AI Software Engineering

Autonomous code agents built on large language models are reshaping software and AI development through tool use, long-horizon reasoning, and self-directed interaction. However, this autonomy introduces a previously unrecognized security risk: agentic interaction fundamentally expands the LLM attack surface, enabling systematic probing and recovery of hidden system prompts that guide model behavior. We identify system prompt extraction as an emergent vulnerability intrinsic to code agents and present \textbf{\textsc{JustAsk}}, a self-evolving framework that autonomously discovers effective extraction strategies through interaction alone. Unlike prior prompt-engineering or dataset-based attacks, \textsc{JustAsk} requires no handcrafted prompts, labeled supervision, or privileged access beyond standard user interaction. It formulates extraction as an online exploration problem, using Upper Confidence Bound-based strategy selection and a hierarchical skill space spanning atomic probes and high-level orchestration. These skills exploit imperfect system-instruction generalization and inherent tensions between helpfulness and safety. Evaluated on \textbf{41} black-box commercial models across multiple providers, \textsc{JustAsk} consistently achieves full or near-complete system prompt recovery, revealing recurring design- and architecture-level vulnerabilities. Our results expose system prompts as a critical yet largely unprotected attack surface in modern agent systems.

The increasing deployment of deep learning systems requires systematic evaluation of their reliability in real-world scenarios. Traditional gradient-based adversarial attacks introduce small perturbations that rarely correspond to realistic failures and mainly assess robustness rather than functional behavior. Generative test generation methods offer an alternative but are often limited to simple datasets or constrained input domains. Although diffusion models enable high-fidelity image synthesis, their computational cost and limited controllability restrict their applicability to large-scale testing. We present HyNeA, a generative testing method that enables direct and efficient control over diffusion-based generation. HyNeA provides dataset-free controllability through hypernetworks, allowing targeted manipulation of the generative process without relying on architecture-specific conditioning mechanisms or dataset-driven adaptations such as fine-tuning. HyNeA employs a distinct training strategy that supports instance-level tuning to identify failure-inducing test cases without requiring datasets that explicitly contain examples of similar failures. This approach enables the targeted generation of realistic failure cases at substantially lower computational cost than search-based methods. Experimental results show that HyNeA improves controllability and test diversity compared to existing generative test generators and generalizes to domains where failure-labeled training data is unavailable.

Large language models (LLMs) are increasingly used for hardware and firmware code generation, but existing studies primarily evaluate functional correctness while largely overlooking security. However, LLM-generated code that appears functionally sound may embed security flaws which could induce catastrophic damages after deployment. This critical research gap motivates us to design a benchmark for assessing security awareness under realistic specifications. In this work, we introduce HardSecBench, a benchmark with 924 tasks spanning Verilog Register Transfer Level (RTL) and firmware-level C, covering 76 hardware-relevant Common Weakness Enumeration (CWE) entries. Each task includes a structured specification, a secure reference implementation, and executable tests. To automate artifact synthesis, we propose a multi-agent pipeline that decouples synthesis from verification and grounds evaluation in execution evidence, enabling reliable evaluation. We evaluate diverse LLMs and find that they often satisfy functional requirements while leaving security risks. We also find that security results vary with prompting. These findings highlight pressing challenges and offer actionable insights for future advancements in LLM-assisted hardware design. Our data and code are available at https://github.com/chenqirui2002/HardSecBench.

Software testing is crucial for ensuring the correctness and reliability of software systems. Automated generation of issue reproduction tests from natural language issue descriptions enhances developer productivity by simplifying root cause analysis, promotes test-driven development -- "test first, write code later", and can be used for improving the effectiveness of automated issue resolution systems like coding agents. Existing methods proposed for this task predominantly rely on closed-source LLMs, with limited exploration of open models. To address this, we propose SWE-Tester -- a novel pipeline for training open-source LLMs to generate issue reproduction tests. First, we curate a high-quality training dataset of 41K instances from 2.6K open-source GitHub repositories and use it to train LLMs of varying sizes and families. The fine-tuned models achieve absolute improvements of up to 10% in success rate and 21% in change coverage on SWT-Bench Verified. Further analysis shows consistent improvements with increased inference-time compute, more data, and larger models. These results highlight the effectiveness of our framework for advancing open-source LLMs in this domain.

LLM-based agents are increasingly capable of complex task execution, yet current agentic systems remain constrained by text-centric paradigms that struggle with long-horizon tasks due to fragile multi-turn dependencies and context drift. We present CaveAgent, a framework that shifts tool use from LLM-as-Text-Generator'' to LLM-as-Runtime-Operator.'' CaveAgent introduces a dual-stream architecture that inverts the conventional paradigm: rather than treating the LLM's text context as the primary workspace with tools as auxiliary, CaveAgent elevates the persistent Python runtime as the central locus of state, with a lightweight semantic stream serving as its orchestrator. Beyond leveraging code generation to resolve interdependent sub-tasks (e.g., loops, conditionals) in a single step, CaveAgent introduces \textit{Stateful Runtime Management}: it injects, manipulates, and retrieves complex Python objects (e.g., DataFrames, database connections) that persist across turns, unlike existing code-based approaches that remain text-bound. CaveAgent further provides a runtime-integrated skill management system that extends the Agent Skills open standard, enabling ecosystem interoperability through executable skill injections. This persistence mechanism serves as a high-fidelity external memory that reduces context drift in multi-turn interactions and preserves processed data for downstream applications without information loss. Evaluations show consistent improvement across challenging benchmarks, enabling CaveAgent to handle data scales that cause context overflow in both JSON-based and code-based agents. The accessible runtime state further provides programmatically verifiable feedback, enabling automated evaluation and reward signal generation without human annotation and establishing a structural foundation for future research in Reinforcement Learning with Verifiable Rewards (RLVR).

