arXiv subjects

Bowen Jin

Publications and source records attributed to Bowen Jin.

At least 37 records · Page 2Linked to original sources

arXiv2025

Learning to Reason as Action Abstractions with Scalable Mid-Training RL

Large language models excel with reinforcement learning (RL), but fully unlocking this potential requires a mid-training stage. An effective mid-training phase should identify a compact set of useful actions and enable fast selection among them through online RL. We formalize this intuition by presenting the first theoretical result on how mid-training shapes post-training: it characterizes an action subspace that minimizes both the value approximation error from pruning and the RL error during subsequent planning. Our analysis reveals two key determinants of mid-training effectiveness: pruning efficiency, which shapes the prior of the initial RL policy, and its impact on RL convergence, which governs the extent to which that policy can be improved via online interactions. These results suggest that mid-training is most effective when the decision space is compact and the effective horizon is short, highlighting the importance of operating in the space of action abstractions rather than primitive actions. Building on these insights, we propose Reasoning as Action Abstractions (RA3), a scalable mid-training algorithm. Specifically, we derive a sequential variational lower bound and optimize it by iteratively discovering temporally-consistent latent structures via RL, followed by fine-tuning on the bootstrapped data. Experiments on code generation tasks demonstrate the effectiveness of our approach. Across multiple base models, RA3 improves the average performance on HumanEval and MBPP by 8 and 4 points over the base model and the next-token prediction baseline. Furthermore, RA3 achieves faster convergence and higher asymptotic performance in RLVR on HumanEval+, MBPP+, LiveCodeBench, and Codeforces.

cs.LG↗

arXiv2025

GRACE: Generative Representation Learning via Contrastive Policy Optimization

Prevailing methods for training Large Language Models (LLMs) as text encoders rely on contrastive losses that treat the model as a black box function, discarding its generative and reasoning capabilities in favor of static embeddings. We introduce GRACE (Generative Representation Learning via Contrastive Policy Optimization), a novel framework that reimagines contrastive signals not as losses to be minimized, but as rewards that guide a generative policy. In GRACE, the LLM acts as a policy that produces explicit, human-interpretable rationales--structured natural language explanations of its semantic understanding. These rationales are then encoded into high-quality embeddings via mean pooling. Using policy gradient optimization, we train the model with a multi-component reward function that maximizes similarity between query positive pairs and minimizes similarity with negatives. This transforms the LLM from an opaque encoder into an interpretable agent whose reasoning process is transparent and inspectable. On MTEB benchmark, GRACE yields broad cross category gains: averaged over four backbones, the supervised setting improves overall score by 11.5% over base models, and the unsupervised variant adds 6.9%, while preserving general capabilities. This work treats contrastive objectives as rewards over rationales, unifying representation learning with generation to produce stronger embeddings and transparent rationales. The model, data and code are available at https://github.com/GasolSun36/GRACE.

cs.CL↗

arXiv2025

CoRank: LLM-Based Compact Reranking with Document Features for Scientific Retrieval

Scientific retrieval is essential for advancing scientific knowledge discovery. Within this process, document reranking plays a critical role in refining first-stage retrieval results. However, standard LLM listwise reranking faces challenges in the scientific domain. First-stage retrieval is often suboptimal in the scientific domain, so relevant documents are ranked lower. Meanwhile, conventional listwise reranking places the full text of candidates into the context window, limiting the number of candidates that can be considered. As a result, many relevant documents are excluded before reranking, constraining overall retrieval performance. To address these challenges, we explore semantic-feature-based compact document representations (e.g., categories, sections, and keywords) and propose CoRank, a training-free, model-agnostic reranking framework for scientific retrieval. It presents a three-stage solution: (i) offline extraction of document features, (ii) coarse-grained reranking using these compact representations, and (iii) fine-grained reranking on full texts of the top candidates from (ii). This integrated process addresses suboptimal first-stage retrieval: Compact representations allow more documents to fit within the context window, improving candidate set coverage, while the final fine-grained ranking ensures a more accurate ordering. Experiments on 5 academic retrieval datasets show that CoRank significantly improves reranking performance across different LLM backbones (average nDCG@10 from 50.6 to 55.5). Overall, these results underscore the synergistic interaction between information extraction and information retrieval, demonstrating how structured semantic features can enhance reranking in the scientific domain.

