Saurabh Sinha

Tyler Stennett, Rangeet Pan, Bridget McGinn et al.

Testing is a core activity in software development workflows, and research on its automation 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 automated test 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 multiple focal methods, involve complex call sequences, and contain elaborate assertions that current automated approaches fail to capture. To address this gap, we propose generating tests from natural language (NL) descriptions of developer intent. We present Sakura, the first agent-based framework for generating structurally complex test cases from NL descriptions. Sakura decomposes NL descriptions into structured blocks and processes them using a multi-agent system consisting of a localization agent that grounds test steps in concrete application code via static analysis, a composition agent that synthesizes compilable test code and iteratively refines it using execution feedback, and a supervisor agent that coordinates agent interactions. To evaluate Sakura, we curate a novel dataset of NL test descriptions at three levels of abstraction, systematically generated from developer-written tests mined from Apache Commons projects. Across 20 applications and 1,464 test scenarios, Sakura significantly outperforms off-the-shelf agentic tools such as Gemini CLI. Specifically, Sakura achieves 50-78% higher test compilability and 38-66% higher coverage overlap with ground-truth tests compared to baselines 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, while also being more cost-effective.

Rangeet Pan, Tyler Stennett, Raju Pavuluri et al.

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.

Rangeet Pan, Raju Pavuluri, Ruikai Huang et al.

Enterprise applications are typically tested at multiple levels, with service-level testing playing an important role in validating application functionality. Existing service-level testing tools, especially for RESTful APIs, often employ fuzzing and/or depend on OpenAPI specifications which are not readily available in real-world enterprise codebases. Moreover, these tools are limited in their ability to generate functional tests that effectively exercise meaningful scenarios. In this work, we present SAINT, a novel white-box testing approach for service-level testing of enterprise Java applications. SAINT combines static analysis, large language models (LLMs), and LLM-based agents to automatically generate endpoint and scenario-based tests. The approach builds two key models: an endpoint model, capturing syntactic and semantic information about service endpoints, and an operation dependency graph, capturing inter-endpoint ordering constraints. SAINT then employs LLM-based agents to generate tests. Endpoint-focused tests aim to maximize code and database interaction coverage. Scenario-based tests are synthesized by extracting application use cases from code and refining them into executable tests via planning, action, and reflection phases of the agentic loop. We evaluated SAINT on eight Java applications, including a proprietary enterprise application. Our results illustrate the effectiveness of SAINT in coverage, fault detection, and scenario generation. Moreover, a developer survey provides strong endorsement of the scenario-based tests generated by SAINT. Overall, our work shows that combining static analysis with agentic LLM workflows enables more effective, functional, and developer-aligned service-level test generation.

Payam Dibaeinia, Saurabh Sinha

The discovery of causal relationships from high-dimensional data is a major open problem in bioinformatics. Machine learning and feature attribution models have shown great promise in this context but lack causal interpretation. Here, we show that a popular feature attribution model estimates a causal quantity reflecting the influence of one variable on another, under certain assumptions. We leverage this insight to implement a new tool, CIMLA, for discovering condition-dependent changes in causal relationships. We then use CIMLA to identify differences in gene regulatory networks between biological conditions, a problem that has received great attention in recent years. Using extensive benchmarking on simulated data sets, we show that CIMLA is more robust to confounding variables and is more accurate than leading methods. Finally, we employ CIMLA to analyze a previously published single-cell RNA-seq data set collected from subjects with and without Alzheimer's disease (AD), discovering several potential regulators of AD.

Ali Reza Ibrahimzada, Kaiyao Ke, Mrigank Pawagi et al.

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.

Shuyang Liu, Yang Chen, Rahul Krishna et al.

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 problem they are solving. Evaluation of such systems is often outcome-centric, judging their performance based on success or failure at the final step. This narrow focus overlooks detailed insights about such systems, failing to explain how agents reason, plan, act, or change their strategies over time. Inspired by the structured representation of conventional software systems as graphs, we introduce Graphectory to systematically encode the temporal and semantic relations in such software systems. Graphectory facilitates the design of process-centric metrics and analyses to assess the quality of agentic workflows independent of final success. Using Graphectory, we analyze 4000 trajectories of two dominant agentic programming workflows, namely SWE-agent and OpenHands, with a combination of four backbone Large Language Models (LLMs), attempting to resolve SWE-bench Verified issues. Our fully automated analyses reveal that: (1) agents using richer prompts or stronger LLMs exhibit more complex Graphectory, reflecting deeper exploration, broader context gathering, and more thorough validation before patch submission; (2) agents' problem-solving strategies vary with both problem difficulty and the underlying LLM -- for resolved issues, the strategies often follow coherent localization-patching-validation steps, while unresolved ones exhibit chaotic, repetitive, or backtracking behaviors; (3) even when successful, agentic programming systems often display inefficient processes, leading to unnecessarily prolonged trajectories.

