arXiv subjects

Silin Chen

Publications and source records attributed to Silin Chen.

At least 19 recordsLinked to original sources

arXiv2026

RSIHub: A Composable Framework for Agent-Evolution Methods

Agent-evolution methods use execution feedback to improve prompts, skills, tools, and orchestration, but their implementations often rebuild the same experimental machinery. We present RSIHub, an open-source framework for building, comparing, and extending these methods on shared infrastructure. Recipes compose reusable operators and declare mutable resources; RSIHub supplies execution, evaluation, recovery, and lineage. Researchers can focus on evolution policy while evaluation stays outside the mutable surface and results remain tied to candidates and evaluation conditions. We instantiate AHE, Hyperagents, A-Evolve, and GEPA without modifying the framework core, keeping method-specific logic in recipes and operators. We evaluate them with MiniSWE and Codex on Terminal Bench 2 and $τ^3$ Banking under fixed model and evaluator configurations. The largest observed overall pass@1 gain is 13.5 percentage points, while method rankings vary across settings and optimization gains do not always transfer to held-out tasks. RSIHub provides a common protocol for comparing evolution policies, inspectable candidate histories, and reusable components for developing new methods.

cs.AI↗

arXiv2026

SWE-at-Scale: Scalable Issue Synthesis from Historical Bug Fixes

As coding agents become increasingly capable, robust evaluation requires a broader and more diverse supply of verifiable software engineering (SWE) tasks. However, real-world tasks are constrained by the natural frequency of issue reporting and the substantial cost of manual curation. Furthermore, existing synthetic approaches rely primarily on the pretrained knowledge of large models coupled with heuristic prompting, often failing to capture the authentic, complex mechanics of software failures. To exponentially scale SWE task production, we introduce SWE-at-Scale, a framework that automatically synthesizes realistic issues by reverse-engineering real-world software fixes. Our key insight is that historical fixes encapsulate deep mechanistic knowledge of bug formation: inverting a fix transforms repair supervision into bug-induction supervision grounded in actual development scenarios. SWE-at-Scale transfers these learned bug patterns to novel code contexts, repeatedly sampling diverse bug typologies to construct executable SWE tasks. Extensive experiments show that SWE-at-Scale generates more diverse and realistic SWE tasks than current synthesis baselines while posing greater challenges to state-of-the-art coding agents. Notably, SWE-at-Scale can generate distinct bug types from a single code context, with bug diversity scaling robustly even up to 200 generations per file. Overall, SWE-at-Scale turns finite real-world fixes into reusable supervision for scalable synthesis of realistic, diverse, and challenging SWE tasks.

cs.SE↗

arXiv2026

From Bench-to-Bedside: A Review of Clinical Trials in Drug Discovery and Development

Clinical trials bridge basic research and clinical application, serving as essential steps in drug development. This review examines clinical trial phases (Phase I [safety assessment], Phase II [efficacy evaluation], Phase III [large-scale validation], and Phase IV [post-marketing surveillance]), highlighting the distinct characteristics and interconnections. Major challenges are identified, including ethical compliance, participant recruitment, and ensuring diversity and representativeness in trial populations, while proposing evidence-based mitigation strategies. To address these challenges, innovative technologies, such as artificial intelligence, big data analytics, and digital health tools, are transforming trial design and implementation, enhancing efficiency and data quality. Looking forward, the review explores how emerging therapies, including gene therapy and immunotherapy, are reshaping trial design requirements and emphasizes the growing importance of regulatory harmonization and global collaboration. Clinical trials remain central to advancing innovative drug development and improving patient outcomes.

cs.CY↗

arXiv2026

From In Silico to In Vitro: A Comprehensive Guide to Validating Bioinformatics Findings

