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Automated Program Repair (APR) agents leverage Large Language Models (LLMs) to autonomously diagnose and fix software bugs through reasoning, planning, and tool use. Despite impressive leaderboard gains on benchmarks such as SWE-bench, little is understood about how these agents take actions, where they fail, and how their behavior compares to that of human developers. This paper presents the first systematic analysis of five state-of-the-art APR agents across 500 real-world repair tasks, tracing their full decision-making pipelines—from issue description to patch validation. Our study reveals that while agents excel at simple fixes, they struggle with logic-intensive bugs, often producing verbose or overfitted patches that merely satisfy existing tests. We find that test generation and regression test selection remain major bottlenecks, with agents frequently failing to reproduce issues or run relevant regression tests. Moreover, most agents operate with primitive tooling (e.g., bash scripts) and lack access to debuggers or program analyzers, which constrains their reasoning and patch quality. These findings highlight key limitations in current APR systems and motivate a shift-left approach—emphasizing early, high-quality test generation and validation—to reduce spurious fixes and improve semantic correctness. We further outline concrete directions for next-generation APR design: (1) richer and more integrated tool ecosystems, (2) diversified agentic architectures that combine complementary strengths, and (3) benchmarks that prioritize semantic repair quality and test generation fidelity over surface-level success metrics. 

Autonomous AI agents are increasingly deployed in open social environments, yet the relationship between their configuration specifications and their emergent social behavior has received little empirical scrutiny. We present a controlled, multi-factor empirical study in which thirteen OpenClaw agents are deployed on Moltbook—a Reddit-like social network built for AI agents—across three systematically varied independent variables: (1) personality specification via SOUL.md, (2) underlying LLM model backbone, and (3) operational rules and memory configuration via AGENTS.md. A default control agent provides a behavioral baseline. Over a one-week observation window spanning approximately 400 autonomous sessions per agent, we collect behavioral, linguistic, and social metrics to assess how configuration layers shape emergent social behavior. We find that personality specification is the dominant behavioral lever, producing substantial variance in response length across agents, while model backbone and operational rules drive systematic but smaller effects on rhetorical style and topic engagement breadth. Our findings contribute empirical evidence to the emerging literature on deployed multi-agent social systems and offer practical guidance for designing agents intended for collaborative or monitoring tasks in real social environments. 

The rise of large language models (LLMs) has led to dramatic improvements across a wide range of natural language tasks. Their performance on certain tasks can be further enhanced by incorporating test-time reasoning techniques. These inference-time advances have been adopted into the code domain, enabling complex software engineering (SWE) tasks such as code generation, test generation and issue resolution. However, the impact of different reasoning techniques on code-centric SWE tasks has not been systematically explored. In this work, we survey code reasoning techniques that underpin these capabilities, with a focus on test-time compute and inference-time reasoning paradigms. We examine a variety of code-specific reasoning methods and progressively build up to SWE agents, which combine planning, tool use, and multi-step interaction. We also compare the impact of different techniques on coding tasks, highlighting their relative importance and outlining open challenges and future research directions. Across commonly used models and benchmarks, we find that approaches exploiting code-specific signals (e.g., structure and execution feedback) are frequently associated with improved performance, motivating a dedicated study of code reasoning beyond natural-language reasoning. Our contributions are: (1) to the best of our knowledge, the first dedicated survey of code reasoning for SWE tasks, highlighting overarching reasoning strategies, hybrid methods, and agentic approaches; (2) a taxonomy of inference-time techniques used to drive code reasoning, accompanied by a curated set of under-explored benchmarks with high potential for SWE evaluation; (3) a comparative analysis of reasoning design patterns across commonly used models and benchmarks; and (4) a synthesis of gaps in current methods and evaluation practices, identifying under-explored areas and concrete opportunities for future research. 

