Papers

Modern artificial-intelligence coding agents can be equipped with tools for checking their own work e.g. a linter, a boot probe, a shell, a screenshot tool. We call this set the agent's verification surface. This study asks whether increasing only that surface, with everything else held fixed, produces a matching growth in the quality of the software the agent ships. We built a minimal coding agent whose tool list is the single controlled variable and used it to implement 1,116 web applications across six models and eight tool configurations. A condition-blind human graded every application against a frozen rubric, and automatic probes stress-tested the API-observable behaviors. Verification's cheapest benefit arrives first, which is to make sure that the application comes up. Without any tools, about one build in seven fails to launch at all and a single boot probe removes nearly all of these failures at roughly 35 percent of a full shell's token cost, while the full shell multiplies the no-tools cost by 2.35. Screenshots help most where mistakes are visible (e.g. element placement, interaction), though even there the gain over a shell is modest and does not survive correction for multiple statistical comparisons. In cases where failures can only be measured rather than seen, such as keeping scrolling smooth over a 100,000-row list, screenshots add nothing. A verification tool improves the output artifact only where its reach covers the way the application actually fails.

Technical operations teams resolve large volumes of incidents by synthesizing fragmented evidence from ticket text, historical cases, system logs, and technical documentation. Existing automation often relies on monolithic generation without explicit evidence modeling or provenance, making outputs difficult to verify when critical signals are sparse across sources. We propose ASTRA, an agentic system for ticket resolution in which a central orchestrator coordinates three specialist information-gathering agents and drives a judge-orchestrator refinement loop to produce evidence-backed troubleshooting reports. TicketSimilarityAgent retrieves relevant historical precedents through dense retrieval and LLM reranking; LogAgent distills hundreds of thousands of log lines into structured, quote-grounded findings using deterministic filtering and constrained LLM analysis; and DomainKnowledgeAgent retrieves relevant technical knowledge via the Model Context Protocol (MCP). Their outputs are transformed into a claim-evidence representation linking each claim to a verbatim source passage, assigning a support level, and preventing cross-attribution. A JudgeAgent scores the report on five criteria, while the OrchestratorAgent converts low scores into targeted follow-up queries for bounded iterative refinement. Evaluated on 987 real-world telecom fault tickets across seven product lines, ASTRA achieves a mean quality score of 4.13/5.0, with 59.9% of reports identifying the fault area at the component-family level or better. Relevance and Clarity scores are 4.88 and 4.94, respectively, while fabricated technical details remain below 3% of error cases. Stratification by fault type reveals that hardware faults remain substantially harder than software or configuration faults (Cohen's d=0.80), pointing to a fundamental limitation of text-based evidence channels for hardware fault diagnosis.

AlphaFold 3 (AF3) enables structure prediction of biomolecular complexes through co-folding multiple interacting molecules, making it increasingly useful for de novo protein design and for large-scale studies of protein-protein, protein-peptide, and other biomolecular interactions. However, systematic co-folding experiments can produce large volumes of output data, particularly when multiple random seeds and samples are generated for each input complex. We introduce FoldKit, a Python package for efficient storage and analysis of large-scale AF3 co-folding results. FoldKit converts raw AF3 outputs into a compact, structured representation while preserving the metadata needed for downstream analysis. The FoldKit Python library provides convenient programmatic access to global, single chain, and interface confidence metrics such as pLDDT, pTM, ipTM, ipAE, and ipSAE, as well as an ensemble-level interface for accessing and aggregating these metrics for a single input across multiple seeds and samples. We benchmark FoldKit on three types of AF3 co-folding datasets: (i) a protein design campaign with 2 chains per input, (ii) a TCR-pMHC dataset with 4 chains per input, and (iii) a pooled-AF3 protein-protein interaction dataset with up to 22 chains per input. We find that FoldKit reduces storage requirements by approximately 5-15-fold compared to native AF3 outputs, depending on dataset composition, while maintaining direct programmatic access to individual predictions, ensembles, and confidence metrics. By reducing storage requirements and facilitating programmatic access to relevant outputs, FoldKit facilitates large-scale computational studies of biomolecular interactions. FoldKit is available from PyPI and can be installed using pip.

Traditional Retrieval-Augmented Generation (RAG) systems treat documents in isolation, failing to capture hierarchical relationships between concepts in complex scientific corpora. This limitation compromises answer quality in specialized domains such as climatology, where conceptual dependencies frequently traverse multiple articles. We propose a hybrid architecture that integrates vector search with GraphRAG, Leiden community detection, and cross-encoder re-ranking, achieving gains of 160% in contextual relevance and 177% in contextual recall compared to classical RAG. These results demonstrate that unifying local and global retrieval significantly outperforms text-span isolation, paving the way for more effective question-answering systems over dispersed scientific literature.

