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arXiv2026

SWE-bench Science: Can Coding Agents Resolve Engineering Tasks in Science?

Software increasingly functions as part of the scientific instrument itself, making failures in scientific code capable of compromising not only program behavior but also the evidence underlying scientific conclusions. Yet existing evaluations of coding agents largely emphasize aggregate task success, providing limited insight into why agents fail when repairing scientific software. We introduce \textbf{SWE-bench Science}, a repository-level benchmark for scientific software engineering comprising 119 tasks from 98 GitHub repositories across 20 scientific domains. Each task is organized into one of three paradigms: Issue-driven, Expert-exploratory, and Engineering-integration. Even the best-performing agent, \textbf{Claude Code with Opus-5 (max), achieves a pass@1 below 50\%}, highlighting the substantial challenges posed by scientific software engineering. We identify four recurring failure mechanisms: deficits in scientific knowledge or abstraction, misguided exploration or surface-level repair, incomplete repair coverage or system integration, and failures to generalize scientific knowledge beyond observed cases in our analysis. We further conduct a paired ablation that removes explicit scientific guidance while preserving the repository and executable engineering context. The results show that scientific knowledge is not uniformly beneficial: well-grounded information can constrain repair and improve average performance and token efficiency, whereas poorly aligned guidance can induce anchoring and does not necessarily improve exact repair success. Together, SWE-bench Science provides a broad testbed for studying both the capabilities and failure mechanisms of coding agents in scientific software engineering.

cs.CL↗

arXiv2026

Software Aging in LLM-Generated Applications: Runtime Evidence, Static Analysis, and Human-Written Comparisons

Large Language Models (LLMs) are increasingly used to generate executable software systems from natural language specifications, accelerating development and reducing manual implementation effort. Although recent studies have investigated the functional correctness, security, maintainability, and robustness of LLM-generated code, little is known about the long-term reliability of such systems under sustained execution. In this paper, we experimentally investigate software aging symptoms in LLM-generated service-based applications across generation-and-execution environments. Using backend scenarios derived from BaxBench, we generated applications targeting JavaScript, Python, and Rust through LLM-based generation platforms, validated them with BaxBench-derived tests, and subjected them to 48-hour workload executions. We monitored memory usage, response time, and throughput and analyzed them using the Mann--Kendall test and Sen's slope estimator. We further complemented the runtime evaluation with static analysis of the generated source code and an exploratory comparison with human-written implementations of related backend scenarios. The results show that memory usage is the most consistent indicator of potential software aging, with statistically significant upward trends in most application-environment combinations, while response time and throughput exhibit more heterogeneous behavior. Static analysis identified plausible code-level aging mechanisms, and the comparison with human-written systems showed that the aging symptoms observed in LLM-generated applications align with degradation patterns also found in manually developed implementations. These findings indicate that functional correctness alone is insufficient to assess the operational reliability of LLM-generated software before deployment in continuously running environments.

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arXiv2026

WiseSpec: Requirements-Driven Agents for Code Generation

Code generation aims to automatically generate source code from task requirements and has attracted significant attention with the rapid advancement of large language models (LLMs). Despite remarkable progress, LLMs often struggle to generate correct code for complex software engineering tasks because task descriptions are frequently incomplete, ambiguous, or lack critical contextual information. Existing approaches primarily improve the capabilities of coding agents through more sophisticated tools, skills, and workflows, while largely overlooking the quality of the task requirements themselves. To address this limitation, we draw inspiration from software requirements engineering and propose WiseSpec, a novel requirements-driven agent framework for repository-level code generation. WiseSpec automatically constructs structured and information-rich requirements, assesses their quality through execution-based evaluation, and iteratively refines them to better guide code generation. Experimental results show that WiseSpec consistently outperforms all baselines, achieving an average improvement of 13.17% in %Resolved.

