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Bowen Zhou

Publications and source records attributed to Bowen Zhou.

At least 55 records · Page 3Linked to original sources
arXiv2026

Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

cs.CL↗
arXiv2026

A Definition and Roadmap for World Models

World models -- internal simulators that learn the structure and dynamics of an environment -- have become one of the most actively debated concepts in AI. From model-based reinforcement learning and video generation to embodied robotics and ultimately, physical AI, researchers across AI subfields are building systems that they call "world models", yet there is no consensus on what a world model fundamentally is, what it should predict, or how it should be built. This perspective article provides a scientific definition of world models, discussions of their key technical aspects, and a staged roadmap for developing effective world models.

cs.AI↗
arXiv2026

WeaveBench: A Long-Horizon, Real-World Benchmark for Computer-Use Agents with Hybrid Interfaces

Computer-use agents (CUAs) increasingly operate in runtimes that combine visual desktop control, command-line execution, code editing, browsers, and external tools. Existing benchmarks, however, often evaluate these interfaces as separable capabilities, leaving long-horizon cross-interface orchestration under-tested. Thus, we introduce WeaveBench, a long-horizon hybrid-interface benchmark with 114 tasks across 8 real-world work domains, grounded in real user requests and publicly verifiable artifacts. Each task requires agents to combine GUI observations/actions with CLI/code operations within a single trajectory. We evaluate these tasks on a real Ubuntu desktop inside deployed CLI-agent runtimes, augmented with a minimal desktop-control plugin. We also propose a companion trajectory-aware judge that inspects deliverables, files, screenshots, logs, and action traces, while detecting shortcut behaviors such as fabricated visual evidence or hard-coded metrics. Across frontier model-runtime pairings, the best PassRate reaches only 41.2%, showing the benchmark remains far from saturated. The trajectory-aware judge further reveals that outcome-only grading substantially overestimates agent performance. Overall, WeaveBench exposes a critical gap in CUA evaluation and provides an effective testbed to measure whether agents can orchestrate GUI, CLI, and code operations across long-horizon real-world tasks.

cs.AI↗
arXiv2026

NatureBench: Can Coding Agents Match the Published SOTA of Nature-Family Papers?

We introduce NatureBench, a cross-discipline benchmark of 90 tasks distilled from peer-reviewed Nature-family publications, designed to evaluate whether AI coding agents can move beyond reproduction toward discovery on real scientific problems. NatureBench is built on NatureGym, an automated pipeline that constructs a standardized, per-task containerized environment from a source paper, addressing the environment-fragmentation problem that has limited the credibility of prior agent-on-research benchmarks. Evaluating ten frontier agent configurations under a strict web-search-disabled protocol, we find that the strongest model surpasses SOTA on only 17.8% of tasks under the g>0.1 criterion. Analysis of method pathways reveals that agents succeed primarily through methodological translation, converting scientific tasks into familiar supervised prediction problems, rather than through genuine scientific invention. Failures are dominated by wrong method choice and insufficient compute budget, not by task misunderstanding. We release the benchmark, the NatureGym pipeline, and a public leaderboard with maintainer-side reproduction. Code: https://github.com/FrontisAI/NatureBench

cs.CL↗
arXiv2026

InternVLA-A1.5: Unifying Understanding, Latent Foresight, and Action for Compositional Generalization

Unified models for robot manipulation aim to equip one policy with both the semantic priors of pretrained VLMs and the physical dynamics learned through future prediction. In practice, existing designs tend to erode the semantics of the pretrained backbone, suffer interference among heterogeneous objectives, and learn future prediction from scratch in pixel space, leaving the dynamics priors of pretrained video generators unexploited. We present InternVLA-A1.5, which builds the policy on a native VLM backbone that keeps training on VQA and subtask prediction, and attaches a lightweight unified expert for continuous action generation. Future prediction is recast as a latent-querying problem, where a small set of learnable foresight tokens condenses the task-relevant future into a compact latent code under the supervision of a frozen pretrained video generation model, so the policy inherits world-model dynamics priors without ever learning pixel-level generation. The video branch is discarded at inference, keeping real-time control. Pretrained on 1.2M robot episodes and 3M multimodal samples, InternVLA-A1.5 achieves the best overall results on all six simulation benchmarks. In the real world, the preserved semantics deliver the strongest compositional generalization on held-out instruction bindings, and the two designs together sustain long-horizon execution.

