Daily Papers

Large language models (LLMs) have shown promise for automated patching, but their effectiveness depends strongly on how they are integrated into patching systems. While prior work explores prompting strategies and individual agent designs, the field lacks a systematic comparison of patching architectures. In this paper, we present a controlled evaluation of four LLM-based patching paradigms -- fixed workflow, single-agent system, multi-agent system, and general-purpose code agents -- using a unified benchmark and evaluation framework. We analyze patch correctness, failure modes, token usage, and execution time across real-world vulnerability tasks. Our results reveal clear architectural trade-offs: fixed workflows are efficient but brittle, single-agent systems balance flexibility and cost, and multi-agent designs improve generalization at the expense of substantially higher overhead and increased risk of reasoning drift on complex tasks. Surprisingly, general-purpose code agents achieve the strongest overall patching performance, benefiting from general-purpose tool interfaces that support effective adaptation across vulnerability types. Overall, we show that architectural design and iteration depth, rather than model capability alone, dominate the reliability and cost of LLM-based automated patching.

Automated Program Repair (APR) improves developer productivity by saving debugging and bug-fixing time. While APR has been extensively explored for C/C++ and Java programs, there is little research on bugs in PHP programs due to the lack of a benchmark PHP bug dataset. This is surprising given that PHP has been one of the most widely used server-side languages for over two decades, being used in a variety of contexts such as e-commerce, social networking, and content management. This paper presents a benchmark dataset of PHP bugs on real-world applications called BUGSPHP, which can enable research on analysis, testing, and repair for PHP programs. The dataset consists of training and test datasets, separately curated from GitHub and processed locally. The training dataset includes more than 600,000 bug-fixing commits. The test dataset contains 513 manually validated bug-fixing commits equipped with developer-provided test cases to assess patch correctness.

Automated program repair (APR) aims to fix software bugs automatically and plays a crucial role in software development and maintenance. With the recent advances in deep learning (DL), an increasing number of APR techniques have been proposed to leverage neural networks to learn bug-fixing patterns from massive open-source code repositories. Such learning-based techniques usually treat APR as a neural machine translation (NMT) task, where buggy code snippets (i.e., source language) are translated into fixed code snippets (i.e., target language) automatically. Benefiting from the powerful capability of DL to learn hidden relationships from previous bug-fixing datasets, learning-based APR techniques have achieved remarkable performance. In this paper, we provide a systematic survey to summarize the current state-of-the-art research in the learning-based APR community. We illustrate the general workflow of learning-based APR techniques and detail the crucial components, including fault localization, patch generation, patch ranking, patch validation, and patch correctness phases. We then discuss the widely-adopted datasets and evaluation metrics and outline existing empirical studies. We discuss several critical aspects of learning-based APR techniques, such as repair domains, industrial deployment, and the open science issue. We highlight several practical guidelines on applying DL techniques for future APR studies, such as exploring explainable patch generation and utilizing code features. Overall, our paper can help researchers gain a comprehensive understanding about the achievements of the existing learning-based APR techniques and promote the practical application of these techniques. Our artifacts are publicly available at https://github.com/QuanjunZhang/AwesomeLearningAPR.

Context engineering has emerged as a pivotal paradigm for unlocking the potential of Large Language Models (LLMs) in Software Engineering (SE) tasks, enabling performance gains at test time without model fine-tuning. Despite its success, existing research lacks a systematic taxonomy of SE-specific context types and a dedicated benchmark to quantify the heterogeneous effects of different contexts across core SE workflows. To address this gap, we propose CL4SE (Context Learning for Software Engineering), a comprehensive benchmark featuring a fine-grained taxonomy of four SE-oriented context types (interpretable examples, project-specific context, procedural decision-making context, and positive & negative context), each mapped to a representative task (code generation, code summarization, code review, and patch correctness assessment). We construct high-quality datasets comprising over 13,000 samples from more than 30 open-source projects and evaluate five mainstream LLMs across nine metrics. Extensive experiments demonstrate that context learning yields an average performance improvement of 24.7% across all tasks. Specifically, procedural context boosts code review performance by up to 33% (Qwen3-Max), mixed positive-negative context improves patch assessment by 30% (DeepSeek-V3), project-specific context increases code summarization BLEU by 14.78% (GPT-Oss-120B), and interpretable examples enhance code generation PASS@1 by 5.72% (DeepSeek-V3). CL4SE establishes the first standardized evaluation framework for SE context learning, provides actionable empirical insights into task-specific context design, and releases a large-scale dataset to facilitate reproducible research in this domain.

A pervasive intuition holds that vision-language models (VLMs) are most trustworthy when their attention maps look sharp: concentrated attention on the queried region should imply a confident, calibrated answer. We test this Attention-Confidence Assumption directly. We instrument three open-weight VLM families (LLaVA-1.5, PaliGemma, Qwen2-VL; 3-7B parameters) with a unified mechanistic pipeline -- the VLM Reliability Probe (VRP) -- that compares attention structure, generation dynamics, and hidden-state geometry against a single correctness label. Three results emerge. (i) Attention structure is a near-zero predictor of correctness (R_pb(C_k,y)=0.001, 95% CI [-0.034,0.036]; R_pb(H_s,y)=-0.012, [-0.047,0.024] on a pooled n=3,090 split), even though attention remains causally necessary for feature extraction (top-30% patch masking drops accuracy by 8.2-11.3 pp, p<0.001). (ii) Reliability becomes legible later in the computation: a single hidden-state linear probe reaches AUROC>0.95 on POPE for two of three families, and self-consistency at K=10 is the strongest behavioral predictor we measure at 10x inference cost (R_pb=0.43). (iii) Causal neuron-level ablations expose a sharp architectural split with direct monitor-design implications: late-fusion LLaVA concentrates reliability in a fragile late bottleneck (-8.3 pp object-identification accuracy after top-5 probe-neuron ablation), whereas early-fusion PaliGemma and Qwen2-VL distribute it widely and absorb destruction of ~50% of their peak-layer hidden dimension with <=1 pp degradation. The takeaway is narrow but consequential: in 3-7B VLMs, reliability is read more reliably off hidden-state geometry, layer-wise margin formation, and sparse late-layer circuits than off attention-map sharpness.

Program repair techniques offer cost-saving benefits for debugging within software development and programming education scenarios. With the proven effectiveness of Large Language Models (LLMs) in code-related tasks, researchers have explored their potential for program repair. However, it is crucial to recognize that existing repair benchmarks may have influenced LLM training data, potentially causing data leakage. To evaluate LLMs' realistic repair capabilities, (1) we introduce an extensive, non-crawled benchmark, referred to as TutorCode, comprising 1,239 C++ defect codes and associated information such as tutor guidance, solution description, failing test cases, and the corrected code. Our work assesses the repair performance of 12 LLMs on TutorCode, measuring repair correctness (TOP-5 and AVG-5) and patch precision (RPSR). (2) We then provide a comprehensive investigation into which types of extra information can help LLMs improve their performance in repairing defects. Among these types, tutor guidance was found to be the most effective information in enhancing LLM repair capabilities. To fully harness LLMs' conversational capabilities and the benefits of augmented information, (3) we introduce a novel conversational semi-automatic repair framework CREF assisting human tutor. It demonstrates a remarkable AVG-5 improvement of 17.2%-24.6% compared to the baseline, achieving an impressive AVG-5 of 76.6% when utilizing GPT-4. These results highlight the potential for enhancing LLMs' repair capabilities through interactions with tutors and historical conversations involving incorrect responses. The successful application of CREF in a real-world educational setting demonstrates its effectiveness in reducing tutors' workload and improving students' learning experience, while also showcasing its promise for facilitating other software engineering tasks, such as code review.

We present SwingArena, a competitive evaluation framework for Large Language Models (LLMs) that closely mirrors real-world software development workflows. Unlike traditional static benchmarks, SwingArena models the collaborative process of software iteration by pairing LLMs as submitters, who generate patches, and reviewers, who create test cases and verify the patches through continuous integration (CI) pipelines. To support these interactive evaluations, we introduce a retrieval-augmented code generation (RACG) module that efficiently handles long-context challenges by providing syntactically and semantically relevant code snippets from large codebases, supporting multiple programming languages (C++, Python, Rust, and Go). This enables the framework to scale across diverse tasks and contexts while respecting token limitations. Our experiments, using over 400 high-quality real-world GitHub issues selected from a pool of 2,300 issues, show that models like GPT-4o excel at aggressive patch generation, whereas DeepSeek and Gemini prioritize correctness in CI validation. SwingArena presents a scalable and extensible methodology for evaluating LLMs in realistic, CI-driven software development settings. More details are available on our project page: swing-bench.github.io

Automated issue solving aims to resolve real-world issues in software repositories. The most popular benchmarks for automated issue solving are SWE-bench and its human-filtered subset SWE-bench Verified. These benchmarks leverage testing to validate generated patches. However, because testing is rarely exhaustive, a patch may pass the tests but nevertheless fail to match the developers' expectations. Unfortunately, it is currently unclear to what extent evaluations performed with SWE-bench suffer from such plausible but incorrect patches. This paper presents an in-depth empirical study of the correctness of plausible patches generated by three state-of-the-art issue-solving tools evaluated on SWE-bench Verified. We extensively test and inspect generated patches, and compare them against human-written ground truth patches. The core of our methodology is a novel technique PatchDiff for differential patch testing, which automatically exposes behavioral discrepancies between two patches. Our findings reveal critical weaknesses in SWE-bench's patch validation mechanism, which causes 7.8% of all patches to count as correct while failing the developer-written test suite. Moreover, our novel automated technique reveals that even more (29.6%) plausible patches induce different behavior than the ground truth patches. These behavioral differences are often due to similar, but divergent implementations (46.8%) and due to generated patches that adapt more behavior than the ground truth patches (27.3%). Our manual inspection shows that 28.6% of behaviorally divergent patches are certainly incorrect. Combined, the different weaknesses lead to an inflation of reported resolution rates by 6.2 absolute percent points. Our findings are a call to arms for more robust and reliable evaluation of issue-solving tools. We envision our automated differential patch testing technique to be useful for this purpose.

We propose patching for large language models (LLMs) like software versions, a lightweight and modular approach for addressing safety vulnerabilities. While vendors release improved LLM versions, major releases are costly, infrequent, and difficult to tailor to customer needs, leaving released models with known safety gaps. Unlike full-model fine-tuning or major version updates, our method enables rapid remediation by prepending a compact, learnable prefix to an existing model. This "patch" introduces only 0.003% additional parameters, yet reliably steers model behavior toward that of a safer reference model. Across three critical domains (toxicity mitigation, bias reduction, and harmfulness refusal) policy patches achieve safety improvements comparable to next-generation safety-aligned models while preserving fluency. Our results demonstrate that LLMs can be "patched" much like software, offering vendors and practitioners a practical mechanism for distributing scalable, efficient, and composable safety updates between major model releases.

Context: Bugs in code are inevitable and can lead to severe consequences, ranging from security vulnerabilities to operational failures. Debugging software remains challenging despite advances in testing and verification, often requiring extensive manual effort. Learning-based automated program repair (APR) has shown promise in reducing the time, effort, and cost of manually fixing bugs. However, existing techniques face several challenges, including language-dependent strategies, limited bug context utilization, and difficulties in handling bugs that span multiple locations in the code. Objective: This paper introduces MultiMend, a learning-based APR approach designed to improve repair performance on multiple programming languages with language-independent context augmentation and multi-hunk patch generation. Method: MultiMend fine-tunes a pre-trained encoder-decoder transformer model (CodeT5) to generate bug-fixing patches. It embeds source code lines and applies retrieval-augmented generation to augment the buggy context with relevant lines during patch generation. The approach systematically constructs patches for multi-hunk bugs to reduce the needed patch validations. We evaluate MultiMend on four benchmarks with four programming languages and compare it with state-of-the-art methods. Results: Experimental results show that MultiMend achieves competitive effectiveness and efficiency against compared tools. Across all benchmarks, MultiMend fixes 2,077 bugs, of which 1,455 are identical to the developer's patch, and 106 are for multi-hunk bugs. Both context augmentation and multi-hunk patch generation positively contribute to the results. Conclusion: MultiMend shows promising performance across benchmarks. The findings highlight its applicability to real-world software maintenance and its potential to reduce manual debugging efforts.

Automated Program Repair (APR) is a task to automatically generate patches for the buggy code. However, most research focuses on generating correct patches while ignoring the consistency between the fixed code and the original buggy code. How to conduct adaptive bug fixing and generate patches with minimal modifications have seldom been investigated. To bridge this gap, we first introduce a novel task, namely AdaPR (Adaptive Program Repair). We then propose a two-stage approach AdaPatcher (Adaptive Patch Generator) to enhance program repair while maintaining the consistency. In the first stage, we utilize a Bug Locator with self-debug learning to accurately pinpoint bug locations. In the second stage, we train a Program Modifier to ensure consistency between the post-modified fixed code and the pre-modified buggy code. The Program Modifier is enhanced with a location-aware repair learning strategy to generate patches based on identified buggy lines, a hybrid training strategy for selective reference and an adaptive preference learning to prioritize fewer changes. The experimental results show that our approach outperforms a set of baselines by a large margin, validating the effectiveness of our two-stage framework for the newly proposed AdaPR task.

Millions of open-source projects with numerous bug fixes are available in code repositories. This proliferation of software development histories can be leveraged to learn how to fix common programming bugs. To explore such a potential, we perform an empirical study to assess the feasibility of using Neural Machine Translation techniques for learning bug-fixing patches for real defects. First, we mine millions of bug-fixes from the change histories of projects hosted on GitHub, in order to extract meaningful examples of such bug-fixes. Next, we abstract the buggy and corresponding fixed code, and use them to train an Encoder-Decoder model able to translate buggy code into its fixed version. In our empirical investigation we found that such a model is able to fix thousands of unique buggy methods in the wild. Overall, this model is capable of predicting fixed patches generated by developers in 9-50% of the cases, depending on the number of candidate patches we allow it to generate. Also, the model is able to emulate a variety of different Abstract Syntax Tree operations and generate candidate patches in a split second.

This paper introduces Patched Round-Trip Correctness (Patched RTC), a novel evaluation technique for Large Language Models (LLMs) applied to diverse software development tasks, particularly focusing on "outer loop" activities such as bug fixing, code review, and documentation updates. Patched RTC extends the original Round-Trip Correctness method to work with any LLM and downstream task, offering a self-evaluating framework that measures consistency and robustness of model responses without human intervention. The study demonstrates a correlation between Patched RTC scores and task-specific accuracy metrics, presenting it as an alternative to the LLM-as-Judge paradigm for open-domain task evaluation. We implement Patched RTC in an open-source framework called patchwork, allowing for transparent evaluation during inference across various patchflows. Experiments comparing GPT-3.5 and GPT-4 models across different software development tasks reveal that Patched RTC effectively distinguishes model performance and task difficulty. The paper also explores the impact of consistency prompts on improving model accuracy, suggesting that Patched RTC can guide prompt refinement and model selection for complex software development workflows.

Automated Program Repair (APR) improves software reliability by generating patches for a buggy program automatically. Recent APR techniques leverage deep learning (DL) to build models to learn to generate patches from existing patches and code corpora. While promising, DL-based APR techniques suffer from the abundant syntactically or semantically incorrect patches in the patch space. These patches often disobey the syntactic and semantic domain knowledge of source code and thus cannot be the correct patches to fix a bug. We propose a DL-based APR approach KNOD, which incorporates domain knowledge to guide patch generation in a direct and comprehensive way. KNOD has two major novelties, including (1) a novel three-stage tree decoder, which directly generates Abstract Syntax Trees of patched code according to the inherent tree structure, and (2) a novel domain-rule distillation, which leverages syntactic and semantic rules and teacher-student distributions to explicitly inject the domain knowledge into the decoding procedure during both the training and inference phases. We evaluate KNOD on three widely-used benchmarks. KNOD fixes 72 bugs on the Defects4J v1.2, 25 bugs on the QuixBugs, and 50 bugs on the additional Defects4J v2.0 benchmarks, outperforming all existing APR tools.

