arXiv:2603.07369v1 Announce Type: new Abstract: How does the brain optimize sensory information for decision-making in new tasks? One hypothesis suggests learning reduces redundancy in neural representations to improve efficiency, while another, based on Bayesian inference, predicts learning increases redundancy by distributing information across neurons. We tested these hypotheses by tracking population responses in macaque cortical area V4 as monkeys learned visual discrimination tasks. We found strong support for the Bayesian predictions: task learning increased redundancy in neural responses over weeks of training and within single trials. This redundancy did not reduce information but instead increased the information carried by individual neurons. These insights suggest sensory processing in the brain reflects a generative rather than discriminative inference process.

arXiv:2603.08035v1 Announce Type: new Abstract: Reward modeling is essential for aligning Large Language Models(LLMs) with human preferences, yet conventional reward models suffer from poor interpretability and heavy reliance on costly expert annotations. While recent rubric-based approaches enhance evaluation transparency, they lack systematic quality control, yielding noisy and redundant criteria, failing to mitigate persistent biases (e.g., verbosity, position) in LLM evaluators, and creating a scalability-reliability trade-off. To address these limitations, we propose CDRRM (Contrast-Driven Rubric Reward Model), a framework built on a novel Contrast-then-Synthesis paradigm for high-quality rubric generation and guided preference judgment. CDRRM first conducts multi-dimensional contrastive profiling on preference pairs to identify causal discriminative factors, then synthesizes these insights into compact, context-aware rubrics to guide preference judg- ments. Extensive experiments on three authoritative benchmarks (RewardBench, RMBench, RMB) demonstrate that CDRRM achieves state-of-the-art performance across diverse domains and effectively mitigates aforementioned evaluation biases. Notably, our approach delivers exceptional data efficiency: training the rubric generator on only 3k high-quality samples empowers a frozen pre-trained judge model to outperform fully fine-tuned baselines. This work offers a scalable, interpretable, and data-efficient path for reward modeling.

arXiv:2603.06961v1 Announce Type: cross Abstract: Quadruped locomotion provides a natural setting for understanding when model-free learning can outperform model-based control design, by exploiting data patterns to bypass the difficulty of optimizing over discrete contacts and the combinatorial explosion of mode changes. We give a principled analysis of why imitation learning with quadrupeds can be inherently effective in a small data regime, based on the structure of its limit cycles, Poincar\'e return maps, and local numerical properties of neural networks. The understanding motivates a new imitation learning method that regulates the alignment between variations in a latent space and those over the output actions. Hardware experiments confirm that a few seconds of demonstration is sufficient to train various locomotion policies from scratch entirely offline with reasonable robustness.

arXiv:2603.08007v1 Announce Type: cross Abstract: Existing aerial Vision-Language Navigation (VLN) methods predominantly adopt a detection-and-planning pipeline, which converts open-vocabulary detections into discrete textual scene graphs. These approaches are plagued by inadequate spatial reasoning capabilities and inherent linguistic ambiguities. To address these bottlenecks, we propose a Visual-Spatial Reasoning (ViSA) enhanced framework for aerial VLN. Specifically, a triple-phase collaborative architecture is designed to leverage structured visual prompting, enabling Vision-Language Models (VLMs) to perform direct reasoning on image planes without the need for additional training or complex intermediate representations. Comprehensive evaluations on the CityNav benchmark demonstrate that the ViSA-enhanced VLN achieves a 70.3\% improvement in success rate compared to the fully trained state-of-the-art (SOTA) method, elucidating its great potential as a backbone for aerial VLN systems.

arXiv:2501.00296v4 Announce Type: replace-cross Abstract: Our aim is to learn to solve long-horizon decision-making problems in complex robotics domains given low-level skills and a handful of short-horizon demonstrations containing sequences of images. To this end, we focus on learning abstract symbolic world models that facilitate zero-shot generalization to novel goals via planning. A critical component of such models is the set of symbolic predicates that define properties of and relationships between objects. In this work, we leverage pretrained vision-language models (VLMs) to propose a large set of visual predicates potentially relevant for decision-making, and to evaluate those predicates directly from camera images. At training time, we pass the proposed predicates and demonstrations into an optimization-based model-learning algorithm to obtain an abstract symbolic world model that is defined in terms of a compact subset of the proposed predicates. At test time, given a novel goal in a novel setting, we use the VLM to construct a symbolic description of the current world state, and then use a search-based planning algorithm to find a sequence of low-level skills that achieves the goal. We demonstrate empirically across experiments in both simulation and the real world that our method can generalize aggressively, applying its learned world model to solve problems with a wide variety of object types, arrangements, numbers of objects, and visual backgrounds, as well as novel goals and much longer horizons than those seen at training time.

