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Siru Ouyang

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8 papers

2 author rows

ICLR Conference 2025 Conference Paper

ChemAgent: Self-updating Memories in Large Language Models Improves Chemical Reasoning

Xiangru Tang
Tianyu Hu
Muyang Ye
Yanjun Shao
Xunjian Yin
Siru Ouyang
Wangchunshu Zhou
Pan Lu

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code ef- effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/ChemAgent.

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NeurIPS Conference 2025 Conference Paper

FGBench: A Dataset and Benchmark for Molecular Property Reasoning at Functional Group-Level in Large Language Models

Xuan Liu
Siru Ouyang
Xianrui Zhong
Jiawei Han
Huimin Zhao

Large language models (LLMs) have gained significant attention in chemistry. However, most existing datasets center on molecular-level property prediction and overlook the role of fine-grained functional group (FG) information. Incorporating FG-level data can provide valuable prior knowledge that links molecular structures with textual descriptions, which can be used to build more interpretable, structure-aware LLMs for reasoning on molecule-related tasks. Moreover, LLMs can learn from such fine-grained information to uncover hidden relationships between specific functional groups and molecular properties, thereby advancing molecular design and drug discovery. Here, we introduce FGBench, a dataset comprising 625K molecular property reasoning problems with functional group information. Functional groups are precisely annotated and localized within the molecule, which ensures the dataset's interoperability thereby facilitating further multimodal applications. FGBench includes both regression and classification tasks on 245 different functional groups across three categories for molecular property reasoning: (1) single functional group impacts, (2) multiple functional group interactions, and (3) direct molecular comparisons. In the benchmark of state-of-the-art LLMs on 7K curated data, the results indicate that current LLMs struggle with FG-level property reasoning, highlighting the need to enhance reasoning capabilities in LLMs for chemistry tasks. We anticipate that the methodology employed in FGBench to construct datasets with functional group-level information will serve as a foundational framework for generating new question–answer pairs, enabling LLMs to better understand fine-grained molecular structure–property relationships. The dataset and evaluation code are available at this \href{https: //github. com/xuanliugit/FGBench}{link}.

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TMLR Journal 2025 Journal Article

Leopard: A Vision Language Model for Text-Rich Multi- Image Tasks

Mengzhao Jia
Wenhao Yu
Kaixin Ma
Tianqing Fang
Zhihan Zhang
Siru Ouyang
Hongming Zhang
Dong Yu

Text-rich images, where text serves as the central visual element guiding the overall understanding, are prevalent in real-world applications, such as presentation slides, scanned documents, and webpage snapshots. Tasks involving multiple text-rich images are especially challenging, as they require not only understanding the content of individual images but reasoning about inter-relationships and logical flows across multiple visual inputs. Despite the importance of these scenarios, current multimodal large language models (MLLMs) struggle to handle such tasks due to two key challenges: (1) the scarcity of high-quality instruction tuning datasets for text-rich multi-image scenarios, and (2) the difficulty in balancing image resolution with visual feature sequence length. To address these challenges, we propose Leopard, a MLLM designed specifically for handling vision-language tasks involving multiple text-rich images. First, we curated about one million high-quality multimodal instruction-tuning data, tailored to text-rich, multi-image scenarios. Second, we proposed an adaptive high-resolution multi-image encoding module to dynamically optimize the allocation of visual sequence length based on the original aspect ratios and resolutions of images. Experiments on a diverse set of benchmarks reveal that our model consistently outperforms state-of-the-art systems, such as Llama-3.2 and Qwen2-VL, in challenging text-rich, multi-image evaluations. Remarkably, our approach achieves outstanding performance using only 1.2M fully open-sourced training instances, outperforming models that rely on large-scale in-house data, highlighting its efficiency and effectiveness. Our code and data are available at https://anonymous.4open.science/r/Leopard-908F.

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NeurIPS Conference 2025 Conference Paper

RAST: Reasoning Activation in LLMs via Small-model Transfer

Siru Ouyang
Xinyu Zhu
Zilin Xiao
Minhao Jiang
Yu Meng
Jiawei Han

Reinforcement learning (RL) has become a powerful approach for improving the reasoning capabilities of large language models (LLMs), as evidenced by recent successes such as OpenAI's o1 and Deepseek-R1. However, applying RL at scale remains intimidatingly resource-intensive, requiring multiple model copies and extensive GPU workloads. On the other hand, while being powerful, recent studies suggest that RL does not fundamentally endow models with new knowledge; rather, it primarily reshapes the model's output distribution to activate reasoning capabilities latent in the base model. Building on this insight, we hypothesize that the changes in output probabilities induced by RL are largely model-size invariant, opening the door to a more efficient paradigm: training a small model with RL and transferring its induced probability shifts to larger base models. To verify our hypothesis, we conduct a token-level analysis of decoding trajectories and find high alignment in RL-induced output distributions across model scales, validating our hypothesis. Motivated by this, we propose RAST, a simple yet effective method that transfers reasoning behaviors by injecting RL-induced probability adjustments from a small RL-trained model into larger models. Experiments across multiple mathematical reasoning benchmarks show that RAST substantially and consistently enhances the reasoning capabilities of base models while requiring significantly lower GPU memory than direct RL training, sometimes even yielding better performance than the RL-trained counterparts. Our findings offer new insights into the nature of RL-driven reasoning and practical strategies for scaling its benefits without incurring its full computational cost. The project page of RAST is available at https: //ozyyshr. github. io/RAST/.

