arXiv subjects

Siru Ouyang

Publications and source records attributed to Siru Ouyang.

34 records · Page 2Linked to original sources

arXiv2025

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

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.

cs.SE↗

arXiv2025

Multimodal Search in Chemical Documents and Reactions

We present a multimodal search tool that facilitates retrieval of chemical reactions, molecular structures, and associated text from scientific literature. Queries may combine molecular diagrams, textual descriptions, and reaction data, allowing users to connect different representations of chemical information. To support this, the indexing process includes chemical diagram extraction and parsing, extraction of reaction data from text in tabular form, and cross-modal linking of diagrams and their mentions in text. We describe the system's architecture, key functionalities, and retrieval process, along with expert assessments of the system. This demo highlights the workflow and technical components of the search system.

cs.IR↗

arXiv2025

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

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 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

cs.CL↗

arXiv2024

Multi-LoRA Composition for Image Generation

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: LoRA Switch, which alternates between different LoRAs at each denoising step, and LoRA Composite, which simultaneously incorporates all LoRAs to guide more cohesive image synthesis. To evaluate the proposed approaches, we establish 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.

cs.CV↗

arXiv2024

Towards End-to-End Open Conversational Machine Reading

In open-retrieval conversational machine reading (OR-CMR) task, machines are required to do multi-turn question answering given dialogue history and a textual knowledge base. Existing works generally utilize two independent modules to approach this problem's two successive sub-tasks: first with a hard-label decision making and second with a question generation aided by various entailment reasoning methods. Such usual cascaded modeling is vulnerable to error propagation and prevents the two sub-tasks from being consistently optimized. In this work, we instead model OR-CMR as a unified text-to-text task in a fully end-to-end style. Experiments on the ShARC and OR-ShARC dataset show the effectiveness of our proposed end-to-end framework on both sub-tasks by a large margin, achieving new state-of-the-art results. Further ablation studies support that our framework can generalize to different backbone models.

cs.CL↗

arXiv2024

Temperature-Centric Investigation of Speculative Decoding with Knowledge Distillation

Speculative decoding stands as a pivotal technique to expedite inference in autoregressive (large) language models. This method employs a smaller draft model to speculate a block of tokens, which the target model then evaluates for acceptance. Despite a wealth of studies aimed at increasing the efficiency of speculative decoding, the influence of generation configurations on the decoding process remains poorly understood, especially concerning decoding temperatures. This paper delves into the effects of decoding temperatures on speculative decoding's efficacy. Beginning with knowledge distillation (KD), we first highlight the challenge of decoding at higher temperatures, and demonstrate KD in a consistent temperature setting could be a remedy. We also investigate the effects of out-of-domain testing sets with out-of-range temperatures. Building upon these findings, we take an initial step to further the speedup for speculative decoding, particularly in a high-temperature generation setting. Our work offers new insights into how generation configurations drastically affect the performance of speculative decoding, and underscores the need for developing methods that focus on diverse decoding configurations. Code is publically available at https://github.com/ozyyshr/TempSpec.

cs.CL↗

arXiv2024

ParallelSpec: Parallel Drafter for Efficient Speculative Decoding

Speculative decoding has proven to be an efficient solution to large language model (LLM) inference, where the small drafter predicts future tokens at a low cost, and the target model is leveraged to verify them in parallel. However, most existing works still draft tokens auto-regressively to maintain sequential dependency in language modeling, which we consider a huge computational burden in speculative decoding. We present ParallelSpec, an alternative to auto-regressive drafting strategies in state-of-the-art speculative decoding approaches. In contrast to auto-regressive drafting in the speculative stage, we train a parallel drafter to serve as an efficient speculative model. ParallelSpec learns to efficiently predict multiple future tokens in parallel using a single model, and it can be integrated into any speculative decoding framework that requires aligning the output distributions of the drafter and the target model with minimal training cost. Experimental results show that ParallelSpec accelerates baseline methods in latency up to 62% on text generation benchmarks from different domains, and it achieves 2.84X overall speedup on the Llama-2-13B model using third-party evaluation criteria.

cs.CL↗

arXiv2024

Structured Chemistry Reasoning with Large Language Models

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. Code is available at \url{https://github.com/ozyyshr/StructChem}.

cs.CL↗

arXiv2024

Investigating Data Contamination for Pre-training Language Models

Language models pre-trained on web-scale corpora demonstrate impressive capabilities on diverse downstream tasks. However, there is increasing concern whether such capabilities might arise from evaluation datasets being included in the pre-training corpus -- a phenomenon known as \textit{data contamination} -- in a manner that artificially increases performance. There has been little understanding of how this potential contamination might influence LMs' performance on downstream tasks. In this paper, we explore the impact of data contamination at the pre-training stage by pre-training a series of GPT-2 models \textit{from scratch}. We highlight the effect of both text contamination (\textit{i.e.}\ input text of the evaluation samples) and ground-truth contamination (\textit{i.e.}\ the prompts asked on the input and the desired outputs) from evaluation data. We also investigate the effects of repeating contamination for various downstream tasks. Additionally, we examine the prevailing n-gram-based definitions of contamination within current LLM reports, pinpointing their limitations and inadequacy. Our findings offer new insights into data contamination's effects on language model capabilities and underscore the need for independent, comprehensive contamination assessments in LLM studies.