Automated program repair (APR) aims to fix software bugs without human intervention and template-based APR has been widely investigated with promising results. However, it is challenging for template-based APR to select the appropriate donor code, which is an important repair ingredient for generating candidate patches. Inappropriate donor code may cause plausible but incorrect patch generation even with correct fix patterns, limiting the repair performance. In this paper, we aim to revisit template-based APR, and propose GAMMA, to directly leverage large pre-trained language models for donor code generation. Our main insight is that instead of retrieving donor code in the local buggy file, we can directly predict the correct code tokens based on the context code snippets and repair patterns by a cloze task. Specifically, (1) GAMMA revises a variety of fix templates from state-of-the-art template-based APR techniques (i.e., TBar) and transforms them into mask patterns. (2) GAMMA adopts a pre-trained language model to predict the correct code for masked code as a fill-in-the-blank task. The experimental results demonstrate that GAMMA correctly repairs 82 bugs on Defects4J-v1.2, which achieves 20.59\% (14 bugs) and 26.15\% (17 bugs) improvement over the previous state-of-the-art template-based approach TBar and learning-based one Recoder. Furthermore, GAMMA repairs 45 bugs and 22 bugs from the additional Defects4J-v2.0 and QuixBugs, indicating the generalizability of GAMMA in addressing the dataset overfitting issue. We also prove that adopting other pre-trained language models can provide substantial advancement, e.g., CodeBERT-based and ChatGPT-based GAMMA is able to fix 80 and 67 bugs on Defects4J-v1.2, indicating the scalability of GAMMA. Overall, our study highlights the promising future of adopting pre-trained models to generate correct patches on top of fix patterns.

Automatic program repair (APR) is crucial to reduce manual debugging efforts for developers and improve software reliability. While conventional search-based techniques typically rely on heuristic rules or a redundancy assumption to mine fix patterns, recent years have witnessed the surge of deep learning (DL) based approaches to automate the program repair process in a data-driven manner. However, their performance is often limited by a fixed set of parameters to model the highly complex search space of APR. To ease such burden on the parametric models, in this work, we propose a novel Retrieval-Augmented Patch Generation framework (RAP-Gen) by explicitly leveraging relevant fix patterns retrieved from a codebase of previous bug-fix pairs. Specifically, we build a hybrid patch retriever to account for both lexical and semantic matching based on the raw source code in a language-agnostic manner, which does not rely on any code-specific features. In addition, we adapt a code-aware language model CodeT5 as our foundation model to facilitate both patch retrieval and generation tasks in a unified manner. We adopt a stage-wise approach where the patch retriever first retrieves a relevant external bug-fix pair to augment the buggy input for the CodeT5 patch generator, which synthesizes a ranked list of repair patch candidates. Notably, RAP-Gen is a generic APR framework that can flexibly integrate different patch retrievers and generators to repair various types of bugs. We thoroughly evaluate RAP-Gen on three benchmarks in two programming languages, including the TFix benchmark in JavaScript, and Code Refinement and Defects4J benchmarks in Java, where the bug localization information may or may not be provided. Experimental results show that RAP-Gen significantly outperforms previous state-of-the-art approaches on all benchmarks, e.g., repairing 15 more bugs on 818 Defects4J bugs.

In rapid release development processes, patches that fix critical issues, or implement high-value features are often promoted directly from the development channel to a stabilization channel, potentially skipping one or more stabilization channels. This practice is called patch uplift. Patch uplift is risky, because patches that are rushed through the stabilization phase can end up introducing regressions in the code. This paper examines patch uplift operations at Mozilla, with the aim to identify the characteristics of uplifted patches that introduce regressions. Through statistical and manual analyses, we quantitatively and qualitatively investigate the reasons behind patch uplift decisions and the characteristics of uplifted patches that introduced regressions. Additionally, we interviewed three Mozilla release managers to understand organizational factors that affect patch uplift decisions and outcomes. Results show that most patches are uplifted because of a wrong functionality or a crash. Uplifted patches that lead to faults tend to have larger patch size, and most of the faults are due to semantic or memory errors in the patches. Also, release managers are more inclined to accept patch uplift requests that concern certain specific components, and-or that are submitted by certain specific developers.

With the increasing usage of open-source software (OSS) components, vulnerabilities embedded within them are propagated to a huge number of underlying applications. In practice, the timely application of security patches in downstream software is challenging. The main reason is that such patches do not explicitly indicate their security impacts in the documentation, which would be difficult to recognize for software maintainers and users. However, attackers can still identify these "secret" security patches by analyzing the source code and generate corresponding exploits to compromise not only unpatched versions of the current software, but also other similar software packages that may contain the same vulnerability due to code cloning or similar design/implementation logic. Therefore, it is critical to identify these secret security patches to enable timely fixes. To this end, we propose a deep learning-based defense system called PatchRNN to automatically identify secret security patches in OSS. Besides considering descriptive keywords in the commit message (i.e., at the text level), we leverage both syntactic and semantic features at the source-code level. To evaluate the performance of our system, we apply it on a large-scale real-world patch dataset and conduct a case study on a popular open-source web server software - NGINX. Experimental results show that the PatchRNN can successfully detect secret security patches with a low false positive rate.

Large Language Models (LLMs) achieve strong program repair performance but often suffer from over-editing, where excessive modifications overwrite correct code and hinder bug localization. We systematically quantify its impact and introduce precise repair task, which maximizes reuse of correct code while fixing only buggy parts. Building on this insight, we propose PRepair, a framework that mitigates over-editing and improves repair accuracy. PRepair has two components: Self-Breaking, which generates diverse buggy programs via controlled bug injection and min-max sampling, and Self-Repairing, which trains models with Edit-Aware Group Relative Policy Optimization (EA-GRPO) using an edit-aware reward to encourage minimal yet correct edits. Experiments show that PRepair improves repair precision by up to 31.4% under fix_1@1, a metric that jointly considers repair correctness and extent, and significantly increases decoding throughput when combined with speculative editing, demonstrating its potential for precise and practical code repair.

Large language models (LLMs) are effective for automated program repair, but plausible patches that pass the full test suite often rewrite more code than necessary, increasing review and maintenance costs. This over-editing is common because most bugs are localized, while standard supervised fine-tuning provides no explicit signal about which tokens should be preserved and which should be changed. We propose PAFT, a preservation-aware fine-tuning method for minimal-edit program repair. PAFT derives token-level preservation signals by aligning buggy and fixed code, combines them with full-sequence masking, and applies an edit-difficulty curriculum. Across Defects4J and HumanEval-Java, PAFT improves pass@1 by up to 65.6% over standard supervised fine-tuning (StdFT) while reducing average edit distance (AED) by up to 32.6%. On Defects4J with DeepSeek-Coder-6.7B, PAFT also outperforms AdaPatcher, a strong preference-based repair baseline, improving pass@1 from 5.9% to 10.1% while reducing median AED from 61.0 to 42.0. Overall, PAFT preserves stable context and concentrates edits on faulty regions, yielding smaller, more localized, plausible patches without inference-time search, reranking, or post-processing.

Deep learning and language models are increasingly dominating automated program repair research. While previous generate-and-validate approaches were able to find and use fix ingredients on a file or even project level, neural language models are limited to the code that fits their input window. In this work we investigate how important identifier ingredients are in neural program repair and present ScanFix, an approach that leverages an additional scanner model to extract identifiers from a bug's file and potentially project-level context. We find that lack of knowledge of far-away identifiers is an important cause of failed repairs. Augmenting repair model input with scanner-extracted identifiers yields relative improvements of up to 31%. However, ScanFix is outperformed by a model with a large input window (> 5k tokens). When passing ingredients from the ground-truth fix, improvements are even higher. This shows that, with refined extraction techniques, ingredient scanning, similar to fix candidate ranking, could have the potential to become an important subtask of future automated repair systems. At the same time, it also demonstrates that this idea is subject to Sutton's bitter lesson and may be rendered unnecessary by new code models with ever-increasing context windows.

Large Language Models (LLMs) have shown impressive capabilities in downstream software engineering tasks such as Automated Program Repair (APR). In particular, there has been a lot of research on repository-level issue-resolution benchmarks such as SWE-Bench. Although there has been significant progress on this topic, we notice that in the process of solving such issues, existing agentic systems tend to hyper-localize on immediately suspicious lines of code and fix them in isolation, without a deeper understanding of the issue semantics, code semantics, or execution semantics. Consequently, many existing systems generate patches that overfit to the user issue, even when a more general fix is preferable. To address this limitation, we introduce SemAgent, a novel workflow-based procedure that leverages issue, code, and execution semantics to generate patches that are complete - identifying and fixing all lines relevant to the issue. We achieve this through a novel pipeline that (a) leverages execution semantics to retrieve relevant context, (b) comprehends issue-semantics via generalized abstraction, (c) isolates code-semantics within the context of this abstraction, and (d) leverages this understanding in a two-stage architecture: a repair stage that proposes fine-grained fixes, followed by a reviewer stage that filters relevant fixes based on the inferred issue-semantics. Our evaluations show that our methodology achieves a solve rate of 44.66% on the SWEBench-Lite benchmark beating all other workflow-based approaches, and an absolute improvement of 7.66% compared to our baseline, which lacks such deep semantic understanding. We note that our approach performs particularly well on issues requiring multi-line reasoning (and editing) and edge-case handling, suggesting that incorporating issue and code semantics into APR pipelines can lead to robust and semantically consistent repairs.

Software vulnerabilities are increasing at an alarming rate. However, manual patching is both time-consuming and resource-intensive, while existing automated vulnerability repair (AVR) techniques remain limited in effectiveness. Recent advances in large language models (LLMs) have opened a new paradigm for AVR, demonstrating remarkable progress. To examine the capability of LLMs in AVR, several vulnerability benchmarks have been proposed recently. However, they still suffer from key limitations of outdated vulnerabilities, limited language coverage, unreliable patch validation, and insufficient reproducibility. To overcome these challenges, we introduce PATCHEVAL, a multilingual benchmark for Go, JavaScript, and Python, languages for which existing benchmarks remain unexplored. PATCHEVAL curates a dataset of 1,000 vulnerabilities drawn from CVEs reported between 2015 and 2025, covering 65 distinct CWEs. A subset of 230 CVEs is further equipped with runtime sandbox environments, enabling patch verification through both security tests and functionality tests. To provide a systematic comparison of LLM-based vulnerability repair, we evaluate a series of state-of-the-art LLMs and agents, presenting an in-depth analysis that empirically yields key insights to guide future research in AVR.

During Automated Program Repair (APR), it can be challenging to synthesize correct patches for real-world systems in general-purpose programming languages. Recent Large Language Models (LLMs) have been shown to be helpful "copilots" in assisting developers with various coding tasks, and have also been directly applied for patch synthesis. However, most LLMs treat programs as sequences of tokens, meaning that they are ignorant of the underlying semantics constraints of the target programming language. This results in plenty of statically invalid generated patches, impeding the practicality of the technique. Therefore, we propose Repilot, a framework to further copilot the AI "copilots" (i.e., LLMs) by synthesizing more valid patches during the repair process. Our key insight is that many LLMs produce outputs autoregressively (i.e., token by token), resembling human writing programs, which can be significantly boosted and guided through a Completion Engine. Repilot synergistically synthesizes a candidate patch through the interaction between an LLM and a Completion Engine, which 1) prunes away infeasible tokens suggested by the LLM and 2) proactively completes the token based on the suggestions provided by the Completion Engine. Our evaluation on a subset of the widely-used Defects4j 1.2 and 2.0 datasets shows that Repilot fixes 66 and 50 bugs, respectively, surpassing the best-performing baseline by 14 and 16 bugs fixed. More importantly, Repilot is capable of producing more valid and correct patches than the base LLM when given the same generation budget.

Automatic program repair (APR) is crucial to improve software reliability. Recently, neural machine translation (NMT) techniques have been used to fix software bugs automatically. While promising, these approaches have two major limitations. Their search space often does not contain the correct fix, and their search strategy ignores software knowledge such as strict code syntax. Due to these limitations, existing NMT-based techniques underperform the best template-based approaches. We propose CURE, a new NMT-based APR technique with three major novelties. First, CURE pre-trains a programming language (PL) model on a large software codebase to learn developer-like source code before the APR task. Second, CURE designs a new code-aware search strategy that finds more correct fixes by focusing on compilable patches and patches that are close in length to the buggy code. Finally, CURE uses a subword tokenization technique to generate a smaller search space that contains more correct fixes. Our evaluation on two widely-used benchmarks shows that CURE correctly fixes 57 Defects4J bugs and 26 QuixBugs bugs, outperforming all existing APR techniques on both benchmarks.

Large Language Models (LLMs) in Software Engineering (SE) can offer assistance for coding. To facilitate a rigorous evaluation of LLMs in practical coding contexts, Carlos et al. introduced the SWE-bench dataset, which comprises 2,294 real-world GitHub issues and their corresponding pull requests, collected from 12 widely used Python repositories. Several impressive LLM-based toolkits recently are developed and evaluated on this dataset. However, a systematic evaluation of the quality of SWE-bench remains missing. In this paper, we addressed this gap by presenting an empirical analysis of the SWE-bench dataset. We conducted a manual screening of instances where SWEAgent + GPT-4 successfully resolved issues by comparing the model-generated patches with the actual pull requests. SWE-Agent+GPT-4 was at the top of SWE-bench leaderboard during the time of our study. Our analysis reveals some critical issues with the SWE-bench dataset: 1) 32.67% of the successful patches involve cheating as the solutions were directly provided in the issue report or the comments. We refer to as solution leakage problem. 2) 31.08% of the passed patches are suspicious patches due to weak test cases, i.e., the tests were not adequate to verify the correctness of a patch. When we filtered out these problematic issues, the resolution rate of SWE-Agent+GPT-4 dropped from 12.47% to 3.97%. We also observed that the same data quality issues also exist in the two variants of SWE-bench, i.e., SWE-bench Lite and SWE-Bench Verified. In addition, over 94% of the issues were created before LLM's knowledge cutoff dates, posing potential data leakage issues.

Automated program repair (APR) using deep learning techniques has become an important area of research in recent years, aiming to automatically generate bug-fixing patches that can improve software reliability and maintainability. However, most existing methods either target a single language or require high computational resources to train multilingual models. In this paper, we propose T5APR, a novel neural program repair approach that provides a unified solution for bug fixing across multiple programming languages. T5APR leverages CodeT5, a powerful pre-trained text-to-text transformer model, and adopts a checkpoint ensemble strategy to improve patch recommendation. We conduct comprehensive evaluations on six well-known benchmarks in four programming languages (Java, Python, C, JavaScript), demonstrating T5APR's competitiveness against state-of-the-art techniques. T5APR correctly fixes 1,985 bugs, including 1,442 bugs that none of the compared techniques has fixed. We further support the effectiveness of our approach by conducting detailed analyses, such as comparing the correct patch ranking among different techniques. The findings of this study demonstrate the potential of T5APR for use in real-world applications and highlight the importance of multilingual approaches in the field of APR.

