arXiv subjects

Saurabh Sinha

Publications and source records attributed to Saurabh Sinha.

At least 19 recordsLinked to original sources

arXiv2026

Tangent: An Empirical Study of Testing Practices for LLM-Based Agent Applications

Agents built on large language models (LLMs) are increasingly used to build applications that perform complex, multi-step tasks involving reasoning, tool use, and interaction with external environments. Despite rapid progress in benchmarking LLM-based agents, very few studies have attempted to understand how such systems are tested in practice. In particular, testing levels, objectives, data patterns, test complexity, and validation strategies for agent applications remain underexplored. In this paper, we present an empirical study of testing practices in LLM-based agent applications using a large corpus of mined open-source projects. We construct a large-scale dataset of agent applications, tools, and tests, and manually label 2,572 test methods from 240 modules. From this analysis, we derive a taxonomy of 23 testing patterns across test fixtures, data, objectives, and assertions, and characterize tests by level (unit, module, integration). We complement this with structured interviews of 10 senior industry practitioners building agentic systems. Our results show that testing of LLM-based agent applications is dominated by narrowly scoped unit tests, with limited coverage of complex interactions, realistic scenarios, and non-functional requirements. Tests frequently rely on simplistic inputs, heavy mocking, and shallow validation, and agent-related tests exhibit low structural complexity. While industry practice places greater emphasis on non-functional testing than open-source projects, both reveal common gaps, including the lack of formal testing foundations, unclear test objectives, and challenges in generating high-quality test data. Based on these findings, we outline research directions toward more systematic and rigorous testing of agent applications, including foundations for agent testability, formalized test objectives, and fault-based testing techniques.

cs.SE↗

arXiv2026

AutoRestTest at the SBFT 2026 Tool Competition

Large input spaces and complex inter-operation dependencies make black-box REST API testing challenging. AutoRestTest combines a Semantic Property Dependency Graph, multi-agent reinforcement learning, and large language models to intelligently explore large API input spaces. In the SBFT 2026 REST League, AutoRestTest ranked first in all three evaluation categories -- fault detection, overall efficiency, and overall effectiveness -- on 11 APIs (317 operations, approximately 29 per API), averaging 67.09 unique server errors and 17.27 successfully processed operations per API under a one-hour testing budget.

cs.SE↗

arXiv2026

Sakura: An Approach for Generating Complex Tests from Natural Language Test Descriptions

Research on automating software testing has spanned several decades. Most existing approaches generate unit tests for individual methods, validate isolated API endpoints, or target user interface (UI) layers, with non-API and non-UI generators typically exercising only a single focal method. Recent empirical evidence shows a substantial gap between such generated tests and developer-written ones, which often span several focal classes and methods, involve multi-step call sequences, and contain chained assertions, all characteristics that current approaches fail to capture. To address this gap, we propose generating tests from natural language (NL) descriptions of developer intent, an expressive and accessible medium for specifying complex test scenarios. We present Sakura, the first agent-based framework for generating structurally complex tests from NL descriptions. Sakura decomposes NL descriptions into structured blocks and processes them with a multi-agent system: a localization agent grounds test steps in concrete application code via static analysis, a composition agent synthesizes compilable test code and iteratively refines it using execution feedback, and a supervisor agent coordinates their interactions. To evaluate Sakura, we curate a novel dataset of NL test descriptions at three levels of abstraction, reflecting different end-user personas, systematically derived from developer-written tests in Apache Commons projects. Across 20 applications and 1,464 test scenarios, Sakura substantially outperforms off-the-shelf agentic tools such as Gemini CLI instantiated with multiple LLMs, achieving 50-78% higher test compilability and 38-66% higher coverage overlap with ground-truth tests using the same models. Moreover, Sakura paired with small open-source models such as Devstral Small 2 and Qwen3-Coder outperforms Gemini CLI using large proprietary models, at lower cost.

