arXiv subjects

Bowen Jin

Publications and source records attributed to Bowen Jin.

At least 19 recordsLinked to original sources

arXiv2026

Simulation of Flagellated Bacteria Near a Solid Surface: Effects of Flagellar Morphology and Ionic Strength

This study systematically investigates the three-stage process of bacterial surface entrapment, characterized by its height and inclination angle. Initially, bacteria swim towards the surface at an approach velocity proportional to motor rotation frequency. Subsequently, the cotangent of the inclination angle decays exponentially with the product of the motor rotation frequency and time during reorientation. Finally, under the combined action of near-field hydrodynamic interactions and DLVO forces, bacteria reach a stable fixed point near the surface. Bacteria with left-handed chiral flagella exhibit a clockwise circular motion on the surface. The stable heights, inclination angles, and radii of curvature of these circular trajectories are collectively determined by the flagellar morphology and ionic strength of the electrolyte solution. Specifically, increasing the contour length of the flagellum reduces the stable inclination angle and increases the radius of curvature. In contrast, decreasing the ionic strength increases the stable height and radius of curvature, while also decreasing the stable inclination angle. Typically, the stable inclination angle falls within $(π/2,π)$, the stable height ranges from several nanometers to over one hundred nanometers, and the radius of curvature spans several to tens of micrometers. Our work explains the observed dispersion of the stable heights.

cond-mat.soft↗

arXiv2026

How Hard Does It Think? Analyzing Step-Aware Reasoning Energy in LLM Chain-of-Thought Trajectories

Understanding how computational effort is allocated across individual chain-of-thought (CoT) reasoning steps remains an open challenge: existing interpretability methods rely on output-level signals or collapse processing depth into a single trajectory-level scalar, leaving step-wise effort opaque. We propose Step-Aware Reasoning Energy (SARE), a geometric framework that quantifies effort at the granularity of individual CoT steps via Centered Kernel Alignment (CKA) between Gram matrices of token hidden states across adjacent transformer layers, capturing inter-token relational structure without requiring eigenvector alignment or cluster correspondence. SARE further contextualizes this energy within reasoning's semantic progression by modeling CoT trajectories as transitions among latent semantic states. Across six reasoning benchmarks and three open-weight LLMs, we find that reasoning energy is highly non-uniform across step types, exhibiting phase-like transitions invisible to trajectory-level metrics; incorrect trajectories show systematically lower energy at critical reasoning junctions; and SARE-based features match or outperform output-based confidence baselines in most settings, indicating that internal geometric dynamics encode predictive information beyond surface-level signals.

cs.AI↗

arXiv2026

Improving Scientific Document Retrieval with Academic Concept Index

Adapting general-domain retrievers to scientific domains is challenging due to the scarcity of large-scale domain-specific relevance annotations and the substantial mismatch in vocabulary and information needs. Recent approaches address these issues through two independent directions that leverage large language models (LLMs): (1) generating synthetic queries for fine-tuning, and (2) generating auxiliary contexts to support relevance matching. However, both directions overlook the diverse academic concepts embedded within scientific documents, often producing redundant or conceptually narrow queries and contexts. To address this limitation, we introduce an academic concept index, which extracts key concepts from papers and organizes them guided by an academic taxonomy. This structured index serves as a foundation for improving both directions. First, we enhance the synthetic query generation with concept coverage-based generation (CCQGen), which adaptively conditions LLMs on uncovered concepts to generate complementary queries with broader concept coverage. Second, we strengthen the context augmentation with concept-focused auxiliary contexts (CCExpand), which leverages a set of document snippets that serve as concise responses to the concept-aware CCQGen queries. Extensive experiments show that incorporating the academic concept index into both query generation and context augmentation leads to higher-quality queries, better conceptual alignment, and improved retrieval performance.

