arXiv subjects

Hongyu Zhang

Publications and source records attributed to Hongyu Zhang.

At least 91 records · Page 5Linked to original sources

arXiv2025

SPENCER: Self-Adaptive Model Distillation for Efficient Code Retrieval

Code retrieval aims to provide users with desired code snippets based on users' natural language queries. With the development of deep learning technologies, adopting pre-trained models for this task has become mainstream. Considering the retrieval efficiency, most of the previous approaches adopt a dual-encoder for this task, which encodes the description and code snippet into representation vectors, respectively. However, the model structure of the dual-encoder tends to limit the model's performance, since it lacks the interaction between the code snippet and description at the bottom layer of the model during training. To improve the model's effectiveness while preserving its efficiency, we propose a framework, which adopts Self-AdaPtive Model Distillation for Efficient CodE Retrieval, named SPENCER. SPENCER first adopts the dual-encoder to narrow the search space and then adopts the cross-encoder to improve accuracy. To improve the efficiency of SPENCER, we propose a novel model distillation technique, which can greatly reduce the inference time of the dual-encoder while maintaining the overall performance. We also propose a teaching assistant selection strategy for our model distillation, which can adaptively select the suitable teaching assistant models for different pre-trained models during the model distillation to ensure the model performance. Extensive experiments demonstrate that the combination of dual-encoder and cross-encoder improves overall performance compared to solely dual-encoder-based models for code retrieval. Besides, our model distillation technique retains over 98% of the overall performance while reducing the inference time of the dual-encoder by 70%.

cs.SE↗

arXiv2025

Adaptive Benders decomposition and enhanced SDDP for multistage stochastic programs with block-separable multistage recourse

This paper proposes an algorithm to efficiently solve multistage stochastic programs with block separable recourse where each recourse problem is a multistage stochastic program with stage-wise independent uncertainty. The algorithm first decomposes the full problem into a reduced master problem and subproblems using Adaptive Benders decomposition. The subproblems are then solved by an enhanced SDDP. The enhancement includes (1) valid bounds at each iteration, (2) a path exploration rule, (3) cut sharing among subproblems, and (4) guaranteed δ-optimal convergence. The cuts for the subproblems are then shared by calling adaptive oracles. The key contribution of the paper is the first algorithm for solving this class of problems. The algorithm is demonstrated on a power system investment planning problem with multi-timescale uncertainty. The case study results show that (1) the proposed algorithm can efficiently solve this type of problem, (2) deterministic wind modelling underestimate the objective function, and (3) stochastic modelling of wind leads to different investment decisions.

math.OC↗

arXiv2025

DaiFu: In-Situ Crash Recovery for Deep Learning Systems

Deep learning (DL) systems have been widely adopted in many areas, and are becoming even more popular with the emergence of large language models. However, due to the complex software stacks involved in their development and execution, crashes are unavoidable and common. Crashes severely waste computing resources and hinder development productivity, so efficient crash recovery is crucial. Existing solutions, such as checkpoint-retry, are too heavyweight for fast recovery from crashes caused by minor programming errors or transient runtime errors. Therefore, we present DaiFu, an in-situ recovery framework for DL systems. Through a lightweight code transformation to a given DL system, DaiFu augments it to intercept crashes in situ and enables dynamic and instant updates to its program running context (e.g., code, configurations, and other data) for agile crash recovery. Our evaluation shows that DaiFu helps reduce the restore time for crash recovery, achieving a 1372x speedup compared with state-of-the-art solutions. Meanwhile, the overhead of DaiFu is negligible (under 0.40%). We also construct a benchmark spanning 7 distinct crash scenarios in DL systems, and show the effectiveness of DaiFu in diverse situations.

cs.SE↗

arXiv2025

OmniESI: A unified framework for enzyme-substrate interaction prediction with progressive conditional deep learning

Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior knowledge of enzyme catalysis to rationally modulate general protein-molecule features that are misaligned with catalytic patterns. To address this issue, we introduce a two-stage progressive framework, OmniESI, for enzyme-substrate interaction prediction through conditional deep learning. By decomposing the modeling of enzyme-substrate interactions into a two-stage progressive process, OmniESI incorporates two conditional networks that respectively emphasize enzymatic reaction specificity and crucial catalysis-related interactions, facilitating a gradual feature modulation in the latent space from general protein-molecule domain to catalysis-aware domain. On top of this unified architecture, OmniESI can adapt to a variety of downstream tasks, including enzyme kinetic parameter prediction, enzyme-substrate pairing prediction, enzyme mutational effect prediction, and enzymatic active site annotation. Under the multi-perspective performance evaluation of in-distribution and out-of-distribution settings, OmniESI consistently delivered superior performance than state-of-the-art specialized methods across seven benchmarks. More importantly, the proposed conditional networks were shown to internalize the fundamental patterns of catalytic efficiency while significantly improving prediction performance, with only negligible parameter increases (0.16%), as demonstrated by ablation studies on key components. Overall, OmniESI represents a unified predictive approach for enzyme-substrate interactions, providing an effective tool for catalytic mechanism cracking and enzyme engineering with strong generalization and broad applicability.

q-bio.BM↗

arXiv2025

Improving Compiler Bug Isolation by Leveraging Large Language Models

Compilers play a foundational role in building reliable software systems, and bugs within them can lead to catastrophic consequences. The compilation process typically involves hundreds of files, making traditional automated bug isolation techniques inapplicable due to scalability or effectiveness issues. Current mainstream compiler bug localization techniques have limitations in test program mutation and resource consumption. Inspired by the recent advances of pre-trained Large Language Models (LLMs), we propose an innovative approach named AutoCBI, which (1) uses LLMs to summarize compiler file functions and (2) employs specialized prompts to guide LLM in reordering suspicious file rankings. This approach leverages four types of information: the failing test program, source file function summaries, lists of suspicious files identified through analyzing test coverage, as well as compilation configurations with related output messages, resulting in a refined ranking of suspicious files. Our evaluation of AutoCBI against state-of-the-art approaches (DiWi, RecBi and FuseFL) on 120 real-world bugs from the widely-used GCC and LLVM compilers demonstrates its effectiveness. Specifically, AutoCBI isolates 66.67%/69.23%, 300%/340%, and 100%/57.14% more bugs than RecBi, DiWi, and FuseFL, respectively, in the Top-1 ranked results for GCC/LLVM. Additionally, the ablation study underscores the significance of each component in our approach.

cs.SE↗

arXiv2025

Empirical Evaluation of Large Language Models in Automated Program Repair

The increasing prevalence of software bugs has made automated program repair (APR) a key research focus. Large language models (LLMs) offer new opportunities for APR, but existing studies mostly rely on smaller, earlier-generation models and Java benchmarks. The repair capabilities of modern, large-scale LLMs across diverse languages and scenarios remain underexplored. To address this, we conduct a comprehensive empirical study of four open-source LLMs, CodeLlama, LLaMA, StarCoder, and DeepSeek-Coder, spanning 7B to 33B parameters, diverse architectures, and purposes. We evaluate them across two bug scenarios (enterprise-grades and algorithmic), three languages (Java, C/C++, Python), and four prompting strategies, analyzing over 600K generated patches on six benchmarks. Key findings include: (1) model specialization (e.g., CodeLlama) can outperform larger general-purpose models (e.g., LLaMA); (2) repair performance does not scale linearly with model size; (3) correct patches often appear early in generation; and (4) prompts significantly affect results. These insights offer practical guidance for designing effective and efficient LLM-based APR systems.

cs.SE↗

arXiv2025

From Informal to Formal -- Incorporating and Evaluating LLMs on Natural Language Requirements to Verifiable Formal Proofs

The research in AI-based formal mathematical reasoning has shown an unstoppable growth trend. These studies have excelled in mathematical competitions like IMO and have made significant progress. This paper focuses on formal verification, an immediate application scenario of formal reasoning, and breaks it down into sub-tasks. We constructed 18k high-quality instruction-response pairs across five formal specification languages (Coq, Lean4, Dafny, ACSL, and TLA+) by distilling gpt-4o and evaluated against ten open-sourced LLMs, including recent popular DeepSeek-R1. We also fine-tuned several 7~8B small models to achieve comparable performance with Deepseek-R1-671B. Interestingly, we observed that fine-tuning with formal data also enhances mathematics, reasoning, and coding capabilities. Fine-tuned models are released at https: //huggingface.co/fm-universe.

cs.AI↗

arXiv2025

Can Large Language Models Understand Intermediate Representations in Compilers?

