arXiv subjects

Yu Kang

Publications and source records attributed to Yu Kang.

At least 19 recordsLinked to original sources

arXiv2026

Update from Hell: Can Coding Agents Survive Hidden Breakage in Dependency Upgrades?

Modern software systems rely heavily on third-party dependencies, but upgrading those dependencies remains a costly maintenance activity. Dependency upgrades do not always preserve the function signatures, type systems, APIs, or runtime semantics assumed by existing code. Consequently, developers often need to perform source code adaptations to accommodate dependency-induced changes. However, such code-level changes are often not explicitly communicated to project maintainers, posing a significant challenge to software reliability. Meanwhile, coding agents have emerged as a new form of software development tool and are increasingly adopted by developers due to their automation capabilities. In this paper, we introduce DEPBENCH, a benchmark consisting of 203 real-world dependency-upgrade tasks across five package ecosystems spanning five language communities, each involving hidden code-level changes that require source code adaptation. We evaluate mainstream coding agents on DEPBENCH. The best completed configuration solves only 104/203 tasks (51.2%), with substantial variation across agent harnesses, models, and ecosystems, highlighting an important gap between current agent capabilities and real-world software maintenance needs.

cs.SE↗

arXiv2026

DPIAgent: Divide, Protocol, Isolate for Agentic Reproduction Test Generation

Reproduction test generation, producing a failing-then-passing test that captures a reported bug, is a critical step in automated software engineering. Existing agentic methods treat this as a monolithic loop, despite the task inherently comprising two subtasks of distinct nature: diagnosing the root cause and writing a fail-to-pass test. Without explicit separation, the agent faces a compound objective with underspecified intermediate goals, leading to goal drift. We propose DPIAgent, a structured agentic framework built on three principles, Divide, Protocol, Isolate (DPI), that mitigates compound-objective ambiguity and goal drift: it Divides the task into single-objective phases of defect exploration and test generation; enforces a handoff Protocol that records the diagnosis and test plan, preventing context loss; and Isolates each phase's action space by tailoring the toolset to its task, preventing irrelevant tools from misleading execution. On SWT-Bench Verified, DPIAgent outperforms seven baselines across three backbone LLMs. With DPI alone it reaches 81.76% success rate on GPT-5, the highest reported among open-source methods, gaining up to 11.88 points over the strongest baseline on GPT-5-Mini; adding test selection further raises it to 86.17%. Our analysis shows that architectural structure and backbone capability are complementary axes rather than substitutes, demonstrating DPI's generalizability across model classes.

cs.SE↗

arXiv2026

Agent Lightning v1.0: Towards Harnessed Agentic RL

Modern agents operate inside agent harnesses that manage tools, context, and control flow, making the harness a critical part of the agent system. Our original Agent Lightning introduced a disaggregated architecture that connects arbitrary agents to RL training through an LLM endpoint proxy, an approach later adopted by frameworks such as verl Uni-Agent, AReaL 2.0, slime, and Polar. We refer to this paradigm as harnessed agentic RL, where the deploy-time harness directly participates in model post-training. Harnessed agentic RL differs fundamentally from traditional agentic RL: the harness, rather than the training engine, owns the environment interaction loop, while the trainer observes only sequences of LLM request-response pairs. This introduces challenges in retokenization, sample merging, advantage calculation, loss normalization, and backend scheduling, which can substantially affect training stability and effectiveness. We present Agent Lightning v1.0, a lightweight framework for harnessed agentic RL implemented in approximately 3,500 lines of code. It supports arbitrary agent harnesses and serves as a practical testbed for studying these challenges. We evaluate it on instruction-following, search, and coding agents, and provide a complete reproducible pipeline for coding-agent RL. Using only 6K training examples and modest compute, RL improves Qwen3.5-9B on SWE-bench Verified from 41.8% to 56.4%, a 14.6-point absolute gain. We release the complete workflow and training scripts to facilitate reproducible research on harnessed agentic RL.

cs.AI↗

arXiv2026

Change2Task: From Repository Changes to Executable Coding Agent Tasks and Environments

