frames, thereby reducing token count, but such frame-wise selection discards essential temporal dynamics, leading to suboptimal reasoning about motion and event continuity. In this work we systematically explore the impact of temporal information and demonstrate that extending selection from isolated key frames to key clips, which are short, temporally coherent segments, improves video understanding. To maintain a fixed computational budget while accommodating the larger token footprint of clips, we propose an adaptive resolution strategy that dynamically balances spatial resolution and clip length, ensuring a constant token count per video. Experiments on three long-form video benchmarks demonstrate that our training-free approach, F2C, outperforms uniform sampling up to 8.1%, 5.6%, and 10.3% on Video-MME, LongVideoBench and MLVU benchmarks, respectively. These results highlight the importance of preserving temporal coherence in frame selection and provide a practical pathway for scaling Video LLMs to real world video understanding applications. Project webpage is available at https://guangyusun.com/f2c .

Multimodal Large Language Models (MLLMs) have achieved strong performance across many tasks, yet most systems remain limited to offline inference, requiring complete inputs before generating outputs. Recent streaming methods reduce latency by interleaving perception and generation, but still enforce a sequential perception-generation cycle, limiting real-time interaction. In this work, we target a fundamental bottleneck that arises when extending MLLMs to real-time video understanding: the global positional continuity constraint imposed by standard positional encoding schemes. While natural in offline inference, this constraint tightly couples perception and generation, preventing effective input-output parallelism. To address this limitation, we propose a parallel streaming framework that relaxes positional continuity through three designs: Overlapped, Group-Decoupled, and Gap-Isolated. These designs enable simultaneous perception and generation, allowing the model to process incoming inputs while producing responses in real time. Extensive experiments reveal that Group-Decoupled achieves the best efficiency-performance balance, maintaining high fluency and accuracy while significantly reducing latency. We further show that the proposed framework yields up to 2x acceleration under balanced perception-generation workloads, establishing a principled pathway toward speak-while-watching real-time systems. We make all our code publicly available: https://github.com/EIT-NLP/Speak-While-Watching.

Large Language Models (LLMs) have achieved remarkable success in source code understanding, yet as software systems grow in scale, computational efficiency has become a critical bottleneck. Currently, these models rely on a text-based paradigm that treats source code as a linear sequence of tokens, which leads to a linear increase in context length and associated computational costs. The rapid advancement of Multimodal LLMs (MLLMs) introduces an opportunity to optimize efficiency by representing source code as rendered images. Unlike text, which is difficult to compress without losing semantic meaning, the image modality is inherently suitable for compression. By adjusting resolution, images can be scaled to a fraction of their original token cost while remaining recognizable to vision-capable models. To explore the feasibility of this approach, we conduct the first systematic study on the effectiveness of MLLMs for code understanding. Our experiments reveal that: (1) MLLMs can effectively understand code with substantial token reduction, achieving up to 8x compression; (2) MLLMs can effectively leverage visual cues such as syntax highlighting, improving code completion performance under 4x compression; and (3) Code-understanding tasks like clone detection exhibit exceptional resilience to visual compression, with some compression ratios even slightly outperforming raw text inputs. Our findings highlight both the potential and current limitations of MLLMs in code understanding, which points out a shift toward image-modality code representation as a pathway to more efficient inference.

Recent advances in multimodal large language models (LLMs) have enabled unified reasoning across images, audio, and video, but extending such capability to brain imaging remains largely unexplored. Bridging this gap is essential to link neural activity with semantic cognition and to develop cross-modal brain representations. To this end, we present fMRI-LM, a foundational model that bridges functional MRI (fMRI) and language through a three-stage framework. In Stage 1, we learn a neural tokenizer that maps fMRI into discrete tokens embedded in a language-consistent space. In Stage 2, a pretrained LLM is adapted to jointly model fMRI tokens and text, treating brain activity as a sequence that can be temporally predicted and linguistically described. To overcome the lack of natural fMRI-text pairs, we construct a large descriptive corpus that translates diverse imaging-based features into structured textual descriptors, capturing the low-level organization of fMRI signals. In Stage 3, we perform multi-task, multi-paradigm instruction tuning to endow fMRI-LM with high-level semantic understanding, supporting diverse downstream applications. Across various benchmarks, fMRI-LM achieves strong zero-shot and few-shot performance, and adapts efficiently with parameter-efficient tuning (LoRA), establishing a scalable pathway toward a language-aligned, universal model for structural and semantic understanding of fMRI.

Fine-grained visual understanding depends on local detail, yet visual encoders face a trade-off between costly full-image high-resolution processing and compact global encoding that can weaken such evidence. Inspired by human active vision, we separate where to look from what to encode. We focus on the latter and introduce FAVE (Foveated Adaptive Visual Encoding), a lightweight variable-resolution ViT that encodes externally selected regions at high acuity while preserving native geometry. We first isolate this encoding problem using oracle ground-truth crops in a controlled small-object regime. On ImageNet objects with a native maximum side of 96 pixels, FAVE improves Top-1 by 9.4 points over a fixed-resolution ViT on the same crop window with 12.7 times lower FLOPs. Increasing global resolution or backbone capacity does not recover the same operating point. We then integrate FAVE as a complementary local branch in FastVLM. Its local tokens are combined with FastVLM's global visual tokens, while the original global pathway and language model remain frozen. With at most 16 additional local tokens, FAVE improves TextVQA by 1.60 points and achieves a 3.3 times controlled TTFT speedup over SmolVLM2-2.2B. On GQA attribute questions, it improves FastVLM-1.5B by 1.31 points, extending the benefit beyond text while narrowing the gap to FastVLM-7B. Together, these results show that selectively allocating high-acuity local capacity provides an efficient complement to broader global representations and model scaling for fine-grained understanding of small objects, text, and attributes.

We introduce MuirBench, a comprehensive benchmark that focuses on robust multi-image understanding capabilities of multimodal LLMs. MuirBench consists of 12 diverse multi-image tasks (e.g., scene understanding, ordering) that involve 10 categories of multi-image relations (e.g., multiview, temporal relations). Comprising 11,264 images and 2,600 multiple-choice questions, MuirBench is created in a pairwise manner, where each standard instance is paired with an unanswerable variant that has minimal semantic differences, in order for a reliable assessment. Evaluated upon 20 recent multi-modal LLMs, our results reveal that even the best-performing models like GPT-4o and Gemini Pro find it challenging to solve MuirBench, achieving 68.0% and 49.3% in accuracy. Open-source multimodal LLMs trained on single images can hardly generalize to multi-image questions, hovering below 33.3% in accuracy. These results highlight the importance of MuirBench in encouraging the community to develop multimodal LLMs that can look beyond a single image, suggesting potential pathways for future improvements.

Comprehending extended audiovisual experiences remains a fundamental challenge for computational systems. Current approaches struggle with temporal integration and cross-modal associations that humans accomplish effortlessly through hippocampal-cortical networks. We introduce HippoMM, a biologically-inspired architecture that transforms hippocampal mechanisms into computational advantages for multimodal understanding. HippoMM implements three key innovations: (i) hippocampus-inspired pattern separation and completion specifically designed for continuous audiovisual streams, (ii) short-to-long term memory consolidation that transforms perceptual details into semantic abstractions, and (iii) cross-modal associative retrieval pathways enabling modality-crossing queries. Unlike existing retrieval systems with static indexing schemes, HippoMM dynamically forms integrated episodic representations through adaptive temporal segmentation and dual-process memory encoding. Evaluations on our challenging HippoVlog benchmark demonstrate that HippoMM significantly outperforms state-of-the-art approaches (78.2% vs. 64.2% accuracy) while providing substantially faster response times (20.4s vs. 112.5s). Our results demonstrate that translating neuroscientific memory principles into computational architectures provides a promising foundation for next-generation multimodal understanding systems. The code and benchmark dataset are publicly available at https://github.com/linyueqian/HippoMM.