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arXiv2026

Towards a Reliable and Practical Eval Pipeline

LLM-based software systems increasingly require effective "evals" as quality gates in the development lifecycle. However, existing work typically addresses individual aspects of eval reliability rather than the full set of practical requirements. We present an end-to-end eval pipeline that combines eval checklist creation, with learned aggregation for checklist responses, to improve agreement across LLM judges and accuracy against human judgments. The framework additionally pro- vides self-consistency, explanations, and prediction uncertainty, and we empirically demonstrate its effectiveness.

cs.AI↗

arXiv2026

Replacing Training with Memory: Listwise Selection for Text-to-SQL

Modern Text-to-SQL systems often follow generate-execute-select pipelines, generating multiple candidate queries then selecting the best one. Listwise selection, by jointly comparing multiple candidates, has been widely adopted, but fine-tuning listwise selectors is costly. We thus propose a fine-tuning-free listwise selector. We replace two major fine-tuning objectives with inference-time strategies: (1) learning selection criteria as ordering and (2) mitigating positional bias. First, we build reusable structured memories instead of learning selection behavior as model parameters. Given a question, MaP-SQL retrieves memories distilled from training data that encode how natural language maps to schema elements, SQL operations, and expected outputs. These memories serve as explicit decision criteria for evaluating candidates in a listwise manner. Second, to mitigate ordering bias of listwise selectors, we aggregate rankings across multiple input permutations, with inference cost optimized by execution results and pointwise scoring. Our approach improves selection accuracy while maintaining efficiency and compatibility with existing large language models. Across Text-to-SQL benchmarks, it produces more stable selection without fine-tuning and fewer unnecessary comparisons than existing methods. On BIRD-dev, it outperforms the previous state-of-the-art selector-based method R^3-SQL by 2.02 execution accuracy points on average using the same candidate sets, with 2.92x fewer tokens.

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arXiv2026

Probabilistic Model Checking of Autoregressive Neural Sequence Models

Test-set accuracy is silent on two issues that matter when deploying autoregressive neural sequence models: how much probability mass the system under test (SUT) places on constraint-violating alternatives that are reachable under sampling and what fraction of the input population satisfies a domain requirement. We answer both with probabilistic model checking. The pipeline extracts a discrete-time Markov chain (DTMC) from the SUT's token-by-token generation, verifies formal PCTL specifications with the PRISM model checker, and aggregates the per-input verdicts into a coverage curve over the input space. A soundness theorem establishes the DTMC as an under-approximation, so every verdict yields a certified interval on the SUT's true reachability probability. The coverage built from those verdicts is, therefore, conservative by construction. A counterexample-guided abstraction refinement (CEGAR) loop adaptively tightens the interval, and a maximum-likelihood algorithm extracts the most probable falsifying trace. Two case studies exercise the pipeline. On a GPT-2 computer-aided process-planning (CAPP) model with 100% test accuracy, the pipeline quantifies the probability mass greedy decoding hides, but that is reachable with sampling; and identifies the smallest training fraction at which an ordering requirement holds population-wide, neither of which test accuracy can report. We then verify the SMILES molecular generator with a 50x larger vocabulary. The only change is an external chemical-validity oracle, and the pipeline identifies the gap between structural completeness and chemical validity.

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arXiv2026

Does Fault Localization Beat a Fresh Attempt? A Placebo-Controlled Study of Test-Guided Code Repair

