arXiv subjects

Pengcheng Jiang

Publications and source records attributed to Pengcheng Jiang.

At least 19 recordsLinked to original sources

arXiv2026

MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry

Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained. To bridge this semantic and chemical knowledge gap, we propose MolE-RAG, a training-free, molecule-centric retrieval-augmented generation framework for LLM-based molecular property prediction. MolE-RAG augments each prediction with three complementary sources of inference-time context: retrieved chemistry literature, molecule-specific information including compound synonyms, identifiers, functional group annotations, and physicochemical descriptors, and structurally similar molecules retrieved from the training set. We evaluate MolE-RAG across nine molecular property prediction tasks using proprietary, chemistry-specialized, and open-source LLMs. Across general-purpose LLMs, MolE-RAG improves ROC-AUC by up to 28 percentage points on classification tasks and reduces regression RMSE by up to 67% relative to a SMILES-only baseline. We further find that the utility of each context source varies across models and tasks, with different models benefiting most from textual retrieval, molecular context, or structural retrieval. These results suggest that molecule-centric retrieval can improve LLM-based molecular property prediction without model fine-tuning while providing a flexible framework for integrating heterogeneous chemical knowledge at inference time.

cs.LG↗

arXiv2026

Harness-1: Reinforcement Learning for Search Agents with State-Externalizing Harnesses

Search agents are often trained as policies over growing transcripts: the model must decide how to search while also remembering what it has seen, which evidence is useful, which constraints remain open, and which claims have actually been checked. We argue that this formulation puts too much routine state management inside the policy: reinforcement learning is forced to optimize both semantic search decisions and recoverable bookkeeping that the environment can maintain more reliably. We introduce Harness-1, a 20B search agent (retrieval subagent) trained with reinforcement learning inside a stateful search harness. The harness maintains environment-side working memory, including a candidate pool, an importance-tagged curated set, compact evidence links, verification records, compressed and deduplicated observations, and budget-aware context rendering. The policy retains the semantic decisions: what to search, which documents to keep or discard, what to verify, and when to stop. Across eight retrieval benchmarks spanning web, finance, patents, and multi-hop QA, Harness-1 achieves 0.730 average curated recall, outperforming the next strongest open search subagent by +11.4 points and remaining competitive with much larger frontier-model searchers. Its gains are especially strong on held-out transfer benchmarks, suggesting that reinforcement learning over explicit search state can produce retrieval behaviors that generalize beyond the training domains. Our code is available at https://github.com/pat-jj/harness-1.

cs.AI↗

arXiv2026

Masking Stale Observations Helps Search Agents -- Until It Doesn't: A Regime Map and Its Mechanism

Long-horizon search agents accumulate large amounts of retrieved content across many tool calls, making context-budget efficiency increasingly important. A minimal intervention is to mask stale observations from the context as the trajectory progresses, but it remains unclear when this form of context management helps and why. We study observation masking through a systematic sweep over various agent backbones (4B to 284B parameters) and three retrievers on offline and live-web agentic search benchmarks. We find that the accuracy gain from masking follows an asymmetric inverted-U shape when plotted against the model's accuracy without context management: a plateau under weak retrievers, a peak when a strong retriever meets a mid-capacity model, and a sharp collapse when the model is saturated. This pattern reflects the interaction between retriever recall and the model's implicit filtering capacity, rather than either factor in isolation. Mechanistically, masking implements a token-for-turn trade-off: it removes observations the model has largely stopped attending to and pages the agent rarely re-opens. The added turns help when they convert failures into successes, but they fail when masking removes evidence the model would otherwise have used. We therefore reframe context management as a regime-dependent intervention and provide a holistic perspective for analyzing context use in agentic deep search. We release our scaffold and trajectories here (https://github.com/i-DeepSearch/observation-masking) to support future research.