A unified audio model must recognize and understand linguistic, paralinguistic, and environmental information while supporting speech synthesis and editing. A key challenge is representation: understanding favors compact features suited to long-context modeling, whereas speech generation requires reconstructible features that preserve fine-grained acoustic detail. We introduce FireRedAudio, a general-purpose audio language model with a shared 9B-parameter LLM. To the best of our knowledge, it is the first publicly disclosed unified audio-language model to provide separate continuous input representations for understanding and generation within a single trainable autoregressive LLM. Audio to be recognized or analyzed is processed by a dedicated Audio Encoder, while speech inputs for generation use a RedAE-based pathway. The LLM directly generates text or conditions a flow-matching DiT to produce continuous acoustic latents. Through progressive multitask training, FireRedAudio supports ASR and audio understanding, with the latter extending to recordings of up to one hour, as well as zero-shot TTS, Instruct TTS, and semantic and acoustic speech editing. Its structured organization of long-form audio achieves second-level timestamp accuracy. Across comprehensive evaluations, FireRedAudio achieves competitive or leading performance in audio understanding and multilingual ASR, strong content accuracy and speaker preservation in zero-shot TTS, leading instruction following in Instruct TTS, and substantial improvements over Ming-UniAudio-Edit in both semantic and acoustic speech editing. These results demonstrate the viability of decoupled continuous input representations for unifying audio understanding and continuous-latent speech generation in a model of moderate scale. Our code is available at https://github.com/FireRedTeam/FireRedAudio.

Chain-of-Thought (CoT) guides large language models (LLMs) to reason step-by-step, and can motivate their logical reasoning ability. While effective for logical tasks, CoT is not conducive to creative problem-solving which often requires out-of-box thoughts and is crucial for innovation advancements. In this paper, we explore the Leap-of-Thought (LoT) abilities within LLMs -- a non-sequential, creative paradigm involving strong associations and knowledge leaps. To this end, we study LLMs on the popular Oogiri game which needs participants to have good creativity and strong associative thinking for responding unexpectedly and humorously to the given image, text, or both, and thus is suitable for LoT study. Then to investigate LLMs' LoT ability in the Oogiri game, we first build a multimodal and multilingual Oogiri-GO dataset which contains over 130,000 samples from the Oogiri game, and observe the insufficient LoT ability or failures of most existing LLMs on the Oogiri game. Accordingly, we introduce a creative Leap-of-Thought (CLoT) paradigm to improve LLM's LoT ability. CLoT first formulates the Oogiri-GO dataset into LoT-oriented instruction tuning data to train pretrained LLM for achieving certain LoT humor generation and discrimination abilities. Then CLoT designs an explorative self-refinement that encourages the LLM to generate more creative LoT data via exploring parallels between seemingly unrelated concepts and selects high-quality data to train itself for self-refinement. CLoT not only excels in humor generation in the Oogiri game but also boosts creative abilities in various tasks like cloud guessing game and divergent association task. These findings advance our understanding and offer a pathway to improve LLMs' creative capacities for innovative applications across domains. The dataset, code, and models will be released online. https://zhongshsh.github.io/CLoT/.

Policy mirror descent (PMD) provides a principled framework for reinforcement learning (RL) by iteratively solving KL-regularized policy improvement subproblems. While this approach has been adopted in training advanced LLMs such as Kimi K1.5/K2, the ideal closed-form PMD updates require reliable partition function estimation, a significant challenge when working with limited rollouts in the vast action spaces of LLMs. We investigate a practical algorithm, termed PMD-mean, that approximates the log-partition term with the mean reward under the sampling policy and performs regression in log-policy space. Specifically, we characterize the population solution of PMD-mean and demonstrate that it implicitly optimizes mirror descent subproblems with an adaptive mixed KL--χ^2 regularizer. This additional χ^2 regularization constrains large probability changes, producing more conservative updates when expected rewards are low and enhancing robustness against finite-sample estimation errors. Experiments on math reasoning tasks show that PMD-mean achieves superior performance with improved stability and time efficiency. These findings deepen our understanding of PMD-mean and illuminate pathways toward principled improvements in RL algorithms for LLMs. Code is available at https://github.com/horizon-rl/OpenKimi.

Large Language Models (LLMs) require efficient knowledge editing (KE) to update factual information, yet existing methods exhibit significant performance decay in multi-hop factual recall. This failure is particularly acute when edits involve intermediate implicit subjects within reasoning chains. Through causal analysis, we reveal that this limitation stems from an oversight of how chained knowledge is dynamically represented and utilized at the neuron level. We discover that during multi hop reasoning, implicit subjects function as query neurons, which sequentially activate corresponding value neurons across transformer layers to accumulate information toward the final answer, a dynamic prior KE work has overlooked. Guided by this insight, we propose ACE: Attribution-Controlled Knowledge Editing for Multi-hop Factual Recall, a framework that leverages neuron-level attribution to identify and edit these critical query-value (Q-V) pathways. ACE provides a mechanistically grounded solution for multi-hop KE, empirically outperforming state-of-the-art methods by 9.44% on GPT-J and 37.46% on Qwen3-8B. Our analysis further reveals more fine-grained activation patterns in Qwen3 and demonstrates that the semantic interpretability of value neurons is orchestrated by query-driven accumulation. These findings establish a new pathway for advancing KE capabilities based on the principled understanding of internal reasoning mechanisms.

Autonomous driving has long relied on modular "Perception-Decision-Action" pipelines, where hand-crafted interfaces and rule-based components often break down in complex or long-tailed scenarios. Their cascaded design further propagates perception errors, degrading downstream planning and control. Vision-Action (VA) models address some limitations by learning direct mappings from visual inputs to actions, but they remain opaque, sensitive to distribution shifts, and lack structured reasoning or instruction-following capabilities. Recent progress in Large Language Models (LLMs) and multimodal learning has motivated the emergence of Vision-Language-Action (VLA) frameworks, which integrate perception with language-grounded decision making. By unifying visual understanding, linguistic reasoning, and actionable outputs, VLAs offer a pathway toward more interpretable, generalizable, and human-aligned driving policies. This work provides a structured characterization of the emerging VLA landscape for autonomous driving. We trace the evolution from early VA approaches to modern VLA frameworks and organize existing methods into two principal paradigms: End-to-End VLA, which integrates perception, reasoning, and planning within a single model, and Dual-System VLA, which separates slow deliberation (via VLMs) from fast, safety-critical execution (via planners). Within these paradigms, we further distinguish subclasses such as textual vs. numerical action generators and explicit vs. implicit guidance mechanisms. We also summarize representative datasets and benchmarks for evaluating VLA-based driving systems and highlight key challenges and open directions, including robustness, interpretability, and instruction fidelity. Overall, this work aims to establish a coherent foundation for advancing human-compatible autonomous driving systems.