Large Language Models (LLMs) are increasingly embedded in agentic frameworks for scientific discovery. First-principles materials computation imposes a demanding standard for autonomy: successful execution depends on internally consistent inputs, supervision of long-running calculations, and verified outputs. Here we present VASP Agent, a coding-agent-centered system that combines reusable domain skills, deterministic tools, workspace-state inspection, runtime evidence, and scientific guardrails to execute multi-step VASP calculations. The system is evaluated across multiple tasks including structural relaxation, bandgap calculation, equilibrium lattice constant determination, and CO/Pt(111) adsorption. VASP Agent completes all evaluated cases, and its computed numerical results are compared with those obtained using pymatgen and other agentic tools. When large deviations occur, the calculation parameters produced by VASP Agent are more appropriate than those produced by LLM-based workflows. Failure analysis shows that errors that terminate fixed pipelines can be diagnosed and recovered under agentic control.

AI coding assistants produce vulnerable code in 45% of security-relevant scenarios~\cite{veracode2025}, yet no public training dataset teaches both traditional web security and AI/ML-specific defenses in a format suitable for instruction tuning. We present SecureCode, a production-grade dataset of 2,185 multi-turn security training examples spanning two domains: web application security (1,435 examples covering the OWASP Top 10 2021 across 11 languages and 9 frameworks, 100% grounded in documented CVEs and security incidents) and AI/ML security (750 examples covering all 10 OWASP LLM Top 10 2025 categories across more than 40 frameworks, including LangChain, OpenAI, and Hugging Face). Every example follows a 4-turn conversational structure -- feature request; vulnerable and secure implementations with attack demonstrations; advanced probing; and defense-in-depth operational guidance -- designed for direct use in instruction tuning pipelines. Quality assurance combines automated structural validation with multi-agent review from seven specialist AI perspectives (more than 10{,}500 assessments) and an 8-phase remediation pipeline, producing a rubric-calibrated mean quality score of 93.8/100 ($σ= 0.93$) for the AI/ML component. Each example provides SIEM integration strategies, infrastructure hardening recommendations, and testing approaches using production frameworks. We release the unified dataset on Hugging Face with domain-specific loading configurations (web, aiml, default), alongside eight fine-tuned open-source models (3B--20B parameters, QLoRA), and an evaluation framework with four security-specific metrics. To our knowledge, SecureCode is the first public dataset that jointly provides OWASP Top 10 2021 web coverage and OWASP LLM Top 10 2025 AI/ML coverage in a unified conversational schema suitable for instruction tuning.

Retrieving code functions, classes or files relevant to a user query, bug report or feature request from large codebases is a fundamental challenge for Large Language Model (LLM)-based coding agents. Agentic approaches typically employ sparse methods like BM25 or dense embedding strategies to identify semantically relevant units. While dense embedding approaches can outperform BM25 by large margins, both ignore the graph-structured characteristics of the codebase. To address this, we propose SpIDER (Spatially Informed Dense Embedding Retrieval), a dense retrieval approach that integrates LLM-based reasoning with graph-based exploration of the codebase. We further introduce SpIDER-Bench, a graph-structured benchmark curated from SWEPolyBench, SWEBench-Verified and Multi-SWE-bench, spanning Python, Java, JavaScript and TypeScript repositories. SpIDER's graph-based candidate expansion attaches a structural reason for inclusion to each surfaced function (its seed and the edge type linking them), making the candidate set auditable while keeping the retrieval budget fixed. The graph is built from per-repository syntax trees, so it can be constructed on-demand at the start of a developer session rather than precomputed offline. Empirical results show that SpIDER consistently improves dense retrieval Recall@20 across every language and benchmark in SpIDER-Bench: by at least 13% relative (+0.05 to +0.12 absolute) along containment edges, rising to at least 27% relative (+0.11 to +0.19 absolute) once call edges are explored.

A program migrated to post-quantum cryptography can verify its own signatures while producing keys or signatures that another implementation rejects. We introduce a contract-based task for migrating a Go file signer from RSA to ML-DSA-44, and compare coding agents with and without structured checker feedback. Both conditions receive the contract, compiler, documentation, and OpenSSL. Across 160 attempts in four local-agent configurations, twelve final patches pass local verification but fail external requirements. Checker access does not increase the observed completion rate in any comparison. Recorded traces show unresolved defects and checks invoked only after a patch is correct. Serving settings also affect completion: reducing only Qwen3.8's context window from 128K to 32K lowers full passes from 36/40 to 4/40. Four exploratory trials using GPT-6 Astra through Codex and Claude Fable 5.1 through Claude Code pass all 40 checks, including both baselines. These findings support evaluating interoperability separately from local agreement and reporting harness and serving limits alongside agent results.

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 0.23x 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 strong performance on code translation between widely used programming languages. However, translation becomes much less reliable for domain-specific code, where correctness depends on framework-specific APIs and execution semantics. One example is translating deep-learning code from PyTorch to JAX, where LLM outputs often contain subtle bugs or non-idiomatic usage that prevents execution or changes behavior. Prior work suggests that curated bug-fix data from LLM-generated code can help improve code generation quality, but such resources are still limited for PyTorch-to-JAX translation. In this work, we introduce T2J, a benchmark of LLM translation bugs paired with developer-written fixes for PyTorch-to-JAX code. We start from 20 kernels in the TorchLeet dataset, translate them to JAX using the weak LLM gpt-4o-mini, and hire software developers to debug and repair the generated JAX implementations. We then use T2J to improve PyTorch-to-JAX translation for the weak LLM gpt-4o-mini via in-context learning. Our evaluation shows that using T2J yields up to 20% improvement of our proposed metric T2J-CodeTrans-Score.