The SWE-Bench Verified leaderboard is approaching saturation, with the top system achieving 78.80%. However, we show that this performance is inflated. Our re-evaluation reveals that one in five "solved" patches from the top-30 agents are semantically incorrect, passing only because weak test suites fail to expose their errors. We present SWE-ABS, an adversarial framework that strengthens test suites through a two-stage pipeline: (1) coverage-driven augmentation using program slicing to target untested code regions, and (2) mutation-driven adversarial testing that synthesizes plausible but incorrect patches to expose semantic blind spots. On SWE-Bench Verified (500 instances), SWE-ABS strengthens 50.2% of instances, a 25.1x improvement over prior work, and rejects 19.71% of previously passing patches. As a result, the top agent's score decreases from 78.80% to 62.20%, leading to significant leaderboard reshuffling, with the previous top-ranked agent dropping to fifth place.

Code Agent development is an extremely active research area, where a reliable performance metric is critical for tracking progress and guiding new developments. This demand is underscored by the meteoric rise in popularity of SWE-Bench. This benchmark challenges code agents to generate patches addressing GitHub issues given the full repository as context. The correctness of generated patches is then evaluated by executing a human-written test suite extracted from the repository after the issue's resolution. However, constructing benchmarks like SWE-Bench requires substantial manual effort to set up historically accurate execution environments for testing. Crucially, this severely limits the number of considered repositories, e.g., just 12 for SWE-Bench. Considering so few repositories, selected for their popularity runs the risk of leading to a distributional mismatch, i.e., the measured performance may not be representative of real-world scenarios potentially misguiding development efforts. In this work, we address this challenge and introduce SetUpAgent, a fully automated system capable of historically accurate dependency setup, test execution, and result parsing. Using SetUpAgent, we generate two new datasets: (i) SWEE-Bench an extended version of SWE-Bench encompassing hundreds of repositories, and (ii) SWA-Bench a benchmark focusing on applications rather than libraries. Comparing these datasets to SWE-Bench with respect to their characteristics and code agent performance, we find significant distributional differences, including lower issue description quality and detail level, higher fix complexity, and most importantly up to 40% lower agent success rates.

Automated Program Repair (APR) can help developers automatically generate patches for bugs. Due to the impressive performance obtained using Large Pre-Trained Language Models (LLMs) on many code related tasks, researchers have started to directly use LLMs for APR. However, prior approaches simply repeatedly sample the LLM given the same constructed input/prompt created from the original buggy code, which not only leads to generating the same incorrect patches repeatedly but also miss the critical information in testcases. To address these limitations, we propose conversational APR, a new paradigm for program repair that alternates between patch generation and validation in a conversational manner. In conversational APR, we iteratively build the input to the model by combining previously generated patches with validation feedback. As such, we leverage the long-term context window of LLMs to not only avoid generating previously incorrect patches but also incorporate validation feedback to help the model understand the semantic meaning of the program under test. We evaluate 10 different LLM including the newly developed ChatGPT model to demonstrate the improvement of conversational APR over the prior LLM for APR approach.

Research shows that grammatical mistakes in a sentence can be corrected by translating it to another language and back using neural machine translation with language models. We investigate whether this correction capability of Large Language Models (LLMs) extends to Automatic Program Repair (APR). Current generative models for APR are pre-trained on source code and fine-tuned for repair. This paper proposes bypassing the fine-tuning step and using Round-Trip Translation (RTT): translation of code from one programming language to another programming or natural language, and back. We hypothesize that RTT with LLMs restores the most commonly seen patterns in code during pre-training, i.e., performs a regression toward the mean, which removes bugs as they are a form of noise w.r.t. the more frequent, natural, bug-free code in the training data. To test this hypothesis, we employ eight recent LLMs pre-trained on code, including the latest GPT versions, and four common program repair benchmarks in Java. We find that RTT with English as an intermediate language repaired 101 of 164 bugs with GPT-4 on the HumanEval-Java dataset. Moreover, 46 of these are unique bugs that are not repaired by other LLMs fine-tuned for APR. Our findings highlight the viability of round-trip translation with LLMs as a technique for automated program repair and its potential for research in software engineering. Keywords: automated program repair, large language model, machine translation

Continuous fuzzing platforms such as OSS-Fuzz uncover large numbers of vulnerabilities, yet the subsequent repair process remains largely manual. Unfortunately, existing Automated Vulnerability Repair (AVR) techniques -- including recent LLM-based systems -- are not directly applicable to continuous fuzzing. This is because these systems are designed and evaluated on a static, single-run benchmark setting, making them ill-suited for the diverse, noisy, and failure-prone environments in continuous fuzzing. To address these issues, we introduce PatchIsland, a system for Continuous Vulnerability Repair (CVR) that tightly integrates with continuous fuzzing pipelines. PatchIsland employs an ensemble of diverse LLM agents. By leveraging multiple LLM agents, PatchIsland can cover a wider range of settings (e.g., different projects, bug types, and programming languages) and also improve operational robustness. In addition, PatchIsland utilizes a two-phase patch-based deduplication to mitigate duplicate crashes and patches, which can be problematic in continuous fuzzing. In our internal evaluation, PatchIsland repaired 84 of 92 vulnerabilities, demonstrating strong repair capability. In the official AIxCC competition, the system operated with no human intervention in a fully autonomous environment and successfully patched 31 out of 43 vulnerabilities, achieving a repair rate of 72.1\%.

Large language models of code (Code-LLMs) have recently brought tremendous advances to code completion, a fundamental feature of programming assistance and code intelligence. However, most existing works ignore the possible presence of bugs in the code context for generation, which are inevitable in software development. Therefore, we introduce and study the buggy-code completion problem, inspired by the realistic scenario of real-time code suggestion where the code context contains potential bugs -- anti-patterns that can become bugs in the completed program. To systematically study the task, we introduce two datasets: one with synthetic bugs derived from semantics-altering operator changes (buggy-HumanEval) and one with realistic bugs derived from user submissions to coding problems (buggy-FixEval). We find that the presence of potential bugs significantly degrades the generation performance of the high-performing Code-LLMs. For instance, the passing rates of CodeGen-2B-mono on test cases of buggy-HumanEval drop more than 50% given a single potential bug in the context. Finally, we investigate several post-hoc methods for mitigating the adverse effect of potential bugs and find that there remains a large gap in post-mitigation performance.

Tremendous efforts have been devoted to automating software debugging, a time-consuming process involving fault localization and repair generation. Recently, Large Language Models (LLMs) have shown great potential in automated debugging. However, we identified three challenges posed to traditional and LLM-based debugging tools: 1) the upstream imperfection of fault localization affects the downstream repair, 2) the deficiency in handling complex logic errors, and 3) the ignorance of program contexts. In this context, we propose the first automated, unified debugging framework, FixAgent, via LLM agent synergy. FixAgent can perform end-to-end localization, repair, and analysis of bugs. Our insight is that LLMs can benefit from general software engineering principles recognized by human developers in debugging, such as rubber duck debugging, enabling a better understanding of program functionality and logic bugs. Hence, we create three designs inspired by rubber ducking to address these challenges. They are agent specialization and synergy, key variable tracking, and program context comprehension, which request LLMs to provide explicit explanations and force them to focus on crucial program logic information. Experiments on the widely used dataset QuixBugs show that FixAgent correctly fixes 79 out of 80 bugs, 9 of which have never been fixed. It also plausibly patches 1.9X more defects than the best-performing repair tool on CodeFlaws, even with no bug location information and fewer than 0.6% sampling times. On average, FixAgent increases about 20% plausible and correct fixes compared to its base model using different LLMs, showing the effectiveness of our designs. Moreover, the correctness rate of FixAgent reaches remarkably 97.26%, indicating that FixAgent can potentially overcome the overfitting issue of the existing approaches.

Many modern software projects evolve rapidly to incorporate new features and security patches. It is important for users to update their dependencies to safer versions, but many still use older, vulnerable package versions because upgrading can be difficult and may break their existing codebase. Software developers can mitigate this problem by backporting security patches to older releases. However, manually backporting is time-consuming and error-prone. The effectiveness of existing automated backporting techniques on general software remains unclear since they typically target only code-hunk or function-level patch porting scenarios and are evaluated with imperfect metrics. To facilitate the development and evaluation of automated backporting techniques, we introduce BackportBench, the first comprehensive benchmark suite for patch backporting problem. BackportBench is a multilingual benchmark that contains 202 patch backporting problems from PyPI, Maven, and npm, each with executable Docker environments and relevant test cases. We evaluated existing patch porting methods and LLM-based techniques that have the potential to adapt to this task using BackportBench. The results show that the agentic method has outperformed traditional patch porting methods, especially on cases that require logical and structural changes. However, the performance varies across different programming languages. Based on the findings, we draw several implications for researchers and software practitioners in future work on automated backporting.

Despite its crucial role in research experiments, code correctness is often presumed only on the basis of the perceived quality of results. This assumption comes with the risk of erroneous outcomes and potentially misleading findings. To address this issue, we posit that the current focus on reproducibility should go hand in hand with the emphasis on software quality. We present a case study in which we identify and fix three bugs in widely used implementations of the state-of-the-art Conformer architecture. Through experiments on speech recognition and translation in various languages, we demonstrate that the presence of bugs does not prevent the achievement of good and reproducible results, which however can lead to incorrect conclusions that potentially misguide future research. As a countermeasure, we propose a Code-quality Checklist and release pangoliNN, a library dedicated to testing neural models, with the goal of promoting coding best practices and improving research software quality within the NLP community.

The rapid advancement of bug-finding techniques has led to the discovery of more vulnerabilities than developers can reasonably fix, creating an urgent need for effective Automated Program Repair (APR) methods. However, the complexity of modern bugs often makes precise root cause analysis difficult and unreliable. To address this challenge, we propose crash-site repair to simplify the repair task while still mitigating the risk of exploitation. In addition, we introduce a template-guided patch generation approach that significantly reduces the token cost of Large Language Models (LLMs) while maintaining both efficiency and effectiveness. We implement our prototype system, WILLIAMT, and evaluate it against state-of-the-art APR tools. Our results show that, when combined with the top-performing agent CodeRover-S, WILLIAMT reduces token cost by 45.9% and increases the bug-fixing rate to 73.5% (+29.6%) on ARVO, a ground-truth open source software vulnerabilities benchmark. Furthermore, we demonstrate that WILLIAMT can function effectively even without access to frontier LLMs: even a local model running on a Mac M4 Mini achieves a reasonable repair rate. These findings highlight the broad applicability and scalability of WILLIAMT.

Correcting bugs using modern Automated Program Repair (APR) can be both time-consuming and resource-expensive. We describe a program repair approach that aims to improve the scalability of modern APR tools. The approach leverages program reduction in the form of program slicing to eliminate code irrelevant to fixing the bug, which improves the APR tool's overall performance. We investigate slicing's impact on all three phases of the repair process: fault localization, patch generation, and patch validation. Our empirical exploration finds that the proposed approach, on average, enhances the repair ability of the TBar APR tool, but we also discovered a few cases where it was less successful. Specifically, on examples from the widely used Defects4J dataset, we obtain a substantial reduction in median repair time, which falls from 80 minutes to just under 18 minutes. We conclude that program reduction can improve the performance of APR without degrading repair quality, but this improvement is not universal. A replication package is available via Zenodo at https://doi.org/10.5281/zenodo.13074333. Keywords: automated program repair, dynamic program slicing, fault localization, test-suite reduction, hybrid techniques.

Diffusion language models are structurally well-suited for iterative error correction, as their non-causal denoising dynamics allow arbitrary positions in a sequence to be revised. However, standard masked diffusion language model (MDLM) training fails to reliably induce this behavior, as models often cannot identify unreliable tokens in a complete input, rendering confidence-guided refinement ineffective. We study corrective behavior in diffusion language models, defined as the ability to assign lower confidence to incorrect tokens and iteratively refine them while preserving correct content. We show that this capability is not induced by conventional masked diffusion objectives and propose a correction-oriented post-training principle that explicitly supervises visible incorrect tokens, enabling error-aware confidence and targeted refinement. To evaluate corrective behavior, we introduce the Code Revision Benchmark (CRB), a controllable and executable benchmark for assessing error localization and in-place correction. Experiments on code revision tasks and controlled settings demonstrate that models trained with our approach substantially outperform standard MDLMs in correction scenarios, while also improving pure completion performance. Our code is publicly available at https://github.com/zhangshuibai/CDLM.

Large Language models (LLMs) can generate complicated source code from natural language prompts. However, LLMs can generate output that deviates from what the user wants, requiring supervision and editing. To support this process, we offer techniques to localize where generations might be misaligned from user intent. We first create a dataset of "Minimal Intent Aligning Patches" of repaired LLM generated programs. Each program uses test cases to verify correctness. After creating a dataset of programs, we measure how well various techniques can assign a well-calibrated probability to indicate which parts of code will be edited in a minimal patch (i.e., give a probability that corresponds with empirical odds it is edited). We compare white-box probing (where we propose a technique for efficient arbitrary-span querying), against black-box reflective and self-consistency based approaches. We find probes with a small supervisor model can achieve low calibration error and Brier Skill Score of approx 0.2 estimating edited lines on code generated by models many orders of magnitude larger. We discuss the generalizability of the techniques, and the connections to AI oversight and control, finding a probe trained only on code shows some signs of generalizing to natural language errors if new probability scaling is allowed.

Automated Program Repair (APR) has evolved significantly with the advent of Large Language Models (LLMs). Fine-tuning LLMs for program repair is a recent avenue of research, with many dimensions which have not been explored. Existing work mostly fine-tunes LLMs with naive code representations and is fundamentally limited in its ability to fine-tune larger LLMs. To address this problem, we propose RepairLLaMA, a novel program repair approach that combines 1) code representations for APR and 2) the state-of-the-art parameter-efficient LLM fine-tuning technique called LoRA. This results in RepairLLaMA producing a highly effective `program repair adapter' for fixing bugs with language models. Our experiments demonstrate the validity of both concepts. First, fine-tuning adapters with program repair specific code representations enables the model to use meaningful repair signals. Second, parameter-efficient fine-tuning helps fine-tuning to converge and contributes to the effectiveness of the repair adapter to fix data-points outside the fine-tuning data distribution. Overall, RepairLLaMA correctly fixes 125 Defects4J v2 and 82 HumanEval-Java bugs, outperforming all baselines.

Activation Patching is a method of directly computing causal attributions of behavior to model components. However, applying it exhaustively requires a sweep with cost scaling linearly in the number of model components, which can be prohibitively expensive for SoTA Large Language Models (LLMs). We investigate Attribution Patching (AtP), a fast gradient-based approximation to Activation Patching and find two classes of failure modes of AtP which lead to significant false negatives. We propose a variant of AtP called AtP*, with two changes to address these failure modes while retaining scalability. We present the first systematic study of AtP and alternative methods for faster activation patching and show that AtP significantly outperforms all other investigated methods, with AtP* providing further significant improvement. Finally, we provide a method to bound the probability of remaining false negatives of AtP* estimates.

To support software developers in finding and fixing software bugs, several automated program repair techniques have been introduced. Given a test suite, standard methods usually either synthesize a repair, or navigate a search space of software edits to find test-suite passing variants. Recent program repair methods are based on deep learning approaches. One of these novel methods, which is not primarily intended for automated program repair, but is still suitable for it, is ChatGPT. The bug fixing performance of ChatGPT, however, is so far unclear. Therefore, in this paper we evaluate ChatGPT on the standard bug fixing benchmark set, QuixBugs, and compare the performance with the results of several other approaches reported in the literature. We find that ChatGPT's bug fixing performance is competitive to the common deep learning approaches CoCoNut and Codex and notably better than the results reported for the standard program repair approaches. In contrast to previous approaches, ChatGPT offers a dialogue system through which further information, e.g., the expected output for a certain input or an observed error message, can be entered. By providing such hints to ChatGPT, its success rate can be further increased, fixing 31 out of 40 bugs, outperforming state-of-the-art.