Rust is claimed to be a type-sound language capable of preventing various undesirable behaviors, including memory bugs. However, rustc, the official Rust compiler, is not immune to defects; it contains soundness bugs, where the compiler accepts programs that should be rejected during type checking. In this work, we present an empirical study of 30 issues that report potential soundness bugs in rustc, collected from the GitHub issue tracker between January 1, 2022 and September 1, 2025. We analyze each issue in depth, focusing on its affected feature, symptom (how the feature is mishandled), consequence (the resulting undesirable behavior), triggering features, community consensus regarding whether it is a bug, and lifecycle, including introduction, discovery, and fix. Furthermore, we investigate existing artifacts, including implementations such as AddressSanitizer, Miri, Chalk, and a-mir-formality, alongside documentation such as the Rust Reference, the FLS, and Rust RFCs to assess their potential as oracles for testing the type soundness of rustc. Our key findings indicate that: (1) Certain soundness bugs, typically triggered by implied bounds or trait objects, compromise memory safety. (2) Sound type checking is challenged by edge cases involving associated types and the interaction between lifetimes and traits. (3) Most bugs persist from the initial introduction of the relevant features and require significant time to be discovered. (4) While AddressSanitizer and Miri can detect soundness bugs that lead to memory bugs, a-mir-formality and Chalk are currently immature despite their potential to identify other bug categories. (5) Existing documentation frequently fails to provide precise explanations of the language semantics.

As AI accelerates vulnerability discovery, remediation throughput may become a greater constraint than prioritisation accuracy. This study evaluates vulnerability remediation as a flow-control problem using Apache Jira, Mozilla Bugzilla, Red Hat security errata, five public Jira organisations, and an npm dependency graph. Apache resolution times are strongly heavy-tailed, while 94-100% of arrivals in the primary issue trackers enter queues estimated to be at or above capacity. Queue-context models provide only moderate predictive discrimination and are largely matched by simple project-level baselines. Severity-to-speed discrimination varies substantially across systems. Flow-control analyses show larger operational effects: transitions from overloaded to draining queues are associated with shorter resolution times, severity-first sequencing reduces critical-item delay at fixed capacity, and capacity reservation can reduce prolonged critical-item delays. Owner-level analyses further show that available capacity is useful only when it is located where demand occurs or can be transferred through relevant expertise connections. These findings support treating vulnerability remediation as a flow-control and capacity-allocation problem rather than solely a ranking problem.

Current approaches to engineering dependable Digital Twins (DTs) of Cyber-Physical Systems lack practical guidance on how qualities such as relevance, verifiability, substitutability and fidelity may be formalised and verified. This need is amplified in Systems-of-Systems (SoS), where reliance is placed on the composition of DTs. The goal of this study is to identify foundational challenges that a framework for DT validation and verification should address in an SoS setting, and to investigate the formalisation of individual DT artefacts as a step towards compositional reasoning. We present a case study based on a DT-enabled greenhouse SoS modelled in VDM-RT (Vienna Development Method, Real-Time), including executable formal models, a property-based account of DT qualities, and an analysis of the obstacles arising when attempting to compose these artefacts at the SoS level. We consider how DT qualities may be operationalised as sets of verifiable properties. Formal modelling and analysis techniques and tools supporting their verification are identified. The study reveals how interpretations of DT qualities must adapt to different architectural roles and how local quality guarantees form assumptions for compositional reasoning. Full formalisation and verification of SoS composition is identified as future work.

AI coding agents, software tools that automate development tasks through reasoning and tool use, are increasingly extended through plugin marketplaces, yet the structure, maintenance, and co-evolution dynamics of these emerging repositories remain empirically unexplored. Unlike traditional software packages that deliver functionality through source code, agent plugins deliver functionality through a combination of natural-language instruction files, scripts, and configuration files, raising the question of whether these plugins are maintained artifacts that co-evolve across components, or one-off artifacts that developers write once and do not need to revisit. To study the maintenance and co-evolution of agent plugins, we conduct an empirical study of 1,926 repositories hosting Claude Code plugin marketplaces, analyzing 8,351 plugins and 77,773 commits across 2,018 marketplaces. We find that the marketplace is expanding rapidly, plugin-touching commit activity growing 8.8x over six months after the October 2025 launch, and plugins targeting Software Engineering tasks accounting for 61.3% of all plugins. Plugin development is predominantly feature-driven, with feature commits occurring at more than twice the rate of conventional open-source software (OSS) (39.6% vs. 17.2%). Claude co-authors 34.9% of all commits, and four commit types (docs, perf, style, and refactor) carry substantially different meanings in plugin repositories than in traditional software. Most component types evolve independently, but within skills directories, natural-language instruction files and implementation scripts co-evolve at above-chance rates, with 78% of co-changes being functionally coupled, representing a new class of maintenance dependency not observed in traditional software engineering.