cs.SE↗

arXiv2026

Hamster: A Large-Scale Study and Characterization of Developer-Written Tests

Automated test generation (ATG), which aims to reduce the cost of manual test suite development, has been investigated for decades and has produced countless techniques based on a variety of approaches: symbolic analysis, search-based, random and adaptive-random, learning-based, and, most recently, large-language-model-based approaches. However, despite this large body of research, there is still a gap in our understanding of the characteristics of developer-written tests and, consequently, our assessment of how well ATG techniques and tools can generate realistic and representative tests. To bridge this gap, we conducted an extensive empirical study of developer-written tests for Java applications, covering 1.7 million test cases from open-source repositories. Our study is the first of its kind to evaluate aspects of developer-written tests that are mostly neglected in the existing literature -- including test scope, test fixtures and assertions, types of inputs, and use of mocking -- and characterize tests accordingly. Based on this characterization, we then compare existing tests with those generated by two state-of-the-art ATG tools. Our results highlight that the vast majority of developer-written tests exhibit characteristics that are beyond the capabilities of current ATG tools. Finally, based on our findings, we identify promising research directions that can help develop more effective tool support for developer testing practices. We believe this work can set the stage for additional research and bring ATG tools closer to generating the types of tests developers write.

cs.SE↗

arXiv2026

Process-Centric Analysis of Agentic Software Systems

Agentic systems are modern software systems: they consist of orchestrated modules, expose interfaces, and are deployed in software pipelines. Unlike conventional programs, their execution, i.e., trajectories, is inherently stochastic and adaptive to the problems they solve. Evaluation of such systems is often outcome-centric. This narrow focus overlooks detailed insights, failing to explain how agents reason, plan, act, or change their strategies. Inspired by the structured representation of conventional software systems as graphs, we introduce Graphectory to systematically encode the temporal and semantic relations in such systems. Using Graphectory, we automatically analyze 4000 trajectories of two dominant agentic programming workflows, SWE-agent and OpenHands, with four backbone Large Language Models (LLMs), attempting to resolve SWE-bench issues. Our automated analyses (completed within four minutes) reveal that: (1) agents using richer prompts or stronger LLMs exhibit more complex Graphectory, reflecting deeper exploration, broader context gathering, and more thorough validation; (2) agents' strategies vary with problem difficulty and the underlying LLM - for resolved issues, strategies often follow coherent localization-patching-validation steps, while unresolved ones exhibit chaotic or backtracking behaviors; and (3) even successful agentic systems often display inefficient processes. We also implement a novel technique for real-time construction and analysis of Graphectory and Langutory during agent execution to flag trajectory issues. Upon detecting such issues, the technique notifies the agent with a diagnostic message and, when applicable, rolls back the trajectory. Experiments show that online monitoring and interventions improve resolution rates by 6.9%-23.5% across models for problematic instances, while significantly shortening trajectories with near-zero overhead.

cs.SE↗

arXiv2026

MAD: Microenvironment-Aware Distillation -- A Pretraining Strategy for Virtual Spatial Omics from Microscopy

Bridging microscopy and omics would allow us to read molecular states from images-at single-cell resolution and tissue scale-without the cost and throughput limits of omics technologies. Self-supervised pretraining offers a scalable approach with minimal labels, yet how to encode single-cell identity within tissue environments-and the extent of biological information such models can capture-remains an open question. Here, we introduce MAD (microenvironment-aware distillation), a pretraining strategy that learns cell-centric embeddings by jointly self-distilling the morphology view and the microenvironment view of the same indexed cell into a unified embedding space. Across diverse tissues and imaging modalities, MAD achieves state-of-the-art prediction performance on downstream tasks including cell subtyping, transcriptomic prediction, and bioinformatic inference. MAD even outperforms foundation models with a similar number of model parameters that have been trained on substantially larger datasets. These results demonstrate that MAD's dual-view joint self-distillation effectively captures the complexity and diversity of cells within tissues. Together, this establishes MAD as a general tool for representation learning in microscopy, enabling virtual spatial omics and biological insights from vast microscopy datasets.

cs.CV↗

arXiv2025

Advancing Automated In-Isolation Validation in Repository-Level Code Translation

Repository-level code translation aims to migrate entire repositories across programming languages while preserving functionality automatically. Despite advancements in repository-level code translation, validating the translations remains challenging. This paper proposes TRAM, which combines context-aware type resolution with mock-based in-isolation validation to achieve high-quality translations between programming languages. Prior to translation, TRAM retrieves API documentation and contextual code information for each variable type in the source language. It then prompts a large language model (LLM) with retrieved contextual information to resolve type mappings across languages with precise semantic interpretations. Using the automatically constructed type mapping, TRAM employs a custom serialization/deserialization workflow that automatically constructs equivalent mock objects in the target language. This enables each method fragment to be validated in isolation, without the high cost of using agents for translation validation, or the heavy manual effort required by existing approaches that rely on language interoperability. TRAM demonstrates state-of-the-art performance in Java-to-Python translation, underscoring the effectiveness of its integration of RAG-based type resolution with reliable in-isolation validation.