Intermediate Representations (IRs) play a critical role in compiler design and program analysis, yet their comprehension by Large Language Models (LLMs) remains underexplored. In this paper, we present an explorative empirical study evaluating the capabilities of six state-of-the-art LLMs: GPT-4, GPT-3, DeepSeek, Gemma 2, Llama 3, and Code Llama, in understanding IRs. Specifically, we assess model performance across four core tasks: control flow graph reconstruction, decompilation, code summarization, and execution reasoning. While LLMs exhibit competence in parsing IR syntax and identifying high-level structures, they consistently struggle with instruction-level reasoning, especially in control flow reasoning, loop handling, and dynamic execution. Common failure modes include misinterpreting branching instructions, omitting critical operations, and relying on heuristic reasoning rather than precise instruction-level logic. Our findings highlight the need for IR-specific enhancements in LLM design. We recommend fine-tuning on structured IR datasets and integrating control-flow-sensitive architectures to improve model effectiveness. All experimental data and source code are publicly available at

cs.LG↗

arXiv2025

MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction

Activity cliff prediction is a critical task in drug discovery and material design. Existing computational methods are limited to handling single binding targets, which restricts the applicability of these prediction models. In this paper, we present the Multi-Grained Target Perception network (MTPNet) to incorporate the prior knowledge of interactions between the molecules and their target proteins. Specifically, MTPNet is a unified framework for activity cliff prediction, which consists of two components: Macro-level Target Semantic (MTS) guidance and Micro-level Pocket Semantic (MPS) guidance. By this way, MTPNet dynamically optimizes molecular representations through multi-grained protein semantic conditions. To our knowledge, it is the first time to employ the receptor proteins as guiding information to effectively capture critical interaction details. Extensive experiments on 30 representative activity cliff datasets demonstrate that MTPNet significantly outperforms previous approaches, achieving an average RMSE improvement of 18.95% on top of several mainstream GNN architectures. Overall, MTPNet internalizes interaction patterns through conditional deep learning to achieve unified predictions of activity cliffs, helping to accelerate compound optimization and design. Codes are available at: https://github.com/ZishanShu/MTPNet.

cs.LG↗

arXiv2025

A Semantic-Aware Layer-Freezing Approach to Computation-Efficient Fine-Tuning of Language Models

Finetuning language models (LMs) is crucial for adapting the models to downstream data and tasks. However, full finetuning is usually costly. Existing work, such as parameter-efficient finetuning (PEFT), often focuses on \textit{how to finetune} but neglects the issue of \textit{where to finetune}. As a pioneering work on reducing the cost of backpropagation (at the layer level) by answering where to finetune, we conduct a semantic analysis of the LM inference process. We first propose using transition traces of the latent representation to compute deviations (or loss). Then, using a derived formula of scaling law, we estimate the gain of each layer in reducing deviation (or loss). Further, we narrow down the scope for finetuning, and also, study the cost-benefit balance of LM finetuning. We perform extensive experiments across well-known LMs and datasets. The results show that our approach is effective and efficient, and outperforms the existing baselines. Our approach is orthogonal to other techniques for improving finetuning efficiency, such as PEFT methods, offering practical values on LM finetuning.

cs.CL↗

arXiv2025

A Silicon Microstrip Detector for Power-Limited and Large Sensitive Area Applications

A silicon microstrip detector (SSD) has been developed to have state of the art spatial resolution and a large sensitive area under stringent power constraints. The design incorporates three floating strips with their bias resistors inserted between two aluminum readout strips. Beam test measurements with the single sensor confirmed that this configuration achieves a total detection efficiency of $99.8 \, \%$ and spatial resolution $7.6 \, \mathrm{μm}$ for MIPs. A double-$η$ algorithm was developed to optimize hit position reconstruction for this SSD. The design can be adapted for large area silicon detectors.