Current open-weight large language models (LLMs) are prone to malicious finetuning attacks, which could compromise the safety alignment of LLMs with only a few steps of supervised finetuning (SFT) on poisoned datasets. Existing alignment-stage defenses are primarily designed to defend against attacks that use parameter-efficient finetuning methods. However, they fail to defend against stronger attacks that use full-parameter finetuning. In this paper, we propose Patcher, a method inspired by adversarial training and bi-level optimization, to combat such attacks. Patcher strengthens the simulated attack by scaling up the optimization steps in the adversarial loop, thus forcing the defender to find model parameters that are insensitive to stronger attacks. Furthermore, we propose an efficient parallel algorithm to implement Patcher, decreasing the wall-clock time of training while preserving Patcher's performance. Extensive experiments show that Patcher substantially improves the model's robustness compared to vanilla SFT alignment, and transfers to diverse attack scenarios and model sizes. Code is available at https://github.com/haomingwen/patcher.

Activation patching is a popular mechanistic interpretability technique, but has many subtleties regarding how it is applied and how one may interpret the results. We provide a summary of advice and best practices, based on our experience using this technique in practice. We include an overview of the different ways to apply activation patching and a discussion on how to interpret the results. We focus on what evidence patching experiments provide about circuits, and on the choice of metric and associated pitfalls.

Recently, self-supervised learning (SSL) was shown to be vulnerable to patch-based data poisoning backdoor attacks. It was shown that an adversary can poison a small part of the unlabeled data so that when a victim trains an SSL model on it, the final model will have a backdoor that the adversary can exploit. This work aims to defend self-supervised learning against such attacks. We use a three-step defense pipeline, where we first train a model on the poisoned data. In the second step, our proposed defense algorithm (PatchSearch) uses the trained model to search the training data for poisoned samples and removes them from the training set. In the third step, a final model is trained on the cleaned-up training set. Our results show that PatchSearch is an effective defense. As an example, it improves a model's accuracy on images containing the trigger from 38.2% to 63.7% which is very close to the clean model's accuracy, 64.6%. Moreover, we show that PatchSearch outperforms baselines and state-of-the-art defense approaches including those using additional clean, trusted data. Our code is available at https://github.com/UCDvision/PatchSearch

Agent benchmarks score submissions with outcome verifiers that are typically hand-written and brittle, leaving them open to reward hacking. We audit 1,968 tasks across five terminal-agent benchmarks and find 323 (16%) hackable by frontier models given only the task description. This corrupts both leaderboard rankings and RL training signal, yet the standard response is manual and reactive. We introduce the hacker-fixer loop, a method for building exploit-resistant verifiers without per-task manual patching. The loop alternates three LLM agents: a hacker tries to pass the verifier without solving the task, a fixer patches the verifier to reject each discovered exploit, and a solver confirms the patched verifier still admits legitimate solutions. The loop iterates: each patch reshapes what the verifier rewards, surfacing the next exploit. We further add verifier access, and let patches transfer across tasks, to broaden the exploits the loop discovers. On KernelBench, the loop drives the attack success rate from 62% to 0% on a held-out corpus of publicly reported exploits. We also find that weaker agents in the loop can defend against much stronger hackers: Gemini 3 Flash's loop drives the stronger Gemini 3.1 Pro and Claude Opus 4.7's attack success rate from 76% and 61% to 0% on KernelBench, and Gemini 3.1 Pro's from 39% to 17% on Terminal Bench across 77 tasks. We release Terminal Wrench (323 hackable environments, 3,632 hack trajectories) as a snapshot of the current attack surface, our patched verifiers, the exploits the loop discovered, and our implementation as a basis for future work.

In recent years, more vulnerabilities have been discovered every day, while manual vulnerability repair requires specialized knowledge and is time-consuming. As a result, many detected or even published vulnerabilities remain unpatched, thereby increasing the exposure of software systems to attacks. Recent advancements in agents based on Large Language Models have demonstrated their increasing capabilities in code understanding and generation, which can be promising to achieve automated vulnerability repair. However, the effectiveness of agents based on static information retrieval is still not sufficient for patch generation. To address the challenge, we propose a program repair agent called VulDebugger that fully utilizes both static and dynamic context, and it debugs programs in a manner akin to humans. The agent inspects the actual state of the program via the debugger and infers expected states via constraints that need to be satisfied. By continuously comparing the actual state with the expected state, it deeply understands the root causes of the vulnerabilities and ultimately accomplishes repairs. We experimentally evaluated VulDebugger on 50 real-life projects. With 60.00% successfully fixed, VulDebugger significantly outperforms state-of-the-art approaches for vulnerability repair.

Large language models (LLMs) have shown impressive effectiveness in various software engineering tasks, including automated program repair (APR). In this study, we take a deep dive into automated bug fixing utilizing LLMs. In contrast to many deep learning-based APR methods that assume known bug locations, rely on line-level localization tools, or address bug prediction and fixing in one step, our approach uniquely employs LLMs to predict bug location at the token level and subsequently utilizes them for bug fixing. This methodological separation of bug localization and fixing using different LLMs enables effective integration of diverse contextual information and improved incorporation of inductive biases. We introduce Toggle: Token-Granulated Bug Localization and Repair, a comprehensive program repair framework that integrates a bug localization model, an adjustment unit, and a bug-fixing model. Toggle takes a buggy function as input and generates a complete corrected function. We investigate various styles of prompting to the bug fixing model to identify the most effective prompts that better utilize the inductive bias and significantly outperform others. Toggle achieves the new state-of-the-art (SOTA) performance on the CodeXGLUE code refinement benchmark, and exhibits better and comparable performance on several other widely-used APR datasets, including Defects4J.

LLM-based code agents treat repositories as unstructured text, applying edits through brittle string matching that frequently fails due to formatting drift or ambiguous patterns. We propose reframing the codebase as a structured action space where agents operate on named AST entities rather than text spans. Our framework, CODESTRUCT, provides readCode for retrieving complete syntactic units and editCode for applying syntax-validated transformations to semantic program elements. Evaluated on SWE-Bench Verified across six LLMs, CODESTRUCT improves Pass@1 accuracy by 1.2-5.0% while reducing token consumption by 12-38% for most models. Models that frequently fail to produce valid patches under text-based interfaces benefit most: GPT-5-nano improves by 20.8% as empty-patch failures drop from 46.6% to 7.2%. On CodeAssistBench, we observe consistent accuracy gains (+0.8-4.4%) with cost reductions up to 33%. Our results show that structure-aware interfaces offer a more reliable foundation for code agents.

Large Language Models (LLMs) often generate code with subtle but critical bugs, especially for complex tasks. Existing automated repair methods typically rely on superficial pass/fail signals, offering limited visibility into program behavior and hindering precise error localization. In addition, without a way to learn from prior failures, repair processes often fall into repetitive and inefficient cycles. To overcome these challenges, we present TraceCoder, a collaborative multi-agent framework that emulates the observe-analyze-repair process of human experts. The framework first instruments the code with diagnostic probes to capture fine-grained runtime traces, enabling deep insight into its internal execution. It then conducts causal analysis on these traces to accurately identify the root cause of the failure. This process is further enhanced by a novel Historical Lesson Learning Mechanism (HLLM), which distills insights from prior failed repair attempts to inform subsequent correction strategies and prevent recurrence of similar mistakes. To ensure stable convergence, a Rollback Mechanism enforces that each repair iteration constitutes a strict improvement toward the correct solution. Comprehensive experiments across multiple benchmarks show that TraceCoder achieves up to a 34.43\% relative improvement in Pass@1 accuracy over existing advanced baselines. Ablation studies verify the significance of each system component, with the iterative repair process alone contributing a 65.61\% relative gain in accuracy. Furthermore, TraceCoder significantly outperforms leading iterative methods in terms of both accuracy and cost-efficiency.

Automated Program Repair (APR) attempts to fix software bugs without human intervention, which plays a crucial role in software development and maintenance. Recently, with the advances in Large Language Models (LLMs), a rapidly increasing number of APR techniques have been proposed with remarkable performance. However, existing LLM-based APR techniques typically adopt trial-and-error strategies, which suffer from two major drawbacks: (1) inherently limited patch effectiveness due to local exploration, and (2) low search efficiency due to redundant exploration. In this paper, we propose APRMCTS, which uses iterative tree search to improve LLM-based APR. APRMCTS incorporates Monte Carlo Tree Search (MCTS) into patch searching by performing a global evaluation of the explored patches and selecting the most promising one for subsequent refinement and generation. APRMCTS effectively resolves the problems of falling into local optima and thus helps improve the efficiency of patch searching. Our experiments on 835 bugs from Defects4J demonstrate that, when integrated with GPT-3.5, APRMCTS can fix a total of 201 bugs, which outperforms all state-of-the-art baselines. Besides, APRMCTS helps GPT-4o-mini, GPT-3.5, Yi-Coder-9B, and Qwen2.5-Coder-7B to fix 30, 27, 37, and 28 more bugs, respectively. More importantly, APRMCTS boasts a significant performance advantage while employing small patch size (16 and 32), notably fewer than the 500 and 10,000 patches adopted in previous studies. In terms of cost, compared to existing state-of-the-art LLM-based APR methods, APRMCTS has time and monetary costs of less than 20% and 50%, respectively. Our extensive study demonstrates that APRMCTS exhibits good effectiveness and efficiency, with particular advantages in addressing complex bugs.

Accurate identification of software vulnerabilities is crucial for system integrity. Vulnerability datasets, often derived from the National Vulnerability Database (NVD) or directly from GitHub, are essential for training machine learning models to detect these security flaws. However, these datasets frequently suffer from significant noise, typically 40% to 75%, due primarily to the automatic and indiscriminate labeling of all changes in vulnerability-fixing commits (VFCs) as vulnerability-related. This misclassification occurs because not all changes in a commit aimed at fixing vulnerabilities pertain to security threats; many are routine updates like bug fixes or test improvements. This paper introduces the first methodology that uses the Large Language Model (LLM) with a heuristic enhancement to automatically identify vulnerability-fixing changes from VFCs, achieving an F1-score of 0.82. VulSifter was applied to a large-scale study, where we conducted a crawl of 127,063 repositories on GitHub, resulting in the acquisition of 5,352,105 commits. VulSifter involves utilizing an LLM to comprehend code semantics and contextual information, while applying heuristics to filter out unrelated changes. We then developed CleanVul, a high-quality dataset comprising 8,198 functions using our LLM heuristic enhancement approach, demonstrating Correctness (90.6%) comparable to established datasets such as SVEN and PrimeVul. To evaluate the CleanVul dataset, we conducted experiments focusing on fine-tuning various LLMs on CleanVul and other high-quality datasets. Evaluation results reveal that LLMs fine-tuned on CleanVul not only exhibit enhanced accuracy but also superior generalization capabilities compared to those trained on uncleaned datasets. Specifically, models trained on CleanVul and tested on PrimeVul achieve accuracy higher than those trained and tested exclusively on PrimeVul.

Activation patching is a standard method in mechanistic interpretability for localizing the components of a model responsible for specific behaviors, but it is computationally expensive to apply at scale. Attribution patching offers a faster, gradient-based approximation, yet suffers from noise and reduced reliability in deep, highly non-linear networks. In this work, we introduce Relevance Patching (RelP), which replaces the local gradients in attribution patching with propagation coefficients derived from Layer-wise Relevance Propagation (LRP). LRP propagates the network's output backward through the layers, redistributing relevance to lower-level components according to local propagation rules that ensure properties such as relevance conservation or improved signal-to-noise ratio. Like attribution patching, RelP requires only two forward passes and one backward pass, maintaining computational efficiency while improving faithfulness. We validate RelP across a range of models and tasks, showing that it more accurately approximates activation patching than standard attribution patching, particularly when analyzing residual stream and MLP outputs in the Indirect Object Identification (IOI) task. For instance, for MLP outputs in GPT-2 Large, attribution patching achieves a Pearson correlation of 0.006, whereas RelP reaches 0.956, highlighting the improvement offered by RelP. Additionally, we compare the faithfulness of sparse feature circuits identified by RelP and Integrated Gradients (IG), showing that RelP achieves comparable faithfulness without the extra computational cost associated with IG.

Optimizing the performance of large-scale software repositories demands expertise in code reasoning and software engineering (SWE) to reduce runtime while preserving program correctness. However, most benchmarks emphasize what to fix rather than how to fix code. We introduce SWE-fficiency, a benchmark for evaluating repository-level performance optimization on real workloads. Our suite contains 498 tasks across nine widely used data-science, machine-learning, and HPC repositories (e.g., numpy, pandas, scipy): given a complete codebase and a slow workload, an agent must investigate code semantics, localize bottlenecks and relevant tests, and produce a patch that matches or exceeds expert speedup while passing the same unit tests. To enable this how-to-fix evaluation, our automated pipeline scrapes GitHub pull requests for performance-improving edits, combining keyword filtering, static analysis, coverage tooling, and execution validation to both confirm expert speedup baselines and identify relevant repository unit tests. Empirical evaluation of state-of-the-art agents reveals significant underperformance. On average, agents achieve less than 0.15x the expert speedup: agents struggle in localizing optimization opportunities, reasoning about execution across functions, and maintaining correctness in proposed edits. We release the benchmark and accompanying data pipeline to facilitate research on automated performance engineering and long-horizon software reasoning.

Large Language Models (LLMs) have shown tremendous promise in automated software engineering. In this paper, we investigate the opportunities of LLMs for automatic regression test generation for programs that take highly structured, human-readable inputs, such as XML parsers or JavaScript interpreters. Concretely, we explore the following regression test generation scenarios for such programs that have so far been difficult to test automatically in the absence of corresponding input grammars: bullet Bug finding. Given a code change (e.g., a commit or pull request), our LLM-based approach generates a test case with the objective of revealing any bugs that might be introduced if that change is applied. bullet Patch testing. Given a patch, our LLM-based approach generates a test case that fails before but passes after the patch. This test can be added to the regression test suite to catch similar bugs in the future. We implement Cleverest, a feedback-directed, zero-shot LLM-based regression test generation technique, and evaluate its effectiveness on 22 commits to three subject programs: Mujs, Libxml2, and Poppler. For programs using more human-readable file formats, like XML or JavaScript, we found Cleverest performed very well. It generated easy-to-understand bug-revealing or bug-reproduction test cases for the majority of commits in just under three minutes -- even when only the code diff or commit message (unless it was too vague) was given. For programs with more compact file formats, like PDF, as expected, it struggled to generate effective test cases. However, the LLM-supplied test cases are not very far from becoming effective (e.g., when used as a seed by a greybox fuzzer or as a starting point by the developer).