Mitigating bias in machine learning systems requires refining our understanding of bias propagation pathways: from societal structures to large-scale data to trained models to impact on society. In this work, we focus on one aspect of the problem, namely bias amplification: the tendency of models to amplify the biases present in the data they are trained on. A metric for measuring bias amplification was introduced in the seminal work by Zhao et al. (2017); however, as we demonstrate, this metric suffers from a number of shortcomings including conflating different types of bias amplification and failing to account for varying base rates of protected attributes. We introduce and analyze a new, decoupled metric for measuring bias amplification, BiasAmp_{rightarrow} (Directional Bias Amplification). We thoroughly analyze and discuss both the technical assumptions and normative implications of this metric. We provide suggestions about its measurement by cautioning against predicting sensitive attributes, encouraging the use of confidence intervals due to fluctuations in the fairness of models across runs, and discussing the limitations of what this metric captures. Throughout this paper, we work to provide an interrogative look at the technical measurement of bias amplification, guided by our normative ideas of what we want it to encompass. Code is located at https://github.com/princetonvisualai/directional-bias-amp

We introduce Motif-2-12.7B, a new open-weight foundation model that pushes the efficiency frontier of large language models by combining architectural innovation with system-level optimization. Designed for scalable language understanding and robust instruction generalization under constrained compute budgets, Motif-2-12.7B builds upon Motif-2.6B with the integration of Grouped Differential Attention (GDA), which improves representational efficiency by disentangling signal and noise-control attention pathways. The model is pre-trained on 5.5 trillion tokens spanning diverse linguistic, mathematical, scientific, and programming domains using a curriculum-driven data scheduler that gradually changes the data composition ratio. The training system leverages the MuonClip optimizer alongside custom high-performance kernels, including fused PolyNorm activations and the Parallel Muon algorithm, yielding significant throughput and memory efficiency gains in large-scale distributed environments. Post-training employs a three-stage supervised fine-tuning pipeline that successively enhances general instruction adherence, compositional understanding, and linguistic precision. Motif-2-12.7B demonstrates competitive performance across diverse benchmarks, showing that thoughtful architectural scaling and optimized training design can rival the capabilities of much larger models.

We present deep observations in targeted regions of the string landscape through a combination of analytic and dedicated numerical methods. Specifically, we devise an algorithm designed for the systematic construction of Type IIB flux vacua in finite regions of moduli space. Our algorithm is universally applicable across Calabi-Yau orientifold compactifications and can be used to enumerate flux vacua in a region given sufficient computational efforts. As a concrete example, we apply our methods to a two-modulus Calabi-Yau threefold, demonstrating that systematic enumeration is feasible and revealing intricate structures in vacuum distributions. Our results highlight local deviations from statistical expectations, providing insights into vacuum densities, superpotential distributions, and moduli mass hierarchies. This approach opens pathways for precise, data-driven mappings of the string landscape, complementing analytic studies and advancing the understanding of the distribution of flux vacua. This allows us to obtain different types of solutions with hierarchical suppressions, e.g.~vacua with small values of the Gukov-Vafa-Witten superpotential |W_0|. We find an example with |W_0| = 5.547 times 10^{-5} at large complex structure, without light directions and the use of non-perturbative effects.

Neural scaling laws describe how pre-training loss decays as power laws with training time, model size, and compute. This position paper argues that the exponents of these power laws are fixed by generic mechanisms: a one-third time scaling due to the strong nonlinearity of Softmax, an inverse width scaling due to representational superposition, and an inverse depth scaling due to ensemble averaging of Transformer layers. These mechanisms are robust to a wide range of data structures and architectural details, placing current large language models in a universality class with fixed exponents. The coefficients, however, are expected to be sensitive to data and architecture details, and directly determine practical quantities such as the optimal model shape and the compute-optimal frontier. We therefore argue that understanding the coefficients is the key to near-term performance improvements, and that a closer examination of the current universality class may reveal pathways to better universality classes.

Zeolites, as representative porous materials, possess intricate three-dimensional frameworks that endow them with high surface areas and remarkable catalytic properties. There are a few factors that give a huge influence on the catalytic properties, including the size and connectivity of these three-dimensional channels and atomic level defects. In additional to that, the surface morphology and thickness variation of zeolites particles are essential to their catalytic performances as well. However, it is a significant challenge to characterize these macroscopic properties of zeolites using conventional techniques due to their sensitivity to electron beams. In this study, we introduce surface-adaptive electron ptychography, an advanced approach based on multi-slice electron ptychography, which enables high-precision reconstruction of both local atomic configurations and global structural features in zeolite nanoparticles. By adaptively optimizing probe defocus and slice thickness during the reconstruction process, SAEP successfully resolves surface morphology, thickness variations and atomic structure simultaneously. This integrated framework facilitates a direct and intuitive correlation between zeolite channel structures and particle thickness. Our findings open new pathways for large-scale, comprehensive structure property analysis of beam-sensitive porous materials, deepening the understanding of their catalytic behavior.

Unified multimodal models (UMMs) integrate image generation and visual understanding, but are existing single-pathway unlearning methods sufficient to suppress target concepts across both? In this work, we study cross-pathway concept unlearning. Our goal is to prevent a model from both generating images of a target concept and identifying it in input images, while preserving other capabilities. To this end, we introduce UUBench, a diagnostic benchmark covering 30 target concepts and 60 semantically related neighboring concepts. Experiments on representative UMMs show that the evaluated single-pathway methods achieve limited joint forgetting: generation-side editors strongly suppress target generation but yield limited forgetting in visual understanding, while understanding-side baselines struggle to achieve substantial forgetting even in their own pathway. Their direct composition also yields limited joint forgetting. We therefore propose UniForget, achieving joint forgetting rates of 80.0% on BAGEL-7B-MoT and 92.7% on Janus-Pro-7B, outperforming representative baselines. Further analysis reveals trade-offs between joint forgetting and capability preservation.

With the rapid growth of information, recommender systems have become integral for providing personalized suggestions and overcoming information overload. However, their practical deployment often encounters "dirty" data, where noise or malicious information can lead to abnormal recommendations. Research on improving recommender systems' robustness against such dirty data has thus gained significant attention. This survey provides a comprehensive review of recent work on recommender systems' robustness. We first present a taxonomy to organize current techniques for withstanding malicious attacks and natural noise. We then explore state-of-the-art methods in each category, including fraudster detection, adversarial training, certifiable robust training against malicious attacks, and regularization, purification, self-supervised learning against natural noise. Additionally, we summarize evaluation metrics and common datasets used to assess robustness. We discuss robustness across varying recommendation scenarios and its interplay with other properties like accuracy, interpretability, privacy, and fairness. Finally, we delve into open issues and future research directions in this emerging field. Our goal is to equip readers with a holistic understanding of robust recommender systems and spotlight pathways for future research and development.

Understanding humor-particularly when it involves complex, contradictory narratives that require comparative reasoning-remains a significant challenge for large vision-language models (VLMs). This limitation hinders AI's ability to engage in human-like reasoning and cultural expression. In this paper, we investigate this challenge through an in-depth analysis of comics that juxtapose panels to create humor through contradictions. We introduce the YesBut (V2), a novel benchmark with 1,262 comic images from diverse multilingual and multicultural contexts, featuring comprehensive annotations that capture various aspects of narrative understanding. Using this benchmark, we systematically evaluate a wide range of VLMs through four complementary tasks spanning from surface content comprehension to deep narrative reasoning, with particular emphasis on comparative reasoning between contradictory elements. Our extensive experiments reveal that even the most advanced models significantly underperform compared to humans, with common failures in visual perception, key element identification, comparative analysis and hallucinations. We further investigate text-based training strategies and social knowledge augmentation methods to enhance model performance. Our findings not only highlight critical weaknesses in VLMs' understanding of cultural and creative expressions but also provide pathways toward developing context-aware models capable of deeper narrative understanding though comparative reasoning.