Software architecture is often only partially captured in code, while much of the design intent lives in evolving project artifacts. In agile projects, work items, user stories, and related tracking documents preserve valuable traces of that intent, but they rarely support direct architectural analysis. This work investigates the recovery of C4 architecture diagrams from historical agile work items using an LLM-based pipeline. The semi-automatic five-step workflow employs a prompt chain, bidirectional traceability, and Chain-of-Thought reasoning to transform unstructured Azure DevOps work items into visual artifacts. Evaluated on two industry projects, we use a mixed-methods design combining qualitative expert interviews with a quantitative stability analysis. Practitioners perceive the generated architectural baselines as accurate and highly useful for system comprehension. Strictly bound by their input data, the artifacts mirror the documented intent, thereby surfacing discrepancies and architectural drift when compared to the implemented reality. Quantitatively, the workflow exhibits high stability for architectural entities but lower stability for their relationships, with relative variance compounding across generation steps. The proposed workflow demonstrates the practical viability of LLM-assisted architectural recovery based on development process artifacts.

Smart contracts are financial programs deployed on blockchains to manage digital assets. To build trust with users and investors, smart contract projects typically publish their source code on blockchain explorers and verify it against the deployed bytecode, making the on-chain program accessible through a human-readable implementation. However, LLM agents are changing the threat model of this disclosure mechanism. By leveraging publicly disclosed source code, recent agent workflows make it increasingly practical to scan contract vulnerabilities for exploits at large scale. In this paper, we propose DeLLMGuard, a smart contract deployment framework that defends against malicious LLM-based vulnerability scanning while preserving public source disclosure and authorized auditing. DeLLMGuard can separate disclosed source code from runtime execution through multiple contract addresses in a real-world blockchain environment. LLM agents must therefore recover additional proxy, delegate, and factory relations before vulnerability analysis. A built-in Verification Layer checks deployment relations, runtime bytecode, source code, and state changes to ensure that the transformation preserves the original business implementation. We evaluate DeLLMGuard on 387 real-world vulnerable contracts with three LLM agents in an environment derived from SCONE-bench. DeLLMGuard reduces overall root-cause correctness from 23.5% to 6.6% and outperforms the closed-source bytecode baseline on the primary non-proxy set. Trace and ablation analyses further show that agents often recover downstream contracts but still fail to identify the vulnerability, indicating that cross-contract recovery remains a major challenge for automated LLM scanning.

Robustness evaluation is essential for deploying machine-learning (ML) systems in real-world settings, where models may face adversarial perturbations, distribution shifts, and other operational stressors. Many open-source tools, including Adversarial Robustness Toolbox, Foolbox, and Robustness Gym, support robustness testing and evaluation. However, little is known about how these tools are maintained, publicly engaged with, and sustained over time, even though practitioners may rely on them to select evaluation dependencies, reproduce robustness assessments, and provide evidence for AI assurance. We present an empirical study of the open-source robustness tooling ecosystem. Starting from a curated seed set derived from prior work, we systematically searched GitHub and identified 28 robustness-tool repositories. We analyzed repository artifacts to characterize observable community engagement, maintenance activity, and project longevity using established software-engineering metrics. Our results show that engagement and maintenance are unevenly distributed, with sustained activity concentrated in a small subset of repositories. At the data collection date of January 21, 2026, five repositories were classified as active, 22 as inactive, and one as archived. These findings highlight the need to treat robustness tools as evolving software systems.

Software testing often relies on assumptions such as reproducible executions and stable correctness criteria. However, many modern software systems exhibit non-deterministic executions and large behavior spaces, making exhaustive exploration impractical and single-run judgments unreliable. These characteristics make it difficult to identify where acceptable behavior ends and problematic behavior begins. Competitive multiplayer games represent a challenging instance of such systems, where balance must be maintained so that no single strategy dominates. Even small parameter changes can trigger abrupt balance disruption, yet detecting such failures requires repeated simulations under non-deterministic outcomes and high-dimensional parameter spaces. In this paper, we formulate game balance regression testing as a boundary-discovery problem under a finite simulation budget. The objective is to efficiently identify inputs near the boundary that separates balanced and unbalanced regions. To address this problem, we propose BBExplorer, which combines multi-directional candidate generation, budget-aware two-stage screening, and adaptive step-size shrinkage for boundary refinement. Experimental results on two games with different levels of complexity show that the approach is strong in low-dimensional settings and remains effective in higher-dimensional ones. It also exhibits stable boundary behavior across unseen random seeds and threshold settings. These results indicate that BBExplorer is effective for practical balance regression testing and, more broadly, for boundary-oriented testing in non-deterministic, budget-constrained systems.