cs.RO↗
arXiv2026

Re:Form -- Reducing Human Annotations in Scalable Formal Software Verification with RL in LLMs: A Preliminary Study on Dafny

Existing informal language-based (e.g., human language) Large Language Models (LLMs) trained with Reinforcement Learning (RL) face a significant challenge: their verification processes, which provide crucial training signals, are neither reliable nor scalable. In fact, the prevalent large proprietary models could hardly generate verifiable programs. A promising yet largely uncharted alternative is formal language-based reasoning. Grounding LLMs in rigorous formal systems where generative models operate in formal language spaces (e.g., Dafny) enables the automatic and mathematically provable verification of their reasoning processes and outcomes. This capability is pivotal for achieving large-scale, reliable formal software verification. It is a common practice to employ human-annotated chain-of-thought and answers to induce the reasoning and coding capabilities of LLMs. Unfortunately, it becomes unacceptably all-consuming to provide such priors for supervising complex programming tasks. In this work, we systematically explore ways to reduce human annotations with the formal language, Dafny, as the main environment for our pilot study. Our pipeline mainly relies on introducing an automatic and scalable data curation pipeline, and careful RL designs integrated with feedback from the formal language verifier. We introduce DafnyComp, a benchmark of compositional formal programs with auto-formalized specifications for specification reasoning. Our supervised fine-tuning (SFT) stage enables even small models (e.g., 0.5B) to generate syntactically valid and verifiable Dafny code, surpassing proprietary models. RL with regularization further improves performance, achieving stronger generalization to out-of-domain tasks and outperforming all strong baselines on the challenging DafnyComp benchmark.

cs.CL↗
arXiv2026

SciIR: A Large-scale Training Dataset and Benchmark for Scientific Image Reasoning Generation

While Text-to-Image (T2I) models have shown remarkable success in generating photorealistic visual content, they still struggle with the rigorous semantic alignment and logical reasoning required for scientific imagery. Inspired by Peirce's Semiotic Triad, we introduce Scientific Image Reasoning (SciIR), a comprehensive resource for training and evaluation of scientific image generation. We formalize scientific reasoning into three core dimensions: Entity Structure (Icon), Scientific Process (Index), and Scientific Law (Symbol). Specifically, to overcome the scarcity of training data in scientific image generation, we elaborately create SciIR-82k, a large-scale dataset containing over 80,000 high-quality scientific image-text pairs from cutting-edge publications. The dataset is hierarchically organized according to the semiotic dimensions and incorporates a Scientific Reasoning Chain-of-Thought (Sci-RCoT) to explicitly model underlying visual logic. For evaluation, we propose SciIR-Bench, which aligns with these three semiotic levels and employs an Atomic Checklist to convert the outcome-oriented scientific accuracy into process-oriented, verifiable, fine-grained questions. Our extensive experiments reveal significant deficiencies in current models' scientific reasoning capabilities. Furthermore, by fine-tuning on the SciIR-82k dataset, we developed the Qwen-Image-SciIR model, which achieves a substantial improvement on the SciIR-Bench, increasing the final score from 35\% to 43\%, laying a solid foundation for future advances in scientific image generation.

cs.CV↗
arXiv2026

MacAgentBench: Benchmarking AI Agents on Real-World macOS Desktop

Computer use agents (CUAs) have advanced rapidly in desktop automation, and a growing number of users deploy CUAs such as OpenClaw on Mac Mini for always-on automation. However, existing benchmarks, including those for macOS, evaluate agents without framework augmentation and rely on binary evaluation. As a result, they fail to capture both the framework capabilities leveraged by modern CUAs and the partial progress on long-horizon, multi-application tasks. We present MacAgentBench, a comprehensive macOS agent benchmark comprising 676 tasks across 25 applications, with nearly 60% involving both GUI and CLI interaction. The benchmark adopts deterministic rule-based evaluation and introduces fine-grained multi-checkpoint scoring with capability annotations for multi-application tasks. Experiments across three frameworks and 16 models show that the best configuration, Claude Opus 4.6 on OpenClaw, attains 73.7% Pass@1, while this advantage is primarily driven by the skill library rather than by framework design. Fine-grained metrics further reveal that models with similar Pass@1 can differ substantially in sub-goal completion. Our code and data are publicly available at https://github.com/JetAstra/MacAgentBench.

