arXiv subjects

Bowen Zhou

Publications and source records attributed to Bowen Zhou.

At least 109 records · Page 6Linked to original sources

arXiv2025

Accurate de novo sequencing of the modified proteome with OmniNovo

Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modified proteome. Standard database search algorithms suffer from a combinatorial explosion of search spaces, limiting the identification of uncharacterized or complex modifications. Here we introduce OmniNovo, a unified deep learning framework for reference-free sequencing of unmodified and modified peptides directly from tandem mass spectra. Unlike existing tools restricted to specific modification types, OmniNovo learns universal fragmentation rules to decipher diverse PTMs within a single coherent model. By integrating a mass-constrained decoding algorithm with rigorous false discovery rate estimation, OmniNovo achieves state-of-the-art accuracy, identifying 51\% more peptides than standard approaches at a 1\% false discovery rate. Crucially, the model generalizes to biological sites unseen during training, illuminating the dark matter of the proteome and enabling unbiased comprehensive analysis of cellular regulation.

q-bio.QM↗

arXiv2025

P1: Mastering Physics Olympiads with Reinforcement Learning

Recent progress in large language models (LLMs) has moved the frontier from puzzle-solving to science-grade reasoning-the kind needed to tackle problems whose answers must stand against nature, not merely fit a rubric. Physics is the sharpest test of this shift, which binds symbols to reality in a fundamental way, serving as the cornerstone of most modern technologies. In this work, we manage to advance physics research by developing large language models with exceptional physics reasoning capabilities, especially excel at solving Olympiad-level physics problems. We introduce P1, a family of open-source physics reasoning models trained entirely through reinforcement learning (RL). Among them, P1-235B-A22B is the first open-source model with Gold-medal performance at the latest International Physics Olympiad (IPhO 2025), and wins 12 gold medals out of 13 international/regional physics competitions in 2024/2025. P1-30B-A3B also surpasses almost all other open-source models on IPhO 2025, getting a silver medal. Further equipped with an agentic framework PhysicsMinions, P1-235B-A22B+PhysicsMinions achieves overall No.1 on IPhO 2025, and obtains the highest average score over the 13 physics competitions. Besides physics, P1 models also present great performance on other reasoning tasks like math and coding, showing the great generalibility of P1 series.

cs.LG↗

arXiv2025

FlowRL: Matching Reward Distributions for LLM Reasoning

We propose FlowRL: matching the full reward distribution via flow balancing instead of maximizing rewards in large language model (LLM) reinforcement learning (RL). Recent advanced reasoning models adopt reward-maximizing methods (\eg, PPO and GRPO), which tend to over-optimize dominant reward signals while neglecting less frequent but valid reasoning paths, thus reducing diversity. In contrast, we transform scalar rewards into a normalized target distribution using a learnable partition function, and then minimize the reverse KL divergence between the policy and the target distribution. We implement this idea as a flow-balanced optimization method that promotes diverse exploration and generalizable reasoning trajectories. We conduct experiments on math and code reasoning tasks: FlowRL achieves a significant average improvement of $10.0\%$ over GRPO and $5.1\%$ over PPO on math benchmarks, and performs consistently better on code reasoning tasks. These results highlight reward distribution-matching as a key step toward efficient exploration and diverse reasoning in LLM reinforcement learning.

cs.LG↗

arXiv2025

A Self-Evolving AI Agent System for Climate Science

Scientific progress in Earth science depends on integrating data across the planet's interconnected spheres. However, the accelerating volume and fragmentation of multi-sphere knowledge and data have surpassed human analytical capacity. This creates a major bottleneck for discovery, especially in climate science. To address this challenge, we introduce EarthLink, the first self-evolving AI agent system designed as an interactive "copilot" for Earth scientists. Through natural language interaction, EarthLink automates the entire research workflow by integrating planning, code execution, data analysis, and physical reasoning into a unified process that directly addresses this limitation. Beyond efficiency, it exhibits human-like cross-disciplinary analytical ability and achieves proficiency comparable to a junior researcher in expert evaluations on core large-scale climate tasks, including model-observation comparison and climate change understanding. When tasked with an open scientific problem, specifically the discovery of precursors of the Atlantic Niño, EarthLink autonomously developed a research strategy, identified sources of predictability, verified its hypotheses with available data, and proposed a physically consistent mechanism. These emerging capabilities enable a new human-AI research paradigm. Scientists can focus on value and result judgments, while AI systems handle complex data analysis and knowledge integration. This accelerates the pace and breadth of discovery in Earth sciences. The system is accessible at our website https://earthlink.intern-ai.org.cn.