Software behavior often changes abruptly at boundaries between input regions, and these transitions are known to be fault-prone. Boundary Value Exploration (BVE) automates boundary discovery by searching for pairs of similar inputs that nevertheless trigger different program behaviors. Existing automated BVE techniques rely on mutation operators hand-engineered for each input type, or even for each function under test, which has confined their use to numeric inputs. We present ABEX, an agentic LLM-based framework that replaces operator engineering with adaptive strategy generation: specialized LLM agents propose, select, and execute boundary-exploration strategies, guided by execution feedback and a quality-diversity (QD) archive. Because strategies are expressed in natural language, they can encode both type-level and function-specific knowledge, and effective strategies can even be stored and reused. We evaluate ABEX in a black-box setting on 20 functions with numeric, string, array, and mixed inputs. On numeric functions, ABEX outperforms a state-of-the-art QD method on 10 of 11 functions, with average QD-scores 11.7x higher. On non-numeric functions, addressed here for the first time in automated black-box BVE, ABEX discovers domain-aligned boundary behaviors for all subjects. Mutation testing shows the discovered boundaries are fault-revealing: with equally sized test suites, ABEX reaches an average mutation score of 86.2% versus 61.9% for the QD baseline, and kills nine times as many hard-to-detect stubborn mutants. An ablation study identifies adaptive strategy generation as the primary driver of these gains.

This paper presents an airborne software development approach for manned and unmanned aerial vehicles aimed at reducing inconsistencies across system, model-based functional, and embedded software domains. In environments influenced by standards such as ARP-4754B and DO-178C, these inconsistencies typically stem from insufficient enforcement across domain boundaries rather than missing process definitions. Building on a previously proposed toolchain centered on a relational interface database, we identify recurring failure modes and propose a repository-centered implementation to address them, tailored to small, resource-constrained teams operating without heavyweight process overhead. Each domain is assigned a primary repository with cross-repository references and dedicated CI pipelines that generate, update, and validate the exchanged artifacts. Automated interface updates, differential change notifications, and consistency checks propagate changes with minimal manual effort and surface inconsistencies before the time-consuming code-generation and compilation steps. An initial implementation in an ongoing experimental project is described, with qualitative feedback from its early use.

Engineering agents that interact with external simulators may need to coordinate design modification with reacquisition of engineering evidence for the modified state. We ask whether first post-edit re-verification changes when explicit verification-cadence guidance is retained versus omitted while verification-relevant state/facts are held constant. Cadence-Guided (CG) retained an instruction to request a new simulation after a substantive modification, whereas Cadence-Omitted (CO) removed that instruction; neither condition used a hard gate. The study therefore measures instruction-conditioned post-edit verification-policy adherence rather than spontaneous recognition that prior evidence has become stale. Using DWSIM as the simulator backend and continuous valve-pressure adjustment, five Alibaba/Qwen models were evaluated on eight synthetic cases; each model-case-condition combination was executed three times via live API calls, yielding 120 evaluation slots per condition. Re-verification was observed in 94/120 CG slots versus 32/120 CO slots; cadence violations occurred in 26/120 versus 87/120; and bounded final success was reached in 95/120 versus 35/120. qwen3.5-35b-a3b showed minimal re-verification (1/24 in CG and 0/24 in CO) and no final success in either condition. Within this bounded protocol, explicit post-edit verification-cadence guidance was associated with more re-verification, fewer cadence violations, and more frequent bounded final success, supporting the treatment of verification cadence as an explicit interaction-protocol component.