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ICLR Conference 2025 Conference Paper

RepoGraph: Enhancing AI Software Engineering with Repository-level Code Graph

Siru Ouyang
Wenhao Yu 0002
Kaixin Ma
Zilin Xiao
Zhihan Zhang 0001
Mengzhao Jia
Jiawei Han 0001
Hongming Zhang 0009

Large Language Models (LLMs) excel in code generation yet struggle with modern AI software engineering tasks. Unlike traditional function-level or file-level coding tasks, AI software engineering requires not only basic coding proficiency but also advanced skills in managing and interacting with code repositories. However, existing methods often overlook the need for repository-level code understanding, which is crucial for accurately grasping the broader context and developing effective solutions. On this basis, we present RepoGraph, a plug-in module that manages a repository-level structure for modern AI software engineering solutions. RepoGraph offers the desired guidance and serves as a repository-wide navigation for AI software engineers. We evaluate RepoGraph on the SWE-bench by plugging it into four different methods of two lines of approaches, where RepoGraph substantially boosts the performance of all systems, leading to a new state-of-the-art among open-source frameworks. Our analyses also demonstrate the extensibility and flexibility of RepoGraph by testing on another repo-level coding benchmark, CrossCodeEval. Our code is available at https://github.com/ozyyshr/RepoGraph.

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AAAI Conference 2024 Conference Paper

Fact-Driven Logical Reasoning for Machine Reading Comprehension

Siru Ouyang
Zhuosheng Zhang
Hai Zhao

Recent years have witnessed an increasing interest in training machines with reasoning ability, which deeply relies on accurately and clearly presented clue forms. The clues are usually modeled as entity-aware knowledge in existing studies. However, those entity-aware clues are primarily focused on commonsense, making them insufficient for tasks that require knowledge of temporary facts or events, particularly in logical reasoning for reading comprehension. To address this challenge, we are motivated to cover both commonsense and temporary knowledge clues hierarchically. Specifically, we propose a general formalism of knowledge units by extracting backbone constituents of the sentence, such as the subject-verb-object formed ``facts''. We then construct a supergraph on top of the fact units, allowing for the benefit of sentence-level (relations among fact groups) and entity-level interactions (concepts or actions inside a fact). Experimental results on logical reasoning benchmarks and dialogue modeling datasets show that our approach improves the baselines substantially, and it is general across backbone models. Code is available at https://github.com/ozyyshr/FocalReasoner.

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TMLR Journal 2024 Journal Article

Multi-LoRA Composition for Image Generation

Ming Zhong
Yelong Shen
Shuohang Wang
Yadong Lu
Yizhu Jiao
Siru Ouyang
Donghan Yu
Jiawei Han

Low-Rank Adaptation (LoRA) is extensively utilized in text-to-image models for the accurate rendition of specific elements like distinct characters or unique styles in generated images. Nonetheless, existing methods face challenges in effectively composing multiple LoRAs, especially as the number of LoRAs to be integrated grows, thus hindering the creation of complex imagery. In this paper, we study multi-LoRA composition through a decoding-centric perspective. We present two training-free methods: \textsc{LoRA Switch}, which alternates between different LoRAs at each denoising step, and \textsc{LoRA Composite}, which simultaneously incorporates all LoRAs to guide more cohesive image synthesis. To evaluate the proposed approaches, we establish \texttt{ComposLoRA}, a new comprehensive testbed as part of this research. It features a diverse range of LoRA categories with 480 composition sets. Utilizing an evaluation framework based on GPT-4V, our findings demonstrate a clear improvement in performance with our methods over the prevalent baseline, particularly evident when increasing the number of LoRAs in a composition. The code, benchmarks, LoRA weights, and all evaluation details are available on our project website: https://maszhongming.github.io/Multi-LoRA-Composition.

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ICML Conference 2024 Conference Paper

Structured Chemistry Reasoning with Large Language Models

Siru Ouyang
Zhuosheng Zhang 0001
Bing Yan
Xuan Liu 0009
Yejin Choi 0001
Jiawei Han 0001
Lianhui Qin

Large Language Models (LLMs) excel in diverse areas, yet struggle with complex scientific reasoning, especially in the field of chemistry. Different from the simple chemistry tasks (e. g. , molecule classification) addressed in previous studies, complex chemistry problems require not only vast knowledge and precise calculation, but also compositional reasoning about rich dynamic interactions of different concepts (e. g. , temperature changes). Our study shows that even advanced LLMs, like GPT-4, can fail easily in different ways. Interestingly, the errors often stem not from a lack of domain knowledge within the LLMs, but rather from the absence of an effective reasoning structure that guides the LLMs to elicit the right knowledge, incorporate the knowledge in step-by-step reasoning, and iteratively refine results for further improved quality. On this basis, we introduce StructChem, a simple yet effective prompting strategy that offers the desired guidance and substantially boosts the LLMs’ chemical reasoning capability. Testing across four chemistry areas—quantum chemistry, mechanics, physical chemistry, and kinetics—StructChem substantially enhances GPT-4’s performance, with up to 30% peak improvement. Our analysis also underscores the unique difficulties of precise grounded reasoning in science with LLMs, highlighting a need for more research in this area.

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