arXiv:2502.08942v3 Announce Type: replace-cross Abstract: While many advances in time series models focus exclusively on numerical data, research on multimodal time series, particularly those involving contextual textual information, remains in its infancy. With recent progress in large language models and time series learning, we revisit the integration of paired texts with time series through the Platonic Representation Hypothesis, which posits that representations of different modalities converge to shared spaces. In this context, we identify that time-series-paired texts may naturally exhibit periodic properties that closely mirror those of the original time series. Building on this insight, we propose a novel framework, Texts as Time Series (TaTS), which considers the time-series-paired texts to be auxiliary variables of the time series. TaTS can be plugged into any existing numerical-only time series models and effectively enable them to handle time series data with paired texts. Through extensive experiments on both multimodal time series forecasting and imputation tasks across benchmark datasets with various existing time series models, we demonstrate that TaTS can enhance multimodal predictive performance without modifying model architectures. Our Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TaTS.

arXiv:2507.17731v2 Announce Type: replace-cross Abstract: Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

arXiv:2508.04594v2 Announce Type: replace-cross Abstract: This work focuses on training graph foundation models (GFMs) that have strong generalization ability in graph-level tasks such as graph classification. Effective GFM training requires capturing information consistent across different domains. We discover that graph structures provide more consistent cross-domain information compared to node features and graph labels. However, traditional GFMs primarily focus on transferring node features from various domains into a unified representation space but often lack structural cross-domain generalization. To address this, we introduce GraphProp, which emphasizes structural generalization. The training process of GraphProp consists of two main phases. First, we train a structural GFM by predicting graph invariants. Since graph invariants are properties of graphs that depend only on the abstract structure, not on particular labellings or drawings of the graph, this structural GFM has a strong ability to capture the abstract structural information and provide discriminative graph representations comparable across diverse domains. In the second phase, we use the representations given by the structural GFM as positional encodings to train a comprehensive GFM. This phase utilizes domain-specific node attributes and graph labels to further improve cross-domain node feature generalization. Our experiments demonstrate that GraphProp significantly outperforms the competitors in supervised learning and few-shot learning, especially in handling graphs without node attributes.

arXiv:2603.03655v1 Announce Type: new Abstract: Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

arXiv:2603.03784v1 Announce Type: new Abstract: World models are essential for planning and evaluation in agentic systems, yet existing approaches lie at two extremes: hand-engineered simulators that offer consistency and reproducibility but are costly to adapt, and implicit neural models that are flexible but difficult to constrain, verify, and debug over long horizons. We seek a principled middle ground that combines the reliability of explicit simulators with the flexibility of learned models, allowing world models to be adapted during online execution. By targeting a broad class of environments whose dynamics are governed by the ordering, timing, and causality of discrete events, such as queueing and service operations, embodied task planning, and message-mediated multi-agent coordination, we advocate explicit, executable discrete-event world models synthesized directly from natural-language specifications. Our approach adopts the DEVS formalism and introduces a staged LLM-based generation pipeline that separates structural inference of component interactions from component-level event and timing logic. To evaluate generated models without a unique ground truth, simulators emit structured event traces that are validated against specification-derived temporal and semantic constraints, enabling reproducible verification and localized diagnostics. Together, these contributions produce world models that are consistent over long-horizon rollouts, verifiable from observable behavior, and efficient to synthesize on demand during online execution.

arXiv:2406.06512v2 Announce Type: replace-cross Abstract: The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.

arXiv:2509.25106v3 Announce Type: replace-cross Abstract: Deep Research Agents (DRAs) can autonomously conduct complex investigations and generate comprehensive reports, demonstrating strong real-world potential. However, existing evaluations mostly rely on close-ended benchmarks, while open-ended deep research benchmarks remain scarce and typically neglect personalized scenarios. To bridge this gap, we introduce Personalized Deep Research Bench (PDR-Bench), the first benchmark for evaluating personalization in DRAs. It pairs 50 diverse research tasks across 10 domains with 25 authentic user profiles that combine structured persona attributes with dynamic real-world contexts, yielding 250 realistic user-task queries. To assess system performance, we propose the PQR Evaluation Framework, which jointly measures Personalization Alignment, Content Quality, and Factual Reliability. Our experiments on a range of systems highlight current capabilities and limitations in handling personalized deep research. This work establishes a rigorous foundation for developing and evaluating the next generation of truly personalized AI research assistants.