REST APIs are widely used in modern software systems, but developers and testers often lack visibility into which parts of an API specification are exercised by a test suite. Traditional coverage analysis usually relies on source-code instrumentation, which is impractical for REST APIs that are distributed, externally maintained, and hence accessible only through black-box execution. This paper presents RESTCov, a lightweight tool that computes structural REST API coverage from an OpenAPI specification and observed HTTP request/response logs, reporting coverage across paths, operations, parameters, media types, status codes, and status classes. RESTCov produces both machine-readable results and a human-readable HTML report, helping users inspect coverage gaps, diagnose specification-log mismatches, and evaluate REST API test suites without requiring access to the implementation. Screencast: https://youtu.be/mNz2P43OyUc Repository: https://github.com/2tolgahan2/RESTCov

Microservice architecture supports software evolution by decomposing a system into small, loosely coupled services that can be deployed independently. Contrary to the expectation of high modularity, prior studies have reported that code clones exist across service boundaries, some of which are co-modified in the same version. Such clones may require changes to be propagated across service boundaries, thereby undermining service independence and increasing maintenance costs. However, existing tools do not support microservice-aware clone analysis. We present CC4M, a microservice-aware clone analysis and visualization tool. CC4M detects and enriches clone pairs with service-boundary, co-modification, file-category, and metric information. The enriched clones are visualized in an interactive scatter plot with explicit service boundaries, supporting metric-based filtering to prioritize clones with potentially higher maintenance impact. Using an open-source microservice application, we illustrate how CC4M helps identify the potential impact scope of code changes. A demo video and the tool are available at https://www.youtube.com/watch?v=0xOIQPFbkUg and https://doi.org/10.5281/zenodo.21204195, respectively.

Large language models increasingly author Infrastructure-as-Code (IaC), where one insecure default is provisioned straight into production. Prior evaluations report vulnerability counts for models only, and so cannot say whether models are worse than the engineers they assist. We present GenIaC-SecBench: 100 deployment scenarios across 12 model configurations from six vendors, open and closed weights, yielding 1,196 artifacts scanned by three policy engines (Checkov, Trivy, KICS) at complete coverage. Crucially we scan 634 human-authored IaC templates with the identical toolchain, giving the first size-matched human security baseline for this task. Vulnerability density is strongly inverse to artifact size (Spearman $\rho=-0.55$, $p<10^{-77}$), so unmatched comparisons measure size, not security. Size-matched, every configuration exceeds the human baseline at $3.21\times$ to $3.87\times$, and the gap widens as tasks get simpler ($4.9\times$ at one resource, $1.4\times$ at twenty or more). A majority of scenarios prescribe a security state rather than specifying function alone, so we stratify by prompt class: pooled the gap is $3.50\times$, and excluding every scenario that explicitly requests an insecure configuration still leaves all configurations above baseline ($2.4\times$ to $4.2\times$). The corpus cannot isolate unprompted default posture, and we say so. Decomposing "reasoning" into standard generation, prompted chain-of-thought, and vendor extended-thinking APIs, extended thinking beats prompted CoT ($-12.0\%$, $p=0.0013$) while prompted CoT alone is indistinguishable from standard ($-1.3\%$, n.s.); it consumes under $1\%$ of the output budget, bounding the effect. Two negative results: more deployable models are not more vulnerable ($r=0.158$, $p=0.625$), and complete-case Friedman is uncomputable here, motivating Skillings-Mack. All code and data are released.

The Android ecosystem faces persistent and rapidly evolving malware threats. Existing machine learning detectors are vulnerable to concept drift because they rely on implementation-specific features whose distributions change over time. Large language models (LLMs) offer strong semantic understanding and zero-shot reasoning, but current LLM-based detectors typically depend on code-centric or single-dimensional evidence, making them susceptible to obfuscation and limiting comprehensive behavior analysis. We present Moirae, a multimodal agent collaborative framework for dynamic Android malware detection. Moirae dynamically collects multimodal runtime evidence and employs ReAct-based specialized agents to analyze complementary behavioral views. The detection process begins by identifying visual deception cues, modeling UI state transitions, and integrating runtime API behaviors to fuse multi-dimensional evidence across user-visible interfaces and hidden backend operations. Experiments on temporally and distributionally unseen datasets show that Moirae achieves an accuracy of 90.06% without fine-tuning, outperforming state-of-the-art baselines and demonstrating strong zero-shot generalization against Android malware concept drift.

Decompilation aims to recover high-level, compilable, and semantically equivalent code from binaries. Traditional decompilers produce pseudo-C that is difficult to read and does not compile, while the recent LLM-assisted approaches generate readable, but semantically incorrect code. LLM-aided iterative recovery is an emerging branch of research, but prior works rely on supplied test suites for semantic recovery. In this work, we present CHISEL, a test suite-free framework to iteratively recover source code from Ghidra-derived pseudo-C. CHISEL uses simple yet effective feedback from a compiler (static analysis) and a coverage-guided fuzzer (differential analysis), augmented by rich observables for grounded divergence detection and feedback, cross-iteration divergence memory, and best candidate retention. We systematically evaluate CHISEL for compilation and semantic recovery, feedback oracle soundness, and iteration overhead on 120 ExeBench functions compiled for the x86-64 architecture, across four optimizations (O0-O3), in both stripped and unstripped variants, using the open-weight Gemma4:31b LLM. CHISEL, with all recommended features, achieves an average of 96.1% re-compilability and 79.8% re-executability rates at an average of 2.1 iterations. Significantly, CHISEL recovers 26% of first-generation execution errors. At the same time, CHISEL feedback oracle falsely accepts only 9.4% candidates. Lastly, CHISEL performs significantly better than two recent prior work on LLM-assisted decompilation.