cs.IR↗

arXiv2025

Search-R1: Training LLMs to Reason and Leverage Search Engines with Reinforcement Learning

Efficiently acquiring external knowledge and up-to-date information is essential for effective reasoning and text generation in large language models (LLMs). Prompting advanced LLMs with reasoning capabilities to use search engines during inference is often suboptimal, as the LLM might not fully possess the capability on how to interact optimally with the search engine. This paper introduces Search-R1, an extension of reinforcement learning (RL) for reasoning frameworks where the LLM learns to autonomously generate (multiple) search queries during step-by-step reasoning with real-time retrieval. Search-R1 optimizes LLM reasoning trajectories with multi-turn search interactions, leveraging retrieved token masking for stable RL training and a simple outcome-based reward function. Experiments on seven question-answering datasets show that Search-R1 improves performance by 41% (Qwen2.5-7B) and 20% (Qwen2.5-3B) over various RAG baselines under the same setting. This paper further provides empirical insights into RL optimization methods, LLM choices, and response length dynamics in retrieval-augmented reasoning. The code and model checkpoints are available at https://github.com/PeterGriffinJin/Search-R1.

cs.CL↗

arXiv2025

Hypercube-Based Retrieval-Augmented Generation for Scientific Question-Answering

Large language models (LLMs) often need to incorporate external knowledge to solve theme-specific problems. Retrieval-augmented generation (RAG) has shown its high promise, empowering LLMs to generate more qualified responses with retrieved external data and knowledge. However, most RAG methods retrieve relevant documents based on either sparse or dense retrieval methods or their combinations, which overlooks the essential, multi-dimensional, and structured semantic information present in documents. This structured information plays a critical role in finding concise yet highly relevant information for domain knowledge-intensive tasks, such as scientific question-answering (QA). In this work, we introduce a multi-dimensional (cube) structure, Hypercube, which can index and allocate documents in a pre-defined multi-dimensional space. Built on the hypercube, we further propose Hypercube-RAG, a novel RAG framework for precise and efficient retrieval. Given a query, Hypercube-RAG first decomposes it based on its entities, phrases, and topics along with pre-defined hypercube dimensions, and then retrieves relevant documents from cubes by aligning these decomposed components with corresponding dimensions. Experiments on three datasets across different domains demonstrate that our method improves response accuracy by 3.7% and retrieval accuracy by 5.3% over the strongest RAG baseline. It also boosts retrieval efficiency (speed) by one or two magnitudes faster than graph-based RAG. Notably, our Hypercube-RAG inherently offers explainability by revealing those underlying dimensions used for retrieval. The code and data are available at https://github.com/JimengShi/Hypercube-RAG.

cs.LG↗

arXiv2025

LLM Alignment as Retriever Optimization: An Information Retrieval Perspective

Large Language Models (LLMs) have revolutionized artificial intelligence with capabilities in reasoning, coding, and communication, driving innovation across industries. Their true potential depends on effective alignment to ensure correct, trustworthy and ethical behavior, addressing challenges like misinformation, hallucinations, bias and misuse. While existing Reinforcement Learning (RL)-based alignment methods are notoriously complex, direct optimization approaches offer a simpler alternative. In this work, we introduce a novel direct optimization approach for LLM alignment by drawing on established Information Retrieval (IR) principles. We present a systematic framework that bridges LLM alignment and IR methodologies, mapping LLM generation and reward models to IR's retriever-reranker paradigm. Building on this foundation, we propose LLM Alignment as Retriever Preference Optimization (LarPO), a new alignment method that enhances overall alignment quality. Extensive experiments validate LarPO's effectiveness with 38.9 % and 13.7 % averaged improvement on AlpacaEval2 and MixEval-Hard respectively. Our work opens new avenues for advancing LLM alignment by integrating IR foundations, offering a promising direction for future research.

cs.CL↗

arXiv2025

Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.

cs.CL↗

arXiv2025

Can Graph Neural Networks Learn Language with Extremely Weak Text Supervision?