cs.IR↗

arXiv2026

Learning Query-Aware Budget-Tier Routing for Runtime Agent Memory

Memory is increasingly central to Large Language Model (LLM) agents operating beyond a single context window, yet most existing systems rely on offline, query-agnostic memory construction that can be inefficient and may discard query-critical information. Although runtime memory utilization is a natural alternative, prior work often incurs substantial overhead and offers limited explicit control over the performance-cost trade-off. In this work, we present \textbf{BudgetMem}, a runtime agent memory framework for explicit, query-aware performance-cost control. BudgetMem structures memory processing as a set of memory modules, each offered in three budget tiers (i.e., \textsc{Low}/\textsc{Mid}/\textsc{High}). A lightweight router performs budget-tier routing across modules to balance task performance and memory construction cost, which is implemented as a compact neural policy trained with reinforcement learning. Using BudgetMem as a unified testbed, we study three complementary strategies for realizing budget tiers: implementation (method complexity), reasoning (inference behavior), and capacity (module model size). Across LoCoMo, LongMemEval, and HotpotQA, BudgetMem surpasses strong baselines when performance is prioritized (i.e., high-budget setting), and delivers better accuracy-cost frontiers under tighter budgets. Moreover, our analysis disentangles the strengths and weaknesses of different tiering strategies, clarifying when each axis delivers the most favorable trade-offs under varying budget regimes.

cs.CL↗

arXiv2026

F-GRPO: Factorized Group-Relative Policy Optimization for Unified Candidate Generation and Ranking

Traditional retrieval pipelines optimize utility through stages of candidate retrieval and reranking, where ranking operates over a predefined candidate set. Large Language Models (LLMs) broaden this into a generative process: given a candidate pool, an LLM can generate a subset and order it within a single autoregressive pass. However, this flexibility introduces a new optimization challenge: the model must search a combinatorial output space while receiving utility feedback only after the full ranked list is generated. Because this feedback is defined over the completed sequence, it cannot distinguish whether a poor result arises from failing to generate a relevant subset or from failing to rank that subset correctly. This credit assignment gap makes end-to-end optimization unstable and sample-inefficient. Existing systems often address this by separating candidate generation from ranking. However, such decoupling remains misaligned with downstream utility because ranking is limited by the candidate set it receives. To bridge this gap, we propose a unified framework that performs both within a single autoregressive rollout and optimizes them end-to-end via factorized group-relative policy optimization (F-GRPO). Our framework factorizes the policy into candidate generation and ranking while sharing a single LLM backbone, and jointly trains them with an order-invariant coverage reward and a position-aware utility reward. To address the resulting phase-specific credit assignment problem, we use separate group-relative advantages for generation and ranking within a two-phase sequence-level objective. Across sequential recommendation and multi-hop question answering benchmarks, F-GRPO improves top-ranked performance over GRPO and decoupled baselines, outperforms supervised alternatives, and remains competitive with strong zero-shot rerankers, with no architectural changes at inference time.

cs.LG↗

arXiv2026

Generating Leakage-Free Benchmarks for Robust RAG Evaluation

Retrieval-augmented generation (RAG) is widely used to augment large language models (LLMs) with external knowledge. However, many benchmark datasets, designed to test RAG performance, comprise many questions that can already be answered from an LLM's parametric memory. This leads to unreliable evaluation. We refer to this phenomenon as knowledge leakage: cases where RAG tasks are solvable without retrieval. This issue worsens over time due to benchmark aging. As benchmarks are reused for training, their contents are increasingly absorbed into model parameters, making them less effective for evaluating retrieval. We introduce SeedRG, a semi-synthetic benchmark generation pipeline that mitigates knowledge leakage and addresses the issue of benchmark aging. Starting from a seed benchmark dataset, SeedRG extracts a reasoning graph from question-context pairs to capture their underlying reasoning structure, and then generates new examples via type-constrained entity replacement. This process produces structurally similar but novel instances that are unlikely to exist in the model's parametric knowledge, while preserving the original reasoning patterns. To ensure quality, we incorporate two verification steps: (1) a reasoning-graph consistency check to maintain task difficulty, and (2) a knowledge-leakage filter to exclude instances answerable without retrieval.

cs.CL↗

arXiv2026

COMPASS: Benchmarking Constrained Optimization in LLM Agents

Human decision-making often involves constrained optimization. As LLM agents are deployed to assist with real-world tasks like travel planning, shopping, and scheduling, they must mirror this capability. We introduce COMPASS, a benchmark that evaluates whether LLM agents can perform constrained optimization in realistic travel planning settings. To success in these tasks, agents must engage in multi-turn conversations with user to gather task information as well as use tools to gather information from the database. Then agents must propose a solution that not only satisfies hard constraints but also optimizes user's utility objective. Evaluating state-of-the-art models, we reveal a significant feasible-optimal gap: while models achieve 70-90% feasibility (constraint satisfaction), they reach only 20-60% optimality (utility optimization). Our analysis shows that tool use is not the bottleneck. Instead, the core limitation is insufficient exploration of the search space, with success strongly correlating with information gathered. Coding agents show a promising approach to mitigate this gap. Together, COMPASS provides a testbed for developing LLM agents that can truly mirror human decision-making by both satisfying constraints and optimizing objectives.