physics.ins-det↗

arXiv2025

SeMe: Training-Free Language Model Merging via Semantic Alignment

Despite the remarkable capabilities of Language Models (LMs) across diverse tasks, no single model consistently outperforms others, necessitating efficient methods to combine their strengths without expensive retraining. Existing model merging techniques, such as parameter averaging and task-guided fusion, often rely on data-dependent computations or fail to preserve internal knowledge, limiting their robustness and scalability. We introduce SeMe (Semantic-based Merging), a novel, data-free, and training-free approach that leverages latent semantic alignment to merge LMs at a fine-grained, layer-wise level. Unlike prior work, SeMe not only preserves model behaviors but also explicitly stabilizes internal knowledge, addressing a critical gap in LM fusion. Through extensive experiments across diverse architectures and tasks, we demonstrate that SeMe outperforms existing methods in both performance and efficiency while eliminating reliance on external data. Our work establishes a new paradigm for knowledge-aware model merging and provides insights into the semantic structure of LMs, paving the way for more scalable and interpretable model composition.

cs.CL↗

arXiv2025

LLMScan: Causal Scan for LLM Misbehavior Detection

Despite the success of Large Language Models (LLMs) across various fields, their potential to generate untruthful, biased and harmful responses poses significant risks, particularly in critical applications. This highlights the urgent need for systematic methods to detect and prevent such misbehavior. While existing approaches target specific issues such as harmful responses, this work introduces LLMScan, an innovative LLM monitoring technique based on causality analysis, offering a comprehensive solution. LLMScan systematically monitors the inner workings of an LLM through the lens of causal inference, operating on the premise that the LLM's `brain' behaves differently when misbehaving. By analyzing the causal contributions of the LLM's input tokens and transformer layers, LLMScan effectively detects misbehavior. Extensive experiments across various tasks and models reveal clear distinctions in the causal distributions between normal behavior and misbehavior, enabling the development of accurate, lightweight detectors for a variety of misbehavior detection tasks.

cs.AI↗

arXiv2025

UICopilot: Automating UI Synthesis via Hierarchical Code Generation from Webpage Designs

Automating the synthesis of User Interfaces (UIs) plays a crucial role in enhancing productivity and accelerating the development lifecycle, reducing both development time and manual effort. Recently, the rapid development of Multimodal Large Language Models (MLLMs) has made it possible to generate front-end Hypertext Markup Language (HTML) code directly from webpage designs. However, real-world webpages encompass not only a diverse array of HTML tags but also complex stylesheets, resulting in significantly lengthy code. The lengthy code poses challenges for the performance and efficiency of MLLMs, especially in capturing the structural information of UI designs. To address these challenges, this paper proposes UICopilot, a novel approach to automating UI synthesis via hierarchical code generation from webpage designs. The core idea of UICopilot is to decompose the generation process into two stages: first, generating the coarse-grained HTML hierarchical structure, followed by the generation of fine-grained code. To validate the effectiveness of UICopilot, we conduct experiments on a real-world dataset, i.e., WebCode2M. Experimental results demonstrate that UICopilot significantly outperforms existing baselines in both automatic evaluation metrics and human evaluations. Specifically, statistical analysis reveals that the majority of human annotators prefer the webpages generated by UICopilot over those produced by GPT-4V.

cs.SE↗

arXiv2025

MHANet: Multi-scale Hybrid Attention Network for Auditory Attention Detection

Auditory attention detection (AAD) aims to detect the target speaker in a multi-talker environment from brain signals, such as electroencephalography (EEG), which has made great progress. However, most AAD methods solely utilize attention mechanisms sequentially and overlook valuable multi-scale contextual information within EEG signals, limiting their ability to capture long-short range spatiotemporal dependencies simultaneously. To address these issues, this paper proposes a multi-scale hybrid attention network (MHANet) for AAD, which consists of the multi-scale hybrid attention (MHA) module and the spatiotemporal convolution (STC) module. Specifically, MHA combines channel attention and multi-scale temporal and global attention mechanisms. This effectively extracts multi-scale temporal patterns within EEG signals and captures long-short range spatiotemporal dependencies simultaneously. To further improve the performance of AAD, STC utilizes temporal and spatial convolutions to aggregate expressive spatiotemporal representations. Experimental results show that the proposed MHANet achieves state-of-the-art performance with fewer trainable parameters across three datasets, 3 times lower than that of the most advanced model. Code is available at: https://github.com/fchest/MHANet.