Code-capable large language model (LLM) agents are embedded in software engineering workflows where they can read, write, and execute code, raising "jailbreak" stakes beyond text-only settings. Prior evaluations emphasize refusal or harmful-text detection, leaving open whether agents compile and run malicious programs. We present JAWS-Bench (Jailbreaks Across WorkSpaces), a benchmark spanning three escalating workspace regimes mirroring attacker capability: empty (JAWS-0), single-file (JAWS-1), and multi-file (JAWS-M). We pair it with a hierarchical, executable-aware Judge Framework that tests (i) compliance, (ii) attack success, (iii) syntactic correctness, and (iv) runtime executability to measure deployable harm. Across seven LLM backends from five families, prompt-only attacks in JAWS-0 achieve 61% compliance; 58% are harmful, 52% parse, and 27% run end-to-end. In JAWS-1, compliance reaches ~100% for stronger models with a mean ASR (Attack Success Rate) ~71%; JAWS-M raises mean ASR to ~75%, with 32% runnable attack code. Wrapping an LLM in an agent increases ASR by 1.6$\times$, by overturning initial refusals during planning and tool use. Additional evaluations with SWE-Agent and OpenAI Codex exhibit similar trends, indicating that JAWS-Bench can be reused across multiple agent frameworks. Category analyses identify which attack classes are most vulnerable and deployable, motivating execution-aware defenses and refusal-preserving agent designs.

We present domain-adapted large language model agents designed to support Cherenkov Telescope Array operation and data analysis. The agents combine contextual knowledge with automated validation and iterative correction to produce more reliable outputs. This approach reduces manual effort, improves consistency, and helps accelerate operational and scientific workflows. The results demonstrate the potential of agentic systems as practical assistants in specialized research environments.

Test-Driven Development (TDD) is a widely adopted practice that requires developers to create and execute tests alongside implementation. With recent advances in Large Language Models (LLMs), developers can shift from manually writing the code to defining tests as executable specifications and delegating code synthesis to AI agents. However, enabling repository-level TDD under developer-written tests is challenging, requiring: (1) specification enhancement: identifying a concise yet representative test subset from large suites with rich task semantics; (2) retrieval augmentation: using tests to guide reasoning and context retrieval; and (3) test-driven refinement: interpreting test feedback for iterative improvement. We propose TENET, an agentic framework for repository-level code generation under the TDD paradigm. TENET includes: (1) a test harness mechanism that selects a concise test suite to maximize diversity of the target usage scenarios; (2) a tailored agent toolset for efficient retrieval and debugging; and (3) a reflection-based refinement workflow that iteratively analyzes failures and updates implementations. TENET consistently outperforms the strongest baselines across backbones, achieving 69.08% and 81.77% Pass@1 on RepoCod and RepoEval with Claude Sonnet 4, improving by 9.49 and 2.17 percentage points, respectively. Additionally, we present the first systematic study of how test suite characteristics influence LLM agent performance in TDD settings.

Fine-tuning large language models for code editing has typically relied on mining commits and pull requests. The working hypothesis has been that commit messages describe human intent in natural language, and patches to code describe the changes that implement that intent. However, much of the previously collected data is noisy: commit messages are terse, human-written commits commingle several unrelated edits, and many commits come from simple, rule-based bots. The recent adoption of software engineering agents changes this landscape. Code changes \emph{co-authored} by humans and agents are often accompanied by substantially more explicit natural-language descriptions of intent and rationale. Moreover, when these changes land in public repositories, they are implicitly filtered by humans: maintainers discard low-quality commits to their projects. We present AgentPack, a corpus of 1.8M code edits co-authored by Claude Code, OpenAI Codex, and Cursor Agent across public GitHub projects up to early October 2025. We describe the identification and curation pipeline, quantify adoption trends of these agents, and analyze the structural properties of the edits. Finally, we show that models fine-tuned on AgentPack can outperform models trained on prior human-only commit corpora, highlighting the potential of using public data from software engineering agents to train future code-editing models.

Machine Learning (ML) pipelines encode quality-relevant decisions across data preparation, training, evaluation, and configuration code. Some recurring source-level quality problems in these pipelines, known as ML code smells, may not cause immediate failures but can harm reproducibility, robustness, efficiency, or maintainability. Detecting ML code smell occurrences is challenging because the decisive evidence is often non-local, spanning helper functions, wrappers, imports, control-flow, and data-flow relations. We present SpecDetect4ML, a static analyser that operationalises 22 ML code smells using CPG views with project-level resolution. We evaluate it on 890 Python ML-based systems comprising more than 20M LOC and a system-level recall benchmark over the complete ML-relevant source subset of 10 selected systems. Under identical ML code smell specifications, CPG-based reasoning raises recall from 68.62% to 88.14% compared with AST-only analysis, while keeping CPG precision comparable at 90.32%. These results show that project-level static reasoning expands the detectable portion of non-local ML code smell occurrences, while configuration-dependent and runtime-only occurrences remain outside our source-only static claims.

API integration is a cornerstone of our digital infrastructure, enabling software systems to connect and interact. However, as shown by many studies, writing or generating correct code to invoke APIs, particularly web APIs, is challenging. Although large language models (LLMs) have become popular in software development, their effectiveness in automating the generation of web API integration code remains unexplored. In order to address this, we present WAPIIBench, a dataset and evaluation pipeline designed to assess the ability of LLMs to generate web API invocation code. Our experiments with several open-source LLMs reveal that generating API invocations poses a significant challenge, resulting in hallucinated endpoints, incorrect argument usage, and other errors. None of the evaluated open-source models was able to solve more than 40% of the tasks.

Multimodal Large Language Models have demonstrated exceptional performance in UI2Code tasks, significantly enhancing website development efficiency. However, these tasks incur substantially higher computational overhead than traditional code generation due to the large number of input image tokens and extensive output code tokens required. Our comprehensive study identifies significant redundancies in both image and code tokens that exacerbate computational complexity and hinder focus on key UI elements, resulting in excessively lengthy and often invalid HTML files. We propose EfficientUICoder, a compression framework for efficient UI code generation with three key components. First, Element and Layout-aware Token Compression preserves essential UI information by detecting element regions and constructing UI element trees. Second, Region-aware Token Refinement leverages attention scores to discard low-attention tokens from selected regions while integrating high-attention tokens from unselected regions. Third, Adaptive Duplicate Token Suppression dynamically reduces repetitive generation by tracking HTML/CSS structure frequencies and applying exponential penalties. Extensive experiments show EfficientUICoder achieves a 55%-60% compression ratio without compromising webpage quality and delivers superior efficiency improvements: reducing computational cost by 44.9%, generated tokens by 41.4%, prefill time by 46.6%, and inference time by 48.8% on 34B-level MLLMs. Code is available at https://github.com/WebPAI/EfficientUICoder.