cs.LG↗

arXiv2025

Towards General Auditory Intelligence: Large Multimodal Models for Machine Listening and Speaking

In the era of large language models (LLMs) and artificial general intelligence (AGI), computer audition must evolve beyond traditional paradigms to fully leverage the capabilities of foundation models, towards more comprehensive understanding, more natural generation and more human-like interaction. Audio, as a modality rich in semantic, emotional, and contextual cues, plays a vital role in achieving naturalistic and embodied machine intelligence. This survey provides a comprehensive review of recent progress in integrating audio into LLMs, with a focus on four key areas: audio comprehension, audio generation, speech-based interaction, and audio-visual understanding. We analyze how LLMs are reshaping audio perception and reasoning, enabling systems to understand sound at a deeper semantic level, generate expressive audio outputs, and engage in human-like spoken interaction. Furthermore, we explore how the fusion of audio and visual modalities enhances situational awareness and cross-modal reasoning, pushing the boundaries of multimodal intelligence. This survey not only synthesizes existing research but also identifies critical challenges and future directions for building audio-native AGI systems capable of perceiving, understanding, and interacting through sound as naturally as humans do.

eess.AS↗

arXiv2025

DePass: Unified Feature Attributing by Simple Decomposed Forward Pass

Attributing the behavior of Transformer models to internal computations is a central challenge in mechanistic interpretability. We introduce DePass, a unified framework for feature attribution based on a single decomposed forward pass. DePass decomposes hidden states into customized additive components, then propagates them with attention scores and MLP's activations fixed. It achieves faithful, fine-grained attribution without requiring auxiliary training. We validate DePass across token-level, model component-level, and subspace-level attribution tasks, demonstrating its effectiveness and fidelity. Our experiments highlight its potential to attribute information flow between arbitrary components of a Transformer model. We hope DePass serves as a foundational tool for broader applications in interpretability.

cs.CL↗

arXiv2025

Memory Decoder: A Pretrained, Plug-and-Play Memory for Large Language Models

Large Language Models (LLMs) have shown strong abilities in general language tasks, yet adapting them to specific domains remains a challenge. Current method like Domain Adaptive Pretraining (DAPT) requires costly full-parameter training and suffers from catastrophic forgetting. Meanwhile, Retrieval-Augmented Generation (RAG) introduces substantial inference latency due to expensive nearest-neighbor searches and longer context. This paper introduces Memory Decoder, a plug-and-play pretrained memory that enables efficient domain adaptation without changing the original model's parameters. Memory Decoder employs a small transformer decoder that learns to imitate the behavior of an external non-parametric retriever. Once trained, Memory Decoder can be seamlessly integrated with any pretrained language model that shares the same tokenizer, requiring no model-specific modifications. Experimental results demonstrate that Memory Decoder enables effective adaptation of various Qwen and Llama models to three distinct specialized domains: biomedicine, finance, and law, reducing perplexity by an average of 6.17 points. Overall, Memory Decoder introduces a novel paradigm centered on a specially pretrained memory component designed for domain-specific adaptation. This memory architecture can be integrated in a plug-and-play manner, consistently enhancing performance across multiple models within the target domain.

cs.CL↗

arXiv2025

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

cs.LG↗

arXiv2025

SDAR: A Synergistic Diffusion-AutoRegression Paradigm for Scalable Sequence Generation