Translating computational predictions into experimentally validated biological knowledge remains one of the central challenges in modern bioinformatics. This review critically examines how in silico findings can be prioritized, tested, and interpreted through experimental validation. We organize the validation process around three recurring challenges: the specificity gap between genome-wide computational predictions and single-target experimental assays; the reproducibility-translatability tension, in which results validated in one model system may not generalize to another; and the scale-depth trade-off between high-throughput candidate discovery and the low-throughput nature of mechanistic validation. Rather than presenting an encyclopedic catalogue of techniques, we compare the strengths, limitations, and common failure modes of major validation approaches, including qPCR, RNA-seq, Western blotting, co-immunoprecipitation, luciferase reporter assays, CRISPR perturbation, and functional phenotypic assays. We also provide structured comparison tables for gene expression, protein-protein interaction, non-coding RNA, regulatory element, and pathway validation, together with decision-making frameworks to guide method selection according to prediction type, biological context, evidence stringency, throughput, and resource constraints. Case studies from cancer genomics, drug target discovery, miRNA regulation, and neurological disease illustrate how multi-step validation workflows can strengthen causal inference and reduce false-positive interpretation. Finally, we discuss how emerging technologies, including CRISPR screens, single-cell and spatial multi-omics, and AI-assisted experimental design, may reshape validation practice by improving scalability, context specificity, and reproducibility.

q-bio.GN↗

arXiv2026

Test vs Mutant: Adversarial LLM Agents for Robust Unit Test Generation

Software testing is a critical, yet resource-intensive phase of the software development lifecycle. Over the years, various automated tools have been developed to aid in this process. Search-based approaches typically achieve high coverage but produce tests with low readability, whereas large language model (LLM)-based methods generate more human-readable tests but often suffer from low coverage and compilability. While the majority of research efforts have focused on improving test coverage and readability, little attention has been paid to enhancing the robustness of bug detection, particularly in exposing corner cases and vulnerable execution paths. To address this gap, we propose AdverTest, a novel adversarial framework for LLM-powered test case generation. AdverTest comprises two interacting agents: a test case generation agent (T) and a mutant generation agent (M). These agents engage in an adversarial loop, where M persistently creates new mutants "hacking" the blind spots of T's current test suite, while T iteratively refines its test cases to "kill" the challenging mutants produced by M. This interaction loop is guided by both coverage and mutation scores, enabling the system to co-evolve toward both high test coverage and bug detection capability. Experimental results in the Defects4J dataset show that our approach improves fault detection rates by 8.56% over the best existing LLM-based methods and by 63.30% over EvoSuite, while also improving line and branch coverage.

cs.SE↗

arXiv2026

Schrödinger's Code Repository: Have LLMs Learned SWE-bench or Memorized It?

Repository-level coding benchmarks have become the standard for evaluating coding agents, yet they inherently suffer from data leakage because they are built upon popular open-source repositories repeatedly used for training. Consequently, strong performance may reflect memorization of canonical repository cues rather than robust repository reasoning. We propose SchrodingerRepo (Schrödinger's Repository), an evaluation framework for testing coding agents under dynamically instantiated repository representations. Instead of repeatedly using a static representation of the test repository, SchrodingerRepo treats the test repository as an evaluation-time latent variable that is dynamically instantiated only when the agent enters the evaluation environment. The instantiated repository preserves the original executable behavior while eroding familiar cues such as naming conventions, file layouts, and implementation patterns through four transformation levels: problem statement reconstruction, namespace remapping, intra-file layout reordering, and functionality-preserving code rewriting. We evaluate popular LLMs on SWE-bench Verified and SWE-QA. Results show that removing familiar repository cues consistently degrades agent performance and substantially increases interaction costs across models. Further analysis reveals that the additional cost is primarily caused by increased difficulty in repository exploration and localization. These findings suggest that current coding agents may partially rely on memorized repository-side cues, highlighting the need for evaluation under dynamically instantiated repository representations.