Saba Ghaffari, Ehsan Saleh, Alexander G. Schwing et al.

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.

Anup Kalia, Jin Xiao, Rahul Krishna et al.

In migrating production workloads to cloud, enterprises often face the daunting task of evolving monolithic applications toward a microservice architecture. At IBM, we developed a tool called Mono2Micro to assist with this challenging task. Mono2Micro performs spatio-temporal decomposition, leveraging well-defined business use cases and runtime call relations to create functionally cohesive partitioning of application classes. Our preliminary evaluation of Mono2Micro showed promising results. How well does Mono2Micro perform against other decomposition techniques, and how do practitioners perceive the tool? This paper describes the technical foundations of Mono2Micro and presents results to answer these two questions. To answer the first question, we evaluated Mono2Micro against four existing techniques on a set of open-source and proprietary Java applications and using different metrics to assess the quality of decomposition and tool's efficiency. Our results show that Mono2Micro significantly outperforms state-of-the-art baselines in specific metrics well-defined for the problem domain. To answer the second question, we conducted a survey of twenty-one practitioners in various industry roles who have used Mono2Micro. This study highlights several benefits of the tool, interesting practitioner perceptions, and scope for further improvements. Overall, these results show that Mono2Micro can provide a valuable aid to practitioners in creating functionally cohesive and explainable microservice decompositions.

Jiashu Han, Kunzan Liu, Yeojin Kim et al.

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.

Toufique Ahmed, Martin Hirzel, Rangeet Pan et al.

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.

Myeongsoo Kim, Tyler Stennett, Saurabh Sinha et al.

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.

Myeongsoo Kim, Saurabh Sinha, Alessandro Orso

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.

Toufique Ahmed, Jatin Ganhotra, Rangeet Pan et al.

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.

Tyler Stennett, Myeongsoo Kim, Saurabh Sinha et al.

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.

Jiaming Shen, Jinfeng Xiao, Xinwei He et al.

Literature search is critical for any scientific research. Different from Web or general domain search, a large portion of queries in scientific literature search are entity-set queries, that is, multiple entities of possibly different types. Entity-set queries reflect user's need for finding documents that contain multiple entities and reveal inter-entity relationships and thus pose non-trivial challenges to existing search algorithms that model each entity separately. However, entity-set queries are usually sparse (i.e., not so repetitive), which makes ineffective many supervised ranking models that rely heavily on associated click history. To address these challenges, we introduce SetRank, an unsupervised ranking framework that models inter-entity relationships and captures entity type information. Furthermore, we develop a novel unsupervised model selection algorithm, based on the technique of weighted rank aggregation, to automatically choose the parameter settings in SetRank without resorting to a labeled validation set. We evaluate our proposed unsupervised approach using datasets from TREC Genomics Tracks and Semantic Scholar's query log. The experiments demonstrate that SetRank significantly outperforms the baseline unsupervised models, especially on entity-set queries, and our model selection algorithm effectively chooses suitable parameter settings.

Faraz Faghri, Sayed Hadi Hashemi, Mohammad Babaeizadeh et al.

In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the bioinformatics community. These top data mining and machine learning algorithms cover classification, clustering, regression, graphical model-based learning, and dimensionality reduction. The goal of this study is to guide the focus of scalable computing experts in the endeavor of applying new storage and scalable computation designs to bioinformatics algorithms that merit their attention most, following the engineering maxim of "optimize the common case".

Parisa Kordjamshidi, Sameer Singh, Daniel Khashabi et al.

Many real world systems need to operate on heterogeneous information networks that consist of numerous interacting components of different types. Examples include systems that perform data analysis on biological information networks; social networks; and information extraction systems processing unstructured data to convert raw text to knowledge graphs. Many previous works describe specialized approaches to perform specific types of analysis, mining and learning on such networks. In this work, we propose a unified framework consisting of a data model -a graph with a first order schema along with a declarative language for constructing, querying and manipulating such networks in ways that facilitate relational and structured machine learning. In particular, we provide an initial prototype for a relational and graph traversal query language where queries are directly used as relational features for structured machine learning models. Feature extraction is performed by making declarative graph traversal queries. Learning and inference models can directly operate on this relational representation and augment it with new data and knowledge that, in turn, is integrated seamlessly into the relational structure to support new predictions. We demonstrate this system's capabilities by showcasing tasks in natural language processing and computational biology domains.