Agentic Software Engineering (SE 3.0) represents a new era where intelligent agents are tasked not with simple code generation, but with achieving complex, goal-oriented SE objectives. To harness these new capabilities while ensuring trustworthiness, we must recognize a fundamental duality within the SE field in the Agentic SE era, comprising two symbiotic modalities: SE for Humans and SE for Agents. This duality demands a radical reimagining of the foundational pillars of SE (actors, processes, tools, and artifacts) which manifest differently across each modality. We propose two purpose-built workbenches to support this vision. The Agent Command Environment (ACE) serves as a command center where humans orchestrate and mentor agent teams, handling outputs such as Merge-Readiness Packs (MRPs) and Consultation Request Packs (CRPs). The Agent Execution Environment (AEE) is a digital workspace where agents perform tasks while invoking human expertise when facing ambiguity or complex trade-offs. This bi-directional partnership, which supports agent-initiated human callbacks and handovers, gives rise to new, structured engineering activities (i.e., processes) that redefine human-AI collaboration, elevating the practice from agentic coding to true agentic software engineering. This paper presents the Structured Agentic Software Engineering (SASE) vision, outlining several of the foundational pillars for the future of SE. The paper culminates in a research roadmap that identifies a few key challenges and opportunities while briefly discussing the resulting impact of this future on SE education. Our goal is not to offer a definitive solution, but to provide a conceptual scaffold with structured vocabulary to catalyze a community-wide dialogue, pushing the SE community to think beyond its classic, human-centric tenets toward a disciplined, scalable, and trustworthy agentic future.

Coding agents powered by large language models are becoming central modules of modern IDEs, helping users perform complex tasks by invoking tools. While powerful, tool invocation opens a substantial attack surface. Prior work has demonstrated attacks against general-purpose and domain-specific agents, but none have focused on the security risks of tool invocation in coding agents. To fill this gap, we conduct the first systematic red-teaming of six popular real-world coding agents: Cursor, Claude Code, Copilot, Windsurf, Cline, and Trae. Our red-teaming proceeds in two phases. In Phase 1, we perform prompt leakage reconnaissance to recover system prompts. We discover a general vulnerability, ToolLeak, which allows malicious prompt exfiltration through benign argument retrieval during tool invocation. In Phase 2, we hijack the agent's tool-invocation behavior using a novel two-channel prompt injection in the tool description and return values, achieving remote code execution (RCE). We adaptively construct payloads using security information leaked in Phase 1. In emulation across five backends, our method outperforms baselines on Claude-Sonnet-4, Claude-Sonnet-4.5, Grok-4, and GPT-5. On real agents, our approach succeeds on 19 of 25 agent-LLM pairs, achieving leakage on every agent using Claude and Grok backends. For tool-invocation hijacking, we obtain RCE on every tested agent-LLM pair, with our two-channel method delivering the highest success rate. We provide case studies on Cursor and Claude Code, analyze security guardrails of external and built-in tools, and conclude with practical defense recommendations.

Qualitative content analysis of open-ended survey responses is a commonly used research method in science education. However, traditional coding approaches are often time-consuming and prone to inconsistency, especially when applied to large datasets. Existing solutions from Natural Language Processing such as supervised classifiers, topic modeling techniques, and generative large language models have limited applicability in analysis of open-ended survey responses, since they demand extensive labeled data, disrupt established qualitative workflows, and/or yield variable results. In this paper, we introduce a text embedding-based classification framework called Deductive Semantic Content Analysis (DeSCA) that requires only a handful of examples per category to run, is transparent and replicable, and fits well with standard qualitative workflows. When benchmarked against human analysis of a physics education survey consisting of 2899 open-ended responses, the method described by our framework achieves high agreement with expert human coders across ten embeddings models on a simulated exhaustive coding task, using approximately 1-2% of the total dataset for training. The method achieves lower agreement on a complete selective coding task; this performance, however, improves with fine-tuning of the text embedding model, which can be done with a small amount of additional data. We unpack these results in terms of the theoretical assumptions of text embeddings, and further demonstrate how embeddings can be used to audit previously-analyzed datasets for coding consistency. These findings demonstrate that text embedding-assisted coding can flexibly scale to thousands of responses without sacrificing interpretability, opening avenues for deductive qualitative analysis at scale.

Issue-to-commit link recovery in software repositories is fundamental to software traceability and project management, yet it remains a challenging task. Prior studies show that only about 42.2% of issues on GitHub are correctly linked to their commits, highlighting the need for more effective solutions. Existing work has explored a range of ML/DL approaches, and more recently, large language models (LLMs) have been applied to this problem. However, these methods face two major limitations. First, LLMs are restricted by limited context windows and cannot simultaneously process all available data sources, such as long commit histories, extensive issue discussions, and large code repositories. Second, most approaches operate on individual issue-commit pairs, where a model independently scores the relevance of a single commit to an issue. This pairwise formulation fails to account for the complex associativity of software fixes, where an issue is often resolved by an aggregate chain of commits rather than a single atomic change. By ignoring these temporal and parental dependencies, existing methods often fail to incorporate the complete resolution logic and might misidentify intermediate commits as final fixes. Furthermore, this strategy is computationally inefficient in large repositories, as it requires exhaustively evaluating an enormous number of candidate pairs. To address these challenges, we present LinkAnchor, the first autonomous LLM-based agent designed specifically for issue-to-commit link recovery. LinkAnchor introduces a lazy-access architecture that allows the underlying LLM to dynamically retrieve only the most relevant contextual data, such as commits, issue comments, and code files, without exceeding token limits.