We propose SDAR, a Synergistic Diffusion-Autoregression paradigm that unifies the training efficiency of autoregressive models with the parallel inference capability of diffusion. Instead of costly end-to-end diffusion training, SDAR performs a lightweight paradigm conversion that transforms a well-trained autoregressive (AR) model into a blockwise diffusion model through brief, data-efficient adaptation. During inference, SDAR generates sequences autoregressively across blocks for global coherence while decoding all tokens within each block in parallel via a discrete diffusion process. Extensive experiments show that AR models remain substantially more compute-efficient than masked diffusion models, providing a strong foundation for adaptation. Building on this insight, SDAR achieves efficient AR-to-diffusion conversion with minimal cost, preserving AR-level performance while enabling parallel generation. Scaling studies across dense and Mixture-of-Experts architectures confirm that SDAR scales without compromise: larger models exhibit stronger robustness to block size and decoding thresholds, yielding greater speedups without accuracy loss. Beyond efficiency, SDAR demonstrates enhanced reasoning and domain adaptability. Our 30B MoE model surpasses its AR counterpart on challenging scientific reasoning benchmarks such as GPQA and ChemBench, and gains further improvements under test-time scaling methods like majority voting and pass@k. Together, these results establish SDAR as a practical paradigm that combines the strengths of autoregression and diffusion for scalable, high-throughput reasoning.

cs.LG↗

arXiv2025

BrainOmni: A Brain Foundation Model for Unified EEG and MEG Signals

Electroencephalography (EEG) and magnetoencephalography (MEG) measure neural activity non-invasively by capturing electromagnetic fields generated by dendritic currents. Although rooted in the same biophysics, EEG and MEG exhibit distinct signal patterns, further complicated by variations in sensor configurations across modalities and recording devices. Existing approaches typically rely on separate, modality- and dataset-specific models, which limits the performance and cross-domain scalability. This paper proposes BrainOmni, the first brain foundation model that generalises across heterogeneous EEG and MEG recordings. To unify diverse data sources, we introduce BrainTokenizer,the first tokenizer that quantises spatiotemporal brain activity into discrete representations. Central to BrainTokenizer is a novel Sensor Encoder that encodes sensor properties such as spatial layout, orientation, and type, enabling compatibility across devices and modalities. Building upon the discrete representations, BrainOmni learns unified semantic embeddings of brain signals by self-supervised pretraining. To the best of our knowledge, it is the first foundation model to support both EEG and MEG signals, as well as the first to incorporate large-scale MEG pretraining. A total of 1,997 hours of EEG and 656 hours of MEG data are curated and standardised from publicly available sources for pretraining. Experiments show that BrainOmni outperforms both existing foundation models and state-of-the-art task-specific models on a range of downstream tasks. It also demonstrates strong generalisation to unseen EEG and MEG devices. Further analysis reveals that joint EEG-MEG (EMEG) training yields consistent improvements across both modalities. Code and checkpoints are publicly available at https://github.com/OpenTSLab/BrainOmni.

eess.SP↗

arXiv2025

InternVLA-M1: A Spatially Guided Vision-Language-Action Framework for Generalist Robot Policy

We introduce InternVLA-M1, a unified framework for spatial grounding and robot control that advances instruction-following robots toward scalable, general-purpose intelligence. Its core idea is spatially guided vision-language-action training, where spatial grounding serves as the critical link between instructions and robot actions. InternVLA-M1 employs a two-stage pipeline: (i) spatial grounding pre-training on over 2.3M spatial reasoning data to determine ``where to act'' by aligning instructions with visual, embodiment-agnostic positions, and (ii) spatially guided action post-training to decide ``how to act'' by generating embodiment-aware actions through plug-and-play spatial prompting. This spatially guided training recipe yields consistent gains: InternVLA-M1 outperforms its variant without spatial guidance by +14.6% on SimplerEnv Google Robot, +17% on WidowX, and +4.3% on LIBERO Franka, while demonstrating stronger spatial reasoning capability in box, point, and trace prediction. To further scale instruction following, we built a simulation engine to collect 244K generalizable pick-and-place episodes, enabling a 6.2% average improvement across 200 tasks and 3K+ objects. In real-world clustered pick-and-place, InternVLA-M1 improved by 7.3%, and with synthetic co-training, achieved +20.6% on unseen objects and novel configurations. Moreover, in long-horizon reasoning-intensive scenarios, it surpassed existing works by over 10%. These results highlight spatially guided training as a unifying principle for scalable and resilient generalist robots. Code and models are available at https://github.com/InternRobotics/InternVLA-M1.