While great success has been achieved in building vision models with Contrastive Language-Image Pre-training (CLIP) over internet-scale image-text pairs, building transferable Graph Neural Networks (GNNs) with CLIP pipeline is challenging because of the scarcity of labeled data and text supervision, different levels of downstream tasks, and the conceptual gaps between domains. In this work, to address these issues, we propose a multi-modal prompt learning paradigm to effectively adapt pre-trained GNN to downstream tasks and data, given only a few semantically labeled samples, each with extremely weak text supervision. Our new paradigm embeds the graphs directly in the same space as the Large Language Models (LLMs) by learning both graph prompts and text prompts simultaneously. We demonstrate the superior performance of our paradigm in few-shot, multi-task-level, and cross-domain settings. Moreover, we build the first CLIP-style zero-shot classification prototype that can generalize GNNs to unseen classes with extremely weak text supervision. The code is available at https://github.com/Violet24K/Morpher.

cs.LG↗

arXiv2025

Acting Less is Reasoning More! Teaching Model to Act Efficiently

Tool-integrated reasoning (TIR) augments large language models (LLMs) with the ability to invoke external tools during long-form reasoning, such as search engines and code interpreters, to solve tasks beyond the capabilities of internal reasoning. While reinforcement learning (RL) has shown promise in training such agents, most of existing approaches typically optimize only for final correctness without considering the efficiency or necessity of external tool use. This often leads to excessive tool calling, incurring high computational costs and hindering the development of internal reasoning capabilities - a phenomenon known as \textit{cognitive offloading}. To this end, we propose Optimal Tool Call-controlled Policy Optimization (OTC-PO), a simple yet effective RL-based framework that encourages models to produce accurate answers with minimal tool calls. Our method introduces a tool-integrated reward that jointly considers answer correctness and corresponding tool use behavior of model to reach that answer. To validate the effectiveness, we introduce the metric of \textit{tool productivity}, defined as the ratio between the number of correct answers and the total number of tool calls across all test cases. This metric reflects how efficiently tool usage contributes to successful task completion, with higher values indicating smarter and more autonomous reasoning. We instantiate this framework within both Proximal Policy Optimization (PPO) and Group Relative Preference Optimization (GRPO), resulting in OTC-PPO and OTC-GRPO. Experiments with Qwen-2.5 and Qwen-Math across multiple QA benchmarks show that our approach reduces tool calls by up to 68.3\% and improves tool productivity by up to 215.4\%, while maintaining comparable answer accuracy.

cs.AI↗

arXiv2025

An Empirical Study on Reinforcement Learning for Reasoning-Search Interleaved LLM Agents

Reinforcement learning (RL) has demonstrated strong potential in training large language models (LLMs) capable of complex reasoning for real-world problem solving. More recently, RL has been leveraged to create sophisticated LLM-based search agents that adeptly combine reasoning with search engine use. While the use of RL for training search agents is promising, the optimal design of such agents remains not fully understood. In particular, key factors -- such as (1) reward formulation, (2) the choice and characteristics of the underlying LLM, and (3) the role of the search engine in the RL process -- require further investigation. In this work, we conduct comprehensive empirical studies to systematically investigate these and offer actionable insights. We highlight several key findings: format rewards are effective in improving final performance, whereas intermediate retrieval rewards have limited impact; the scale and initialization of the LLM (general-purpose vs. reasoning-specialized) significantly influence RL outcomes; and the choice of search engine plays a critical role in shaping RL training dynamics and the robustness of the trained agent during inference. These establish important guidelines for successfully building and deploying LLM-based search agents in real-world applications. Code is available at https://github.com/PeterGriffinJin/Search-R1.

cs.CL↗

arXiv2025

Demystifying and Enhancing the Efficiency of Large Language Model Based Search Agents