cs.HC↗

arXiv2025

ListenNet: A Lightweight Spatio-Temporal Enhancement Nested Network for Auditory Attention Detection

Auditory attention detection (AAD) aims to identify the direction of the attended speaker in multi-speaker environments from brain signals, such as Electroencephalography (EEG) signals. However, existing EEG-based AAD methods overlook the spatio-temporal dependencies of EEG signals, limiting their decoding and generalization abilities. To address these issues, this paper proposes a Lightweight Spatio-Temporal Enhancement Nested Network (ListenNet) for AAD. The ListenNet has three key components: Spatio-temporal Dependency Encoder (STDE), Multi-scale Temporal Enhancement (MSTE), and Cross-Nested Attention (CNA). The STDE reconstructs dependencies between consecutive time windows across channels, improving the robustness of dynamic pattern extraction. The MSTE captures temporal features at multiple scales to represent both fine-grained and long-range temporal patterns. In addition, the CNA integrates hierarchical features more effectively through novel dynamic attention mechanisms to capture deep spatio-temporal correlations. Experimental results on three public datasets demonstrate the superiority of ListenNet over state-of-the-art methods in both subject-dependent and challenging subject-independent settings, while reducing the trainable parameter count by approximately 7 times. Code is available at:https://github.com/fchest/ListenNet.

cs.HC↗

arXiv2025

OmniGIRL: A Multilingual and Multimodal Benchmark for GitHub Issue Resolution

The GitHub issue resolution task aims to resolve issues reported in repositories automatically. With advances in large language models (LLMs), this task has gained increasing attention, and several benchmarks are proposed to evaluate the issue resolution ability of LLMs. However, existing benchmarks have three main limitations. First, current benchmarks focus on a single programming language, limiting the evaluation of issues from repositories across different languages. Second, they usually cover a narrow range of domains, which may fail to represent the diversity of real-world issues. Third, existing benchmarks rely solely on textual information in issue descriptions, overlooking multimodal information such as images in issues. In this paper, we propose OmniGIRL, a GitHub Issue ResoLution benchmark that is multilingual, multimodal, and multi-domain. OmniGIRL includes 959 task instances, which are collected from repositories across four programming languages (i.e., Python, JavaScript, TypeScript, and Java) and eight different domains. Our evaluation shows that current LLMs show limited performances on OmniGIRL. Notably, the best-performing model, GPT-4o, resolves only 8.6% of the issues. Besides, we find that current LLMs struggle to resolve issues requiring understanding images. The best performance is achieved by Claude-3.5-Sonnet, which resolves only 10.5% of the issues with image information. Finally, we analyze the reasons behind current LLMs' failure on OmniGIRL, providing insights for future improvements.

cs.SE↗

arXiv2025

AdaCoder: An Adaptive Planning and Multi-Agent Framework for Function-Level Code Generation

Recently, researchers have proposed many multi-agent frameworks for function-level code generation, which aim to improve software development productivity by automatically generating function-level source code based on task descriptions. A typical multi-agent framework consists of Large Language Model (LLM)-based agents that are responsible for task planning, code generation, testing, debugging, etc. Studies have shown that existing multi-agent code generation frameworks perform well on ChatGPT. However, their generalizability across other foundation LLMs remains unexplored systematically. In this paper, we report an empirical study on the generalizability of four state-of-the-art multi-agent code generation frameworks across six open-source LLMs with varying parameter sizes, architectures, and performance levels. Our study reveals the unstable generalizability of existing frameworks on diverse foundation LLMs. Based on the findings obtained from the empirical study, we propose AdaCoder, a novel adaptive planning, multi-agent framework for function-level code generation. AdaCoder has two phases. Phase-1 is an initial code generation step without planning, which uses an LLM-based coding agent and a script-based testing agent to unleash LLM's native power, identify cases beyond LLM's power, and determine the errors hindering execution. Phase-2 adds a rule-based debugging agent and an LLM-based planning agent for iterative code generation with planning. Our evaluation shows that AdaCoder achieves higher generalizability on diverse LLMs. Compared to the best baseline MapCoder, AdaCoder is on average 27.69% higher in Pass@1, 16 times faster in inference, and 12 times lower in token consumption.

cs.SE↗