Multimodal Large Language Models (MLLMs) are increasingly being deployed as automated content moderators. Within this landscape, we uncover a critical threat: Adversarial Smuggling Attacks. Unlike adversarial perturbations (for misclassification) and adversarial jailbreaks (for harmful output generation), adversarial smuggling exploits the Human-AI capability gap. It encodes harmful content into human-readable visual formats that remain AI-unreadable, thereby evading automated detection and enabling the dissemination of harmful content. We classify smuggling attacks into two pathways: (1) Perceptual Blindness, disrupting text recognition; and (2) Reasoning Blockade, inhibiting semantic understanding despite successful text recognition. To evaluate this threat, we constructed SmuggleBench, the first comprehensive benchmark comprising 1,700 adversarial smuggling attack instances. Evaluations on SmuggleBench reveal that both proprietary (e.g., GPT-5) and open-source (e.g., Qwen3-VL) state-of-the-art models are vulnerable to this threat, producing Attack Success Rates (ASR) exceeding 90%. By analyzing the vulnerability through the lenses of perception and reasoning, we identify three root causes: the limited capabilities of vision encoders, the robustness gap in OCR, and the scarcity of domain-specific adversarial examples. We conduct a preliminary exploration of mitigation strategies, investigating the potential of test-time scaling (via CoT) and adversarial training (via SFT) to mitigate this threat. Our code is publicly available at https://github.com/zhihengli-casia/smugglebench.

Visual generation grounded in Visual Foundation Model (VFM) representations offers a highly promising unified pathway for integrating visual understanding, perception, and generation. Despite this potential, training large-scale text-to-image diffusion models entirely within the VFM representation space remains largely unexplored. To bridge this gap, we scale the SVG (Self-supervised representations for Visual Generation) framework, proposing SVG-T2I to support high-quality text-to-image synthesis directly in the VFM feature domain. By leveraging a standard text-to-image diffusion pipeline, SVG-T2I achieves competitive performance, reaching 0.75 on GenEval and 85.78 on DPG-Bench. This performance validates the intrinsic representational power of VFMs for generative tasks. We fully open-source the project, including the autoencoder and generation model, together with their training, inference, evaluation pipelines, and pre-trained weights, to facilitate further research in representation-driven visual generation.

Physics-informed neural networks (PINNs) provide a promising machine learning framework for solving partial differential equations, but their training often breaks down on challenging problems, sometimes converging to physically incorrect solutions despite achieving small residual losses. This failure, we argue, is not merely an optimization difficulty. Rather, it reflects a fundamental weakness of the empirical PDE residual loss, which can admit trivial or spurious solutions during training. From this perspective, we revisit pseudo-time stepping, a technique that has recently shown strong empirical success in PINNs. We show that its main benefit is not simply to ease optimization; instead, when combined with collocation-point resampling, it helps reveal and avoid spurious solutions. At the same time, we find that the effectiveness of pseudo-time stepping depends critically on the choice of step size, which cannot be tuned reliably from the training loss alone. To overcome this limitation, we propose an adaptive pseudo-time stepping strategy that selects the step size from a finite-difference surrogate of the local residual Jacobian, yielding the largest step permitted by local stability without per-problem tuning. Across a diverse set of PDE benchmarks, the proposed method consistently improves both accuracy and robustness. Together, these findings provide a clearer understanding of why PINNs fail and suggest a practical pathway toward more reliable physics-informed learning. All code and data accompanying this manuscript are available at https://github.com/sifanexisted/jaxpi2.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

A significant ``modality gap" exists between the abundance of text-only data and the increasing power of multimodal models. This work systematically investigates whether images generated on-the-fly by Text-to-Image (T2I) models can serve as a mechanism to unlock latent visual priors for text-centric reasoning. Through a comprehensive evaluation framework on text classification, we analyze the impact of critical variables, including T2I model quality (e.g., Flux.1, SDXL), prompt engineering strategies, and multimodal fusion architectures. Our findings demonstrate that this ``synthetic perception" can yield significant performance gains by effectively projecting text into a visual semantic space, even when augmenting strong large language model baselines like Llama-3 and Qwen-2.5. We show that this approach serves as a form of cross-modal probing, mitigating the sensory deprivation inherent in pure text training. However, the effectiveness is highly conditional, depending on the semantic alignment between text and the generated image, the task's visual groundability, and the generative fidelity of the T2I model. Our work establishes a rigorous benchmark for this paradigm, demonstrating its viability as a pathway to enrich language understanding in traditionally unimodal scenarios.

While feed-forward 3D Gaussian Splatting (3DGS) enables efficient 3D reconstruction, achieving high-fidelity rendering remains challenging. Existing pixel-aligned approaches suffer from spatial inflexibility and massive structural redundancy, whereas query-based methods lack 3D priors and entangle geometry with appearance, yielding blurry, pose-dependent results. To overcome these deficiencies, we propose QuerySplat, a feed-forward 3DGS framework driven by geometric priors and explicit appearance decoupling. Specifically, we design a dual-branch query-based decoder: the geometry branch leverages a pretrained Vision Geometric Model for spatial understanding, which intrinsically endows QuerySplat with pose-free modeling capabilities, while the appearance branch recovers high-frequency details through a dedicated pathway separated from geometric attribute regression. Extensive experiments demonstrate that QuerySplat mitigates the blurry rendering issues of early query-based models and consistently outperforms pixel-aligned approaches in rendering fidelity. On the challenging DL3DV benchmark, it achieves state-of-the-art novel view synthesis performance, with average PSNR gains of 2.30 dB and 1.04 dB over the best pose-free and pose-required baselines, respectively. Project Page: https://inspatio.github.io/querysplat.

Agentic assistants capable of proactive, personalized interactions require structured models of user intent and workflow. However, building these models from raw, unstructured screen activity remains an open challenge. We present SERUM, a multi-pass framework that extracts finite-state behavioral models directly from unstructured egocentric video using hierarchical VLM annotation. Processing screen recordings through a sliding window, SERUM alternates between activity-recognition and intent-inference passes, with each pass refining labels using accumulated prior context to reduce hallucination and temporal conflation seen in single-pass annotation. Synonymous states are then merged via sentence embeddings and human-calibrated thresholds into a compact, coherent taxonomy. We evaluate behavioral structure by fitting first-order Markov models over the resulting label sequences (both actions and intents) and measuring predictive accuracy against frequency baselines. Across 61 egocentric videos in four domains (coding, cooking, physical activities, and daily life), we find: (1) iterative label refinement converges to a stable state vocabulary, which we term schematic equilibrium, after several passes; (2) normalized Markov models achieve substantially lower perplexity and higher action predictions than frequency baselines, with the largest gains on structured tasks like coding; and (3) human annotators rate final-pass labels as accurate and meaningfully improved over first-pass labels. To our knowledge, SERUM is the first system to produce interpretable process models from unstructured egocentric screen video without manual annotation, opening a scalable pathway for user modeling and behavioral understanding in the wild. Our demo, code, and results are publicly available

Despite the rapid progress of Multimodal Large Language Models (MLLMs) in 2D vision-language tasks, robust multi-view spatial reasoning remains a fundamental bottleneck due to the lack of structured 3D cognitive pathways in existing datasets. To address this, we introduce MV-STRIDE, a Multi-View hierarchical SpaTial Reasoning dataset with Interdependent and DEcomposed capabilitiEs. Moving beyond flat data structures, MV-STRIDE explicitly models the dependency relationships between foundational perception, scene understanding, and complex contextual reasoning, providing a coherent learning pathway aligned with human spatial cognition. We develop a systematic QA generation pipeline leveraging diverse 3D scene sources that enforces cross-view dependency constraints to prevent single-view solvability, generating multi-level spatial reasoning tasks supported by cognitively grounded chain-of-thought supervision for complex inference. Extensive evaluations demonstrate that our multi-stage training framework based on our hierarchical dataset achieves state-of-the-art performance across multiple spatial reasoning benchmarks, notably the multi-view oriented MMSI-Bench. Our approach enables MLLMs to maintain robust, 3D-consistent spatial reasoning across diverse viewpoints. The code and dataset are available at https://co1dspring.github.io/MV-STRIDE/.