cs.SE↗

arXiv2025

AlphaTrans: A Neuro-Symbolic Compositional Approach for Repository-Level Code Translation and Validation

Code translation transforms programs from one programming language (PL) to another. Several rule-based transpilers have been designed to automate code translation between different pairs of PLs. However, the rules can become obsolete as the PLs evolve and cannot generalize to other PLs. Recent studies have explored the automation of code translation using Large Language Models (LLMs). One key observation is that such techniques may work well for crafted benchmarks but fail to generalize to the scale and complexity of real-world projects with dependencies, custom types, PL-specific features, etc. We propose AlphaTrans, a neuro-symbolic approach to automate repository-level code translation. AlphaTrans translates both source and test code, and employs multiple levels of validation to ensure the translation preserves the functionality of the source program. To break down the problem for LLMs, AlphaTrans leverages program analysis to decompose the program into fragments and translates them in the reverse call order. We leveraged AlphaTrans to translate ten real-world open-source projects consisting of <836, 8575, 2719> classes, methods, and tests. AlphaTrans breaks down these projects into 17874 fragments and translates the entire repository. 96.40% of the translated fragments are syntactically correct, and AlphaTrans validates the translations' runtime behavior and functional correctness for 27.03% and 25.14% of fragments. On average, the integrated translation and validation take 34 hours to translate a project, showing its scalability in practice. For the incorrect translations, AlphaTrans generates a report including existing translation, stack trace, test errors, or assertion failures. We provided these artifacts to two developers to fix the translation bugs in four projects. They were able to fix the issues in 20.1 hours on average and achieve all passing tests.

cs.SE↗

arXiv2025

Otter: Generating Tests from Issues to Validate SWE Patches

While there has been plenty of work on generating tests from existing code, there has been limited work on generating tests from issues. A correct test must validate the code patch that resolves the issue. This paper focuses on the scenario where that code patch does not yet exist. Doing so supports two major use-cases. First, it supports TDD (test-driven development), the discipline of "test first, write code later" that has well-documented benefits for human software engineers. Second, it also validates SWE (software engineering) agents, which generate code patches for resolving issues. This paper introduces TDD-Bench-Verified, a benchmark for generating tests from issues, and Otter, an LLM-based solution for this task. Otter augments LLMs with rule-based analysis to check and repair their outputs, and introduces a novel self-reflective action planner. Experiments show Otter outperforming state-of-the-art systems for generating tests from issues, in addition to enhancing systems that generate patches from issues. We hope that Otter helps make developers more productive at resolving issues and leads to more robust, well-tested code.

cs.SE↗

arXiv2025

LlamaRestTest: Effective REST API Testing with Small Language Models

Modern web services rely heavily on REST APIs, typically documented using the OpenAPI specification. The widespread adoption of this standard has resulted in the development of many black-box testing tools that generate tests based on OpenAPI specifications. Although Large Language Models (LLMs) have shown promising test-generation abilities, their application to REST API testing remains mostly unexplored. We present LlamaRestTest, a novel approach that employs two custom LLMs-created by fine-tuning and quantizing the Llama3-8B model using mined datasets of REST API example values and inter-parameter dependencies-to generate realistic test inputs and uncover inter-parameter dependencies during the testing process by analyzing server responses. We evaluated LlamaRestTest on 12 real-world services (including popular services such as Spotify), comparing it against RESTGPT, a GPT-powered specification-enhancement tool, as well as several state-of-the-art REST API testing tools, including RESTler, MoRest, EvoMaster, and ARAT-RL. Our results demonstrate that fine-tuning enables smaller models to outperform much larger models in detecting actionable parameter-dependency rules and generating valid inputs for REST API testing. We also evaluated different tool configurations, ranging from the base Llama3-8B model to fine-tuned versions, and explored multiple quantization techniques, including 2-bit, 4-bit, and 8-bit integer formats. Our study shows that small language models can perform as well as, or better than, large language models in REST API testing, balancing effectiveness and efficiency. Furthermore, LlamaRestTest outperforms state-of-the-art REST API testing tools in code coverage achieved and internal server errors identified, even when those tools use RESTGPT-enhanced specifications.