The application of Large Language Models (LLMs) is growing in the productive completion of Software Engineering tasks. Yet, studies investigating productive prompting techniques often employed a limited problem space, focusing primarily on well-known prompting patterns and targeting function-level SE practices. We identify significant gaps in real-world workflows that involve complexities beyond class-level (e.g., multi-class dependencies) and different features that can impact Human-LLM Interaction (HLI) processes in code generation. To address these issues, we designed an experiment to comprehensively analyze HLI features related to code generation productivity. Our study presents two project-level benchmark tasks that extend beyond function-level evaluations. We conducted a user study with 36 participants from diverse backgrounds, asking them to solve the assigned tasks by interacting with the GPT assistant using specific prompting patterns. We also examined participants' experiences and behavioral features during interactions by analyzing screen recordings and GPT chat logs. Our empirical investigation, based on statistical guidance, revealed (1) that three out of 15 HLI features emerged as consistently supported factors for productivity; (2) five primary guidelines for enhancing productivity for HLI processes; and (3) a taxonomy of 29 runtime and logic errors that can occur during HLI processes, along with suggested mitigation plans.

Atomic commits, which address a single development concern, are a best practice in software development. In practice, however, developers often produce tangled commits that mix unrelated changes, complicating code review and maintenance. Prior untangling approaches (rule-based, feature-based, or graph-based) have made progress but typically rely on shallow signals and struggle to distinguish explicit dependencies (e.g., control/data flow) from implicit ones (e.g., semantic or conceptual relationships). In this paper, we propose ColaUntangle, a new collaborative consultation framework for commit untangling that models both explicit and implicit dependencies among code changes. ColaUntangle integrates Large Language Model (LLM)-driven agents in a multi-agent architecture: one agent specializes in explicit dependencies, another in implicit ones, and a reviewer agent synthesizes their perspectives through iterative consultation. To capture structural and contextual information, we construct Explicit and Implicit Contexts, enabling agents to reason over code relationships with both symbolic and semantic depth. We evaluate ColaUntangle on two widely-used datasets (1,612 C# and 14k Java tangled commits). Experimental results show that ColaUntangle outperforms the best-performing baseline, achieving an improvement of 44% on the C# dataset and 82% on the Java dataset. These findings highlight the potential of LLM-based collaborative frameworks for advancing automated commit untangling tasks.

Large Language Models (LLMs) for code generation (i.e., Code LLMs) have demonstrated impressive capabilities in AI-assisted software development and testing. However, recent studies have shown that these models are prone to generating vulnerable or even malicious code under adversarial settings. Existing red-teaming approaches rely on extensive human effort, limiting their scalability and practicality, and generally overlook the interactive nature of real-world AI-assisted programming, which often unfolds over multiple turns. To bridge these gaps, we present RedCoder, a red-teaming agent that engages victim models in multi-turn conversation to elicit vulnerable code. The pipeline to construct RedCoder begins with a multi-agent gaming process that simulates adversarial interactions, yielding a set of prototype conversations and an arsenal of reusable attack strategies. We then fine-tune an LLM on these prototype conversations to serve as the backbone of RedCoder. Once deployed, RedCoder autonomously engages Code LLMs in multi-turn conversations, dynamically retrieving relevant strategies from the arsenal to steer the dialogue toward vulnerability-inducing outputs. Experiments across multiple Code LLMs show that our approach outperforms prior single-turn and multi-turn red-team methods in inducing vulnerabilities in code generation, offering a scalable and effective tool for evaluating the security boundaries of modern code-generation systems.

The rise of large language models (LLMs) has led to dramatic improvements across a wide range of natural language tasks. Their performance on certain tasks can be further enhanced by incorporating test-time reasoning techniques. These inference-time advances have been adopted into the code domain, enabling complex software engineering (SWE) tasks such as code generation, test generation and issue resolution. However, the impact of different reasoning techniques on code-centric SWE tasks has not been systematically explored. In this work, we survey code reasoning techniques that underpin these capabilities, with a focus on test-time compute and inference-time reasoning paradigms. We examine a variety of code-specific reasoning methods and progressively build up to SWE agents, which combine planning, tool use, and multi-step interaction. We also compare the impact of different techniques on coding tasks, highlighting their relative importance and outlining open challenges and future research directions. Across commonly used models and benchmarks, we find that approaches exploiting code-specific signals (e.g., structure and execution feedback) are frequently associated with improved performance, motivating a dedicated study of code reasoning beyond natural-language reasoning.

Fuzzing frameworks like syzkaller have uncovered thousands of Linux kernel crashes, many of which are critical and security-sensitive. However, the ability to rapidly repair these crashes has not kept pace, particularly given the complexity and low-level nature of kernel code. Predominantly targeting user-space applications, existing LLM-based program repair techniques are not tailored to the unique challenges posed by kernel fuzz bugs-such as the absence of natural language bug reports, lack of exhaustive test oracles, and highly specialized crash artifacts. Thus, in this work, we first identify the prevalent bottlenecks that generic agents struggle with in complex systems such as the Linux kernel. Guided by these findings, we then build kAgent, a workflow-based agent inspired by how kernel developers diagnose and fix bugs, and kGym++, the co-designed toolstack supporting kAgent's requests. kAgent inspects relevant execution logs, generates execution-grounded natural language hypotheses, synthesizes candidate patches, validates patches through crash reproduction, and iteratively refines its reasoning. We ablate these agentic system features in kAgent and quantitatively analyze their contributions to the overall performance. We also report our experience on building agents for kernel crash repair. Although derived from this work on Linux, we note that our experience applies broadly to fuzzing-discovered bugs in complex systems software. We evaluate kAgent on kBenchSyz and show that it can repair up to 54.5% of crashes without localization and 65% with correct file hints. We also show kAgent's generalization on a few wild Syzkaller bugs, and how different patch types offer varying utility to developers who debug complex system software.