Fault localization can focus a code model's repair on the statements a failing test implicates, but a targeted edit may succeed merely because it is small, and a second model call may succeed without using the failure at all. We separate these explanations with three arms applied to the same failed candidate: blind whole-solution resampling, spectrum-based localization followed by suspect-span infilling, and same-length infilling at a disjoint random code span. Across three frozen 26-32B models, three benchmarks and 488 failing candidates, plus a separately declared 24B fourth model from a third family, three results follow. First, localization is rarely available: only 9.0% of failing candidates expose a failing public test with a usable spectrum. Second, among the 177 candidates localizable from a strong suite, localized infilling loses decisively to blind resampling at a matched attempt count (3:40, p = 3.0 x 10^-9), opposite to our hypothesis; the loss replicates in a third family at -11.3 points (95% CI [-16.6, -6.8]), and widening the edit does not rescue it. Third, against the random-span placebo localized infilling leads pooled (11:1, Holm-adjusted p = .019), but that lead resolves in no individual model under the analysis our shipped plan designates primary (best Holm p = .087), so we report the location effect as suggestive rather than established. Re-pricing attempts as tokens narrows but does not overturn this: a span attempt spends 21.7 generated tokens against 371.1, yet 16 localized attempts reach 6.8% while one blind attempt already reaches 10.1%. Infilling reproduces the removed span verbatim in 48.9% of attempts, which is why more budget does not help. We restrict every localization conclusion to the 24-32B models tested.

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arXiv2026

Fine-Tuning Large Language Models to Classify Pull Request-Issue Alignments: Going Beyond Prompting

Context: Accurate alignment between pull requests (PRs) and corresponding issues is crucial for efficient software development and maintaining code quality, as misalignments can reduce traceability, hinder defect localization, and decrease maintainability. Objective: This study aims to improve automated PR-issue alignment classification by leveraging fine-tuned large language models (LLMs) across multiple alignment categories, and conducts interpretability analysis to investigate the effects of PR-issue fields on the predictions of fine-tuned LLMs. Method: Our methodology consists of dataset preparation, LLM fine-tuning, and interpretability analysis. We first extended an existing dataset and applied data augmentation to address class imbalance. GPT-4o was then fine-tuned via instruction tuning, and open-source LLMs including CodeLlama-7B, CodeQwen1.5-7B, StableCode-3B, CodeGemma-7B, and Deepseek-Coder-6.7B were fine-tuned using classification-specific heads. Interpretability analysis using Shapley Additive Explanations (SHAP) was conducted to examine the influence of PR-issue fields on predictions for the best-performing open-source LLM. Results: Fine-tuned LLMs outperformed baseline models, achieving average improvements of 6.15% in accuracy and F1-micro, 14.69% in F1-macro, and 6.15% in recall. CodeLlama-7B emerged as the best-performing fine-tuned LLM overall, while interpretability analysis revealed that code diffs together with issue body and PR body contents exert the greatest influence on predictions. Conclusions: Fine-tuning substantially enhances PR-issue alignment classification, improving both accuracy and efficiency. Interpretability analysis provides actionable insights into the dataset features driving alignment decisions, deepening understanding of how LLMs reason over software artifacts.

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arXiv2026

Reliable LLM-Generated Programs for High-Energy Physics Experiments through Graph-Grounded Software Knowledge

Extracting physics information from modern particle-physics experiments requires multistage analyses implemented on top of large and highly interconnected software ecosystems. General-purpose large language models (LLMs) often produce unreliable programs for such tasks because a user request alone rarely specifies the required APIs, dependencies, and usage conventions. We organize these software relations before generation and retrieve task-relevant knowledge at inference time. Using the open-source ROOT framework as a representative and reproducible testbed, we evaluate a complete grounding system that combines hybrid retrieval over a heterogeneous software knowledge graph, skill-selected workflow examples, and execution-guided repair. On a benchmark of 275 ROOT tasks, grounding improves first-attempt execution from 58.5% to 76.0% under Claude Code orchestration and from 51.3% to 64.0% under standalone orchestration. Final success increases from 90.5% to 96.0% and from 78.9% to 90.9%, respectively, while the average generation cost per successful task increases by only 1.3% and 3.2%. The gains persist under a strong coding agent, indicating that explicit software knowledge remains valuable even when agentic scaffolding is already in place. Because the method captures software relations common to large codebases rather than facts specific to ROOT or a particular model, it should transfer to other experiment frameworks and proprietary software, especially where documentation is sparse or internal dependencies are complex.