Open-Source Software (OSS) vulnerabilities bring great challenges to the software security and pose potential risks to our society. Enormous efforts have been devoted into automated vulnerability detection, among which deep learning (DL)-based approaches have proven to be the most effective. However, the current labeled data present the following limitations: (1) Tangled Patches: Developers may submit code changes unrelated to vulnerability fixes within patches, leading to tangled patches. (2) Lacking Inter-procedural Vulnerabilities: The existing vulnerability datasets typically contain function-level and file-level vulnerabilities, ignoring the relations between functions, thus rendering the approaches unable to detect the inter-procedural vulnerabilities. (3) Outdated Patches: The existing datasets usually contain outdated patches, which may bias the model during training. To address the above limitations, in this paper, we propose an automated data collection framework and construct the first repository-level high-quality vulnerability dataset named ReposVul. The proposed framework mainly contains three modules: (1) A vulnerability untangling module, aiming at distinguishing vulnerability-fixing related code changes from tangled patches, in which the Large Language Models (LLMs) and static analysis tools are jointly employed. (2) A multi-granularity dependency extraction module, aiming at capturing the inter-procedural call relationships of vulnerabilities, in which we construct multiple-granularity information for each vulnerability patch, including repository-level, file-level, function-level, and line-level. (3) A trace-based filtering module, aiming at filtering the outdated patches, which leverages the file path trace-based filter and commit time trace-based filter to construct an up-to-date dataset.

Patch backporting, the process of migrating mainline security patches to older branches, is an essential task in maintaining popular open-source projects (e.g., Linux kernel). However, manual backporting can be labor-intensive, while existing automated methods, which heavily rely on predefined syntax or semantic rules, often lack agility for complex patches. In this paper, we introduce PORTGPT, an LLM-agent for end-to-end automation of patch backporting in real-world scenarios. PORTGPT enhances an LLM with tools to access code on-demand, summarize Git history, and revise patches autonomously based on feedback (e.g., from compilers), hence, simulating human-like reasoning and verification. PORTGPT achieved an 89.15% success rate on existing datasets (1815 cases), and 62.33% on our own dataset of 146 complex cases, both outperforms state-of-the-art of backporting tools. We contributed 9 backported patches from PORTGPT to the Linux kernel community and all patches are now merged.

Vision Language Models (VLMs) are improving quickly, but standard benchmarks can hide systematic failures that reduce real world trust. We introduce MATS (Multimodal Audit for Truthful Spatialization), a compact behavioral audit that measures whether models reject visually contradicted statements, and two metrics Spatial Consistency Score (SCS) and Incorrect Agreement Rate (IAR). Instruction tuned generative VLMs (LLaVA 1.5, QwenVLchat) exhibit very low SCS and high IAR, while contrastive encoders (CLIP, SigLIP) are far more robust. Activation patching causally localizes failure loci (mid to late cross attention for generative models, pooled projection components for contrastive models) and suggests concrete repair paths.

Automated program repair (APR) aims to help developers improve software reliability by generating patches for buggy programs. Although many code language models (CLM) are developed and effective in many software tasks such as code completion, there has been little comprehensive, in-depth work to evaluate CLMs' fixing capabilities and to fine-tune CLMs for the APR task. Firstly, this work is the first to evaluate ten CLMs on four APR benchmarks, which shows that surprisingly, the best CLM, as is, fixes 72% more bugs than the state-of-the-art deep-learning (DL)-based APR techniques. Secondly, one of the four APR benchmarks was created by us in this paper to avoid data leaking for a fair evaluation. Thirdly, it is the first work to fine-tune CLMs with APR training data, which shows that fine-tuning brings 31%-1,267% improvement to CLMs and enables them to fix 46%-164% more bugs than existing DL-based APR techniques. Fourthly, this work studies the impact of buggy lines, showing that CLMs, as is, cannot make good use of the buggy lines to fix bugs, yet fine-tuned CLMs could potentially over-rely on buggy lines. Lastly, this work analyzes the size, time, and memory efficiency of different CLMs. This work shows promising directions for the APR domain, such as fine-tuning CLMs with APR-specific designs, and also raises awareness of fair and comprehensive evaluations of CLMs and calls for more transparent reporting of open-source repositories used in the pre-training data to address the data leaking problem.

Many recent language model (LM) interpretability studies have adopted the circuits framework, which aims to find the minimal computational subgraph, or circuit, that explains LM behavior on a given task. Most studies determine which edges belong in a LM's circuit by performing causal interventions on each edge independently, but this scales poorly with model size. Edge attribution patching (EAP), gradient-based approximation to interventions, has emerged as a scalable but imperfect solution to this problem. In this paper, we introduce a new method - EAP with integrated gradients (EAP-IG) - that aims to better maintain a core property of circuits: faithfulness. A circuit is faithful if all model edges outside the circuit can be ablated without changing the model's performance on the task; faithfulness is what justifies studying circuits, rather than the full model. Our experiments demonstrate that circuits found using EAP are less faithful than those found using EAP-IG, even though both have high node overlap with circuits found previously using causal interventions. We conclude more generally that when using circuits to compare the mechanisms models use to solve tasks, faithfulness, not overlap, is what should be measured.

Large language models (LLMs) have significantly advanced autonomous software engineering, leading to a growing number of software engineering agents that assist developers in automatic program repair. Issue localization forms the basis for accurate patch generation. However, because of limitations caused by the context window length of LLMs, existing issue localization methods face challenges in balancing concise yet effective contexts and adequately comprehensive search spaces. In this paper, we introduce CoSIL, an LLM driven, simple yet powerful function level issue localization method without training or indexing. CoSIL reduces the search space through module call graphs, iteratively searches the function call graph to obtain relevant contexts, and uses context pruning to control the search direction and manage contexts effectively. Importantly, the call graph is dynamically constructed by the LLM during search, eliminating the need for pre-parsing. Experiment results demonstrate that CoSIL achieves a Top-1 localization success rate of 43 percent and 44.6 percent on SWE bench Lite and SWE bench Verified, respectively, using Qwen2.5 Coder 32B, outperforming existing methods by 8.6 to 98.2 percent. When CoSIL is applied to guide the patch generation stage, the resolved rate further improves by 9.3 to 31.5 percent.

LLM-based multi-agent pipelines flip from correct to incorrect answers under simulated peer disagreement at rates we term yield, a vulnerability widely attributed to RLHF-induced sycophancy. We test this attribution across four model families and find it largely wrong: pretrained base models exhibit the same substitution pattern as their Instruct variants, averaging higher yield than Instruct. Using activation patching, we localize the corruption to a narrow mid-layer window where attention carries the causal weight and MLP contribution is negligible; patching above this window restores 96% of the clean-to-pressured P(correct) gap. The attack surface decomposes into two independent factors (channel framing and consensus strength) whose interaction produces a 47.5 percentage-point yield gap at majority consensus, preserved across jury sizes N in {4, 5, 6}. Two converging activation-space interventions show that pressure suppresses clean-reasoning features rather than activating a new sycophancy circuit. A single correctly-arguing dissenter reduces yield by 54-73 percentage points across all framings tested, whereas the strongest prompt-level defense fails on attack variants outside its design surface. Mitigations should target the mechanism, structured dissent at the pipeline level, rather than prompt-level defenses.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

Automated generate-and-validate (G&V) program repair techniques typically rely on hard-coded rules, only fix bugs following specific patterns, and are hard to adapt to different programming languages. We propose ENCORE, a new G&V technique, which uses ensemble learning on convolutional neural machine translation (NMT) models to automatically fix bugs in multiple programming languages. We take advantage of the randomness in hyper-parameter tuning to build multiple models that fix different bugs and combine them using ensemble learning. This new convolutional NMT approach outperforms the standard long short-term memory (LSTM) approach used in previous work, as it better captures both local and long-distance connections between tokens. Our evaluation on two popular benchmarks, Defects4J and QuixBugs, shows that ENCORE fixed 42 bugs, including 16 that have not been fixed by existing techniques. In addition, ENCORE is the first G&V repair technique to be applied to four popular programming languages (Java, C++, Python, and JavaScript), fixing a total of 67 bugs across five benchmarks.

Commit messages are a valuable resource in comprehension of software evolution, since they provide a record of changes such as feature additions and bug repairs. Unfortunately, programmers often neglect to write good commit messages. Different techniques have been proposed to help programmers by automatically writing these messages. These techniques are effective at describing what changed, but are often verbose and lack context for understanding the rationale behind a change. In contrast, humans write messages that are short and summarize the high level rationale. In this paper, we adapt Neural Machine Translation (NMT) to automatically "translate" diffs into commit messages. We trained an NMT algorithm using a corpus of diffs and human-written commit messages from the top 1k Github projects. We designed a filter to help ensure that we only trained the algorithm on higher-quality commit messages. Our evaluation uncovered a pattern in which the messages we generate tend to be either very high or very low quality. Therefore, we created a quality-assurance filter to detect cases in which we are unable to produce good messages, and return a warning instead.

Interactive LLM agents are becoming part of daily work, but they do not reliably become easier to work with over time: a correction remembered in one session may still be violated in the next. We study this gap between preference access and preference compliance. In tasks derived from anonymized real-user friction cases, Mem0 memory still leaves 57.5% of applicable preference checks violated. We introduce Test-time Rule Acquisition and Compiled Enforcement (TRACE), a drop-in skill-layer pipeline for coding-agent runtimes that mines user corrections, rewrites them as atomic rules, and compiles them into runtime checks that must pass before an agent completes future tasks. Unlike runtime checks written ahead of time by developers, TRACE skills come from the user's own chat corrections. We evaluate TRACE with simulated user-in-the-loop experiments on ClawArena coding-agent tasks and MemoryArena-derived memory-intensive tasks. On ClawArena, TRACE reduces held-out preference violation from 100.0% to 37.6% on in-distribution tasks and from 100.0% to 2.0% on out-of-distribution tasks. On MemoryArena-derived tasks, TRACE reduces in-distribution violation from 100.0% to 60.5% while matching or exceeding the strongest memory baseline on task pass. These results suggest that compiling corrections into runtime enforcement can address a repeated-friction failure mode that memory alone does not reliably solve, reducing the need for users to restate the same correction across future sessions. Experiment code is available at https://github.com/YujunZhou/TRACE_exp, and the deployable skill is available at https://github.com/YujunZhou/tellonce.

Language Models (LMs) have become widely used in software engineering, especially for tasks such as code generation, where they are referred to as code LMs. These models have proven effective in generating code, making it easier for developers to automate coding activities. However, research has highlighted a significant limitation: despite their effectiveness, LMs often produce code that is incorrect, buggy, or not fully functional. Updating these models with limited data can be prohibitively challenging, yet it is essential to maximize their utility. This may require hot-fix techniques (updating models with limited data) to resolve. In this paper, we propose Model Improvement via Neuron Targeting (MINT), a novel approach for repairing code LMs. MINT leverages the semantic property of language models to perform neuron-level repairs in a novel way. Further, by analyzing the relationships between the model's latent representations, the incorrect outputs, and the desired outputs, MINT determines which neurons are worth updating. This approach ensures that only the neurons crucial to the model's failure are targeted, avoiding unnecessary changes and allowing for a more efficient and precise repair process. MINT is effective, efficient, and reliable, capable of correcting a neural model by patching a minimum number of neurons (usually one or two neurons). Our approach is evaluated on three coding tasks: line-level code generation, shellcode generation, and intent-to-bash translation. The experimental results demonstrate that the proposed approach significantly outperforms the state-of-the-art in both effectiveness and efficiency measures. In addition, we analyze and discuss the side effects of model repair techniques, including the balance between generalization and specificity, and the performance after multiple repairs in succession.

Unlike code completion, debugging requires localizing faults and applying targeted edits. We observe that frontier LLMs often regenerate correct but over-edited solutions during debugging. To evaluate how far LLMs are from precise debugging, we introduce the Precise Debugging Benchmark (PDB) framework, which automatically converts any coding dataset into a debugging benchmark with precision-aware evaluation. PDB generates buggy programs by synthesizing verified atomic bugs and composing them into multi-bug programs. We define two novel metrics, edit-level precision and bug-level recall, which measures how many necessary edits are made and how many bugs are resolved. We release two evaluation benchmarks: PDB-Single-Hard on single-line bugs, and PDB-Multi on multi-line bugs. Experiments show that frontier models, such as GPT-5.1-Codex and DeepSeek-V3.2-Thinking, achieve unit-test pass rates above 76% but exhibit precision below 45%, even when explicitly instructed to perform minimal debugging. Finally, we show that iterative and agentic debugging strategies do not substantially improve precision or recall, highlighting the need to rethink post-training pipelines for coding models.

Most programmers make mistakes when writing code. Some of these mistakes are small and require few edits to the original program -- a class of errors recently termed last mile mistakes. These errors break the flow for experienced developers and can stump novice programmers. Existing automated repair techniques targeting this class of errors are language-specific and do not easily carry over to new languages. Transferring symbolic approaches requires substantial engineering and neural approaches require data and retraining. We introduce RING, a multilingual repair engine powered by a large language model trained on code (LLMC) such as Codex. Such a multilingual engine enables a flipped model for programming assistance, one where the programmer writes code and the AI assistance suggests fixes, compared to traditional code suggestion technology. Taking inspiration from the way programmers manually fix bugs, we show that a prompt-based strategy that conceptualizes repair as localization, transformation, and candidate ranking, can successfully repair programs in multiple languages with minimal effort. We present the first results for such a multilingual repair engine by evaluating on 6 different languages and comparing performance to language-specific repair engines. We show that RING can outperform language-specific repair engines for three of these languages.

The issue-resolving task, where a model generates patches to fix real-world bugs, has emerged as a critical benchmark for evaluating the capabilities of large language models (LLMs). While SWE-bench and its variants have become standard in this domain, they suffer from key limitations: they have not been updated since their initial releases, cover a narrow set of repositories, and depend heavily on manual effort for instance construction and environment setup. These factors hinder scalability and introduce risks of overfitting and data contamination. In this work, we present SWE-bench-Live, a live-updatable benchmark designed to overcome these challenges. Our initial release consists of 1,319 tasks derived from real GitHub issues created since 2024, spanning 93 repositories. Each task is accompanied by a dedicated Docker image to ensure reproducible execution. Central to our benchmark is \method, an automated curation pipeline that streamlines the entire process from instance creation to environment setup, removing manual bottlenecks and enabling scalability and continuous updates. We evaluate a range of state-of-the-art agent frameworks and LLMs on SWE-bench-Live, revealing a substantial performance gap compared to static benchmarks like SWE-bench, even under controlled evaluation conditions. To better understand this discrepancy, we perform detailed analyses across repository origin, issue recency, and task difficulty. By providing a fresh, diverse, and executable benchmark grounded in live repository activity, SWE-bench-Live facilitates rigorous, contamination-resistant evaluation of LLMs and agents in dynamic, real-world software development settings.

These days deep neural networks are ubiquitously used in a wide range of tasks, from image classification and machine translation to face identification and self-driving cars. In many applications, a single model error can lead to devastating financial, reputational and even life-threatening consequences. Therefore, it is crucially important to correct model mistakes quickly as they appear. In this work, we investigate the problem of neural network editing - how one can efficiently patch a mistake of the model on a particular sample, without influencing the model behavior on other samples. Namely, we propose Editable Training, a model-agnostic training technique that encourages fast editing of the trained model. We empirically demonstrate the effectiveness of this method on large-scale image classification and machine translation tasks.

AI-driven program repair uses AI models to repair buggy software by producing patches. Rapid advancements in AI surely impact state-of-the-art performance of program repair. Yet, grasping this progress requires frequent and standardized evaluations. We propose RepairBench, a novel leaderboard for AI-driven program repair. The key characteristics of RepairBench are: 1) it is execution-based: all patches are compiled and executed against a test suite, 2) it assesses frontier models in a frequent and standardized way. RepairBench leverages two high-quality benchmarks, Defects4J and GitBug-Java, to evaluate frontier models against real-world program repair tasks. We publicly release the evaluation framework of RepairBench. We will update the leaderboard as new frontier models are released.