Scaling coding agents requires a continuing supply of executable data for training, benchmarking, and continuous evaluation. Each task must couple a realistic software state with a specification, development tools, and reliable verification. To expand this supply, we present Change2Task, a system grounded in repository history that converts merged pull requests into verified tasks on healthy modern revisions of the same repository. It aligns historical evidence with evolved code, reconstructs task states through Patch Reversal, Code Mapping, or Agent Reconstruction, and validates the lifecycle from a healthy base to a task state and a restored state. By deriving multiple tasks grounded in developer evidence from maintained environments, Change2Task provides executable data for coding agent training and evaluation while reducing repeated environment setup, storage, and task construction effort. We evaluate the system through five common and widely adopted coding agent task families: Bug Fix, Feature Addition, Test Generation, Application Programming Interface Migration, and Security Repair. Starting from 1,130 source changes eligible for construction, Change2Task achieves 79.6% verified task construction success across these task families. On a matched candidate set, it recovers 29.2% more verified tasks than a construction baseline based on pull requests. Historical and reconstructed cases achieve up to 98.0% matched outcome agreement under agent evaluation, while reuse of modern bases reduces measured expenditure across the complete pipeline by 10.8%.

cs.SE↗

arXiv2026

Towards a Systems Foundation for Agentic Cloud Management

Agentic cloud management is emerging as a practice to automate laborious operations, minimize toil, and improve responsiveness. Despite the rapid development of autonomous management agents, we argue that the fundamental missing piece is a systems foundation to enable safe, effective operations across agents and between agents and human operators. In this paper, we advocate for the need of such a systems foundation and share our efforts on developing CloudWeaver, an agentic management substrate that works across existing cloud-user interfaces and future agent-native interfaces. Specifically, we discuss how CloudWeaver (1) scopes the context of individual agent sessions with local views of cloud resources and (2) coordinates concurrent management operations on shared cloud resources. CloudWeaver offers strong safety guarantees and attributable feedback in the presence of conflicting intents, while preserving concurrency between independent operations. We validate CloudWeaver using a representative Azure API workload.

cs.MA↗

arXiv2026

Beyond Fail-to-Pass: Iterative Hardening of Co-Generated Bug Reproduction Tests and Fixes

Large language models (LLMs) have made automated program repair (APR) increasingly practical for real-world bugs, but repairing directly from bug reports remains underconstrained. Bug reproduction tests (BRTs) help close this gap by turning a bug report into an executable, bug-specific signal that can guide repair and validate candidate patches. Existing work has therefore studied BRT generation as a core subproblem in APR and mainly evaluates a generated BRT using the fail-to-pass (F->P) criterion, which requires the test to fail on the buggy code but pass on the golden fix. We show that F->P alone is insufficient when the goal of a BRT is to improve downstream repair. In particular, some F->P BRTs are lax, reproducing the observed symptom yet still admitting plausible-but-incorrect patches. We formalize this missing quality dimension by separating F->P BRTs into rigorous and lax ones, and show empirically that only the former consistently improve repair success. We further find that co-generation introduces test--fix error coupling, where the in-trajectory fail-to-pass (F->P) check can pass even when both the generated patch and generated test are wrong. Based on these findings, we propose CoHarden, a co-generation framework that uses the Lax signal as an in-loop convergence criterion. CoHarden first generates a test before any fix, then iteratively hardens the test and fix against surviving mutation patches until the generated test no longer admits Lax regressions. Experiments show that CoHarden reaches 69.4% Resolved and 78.9% F->P on SWE-bench Verified, outperforming the strongest fix-only and cogeneration baselines by +9.6 and +7.9 percentage points in Resolved, respectively, with consistent gains across LLM backbones and benchmarks.

cs.SE↗

arXiv2026

DepRepair: LLM-Based Source-Code Repair for Dependency Breaking Changes

Modern software projects depend on numerous third-party libraries, whose updates often introduce breaking changes. Adapting consumer code to such changes remains labor-intensive and error-prone. Existing work either characterizes dependency breaking changes without producing a verified consumer-side patch, or studies automated repair only in settings where the failure and repair context are contained within the target repository. However, dependency breaking changes violate this assumption: the decisive repair evidence lies upstream in release notes and API diffs, and no failing test localizes where the consumer breaks, leaving the repair under-informed. To study this cross-repository problem on real data, we introduce DepBench, a benchmark of 95 real-world dependency-update instances across four ecosystems, each paired with a Docker-based executable oracle that runs the consumer's own tests. To address these challenges, we propose DepRepair, a single-call LLM approach that grounds repair in structured upstream evidence through three components: an evidence filter that distills relevant upstream changes, a usage locator that identifies affected consumer sites, and a subcategory-aware guide that tailors repairs to the breaking-change type. Evaluated on DepBench, DepRepair attains the highest executable pass rate on each backbone, achieving 89.5% with GPT-5.5 and 82.1% with Claude Opus 4.6. We further find that raw upstream evidence reduces LLM and agent pass rates by 7--23 percentage points, whereas structured evidence consistently improves them.