cs.LG↗

arXiv2026

Generate, Filter, Control, Replay: A Comprehensive Survey of Rollout Strategies for LLM Reinforcement Learning

Reinforcement learning (RL) has become a central post-training tool for improving the reasoning abilities of large language models (LLMs). In these systems, the rollout, the trajectory sampled from a prompt to termination, including intermediate reasoning steps and optional tool or environment interactions, determines the data the optimizer learns from, yet rollout design is often underreported. This survey provides an optimizer-agnostic view of rollout strategies for RL-based post-training of reasoning LLMs. We formalize rollout pipelines with unified notation and introduce Generate-Filter-Control-Replay (GFCR), a lifecycle taxonomy that decomposes rollout pipelines into four modular stages: Generate proposes candidate trajectories and topologies; Filter constructs intermediate signals via verifiers, judges, critics; Control allocates compute and makes continuation/branching/stopping decisions under budgets; and Replay retains and reuses artifacts across rollouts without weight updates, including self-evolving curricula that autonomously generate new training tasks. We complement GFCR with a criterion taxonomy of reliability, coverage, and cost sensitivity that characterizes rollout trade-offs. Using this framework, we synthesize methods spanning RL with verifiable rewards, process supervision, judge-based gating, guided and tree/segment rollouts, adaptive compute allocation, early-exit and partial rollouts, throughput optimization, and replay/recomposition for self-improvement. We ground the framework with case studies in math, code/SQL, multimodal reasoning, tool-using agents, and agentic skill benchmarks that evaluate skill induction, reuse, and cross-task transfer. Finally, we provide a diagnostic index that maps common rollout pathologies to GFCR modules and mitigation levers, alongside open challenges for building reproducible, compute-efficient, and trustworthy rollout pipelines.

cs.LG↗

arXiv2026

Incentivizing Temporal-Awareness in Egocentric Video Understanding Models

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.

cs.CV↗

arXiv2026

RM-R1: Reward Modeling as Reasoning

Reward modeling is essential for aligning large language models with human preferences through reinforcement learning. To provide accurate reward signals, a reward model (RM) should stimulate deep thinking and conduct interpretable reasoning before assigning a score or a judgment. Inspired by recent advances of long chain-of-thought on reasoning-intensive tasks, we hypothesize and validate that integrating reasoning into reward modeling significantly enhances RM's interpretability and performance. We introduce a new class of generative reward models, Reasoning Reward Models (ReasRMs), which formulate reward modeling as a reasoning task. We propose a reasoning-oriented training pipeline and train a family of ReasRMs, RM-R1. RM-R1 features a chain-of-rubrics (CoR) mechanism -- self-generating sample-level chat rubrics or math/code solutions, and evaluating candidate responses against them. The training of RM-R1 consists of two key stages: (1) distillation of high-quality reasoning chains and (2) reinforcement learning with verifiable rewards. Empirically, our models achieve superior performance across three reward model benchmarks on average, outperforming much larger open-weight models (e.g., INF-ORM-Llama3.1-70B) and proprietary ones (e.g., GPT-4o) by up to 4.9%. Beyond final performance, we perform thorough analyses to understand the key ingredients of successful ReasRM training.

cs.CL↗

arXiv2026

mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. Experiments on FDA-approved drugs showed that mCLM is capable of significantly improving chemical functions. mCLM, with only 3B parameters, also achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

cs.AI↗

arXiv2026

Morphological Effects on Bacterial Brownian Motion: Validation of a Chiral Two-Body Model