cs.CL↗

arXiv2026

Retrieval is Cheap, Show Me the Code: Executable Multi-Hop Reasoning for Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) has become a standard approach for knowledge-intensive question answering, but existing systems remain brittle on multi-hop questions, where solving the task requires chaining multiple retrieval and reasoning steps. Key challenges are that current methods represent reasoning through free-form natural language, where intermediate states are implicit, retrieval queries can drift from intended entities, and errors are detected by the same model that produces them making self-reflection an unreliable, ungrounded signal. We observe that multi-hop question answering is a typical form of step-by-step computation, and that this structured process aligns closely with how code-specialized language models are trained to operate. Motivated by this, we introduce \pyrag, a framework that reformulates multi-hop RAG as program synthesis and execution. Instead of free-form reasoning trajectories, \pyrag represents the reasoning process as an executable Python program over retrieval and QA tools, exposing intermediate states as variables, producing deterministic feedback through execution, and yielding an inspectable trace of the entire reasoning process. This formulation further enables compiler-grounded self-repair and execution-driven adaptive retrieval without any additional training. Experiments on five QA benchmarks (PopQA, HotpotQA, 2WikiMultihopQA, MuSiQue, and Bamboogle) show that \pyrag consistently outperforms strong baselines under both training-free and RL-trained settings, with especially large gains on compositional multi-hop datasets. Our code, data and models are publicly available at https://github.com/GasolSun36/PyRAG.

cs.AI↗

arXiv2026

Learning to Predict Future-Aligned Research Proposals with Language Models

Large language models (LLMs) are increasingly used to assist ideation in research, but evaluating the quality of LLM-generated research proposals remains difficult: novelty and soundness are hard to measure automatically, and large-scale human evaluation is costly. We propose a verifiable alternative by reframing proposal generation as a time-sliced scientific forecasting problem. Given a research question and inspiring papers available before a cutoff time, the model generates a structured proposal and is evaluated by whether it anticipates research directions that appear in papers published after the time. We operationalize this objective with the Future Alignment Score (FAS), computed via retrieval and LLM-based semantic scoring against a held-out future corpus. To train models, we build a time-consistent dataset of 21,835 paper occurrences across 3,642 instances from targets and their pre-cutoff citations, and synthesize reasoning traces that teach gap identification and inspiration borrowing. Across Llama-3.1 and Qwen2.5 models, future-aligned tuning improves future alignment over unaligned baselines (up to +10.6% overall FAS), and domain-expert human evaluation corroborates improved proposal quality. Finally, we demonstrate practical impact by implementing two model-generated proposals with a code agent, obtaining 4.17% accuracy gain on MATH from a new prompting strategy and consistent improvements for a novel model-merging method. Our code and data are publicly available at https://github.com/Arthur-Heng/future-aligned-proposals.

cs.CL↗

arXiv2026

Efficient, Property-Aligned Fan-Out Retrieval via RL-Compiled Diffusion

Many modern retrieval problems are set-valued: given a broad intent, the system must return a collection of results that optimizes higher-order properties (e.g., diversity, coverage, complementarity, coherence) while remaining grounded with respect to a fixed database. Set-valued objectives are typically non-decomposable and are not captured by existing supervised (query, content) datasets which only prioritize top-1 retrieval. Consequently, fan-out retrieval is often employed to generate diverse subqueries to retrieve item sets. While reinforcement learning (RL) can optimize set-level objectives via interaction, deploying an RL-tuned LLM for fan-out retrieval is prohibitively expensive at inference time. Conversely, diffusion-based generative retrieval enables efficient single-pass fan-out in embedding space, but requires objective-aligned training targets. To address these issues, we propose R4T (Retrieve-for-Train), which uses RL once as an objective transducer in a three-step process: (i) train a fan-out LLM with composite set-level rewards, (ii) synthesize objective-consistent training pairs, and (iii) train a lightweight diffusion retriever to model the conditional distribution of set-valued outputs. Across large-scale fashion and music benchmarks consisting of curated item sets, we show that R4T improves retrieval quality relative to strong baselines while reducing query-time fan-out latency by an order of magnitude.