cs.SE↗

arXiv2026

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling

Understanding and generation are often treated as two separate paradigms in training deep neural networks, despite the fact that both are trained with closely related objectives such as denoising and masked prediction. While prior studies have shown that generative models often learn suboptimal representations for understanding tasks in vision, it is less understood whether a similar gap exists in the protein domain. In this work, we systematically investigate this question by benchmarking state-of-the-art protein generative models on widely-used protein understanding tasks, and observe that these models exhibit consistently poor performance compared to existing protein encoders. Furthermore, inspired by the Representation Alignment (REPA) framework, we propose to explicitly align generative protein diffusion models with pretrained protein understanding models during training. Experiments on the MotifBench demonstrate that representation alignment significantly improves functional protein generation, boosting the MotifBench score of Protpardelle-1c from 39.2 to 47.1, corresponding to a 20% relative improvement. Our results suggest that representation alignment provides a general and effective mechanism for bridging understanding and generation in protein structure modeling.

cs.CE↗

arXiv2026

Can Large Language Models Generate Observability-Aware Code?

Recent advances in coding agents have enabled the generation of increasingly complex software systems. While existing evaluations primarily focus on functional correctness, production systems must expose failure evidence to support observability. In this paper, we present a systematic study of observability in agent-generated systems. We examine whether agents can reconstruct source-level diagnostic semantics by restoring observability artifacts in 10 open-source and 8 industrial repositories. We also evaluate whether these artifacts translate into effective fault signals at runtime through 200 generated microservice systems deployed on Kubernetes with 13 injected faults. Our results reveal a consistent gap between diagnostic semantics at the source level and fault signals (i.e., explicit, fault-specific evidence) at runtime. At the source level, agents partially recover observability artifacts but struggle to capture key diagnostic semantics. At runtime, generated systems expose fault signals for only a small fraction of failures (up to 13.99\%), despite the presence of logging, suggesting that the generated observability artifacts may lack the failure-specific semantics needed to effectively expose faults. We further introduce an observability-oriented skill, which can serve as a guidance to improve both diagnostic semantics and fault-signal exposure, but the gains remain limited, indicating that the gap is not easily addressed. More broadly, our findings suggest that current evaluations focusing primarily on functional correctness may overlook observability as an important dimension of practical software quality.

cs.SE↗

arXiv2026

An accurate nucleic acid-small molecule docking framework via geometric deep learning with large-scale pretraining

Nucleic acids are increasingly recognized as therapeutic targets beyond conventional protein-centered drug discovery, yet accurate and efficient docking of small molecules to nucleic acid structures remains challenging. Physics-based docking methods often show limited accuracy and efficiency, whereas deep learning approaches are constrained by the scarcity of experimentally resolved nucleic acid-ligand complexes. Here, we present NucleoDock, a deep learning framework for nucleic acid-small molecule docking. To address data scarcity, NucleoDock combines physics-guided large-scale pretraining on millions of docking-generated synthetic complexes with fine-tuning on curated experimental co-crystal structures. It further integrates sequence- and structure-informed nucleotide representations with atomistic three-dimensional features to capture both biological context and binding-site geometry. A mixture density network-based geometric scoring head is used to model conditional interaction-distance distributions for pose ranking. On an external benchmark of 125 nucleic acid-ligand complexes, NucleoDock achieved a top-1 success rate of 56 percent at an RMSD cutoff of 2.0 Angstrom, outperforming rDock with 29 percent, while generating 100 poses in approximately 5 seconds per complex. Retrospective virtual screening on the ROBIN benchmark further showed improved early enrichment. NucleoDock represents a step toward bridging the methodological gap between protein- and nucleic acid-directed computational drug discovery.