The task of issue resolving is to modify a codebase to generate a patch that addresses a given issue. However, existing benchmarks, such as SWE-bench, focus almost exclusively on Python, making them insufficient for evaluating Large Language Models (LLMs) across diverse software ecosystems. To address this, we introduce a multilingual issue-resolving benchmark, called Multi-SWE-bench, covering Java, TypeScript, JavaScript, Go, Rust, C, and C++. It includes a total of 1,632 high-quality instances, which were carefully annotated from 2,456 candidates by 68 expert annotators, ensuring that the benchmark can provide an accurate and reliable evaluation. Based on Multi-SWE-bench, we evaluate a series of state-of-the-art models using three representative methods (Agentless, SWE-agent, and OpenHands) and present a comprehensive analysis with key empirical insights. In addition, we launch a Multi-SWE-RL open-source community, aimed at building large-scale reinforcement learning (RL) training datasets for issue-resolving tasks. As an initial contribution, we release a set of 4,723 well-structured instances spanning seven programming languages, laying a solid foundation for RL research in this domain. More importantly, we open-source our entire data production pipeline, along with detailed tutorials, encouraging the open-source community to continuously contribute and expand the dataset. We envision our Multi-SWE-bench and the ever-growing Multi-SWE-RL community as catalysts for advancing RL toward its full potential, bringing us one step closer to the dawn of AGI.

As machine learning tools progress, the inevitable question arises: How can machine learning help us write better code? With significant progress being achieved in natural language processing with models like GPT-3 and Bert, the applications of natural language processing techniques to code are starting to be explored. Most of the research has been focused on automatic program repair (APR), and while the results on synthetic or highly filtered datasets are promising, such models are hard to apply in real-world scenarios because of inadequate bug localization. We propose BigIssue: a benchmark for realistic bug localization. The goal of the benchmark is two-fold. We provide (1) a general benchmark with a diversity of real and synthetic Java bugs and (2) a motivation to improve bug localization capabilities of models through attention to the full repository context. With the introduction of BigIssue, we hope to advance the state of the art in bug localization, in turn improving APR performance and increasing its applicability to the modern development cycle.

Large language models (LLMs) are transforming automated program repair (APR) through agent-based approaches that localize bugs, generate patches, and verify fixes. However, the lack of high-quality, scalable training datasets, especially those with verifiable outputs and intermediate reasoning traces-limits progress, particularly for open-source models. In this work, we present SWE-Synth, a framework for synthesizing realistic, verifiable, and process-aware bug-fix datasets at the repository level. SWE-Synth leverages LLM agents to simulate debugging workflows, producing not only bug-fix pairs but also test cases and structured repair trajectories. Compared to manually curated datasets, our method scales with minimal human effort while preserving contextual richness and correctness. Experiments show that models trained on SWE-Synth outperform those trained on real-world datasets by 2.3% on SWE-Bench Lite. Our results highlight the potential of synthetic, agent-generated data to advance the state of the art in APR and software engineering automation.

Issue resolution has made remarkable progress thanks to the advanced reasoning capabilities of large language models (LLMs). Recently, agent-based frameworks such as SWE-agent have further advanced this progress by enabling autonomous, tool-using agents to tackle complex software engineering tasks. While existing agent-based issue resolution approaches are primarily based on agents' independent explorations, they often get stuck in local solutions and fail to identify issue patterns that span across different parts of the codebase. To address this limitation, we propose SWE-Debate, a competitive multi-agent debate framework that encourages diverse reasoning paths and achieves more consolidated issue localization. SWE-Debate first creates multiple fault propagation traces as localization proposals by traversing a code dependency graph. Then, it organizes a three-round debate among specialized agents, each embodying distinct reasoning perspectives along the fault propagation trace. This structured competition enables agents to collaboratively converge on a consolidated fix plan. Finally, this consolidated fix plan is integrated into an MCTS-based code modification agent for patch generation. Experiments on the SWE-bench benchmark show that SWE-Debate achieves new state-of-the-art results in open-source agent frameworks and outperforms baselines by a large margin.

We present Code Comparison Tuning (CCT), a simple and effective tuning method for code large language models (Code LLMs) to better handle subtle code errors. Specifically, we integrate the concept of comparison into instruction tuning, both at the token and sequence levels, enabling the model to discern even the slightest deviations in code. To compare the original code with an erroneous version containing manually added code errors, we use token-level preference loss for detailed token-level comparisons. Additionally, we combine code segments to create a new instruction tuning sample for sequence-level comparisons, enhancing the model's bug-fixing capability. Experimental results on the HumanEvalFix benchmark show that CCT surpasses instruction tuning in pass@1 scores by up to 4 points across diverse code LLMs, and extensive analysis demonstrates the effectiveness of our method.

Automated program repair (APR) has recently shifted toward large language models and agent-based systems, yet most systems rely on local snapshot context, overlooking repository history. Prior work shows that repository history helps repair single-line bugs, since the last commit touching the buggy line is often the bug-introducing one. In this paper, we investigate whether repository history can also improve agentic APR systems at scale, especially for complex multi-hunk bugs. We present HAFixAgent, a History-Aware Bug-Fixing Agent that injects blame-derived repository heuristics into its repair loop. A preliminary study of all 854 real-world bugs from Defects4J motivates our design, showing that bug-relevant history is both widely available and highly concentrated. Empirical comparison of HAFixAgent with two state-of-the-art baselines shows: (1) Effectiveness: HAFixAgent significantly improves over the agent-based baseline (by 212.3%) and the multi-hunk baseline (by 29.9%). (2) Efficiency: history does not significantly increase agent steps and keeps token costs comparable, with notably lower median costs for complex multi-file-multi-hunk bugs. (3) Practicality: combining different historical heuristics repairs more bugs, offering a clear cost-benefit trade-off. HAFixAgent offers a practical recipe for history-aware agentic APR: ground the agent in version control history, prioritize diff-based historical context, and integrate complementary heuristics when needed.

Large language models (LLMs) have demonstrated remarkable capabilities on a broad spectrum of downstream tasks. Within the realm of software engineering, specialized tasks on code, such as program repair, present unique challenges, necessitating fine-tuning to unlock state-of-the-art performance. Fine-tuning approaches proposed in the literature for LLMs on program repair tasks are however generally overlooking the need to reason about the logic behind code changes, beyond syntactic patterns in the data. High-performing fine-tuning experiments also usually come at very high computational costs. With MORepair, we propose a novel perspective on the learning focus of LLM fine-tuning for program repair: we not only adapt the LLM parameters to the syntactic nuances of the task of code transformation (objective 1), but we also specifically fine-tune the LLM with respect to the logical reason behind the code change in the training data (objective 2). Such a multi-objective fine-tuning will instruct LLMs to generate high-quality patches. We apply MORepair to fine-tune four open-source LLMs with different sizes and architectures. Experimental results on C++ and Java repair benchmarks show that the implemented fine-tuning effectively boosts LLM repair performance by 7.6% to 10% in Top-10 repair suggestions. We further show that our fine-tuning strategy yields superior performance compared to the incumbent state-of-the-art in fine-tuned models for program repair, Fine-tune-CoT and RepairLLaMA.

Large Language Models (LLMs) for code generation evolve rapidly through fine-tuning, merging, or new model releases. However, such updates can introduce regressions, not only in correctness but also in code quality and performance. To address this, we present ReCatcher, a regression testing framework for Python code generation. ReCatcher systematically compares two LLMs, typically a current model and a candidate update, across three dimensions: logical correctness, static code quality, and execution performance. We apply ReCatcher to assess regressions across three update scenarios, fine-tuning, merging, and model release, using CodeLlama, DeepSeek-Coder, and GPT-4o. Our evaluation shows that fine-tuning with cross-language datasets increases syntax errors by up to 12%. Merging with general-purpose models like Llama2 leads to regressions in correctness by up to 18%. GPT-4o introduces regressions of up to 50% in handling missing imports compared to GPT-3.5-turbo, while GPT-4o-mini suffers up to 80% performance degradation in execution time versus GPT-4o. Overall, logical correctness, performance, and error handling (e.g., syntax errors and missing imports) are the most regression-prone areas. Comparing ReCatcher with baseline solutions, it presents better and consistent accuracy across logical and performance aspects. ReCatcher highlights the importance of systematic regression evaluation before adopting new models, while assisting researchers and practitioners in making more informed update decisions.

The advent of Large Language Models (LLMs) has spurred the development of coding agents for real-world code generation. As a widely used benchmark for evaluating the code generation capabilities of these agents, SWE-Bench uses real-world problems based on GitHub issues and their corresponding pull requests. However, the manually written test cases included in these pull requests are often insufficient, allowing generated patches to pass the tests without resolving the underlying issue. To address this challenge, we introduce UTGenerator, an LLM-driven test case generator that automatically analyzes codebases and dependencies to generate test cases for real-world Python projects. Building on UTGenerator, we propose UTBoost, a comprehensive framework for test case augmentation. In our evaluation, we identified 36 task instances with insufficient test cases and uncovered 345 erroneous patches incorrectly labeled as passed in the original SWE Bench. These corrections, impacting 40.9% of SWE-Bench Lite and 24.4% of SWE-Bench Verified leaderboard entries, yield 18 and 11 ranking changes, respectively.

Large language models (LLMs), such as OpenAI's Codex, have demonstrated their potential to generate code from natural language descriptions across a wide range of programming tasks. Several benchmarks have recently emerged to evaluate the ability of LLMs to generate functionally correct code from natural language intent with respect to a set of hidden test cases. This has enabled the research community to identify significant and reproducible advancements in LLM capabilities. However, there is currently a lack of benchmark datasets for assessing the ability of LLMs to generate functionally correct code edits based on natural language descriptions of intended changes. This paper aims to address this gap by motivating the problem NL2Fix of translating natural language descriptions of code changes (namely bug fixes described in Issue reports in repositories) into correct code fixes. To this end, we introduce Defects4J-NL2Fix, a dataset of 283 Java programs from the popular Defects4J dataset augmented with high-level descriptions of bug fixes, and empirically evaluate the performance of several state-of-the-art LLMs for the this task. Results show that these LLMS together are capable of generating plausible fixes for 64.6% of the bugs, and the best LLM-based technique can achieve up to 21.20% top-1 and 35.68% top-5 accuracy on this benchmark.

Machine learning models are known to be susceptible to adversarial perturbation. One famous attack is the adversarial patch, a sticker with a particularly crafted pattern that makes the model incorrectly predict the object it is placed on. This attack presents a critical threat to cyber-physical systems that rely on cameras such as autonomous cars. Despite the significance of the problem, conducting research in this setting has been difficult; evaluating attacks and defenses in the real world is exceptionally costly while synthetic data are unrealistic. In this work, we propose the REAP (REalistic Adversarial Patch) benchmark, a digital benchmark that allows the user to evaluate patch attacks on real images, and under real-world conditions. Built on top of the Mapillary Vistas dataset, our benchmark contains over 14,000 traffic signs. Each sign is augmented with a pair of geometric and lighting transformations, which can be used to apply a digitally generated patch realistically onto the sign. Using our benchmark, we perform the first large-scale assessments of adversarial patch attacks under realistic conditions. Our experiments suggest that adversarial patch attacks may present a smaller threat than previously believed and that the success rate of an attack on simpler digital simulations is not predictive of its actual effectiveness in practice. We release our benchmark publicly at https://github.com/wagner-group/reap-benchmark.

Large Language Models (LLMs) have shown remarkable aptitude in code generation but still struggle on challenging programming tasks. Self-repair -- in which the model debugs and fixes mistakes in its own code -- has recently become a popular way to boost performance in these settings. However, only very limited studies on how and when self-repair works effectively exist in the literature, and one might wonder to what extent a model is really capable of providing accurate feedback on why the code is wrong when that code was generated by the same model. In this paper, we analyze GPT-3.5 and GPT-4's ability to perform self-repair on APPS, a challenging dataset consisting of diverse coding challenges. To do so, we first establish a new evaluation strategy dubbed pass@t that measures the pass rate of the tasks against the total number of tokens sampled from the model, enabling a fair comparison to purely sampling-based approaches. With this evaluation strategy, we find that the effectiveness of self-repair is only seen in GPT-4. We also observe that self-repair is bottlenecked by the feedback stage; using GPT-4 to give feedback on the programs generated by GPT-3.5 and using expert human programmers to give feedback on the programs generated by GPT-4, we unlock significant performance gains.

The exponential growth of AI-generated images (AIGIs) underscores the urgent need for robust and generalizable detection methods. In this paper, we establish two key principles for AIGI detection through systematic analysis: (1) All Patches Matter: Unlike conventional image classification where discriminative features concentrate on object-centric regions, each patch in AIGIs inherently contains synthetic artifacts due to the uniform generation process, suggesting that every patch serves as an important artifact source for detection. (2) More Patches Better: Leveraging distributed artifacts across more patches improves detection robustness by capturing complementary forensic evidence and reducing over-reliance on specific patches, thereby enhancing robustness and generalization. However, our counterfactual analysis reveals an undesirable phenomenon: naively trained detectors often exhibit a Few-Patch Bias, discriminating between real and synthetic images based on minority patches. We identify Lazy Learner as the root cause: detectors preferentially learn conspicuous artifacts in limited patches while neglecting broader artifact distributions. To address this bias, we propose the Panoptic Patch Learning (PPL) framework, involving: (1) Random Patch Replacement that randomly substitutes synthetic patches with real counterparts to compel models to identify artifacts in underutilized regions, encouraging the broader use of more patches; (2) Patch-wise Contrastive Learning that enforces consistent discriminative capability across all patches, ensuring uniform utilization of all patches. Extensive experiments across two different settings on several benchmarks verify the effectiveness of our approach.

OpenAI's Codex, a GPT-3 like model trained on a large code corpus, has made headlines in and outside of academia. Given a short user-provided description, it is capable of synthesizing code snippets that are syntactically and semantically valid in most cases. In this work, we want to investigate whether Codex is able to localize and fix bugs, a task of central interest in the field of automated program repair. Our initial evaluation uses the multi-language QuixBugs benchmark (40 bugs in both Python and Java). We find that, despite not being trained for APR, Codex is surprisingly effective, and competitive with recent state of the art techniques. Our results also show that Codex is slightly more successful at repairing Python than Java.

Localizing behaviors of neural networks to a subset of the network's components or a subset of interactions between components is a natural first step towards analyzing network mechanisms and possible failure modes. Existing work is often qualitative and ad-hoc, and there is no consensus on the appropriate way to evaluate localization claims. We introduce path patching, a technique for expressing and quantitatively testing a natural class of hypotheses expressing that behaviors are localized to a set of paths. We refine an explanation of induction heads, characterize a behavior of GPT-2, and open source a framework for efficiently running similar experiments.

The rapid advancement of Large Language Models (LLMs) in software engineering has revealed critical limitations in existing benchmarks, particularly the widely used SWE-bench dataset. Recent studies have uncovered severe data contamination issues, e.g. SWE-bench reports 32.67% of successful patches involve direct solution leakage and 31.08% pass due to inadequate test cases. We introduce SWE-MERA, a dynamic, continuously updated benchmark designed to address these fundamental challenges through an automated collection of real-world GitHub issues and rigorous quality validation. Our approach implements a reliable pipeline that ensures quality while minimizing contamination risks, resulting in approximately 10,000 potential tasks with 300 samples currently available. Evaluation using the Aider coding agent demonstrates strong discriminative power in state-of-the-art models. We report performance across a dozen recent LLMs evaluated on tasks collected between September 2024 and June 2025.