While software requirements are often expressed in natural language, verifying the correctness of a program against such requirements is a hard and underexplored problem. Large language models (LLMs) are promising candidates for addressing this challenge, however our experience shows that they are ineffective in this task, often failing to detect even straightforward bugs. To address this gap, we introduce HoarePrompt, a novel approach that adapts fundamental ideas from program verification to natural language artifacts. Inspired from the strongest postcondition calculus, HoarePrompt employs a systematic, step-by-step process in which an LLM generates natural language descriptions of reachable program states at various code points. To manage loops, we propose few-shot-driven k-induction, an adaptation of the k-induction method widely used in model checking. Once program states are described, HoarePrompt leverages the LLM to assess whether the program, annotated with these state descriptions, conforms to the natural language requirements. For evaluating the quality of classifiers of program correctness with respect to natural language requirements, we constructed CoCoClaNeL, a challenging dataset of solutions to programming competition problems. Our experiments show that HoarePrompt improves the MCC by 61% compared to directly using Zero-shot-CoT prompts for correctness classification. Furthermore, HoarePrompt outperforms a classifier that assesses correctness via LLM-based test generation by an MCC increase of 106%. The inductive reasoning mechanism contributes a 26% boost to MCC, underscoring its effectiveness in managing loops.

We introduce BigO(Bench), a novel coding benchmark designed to evaluate the capabilities of generative language models in understanding and generating code with specified time and space complexities. This benchmark addresses the gap in current evaluations that often overlook the ability of models to comprehend and produce code constrained by computational complexity. BigO(Bench) includes tooling to infer the algorithmic complexity of any Python function from profiling measurements, including human- or LLM-generated solutions. BigO(Bench) also includes of set of 3,105 coding problems and 1,190,250 solutions from Code Contests annotated with inferred (synthetic) time and space complexity labels from the complexity framework, as well as corresponding runtime and memory footprint values for a large set of input sizes. We present results from evaluating multiple state-of-the-art language models on this benchmark, highlighting their strengths and weaknesses in handling complexity requirements. In particular, token-space reasoning models are unrivaled in code generation but not in complexity understanding, hinting that they may not generalize well to tasks for which no reward was given at training time.

Generative Pretrained Transformers (GPTs) are foundational Large Language Models (LLMs) for text generation. However, individual LLMs often produce inconsistent outputs and exhibit biases, limiting their representation of diverse language patterns. The closed-source nature of many powerful LLMs further restricts industry applications due to data privacy concerns. Inspired by successes in text generation, LLM ensemble techniques are now increasingly explored for code generation. This article reviews these emerging ensemble approaches to enhance understanding, encourage further research, and promote practical implementation in both text and code generation. We categorize LLM ensembles into seven main methods - weight merging, knowledge fusion, mixture-of-experts, reward ensemble, output ensemble, routing, and cascading - analyzing capabilities of those approaches. Our findings highlight key benefits such as improved diversity representation, enhanced output quality, and greater application flexibility. These insights aid model selection for real-world tasks and crucially, lay groundwork for extending ensemble strategies to multimodal LLMs.

Large Language Models (LLMs) have shown tremendous promise in automated software engineering. In this paper, we investigate LLMs for just-in-time regression test generation for programs, like parsers, interpreters, or compilers, that take highly structured, human-readable inputs. When a bug fix or code change is committed, the repository (as part of CI/CD) runs an LLM for a few minutes to generate regression tests that exercise the changed code and potentially trigger bugs. We frame LLM-based regression test generation as a machine translation task that takes the developer-provided commit message, the code change, and the input format name (e.g., XML), and produces regression tests for the described change in that format. Testing 72 commits to Mujs, Libxml2, Poppler, JerryScript, Z3, PHP, JQ, and MicroPython, our feedback-directed, zero-shot prototype Cleverest performed well, even without the code change. In under 2 minutes on average, Cleverest found as many bugs as the state-of-the-art directed greybox fuzzer WAFLGo did in 24 hours, even though WAFLGo started with a commit-reaching seed corpus in most cases. Using the Cleverest-generated tests as a seed corpus in coverage-guided greybox fuzzing doubles the number of bugs found; we call this integration ClevFuzz. We also find that some commit messages are more expressive than others, thus we ask how it impacts Cleverest's effectiveness. Cleverest picks up on the change intention: e.g., given a commit message that a patch changes how floating point variables are treated in the Mujs JavaScript interpreter, Cleverest generates JavaScript programs that contain floating point variables. Minimally changing commit messages to reduce or increase their information substantially impacts effectiveness: adding 17 words on average (max. 43) to make ineffective commit messages more expressive significantly increased the number of bugs found.

Code-related benchmarks play a critical role in evaluating large language models (LLMs), yet their quality fundamentally shapes how the community interprets model capabilities. In the past few years, awareness of benchmark quality has grown. Yet, after a decade-scale (2014-2025) survey over 672 code benchmarks, we observed a lag between growing awareness and actual practice. For example, in 2025 alone, the number of benchmarks that ignore code coverage when providing test cases nearly matches the total count accumulated across the previous ten years. In response, we take a clear position: Code benchmarks must prioritize rigor in benchmark construction, reliability in evaluation, and reproducibility in release. To operationalize this position, we introduce a code benchmark guideline HOW2BENCH with 55 checklists. Finally, our further human study also exposed that the current issues not only stem from the significant effort required, but also from a lack of awareness regarding their importance.