cs.SE↗

arXiv2026

Repo0: Design-Driven Zero-to-All Code Generation

Large language model agents have made substantial progress in code generation, yet most existing systems assume a predefined repository architecture. This assumption does not hold in zero-to-all code generation, where an agent must construct an entire software project directly from natural-language requirements while maintaining a modular repository architecture throughout development. We present Repo0, a continuous structural evolution framework for zero-to-all code generation. Repo0 maintains an explicit architectural state instantiated as a Dual-Directed-Acyclic-Graph (Dual-DAG), consisting of a requirement-level DAG, a component-level DAG, and their alignment relation. Starting from natural-language requirements, it iteratively evolves component boundaries through structural actions guided by modularity metrics until structural convergence, after which the converged architecture guides test-driven development code generation. We evaluate Repo0 on six real-world repositories from RepoCraft using GPT-5 mini and DeepSeek V3.2. Repo0 achieves the highest Functionality Coverage and Pass Rate across all settings. Compared with RPG, the strongest repository-planning baseline, Repo0 improves Functionality Coverage by up to 20.08 percentage points and Pass Rate by up to 29.74 percentage points. Ablation and structural-evolution analyses further demonstrate the importance of the Dual-DAG architectural state, modularity-guided structural evolution, and explicit structural convergence.

cs.SE↗

arXiv2026

SkillForge: Self-Distilling Agents for Project-Specific Issue Resolution

Large language model (LLM) based agents have demonstrated remarkable proficiency in automated software issue resolution, yet they often struggle to resolve issues in a specific repository because they lack project-specific knowledge. Existing self-evolving approaches acquire such knowledge from repository history or online repair trajectories, but they either depend on available historical issue-resolution signals or incur substantial per-issue test-time exploration cost. In this paper, we propose SkillForge, a self-distillation framework that proactively acquires project-specific knowledge from the repository itself. Instead of waiting for real issues to expose project-specific knowledge gaps, SkillForge synthesizes project-specific issues by re-implementing test-covered core functionalities of the repository. By resolving these synthetic issues, SkillForge distills reusable project-specific knowledge into entity-grounded skills and associates them with relevant repository entities for future issue resolution. Extensive experiments using both open-source and closed-source models show that SkillForge consistently improves issue resolution performance over strong baselines. These results demonstrate that proactively acquiring project-specific knowledge before solving real issues substantially improves downstream software issue resolution.

cs.SE↗

arXiv2026

LLM Agents Can See Code Repositories

Coding agents powered by large language models have demonstrated strong performance on software engineering tasks. Yet most agents consume repositories almost entirely as text, which differs from how human developers use visual structure such as folder hierarchies and dependency relationships to orient themselves in large codebases. With multimodal large language models (MLLMs), it is an open question whether agents can effectively benefit from visual representations of repositories. This paper presents the first systematic empirical study of visual repository representations for LLM-based agents on repository-level issue resolution. We evaluate four recent multimodal models. Our results show that a strictly vision-only setup degrades accuracy and increases token cost, because agents lack sufficient symbolic detail and compensate with repeated visual queries. In contrast, integrating visual graphs of repository structure as a supplementary modality alongside standard text interfaces helps agents understand structure more efficiently: input token consumption decreases by up to 26% while issue-resolution accuracy is maintained or improved. Visualization is most useful during fault localization and when the agent autonomously controls exploration depth. These findings point to a practical hybrid text-and-vision design for next-generation coding agents.

cs.SE↗

arXiv2026

Know Before Fix: QA-Driven Repository Knowledge Acquisition for Software Issue Resolution

LLM-based coding agents have significantly advanced automated software issue resolution, yet they remain highly prone to factual errors caused by insufficient repository understanding. Recent methods attempt to mitigate this limitation through pre-repair repository exploration; however, their fix-driven strategies explore repositories without identifying the agent's knowledge gaps, often yielding imprecise context that fails to bridge the underlying understanding deficit. In this paper, we propose ACQUIRE, a QA-driven framework for software issue resolution. Mirroring how experienced developers first comprehend unfamiliar code before attempting a fix, ACQUIRE explicitly acquires repository knowledge prior to repair. The framework decouples knowledge acquisition from patch generation through two stages: in the first stage, a Questioner and an Answerer collaborate to acquire structured repository knowledge, where the Questioner poses targeted questions and the Answerer produces evidence-grounded answers through autonomous exploration; in the second stage, the Resolver leverages the resulting QA knowledge to generate informed patches. By transforming implicit knowledge gaps into explicit, factually reliable understanding, ACQUIRE accelerates knowledge-intensive repair stages and enables more accurate resolution. Experiments on SWE-bench Verified demonstrate that ACQUIRE consistently outperforms representative pre-repair methods, raising Pass@1 by up to 4.4 percentage points with modest additional cost and time.