Large Language Model (LLM)-based search agents have shown remarkable capabilities in solving complex tasks by dynamically decomposing problems and addressing them through interleaved reasoning and retrieval. However, this interleaved paradigm introduces substantial efficiency bottlenecks. First, we observe that both highly accurate and overly approximate retrieval methods degrade system efficiency: exact search incurs significant retrieval overhead, while coarse retrieval requires additional reasoning steps during generation. Second, we identify inefficiencies in system design, including improper scheduling and frequent retrieval stalls, which lead to cascading latency -- where even minor delays in retrieval amplify end-to-end inference time. To address these challenges, we introduce SearchAgent-X, a high-efficiency inference framework for LLM-based search agents. SearchAgent-X leverages high-recall approximate retrieval and incorporates two key techniques: priority-aware scheduling and non-stall retrieval. Extensive experiments demonstrate that SearchAgent-X consistently outperforms state-of-the-art systems such as vLLM and HNSW-based retrieval across diverse tasks, achieving up to 3.4$\times$ higher throughput and 5$\times$ lower latency, without compromising generation quality. SearchAgent-X is available at https://github.com/tiannuo-yang/SearchAgent-X.

cs.AI↗

arXiv2025

CoDiCast: Conditional Diffusion Model for Global Weather Prediction with Uncertainty Quantification

Accurate weather forecasting is critical for science and society. Yet, existing methods have not managed to simultaneously have the properties of high accuracy, low uncertainty, and high computational efficiency. On one hand, to quantify the uncertainty in weather predictions, the strategy of ensemble forecast (i.e., generating a set of diverse predictions) is often employed. However, traditional ensemble numerical weather prediction (NWP) is computationally intensive. On the other hand, most existing machine learning-based weather prediction (MLWP) approaches are efficient and accurate. Nevertheless, they are deterministic and cannot capture the uncertainty of weather forecasting. In this work, we propose CoDiCast, a conditional diffusion model to generate accurate global weather prediction, while achieving uncertainty quantification with ensemble forecasts and modest computational cost. The key idea is to simulate a conditional version of the reverse denoising process in diffusion models, which starts from pure Gaussian noise to generate realistic weather scenarios for a future time point. Each denoising step is conditioned on observations from the recent past. Ensemble forecasts are achieved by repeatedly sampling from stochastic Gaussian noise to represent uncertainty quantification. CoDiCast is trained on a decade of ERA5 reanalysis data from the European Centre for Medium-Range Weather Forecasts (ECMWF). Experimental results demonstrate that our approach outperforms several existing data-driven methods in accuracy. Our conditional diffusion model, CoDiCast, can generate 6-day global weather forecasts, at 6-hour steps and $5.625^\circ$ latitude-longitude resolution, for over 5 variables, in about 12 minutes on a commodity A100 GPU machine with 80GB memory. The open-souced code is provided at https://github.com/JimengShi/CoDiCast.

cs.LG↗

arXiv2025

GRAPHGPT-O: Synergistic Multimodal Comprehension and Generation on Graphs

The rapid development of Multimodal Large Language Models (MLLMs) has enabled the integration of multiple modalities, including texts and images, within the large language model (LLM) framework. However, texts and images are usually interconnected, forming a multimodal attributed graph (MMAG). It is underexplored how MLLMs can incorporate the relational information (\textit{i.e.}, graph structure) and semantic information (\textit{i.e.,} texts and images) on such graphs for multimodal comprehension and generation. In this paper, we propose GraphGPT-o, which supports omni-multimodal understanding and creation on MMAGs. We first comprehensively study linearization variants to transform semantic and structural information as input for MLLMs. Then, we propose a hierarchical aligner that enables deep graph encoding, bridging the gap between MMAGs and MLLMs. Finally, we explore the inference choices, adapting MLLM to interleaved text and image generation in graph scenarios. Extensive experiments on three datasets from different domains demonstrate the effectiveness of our proposed method. Datasets and codes will be open-sourced upon acceptance.

cs.AI↗

arXiv2025

Chain-of-Factors Paper-Reviewer Matching

With the rapid increase in paper submissions to academic conferences, the need for automated and accurate paper-reviewer matching is more critical than ever. Previous efforts in this area have considered various factors to assess the relevance of a reviewer's expertise to a paper, such as the semantic similarity, shared topics, and citation connections between the paper and the reviewer's previous works. However, most of these studies focus on only one factor, resulting in an incomplete evaluation of the paper-reviewer relevance. To address this issue, we propose a unified model for paper-reviewer matching that jointly considers semantic, topic, and citation factors. To be specific, during training, we instruction-tune a contextualized language model shared across all factors to capture their commonalities and characteristics; during inference, we chain the three factors to enable step-by-step, coarse-to-fine search for qualified reviewers given a submission. Experiments on four datasets (one of which is newly contributed by us) spanning various fields such as machine learning, computer vision, information retrieval, and data mining consistently demonstrate the effectiveness of our proposed Chain-of-Factors model in comparison with state-of-the-art paper-reviewer matching methods and scientific pre-trained language models.