Vulnerability datasets underpin a wide range of security research, including vulnerability detection, automated remediation, and secure code generation. However, existing datasets sacrifice at least one of three desirable properties: diversity (of language or vulnerability type), reproducibility/executability, or realism. We therefore present GraftyVul, a system that constructs vulnerable programs by grafting real-world vulnerabilities into open-source projects. This grounds the dataset in vulnerabilities observed in real-world contexts while harnessing known good build and test environments, enabling exploit-verification scripts to guarantee that an introduced vulnerability successfully alters a program's behaviour. Using GraftyVul, we generate 212 verified and exploitable vulnerable programs spanning five programming languages (Python, TypeScript, Java, Go, and C#) across 23 CWE categories. To evaluate fidelity, we introduce a language- and context-agnostic semantic embedding that compares vulnerabilities by sink, mechanism and host-feature rather than surface code. This approach outperforms standard code embeddings on cross-language clone and CWE classification. These embeddings demonstrate that GraftyVul samples retain a strong semantic signature to their source vulnerability. We additionally compare GraftyVul against 13 widely used datasets, where it attains competitive diversity while being the only reproducible-exploit dataset with broad language and CWE coverage. Finally, we illustrate GraftyVul's practical utility through an industrial case study evaluating a production vulnerability remediation system.

AI-assisted qualitative data analysis (QDA) offers unprecedented opportunities to streamline software engineering (SE) research, yet uncritical use risks compromising analytical rigor and flooding the field with accelerated production of low-quality research. While tactical best practices will naturally evolve over time, SE researchers currently lack strategic guidance to identify and mitigate methodological risks when attempting AI-assisted QDA. Based on our decades of qualitative SE research expertise and experience combined with an understanding of the emerging landscape of AI-assisted QDA, this paper presents a catalog of antipatterns in AI-assisted QDA - a set of assumptions and practices that initially appear advantageous but ultimately undermine analytical rigor and validity. The antipatterns are grouped into three categories reflecting escalating impact: Dangerous Drivers, Operational Missteps, and Analytical Failures. As more SE researchers attempt AI-assisted QDA, these antipatterns will help them identify and avoid common temptations and pitfalls, while reviewers can be equipped with the vocabulary and criteria to call out problematic and failed practice. Ultimately, this catalog of antipatterns can serve as a stepping stone in our responsible methodological evolution toward principled and meaningful human-AI collaboration in qualitative research.

Reverse engineering is essential for software security analysis and vulnerability detection. Decompilation, the process of lifting binaries to high-level pseudocode, is central to this task. However, production binaries are hostile environments: aggressive compiler optimizations and adversarial obfuscation jointly mangle control structures, obscure variable intents, and disguise high-level program logic. Consequently, existing LLM-based decompilation tools frequently suffer from structural collapse and semantic hallucinations. We present ReSource, the first multi-phase LLM framework designed for transformation-agnostic source recovery. To tackle these intertwined distortions, ReSource conceptualizes the binary-to-source discrepancies into three orthogonal tiers, namely lexical, syntactic, and semantic, and decouples the recovery process accordingly. First, to ground the LLM and prevent logic drift, it retrieves empirical priors from a curated Semantic Distortion Database. Second, to resolve control-flow flattening, it integrates a lightweight predictor to reconstruct the source-level structural skeleton. Finally, a contextual lexical deduction stage refines identifiers to restore human readability. Evaluated on a massive benchmark of over 80,000 decompiled-source function pairs across three optimization levels and four obfuscation techniques, ReSource achieves an 83% Top-5 source retrieval accuracy and an average similarity score of 0.66. By maintaining robust semantic identifiability where state-of-the-art baselines (DeGPT, LLM4Decompile, and FidelityGPT) severely overfit or degrade, ReSource provides a scalable and reliable foundation for downstream security analysis.