cs.IR↗

arXiv2026

Condition-Gated Reasoning for Context-Dependent Biomedical Question Answering

Current biomedical question answering (QA) systems often assume that medical knowledge applies uniformly, yet real-world clinical reasoning is inherently conditional: nearly every decision depends on patient-specific factors such as comorbidities and contraindications. Existing benchmarks do not evaluate such conditional reasoning, and retrieval-augmented or graph-based methods lack explicit mechanisms to ensure that retrieved knowledge is applicable to given context. To address this gap, we propose CondMedQA, the first benchmark for conditional biomedical QA, consisting of multi-hop questions whose answers vary with patient conditions. Furthermore, we propose Condition-Gated Reasoning (CGR), a novel framework that constructs condition-aware knowledge graphs and selectively activates or prunes reasoning paths based on query conditions. Our findings show that CGR more reliably selects condition-appropriate answers while matching or exceeding state-of-the-art performance on biomedical QA benchmarks, highlighting the importance of explicitly modeling conditionality for robust medical reasoning.

cs.CL↗

arXiv2026

A Multi-objective Evolutionary Algorithm Based on Bi-population with Uniform Sampling for Neural Architecture Search

Neural architecture search (NAS) automates neural network design, improving efficiency over manual approaches. However, efficiently discovering high-performance neural network architectures that simultaneously optimize multiple objectives remains a significant challenge in NAS. Existing methods often suffer from limited population diversity and inadequate exploration of the search space, particularly in regions with extreme complexity values. To address these challenges, we propose MOEA-BUS, an innovative multi-objective evolutionary algorithm based on bi-population with uniform sampling for neural architecture search, aimed at simultaneously optimizing both accuracy and network complexity. In MOEA-BUS, a novel uniform sampling method is proposed to initialize the population, ensuring that architectures are distributed uniformly across the objective space. Furthermore, to enhance exploration, we deploy a bi-population framework where two populations evolve synergistically, facilitating comprehensive search space coverage. Experiments on CIFAR-10 and ImageNet demonstrate MOEA-BUS's superiority, achieving top-1 accuracies of 98.39% on CIFAR-10, and 80.03% on ImageNet. Notably, it achieves 78.28% accuracy on ImageNet with only 446M MAdds. Ablation studies confirm that both uniform sampling and bi-population mechanisms enhance population diversity and performance. Additionally, in terms of the Kendall's tau coefficient, the SVM achieves an improvement of at least 0.035 compared to the other three commonly used machine learning models, and uniform sampling provided an enhancement of approximately 0.07.

cs.NE↗

arXiv2026

Steer2Adapt: Dynamically Composing Steering Vectors Elicits Efficient Adaptation of LLMs

Activation steering has emerged as a promising approach for efficiently adapting large language models (LLMs) to downstream behaviors. However, most existing steering methods rely on a single static direction per task or concept, making them inflexible under task variation and inadequate for complex tasks that require multiple coordinated capabilities. To address this limitation, we propose STEER2ADAPT, a lightweight framework that adapts LLMs by composing steering vectors rather than learning new ones from scratch. In many domains (e.g., reasoning or safety), tasks share a small set of underlying concept dimensions. STEER2ADAPT captures these dimensions as a reusable, low-dimensional semantic prior subspace, and adapts to new tasks by dynamically discovering a linear combination of basis vectors from only a handful of examples. Experiments across 9 tasks and 3 models in both reasoning and safety domains demonstrate the effectiveness of STEER2ADAPT, achieving an average improvement of 8.2%. Extensive analyses further show that STEER2ADAPT is a data-efficient, stable, and transparent inference-time adaptation method for LLMs.

cs.AI↗

arXiv2026

Rethinking the Reranker: Boundary-Aware Evidence Selection for Robust Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) systems remain brittle under realistic retrieval noise, even when the required evidence appears in the top-K results. A key reason is that retrievers and rerankers optimize solely for relevance, often selecting either trivial, answer-revealing passages or evidence that lacks the critical information required to answer the question, without considering whether the evidence is suitable for the generator. We propose BAR-RAG, which reframes the reranker as a boundary-aware evidence selector that targets the generator's Goldilocks Zone -- evidence that is neither trivially easy nor fundamentally unanswerable for the generator, but is challenging yet sufficient for inference and thus provides the strongest learning signal. BAR-RAG trains the selector with reinforcement learning using generator feedback, and adopts a two-stage pipeline that fine-tunes the generator under the induced evidence distribution to mitigate the distribution mismatch between training and inference. Experiments on knowledge-intensive question answering benchmarks show that BAR-RAG consistently improves end-to-end performance under noisy retrieval, achieving an average gain of 10.3 percent over strong RAG and reranking baselines while substantially improving robustness. Code is publicly avaliable at https://github.com/GasolSun36/BAR-RAG.