We systematically investigate how flagellar morphology governs the stability of bacterial Brownian motion, evaluating the effectiveness of a simplified chiral two-body model. This model, which effectively captures the specific bacterial morphology and significantly reduces computational cost, is used for simulating bacterial Brownian motion. Our results demonstrate that the model accurately reproduces the Brownian motion of bacteria for contour lengths $Λ\ge5.0$~\si{μm}, helix radii $0.2\le R\le 0.5$~\si{μm}, and pitch angles $π/6\leθ\le2π/9$. We find that the translational and rotational velocities of bacteria depend linearly on the motor rotation rate, independent of dynamic viscosity. Increasing helix radius and contour length leads to more elongated trajectories and enhances their linearity. Furthermore, longer contour lengths improve the stability of the bacterial forward motion. Collectively, these findings demonstrate the essential role of flagella in stabilizing bacterial Brownian motion and confirm the effectiveness of the chiral two-body model for simulating this phenomenon.

physics.flu-dyn↗

arXiv2026

Benchmarking Retrieval-Augmented Generation for Chemistry

Retrieval-augmented generation (RAG) has emerged as a powerful framework for enhancing large language models (LLMs) with external knowledge, particularly in scientific domains that demand specialized and dynamic information. Despite its promise, the application of RAG in the chemistry domain remains underexplored, primarily due to the lack of high-quality, domain-specific corpora and well-curated evaluation benchmarks. In this work, we introduce ChemRAG-Bench, a comprehensive benchmark designed to systematically assess the effectiveness of RAG across a diverse set of chemistry-related tasks. The accompanying chemistry corpus integrates heterogeneous knowledge sources, including scientific literature, the PubChem database, PubMed abstracts, textbooks, and Wikipedia entries. In addition, we present ChemRAG-Toolkit, a modular and extensible RAG toolkit that supports five retrieval algorithms and eight LLMs. Using ChemRAG-Toolkit, we demonstrate that RAG yields a substantial performance gain -- achieving an average relative improvement of 17.4% over direct inference methods. We further conduct in-depth analyses on retriever architectures, corpus selection, and the number of retrieved passages, culminating in practical recommendations to guide future research and deployment of RAG systems in the chemistry domain. The code and data is available at https://chemrag.github.io.

cs.CL↗

arXiv2026

MultiCube-RAG for Multi-hop Question Answering

Multi-hop question answering (QA) necessitates multi-step reasoning and retrieval across interconnected subjects, attributes, and relations. Existing retrieval-augmented generation (RAG) methods struggle to capture these structural semantics accurately, resulting in suboptimal performance. Graph-based RAGs structure such information in graphs, but the resulting graphs are often noisy and computationally expensive. Moreover, most methods rely on single-step retrieval, neglecting the need for multi-hop reasoning processes. Recent training-based approaches attempt to incentivize the large language models (LLMs) for iterative reasoning and retrieval, but their training processes are prone to unstable convergence and high computational overhead. To address these limitations, we devise an ontology-based cube structure with multiple and orthogonal dimensions to model structural subjects, attributes, and relations. Built on the cube structure, we propose MultiCube-RAG, a training-free method consisting of multiple cubes for multi-step reasoning and retrieval. Each cube specializes in modeling a class of subjects, so that MultiCube-RAG flexibly selects the most suitable cubes to acquire the relevant knowledge precisely. To enhance the query-based reasoning and retrieval, our method decomposes a complex multi-hop query into a set of simple subqueries along cube dimensions and conquers each of them sequentially. Experiments on four multi-hop QA datasets show that MultiCube-RAG improves response accuracy by 8.9% over the average performance of various baselines. Notably, we also demonstrate that our method performs with greater efficiency and inherent explainability.

cs.CL↗

arXiv2025

Deep Research: A Systematic Survey

Large language models (LLMs) have rapidly evolved from text generators into powerful problem solvers. Yet, many open tasks demand critical thinking, multi-source, and verifiable outputs, which are beyond single-shot prompting or standard retrieval-augmented generation. Recently, numerous studies have explored Deep Research (DR), which aims to combine the reasoning capabilities of LLMs with external tools, such as search engines, thereby empowering LLMs to act as research agents capable of completing complex, open-ended tasks. This survey presents a comprehensive and systematic overview of deep research systems, including a clear roadmap, foundational components, practical implementation techniques, important challenges, and future directions. Specifically, our main contributions are as follows: (i) we formalize a three-stage roadmap and distinguish deep research from related paradigms; (ii) we introduce four key components: query planning, information acquisition, memory management, and answer generation, each paired with fine-grained sub-taxonomies; (iii) we summarize optimization techniques, including prompting, supervised fine-tuning, and agentic reinforcement learning; and (iv) we consolidate evaluation criteria and open challenges, aiming to guide and facilitate future development. As the field of deep research continues to evolve rapidly, we are committed to continuously updating this survey to reflect the latest progress in this area.