q-bio.BM↗

arXiv2026

SWE-Edit: Rethinking Code Editing for Efficient SWE-Agent

Large language model agents have made strong progress on software engineering, yet current systems suffer from a context coupling problem: the standard code editing interface conflates code inspection, modification planning, and edit execution within a single context window, forcing agents to interleave exploratory viewing with strictly formatted edit generation. Irrelevant context accumulates and edit reliability degrades. We propose SWE-Edit, which decomposes the editing interface into two specialized subagents: a Viewer that extracts task-relevant code on demand, and an Editor that executes modifications from high-level natural language plans -- letting the main agent focus on reasoning while delegating context-intensive operations to clean context windows. On SWE-Bench Verified, this decomposition raises resolve rate by 2.1 pp and cuts inference cost by 17.9%, with consistent gains across multiple reasoning-model families (Kimi-K2, MiniMax-M2.1, GLM-4.7). We further show that effective edit-format selection can be trained into a small model rather than requiring frontier-scale capacity: GRPO training on Qwen3-8B with an adaptive find-replace/whole-file-rewrite policy improves edit success by 12.5 pp and brings an 8B open-source editor to parity with GPT-5-nano on downstream SWE-Bench resolve rate. To enable rapid editor iteration, we release PR-Edit, a lightweight evaluation whose scores correlate strongly with SWE-Bench resolve rate. We release our code at https://github.com/microsoft/SWE-Edit.

cs.SE↗

arXiv2026

ORACLE-SWE: Quantifying the Contribution of Oracle Information Signals on SWE Agents

Recent advances in language model (LM) agents have significantly improved automated software engineering (SWE). Prior work has proposed various agentic workflows and training strategies as well as analyzed failure modes of agentic systems on SWE tasks, focusing on several contextual information signals: Reproduction Test, Regression Test, Edit Location, Execution Context, and API Usage. However, the individual contribution of each signal to overall success remains underexplored, particularly their ideal contribution when intermediate information is perfectly obtained. To address this gap, we introduce Oracle-SWE, a unified method to isolate and extract oracle information signals from SWE benchmarks and quantify the impact of each signal on agent performance. To further validate the pattern, we evaluate the performance gain of signals extracted by strong LMs when provided to a base agent, approximating real-world task-resolution settings. These evaluations aim to guide research prioritization for autonomous coding systems.

cs.MA↗

arXiv2026

RepoLaunch: Automating Build and Management of Code Repositories across Languages and Platforms

Language model (LM) agents have driven substantial progress in automated software engineering (SWE), yet building and testing software repositories at scale remains a largely manual and labor-intensive bottleneck. In this work, we introduce RepoLaunch, a novel agentic framework that automatically resolves dependencies, compiles source code, and extracts test results across diverse programming languages and operating systems. RepoLaunch achieves a 78% build success rate, outperforming the Python/Linux-only prior system by 18%. To demonstrate its application, we further present a fully automated pipeline for SWE dataset creation driven by RepoLaunch, which only requires human input at the task-design stage. RepoLaunch is open-sourced, and its automated task-generation pipeline has already been adopted by several recent works on agentic benchmarking and training.

cs.SE↗

arXiv2026

DRIFT: Diffusion-based Rule-Inferred For Trajectories

Trajectory generation for mobile robots in unstructured environments faces a critical dilemma: balancing kinematic smoothness for safe execution with terminal precision for fine-grained tasks. Existing generative planners often struggle with this trade-off, yielding either smooth but imprecise paths or geometrically accurate but erratic motions. To address the aforementioned shortcomings, this article proposes DRIFT (Diffusion-based Rule-Inferred for Trajectories), a conditional diffusion framework designed to generate high-fidelity reference trajectories by integrating two complementary inductive biases. First, a Relational Inductive Bias, realized via a GNN-based Structured Scene Perception (SSP) module, encodes global topological constraints to ensure holistic smoothness. Second, a Temporal Attention Bias, implemented through a novel Graph-Conditioned Time-Aware GRU (GTGRU), dynamically attends to sparse obstacles and targets for precise local maneuvering. In the end, quantitative results demonstrate that DRIFT reconciles these conflicting objectives, achieving centimeter-level imitation fidelity (0.041m FDE) and competitive smoothness (27.19 Jerk). This balance yields highly executable reference plans for downstream control.

cs.RO↗

arXiv2026

TestExplora: Benchmarking LLMs for Proactive Bug Discovery via Repository-Level Test Generation