cs.SE↗

arXiv2026

A Unified Geometric Space for Topological Alignment Between Transformer-Based Models and Human Brain Networks

Whether artificial neural networks organize information comparably to the human brain remains unclear. Prior brain--AI alignment studies are constrained by specific inputs and tasks, limiting cross-modal comparison. Here we introduce a brain--model topological alignment space, mapping Transformer attention topology onto human intrinsic connectivity networks (ICNs) to enable task-free, modality-agnostic comparison. Analyzing 151 Transformer-based models with 62,480 attention head graphs, we observe a continuous arc-shaped distribution reflecting varying alignment. Models optimized for global semantics aligned with higher-order ICNs, while local-detail models aligned with sensory ICNs. Non-intuitive findings include reduced alignment in DINOv2 compared to its predecessors and a counterintuitive scaling inversion in distilled DeiT models, while fine-tuning and instruction tuning had limited effect. Alignment scores showed no significant correlation with ImageNet accuracy (r = 0.266, p = 0.156). This work offers a quantitative framework for comparing the organizational principles of artificial and biological systems.

cs.AI↗

arXiv2026

SWE-Exp: Experience-Driven Software Issue Resolution

Recent advances in large language model (LLM) agents have shown remarkable progress in software issue resolution, leveraging advanced techniques such as multi-agent collaboration and Monte Carlo Tree Search (MCTS). However, current agents act as memoryless explorers - treating each problem separately without retaining or reusing knowledge from previous repair experiences. This leads to redundant exploration of failed trajectories and missed chances to adapt successful issue resolution methods to similar problems. To address this problem, we introduce SWE-Exp, an experience-enhanced approach that distills concise and actionable experience from prior agent trajectories, enabling continuous learning across issues. Our method introduces a multi-faceted experience bank that captures both successful and failed repair attempts. Specifically, it extracts reusable issue resolution knowledge at different levels - from high-level problem comprehension to specific code changes. Experiments show that SWE-Exp achieves a Pass@1 resolution rate of 73.0% on SWE-Bench Verified using the state-of-the-art LLM Claude 4 Sonnet, significantly outperforming prior results under other agent frameworks. Our approach establishes a new paradigm in which automated software engineering agents systematically accumulate and leverage repair expertise, fundamentally shifting from trial-and-error exploration to strategic, experience-driven issue resolution.

cs.SE↗

arXiv2025

FedDyMem: Efficient Federated Learning with Dynamic Memory and Memory-Reduce for Unsupervised Image Anomaly Detection

Unsupervised image anomaly detection (UAD) has become a critical process in industrial and medical applications, but it faces growing challenges due to increasing concerns over data privacy. The limited class diversity inherent to one-class classification tasks, combined with distribution biases caused by variations in products across and within clients, poses significant challenges for preserving data privacy with federated UAD. Thus, this article proposes an efficient federated learning method with dynamic memory and memory-reduce for unsupervised image anomaly detection, called FedDyMem. Considering all client data belongs to a single class (i.e., normal sample) in UAD and the distribution of intra-class features demonstrates significant skewness, FedDyMem facilitates knowledge sharing between the client and server through the client's dynamic memory bank instead of model parameters. In the local clients, a memory generator and a metric loss are employed to improve the consistency of the feature distribution for normal samples, leveraging the local model to update the memory bank dynamically. For efficient communication and data privacy, a memory-reduce method based on weighted averages is proposed to significantly decrease the scale of memory banks. This reduced representation inherently, thereby mitigating the risk of data reconstruction. On the server, global memory is constructed and distributed to individual clients through k-means aggregation. Experiments conducted on six industrial and medical datasets, comprising a mixture of six products or health screening types derived from eleven public datasets, demonstrate the effectiveness of FedDyMem.

cs.DC↗

arXiv2025

Deep Learning and Machine Learning -- Python Data Structures and Mathematics Fundamental: From Theory to Practice