Semantic vision encoders have become a central visual interface for multimodal understanding and semantic conditioning in image generation. However, their final tokens discard fine-grained visual details, leading to poor pixel reconstruction and limiting their use in reconstruction-sensitive tasks such as image generation and editing. In this work, we ask whether understanding, generation, and editing can be modeled in a single visual representation space built from a pretrained semantic ViT. We show that the frozen Transformer blocks of a semantic ViT are not intrinsically unable to preserve visual details. Instead, the original patch parameterization drives the representation toward semantic abstraction, making fine-grained information difficult to recover from the final tokens. Based on this observation, we introduce Patch Reparameterization, which preserves the original semantic pathway while adding a reconstruction-aware patch embedding that provides fine-grained visual information to the same frozen ViT blocks. The resulting unified representation preserves multimodal understanding while enabling high-fidelity image reconstruction and a favorable reconstruction--generation trade-off. We further scale this representation into UniSpace, an 8B Mixture-of-Transformer-Experts model that performs understanding, generation, and editing in the same visual space without a separate VAE pathway. System-level evaluations demonstrate practical text-to-image generation and instruction-based image editing, showing that a reparameterized pretrained ViT can serve as a unified visual interface for scalable multimodal modeling.

Video reasoning requires models to locate and track question-relevant evidence across frames. While reinforcement learning (RL) with verifiable rewards improves accuracy, it still struggles to achieve reliable spatio-temporal grounding during the reasoning process. Moreover, improving grounding typically relies on scaled training data or inference-time perception tools, which increases annotation cost or computational cost. To address this challenge, we propose VisonCoach, an input-adaptive RL framework that improves spatio-temporal grounding through visual prompting as training-time guidance. During RL training, visual prompts are selectively applied to challenging inputs to amplify question-relevant evidence and suppress distractors. The model then internalizes these improvements through self-distillation, enabling grounded reasoning directly on raw videos without visual prompting at inference. VisonCoach consists of two components: (1) Visual Prompt Selector, which predicts appropriate prompt types conditioned on the video and question, and (2) Spatio-Temporal Reasoner, optimized with RL under visual prompt guidance and object-aware grounding rewards that enforce object identity consistency and multi-region bounding-box overlap. Extensive experiments demonstrate that VisonCoach achieves state-of-the-art performance under comparable settings, across diverse video reasoning, video understanding, and temporal grounding benchmarks (V-STAR, VideoMME, World-Sense, VideoMMMU, PerceptionTest, and Charades-STA), while maintaining a single efficient inference pathway without external tools. Our results show that visual prompting during training improves grounded video reasoning, while self-distillation enables the model to internalize this ability without requiring prompts at inference time.

Vision-Language Models (VLMs) have achieved significant progress in multimodal understanding tasks, demonstrating strong capabilities particularly in general tasks such as image captioning and visual reasoning. However, when dealing with specialized cultural heritage domains like 3D vase artifacts, existing models face severe data scarcity issues and insufficient domain knowledge limitations. Due to the lack of targeted training data, current VLMs struggle to effectively handle such culturally significant specialized tasks. To address these challenges, we propose the VaseVQA-3D dataset, which serves as the first 3D visual question answering dataset for ancient Greek pottery analysis, collecting 664 ancient Greek vase 3D models with corresponding question-answer data and establishing a complete data construction pipeline. We further develop the VaseVLM model, enhancing model performance in vase artifact analysis through domain-adaptive training. Experimental results validate the effectiveness of our approach, where we improve by 12.8% on R@1 metrics and by 6.6% on lexical similarity compared with previous state-of-the-art on the VaseVQA-3D dataset, significantly improving the recognition and understanding of 3D vase artifacts, providing new technical pathways for digital heritage preservation research. Code: https://github.com/AIGeeksGroup/VaseVQA-3D. Website: https://aigeeksgroup.github.io/VaseVQA-3D.

Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but rather from the sparsity it introduces. We conducted a comprehensive analysis of all relevant pathway-based neural network models for predictive tasks, critically evaluating each study's contributions. From this review, we curated a subset of methods for which the source code was publicly available. The comparison of the biologically informed state-of-the-art deep learning models and their randomized counterparts showed that models based on randomized information performed equally well as biologically informed ones across different metrics and datasets. Notably, in 3 out of the 15 analyzed models, the randomized versions even outperformed their biologically informed counterparts. Moreover, pathway-informed models did not show any clear advantage in interpretability, as randomized models were still able to identify relevant disease biomarkers despite lacking explicit pathway information. Our findings suggest that pathway annotations may be too noisy or inadequately explored by current methods. Therefore, we propose a methodology that can be applied to different domains and can serve as a robust benchmark for systematically comparing novel pathway-informed models against their randomized counterparts. This approach enables researchers to rigorously determine whether observed performance improvements can be attributed to biological insights.

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

Large language models (LLMs) have made remarkable strides in various natural language processing tasks, but their performance on complex reasoning problems remains hindered by a lack of explainability and trustworthiness. This issue, often manifesting as hallucinations or unattributable reasoning processes, limits their applicability in complex reasoning scenarios. To address this, we propose Knowledge Graph-constrained Trajectory Reasoning Attribution and Chain Explanation Supervision (KG-TRACES), a novel framework that enhances the reasoning ability of LLMs through explicit supervision over reasoning paths and processes. KG-TRACES jointly supervises the model to: (1) predict symbolic relation paths, (2) predict full triple-level reasoning paths, and (3) generate attribution-aware reasoning processes grounded in the reasoning paths. At inference phase, the model adapts to both KG-available and KG-unavailable scenarios, retrieving reasoning paths from a KG when possible or predicting plausible reasoning paths with only intrinsic knowledge when not. This design enables the model to reason in an explainable and source-attributable pattern. Through extensive experiments on complex reasoning tasks, we demonstrate that KG-TRACES significantly outperforms existing SOTA: it improves Hits@1 by 1.6% and F1 by 4.7% on WebQSP, and achieves improvements of 4.8% in Hits@1 and 2.1% in F1 on CWQ. Moreover, we show its transferability to specialized domains such as medicine. By visualizing the intermediate steps of reasoning processes, we further show that the explicit supervision introduced by KG-TRACES leads to more stable and goal-directed reasoning processes, aligning closely with correct answers. Code is available at https://github.com/Edaizi/KG-TRACES.

Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

Cross-entropy pretraining and preference alignment update the same transformer weights, but leave geometrically distinct traces. We characterise this asymmetry with a relative-subspace-fraction probe that tracks how weight deltas align with residual-stream activation subspaces and with the prediction subspace defined by the unembedding. Alignment deltas concentrate in the read pathway (W_Q, W_K), along principal directions of attention-input activations, while remaining near-isotropic in the write pathway (W_O, W_2) relative to the prediction subspace. We explain this pattern through anisotropic gradient accumulation: updates to a matrix W are sums of outer products δ_t a_t^top, and inherit directional structure from whichever side has concentrated covariance. For read-pathway matrices, this side is the input activation a_t, whose covariance is spiked in trained transformers and therefore produces objective-agnostic concentration. For write-pathway matrices, the relevant side is the upstream gradient δ_t, whose anisotropy depends on the loss. Cross-entropy supplies the canonical sharp per-sample signal, inducing write-pathway prediction geometry during pretraining; alignment objectives typically add little further write-side concentration. We support this explanation with a within-checkpoint trajectory, a graded contrastive-objective control, and a closed-form rank-1 intervention with matched direction controls, providing causal evidence for the proposed weight-space geometry.

Reasoning is central to a wide range of intellectual activities, and while the capabilities of large language models (LLMs) continue to advance, their performance in reasoning tasks remains limited. The processes and mechanisms underlying reasoning are not yet fully understood, but key elements include path exploration, selection of relevant knowledge, and multi-step inference. Problems are solved through the synthesis of these components. In this paper, we propose a benchmark that focuses on a specific aspect of reasoning ability: the direct evaluation of multi-step inference. To this end, we design a special reasoning task where multi-step inference is specifically focused by largely eliminating path exploration and implicit knowledge utilization. Our dataset comprises pairs of explicit instructions and corresponding questions, where the procedures necessary for solving the questions are entirely detailed within the instructions. This setup allows models to solve problems solely by following the provided directives. By constructing problems that require varying numbers of steps to solve and evaluating responses at each step, we enable a thorough assessment of state-of-the-art LLMs' ability to follow instructions. To ensure the robustness of our evaluation, we include multiple distinct tasks. Furthermore, by comparing accuracy across tasks, utilizing step-aware metrics, and applying separately defined measures of complexity, we conduct experiments that offer insights into the capabilities and limitations of LLMs in reasoning tasks. Our findings have significant implications for the development of LLMs and highlight areas for future research in advancing their reasoning abilities. Our dataset is available at https://huggingface.co/datasets/ifujisawa/procbench and code at https://github.com/ifujisawa/proc-bench.

Explainability has become an important topic in computer science and artificial intelligence, leading to a subfield called Explainable Artificial Intelligence (XAI). The goal of providing or seeking explanations is to achieve (better) 'understanding' on the part of the explainee. However, what it means to 'understand' is still not clearly defined, and the concept itself is rarely the subject of scientific investigation. This conceptual article aims to present a model of forms of understanding for XAI-explanations and beyond. From an interdisciplinary perspective bringing together computer science, linguistics, sociology, philosophy and psychology, a definition of understanding and its forms, assessment, and dynamics during the process of giving everyday explanations are explored. Two types of understanding are considered as possible outcomes of explanations, namely enabledness, 'knowing how' to do or decide something, and comprehension, 'knowing that' -- both in different degrees (from shallow to deep). Explanations regularly start with shallow understanding in a specific domain and can lead to deep comprehension and enabledness of the explanandum, which we see as a prerequisite for human users to gain agency. In this process, the increase of comprehension and enabledness are highly interdependent. Against the background of this systematization, special challenges of understanding in XAI are discussed.

Convolutional Neural Networks (CNNs) have exhibited great performance in discriminative feature learning for complex visual tasks. Besides discrimination power, interpretability is another important yet under-explored property for CNNs. One difficulty in the CNN interpretability is that filters and image classes are entangled. In this paper, we introduce a novel pathway to alleviate the entanglement between filters and image classes. The proposed pathway groups the filters in a late conv-layer of CNN into class-specific clusters. Clusters and classes are in a one-to-one relationship. Specifically, we use the Bernoulli sampling to generate the filter-cluster assignment matrix from a learnable filter-class correspondence matrix. To enable end-to-end optimization, we develop a novel reparameterization trick for handling the non-differentiable Bernoulli sampling. We evaluate the effectiveness of our method on ten widely used network architectures (including nine CNNs and a ViT) and five benchmark datasets. Experimental results have demonstrated that our method PICNN (the combination of standard CNNs with our proposed pathway) exhibits greater interpretability than standard CNNs while achieving higher or comparable discrimination power.

Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at https://github.com/Jun-Hyeong-Kim/AdaPath.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

Gradient descent is the method of choice for training large artificial intelligence systems. As these systems become larger, a better understanding of the mechanisms behind gradient training would allow us to alleviate compute costs and help steer these systems away from harmful behaviors. To that end, we suggest utilizing the circuit perspective brought forward by mechanistic interpretability. After laying out our intuition, we illustrate how it enables us to design a curriculum for efficient learning in a controlled setting. The code is available at https://github.com/facebookresearch/pal.

Grokking, i.e., test performance keeps improving long after training loss converged, has been recently witnessed in neural network training, making the mechanism of generalization and other emerging capabilities such as reasoning mysterious. While prior studies usually train small models on a few toy or highly-specific tasks for thousands of epochs, we conduct the first study of grokking on checkpoints during one-pass pretraining of a 7B large language model (LLM), i.e., OLMoE. We compute the training loss and evaluate generalization on diverse benchmark tasks, including math reasoning, code generation, and commonsense/domain-specific knowledge retrieval tasks. Our study, for the first time, verifies that grokking still happens in the pretraining of large-scale foundation models, though different data may enter grokking stages asynchronously. We further demystify grokking's "emergence of generalization" by investigating LLM internal dynamics. Specifically, we find that training samples' pathways (i.e., expert choices across layers) evolve from random, instance-specific to more structured and shareable between samples during grokking. Also, the complexity of a sample's pathway reduces despite the converged loss. These indicate a memorization-to-generalization conversion, providing a mechanistic explanation of delayed generalization. In the study, we develop two novel metrics to quantify pathway distance and the complexity of a single pathway. We show their ability to predict the generalization improvement on diverse downstream tasks. They are efficient, simple to compute and solely dependent on training data. Hence, they have practical value for pretraining, enabling us to monitor the generalization performance without finetuning and test. Theoretically, we show that more structured pathways reduce model complexity and improve the generalization bound.

Vision Transformer models exhibit immense power yet remain opaque to human understanding, posing challenges and risks for practical applications. While prior research has attempted to demystify these models through input attribution and neuron role analysis, there's been a notable gap in considering layer-level information and the holistic path of information flow across layers. In this paper, we investigate the significance of influential neuron paths within vision Transformers, which is a path of neurons from the model input to output that impacts the model inference most significantly. We first propose a joint influence measure to assess the contribution of a set of neurons to the model outcome. And we further provide a layer-progressive neuron locating approach that efficiently selects the most influential neuron at each layer trying to discover the crucial neuron path from input to output within the target model. Our experiments demonstrate the superiority of our method finding the most influential neuron path along which the information flows, over the existing baseline solutions. Additionally, the neuron paths have illustrated that vision Transformers exhibit some specific inner working mechanism for processing the visual information within the same image category. We further analyze the key effects of these neurons on the image classification task, showcasing that the found neuron paths have already preserved the model capability on downstream tasks, which may also shed some lights on real-world applications like model pruning. The project website including implementation code is available at https://foundation-model-research.github.io/NeuronPath/.