Given that Large Language Models (LLMs) are increasingly applied to automate software development, comprehensive software assurance spans three distinct goals: regression prevention, reactive reproduction, and proactive discovery. Current evaluations systematically overlook the third goal. Specifically, they either treat existing code as ground truth (a compliance trap) for regression prevention, or depend on post-failure artifacts (e.g., issue reports) for bug reproduction-so they rarely surface defects before failures. To bridge this gap, we present TestExplora, a benchmark designed to evaluate LLMs as proactive testers within full-scale, realistic repository environments. TestExplora contains 2,389 tasks from 482 repositories and hides all defect-related signals. Models must proactively find bugs by comparing implementations against documentation-derived intent, using documentation as the oracle. Furthermore, to keep evaluation sustainable and reduce leakage, we propose continuous, time-aware data collection. Our evaluation reveals a significant capability gap: state-of-the-art models achieve a maximum Fail-to-Pass (F2P) rate of only 16.06%. Further analysis indicates that navigating complex cross-module interactions and leveraging agentic exploration are critical to advancing LLMs toward autonomous software quality assurance. Consistent with this, SWEAgent instantiated with GPT-5-mini achieves an F2P of 17.27% and an F2P@5 of 29.7%, highlighting the effectiveness and promise of agentic exploration in proactive bug discovery tasks.

cs.SE↗

arXiv2026

AntigenLM: Structure-Aware DNA Language Modeling for Influenza

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact, aligned functional units. This structure-aware pretraining enables AntigenLM to capture evolutionary constraints and generalize across tasks. Fine-tuned on time-series hemagglutinin (HA) and neuraminidase (NA) sequences, AntigenLM accurately forecasts future antigenic variants across regions and subtypes, including those unseen during training, outperforming phylogenetic and evolution-based models. It also achieves near-perfect subtype classification. Ablation studies show that disrupting genomic structure through fragmentation or shuffling severely degrades performance, revealing the importance of preserving functional-unit integrity in DNA language modeling. AntigenLM thus provides both a powerful framework for antigen evolution prediction and a general principle for building biologically grounded DNA foundation models.

q-bio.GN↗

arXiv2026

Closing the Loop: Universal Repository Representation with RPG-Encoder

Current repository agents encounter a reasoning disconnect due to fragmented representations, as existing methods rely on isolated API documentation or dependency graphs that lack semantic depth. We consider repository comprehension and generation to be inverse processes within a unified cycle: generation expands intent into implementation, while comprehension compresses implementation back into intent. To address this, we propose RPG-Encoder, a framework that generalizes the Repository Planning Graph (RPG) from a static generative blueprint into a unified, high-fidelity representation. RPG-Encoder closes the reasoning loop through three mechanisms: (1) Encoding raw code into the RPG that combines lifted semantic features with code dependencies; (2) Evolving the topology incrementally to decouple maintenance costs from repository scale, reducing overhead by 95.7%; and (3) Operating as a unified interface for structure-aware navigation. In evaluations, RPG-Encoder establishes state-of-the-art localization performance on SWE-bench Verified with 93.7% Acc@5 and exceeds the best baseline by over 10% in localization accuracy on SWE-bench Live Lite. These results highlight our superior fine-grained precision in complex codebases. Furthermore, it achieves 98.5% reconstruction coverage on RepoCraft, confirming RPG's high-fidelity capacity to mirror the original codebase and closing the loop between intent and implementation.

cs.CL↗

arXiv2026

DA-SPS: A Dual-stage Network based on Singular Spectrum Analysis, Patching-strategy and Spearman-correlation for Multivariate Time-series Prediction

Multivariate time-series forecasting, as a typical problem in the field of time series prediction, has a wide range of applications in weather forecasting, traffic flow prediction, and other scenarios. However, existing works do not effectively consider the impact of extraneous variables on the prediction of the target variable. On the other hand, they fail to fully extract complex sequence information based on various time patterns of the sequences. To address these drawbacks, we propose a DA-SPS model, which adopts different modules for feature extraction based on the information characteristics of different variables. DA-SPS mainly consists of two stages: the target variable processing stage (TVPS) and the extraneous variables processing stage (EVPS). In TVPS, the model first uses Singular Spectrum Analysis (SSA) to process the target variable sequence and then uses Long Short-Term Memory (LSTM) and P-Conv-LSTM which deploys a patching strategy to extract features from trend and seasonality components, respectively. In EVPS, the model filters extraneous variables that have a strong correlation with the target variate by using Spearman correlation analysis and further analyses them using the L-Attention module which consists of LSTM and attention mechanism. Finally, the results obtained by TVPS and EVPS are combined through weighted summation and linear mapping to produce the final prediction. The results on four public datasets demonstrate that the DA-SPS model outperforms existing state-of-the-art methods. Additionally, its performance in real-world scenarios is further validated using a private dataset collected by ourselves, which contains the test items' information on laptop motherboards.

cs.LG↗