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arXiv2026

Hints Help But Do They Teach? Evaluating Skills Transfer in Code Generation

When a hint turns a failing generated program into a passing one, does it provide missing information or merely steer the model toward a solution it could already produce? We test these hypotheses on HumanEval+ and MBPP+ using executable evaluation. For Qwen2.5-3B-Instruct, adaptive relevant hints rescue 36 of 79 selected failures; an unrelated hint rescues 19, while eight unhinted samples solve 46 and recover 31 of the 36 relevant-hint rescues. Phi-3.5-mini shows the same pattern: relevant hints rescue 42 of 101 failures, an unrelated hint rescues 17, and unhinted sampling solves 57, including 36 of the 42 relevant-hint rescues. Because the hint conditions use different attempt budgets, these comparisons do not isolate a purely semantic effect. Mechanistic tests on Qwen identify a stable activation direction shared by relevant and unrelated hints. Persistently adding this direction yields 14 rescues and 18 regressions, with no detectable net accuracy gain; learned low-rank interventions have a positive but imprecise estimated effect. Full textual specifications solve 22 of 24 context-defined problems, versus 5-11 for tested virtual-KV prefixes. Post-generation hidden-state probes transfer across benchmarks, with pooled AUROC 0.806 and 0.780, but their top-one selection advantage over token confidence is statistically unresolved. Overall, relevant hints can rescue failures, but most rescued solutions are already reachable through ordinary sampling, and the internal interventions tested here do not establish task-general capability transfer.

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arXiv2026

Smart Contracts Claimed Vulnerable by the CVE Database, with Labels and Source Locations

The Common Vulnerabilities and Exposures (CVE) database catalogs vulnerability claims in hard- and software, among them those pertaining to blockchain programs a.k.a. smart contracts. We present CVE-Smart-Contracts, a curated dataset of CVE records up to July 2026 referring to Ethereum smart contracts. The dataset contains the vulnerable artifacts (source code and runtime bytecode), labels according to three taxonomies, and function-level locations. The retrieval of CVE records, collection of additional evidence, validation of the correspondence between records and artifacts, label assignment, and vulnerability localization are automated, leaving 15% to manual analysis. The dataset does not validate the original vulnerability claims, but marks a few records obviously wrong as `refuted'. For the sake of reproducibility, all external inputs are retained, so that rerunning the pipelines results in the same outputs. The dataset comprises 491 records linked to deployed contracts, 26 referring to projects (mostly libraries), 45 without validated artifacts, and six records with refuted claims. The dataset supports empirical security research, in particular the evaluation of code analysis and repair techniques.

cs.CR↗

arXiv2026

Athena: Vulnerability-Affected Library Identification via Knowledge Graph Completion

A single vulnerability in a widely used library can cascade through millions of dependent applications, yet more than half of vulnerability database entries contain missing or incorrect affected-library information. Existing automated approaches neglect the relational structure of vulnerability databases, treating identification as an isolated text retrieval problem. In this paper, we propose Athena, the first graph-based approach for vulnerability affected library identification. Athena models vulnerability databases as a knowledge graph and reformulates the identification problem as knowledge graph completion (KGC). It comprises three key modules: a Modeling module that constructs a security knowledge graph integrating CVEs, libraries, CWE weakness types, CPE products, and software ecosystems; a Completion module that applies a modular KGC backbone to predict missing affected libraries for a given CVE via link prediction; and a Re-ranking module that retrieves KGC candidates and rescores them using a fine-tuned LLM augmented with knowledge graph embeddings, jointly leveraging structural and textual information. Our experiments on VulLib demonstrate that Athena significantly outperforms four state-of-the-art baselines, achieving a 32% improvement in Avg. F1 over the best baseline (i.e., VulLibGen). Notably, our KGC backbone with only 110M parameters already surpasses VulLibGen's best configuration at 7B parameters, demonstrating the effectiveness of graph-based modeling; the re-ranking module then provides substantial further gains, consistently outperforming the best baseline across all evaluated LLM backbones.