cs.SE↗

arXiv2025

AutoRestTest: A Tool for Automated REST API Testing Using LLMs and MARL

As REST APIs have become widespread in modern web services, comprehensive testing of these APIs is increasingly crucial. Because of the vast search space of operations, parameters, and parameter values, along with their dependencies and constraints, current testing tools often achieve low code coverage, resulting in suboptimal fault detection. To address this limitation, we present AutoRestTest, a novel tool that integrates the Semantic Property Dependency Graph (SPDG) with Multi-Agent Reinforcement Learning (MARL) and large language models (LLMs) for effective REST API testing. AutoRestTest determines operation-dependent parameters using the SPDG and employs five specialized agents (operation, parameter, value, dependency, and header) to identify dependencies of operations and generate operation sequences, parameter combinations, and values. Through an intuitive command-line interface, users can easily configure and monitor tests with successful operation count, unique server errors detected, and time elapsed. Upon completion, AutoRestTest generates a detailed report highlighting errors detected and operations exercised. In this paper, we introduce our tool and present preliminary findings, with a demonstration video available at https://www.youtube.com/watch?v=VVus2W8rap8.

cs.SE↗

arXiv2025

A Multi-Agent Approach for REST API Testing with Semantic Graphs and LLM-Driven Inputs

As modern web services increasingly rely on REST APIs, their thorough testing has become crucial. Furthermore, the advent of REST API documentation languages, such as the OpenAPI Specification, has led to the emergence of many black-box REST API testing tools. However, these tools often focus on individual test elements in isolation (e.g., APIs, parameters, values), resulting in lower coverage and less effectiveness in fault detection. To address these limitations, we present AutoRestTest, the first black-box tool to adopt a dependency-embedded multi-agent approach for REST API testing that integrates multi-agent reinforcement learning (MARL) with a semantic property dependency graph (SPDG) and Large Language Models (LLMs). Our approach treats REST API testing as a separable problem, where four agents -- API, dependency, parameter, and value agents -- collaborate to optimize API exploration. LLMs handle domain-specific value generation, the SPDG model simplifies the search space for dependencies using a similarity score between API operations, and MARL dynamically optimizes the agents' behavior. Our evaluation of AutoRestTest on 12 real-world REST services shows that it outperforms the four leading black-box REST API testing tools, including those assisted by RESTGPT (which generates realistic test inputs using LLMs), in terms of code coverage, operation coverage, and fault detection. Notably, AutoRestTest is the only tool able to trigger an internal server error in the Spotify service. Our ablation study illustrates that each component of AutoRestTest -- the SPDG, the LLM, and the agent-learning mechanism -- contributes to its overall effectiveness.

cs.SE↗

arXiv2025

ASTER: Natural and Multi-language Unit Test Generation with LLMs

Implementing automated unit tests is an important but time-consuming activity in software development. To assist developers in this task, many techniques for automating unit test generation have been developed. However, despite this effort, usable tools exist for very few programming languages. Moreover, studies have found that automatically generated tests suffer poor readability and do not resemble developer-written tests. In this work, we present a rigorous investigation of how large language models (LLMs) can help bridge the gap. We describe a generic pipeline that incorporates static analysis to guide LLMs in generating compilable and high-coverage test cases. We illustrate how the pipeline can be applied to different programming languages, specifically Java and Python, and to complex software requiring environment mocking. We conducted an empirical study to assess the quality of the generated tests in terms of code coverage and test naturalness -- evaluating them on standard as well as enterprise Java applications and a large Python benchmark. Our results demonstrate that LLM-based test generation, when guided by static analysis, can be competitive with, and even outperform, state-of-the-art test-generation techniques in coverage achieved while also producing considerably more natural test cases that developers find easy to understand. We also present the results of a user study, conducted with 161 professional developers, that highlights the naturalness characteristics of the tests generated by our approach.

cs.SE↗

arXiv2024

TDD-Bench Verified: Can LLMs Generate Tests for Issues Before They Get Resolved?