cs.CL↗

arXiv2025

Adaptation of Agentic AI: A Survey of Post-Training, Memory, and Skills

Large language model (LLM) agents are moving beyond prompting alone. ChatGPT marked the rise of general-purpose LLM assistants, DeepSeek showed that on-policy reinforcement learning with verifiable rewards can improve reasoning and tool use, and OpenClaw highlights a newer direction in which agents accumulate persistent memory and reusable skills. Yet the research landscape remains fragmented across post-training, retrieval, memory, and skill systems. This survey studies these developments under a single notion of \emph{adaptation}: improving an agent, its tools, or their interaction after pretraining. We organize the field with a four-paradigm framework spanning agent adaptation and tool adaptation. On the agent side, A1 (tool-execution-signaled) and A2 (agent-output-signaled) improve the agent itself through supervised fine-tuning, preference optimization, and reinforcement learning with verifiable rewards. On the tool side, T1 (agent-agnostic) provides reusable pre-trained modules any agent can call, while T2 (agent-supervised) uses the agent's outputs to train memory systems, skill libraries, or lightweight subagents. Using this framework, we review post-training methods, adaptive memory architectures, and agent skills; compare their trade-offs in cost, flexibility, and generalization; and summarize evaluation practices across deep research, software development, computer use, and drug discovery. We conclude by outlining open problems in agent-tool co-adaptation, continual learning, safety, and efficient deployment.

cs.AI↗

arXiv2025

PairSem: LLM-Guided Pairwise Semantic Matching for Scientific Document Retrieval

Scientific document retrieval is a critical task for enabling knowledge discovery and supporting research across diverse domains. However, existing dense retrieval methods often struggle to capture fine-grained scientific concepts in texts due to their reliance on holistic embeddings and limited domain understanding. Recent approaches leverage large language models (LLMs) to extract fine-grained semantic entities and enhance semantic matching, but they typically treat entities as independent fragments, overlooking the multi-faceted nature of scientific concepts. To address this limitation, we propose Pairwise Semantic Matching (PairSem), a framework that represents relevant semantics as entity-aspect pairs, capturing complex, multi-faceted scientific concepts. PairSem is unsupervised, base retriever-agnostic, and plug-and-play, enabling precise and context-aware matching without requiring query-document labels or entity annotations. Extensive experiments on multiple datasets and retrievers demonstrate that PairSem significantly improves retrieval performance, highlighting the importance of modeling multi-aspect semantics in scientific information retrieval.

cs.IR↗

arXiv2025

RareAgent: Self-Evolving Reasoning for Drug Repurposing in Rare Diseases

Computational drug repurposing for rare diseases is especially challenging when no prior associations exist between drugs and target diseases. Therefore, knowledge graph completion and message-passing GNNs have little reliable signal to learn and propagate, resulting in poor performance. We present RareAgent, a self-evolving multi-agent system that reframes this task from passive pattern recognition to active evidence-seeking reasoning. RareAgent organizes task-specific adversarial debates in which agents dynamically construct evidence graphs from diverse perspectives to support, refute, or entail hypotheses. The reasoning strategies are analyzed post hoc in a self-evolutionary loop, producing textual feedback that refines agent policies, while successful reasoning paths are distilled into transferable heuristics to accelerate future investigations. Comprehensive evaluations reveal that RareAgent improves the indication AUPRC by 18.1% over reasoning baselines and provides a transparent reasoning chain consistent with clinical evidence.