Static analysis tools are widely used for vulnerability detection as they understand programs with complex behavior and millions of lines of code. Despite their popularity, static analysis tools are known to generate an excess of false positives. The recent ability of Machine Learning models to understand programming languages opens new possibilities when applied to static analysis. However, existing datasets to train models for vulnerability identification suffer from multiple limitations such as limited bug context, limited size, and synthetic and unrealistic source code. We propose D2A, a differential analysis based approach to label issues reported by static analysis tools. The D2A dataset is built by analyzing version pairs from multiple open source projects. From each project, we select bug fixing commits and we run static analysis on the versions before and after such commits. If some issues detected in a before-commit version disappear in the corresponding after-commit version, they are very likely to be real bugs that got fixed by the commit. We use D2A to generate a large labeled dataset to train models for vulnerability identification. We show that the dataset can be used to build a classifier to identify possible false alarms among the issues reported by static analysis, hence helping developers prioritize and investigate potential true positives first.

Software is used in critical applications in our day-to-day life and it is important to ensure its correctness. One popular approach to assess correctness is to evaluate software on tests. If a test fails, it indicates a fault in the software under test; if all tests pass correctly, one may assume that the software is correct. However, the reliability of these results depends on the test suite considered, and there is a risk of false negatives (i.e. software that passes all available tests but contains bugs because some cases are not tested). Therefore, it is important to consider error-inducing test cases when evaluating software. To support data-driven creation of such a test-suite, which is especially of interest for testing software synthesized from large language models, we curate a dataset (Codehacks) of programming problems together with corresponding error-inducing test cases (i.e., "hacks"). This dataset is collected from the wild, in particular, from the Codeforces online judge platform. The dataset comprises 288,617 hacks for 5,578 programming problems, each with a natural language description, as well as the source code for 2,196 submitted solutions to these problems that can be broken with their corresponding hacks. Keywords: competitive programming, language model, dataset

APR (Automated Program Repair) aims to automatically locate program defects, generate patches and validate the repairs. Existing techniques for APR are often combined with LLMs (Large Language Models), which leverages the code-related knowledge of LLMs to improve repair effectiveness. Current LLM-based APR methods typically utilize test cases only during the inference stage, adopting an iterative approach that performs repair first and validates it through test execution afterward. This conventional paradigm neglects two important aspects: the potential contribution of test cases in the training phase, and the possibility of leveraging testing prior to repair. To address this, we propose Repair-R1, which introduces test cases into the model's training phase and shifts test generation to precede repair. The model is required to first generate discriminative test cases that can distinguish defective behaviors, and then perform repair based on these tests. This enables the model to better locate defects and understand the underlying causes of defects, thereby improving repair effectiveness. We implement Repair-R1 with three different backbone models, using RL (reinforcement learning) to co-optimize test generation and bug repair. Experimental results on four widely adopted benchmarks demonstrate the superiority of Repair-R1. Specially, compared to vanilla models, Repair-R1 improves repair success rate by 2.68\% to 48.29\%, test generation success rate by 16.38\% to 53.28\%, and test coverage by 0.78\% to 53.96\%. We publish the code and weights at https://github.com/Tomsawyerhu/APR-RL and https://huggingface.co/tomhu/Qwen3-4B-RL-5000-step.

To evaluate code large language models (LLMs), research has relied on a few small manually curated benchmarks, such as HumanEval and MBPP, which represent a narrow part of the real-world software domains. In this work, we introduce round-trip correctness (RTC) as an alternative evaluation method. RTC allows Code LLM evaluation on a broader spectrum of real-world software domains without the need for costly human curation. RTC rests on the idea that we can ask a model to make a prediction (e.g., describe some code using natural language), feed that prediction back (e.g., synthesize code from the predicted description), and check if this round-trip leads to code that is semantically equivalent to the original input. We show how to employ RTC to evaluate code synthesis and editing. We find that RTC strongly correlates with model performance on existing narrow-domain code synthesis benchmarks while allowing us to expand to a much broader set of domains and tasks which was not previously possible without costly human annotations.

Software updates, including bug repair and feature additions, are frequent in modern applications but they often leave test suites outdated, resulting in undetected bugs and increased chances of system failures. A recent study by Meta revealed that 14%-22% of software failures stem from outdated tests that fail to reflect changes in the codebase. This highlights the need to keep tests in sync with code changes to ensure software reliability. In this paper, we present UTFix, a novel approach for repairing unit tests when their corresponding focal methods undergo changes. UTFix addresses two critical issues: assertion failure and reduced code coverage caused by changes in the focal method. Our approach leverages language models to repair unit tests by providing contextual information such as static code slices, dynamic code slices, and failure messages. We evaluate UTFix on our generated synthetic benchmarks (Tool-Bench), and real-world benchmarks. Tool- Bench includes diverse changes from popular open-source Python GitHub projects, where UTFix successfully repaired 89.2% of assertion failures and achieved 100% code coverage for 96 tests out of 369 tests. On the real-world benchmarks, UTFix repairs 60% of assertion failures while achieving 100% code coverage for 19 out of 30 unit tests. To the best of our knowledge, this is the first comprehensive study focused on unit test in evolving Python projects. Our contributions include the development of UTFix, the creation of Tool-Bench and real-world benchmarks, and the demonstration of the effectiveness of LLM-based methods in addressing unit test failures due to software evolution.

Large language models (LLMs) have shown strong performance on automated software engineering tasks, yet existing benchmarks focus primarily on general-purpose libraries or web applications, leaving mobile application development largely unexplored despite its strict platform constraints, framework-driven lifecycles, and complex platform API interactions. We introduce MobileDev-Bench, a benchmark comprising 384 real-world issue-resolution tasks collected from 18 production mobile applications spanning Android Native (Java/Kotlin), React Native (TypeScript), and Flutter (Dart). Each task pairs an authentic developer-reported issue with executable test patches, enabling fully automated validation of model-generated fixes within mobile build environments. The benchmark exhibits substantial patch complexity: fixes modify 12.5 files and 324.9 lines on average, and 35.7% of instances require coordinated changes across multiple artifact types, such as source and manifest files. Evaluation of four state-of-the-art code-capable LLMs, GPT- 5.2, Claude Sonnet 4.5, Gemini Flash 2.5, and Qwen3-Coder, yields low end-to-end resolution rates of 3.39%-5.21%, revealing significant performance gaps compared to prior benchmarks. Further analysis reveals systematic failure modes, with fault localization across multi-file and multi-artifact changes emerging as the primary bottleneck.

Large Language Models (LLMs) and other automated techniques have been increasingly used to support software developers by generating software artifacts such as code snippets, patches, and comments. However, accurately assessing the correctness of these generated artifacts remains a significant challenge. On one hand, human evaluation provides high accuracy but is labor-intensive and lacks scalability. On the other hand, many automatic evaluation metrics are scalable and require minimal human effort, but they often fail to accurately reflect the actual correctness of generated software artifacts. In this paper, we present SE-Jury, the first evaluation metric for LLM-as-Ensemble-Judge specifically designed to accurately assess the correctness of generated software artifacts. SE-Jury first defines five distinct evaluation strategies, each implemented by an independent judge. A dynamic team selection mechanism then identifies the most appropriate subset of judges as a team to produce a final correctness score through ensembling. We evaluate SE-Jury across a diverse set of software engineering (SE) benchmarks that span three popular SE tasks: code generation, automated program repair, and code summarization. Results demonstrate that SE-Jury consistently achieves a higher correlation with human judgments, with improvements ranging from 29.6% to 140.8% over existing automatic metrics. SE-Jury reaches agreement levels with human annotators that are close to inter-annotator agreement in code generation and program repair. These findings underscore SE-Jury's potential as a scalable and reliable alternative to human evaluation in these SE tasks.

Code generation models have achieved impressive performance. However, they tend to be brittle as slight edits to a prompt could lead to very different generations; these robustness properties, critical for user experience when deployed in real-life applications, are not well understood. Most existing works on robustness in text or code tasks have focused on classification, while robustness in generation tasks is an uncharted area and to date there is no comprehensive benchmark for robustness in code generation. In this paper, we propose ReCode, a comprehensive robustness evaluation benchmark for code generation models. We customize over 30 transformations specifically for code on docstrings, function and variable names, code syntax, and code format. They are carefully designed to be natural in real-life coding practice, preserve the original semantic meaning, and thus provide multifaceted assessments of a model's robustness performance. With human annotators, we verified that over 90% of the perturbed prompts do not alter the semantic meaning of the original prompt. In addition, we define robustness metrics for code generation models considering the worst-case behavior under each type of perturbation, taking advantage of the fact that executing the generated code can serve as objective evaluation. We demonstrate ReCode on SOTA models using HumanEval, MBPP, as well as function completion tasks derived from them. Interesting observations include: better robustness for CodeGen over InCoder and GPT-J; models are most sensitive to syntax perturbations; more challenging robustness evaluation on MBPP over HumanEval.

Efficient bug resolution is critical for maintaining software quality and user satisfaction. However, specific bug reports experience unusually long resolution times, which may indicate underlying process inefficiencies or complex issues. This study presents a comprehensive analysis of bug resolution anomalies across seven prominent open-source repositories: Cassandra, Firefox, Hadoop, HBase, SeaMonkey, Spark, and Thunderbird. Utilizing statistical methods such as Z-score and Interquartile Range (IQR), we identify anomalies in bug resolution durations. To understand the thematic nature of these anomalies, we apply Term Frequency-Inverse Document Frequency (TF-IDF) for textual feature extraction and KMeans clustering to group similar bug summaries. Our findings reveal consistent patterns across projects, with anomalies often clustering around test failures, enhancement requests, and user interface issues. This approach provides actionable insights for project maintainers to prioritize and effectively address long-standing bugs.

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.

Large language models (LLMs) and LLM-based Agents have been applied to fix bugs automatically, demonstrating the capability in addressing software defects by engaging in development environment interaction, iterative validation and code modification. However, systematic analysis of these agent and non-agent systems remain limited, particularly regarding performance variations among top-performing ones. In this paper, we examine seven proprietary and open-source systems on the SWE-bench Lite benchmark for automated bug fixing. We first assess each system's overall performance, noting instances solvable by all or none of these sytems, and explore why some instances are uniquely solved by specific system types. We also compare fault localization accuracy at file and line levels and evaluate bug reproduction capabilities, identifying instances solvable only through dynamic reproduction. Through analysis, we concluded that further optimization is needed in both the LLM itself and the design of Agentic flow to improve the effectiveness of the Agent in bug fixing.

High quality bugs are key to training the next generation of language model based software engineering (SWE) agents. We introduce a novel method for synthetic generation of difficult and diverse bugs. Our method instructs SWE Agents to introduce a feature into the codebase whereby they may unintentionally break tests, resulting in bugs. Prior approaches often induce an out-of-distribution effect by generating bugs intentionally (e.g. by introducing local perturbation to existing code), which does not reflect realistic development processes. We perform qualitative analysis to demonstrate that our approach for generating bugs more closely reflects the patterns found in human-authored edits. Through extensive experiments, we demonstrate that our bugs provide more efficient training data for supervised fine-tuning, outperforming other bug datasets by 2% with half the training data (1.2k vs. 3k bugs). We train on our newly generated bugs in addition to existing bug datasets to get FrogBoss a state-of-the-art 32B parameter model on SWE-bench Verified with a pass@1 of 54.6% and FrogMini a state-of-the-art 14B model on SWE-bench Verified with a pass@1 of 45.3% on SWE-bench Verified averaged over three seeds.

Large language models (LLMs) now write code in settings where misreading a single word can break safety or cost money, yet we still expect them to overlook stray typos. To probe where useful robustness ends and harmful insensitivity begins, we compile 50 LeetCode problems and craft three minimal prompt perturbations that should vary in importance: (i) progressive underspecification deleting 10 % of words per step; (ii) lexical flip swapping a pivotal quantifier ("max" to "min"); and (iii) jargon inflation replacing a common noun with an obscure technical synonym. Six frontier models, including three "reasoning-tuned" versions, solve each mutated prompt, and their Python outputs are checked against the original test suites to reveal whether they reused the baseline solution or adapted. Among 11 853 generations we observe a sharp double asymmetry. Models remain correct in 85 % of cases even after 90 % of the prompt is missing, showing over-robustness to underspecification, yet only 54 % react to a single quantifier flip that reverses the task, with reasoning-tuned variants even less sensitive than their bases. Jargon edits lie in between, passing through 56 %. Current LLMs thus blur the line between harmless noise and meaning - changing edits, often treating both as ignorable. Masking salient anchors such as function names can force re - evaluation. We advocate evaluation and training protocols that reward differential sensitivity: stay steady under benign noise but adapt - or refuse - when semantics truly change.

We release Terminal Wrench, a subset of 331 terminal-agent benchmark environments, copied from the popular open benchmarks that are demonstrably reward-hackable. The data set includes 3,632 hack trajectories and 2,352 legitimate baseline trajectories across three frontier models (Claude Opus 4.6, Gemini 3.1 Pro, GPT-5.4). Each entry preserves the original task definition alongside full attack trajectories that show how the verifier was bypassed. It also includes cases where the task was not solved as intended. The tasks span system administration, machine learning, software engineering, and security challenges; the exploits range from simple output spoofing to stack-frame introspection, standard-library patching, and rootkit-style binary hijacking. Crucially, these exploits are specific to each task, rather than the evaluation harness, making them harder to patch. We also present a monitorability study in which hack trajectories are sanitized or stripped of reasoning traces and then scored by an LLM judge, showing that detection degrades meaningfully when chain-of-thought is removed (AUC drops from 0.97 to 0.92). The data set is publicly available at https://github.com/few-sh/terminal-wrench.

In this study, we evaluated the capability of Large Language Models (LLMs), particularly OpenAI's GPT-4, in detecting software vulnerabilities, comparing their performance against traditional static code analyzers like Snyk and Fortify. Our analysis covered numerous repositories, including those from NASA and the Department of Defense. GPT-4 identified approximately four times the vulnerabilities than its counterparts. Furthermore, it provided viable fixes for each vulnerability, demonstrating a low rate of false positives. Our tests encompassed 129 code samples across eight programming languages, revealing the highest vulnerabilities in PHP and JavaScript. GPT-4's code corrections led to a 90% reduction in vulnerabilities, requiring only an 11% increase in code lines. A critical insight was LLMs' ability to self-audit, suggesting fixes for their identified vulnerabilities and underscoring their precision. Future research should explore system-level vulnerabilities and integrate multiple static code analyzers for a holistic perspective on LLMs' potential.

Code agents are increasingly trusted to autonomously fix bugs on platforms such as GitHub, yet their security evaluation focuses almost exclusively on functional correctness. In this paper, we reveal a novel type of threat to real-world code agents: Functionally Correct yet Vulnerable (FCV) patches, which pass all test cases but contain vulnerable code. With our proposed FCV-Attack, which can be deliberately crafted by malicious attackers or implicitly introduced by benign developers, we show that SOTA LLMs (e.g., ChatGPT and Claude) and agent scaffolds (e.g., SWE-agent and OpenHands) are all vulnerable to this FCV threat; across 12 agent-model combinations on SWE-Bench, the attack only requires black-box access and a single query to the code agent to perform the attack. For example, for CWE-538 (information exposure vulnerability), the FCV-Attack attains an attack success rate of 40.7% on GPT-5 Mini + OpenHands. Our results reveal an important security threat overlooked by current evaluation paradigms and urge the development of security-aware defenses for code agents.