Mechanistic interpretability seeks to understand the neural mechanisms that enable specific behaviors in Large Language Models (LLMs) by leveraging causality-based methods. While these approaches have identified neural circuits that copy spans of text, capture factual knowledge, and more, they remain unusable for multimodal models since adapting these tools to the vision-language domain requires considerable architectural changes. In this work, we adapt a unimodal causal tracing tool to BLIP to enable the study of the neural mechanisms underlying image-conditioned text generation. We demonstrate our approach on a visual question answering dataset, highlighting the causal relevance of later layer representations for all tokens. Furthermore, we release our BLIP causal tracing tool as open source to enable further experimentation in vision-language mechanistic interpretability by the community. Our code is available at https://github.com/vedantpalit/Towards-Vision-Language-Mechanistic-Interpretability.

Mechanistic interpretability aims to understand the computational mechanisms underlying neural networks' capabilities in order to accomplish concrete scientific and engineering goals. Progress in this field thus promises to provide greater assurance over AI system behavior and shed light on exciting scientific questions about the nature of intelligence. Despite recent progress toward these goals, there are many open problems in the field that require solutions before many scientific and practical benefits can be realized: Our methods require both conceptual and practical improvements to reveal deeper insights; we must figure out how best to apply our methods in pursuit of specific goals; and the field must grapple with socio-technical challenges that influence and are influenced by our work. This forward-facing review discusses the current frontier of mechanistic interpretability and the open problems that the field may benefit from prioritizing.

Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes from a systems biological point of view. The integration of known cancer genes onto protein and signaling networks reveals the characteristics of cancer genes within networks. This approach shows that cancer genes often function as network hub proteins which are involved in many cellular processes and form focal nodes in the information exchange between many signaling pathways. Literature mining allows constructing gene-gene networks, in which new cancer genes can be identified. The gene expression profiles of cancer cells are used for reconstructing gene regulatory networks. By doing so, the genes, which are involved in the regulation of cancer progression, can be picked up from these networks after which their functions can be further confirmed in the laboratory.

In this paper, we introduce agentic unlearning which removes specified information from both model parameters and persistent memory in agents with closed-loop interaction. Existing unlearning methods target parameters alone, leaving two critical gaps: (i) parameter-memory backflow, where retrieval reactivates parametric remnants or memory artifacts reintroduce sensitive content, and (ii) the absence of a unified strategy that covers both parameter and memory pathways. We present Synchronized Backflow Unlearning (SBU), a framework that unlearns jointly across parameter and memory pathways. The memory pathway performs dependency closure-based unlearning that prunes isolated entities while logically invalidating shared artifacts. The parameter pathway employs stochastic reference alignment to guide model outputs toward a high-entropy prior. These pathways are integrated via a synchronized dual-update protocol, forming a closed-loop mechanism where memory unlearning and parametric suppression reinforce each other to prevent cross-pathway recontamination. Experiments on medical QA benchmarks show that SBU reduces traces of targeted private information across both pathways with limited degradation on retained data.

Advanced models such as OpenAI o1 exhibit impressive problem-solving capabilities through step-by-step reasoning. However, they may still falter on more complex problems, making errors that disrupt their reasoning paths. We attribute this to the expansive solution space, where each step has the risk of diverging into mistakes. To enhance language model reasoning, we introduce a specialized training framework called Reasoning Paths Optimization (RPO), which enables learning to reason and explore from diverse paths. Our approach encourages favorable branches at each reasoning step while penalizing unfavorable ones, enhancing the model's overall problem-solving performance. Reasoning Paths Optimization does not rely on large-scale human-annotated rationales or outputs from closed-source models, making it scalable and data-efficient. We focus on multi-step reasoning tasks, such as math word problems and science-based exam questions. The experiments demonstrate that our framework significantly enhances the reasoning performance of large language models, with up to 3.1% and 4.3% improvement on GSM8K and MMLU (STEM) respectively. Our data and code can be found at https://reasoning-paths.github.io.

Vision-Language Models (VLMs) are advancing computational pathology with superior visual understanding capabilities. However, current systems often reduce diagnosis to directly output conclusions without verifiable evidence-linked reasoning, which severely limits clinical trust and hinders expert error rectification. To address these barriers, we construct PathReasoner, the first large-scale dataset of whole-slide image (WSI) reasoning. Unlike previous work reliant on unverified distillation, we develop a rigorous knowledge-guided generation pipeline. By leveraging medical knowledge graphs, we explicitly align structured pathological findings and clinical reasoning with diagnoses, generating over 20K high-quality instructional samples. Based on the database, we propose PathReasoner-R1, which synergizes trajectory-masked supervised fine-tuning with reasoning-oriented reinforcement learning to instill structured chain-of-thought capabilities. To ensure medical rigor, we engineer a knowledge-aware multi-granular reward function incorporating an Entity Reward mechanism strictly aligned with knowledge graphs. This effectively guides the model to optimize for logical consistency rather than mere outcome matching, thereby enhancing robustness. Extensive experiments demonstrate that PathReasoner-R1 achieves state-of-the-art performance on both PathReasoner and public benchmarks across various image scales, equipping pathology models with transparent, clinically grounded reasoning capabilities. Dataset and code are available at https://github.com/cyclexfy/PathReasoner-R1.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

Understanding commonsense causality is a unique mark of intelligence for humans. It helps people understand the principles of the real world better and benefits the decision-making process related to causation. For instance, commonsense causality is crucial in judging whether a defendant's action causes the plaintiff's loss in determining legal liability. Despite its significance, a systematic exploration of this topic is notably lacking. Our comprehensive survey bridges this gap by focusing on taxonomies, benchmarks, acquisition methods, qualitative reasoning, and quantitative measurements in commonsense causality, synthesizing insights from over 200 representative articles. Our work aims to provide a systematic overview, update scholars on recent advancements, provide a pragmatic guide for beginners, and highlight promising future research directions in this vital field.

Adaptive hierarchical systems accumulate routing state as they learn which components to select. We show that this state already defines a coherent attribution over the hierarchy. A leaf receives the product of the local routing weights on its path, while an internal node receives the corresponding prefix product. The same learned state can therefore be read consistently at group and component levels, and every finer readout sums exactly to its coarser counterpart. This attribution describes the preferences learned by the deployed router rather than an intrinsic or counterfactual value of a component. Across LLM, Census, agentic, and telecom-network hierarchies, the learned state contains meaningful structure at several levels, and the clearest organisation need not occur at the leaves. In the telecom study, Site- or Region-level readouts usually reveal clearer structure than Cell-level readouts. Comparison with Shapley attribution can then show whether the preferences learned in deployment match capabilities revealed by counterfactual coalitions. The result is a hierarchical explanation that requires no separate attribution model: the same routing state supports consistent explanations at several levels of the system.

Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical impact requires models that generalize across cancer types and capture biologically coherent signals. Prior work is often limited to per-cancer settings and variance-based evaluation, leaving functional relevance underexplored. We introduce HistoPrism, an efficient transformer-based architecture for pan-cancer prediction of gene expression from histology. To evaluate biological meaning, we introduce a pathway-level benchmark, shifting assessment from isolated gene-level variance to coherent functional pathways. HistoPrism not only surpasses prior state-of-the-art models on highly variable genes , but also more importantly, achieves substantial gains on pathway-level prediction, demonstrating its ability to recover biologically coherent transcriptomic patterns. With strong pan-cancer generalization and improved efficiency, HistoPrism establishes a new standard for clinically relevant transcriptomic modeling from routinely available histology.