cs.RO↗

arXiv2025

A Survey of Reinforcement Learning for Large Reasoning Models

In this paper, we survey recent advances in Reinforcement Learning (RL) for reasoning with Large Language Models (LLMs). RL has achieved remarkable success in advancing the frontier of LLM capabilities, particularly in addressing complex logical tasks such as mathematics and coding. As a result, RL has emerged as a foundational methodology for transforming LLMs into LRMs. With the rapid progress of the field, further scaling of RL for LRMs now faces foundational challenges not only in computational resources but also in algorithm design, training data, and infrastructure. To this end, it is timely to revisit the development of this domain, reassess its trajectory, and explore strategies to enhance the scalability of RL toward Artificial SuperIntelligence (ASI). In particular, we examine research applying RL to LLMs and LRMs for reasoning abilities, especially since the release of DeepSeek-R1, including foundational components, core problems, training resources, and downstream applications, to identify future opportunities and directions for this rapidly evolving area. We hope this review will promote future research on RL for broader reasoning models. Github: https://github.com/TsinghuaC3I/Awesome-RL-for-LRMs

cs.CL↗

arXiv2025

Mission Impossible: Feedback-Guided Dynamic Interactive Planning for Improving Reasoning on LLMs

Recent advancements in language agents have led to significant improvements in multi-hop reasoning tasks. However, existing approaches often struggle with handling open-domain problems, which require massive information retrieval due to their reliance on a fixed sequence of actions. To address this, we propose Feedback-Guided Dynamic Interactive Planning (FGDIP), a novel framework tailored to enhance reasoning in LLMs by utilizing dynamic and adaptive strategies for information exploration in open-domain multi-hop reasoning tasks. Our approach begins by identifying key entities relevant to the problem, which serve as the initial nodes in the reasoning process. From these initial nodes, we then generate reasoning child nodes with the process being refined through a combination of historical error analysis and real-time feedback, which allows the framework to dynamically adjust and optimize its reasoning strategies. By integrating depth-first search with an innovative node generation technique, our framework adapts based on both prior error paths and concurrently generated nodes at the same hierarchical level. This dynamic strategy effectively expands the search space while ensuring the reasoning process systematically converges toward accurate solutions. Experimental results show that FGDIP achieved up to 54.47% F1 score on the HotpotQA dataset and 70.05% on the StrategyQA dataset, surpassing the best baseline by 5.03% and 7.25% respectively, highlighting its versatility and potential to enhance language agents in multi-hop reasoning tasks.

cs.CL↗

arXiv2025

MinerU2.5: A Decoupled Vision-Language Model for Efficient High-Resolution Document Parsing

We introduce MinerU2.5, a 1.2B-parameter document parsing vision-language model that achieves state-of-the-art recognition accuracy while maintaining exceptional computational efficiency. Our approach employs a coarse-to-fine, two-stage parsing strategy that decouples global layout analysis from local content recognition. In the first stage, the model performs efficient layout analysis on downsampled images to identify structural elements, circumventing the computational overhead of processing high-resolution inputs. In the second stage, guided by the global layout, it performs targeted content recognition on native-resolution crops extracted from the original image, preserving fine-grained details in dense text, complex formulas, and tables. To support this strategy, we developed a comprehensive data engine that generates diverse, large-scale training corpora for both pretraining and fine-tuning. Ultimately, MinerU2.5 demonstrates strong document parsing ability, achieving state-of-the-art performance on multiple benchmarks, surpassing both general-purpose and domain-specific models across various recognition tasks, while maintaining significantly lower computational overhead.

cs.CV↗

arXiv2025

Process Reinforcement through Implicit Rewards

Dense process rewards have proven a more effective alternative to the sparse outcome-level rewards in the inference-time scaling of large language models (LLMs), particularly in tasks requiring complex multi-step reasoning. While dense rewards also offer an appealing choice for the reinforcement learning (RL) of LLMs since their fine-grained rewards have the potential to address some inherent issues of outcome rewards, such as training efficiency and credit assignment, this potential remains largely unrealized. This can be primarily attributed to the challenges of training process reward models (PRMs) online, where collecting high-quality process labels is prohibitively expensive, making them particularly vulnerable to reward hacking. To address these challenges, we propose PRIME (Process Reinforcement through IMplicit rEwards), which enables online PRM updates using only policy rollouts and outcome labels through implict process rewards. PRIME combines well with various advantage functions and forgoes the dedicated reward model training phrase that existing approaches require, substantially reducing the development overhead. We demonstrate PRIME's effectiveness on competitional math and coding. Starting from Qwen2.5-Math-7B-Base, PRIME achieves a 15.1% average improvement across several key reasoning benchmarks over the SFT model. Notably, our resulting model, Eurus-2-7B-PRIME, surpasses Qwen2.5-Math-7B-Instruct on seven reasoning benchmarks with 10% of its training data.