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arXiv2026

Continuous Autonomous Refactoring: A Research Roadmap for AI-Driven Code Quality Maintenance

Large language models have shown promising capabilities in code refactoring, but existing approaches remain limited to method-level tasks. In this paper, we envision LLM-based refactoring as a continuous component of software maintenance rather than a tool invoked only for occasional manual refactoring. Under this vision, AI agents continuously monitor, evaluate, and improve codebases against explicit and evolving notions of software quality. We present a roadmap organized around five dimensions: the multi-objective optimization problem, quality definition and evaluation, multi-timescale integration of heterogeneous signals, architecture and design pattern, and trust in autonomous refactoring. We further identify integration into continuous delivery pipelines and cost considerations as cross-cutting concerns. For each dimension, we analyze the underlying challenges and pose open research questions. These dimensions define a research agenda for advancing autonomous refactoring from isolated code improvements to system-level quality maintenance.

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arXiv2026

What Does an Agentic Software Engineering Benchmark Measure? Profiling Task Demands and Agent Behaviour Beyond What Category Labels Reveal

Agentic software engineering benchmarks are typically summarized by nominal category labels such as "bug fix" or "feature implementation," yet benchmarks carrying the same label are built through very different curation pipelines. A label thus reveals little about the engineering work a benchmark demands. We introduce the Spread--Novelty--Centrality (SNC) profile, a three-axis characterization of the demands of repository-level coding tasks, grounded in empirical software engineering research. We apply the profile to five widely used benchmarks and 14,922 trajectories of two model families at three scales, and report three findings. (1) A label is an unreliable proxy for task demands, as every pair of benchmarks is statistically separated on at least two SNC axes, and the separations trace back to specific curation decisions. (2) Agent behaviour reveals demands that the human-written gold solution cannot. Agents produce larger solutions than the gold where problem statements withhold hints and smaller ones where curation inflates the gold. How a task is phrased shapes what an agent produces. (3) Task demands correlate with success uniformly, with resolved runs concentrating in the low-SNC region for every family and scale, whereas the behavioural signatures of success are family-specific. Claude succeeds by matching the scope of the gold solution, and its parity share on files rises from $0.17$ at the smallest scale to $0.54$ at the largest. Qwen succeeds by exceeding the gold scope at every scale, and editing too little marks failure for both families.

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arXiv2026

HarnessDev: Can LLMs Create and Evolve Their Own Agent Harness?

As agents move from research prototypes to deployed tools, their capability increasingly depends on model-external execution infrastructure, commonly termed the agent harness. Changing this harness while holding model weights fixed can substantially alter task performance. Current agent evaluations typically report downstream performance under a chosen harness, leaving a model's ability to develop the harness itself comparatively underexplored. We introduce HarnessDev, a benchmark that shifts the unit of evaluation from task outputs to runnable infrastructure. HarnessDev covers two stages. In Creation, the agent starts from a minimal seed and a small number of cases, then builds a complete execution system. In Evolution, it starts from its own created harness and iteratively revises it using downstream execution feedback, with the goal of improving benchmark performance. We then evaluate each constructed harness on capability (task success on held-out benchmarks) and efficiency (execution-token cost). The reported Creation results cover six creator LLMs, four domains, and five downstream benchmarks totaling 2,207 unique downstream instances, with hidden evaluation tasks withheld from development. We find that generated harnesses remain substantially behind mature human-engineered references on code and on search and research, while matching or exceeding the selected references on writing and machine-learning experimentation, with large variation in execution cost. Evolution produces some performance gains, but they are unstable and transfer only partially to held-out tasks. Experiments with a fixed runtime model further show that the gains depend strongly on the model executing the harness, indicating limited transfer across models.