Stepwise inference protocols, such as scratchpads and chain-of-thought, help language models solve complex problems by decomposing them into a sequence of simpler subproblems. Despite the significant gain in performance achieved via these protocols, the underlying mechanisms of stepwise inference have remained elusive. To address this, we propose to study autoregressive Transformer models on a synthetic task that embodies the multi-step nature of problems where stepwise inference is generally most useful. Specifically, we define a graph navigation problem wherein a model is tasked with traversing a path from a start to a goal node on the graph. Despite is simplicity, we find we can empirically reproduce and analyze several phenomena observed at scale: (i) the stepwise inference reasoning gap, the cause of which we find in the structure of the training data; (ii) a diversity-accuracy tradeoff in model generations as sampling temperature varies; (iii) a simplicity bias in the model's output; and (iv) compositional generalization and a primacy bias with in-context exemplars. Overall, our work introduces a grounded, synthetic framework for studying stepwise inference and offers mechanistic hypotheses that can lay the foundation for a deeper understanding of this phenomenon.

We introduce directional routing, a lightweight mechanism that gives each transformer attention head learned suppression directions controlled by a shared router, at 3.9% parameter cost. We train a 433M-parameter model alongside an identical baseline in a single run, then trace the resulting circuits through mechanistic interpretability. Routing becomes the model's dominant computational pathway. Disabling it collapses factual recall to near-zero probability across all 8 test prompts and drops induction accuracy from 93.4% to 0.0%. Knocking out individual attention heads has negligible effect: the primary mover head's removal actually increases target probability, and induction heads retain 98.6% accuracy without their strongest member. The coordination mechanism is irreplaceable; the components it coordinates are not. The model also self-organizes, without explicit pressure, into two regimes: domain-adaptive routing in early layers and fixed syntactic pruning in late layers, where the least-varying layer is the most critical (+42.6 PPL when disabled). Routing reduces perplexity 31-56% relative to the baseline, though downstream multiple-choice benchmarks do not yet reflect these gains.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

Motivation: Interpretability is not optional in biology: understanding gene regulation requires models whose learned structure can be directly interrogated, not merely accurate predictors whose internals resist mapping onto regulatory relationships. We ask whether an architecture mirroring the central dogma yields attention and gradient maps that recover known regulatory elements and networks in inspectable form. Results: Central Dogma Transformer II (CDT-II) mirrors the central dogma in its architecture -- DNA self-attention, RNA self-attention, and DNA-to-RNA cross-attention -- requiring only genomic embeddings and raw per-cell expression. On K562 CRISPR interference (CRISPRi) data with five genes held out entirely, CDT-II predicts perturbation effects (per-gene mean r = 0.84), recovers the GFI1B regulatory network (6.6-fold enrichment, P = 3.5 x 10^-17), and concentrates cross-attention on ENCODE regulatory elements including CTCF sites (mean 7.67x across 28 target genes, P < 0.001). Gradient attribution predicts consequences of perturbing therapeutic targets (mean r = 0.82). For TFRC, target of the anti-TfR1 antibody PPMX-T003, it identifies erythrocyte-structure, iron-dependent DNA-synthesis and oxidative-stress genes, matching anemia and ferroptosis reported clinically and preclinically -- without clinical data as input. CDT-II acts as an AI microscope, surfacing clinically relevant regulatory structure from perturbation experiments alone. Availability: Source code is available at https://github.com/nobusama/CDT2. Pre-computed embeddings, training data, and model weights are available at https://huggingface.co/datasets/nobusama17/CDT2-data.

Large Language Models (LLMs) are prone to hallucination, the generation of plausible yet factually incorrect statements. This work investigates the intrinsic, architectural origins of this failure mode through three primary contributions.First, to enable the reliable tracing of internal semantic failures, we propose Distributional Semantics Tracing (DST), a unified framework that integrates established interpretability techniques to produce a causal map of a model's reasoning, treating meaning as a function of context (distributional semantics). Second, we pinpoint the model's layer at which a hallucination becomes inevitable, identifying a specific commitment layer where a model's internal representations irreversibly diverge from factuality. Third, we identify the underlying mechanism for these failures. We observe a conflict between distinct computational pathways, which we interpret using the lens of dual-process theory: a fast, heuristic associative pathway (akin to System 1) and a slow, deliberate contextual pathway (akin to System 2), leading to predictable failure modes such as Reasoning Shortcut Hijacks. Our framework's ability to quantify the coherence of the contextual pathway reveals a strong negative correlation (rho = -0.863) with hallucination rates, implying that these failures are predictable consequences of internal semantic weakness. The result is a mechanistic account of how, when, and why hallucinations occur within the Transformer architecture.

When studying unconstrained behaviour and allowing mice to leave their cage to navigate a complex labyrinth, the mice exhibit foraging behaviour in the labyrinth searching for rewards, returning to their home cage now and then, e.g. to drink. Surprisingly, when executing such a ``home run'', the mice do not follow the exact reverse path, in fact, the entry path and home path have very little overlap. Recent work proposed a hierarchical active inference model for navigation, where the low level model makes inferences about hidden states and poses that explain sensory inputs, whereas the high level model makes inferences about moving between locations, effectively building a map of the environment. However, using this ``map'' for planning, only allows the agent to find trajectories that it previously explored, far from the observed mice's behaviour. In this paper, we explore ways of incorporating before-unvisited paths in the planning algorithm, by using the low level generative model to imagine potential, yet undiscovered paths. We demonstrate a proof of concept in a grid-world environment, showing how an agent can accurately predict a new, shorter path in the map leading to its starting point, using a generative model learnt from pixel-based observations.

LLMs cannot forget the way we delete a file. Strangely, we are asked to remove something that was never put anywhere in particular. What the model took from a piece of text is now smeared across billions of weights. Existing methods rewrite all of them to change one thing, and none of them say which part produced that change. To address this, we introduce Causal Routing for Unlearning (CRU) by asking where the concept is expressed in the model and suppressing only that part. One untrained forward pass over the forget set ranks neurons by how their activations vary. Then, small routing modules on those neurons gate and suppress only the concepts that need to be forgotten. In CRU, the base model is frozen, and any change in behavior is caused only by the gated neurons; hence, why the routing is causal. Due to our parameter efficiency (only ~0.01% as many parameters as the base model), unlearning a concept costs 14 GiB, whereas the baselines require 71 GiB. On TOFU, CRU is indistinguishable from the retained model (p > 0.05, KS test) and is never Pareto-dominated, whereas every compared baseline matches its forgetting on the larger-forget batches only by collapsing utility. On RWKU, it achieves an adversarial-probe recall of 0.052, compared to 0.250 for the strongest baseline, meaning the knowledge is gone, not merely harder to reach. Thus, deciding on the intervention at query time, rather than fixing it beforehand, is the axis along which we argue that unlearning should proceed.

Next-generation sequencing technologies, including RNA-sequencing, provide genome-wide measurements of gene expression and enable broad explorations of biomarkers and mechanisms underlying disease and treatment response. Bioinformatics tools for processing this data, such as differential expression analysis, are largely univariate, linear, and rely on predefined pathway knowledge annotations, which limits their ability to capture nonlinear and multivariate gene interactions. This paper explores the application of causal discovery to characterizing transcriptional responses to radiation as a function of dose rate in human cells. By jointly modeling radiation perturbations and gene expression, we learn directed gene networks that capture important regulatory relationships beyond correlation and exhibit significant enrichment of known radiation response pathways compared to baseline approaches. We find that inferred causal graphs reveal structured network features such as high in-degree housekeeping genes and high out-degree transcription factors. Further analysis suggests a hierarchical organization of stress response pathways and triggered cell death pathways. This work highlights the potential of causal discovery in healthcare settings with applications to understanding response mechanisms, identifying regulatory targets, and improving interpretation of complex genomic data.