cs.AI↗
arXiv2026

TMPO: Trajectory Matching Policy Optimization for Diverse and Efficient Diffusion Alignment

Reinforcement learning (RL) has shown extraordinary potential in aligning diffusion models to downstream tasks, yet most of them still suffer from significant reward hacking, which degrades generative diversity and quality by inducing visual mode collapse and amplifying unreliable rewards. We identify the root cause as the mode-seeking nature of these methods, which maximize expected reward without effectively constraining probability distribution over acceptable trajectories, causing concentration on a few high-reward paths. In contrast, we propose Trajectory Matching Policy Optimization (TMPO), which replaces scalar reward maximization with trajectory-level reward distribution matching. Specifically, TMPO introduces a Softmax Trajectory Balance (Softmax-TB) objective to match the policy probabilities of K trajectories to a reward-induced Boltzmann distribution. We prove that this objective inherits the mode-covering property of forward KL divergence, preserving coverage over all acceptable trajectories while optimizing reward. To further reduce multi-trajectory training time on large-scale flow-matching models, TMPO incorporates Dynamic Stochastic Tree Sampling, where trajectories share denoising prefixes and branch at dynamically scheduled steps, reducing redundant computation while improving training effectiveness. Extensive results across diverse alignment tasks such as human preference, compositional generation and text rendering show that TMPO improves generative diversity over state-of-the-art methods by 9.1%, and achieves competitive performance in all downstream and efficiency metrics, attaining the optimal trade-off between reward and diversity.

cs.LG↗
arXiv2026

Post-Trained MoE Can Skip Half Experts via Self-Distillation

Mixture-of-Experts (MoE) scales language models efficiently through sparse expert activation, and its dynamic variant further reduces computation by adjusting the activated experts in an input-dependent manner. Existing dynamic MoE methods usually rely on pre-training from scratch or task-specific adaptation, leaving the practical conversion of fully trained MoE underexplored. Enabling such adaptation would directly alleviate the inference costs by allowing easy tokens to bypass unnecessary expert during serving. This paper introduces Zero-Expert Self-Distillation Adaptation (ZEDA), a low-cost framework that transforms post-trained static MoE models into efficient dynamic ones. To stabilize this architectural conversion, ZEDA injects parameter-free zero-output experts into each MoE layer and adapts the augmented model through two-stage self-distillation, utilizing the original MoE as a frozen teacher and applying a group-level balancing loss. On Qwen3-30B-A3B and GLM-4.7-Flash across 11 benchmarks spanning math, code, and instruction following, ZEDA eliminates over 50% of expert FLOPs at marginal accuracy loss. It outperforms the strongest dynamic MoE baseline by 6.1 and 4.0 points on the two models, and delivers ~1.20$\times$ end-to-end inference speedup.

cs.LG↗
arXiv2026

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model

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 $50\times$ 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.

q-bio.BM↗
arXiv2026

AMix-2: Establishing Protein as a Native Modality in Large Language Models

We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design within a single foundation model. AMix-2 is built upon two key ideas: (1) a unified protein-text formulation that embeds natural language and protein sequence in a shared token space, enabling one model to perform biological reasoning and conditional design instead of separate downstream task-specialized models; and (2) a block-wise diffusion language modeling backbone that combines causal generation across blocks with bidirectional context and iterative refinement within blocks. This scheme better matches the intrinsic nature of proteins than a strict left-to-right factorization. To evaluate protein foundation models under realistic generalization settings, we further introduce ProteinArena, a comprehensive benchmark with time-aware and homology-aware protocols across various understanding and design tasks, and with baselines covering classical bioinformatics tools, protein-specialized models and LLMs. On ProteinArena, AMix-2 outperforms frontier LLMs and demonstrates competitive performance to task-specific protein models. Controlled experiments further show that the diffusion-based paradigm generally surpasses its autoregressive counterpart, highlighting the advantage of flexible generation order for protein sequences. We release both AMix-2 and ProteinArena to facilitate open research in protein foundation models.