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arXiv2026

The Data Problem in Software Vulnerability Analysis: Artifacts, Quality, and Consumption

Learning- and LLM-based software vulnerability analysis is only as trustworthy as the data it is trained and evaluated on, yet that data is rarely examined as a first-class object. We investigate the data behind vulnerability analysis through a dataset-centric taxonomy that separates what an artifact is (code, metadata, patches, tests/PoCs, reasoning, traces), how good it is (realism, label evidence, scale, diversity, leakage, availability), and what it is used for. From a systematically assembled corpus of 1522 papers covering 2016-2026 plus foundational earlier work we deep-code a tiered set of 111 anchor papers, backing every affirmative rubric-graded value with a verbatim span, and we report, per attribute, both how much it has been studied and how well datasets achieve it. The results trace an evidence ladder: executable artifacts are the only major type where 15 of the 24 datasets are both graded real-world and carry labels that received an independent check, while code-sample datasets-the largest category in both the auto-tagged corpus and the anchor set-are the least realistic: 20 of the 41 draw their vulnerabilities from authentic projects or CVEs, but only 3 keep the sample at the unit the code is deployed in, and only 2 do both-though these are coarse component tests, and just one code-sample dataset meets the codebook's stricter full-context real-world grade. Among these, leakage goes unaddressed by 49 of the 90 datasets where it applies, more than a quarter say nothing about availability, reasoning data has arrived only recently and is mostly model-generated, and primary trace corpora remain limited to three datasets, the total after a corpus-wide screen and a full-text check of every candidate it surfaced, with further datasets releasing traces secondarily behind benchmarks and harnesses.

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arXiv2026

Adaptive Critical Token-Aware Retrieval for Repository-Level Code Generation

The repository-level code generation task requires synthesizing code that satisfies task requirements while remaining consistent with the target repository context. Since real-world repositories often exceed the input length limits of LLMs, existing approaches commonly adopt retrieval-augmented generation (RAG) to provide repository-specific context. Despite improving repository-context retrieval, existing methods typically provide context as task-level support, without explicitly identifying the critical tokens that require fine-grained repository context during generation. During the autoregressive generation process of LLMs, errors often concentrate at a small number of decisive positions: once such tokens are generated incorrectly, subsequent code may follow an incorrect semantic path and eventually lead to functional failure. We refer to these positions as "critical tokens". In this paper, we propose ACToR, an adaptive critical token-aware retrieval framework for repository-level code generation. ACToR identifies critical tokens during generation and triggers targeted retrieval on demand to provide repository context at these decisive positions. In addition, we design a position-aware weighting method for dense retrievers to prioritize context that is more informative for generation. We evaluate ACToR on two representative repository-level benchmarks, RepoExec and CoderEval. Experimental results show that ACToR consistently outperforms state-of-the-art methods, achieving relative improvements of 8.4% on RepoExec and 15.4% on CoderEval. Beyond performance gains, we systematically quantify the impact of critical tokens, revealing their central role in major generation failures and highlighting the necessity of targeted retrieval strategies. We provide the code and data at https://github.com/DeepSoftwareAnalytics/ACToR.

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arXiv2026

Efficient SWE Agent Benchmarking via Trajectory-Aware Evaluation

Evaluating software engineering agents on realistic benchmarks is costly, since each task may require multi-step code exploration, modification, and test execution. Existing efficient evaluation methods select representative subsets to estimate full-benchmark performance, but are largely result-only: they fit historical pass/fail response matrices or static task semantics, discarding how agents solve problems. We propose PTA-IRT, a Privileged Trajectory-Aware Item Response Theory framework that fuses process and outcome signals. Historical execution trajectories supply process-level evidence beyond pass/fail, such as explored context, attempted edits, and solving paths, which PTA-IRT uses as privileged information for calibration subset selection and ability estimation. Under low calibration budgets, PTA-IRT consistently outperforms prior IRT baselines on score and ranking recovery across four SWE benchmarks. Code and data are publicly available at https://github.com/DeepSoftwareAnalytics/PTA-IRT.

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