Large language models (LLMs) have shown strong performance in automated code generation, with few-shot prompting widely used for its simplicity and effectiveness. However, few-shot methods depend on curated or manually crafted reference examples, limiting their applicability in data-free coding scenarios such as real-world data-free coding scenarios and benchmarks without training sets. Existing methods that generate reference examples via recitation or analogy cannot guarantee their authenticity or accuracy. Inspired by human metamemory, we propose a novel metamemory agent to enhance one-time code generation in data-free coding scenarios. The agent guides LLMs to recall relevant prior knowledge, evaluate confidence in recalled information, and selectively exploit reliable content for problem solving. This agent removes the need for external reference examples, improves the authenticity and accuracy of recalled knowledge, and adaptively tailors the recall&evaluation process to each task. Extensive experiments demonstrate that the proposed metamemory agent significantly improves one-time code generation quality across data-free coding scenarios. The AI contribution is the metamemory agent, which makes self-recalled examples reliable through confidence evaluation and selection; the engineering application is data-free automated code generation, validated on eight public benchmarks.

Recent advancements in large language models (LLMs) have demonstrated their potential in automating the scientific research ideation. Existing approaches primarily focus on prompting techniques, often producing ideas misaligned with expert standards - novelty, feasibility, and effectiveness, which are widely recognized by the research community as the three key subdimensions of high-quality ideas. Also, balancing these dimensions remains challenging due to their inherent trade-offs. To address these limitations, we propose the first framework that employs a two-stage approach combining Supervised Fine-Tuning (SFT) and controllable Reinforcement Learning (RL) for the task. In the SFT stage, the model learns foundational patterns from pairs of research papers and their corresponding follow-up ideas. In the RL stage, multi-dimensional reward models guided by fine-grained feedback evaluate and optimize the model across key dimensions. During inference, dimensional controllers coordinated by a sentence-level decoder enable dynamic context-aware steering of the idea generation process. Our framework provides a balanced approach to research idea generation, achieving high-quality outcomes in the experiment by dynamically navigating the trade-offs among novelty, feasibility, and effectiveness.

Context: Machine Learning (ML) significantly impacts Software Engineering (SE), but studies mainly focus on practitioners, neglecting researchers. This overlooks practices and challenges in teaching, researching, or reviewing ML applications in SE. Objective: This study aims to contribute to the knowledge, about the synergy between ML and SE from the perspective of SE researchers, by providing insights into the practices followed when researching, teaching, and reviewing SE studies that apply ML. Method: We analyzed SE researchers familiar with ML or who authored SE articles using ML, along with the articles themselves. We examined practices, SE tasks addressed with ML, challenges faced, and reviewers' and educators' perspectives using grounded theory coding and qualitative analysis. Results: We found diverse practices focusing on data collection, model training, and evaluation. Some recommended practices (e.g., hyperparameter tuning) appeared in less than 20% of literature. Common challenges involve data handling, model evaluation (incl. non-functional properties), and involving human expertise in evaluation. Hands-on activities are common in education, though traditional methods persist. Conclusion: Despite accepted practices in applying ML to SE, significant gaps remain. By enhancing guidelines, adopting diverse teaching methods, and emphasizing underrepresented practices, the SE community can bridge these gaps and advance the field.

Large language models (LLMs) are increasingly used for program synthesis, yet they often generate code that is functionally plausible but insecure. Progress in secure code generation has been hindered by benchmarks that are small, non-executable, leak mitigation details, or rely on noisy analyzers and subjective judgments, making it difficult to measure whether security improves without sacrificing correctness. We address these gaps with CodeSecEval, an execution-based benchmark for secure code generation, comprising 255 Python tasks spanning 77 CWE categories. Each task provides paired insecure and secure implementations together with executable functional and vulnerability-targeted security tests, enabling precise and reproducible evaluation of secure code generation and insecure-code repair. Building on CodeSecEval, we propose SecAwareCoder, an agent-based framework that shifts code generation toward secure-by-construction synthesis. SecAwareCoder performs task-adaptive threat modeling to identify security-sensitive regions and derive task-grounded vulnerability hypotheses, uses these hypotheses to guide both constraint-aware code generation and security-aware test synthesis, and leverages execution feedback for targeted refinement. Experiments across multiple LLM backbones show that SecAwareCoder consistently improves Pass@1 and security robustness over prompting and analyzer-driven baselines, narrowing the security--correctness gap in LLM code generation.

Large Language Models (LLMs) struggle with reliably generating highly structured outputs, such as program code, mathematical formulas, or well-formed markup. Constrained decoding approaches mitigate this problem by greedily restricting what tokens an LLM can output at each step to guarantee that the output matches a given constraint. Specifically, in grammar-constrained decoding (GCD), the LLM's output must follow a given grammar. In this paper, we demonstrate that GCD techniques (and in general constrained decoding techniques) can distort the LLM's distribution, leading to outputs that are grammatical but appear with likelihoods that are not proportional to the ones given by the LLM, and so ultimately are low-quality. We call the problem of aligning sampling with a grammar constraint, grammar-aligned decoding (GAD), and propose adaptive sampling with approximate expected futures (ASAp), a decoding algorithm that guarantees the output to be grammatical while provably producing outputs that match the conditional probability of the LLM's distribution conditioned on the given grammar constraint. Our algorithm uses prior sample outputs to soundly overapproximate the future grammaticality of different output prefixes. Our evaluation on code generation and structured NLP tasks shows how ASAp often produces outputs with higher likelihood (according to the LLM's distribution) than existing GCD techniques, while still enforcing the desired grammatical constraints.

The growing complexity of software calls for innovative solutions that support the deployment of reliable and secure software. Machine Learning (ML) has shown its applicability to various complex problems and is frequently used in the dependability domain, both for supporting systems design and verification activities. However, using ML is complex and highly dependent on the problem in hand, increasing the probability of mistakes that compromise the results. In this paper, we introduce Propheticus, a ML framework that can be used to create predictive models for reliable and secure software systems. Propheticus attempts to abstract the complexity of ML whilst being easy to use and accommodating the needs of the users. To demonstrate its use, we present two case studies (vulnerability prediction and online failure prediction) that show how it can considerably ease and expedite a thorough ML workflow.