cs.CL↗

arXiv2025

Controlling Performance and Budget of a Centralized Multi-agent LLM System with Reinforcement Learning

Large language models (LLMs) exhibit complementary strengths across domains and come with varying inference costs, motivating the design of multi-agent LLM systems where specialized models collaborate efficiently. Existing approaches predominantly rely on decentralized frameworks, which invoke multiple LLMs for every input and thus lead to substantial and uncontrolled inference costs. In this work, we introduce a centralized multi-LLM framework, where a controller LLM selectively coordinates a pool of expert models in a cost-efficient and cost-controllable manner. We formulate this coordination problem as reinforcement learning with dual objectives: maximizing task performance while minimizing the overall inference cost. In addition, we expect the multi-agent system to have adapted behavior with different budget conditions during inference. To this end, we propose CoRL, a reinforcement learning framework that optimizes the performance cost trade-off in a controllable multi-budget setting. Experiments on four diverse benchmarks demonstrate that CoRL enables a single system to surpass the best expert LLM under high-budget settings, while maintaining strong performance in more economical low-budget modes, highlighting the effectiveness of centralized coordination for scalable and cost-efficient multi-agent LLM systems.

cs.CL↗

arXiv2025

Hybrid Latent Reasoning via Reinforcement Learning

Recent advances in large language models (LLMs) have introduced latent reasoning as a promising alternative to autoregressive reasoning. By performing internal computation with hidden states from previous steps, latent reasoning benefit from more informative features rather than sampling a discrete chain-of-thought (CoT) path. Yet latent reasoning approaches are often incompatible with LLMs, as their continuous paradigm conflicts with the discrete nature of autoregressive generation. Moreover, these methods rely on CoT traces for training and thus fail to exploit the inherent reasoning patterns of LLMs. In this work, we explore latent reasoning by leveraging the intrinsic capabilities of LLMs via reinforcement learning (RL). To this end, we introduce hybrid reasoning policy optimization (HRPO), an RL-based hybrid latent reasoning approach that (1) integrates prior hidden states into sampled tokens with a learnable gating mechanism, and (2) initializes training with predominantly token embeddings while progressively incorporating more hidden features. This design maintains LLMs' generative capabilities and incentivizes hybrid reasoning using both discrete and continuous representations. In addition, the hybrid HRPO introduces stochasticity into latent reasoning via token sampling, thereby enabling RL-based optimization without requiring CoT trajectories. Extensive evaluations across diverse benchmarks show that HRPO outperforms prior methods in both knowledge- and reasoning-intensive tasks. Furthermore, HRPO-trained LLMs remain interpretable and exhibit intriguing behaviors like cross-lingual patterns and shorter completion lengths, highlighting the potential of our RL-based approach and offer insights for future work in latent reasoning.

cs.CL↗

arXiv2025

Structure-R1: Dynamically Leveraging Structural Knowledge in LLM Reasoning through Reinforcement Learning

Large language models (LLMs) have demonstrated remarkable advances in reasoning capabilities. However, their performance remains constrained by limited access to explicit and structured domain knowledge. Retrieval-Augmented Generation (RAG) addresses this by incorporating external information as context to augment reasoning. Nevertheless, traditional RAG systems typically operate over unstructured and fragmented text, resulting in low information density and suboptimal reasoning. To overcome these limitations, we propose \textsc{Structure-R1}, a novel framework that transforms retrieved content into structured representations optimized for reasoning. Leveraging reinforcement learning, \textsc{Structure-R1} learns a content representation policy that dynamically generates and adapts structural formats based on the demands of multi-step reasoning. Unlike prior methods that rely on fixed schemas, our approach adopts a generative paradigm capable of producing task-specific structures tailored to individual queries. To ensure the quality and reliability of these representations, we introduce a self-reward structural verification mechanism that checks whether the generated structures are both correct and self-contained. Extensive experiments on seven knowledge-intensive benchmarks show that \textsc{Structure-R1} consistently achieves competitive performance with a 7B-scale backbone model and matches the performance of much larger models. Additionally, our theoretical analysis demonstrates how structured representations enhance reasoning by improving information density and contextual clarity. Our code and data are available at: https://github.com/jlwu002/sr1.

cs.CL↗