cs.AI↗

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

Topic Coverage-based Demonstration Retrieval for In-Context Learning

The effectiveness of in-context learning relies heavily on selecting demonstrations that provide all the necessary information for a given test input. To achieve this, it is crucial to identify and cover fine-grained knowledge requirements. However, prior methods often retrieve demonstrations based solely on embedding similarity or generation probability, resulting in irrelevant or redundant examples. In this paper, we propose TopicK, a topic coverage-based retrieval framework that selects demonstrations to comprehensively cover topic-level knowledge relevant to both the test input and the model. Specifically, TopicK estimates the topics required by the input and assesses the model's knowledge on those topics. TopicK then iteratively selects demonstrations that introduce previously uncovered required topics, in which the model exhibits low topical knowledge. We validate the effectiveness of TopicK through extensive experiments across various datasets and both open- and closed-source LLMs. Our source code is available at https://github.com/WonbinKweon/TopicK_EMNLP2025.

cs.CL↗

arXiv2025

A Survey on Retrieval And Structuring Augmented Generation with Large Language Models

Large Language Models (LLMs) have revolutionized natural language processing with their remarkable capabilities in text generation and reasoning. However, these models face critical challenges when deployed in real-world applications, including hallucination generation, outdated knowledge, and limited domain expertise. Retrieval And Structuring (RAS) Augmented Generation addresses these limitations by integrating dynamic information retrieval with structured knowledge representations. This survey (1) examines retrieval mechanisms including sparse, dense, and hybrid approaches for accessing external knowledge; (2) explore text structuring techniques such as taxonomy construction, hierarchical classification, and information extraction that transform unstructured text into organized representations; and (3) investigate how these structured representations integrate with LLMs through prompt-based methods, reasoning frameworks, and knowledge embedding techniques. It also identifies technical challenges in retrieval efficiency, structure quality, and knowledge integration, while highlighting research opportunities in multimodal retrieval, cross-lingual structures, and interactive systems. This comprehensive overview provides researchers and practitioners with insights into RAS methods, applications, and future directions.

cs.CL↗

arXiv2025

Structure-Augmented Reasoning Generation

Recent advances in Large Language Models (LLMs) have significantly improved complex reasoning capabilities. Retrieval-Augmented Generation (RAG) has further extended these capabilities by grounding generation in dynamically retrieved evidence, enabling access to information beyond the model's training parameters. However, while RAG addresses knowledge availability, standard pipelines treat retrieved documents as independent, unstructured text chunks, forcing models to implicitly connect information across fragmented context. This limitation becomes critical for multi-hop queries, where answering correctly requires synthesizing information scattered across different documents. We present Structure-Augmented Reasoning Generation (SARG), a post-retrieval framework that addresses this gap by materializing explicit reasoning structures from retrieved context. SARG operates in three stages: extracting relational triples from retrieved documents via few-shot prompting, organizing these triples into a domain-adaptive knowledge graph, and performing multi-hop traversal to identify relevant reasoning chains. These chains, along with their associated text chunks, are then integrated into the generation prompt to explicitly guide the model's reasoning process. Importantly, SARG doesn't require custom retrievers or domain-specific fine-tuning. Instead, it functions as a modular layer compatible with all existing RAG pipelines. Extensive experiments on open-domain QA benchmarks and specialized reasoning datasets in finance and medicine demonstrate that SARG significantly outperforms state-of-the-art flat-context RAG baselines in both factual accuracy and reasoning coherence. Furthermore, by surfacing the exact traversal paths used during generation, SARG provides fully traceable and interpretable inference.

cs.CL↗

arXiv2025

Zero-Shot Open-Schema Entity Structure Discovery

Entity structure extraction, which aims to extract entities and their associated attribute-value structures from text, is an essential task for text understanding and knowledge graph construction. Existing methods based on large language models (LLMs) typically rely heavily on predefined entity attribute schemas or annotated datasets, often leading to incomplete extraction results. To address these challenges, we introduce Zero-Shot Open-schema Entity Structure Discovery (ZOES), a novel approach to entity structure extraction that does not require any schema or annotated samples. ZOES operates via a principled mechanism of enrichment, refinement, and unification, based on the insight that an entity and its associated structure are mutually reinforcing. Experiments demonstrate that ZOES consistently enhances LLMs' ability to extract more complete entity structures across three different domains, showcasing both the effectiveness and generalizability of the method. These findings suggest that such an enrichment, refinement, and unification mechanism may serve as a principled approach to improving the quality of LLM-based entity structure discovery in various scenarios.

cs.CL↗