As long-horizon coding agents produce more code than any developer can review, oversight collapses onto a single surface: the automated test suite. Reward hacking naturally arises in this setup, as the agent optimizes for passing tests while deviating from the users true goal. We study this reward hacking phenomenon by decompose software engineering tasks into three parts: (i) a natural language description of the specification (ii) visible validation tests that exercise specified features in isolation, and (iii) held-out tests that compose those same features to simulate real-world usage. Based on the specification and the visible validation test suites, a genuine agent would be able to generate a solution that can also pass all of the held-out tests. Therefore we use the gap in pass rates on these two suites to quantify reward hacking. Based on this methodology, we introduce SpecBench, a benchmark comprising 30 systems-level programming tasks ranging from short horizon tasks like building a JSON parser to ultra long horizon tasks like building an entire OS kernel from scratch. Large-scale experiments reveal a consistent pattern: while every frontier agent saturates the visible suite, reward hacking persists, with smaller models exhibiting larger gaps on holdout suites. The gap also scales sharply with task length: it grows by 28 percentage points for every tenfold increase in code size. Failures range from subtle feature isolation to deliberate exploits, including a 2,900-line hash-table "compiler" that memorizes test inputs. SpecBench offers a principled testbed for measuring whether coding agents build genuine working systems or merely game the test suites developers hand them.

Language generation is almost universally treated as a sequential process: autoregressive models emit one token at a time, while diffusion language models replace token-level seriality with a long trajectory of iterative refinement. In this work, we introduce PlaidQ, a 0.7B continuous diffusion language model for code generation, and show that its trajectory can be aggressively distilled into only a few denoising steps---or even one, enabling efficient code generation. PlaidQ repurposes a pretrained autoregressive model as a bidirectional denoiser over continuous token embeddings. We distill PlaidQ with distribution matching for few-step generation and paired-trajectory supervision for one-step generation. At matched model scale, PlaidQ is competitive with discrete diffusion language models on code generation. Distillation then shifts the quality--compute frontier: a 16-step student reaches 31.78 and 40.49 pass@10 on HumanEval and MBPP+, surpassing the same PlaidQ teacher sampled for 512 steps. At the extreme, paired-trajectory distillation achieves 7.07 pass@1 on HumanEval with a single denoising step, producing functionally correct programs. Together, these results establish continuous diffusion as a viable path to few-step and one-step code generation. Broadly, continuous diffusion is not merely another representation for language: it provides an interface through which language models can inherit the acceleration and distillation machinery of continuous diffusion modeling. Training and inference code and model checkpoints are available at https://github.com/pengzhangzhi/plaidq.

Generative models now write application code, harden and monitor it, and probe it for exploitable flaws, so that one family of models increasingly plays builder, defender and breaker at once. The prevailing view treats full autonomy as the natural end point of assistance. This article argues for a narrower and more defensible position than a blanket requirement for human oversight. We define the shared generative substrate as the set of upstream dependencies (training corpus, model family, alignment procedure, vendor, toolchain) that induce correlated errors, and we define independence as a measurable property of pairs of lifecycle roles rather than an attribute of any participant. A coincident-failure model in the tradition of Eckhardt and Lee shows why organisational independence, the proxy on which verification standards have relied, no longer implies statistical independence once roles share a substrate; it also shows that heterogeneous models, deterministic analysers and formal verification can restore independence for the fault classes they cover. What remains for humans is specific: authority over the specification against which every machine oracle is judged, accountability that current governance instruments do not permit to be delegated, and last-resort authority to halt. We translate this into an operational framework with five autonomy levels, three distinct human roles and five decision criteria (consequence, reversibility, time-criticality, verifiability and adversarial exposure), apply it to build, defend and test actions, and specify how independence and oversight effectiveness can be measured. The central claims are stated as testable hypotheses with a protocol for refuting them.

AI agents increasingly act through tools and delegated authority, but general incident repositories rarely capture the mechanisms needed to compare public failures with agent-security evaluations. We present the Agent Incident Registry (AIR) (Project page: https://enkryptai.com/air), a source-linked catalog containing 487 records of agent-related events disclosed from 2022 through 2026. Each record includes supporting evidence, a stable identifier, and missingness-aware labels for causal role, disclosure class, mechanism, and outcome. Among the 336 generative-system records in which the agent acted, 81 involved realized harm (24%). Realized outcomes concentrate in in-the-wild and safety-failure records, while responsible disclosures and research demonstrations are overwhelmingly demonstrated; the aggregate share therefore characterizes collection composition rather than deployment risk. After initial curation, a second human reviewer checked all 487 records and their existing labels for completeness and correctness. In a deployment-analogue audit, InjecAgent's 1,054 cases occupy three of AIR's twelve surfaces and are all attacker-triggered, whereas AIR contains 92 no-adversary safety failures. AIR supports source-grounded case retrieval and evaluation-scope auditing, not failure-rate or control-efficacy estimation.

An agent skill is a folder containing a SKILL.md file with instructions for a language-model agent, optionally accompanied by scripts and reference files. The agent loads the skill when it judges that a task matches the skill description. Anthropic introduced the format in October 2025 as an open specification. Nine months later, public GitHub repositories hold millions of skill files. Skills are unlike the artifacts that software engineering researchers usually mine: they are written mainly in natural language, a model selects them probabilistically at run time, and no compiler or type checker verifies the selection. Skills also have no central registry or package manager; developers reuse them by copying folders between repositories. How developers write, reuse, and maintain skills is therefore an empirical question, and no existing dataset records this population. We present GitSkills, a dataset of 3,797,117 SKILL.md files collected from 282,200 public repositories in July 2026. The dataset retains every file occurrence with its repository, path, and content hash. We group identical files into 1,877,981 distinct contents and enrich one representative per group with the full text, parsed front matter, folder contents, repository metadata, and, for a subset, the commit history of the file. A single self-contained SQLite file supports research on the adoption, reuse, structure, authorship, maintenance, and security of agent skills.