Coding agents are now commonly evaluated on the SWE-bench family of benchmarks, whose tasks are built from curated GitHub issues: long, structured, and information-rich. Real user requests, however, are typically far shorter and less structured. To characterize this gap, we define a six-category information taxonomy and four dimensions of linguistic style, and apply them to real user prompts from SWE-chat and problem statements from SWE-bench Verified and Pro. We find that requests carrying only a problem statement, alone or with limited additional context, account for 88% of real prompts but just 7% of benchmark problems. Furthermore, 87% of real prompts are casually written whereas 94% of benchmark problems are formal. Guided by these observations, we introduce RealSWE, 381 multi-variant task families derived from SWE-bench Verified and Pro. Variants within each family share the same underlying task and gold patch while differing only in information composition and linguistic style. Evaluating seven contemporary LLMs with RealSWE, we find that i) realistic inputs reduce resolution rates by 6.4 pp on average and can change model rankings. Controlled analysis further shows that ii) including Desired Behavior and Motivation significantly affects performance, whereas Environment Information and Reproduction Steps merely add tokens without measurable benefit; iii) linguistic style has only small, model-dependent effects. These findings provide actionable guidance for users and agents: explicitly stating the desired behavior and motivation, which most real prompts omit, substantially improves the LLM's software engineering performance.

Slow queries frequently cause severe performance bottlenecks in database management systems. Diagnosing their root causes online risks exacerbating resource contention, while data privacy regulations often prohibit copying production data to test environments. Synthesizing a proxy database from non-intrusive metadata that induces the query optimizer to generate the same physical execution plans is therefore critical for offline diagnosis. High-fidelity reproduction requires preserving global statistical distributions while enforcing exact local cardinalities. Existing data-driven and workload-aware approaches cannot satisfy both requirements simultaneously. We present DBRepro, an automated end-to-end framework that formulates database generation as a constrained distribution synthesis problem. DBRepro initializes a global distribution from lightweight column statistics, extracts execution constraints from target queries, and progressively adjusts the distribution to satisfy these constraints while preserving the global distribution. Experiments on TPC-H and SSB show that DBRepro reduces cardinality error by up to 20.3% over a data-driven baseline while maintaining identical plan consistency. Compared with a workload-aware baseline, it reproduces 15% more consistent execution plans and reduces latency proportion error by 21.5%. We further validate DBRepro on a nearly 1 TB real-world dataset managed by KingbaseES, where it reproduces the execution performance of complex slow queries with high fidelity.

Prospective silent trials provide an important bridge between retrospective validation of artificial intelligence (AI) models and their use in clinical care by evaluating model performance and operational reliability on live clinical data without influencing patient management. In computational pathology, conducting silent trials requires integration across laboratory information systems, digital pathology infrastructure, computational resources, and model inference pipelines, and these workflows are often implemented using application-specific software. We developed the Silent Trial Engine for Pathology (STEP), a reusable software platform for orchestrating prospective silent trials of computational pathology AI models across heterogeneous clinical and computational environments. STEP separates common trial orchestration from institution-specific data access and compute infrastructure through modular adapter interfaces. The platform supports scheduled case discovery, per-slide inference submission, deterministic idempotency, failure recovery, result and ancillary-data ingestion, persistent trial and run state, and audit logging, with compute adapters supporting local execution and high-performance computing environments using LSF and Slurm. STEP was deployed at three institutions to support prospective silent evaluation of EAGLE, an AI model for predicting EGFR mutation status from hematoxylin and eosin-stained whole-slide images. By separating trial-level workflow logic from site-specific integrations, STEP enables a common execution framework to operate across heterogeneous pathology environments while maintaining durable and auditable trial state. This approach may reduce duplicated engineering effort and facilitate systematic real-world evaluation of computational pathology AI before interventional clinical deployment.

When machine learning classifiers are retrained, inputs correctly classified by the previous model version may be misclassified by the updated version, creating regression faults that are costly to detect because verifying predictions against ground truth may require human annotation, expert review, or expensive simulation rather than inexpensive model inference. Test input prioritization addresses this problem by ranking inputs so that a limited verification budget reveals as many regression faults as possible. Existing approaches rely predominantly on single-model confidence scores and do not exploit how predictions, decision boundaries, and local neighborhoods change between model versions. We propose RiskBlend, a classifier-agnostic prioritization framework that combines four complementary risk signals: historical failure patterns, prediction shift, decision-boundary shift, and neighborhood change. These signals are combined using validation-learned APFD-squared weighting. Across four datasets, five classifiers, four regression-update scenarios, and 15 random seeds, totaling 1,200 experimental configurations, RiskBlend achieves the highest average APFD in all 80 dataset-classifier-scenario combinations, with improvements of up to 0.32 APFD over the strongest baseline. Confidence-based methods remain competitive primarily for linear classifiers on sparse categorical features, which we attribute to feature-space geometry. The results show that cross-version behavioral signals provide important complementary information for prioritizing regression faults in machine learning systems.