This book provides a comprehensive introduction to the foundational concepts of machine learning (ML) and deep learning (DL). It bridges the gap between theoretical mathematics and practical application, focusing on Python as the primary programming language for implementing key algorithms and data structures. The book covers a wide range of topics, including basic and advanced Python programming, fundamental mathematical operations, matrix operations, linear algebra, and optimization techniques crucial for training ML and DL models. Advanced subjects like neural networks, optimization algorithms, and frequency domain methods are also explored, along with real-world applications of large language models (LLMs) and artificial intelligence (AI) in big data management. Designed for both beginners and advanced learners, the book emphasizes the critical role of mathematical principles in developing scalable AI solutions. Practical examples and Python code are provided throughout, ensuring readers gain hands-on experience in applying theoretical knowledge to solve complex problems in ML, DL, and big data analytics.

cs.LG↗

arXiv2025

Deep Learning, Machine Learning -- Digital Signal and Image Processing: From Theory to Application

Digital Signal Processing (DSP) and Digital Image Processing (DIP) with Machine Learning (ML) and Deep Learning (DL) are popular research areas in Computer Vision and related fields. We highlight transformative applications in image enhancement, filtering techniques, and pattern recognition. By integrating frameworks like the Discrete Fourier Transform (DFT), Z-Transform, and Fourier Transform methods, we enable robust data manipulation and feature extraction essential for AI-driven tasks. Using Python, we implement algorithms that optimize real-time data processing, forming a foundation for scalable, high-performance solutions in computer vision. This work illustrates the potential of ML and DL to advance DSP and DIP methodologies, contributing to artificial intelligence, automated feature extraction, and applications across diverse domains.

cs.CV↗

arXiv2025

Large Language Models and Cognitive Science: A Comprehensive Review of Similarities, Differences, and Challenges

This comprehensive review explores the intersection of Large Language Models (LLMs) and cognitive science, examining similarities and differences between LLMs and human cognitive processes. We analyze methods for evaluating LLMs cognitive abilities and discuss their potential as cognitive models. The review covers applications of LLMs in various cognitive fields, highlighting insights gained for cognitive science research. We assess cognitive biases and limitations of LLMs, along with proposed methods for improving their performance. The integration of LLMs with cognitive architectures is examined, revealing promising avenues for enhancing artificial intelligence (AI) capabilities. Key challenges and future research directions are identified, emphasizing the need for continued refinement of LLMs to better align with human cognition. This review provides a balanced perspective on the current state and future potential of LLMs in advancing our understanding of both artificial and human intelligence.

cs.AI↗

arXiv2025

From Text to Multimodality: Exploring the Evolution and Impact of Large Language Models in Medical Practice

Large Language Models (LLMs) have rapidly evolved from text-based systems to multimodal platforms, significantly impacting various sectors including healthcare. This comprehensive review explores the progression of LLMs to Multimodal Large Language Models (MLLMs) and their growing influence in medical practice. We examine the current landscape of MLLMs in healthcare, analyzing their applications across clinical decision support, medical imaging, patient engagement, and research. The review highlights the unique capabilities of MLLMs in integrating diverse data types, such as text, images, and audio, to provide more comprehensive insights into patient health. We also address the challenges facing MLLM implementation, including data limitations, technical hurdles, and ethical considerations. By identifying key research gaps, this paper aims to guide future investigations in areas such as dataset development, modality alignment methods, and the establishment of ethical guidelines. As MLLMs continue to shape the future of healthcare, understanding their potential and limitations is crucial for their responsible and effective integration into medical practice.

cs.CY↗

arXiv2025

Deep Learning and Machine Learning -- Object Detection and Semantic Segmentation: From Theory to Applications

An in-depth exploration of object detection and semantic segmentation is provided, combining theoretical foundations with practical applications. State-of-the-art advancements in machine learning and deep learning are reviewed, focusing on convolutional neural networks (CNNs), YOLO architectures, and transformer-based approaches such as DETR. The integration of artificial intelligence (AI) techniques and large language models for enhancing object detection in complex environments is examined. Additionally, a comprehensive analysis of big data processing is presented, with emphasis on model optimization and performance evaluation metrics. By bridging the gap between traditional methods and modern deep learning frameworks, valuable insights are offered for researchers, data scientists, and engineers aiming to apply AI-driven methodologies to large-scale object detection tasks.

cs.CV↗