cs.LG↗

arXiv2025

V-GameGym: Visual Game Generation for Code Large Language Models

Code large language models have demonstrated remarkable capabilities in programming tasks, yet current benchmarks primarily focus on single modality rather than visual game development. Most existing code-related benchmarks evaluate syntax correctness and execution accuracy, overlooking critical game-specific metrics such as playability, visual aesthetics, and user engagement that are essential for real-world deployment. To address the gap between current LLM capabilities in algorithmic problem-solving and competitive programming versus the comprehensive requirements of practical game development, we present V-GameGym, a comprehensive benchmark comprising 2,219 high-quality samples across 100 thematic clusters derived from real-world repositories, adopting a novel clustering-based curation methodology to ensure both diversity and structural completeness. Further, we introduce a multimodal evaluation framework with an automated LLM-driven pipeline for visual code synthesis using complete UI sandbox environments. Our extensive analysis reveals that V-GameGym effectively bridges the gap between code generation accuracy and practical game development workflows, providing quantifiable quality metrics for visual programming and interactive element generation.

cs.SE↗

arXiv2025

ScaleCUA: Scaling Open-Source Computer Use Agents with Cross-Platform Data

Vision-Language Models (VLMs) have enabled computer use agents (CUAs) that operate GUIs autonomously, showing great potential, yet progress is limited by the lack of large-scale, open-source computer use data and foundation models. In this work, we introduce ScaleCUA, a step toward scaling open-source CUAs. It offers a large-scale dataset spanning 6 operating systems and 3 task domains, built via a closed-loop pipeline uniting automated agents with human experts. Trained on this scaled-up data, ScaleCUA can operate seamlessly across platforms. Specifically, it delivers strong gains over baselines (+26.6 on WebArena-Lite-v2, +10.7 on ScreenSpot-Pro) and sets new state-of-the-art results (94.4% on MMBench-GUI L1-Hard, 60.6% on OSWorld-G, 47.4% on WebArena-Lite-v2). These findings underscore the power of data-driven scaling for general-purpose computer use agents. We will release data, models, and code to advance future research: https://github.com/OpenGVLab/ScaleCUA.

cs.CV↗

arXiv2025

MARS2 2025 Challenge on Multimodal Reasoning: Datasets, Methods, Results, Discussion, and Outlook

This paper reviews the MARS2 2025 Challenge on Multimodal Reasoning. We aim to bring together different approaches in multimodal machine learning and LLMs via a large benchmark. We hope it better allows researchers to follow the state-of-the-art in this very dynamic area. Meanwhile, a growing number of testbeds have boosted the evolution of general-purpose large language models. Thus, this year's MARS2 focuses on real-world and specialized scenarios to broaden the multimodal reasoning applications of MLLMs. Our organizing team released two tailored datasets Lens and AdsQA as test sets, which support general reasoning in 12 daily scenarios and domain-specific reasoning in advertisement videos, respectively. We evaluated 40+ baselines that include both generalist MLLMs and task-specific models, and opened up three competition tracks, i.e., Visual Grounding in Real-world Scenarios (VG-RS), Visual Question Answering with Spatial Awareness (VQA-SA), and Visual Reasoning in Creative Advertisement Videos (VR-Ads). Finally, 76 teams from the renowned academic and industrial institutions have registered and 40+ valid submissions (out of 1200+) have been included in our ranking lists. Our datasets, code sets (40+ baselines and 15+ participants' methods), and rankings are publicly available on the MARS2 workshop website and our GitHub organization page https://github.com/mars2workshop/, where our updates and announcements of upcoming events will be continuously provided.

cs.CV↗