Integrating Large Language Models (LLMs) into the Software Development Life Cycle (SDLC) can improve developer productivity, but it also introduces security, privacy, and compliance risks during model selection. Regulations and frameworks such as the EU AI Act, the NIST AI Risk Management Framework (RMF), the General Data Protection Regulation (GDPR), the Lei Geral de Proteção de Dados (LGPD), and ISO/IEC 42001 establish obligations that are often difficult to translate into operational criteria for technical decision-making. This paper proposes a model to support governance and compliance in LLM selection for software engineering projects. The model is developed through Design Science Research (DSR) and is structured in three layers: (i) regulatory requirements, (ii) organizational governance capabilities, instantiated by a multi-criteria decision matrix with knock-out and weighted scoring criteria, and (iii) productivity and sustainability outcomes, operationalized by the LLM governance assessment protocol (PAG-LLM). A regulatory feedback loop connects operational results back to the normative layer, enabling iterative refinement of the model. A pilot evaluation with 20 adversarial scenarios based on Common Weakness Enumeration (CWE) and the OWASP Top 10 suggests distinct risk profiles between commercial cloud-based LLMs and local open-source LLMs. The results provide preliminary evidence that regulatory disqualification logic, particularly K.O. criteria, can prevent the selection of technically competitive models that nonetheless pose unacceptable compliance risks, demonstrating the feasibility of governance-oriented LLM selection in software engineering projects.

Background. LLM outputs are highly sensitive to prompt formulation: small wording changes can substantially affect output quality. This matters in software engineering, where prompts guide requirements analysis, code generation, and artefact synthesis. Poor formulations yield unreliable artefacts, yet practitioners lack principled ways to assess a prompt before inference, making selection depend on costly LLM calls and trial-and-error refinement. Aims. We investigate whether measurable linguistic properties of prompts can predict LLM performance before inference, enabling low-cost prompt selection and refinement, validated on binary requirements classification targeting F1, F2, precision, and recall. Method. We generate 9,000 linguistically controlled prompt variants from 100 initial prompts by varying 30 linguistic metrics, evaluated with five open-source LLMs on 625 annotated requirements. Regression predictors are trained via stratified 10-fold cross-validation with permutation-based significance testing; feature importance analysis identifies cross-LLM and model-specific predictors. Results. Linguistic features significantly predict prompt performance across all targets (R2 in [0.38,0.42], q<0.05). Syntactic and morphosyntactic features drive most predictive signal; cross-LLM predictors include compound dependency distribution, conjunction density, and word/sentence length, reflecting sensitivity to domain vocabulary and complex structures. Conclusions. Results suggest practical implications for prompt engineering, including overlap between linguistic patterns that reduce LLM performance and those that increase human comprehension difficulty, and the irrelevance of lexical variety as a quality dimension. More broadly, linguistic profiling combined with standard regression provides an effective, interpretable, low-cost prior before costly optimisation pipelines.

Ensuring the reliability of deep learning-based image retrieval systems is a software engineering challenge. This paper presents a dual contribution: (1) a literature review of augmentation and generation techniques which resulted in the identification of 50 techniques which we organized into a ten-category taxonomy, and (2) a large-scale empirical study that evaluates these techniques as test generators for embedding-based image retrieval systems. Augmented images are embedded using Amazon Titan and OpenCLIP, and evaluated across four analytical dimensions: (1) embedding-space similarity, (2) embedding uncertainty measured via four estimators, (3) semantic realism scored by LLaVA, and (4) retrieval failure rate. Experiments are performed on three datasets: CIFAR-10, ImageNet-1K, and a dataset from an industrial partner (March Networks). Across all evaluated datasets and embedding models, and under the single severity level tested for each technique, weather simulation and SaSPA are the image augmentation/generation techniques that produce the highest embedding uncertainty and failure rates while maintaining a favorable balance between performance stability, visual realism, and augmentation effectiveness. The results we discuss are configuration-specific and may shift under milder or stronger perturbation settings. In contrast, GAN-based augmentation techniques are among the lowest in realism, indicating the presence of synthetic artifacts and perceptual inconsistencies that reduce their suitability to produce realistic test inputs. Overall, our findings provide practical guidelines for selecting augmentation techniques that maximize test diversity while preserving realistic image characteristics, thereby enabling the construction of comprehensive and effective test suites for image retrieval systems while reducing the cost of manual data labeling through the use of metamorphic testing.