cs.IR↗

arXiv2025

Improving Scientific Document Retrieval with Concept Coverage-based Query Set Generation

In specialized fields like the scientific domain, constructing large-scale human-annotated datasets poses a significant challenge due to the need for domain expertise. Recent methods have employed large language models to generate synthetic queries, which serve as proxies for actual user queries. However, they lack control over the content generated, often resulting in incomplete coverage of academic concepts in documents. We introduce Concept Coverage-based Query set Generation (CCQGen) framework, designed to generate a set of queries with comprehensive coverage of the document's concepts. A key distinction of CCQGen is that it adaptively adjusts the generation process based on the previously generated queries. We identify concepts not sufficiently covered by previous queries, and leverage them as conditions for subsequent query generation. This approach guides each new query to complement the previous ones, aiding in a thorough understanding of the document. Extensive experiments demonstrate that CCQGen significantly enhances query quality and retrieval performance.

cs.IR↗

arXiv2025

Deep Learning and Foundation Models for Weather Prediction: A Survey

Physics-based numerical models have been the bedrock of atmospheric sciences for decades, offering robust solutions but often at the cost of significant computational resources. Deep learning (DL) models have emerged as powerful tools in meteorology, capable of analyzing complex weather and climate data by learning intricate dependencies and providing rapid predictions once trained. While these models demonstrate promising performance in weather prediction, often surpassing traditional physics-based methods, they still face critical challenges. This paper presents a comprehensive survey of recent deep learning and foundation models for weather prediction. We propose a taxonomy to classify existing models based on their training paradigms: deterministic predictive learning, probabilistic generative learning, and pre-training and fine-tuning. For each paradigm, we delve into the underlying model architectures, address major challenges, offer key insights, and propose targeted directions for future research. Furthermore, we explore real-world applications of these methods and provide a curated summary of open-source code repositories and widely used datasets, aiming to bridge research advancements with practical implementations while fostering open and trustworthy scientific practices in adopting cutting-edge artificial intelligence for weather prediction. The related sources are available at https://github.com/JimengShi/ DL-Foundation-Models-Weather.

cs.LG↗

arXiv2024

Large Language Models on Graphs: A Comprehensive Survey

Large language models (LLMs), such as GPT4 and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data is associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data is paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graphs (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-attributed graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we discuss the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

cs.CL↗

arXiv2024

Grasping the Essentials: Tailoring Large Language Models for Zero-Shot Relation Extraction

Relation extraction (RE) aims to identify semantic relationships between entities within text. Despite considerable advancements, existing models predominantly require extensive annotated training data, which is both costly and labor-intensive to collect. Moreover, these models often struggle to adapt to new or unseen relations. Few-shot learning, aiming to lessen annotation demands, typically provides incomplete and biased supervision for target relations, leading to degraded and unstable performance. To accurately and explicitly describe relation semantics while minimizing annotation demands, we explore the definition only zero-shot RE setting where only relation definitions expressed in natural language are used to train a RE model. We introduce REPaL, comprising three stages: (1) We leverage large language models (LLMs) to generate initial seed instances from relation definitions and an unlabeled corpus. (2) We fine-tune a bidirectional Small Language Model (SLM) with initial seeds to learn relations for the target domain. (3) We expand pattern coverage and mitigate bias from initial seeds by integrating feedback from the SLM's predictions on the unlabeled corpus and the synthesis history. To accomplish this, we leverage the multi-turn conversation ability of LLMs to generate new instances in follow-up dialogues, informed by both the feedback and synthesis history. Studies reveal that definition-oriented seed synthesis enhances pattern coverage whereas indiscriminately increasing seed quantity leads to performance saturation. Experiments on two datasets show REPaL significantly improved cost-effective zero-shot performance by large margins.

cs.CL↗