cs.CL↗

arXiv2023

Instruct and Extract: Instruction Tuning for On-Demand Information Extraction

Large language models with instruction-following capabilities open the door to a wider group of users. However, when it comes to information extraction - a classic task in natural language processing - most task-specific systems cannot align well with long-tail ad hoc extraction use cases for non-expert users. To address this, we propose a novel paradigm, termed On-Demand Information Extraction, to fulfill the personalized demands of real-world users. Our task aims to follow the instructions to extract the desired content from the associated text and present it in a structured tabular format. The table headers can either be user-specified or inferred contextually by the model. To facilitate research in this emerging area, we present a benchmark named InstructIE, inclusive of both automatically generated training data, as well as the human-annotated test set. Building on InstructIE, we further develop an On-Demand Information Extractor, ODIE. Comprehensive evaluations on our benchmark reveal that ODIE substantially outperforms the existing open-source models of similar size. Our code and dataset are released on https://github.com/yzjiao/On-Demand-IE.

cs.CL↗

arXiv2023

The Shifted and The Overlooked: A Task-oriented Investigation of User-GPT Interactions

Recent progress in Large Language Models (LLMs) has produced models that exhibit remarkable performance across a variety of NLP tasks. However, it remains unclear whether the existing focus of NLP research accurately captures the genuine requirements of human users. This paper provides a comprehensive analysis of the divergence between current NLP research and the needs of real-world NLP applications via a large-scale collection of user-GPT conversations. We analyze a large-scale collection of real user queries to GPT. We compare these queries against existing NLP benchmark tasks and identify a significant gap between the tasks that users frequently request from LLMs and the tasks that are commonly studied in academic research. For example, we find that tasks such as ``design'' and ``planning'' are prevalent in user interactions but are largely neglected or different from traditional NLP benchmarks. We investigate these overlooked tasks, dissect the practical challenges they pose, and provide insights toward a roadmap to make LLMs better aligned with user needs.

cs.CL↗

arXiv2023

Ontology Enrichment for Effective Fine-grained Entity Typing

Fine-grained entity typing (FET) is the task of identifying specific entity types at a fine-grained level for entity mentions based on their contextual information. Conventional methods for FET require extensive human annotation, which is time-consuming and costly. Recent studies have been developing weakly supervised or zero-shot approaches. We study the setting of zero-shot FET where only an ontology is provided. However, most existing ontology structures lack rich supporting information and even contain ambiguous relations, making them ineffective in guiding FET. Recently developed language models, though promising in various few-shot and zero-shot NLP tasks, may face challenges in zero-shot FET due to their lack of interaction with task-specific ontology. In this study, we propose OnEFET, where we (1) enrich each node in the ontology structure with two types of extra information: instance information for training sample augmentation and topic information to relate types to contexts, and (2) develop a coarse-to-fine typing algorithm that exploits the enriched information by training an entailment model with contrasting topics and instance-based augmented training samples. Our experiments show that OnEFET achieves high-quality fine-grained entity typing without human annotation, outperforming existing zero-shot methods by a large margin and rivaling supervised methods.

cs.CL↗

arXiv2023

ReactIE: Enhancing Chemical Reaction Extraction with Weak Supervision

Structured chemical reaction information plays a vital role for chemists engaged in laboratory work and advanced endeavors such as computer-aided drug design. Despite the importance of extracting structured reactions from scientific literature, data annotation for this purpose is cost-prohibitive due to the significant labor required from domain experts. Consequently, the scarcity of sufficient training data poses an obstacle to the progress of related models in this domain. In this paper, we propose ReactIE, which combines two weakly supervised approaches for pre-training. Our method utilizes frequent patterns within the text as linguistic cues to identify specific characteristics of chemical reactions. Additionally, we adopt synthetic data from patent records as distant supervision to incorporate domain knowledge into the model. Experiments demonstrate that ReactIE achieves substantial improvements and outperforms all existing baselines.

cs.CL↗

arXiv2023

Fact-driven Logical Reasoning for Machine Reading Comprehension

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 \url{https://github.com/ozyyshr/FocalReasoner}.

cs.CL↗

arXiv2021

Smoothing Dialogue States for Open Conversational Machine Reading

Conversational machine reading (CMR) requires machines to communicate with humans through multi-turn interactions between two salient dialogue states of decision making and question generation processes. In open CMR settings, as the more realistic scenario, the retrieved background knowledge would be noisy, which results in severe challenges in the information transmission. Existing studies commonly train independent or pipeline systems for the two subtasks. However, those methods are trivial by using hard-label decisions to activate question generation, which eventually hinders the model performance. In this work, we propose an effective gating strategy by smoothing the two dialogue states in only one decoder and bridge decision making and question generation to provide a richer dialogue state reference. Experiments on the OR-ShARC dataset show the effectiveness of our method, which achieves new state-of-the-art results.

cs.CL↗

arXiv2021

Dialogue Graph Modeling for Conversational Machine Reading

Conversational Machine Reading (CMR) aims at answering questions in a complicated manner. Machine needs to answer questions through interactions with users based on given rule document, user scenario and dialogue history, and ask questions to clarify if necessary. In this paper, we propose a dialogue graph modeling framework to improve the understanding and reasoning ability of machine on CMR task. There are three types of graph in total. Specifically, Discourse Graph is designed to learn explicitly and extract the discourse relation among rule texts as well as the extra knowledge of scenario; Decoupling Graph is used for understanding local and contextualized connection within rule texts. And finally a global graph for fusing the information together and reply to the user with our final decision being either "Yes/No/Irrelevant" or to ask a follow-up question to clarify.

cs.CL↗