Sequence-to-sequence models have been used to transform erroneous programs into correct ones when trained with a large enough dataset. Some recent studies also demonstrated strong empirical evidence that code review could improve the program repair further. Large language models, trained with Natural Language (NL) and Programming Language (PL), can contain inherent knowledge of both. In this study, we investigate if this inherent knowledge of PL and NL can be utilized to improve automated program repair. We applied PLBART and CodeT5, two state-of-the-art language models that are pre-trained with both PL and NL, on two such natural language-based program repair datasets and found that the pre-trained language models fine-tuned with datasets containing both code review and subsequent code changes notably outperformed each of the previous models. With the advent of code generative models like Codex and GPT-3.5-Turbo, we also performed zero-shot and few-shots learning-based prompt engineering to assess their performance on these datasets. However, the practical application of using LLMs in the context of automated program repair is still a long way off based on our manual analysis of the generated repaired codes by the learning models.

Automatic program repair seeks to generate correct code from buggy programs, with most approaches searching the correct program in a discrete, symbolic space of source code tokens. This symbolic search is fundamentally limited by its inability to directly reason about program behavior. We introduce Gradient-Based Program Repair (GBPR), a new paradigm that reframes program repair as continuous optimization in a differentiable numerical program space. Our core insight is to compile symbolic programs into differentiable numerical representations, enabling search in the numerical program space directly guided by program behavior. To evaluate GBPR, we present RaspBugs, a new benchmark of 1,466 buggy symbolic RASP programs and their respective numerical representations. Our experiments demonstrate that GBPR can effectively repair buggy symbolic programs by gradient-based optimization in the numerical program space, with convincing repair trajectories. To our knowledge, we are the first to state program repair as continuous optimization in a numerical program space. Our work establishes a new direction for program repair research, bridging two rich worlds: continuous optimization and program behavior.

Security vulnerability repair is a difficult task that is in dire need of automation. Two groups of techniques have shown promise: (1) large code language models (LLMs) that have been pre-trained on source code for tasks such as code completion, and (2) automated program repair (APR) techniques that use deep learning (DL) models to automatically fix software bugs. This paper is the first to study and compare Java vulnerability repair capabilities of LLMs and DL-based APR models. The contributions include that we (1) apply and evaluate five LLMs (Codex, CodeGen, CodeT5, PLBART and InCoder), four fine-tuned LLMs, and four DL-based APR techniques on two real-world Java vulnerability benchmarks (Vul4J and VJBench), (2) design code transformations to address the training and test data overlapping threat to Codex, (3) create a new Java vulnerability repair benchmark VJBench, and its transformed version VJBench-trans and (4) evaluate LLMs and APR techniques on the transformed vulnerabilities in VJBench-trans. Our findings include that (1) existing LLMs and APR models fix very few Java vulnerabilities. Codex fixes 10.2 (20.4%), the most number of vulnerabilities. (2) Fine-tuning with general APR data improves LLMs' vulnerability-fixing capabilities. (3) Our new VJBench reveals that LLMs and APR models fail to fix many Common Weakness Enumeration (CWE) types, such as CWE-325 Missing cryptographic step and CWE-444 HTTP request smuggling. (4) Codex still fixes 8.3 transformed vulnerabilities, outperforming all the other LLMs and APR models on transformed vulnerabilities. The results call for innovations to enhance automated Java vulnerability repair such as creating larger vulnerability repair training data, tuning LLMs with such data, and applying code simplification transformation to facilitate vulnerability repair.

Static analysis is a cornerstone for software vulnerability detection, yet it often struggles with the classic precision-scalability trade-off. In practice, such tools often produce high false positive rates, particularly in large codebases like the Linux kernel. This imprecision can arise from simplified vulnerability modeling and over-approximation of path and data constraints. While large language models (LLMs) show promise in code understanding, their naive application to program analysis yields unreliable results due to inherent reasoning limitations. We introduce BugLens, a post-refinement framework that significantly improves static analysis precision. BugLens guides an LLM to follow traditional analysis steps by assessing buggy code patterns for security impact and validating the constraints associated with static warnings. Evaluated on real-world Linux kernel bugs, BugLens raises precision from 0.10 (raw) and 0.50 (semi-automated refinement) to 0.72, substantially reducing false positives and revealing four previously unreported vulnerabilities. Our results suggest that a structured LLM-based workflow can meaningfully enhance the effectiveness of static analysis tools.

Bug-fix benchmarks are fundamental in advancing various sub-fields of software engineering such as automatic program repair (APR) and fault localization (FL). A good benchmark must include recent examples that accurately reflect technologies and development practices of today. To be executable in the long term, a benchmark must feature test suites that do not degrade overtime due to, for example, dependencies that are no longer available. Existing benchmarks fail in meeting both criteria. For instance, Defects4J, one of the foremost Java benchmarks, last received an update in 2020. Moreover, full-reproducibility has been neglected by the majority of existing benchmarks. In this paper, we present GitBug-Actions: a novel tool for building bug-fix benchmarks with modern and fully-reproducible bug-fixes. GitBug-Actions relies on the most popular CI platform, GitHub Actions, to detect bug-fixes and smartly locally execute the CI pipeline in a controlled and reproducible environment. To the best of our knowledge, we are the first to rely on GitHub Actions to collect bug-fixes. To demonstrate our toolchain, we deploy GitBug-Actions to build a proof-of-concept Go bug-fix benchmark containing executable, fully-reproducible bug-fixes from different repositories. A video demonstrating GitBug-Actions is available at: https://youtu.be/aBWwa1sJYBs.

Large Language Models (LLMs) have been gaining increasing attention and demonstrated promising performance across a variety of Software Engineering (SE) tasks, such as Automated Program Repair (APR), code summarization, and code completion. For example, ChatGPT, the latest black-box LLM, has been investigated by numerous recent research studies and has shown impressive performance in various tasks. However, there exists a potential risk of data leakage since these LLMs are usually close-sourced with unknown specific training details, e.g., pre-training datasets. In this paper, we seek to review the bug-fixing capabilities of ChatGPT on a clean APR benchmark with different research objectives. We first introduce {\benchmark}, a new benchmark with buggy and the corresponding fixed programs from competitive programming problems starting from 2023, after the training cutoff point of ChatGPT. The results on {\benchmark} show that ChatGPT is able to fix 109 out of 151 buggy programs using the basic prompt within 35 independent rounds, outperforming state-of-the-art LLMs CodeT5 and PLBART by 27.5\% and 62.4\% prediction accuracy. We also investigate the impact of three types of prompts, i.e., problem description, error feedback, and bug localization, leading to additional 34 fixed bugs. Besides, we provide additional discussion from the interactive nature of ChatGPT to illustrate the capacity of a dialog-based repair workflow with 9 additional fixed bugs. Inspired by the findings, we further pinpoint various challenges and opportunities for advanced SE study equipped with such LLMs (e.g.,~ChatGPT) in the near future. More importantly, our work calls for more research on the reevaluation of the achievements obtained by existing black-box LLMs across various SE tasks, not limited to ChatGPT on APR.

LLMs have long demonstrated remarkable effectiveness in automatic program repair (APR), with OpenAI's ChatGPT being one of the most widely used models in this domain. Through continuous iterations and upgrades of GPT-family models, their performance in fixing bugs has already reached state-of-the-art levels. However, there are few works comparing the effectiveness and variations of different versions of GPT-family models on APR. In this work, inspired by the recent public release of the GPT-o1 models, we conduct the first study to compare the effectiveness of different versions of the GPT-family models in APR. We evaluate the performance of the latest version of the GPT-family models (i.e., O1-preview and O1-mini), GPT-4o, and the historical version of ChatGPT on APR. We conduct an empirical study of the four GPT-family models against other LLMs and APR techniques on the QuixBugs benchmark from multiple evaluation perspectives, including repair success rate, repair cost, response length, and behavior patterns. The results demonstrate that O1's repair capability exceeds that of prior GPT-family models, successfully fixing all 40 bugs in the benchmark. Our work can serve as a foundation for further in-depth exploration of the applications of GPT-family models in APR.

Large language models frequently fail to produce correct code on their first attempt, yet most benchmarks evaluate them in a single-shot setting. We investigate iterative self-repair (feeding execution errors back to the model for correction) across seven models spanning three families and both open-weight and proprietary providers: Llama 3.1 8B, Llama 3.3 70B, Llama 4 Scout (MoE, 16 experts), Llama 4 Maverick (MoE, 128 experts), Qwen3 32B, Gemini 2.5 Flash, and Gemini 2.5 Pro. On HumanEval (164 problems) and MBPP Sanitized (257 problems) with up to five attempts, self-repair universally improves pass rates: +4.9 to +17.1 pp on HumanEval and +16.0 to +30.0 pp on MBPP. Gemini 2.5 Flash achieves the highest final pass rates (96.3% HumanEval, 93.8% MBPP). Most gains concentrate in the first two rounds.Error-type analysis shows assertion errors (logical mistakes) are the hardest to repair at ~45%, while syntax and name errors are repaired at substantially higher rates, connecting to broader findings on the limits of LLM self-correction. Prior work found that weaker models fail at self-repair or require fine-tuning; we show that modern instruction-tuned models succeed with prompting alone, even at 8B scale. We also provide the first comparison of dense and MoE architectures for self-repair, and extend the repair-vs-resampling tradeoff analysis to modern models. A prompt ablation reveals chain-of-thought repair yields up to +5.5 pp additional self-repair gain (measured as improvement in repair delta) over minimal prompting for capable models.

Machine Learning models increasingly face data integrity challenges due to the use of large-scale training datasets drawn from the Internet. We study what model developers can do if they detect that some data was manipulated or incorrect. Such manipulated data can cause adverse effects including vulnerability to backdoored samples, systemic biases, and reduced accuracy on certain input domains. Realistically, all manipulated training samples cannot be identified, and only a small, representative subset of the affected data can be flagged. We formalize Corrective Machine Unlearning as the problem of mitigating the impact of data affected by unknown manipulations on a trained model, only having identified a subset of the corrupted data. We demonstrate that the problem of corrective unlearning has significantly different requirements from traditional privacy-oriented unlearning. We find most existing unlearning methods, including retraining-from-scratch without the deletion set, require most of the manipulated data to be identified for effective corrective unlearning. However, one approach, Selective Synaptic Dampening, achieves limited success, unlearning adverse effects with just a small portion of the manipulated samples in our setting, which shows encouraging signs for future progress. We hope our work spurs research towards developing better methods for corrective unlearning and offers practitioners a new strategy to handle data integrity challenges arising from web-scale training. Code is available at https://github.com/drimpossible/corrective-unlearning-bench.

Although LLMs have shown promising potential in vulnerability detection, this study reveals their limitations in distinguishing between vulnerable and similar-but-benign patched code (only 0.06 - 0.14 accuracy). It shows that LLMs struggle to capture the root causes of vulnerabilities during vulnerability detection. To address this challenge, we propose enhancing LLMs with multi-dimensional vulnerability knowledge distilled from historical vulnerabilities and fixes. We design a novel knowledge-level Retrieval-Augmented Generation framework Vul-RAG, which improves LLMs with an accuracy increase of 16% - 24% in identifying vulnerable and patched code. Additionally, vulnerability knowledge generated by Vul-RAG can further (1) serve as high-quality explanations to improve manual detection accuracy (from 60% to 77%), and (2) detect 10 previously-unknown bugs in the recent Linux kernel release with 6 assigned CVEs.

Large language models (LLMs) have advanced rapidly from conversational problem solving to addressing real-world tasks involving tool use, such as software engineering (SWE). Recent LLM-powered toolkits, such as OpenAI Codex and Cursor, have offered end-to-end automation of the software development process. However, building effective SWE agents remains challenging due to the lack of high-quality training data and effective test cases. To address this issue, we present SWE-Dev, an SWE agent built upon open-source LLMs. First, we develop a robust pipeline to synthesize test cases for patch evaluation. Second, we scale up agent trajectories to construct the training data for building SWE-Dev. Experiments on the SWE-bench-Verified benchmark show that the SWE-Dev models can achieve top performance among all open SWE agents. Specifically, the success rates of the SWE-Dev 7B and 32B parameter models reach 23.4% and 36.6%, respectively, outperforming state-of-the-art open-source models. All code, models, and datasets are publicly available at https://github.com/THUDM/SWE-Dev.

Text-agent environments are typically modeled as partially observable Markov decision processes (POMDPs), assuming that the simulator's latent state and transition dynamics are hidden from the agent. Yet little work has examined whether executable code can be induced to serve as a world model for prediction and planning under partial observability. We introduce PatchWorld, a gradient-free framework that turns offline trajectories into executable Python world models through counterexample-guided code repair. Instead of predicting the next observation with a black-box model, PatchWorld induces symbolic belief-state programs whose action updates can be inspected, replayed, and locally patched. Across seven AgentGym environments, PatchWorld-Simple achieves the highest code-based planning score among evaluated methods, reaching 76.4\% macro success in live one-step lookahead while invoking no LLM calls inside the world-model prediction module itself. We further find that a human-specified residual-memory bias improves surface observation fidelity but weakens decision utility. This exposes a tradeoff in executable world models, since improving observation fidelity can come at the expense of action-discriminative dynamics, and vice versa. Code is available at https://github.com/HKBU-KnowComp/PatchWorld.

Preference learning enhances Code LLMs beyond supervised fine-tuning by leveraging relative quality comparisons. Existing methods construct preference pairs from candidates based on test case success, treating the higher pass rate sample as positive and the lower as negative. However, this approach does not pinpoint specific errors in the code, which prevents the model from learning more informative error correction patterns, as aligning failing code as a whole lacks the granularity needed to capture meaningful error-resolution relationships. To address these issues, we propose IterPref, a new preference alignment framework that mimics human iterative debugging to refine Code LLMs. IterPref explicitly locates error regions and aligns the corresponding tokens via a tailored DPO algorithm. To generate informative pairs, we introduce the CodeFlow dataset, where samples are iteratively refined until passing tests, with modifications capturing error corrections. Extensive experiments show that a diverse suite of Code LLMs equipped with IterPref achieves significant performance gains in code generation and improves on challenging tasks like BigCodeBench. In-depth analysis reveals that IterPref yields fewer errors. Our code and data will be made publicaly available.

Language models (LMs) are susceptible to in-context reward hacking, where they exploit flaws in tainted or faulty written specifications or rubrics to achieve high scores without fulfilling the user's true intent. We introduce Specification Self-Correction (SSC), a novel, test-time framework that enables an LM to identify and correct flaws within its own guiding specification. SSC employs a multi-step inference process where the model first generates a response based on a potentially tainted specification, critiques its output, and then revises the specification itself to remove the exploitable loophole. A final, more robust response is then generated using this self-corrected specification. Across experiments spanning creative writing and agentic coding tasks with several LMs, we demonstrate that while models initially game tainted specifications in 50-70\% of cases, the SSC process reduces this vulnerability by over 90\%. This dynamic repair occurs at inference time, requires no weight modification, and leads to more robustly aligned model behavior. Code at https://github.com/vicgalle/specification-self-correction .

Saliency maps are increasingly used as design guidance in siRNA efficacy prediction, yet attribution methods are rarely validated before motivating sequence edits. We introduce a pre-synthesis gate: a protocol for counterfactual sensitivity faithfulness that tests whether mutating high-saliency positions changes model output more than composition-matched controls. Cross-dataset transfer reveals two failure modes that would otherwise go undetected: faithful-but-wrong (saliency valid, predictions fail) and inverted saliency (top-saliency edits less impactful than random). Strikingly, models trained on mRNA-level assays collapse on a luciferase reporter dataset, demonstrating that protocol shifts can silently invalidate deployment. Across four benchmarks, 19/20 fold instances pass; the single failure shows inverted saliency. A biology-informed regularizer (BioPrior) strengthens saliency faithfulness with modest, dataset-dependent predictive trade-offs. Our results establish saliency validation as essential pre-deployment practice for explanation-guided therapeutic design. Code is available at https://github.com/shadi97kh/BioPrior.