Test-driven development (TDD) is the practice of writing tests first and coding later, and the proponents of TDD expound its numerous benefits. For instance, given an issue on a source code repository, tests can clarify the desired behavior among stake-holders before anyone writes code for the agreed-upon fix. Although there has been a lot of work on automated test generation for the practice "write code first, test later", there has been little such automation for TDD. Ideally, tests for TDD should be fail-to-pass (i.e., fail before the issue is resolved and pass after) and have good adequacy with respect to covering the code changed during issue resolution. This paper introduces TDD-Bench Verified, a high-quality benchmark suite of 449 issues mined from real-world GitHub code repositories. The benchmark's evaluation harness runs only relevant tests in isolation for simple yet accurate coverage measurements, and the benchmark's dataset is filtered both by human judges and by execution in the harness. This paper also presents Auto-TDD, an LLM-based solution that takes as input an issue description and a codebase (prior to issue resolution) and returns as output a test that can be used to validate the changes made for resolving the issue. Our evaluation shows that Auto-TDD yields a better fail-to-pass rate than the strongest prior work while also yielding high coverage adequacy. Overall, we hope that this work helps make developers more productive at resolving issues while simultaneously leading to more robust fixes.

cs.SE↗

arXiv2024

Perspective on recent developments and challenges in regulatory and systems genomics

Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective, we discuss recent computational progress and challenges towards solving this fundamental problem. We describe how cis-regulatory elements are mapped and how their sequence rules can be learned and interpreted with sequence-to-function neural networks, with the goal of identifying genetic variants in human disease. We also discuss how studies of the 3D chromatin organization could help identifying long-range regulatory effects and how current methods for mapping gene regulatory networks could better describe biological processes. We point out current gaps in knowledge along with technical limitations and benchmarking challenges of computational methods. Finally, we discuss newly emerging technologies, such as spatial transcriptomics, and outline strategies for creating a more general model of the cis-regulatory code that is more broadly applicable across cell types and individuals.

q-bio.GN↗

arXiv2024

Codellm-Devkit: A Framework for Contextualizing Code LLMs with Program Analysis Insights

Large Language Models for Code (or code LLMs) are increasingly gaining popularity and capabilities, offering a wide array of functionalities such as code completion, code generation, code summarization, test generation, code translation, and more. To leverage code LLMs to their full potential, developers must provide code-specific contextual information to the models. These are typically derived and distilled using program analysis tools. However, there exists a significant gap--these static analysis tools are often language-specific and come with a steep learning curve, making their effective use challenging. These tools are tailored to specific program languages, requiring developers to learn and manage multiple tools to cover various aspects of the their code base. Moreover, the complexity of configuring and integrating these tools into the existing development environments add an additional layer of difficulty. This challenge limits the potential benefits that could be gained from more widespread and effective use of static analysis in conjunction with LLMs. To address this challenge, we present codellm-devkit (hereafter, `CLDK'), an open-source library that significantly simplifies the process of performing program analysis at various levels of granularity for different programming languages to support code LLM use cases. As a Python library, CLDK offers developers an intuitive and user-friendly interface, making it incredibly easy to provide rich program analysis context to code LLMs. With this library, developers can effortlessly integrate detailed, code-specific insights that enhance the operational efficiency and effectiveness of LLMs in coding tasks. CLDK is available as an open-source library at https://github.com/IBM/codellm-devkit.

cs.SE↗

arXiv2024

Robust Model-Based Optimization for Challenging Fitness Landscapes

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

cs.LG↗

arXiv2024

Leveraging Large Language Models to Improve REST API Testing

The widespread adoption of REST APIs, coupled with their growing complexity and size, has led to the need for automated REST API testing tools. Current tools focus on the structured data in REST API specifications but often neglect valuable insights available in unstructured natural-language descriptions in the specifications, which leads to suboptimal test coverage. Recently, to address this gap, researchers have developed techniques that extract rules from these human-readable descriptions and query knowledge bases to derive meaningful input values. However, these techniques are limited in the types of rules they can extract and prone to produce inaccurate results. This paper presents RESTGPT, an innovative approach that leverages the power and intrinsic context-awareness of Large Language Models (LLMs) to improve REST API testing. RESTGPT takes as input an API specification, extracts machine-interpretable rules, and generates example parameter values from natural-language descriptions in the specification. It then augments the original specification with these rules and values. Our evaluations indicate that RESTGPT outperforms existing techniques in both rule extraction and value generation. Given these promising results, we outline future research directions for advancing REST API testing through LLMs.

cs.SE↗