Understanding and reasoning about code semantics is essential for enhancing code LLMs' abilities to solve real-world software engineering (SE) tasks. Although several code reasoning benchmarks exist, most rely on synthetic datasets or educational coding problems and focus on coarse-grained reasoning tasks such as input/output prediction, limiting their effectiveness in evaluating LLMs in practical SE contexts. To bridge this gap, we propose CodeSense, the first benchmark that makes available a spectrum of fine-grained code reasoning tasks concerned with the software engineering of real-world code. We collected Python, C and Java software projects from real-world repositories. We executed tests from these repositories, collected their execution traces, and constructed a ground truth dataset for fine-grained semantic reasoning tasks. We then performed comprehensive evaluations on state-of-the-art LLMs. Our results show a clear performance gap for the models to handle fine-grained reasoning tasks. Although prompting techniques such as chain-of-thought and in-context learning helped, the lack of code semantics in LLMs fundamentally limit models' capabilities of code reasoning. Besides dataset, benchmark and evaluation, our work produced an execution tracing framework and tool set that make it easy to collect ground truth for fine-grained SE reasoning tasks, offering a strong basis for future benchmark construction and model post training. Our code and data are located at \url{https://codesense-bench.github.io/}. 

This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). By assigning a unique vector embedding to each short sequence, it is possible to more efficiently cluster and improve upon compression performance for the string representations of cDNA libraries. Furthermore, by studying alternative coordinate vector embeddings trained on the context of codon triplets, we can demonstrate clustering based on amino acid properties. Employing this sequence embedding method to encode barcodes and cDNA sequences, we can improve the time complexity of similarity searches. By pairing vector embeddings with an algorithm that determines the vector proximity in Euclidean space, this approach enables quicker and more flexible sequence searches. 

This paper introduces a novel code-to-code search technique that enhances the performance of Large Language Models (LLMs) by including both static and dynamic features as well as utilizing both similar and dissimilar examples during training. We present the first-ever code search method that encodes dynamic runtime information during training without the need to execute either the corpus under search or the search query at inference time and the first code search technique that trains on both positive and negative reference samples. To validate the efficacy of our approach, we perform a set of studies demonstrating the capability of enhanced LLMs to perform cross-language code-to-code search. Our evaluation demonstrates that the effectiveness of our approach is consistent across various model architectures and programming languages. We outperform the state-of-the-art crosslanguage search tool by up to 44.7%. Moreover, our ablation studies reveal that even a single positive and negative reference sample in the training process results in substantial performance improvements demonstrating both similar and dissimilar references are important parts of code search. Importantly, we show that enhanced well-crafted, fine-tuned models consistently outperform enhanced larger modern LLMs without fine tuning, even when enhancing the largest available LLMs highlighting the importance for open-sourced models. To ensure the reproducibility and extensibility of our research, we present an open-sourced implementation of our tool and training procedures called REINFOREST. 

Code Large Language Models (Code LLMs) have excelled at tasks like code completion but often miss deeper semantics such as execution effects and dynamic states. This paper aims to bridge the gap between Code LLMs' reliance on static text data and the need for semantic understanding for complex tasks like debugging and program repair. We introduce a novel strategy, monologue reasoning, to train Code LLMs to reason comprehensive semantics, encompassing high-level functional descriptions, local execution effects of individual statements, and overall input/output behavior, thereby linking static code text with dynamic execution states. We begin by collecting PyX, a clean Python corpus of fully executable code samples with functional descriptions and test cases. We propose training Code LLMs not only to write code but also to understand code semantics by reasoning about key properties, constraints, and execution behaviors using natural language, mimicking human verbal debugging, i.e., rubber-duck debugging. This approach led to the development of SemCoder, a Code LLM with only 6.7B parameters, which shows competitive performance with GPT-3.5-turbo on code generation and execution reasoning tasks. SemCoder achieves 79.3% on HumanEval (GPT-3.5-turbo: 76.8%), 63.6% on CRUXEval-I (GPT-3.5-turbo: 50.3%), and 63.9% on CRUXEval-O (GPT-3.5-turbo: 59.0%). We also study the effectiveness of SemCoder's monologue-style execution reasoning compared to concrete scratchpad reasoning, showing that our approach integrates semantics from multiple dimensions more smoothly. Finally, we demonstrate the potential of applying learned semantics to improve Code LLMs' debugging and self-refining capabilities. Our data, code, and models are available at: https://github.com/ARiSE-Lab/SemCoder.