arXiv:2603.02406v1 Announce Type: cross Abstract: Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.

arXiv:2603.03195v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models are a promising path toward embodied intelligence, yet they often overlook the predictive and temporal-causal structure underlying visual dynamics. World-model VLAs address this by predicting future frames, but waste capacity reconstructing redundant backgrounds. Latent-action VLAs encode frame-to-frame transitions compactly, but lack temporally continuous dynamic modeling and world knowledge. To overcome these limitations, we introduce CoWVLA (Chain-of-World VLA), a new "Chain of World" paradigm that unifies world-model temporal reasoning with a disentangled latent motion representation. First, a pretrained video VAE serves as a latent motion extractor, explicitly factorizing video segments into structure and motion latents. Then, during pre-training, the VLA learns from an instruction and an initial frame to infer a continuous latent motion chain and predict the segment's terminal frame. Finally, during co-fine-tuning, this latent dynamic is aligned with discrete action prediction by jointly modeling sparse keyframes and action sequences in a unified autoregressive decoder. This design preserves the world-model benefits of temporal reasoning and world knowledge while retaining the compactness and interpretability of latent actions, enabling efficient visuomotor learning. Extensive experiments on robotic simulation benchmarks show that CoWVLA outperforms existing world-model and latent-action approaches and achieves moderate computational efficiency, highlighting its potential as a more effective VLA pretraining paradigm. The project website can be found at https://fx-hit.github.io/cowvla-io.

arXiv:2410.04949v3 Announce Type: replace-cross Abstract: Judicial efficiency is critical to social stability. However, in many countries worldwide, grassroots courts face substantial case backlogs, and judicial decisions remain heavily dependent on judges' cognitive efforts, with insufficient intelligent tools to enhance efficiency. To address this issue, we propose a highly efficient law article recommendation approach combining a Knowledge Graph (KG) and a Large Language Model (LLM). First, we construct a Case-Enhanced Law Article Knowledge Graph (CLAKG) to store current law articles, historical case information, and their interconnections, alongside an LLM-based automated construction method. Building on this, we propose a closed-loop law article recommendation framework integrating graph embedding-based retrieval and KG-grounded LLM reasoning. Experiments on judgment documents from China Judgments Online demonstrate that our method boosts law article recommendation accuracy from 0.549 to 0.694, outperforming strong baselines significantly. To support reproducibility and future research, all source code and processed datasets are publicly available on GitHub (see Data Availability Statement).

arXiv:2507.01352v3 Announce Type: replace-cross Abstract: Despite the critical role of reward models (RMs) in Reinforcement Learning from Human Feedback (RLHF), current state-of-the-art open RMs perform poorly on most existing evaluation benchmarks, failing to capture nuanced human preferences. We hypothesize that this brittleness stems primarily from limitations in preference datasets, which are often narrowly scoped, synthetically labeled, or lack rigorous quality control. To address these challenges, we present SynPref-40M, a large-scale preference dataset comprising 40 million preference pairs. To enable data curation at scale, we design a human-AI synergistic two-stage pipeline that leverages the complementary strengths of human annotation quality and AI scalability. In this pipeline, humans provide verified annotations, while LLMs perform automatic curation based on human guidance. Training on this preference mixture, we introduce Skywork-Reward-V2, a suite of eight reward models ranging from 0.6B to 8B parameters, trained on a carefully curated subset of 26 million preference pairs from SynPref-40M. We demonstrate that Skywork-Reward-V2 is versatile across a wide range of capabilities, including alignment with human preferences, objective correctness, safety, resistance to stylistic biases, and best-of-N scaling. These reward models achieve state-of-the-art performance across seven major reward model benchmarks, outperform generative reward models, and demonstrate strong downstream performance. Ablation studies confirm that effectiveness stems not only from data scale but also from high-quality curation. The Skywork-Reward-V2 series represents substantial progress in open reward models, demonstrating how human-AI curation synergy can unlock significantly higher data quality.