q-bio.BM↗
arXiv2026

MolClaw: An Autonomous Agent with Hierarchical Skills for Drug Molecule Evaluation, Screening, and Optimization

Computational drug discovery, particularly the complex workflows of drug molecule screening and optimization, requires orchestrating dozens of specialized tools in multi-step workflows, yet current AI agents struggle to maintain robust performance and consistently underperform in these high-complexity scenarios. Here we present MolClaw, an autonomous agent that leads drug molecule evaluation, screening, and optimization. It unifies over 30 specialized domain resources through a three-tier hierarchical skill architecture (70 skills in total) that facilitates agent long-term interaction at runtime: tool-level skills standardize atomic operations, workflow-level skills compose them into validated pipelines with quality check and reflection, and a discipline-level skill supplies scientific principles governing planning and verification across all scenarios in the field. Additionally, we introduce MolBench, a benchmark comprising molecular screening, optimization, and end-to-end discovery challenges spanning 8 to 50+ sequential tool calls. MolClaw achieves state-of-the-art performance across all metrics, and ablation studies confirm that gains concentrate on tasks that demand structured workflows while vanishing on those solvable with ad hoc scripting, establishing workflow orchestration competence as the primary capability bottleneck for AI-driven drug discovery.

cs.AI↗
arXiv2026

AOT-POT: Adaptive Operator Transformation for Large-Scale PDE Pre-training

Pre-training neural operators on diverse partial differential equation (PDE) datasets has emerged as a promising direction for building general-purpose surrogate models in scientific machine learning. However, the inherent complexity and structural diversity of PDE solution operators make multi-PDE pre-training fundamentally challenging. Existing methods mainly address this by increasing model capacity, while leaving the target solution operators unchanged. Inspired by classical numerical analysis, we instead propose to transform complex and diverse solution operators into simpler, better-aligned forms that are easier to model jointly. Since the optimal transformation varies across PDE types, it must be adaptive and input-dependent, allowing a single neural operator to approximate an entire family of operators. We instantiate this idea as AOT-POT (adaptive operator-transformation for pre-training operator transformer), which expands hidden representations into multiple parallel streams, adaptively aggregates and redistributes them before and after each sub-layer, and mixes streams through Sinkhorn-projected doubly stochastic matrices for stable training. These mechanisms together reshape diverse solution operators into a unified form that can be effectively modeled by a single architecture. Empirically, AOT-POT achieves state-of-the-art performance on 12 PDE benchmarks with only 3\% additional parameters, reducing relative L2 error by up to 77.6\% (40.9\% on average). Fine-tuning AOT-POT further reduces L2 error by up to 92\% on in-domain PDEs and 89\% on out-of-domain PDEs (unseen types during pre-training), demonstrating that adaptive operator transformation is an effective and complementary direction for advancing PDE foundation models beyond simply scaling model capacity.

cs.LG↗
arXiv2026

LENS: Multi-level Evaluation of Multimodal Reasoning with Large Language Models

Multimodal Large Language Models (MLLMs) have achieved significant advances in integrating visual and linguistic information, yet their ability to reason about complex and real-world scenarios remains limited. The existing benchmarks are usually constructed in the task-oriented manner without guarantee that different task samples come from the same data distribution, thus they often fall short in evaluating the synergistic effects of lower-level perceptual capabilities on higher-order reasoning. To lift this limitation, we contribute Lens, a multi-level benchmark with 3.4K contemporary images and 60K+ human-authored questions covering eight tasks and 12 daily scenarios, forming three progressive task tiers, i.e., perception, understanding, and reasoning. One feature is that each image is equipped with rich annotations for all tasks. Thus, this dataset intrinsically supports to evaluate MLLMs to handle image-invariable prompts, from basic perception to compositional reasoning. In addition, our images are manully collected from the social media, in which 53% were published later than Jan. 2025. We evaluate 15+ frontier MLLMs such as Qwen2.5-VL-72B, InternVL3-78B, GPT-4o and two reasoning models QVQ-72B-preview and Kimi-VL. These models are released later than Dec. 2024, and none of them achieve an accuracy greater than 60% in the reasoning tasks. Project page: https://github.com/Lens4MLLMs/lens. ICCV 2025 workshop page: https://lens4mllms.github.io/mars2-workshop-iccv2025/

cs.CV↗
arXiv2026

Achieving Gold-Medal-Level Olympiad Reasoning via Simple and Unified Scaling

Recent progress in reasoning models has substantially advanced long-horizon mathematical and scientific problem solving, with several systems now reaching gold-medal-level performance on International Mathematical Olympiad (IMO) and International Physics Olympiad (IPhO) problems. In this paper, we introduce a simple and unified recipe for converting a post-trained reasoning backbone into a rigorous olympiad-level solver. The recipe first uses a reverse-perplexity curriculum for SFT to instill rigorous proof-search and self-checking behaviors, then scales these behaviors through a two-stage RL pipeline that progresses from RL with verifiable rewards to more delicate proof-level RL, and finally boosts solving performance with test-time scaling. Applying this recipe, we train a 30B-A3B backbone with SFT on around 340K sub-8K-token trajectories followed by 200 RL steps. The resulting model, SU-01, supports stable reasoning on difficult problems with trajectories exceeding 100K tokens, while achieving gold-medal-level performance on mathematical and physical olympiad competitions, including IMO 2025/USAMO 2026 and IPhO 2024/2025. It also demonstrates strong generalization of scientific reasoning to domains beyond mathematics and physics.

cs.AI↗
arXiv2026

RL-RIG: A Generative Spatial Reasoner via Intrinsic Reflection

Recent advancements in image generation have achieved impressive results in producing high-quality images. However, existing image generation models still generally struggle with a spatial reasoning dilemma, lacking the ability to accurately capture fine-grained spatial relationships from the prompt and correctly generate scenes with structural integrity. To mitigate this dilemma, we propose RL-RIG, a Reinforcement Learning framework for Reflection-based Image Generation. Our architecture comprises four primary components: Diffuser, Checker, Actor, and Inverse Diffuser, following a Generate-Reflect-Edit paradigm to spark the Chain of Thought reasoning ability in image generation for addressing the dilemma. To equip the model with better intuition over generation trajectories, we further develop Reflection-GRPO to train the VLM Actor for edit prompts and the Image Editor for better image quality under a given prompt, respectively. Unlike traditional approaches that solely produce visually stunning yet structurally unreasonable content, our evaluation metrics prioritize spatial accuracy, utilizing Scene Graph IoU and employing a VLM-as-a-Judge strategy to assess the spatial consistency of generated images on LAION-SG dataset. Experimental results show that RL-RIG outperforms existing state-of-the-art open-source models by up to 11% in terms of controllable and precise spatial reasoning in image generation.

cs.CV↗
arXiv2026

Teaching Thinking Models to Reason with Tools: A Full-Pipeline Recipe for Tool-Integrated Reasoning

Tool-integrated reasoning (TIR) offers a direct way to extend thinking models beyond the limits of text-only reasoning. Paradoxically, we observe that tool-enabled evaluation can degrade reasoning performance even when the strong thinking models make almost no actual tool calls. In this paper, we investigate how to inject natural tool-use behavior into a strong thinking model without sacrificing its no-tool reasoning ability, and present a comprehensive TIR recipe. We highlight that (i) the effectiveness of TIR supervised fine-tuning (SFT) hinges on the learnability of teacher trajectories, which should prioritize problems inherently suited for tool-augmented solutions; (ii) controlling the proportion of tool-use trajectories could mitigate the catastrophic forgetting of text-only reasoning capacity; (iii) optimizing for pass@k and response length instead of training loss could maximize TIR SFT gains while preserving headroom for reinforcement learning (RL) exploration; (iv) a stable RL with verifiable rewards (RLVR) stage, built upon suitable SFT initialization and explicit safeguards against mode collapse, provides a simple yet remarkably effective solution. When applied to Qwen3 thinking models at 4B and 30B scales, our recipe yields models that achieve state-of-the-art performance in a wide range of benchmarks among open-source models, such as 96.7% and 99.2% on AIME 2025 for 4B and 30B, respectively.

cs.CL↗