arXiv:2509.12610v2 Announce Type: replace-cross Abstract: Predicates are foundational components in data analysis systems. However, modern workloads increasingly involve unstructured documents, which demands semantic understanding, beyond traditional value-based predicates. Given enormous documents and ad-hoc queries, while Large Language Models (LLMs) demonstrate powerful zero-shot capabilities, their high inference cost leads to unacceptable overhead. Therefore, we introduce \textsc{ScaleDoc}, a novel system that addresses this by decoupling predicate execution into an offline representation phase and an optimized online filtering phase. In the offline phase, \textsc{ScaleDoc} leverages a LLM to generate semantic representations for each document. Online, for each query, it trains a lightweight proxy model on these representations to filter the majority of documents, forwarding only the ambiguous cases to the LLM for final decision. Furthermore, \textsc{ScaleDoc} proposes two core innovations to achieve significant efficiency: (1) a contrastive-learning-based framework that trains the proxy model to generate reliable predicating decision scores; (2) an adaptive cascade mechanism that determines the effective filtering policy while meeting specific accuracy targets. Our evaluations across three datasets demonstrate that \textsc{ScaleDoc} achieves over a 2$\times$ end-to-end speedup and reduces expensive LLM invocations by up to 85\%, making large-scale semantic analysis practical and efficient.

arXiv:2509.15927v4 Announce Type: replace-cross Abstract: Auto-bidding is a critical tool for advertisers to improve advertising performance. Recent progress has demonstrated that AI-Generated Bidding (AIGB), which learns a conditional generative planner from offline data, achieves superior performance compared to typical offline reinforcement learning (RL)-based auto-bidding methods. However, existing AIGB methods still face a performance bottleneck due to their inherent inability to explore beyond the static dataset with feedback. To address this, we propose \textbf{AIGB-Pearl} (\emph{\textbf{P}lanning with \textbf{E}valu\textbf{A}tor via \textbf{RL}}), a novel method that integrates generative planning and policy optimization. The core of AIGB-Pearl lies in constructing a trajectory evaluator to assess the quality of generated scores and designing a provably sound KL-Lipschitz-constrained score-maximization scheme to ensure safe and efficient exploration beyond the offline dataset. A practical algorithm that incorporates the synchronous coupling technique is further developed to ensure the model regularity required by the proposed scheme. Extensive experiments on both simulated and real-world advertising systems demonstrate the state-of-the-art performance of our approach.

arXiv:2602.12705v3 Announce Type: replace-cross Abstract: We present MedXIAOHE, a medical vision-language foundation model designed to advance general-purpose medical understanding and reasoning in real-world clinical applications. MedXIAOHE achieves state-of-the-art performance across diverse medical benchmarks and surpasses leading closed-source multimodal systems on multiple capabilities. To achieve this, we propose an entity-aware continual pretraining framework that organizes heterogeneous medical corpora to broaden knowledge coverage and reduce long-tail gaps (e.g., rare diseases). For medical expert-level reasoning and interaction, MedXIAOHE incorporates diverse medical reasoning patterns via reinforcement learning and tool-augmented agentic training, enabling multi-step diagnostic reasoning with verifiable decision traces. To improve reliability in real-world use, MedXIAOHE integrates user-preference rubrics, evidence-grounded reasoning, and low-hallucination long-form report generation, with improved adherence to medical instructions. We release this report to document our practical design choices, scaling insights, and evaluation framework, hoping to inspire further research.

arXiv:2602.18479v1 Announce Type: cross Abstract: This paper presents a large language model (LLM) agent named AgentCAT, which extracts and analyzes catalytic reaction data from chemical engineering papers, %and supports natural language based interactive analysis of the extracted data. AgentCAT serves as an alternative to overcome the long-standing data bottleneck in chemical engineering field, and its natural language based interactive data analysis functionality is friendly to the community. AgentCAT also presents a formal abstraction and challenge analysis of the catalytic reaction data extraction task in an artificial intelligence-friendly manner. This abstraction would help the artificial intelligence community understand this problem and in turn would attract more attention to address it. Technically, the complex catalytic process leads to complicated dependency structure in catalytic reaction data with respect to elementary reaction steps, molecular behaviors, measurement evidence, etc. This dependency structure makes it challenging to guarantee the correctness and completeness of data extraction, as well as representing them for analysis. AgentCAT addresses this challenge and it makes four folds of technical contributions: (1) a schema-governed extraction pipeline with progressive schema evolution, enabling robust data extraction from chemical engineering papers; (2) a dependency-aware reaction-network knowledge graph that links catalysts/active sites, synthesis-derived descriptors, mechanistic claims with evidence, and macroscopic outcomes, preserving process coupling and traceability; (3) a general querying module that supports natural-language exploration and visualization over the constructed graph for cross-paper analysis; (4) an evaluation on $\sim$800 peer-reviewed chemical engineering publications demonstrating the effectiveness of AgentCAT.