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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. In this work, we focus on the scenario where the code patch does not exist yet. This approach 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 Otter, an LLM-based solution for generating tests from issues. Otter augments LLMs with rule-based analysis to check and repair their outputs, and introduces a novel self-reflective action planning stage. 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.

As REST APIs have become widespread in modern web services, comprehensive testing of these APIs has become increasingly crucial. Due to the vast search space consisting of operations, parameters, and parameter values along with their complex dependencies and constraints, current testing tools suffer from low code coverage, leading to suboptimal fault detection. To address this limitation, we present a novel tool, AutoRestTest, which integrates the Semantic Operation Dependency Graph (SODG) with Multi-Agent Reinforcement Learning (MARL) and large language models (LLMs) for effective REST API testing. AutoRestTest determines operation-dependent parameters using the SODG and employs five specialized agents (operation, parameter, value, dependency, and header) to identify dependencies of operations and generate operation sequences, parameter combinations, and values. AutoRestTest provides a command-line interface and continuous telemetry on 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 results., Comment: To be published in the 47th IEEE/ACM International Conference on Software Engineering - Demonstration Track (ICSE-Demo 2025)

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 these specifications. Recent advancements in Natural Language Processing (NLP), particularly with Large Language Models (LLMs), have enhanced REST API testing by extracting actionable rules and generating input values from the human-readable portions of the specification. However, these advancements overlook the potential of continuously refining the identified rules and test inputs based on server responses. To address this limitation, we present LlamaRestTest, a novel approach that employs two custom LLMs to generate realistic test inputs and uncover parameter dependencies during the testing process by incorporating server responses. These LLMs are created by fine-tuning the Llama3-8b model, using mined datasets of REST API example values and inter-parameter dependencies. 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 show that fine-tuning enables smaller LLMs to outperform larger models in detecting actionable rules and generating inputs for REST API testing. We evaluated configurations from the base Llama3-8B to fine-tuned versions and explored 2-bit, 4-bit, and 8-bit quantization for efficiency. LlamaRestTest surpasses state-of-the-art tools in code coverage and error detection, even with RESTGPT-enhanced specifications, and an ablation study highlights the impact of its novel components., Comment: To be published in the ACM International Conference on the Foundations of Software Engineering (FSE 2025)

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.

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., Comment: To be published in the 47th IEEE/ACM International Conference on Software Engineering (ICSE 2025)

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.

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.

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.

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., Comment: Accepted at ICSE-SEIP, 2025

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., Comment: To be published in the 46th IEEE/ACM International Conference on Software Engineering - New Ideas and Emerging Results Track (ICSE-NIER 2024)

Modern web services increasingly rely on REST APIs. Effectively testing these APIs is challenging due to the vast search space to be explored, which involves selecting API operations for sequence creation, choosing parameters for each operation from a potentially large set of parameters, and sampling values from the virtually infinite parameter input space. Current testing tools lack efficient exploration mechanisms, treating all operations and parameters equally (i.e., not considering their importance or complexity) and lacking prioritization strategies. Furthermore, these tools struggle when response schemas are absent in the specification or exhibit variants. To address these limitations, we present an adaptive REST API testing technique that incorporates reinforcement learning to prioritize operations and parameters during exploration. Our approach dynamically analyzes request and response data to inform dependent parameters and adopts a sampling-based strategy for efficient processing of dynamic API feedback. We evaluated our technique on ten RESTful services, comparing it against state-of-the-art REST testing tools with respect to code coverage achieved, requests generated, operations covered, and service failures triggered. Additionally, we performed an ablation study on prioritization, dynamic feedback analysis, and sampling to assess their individual effects. Our findings demonstrate that our approach outperforms existing REST API testing tools in terms of effectiveness, efficiency, and fault-finding ability., Comment: To be published in the 38th IEEE/ACM International Conference on Automated Software Engineering (ASE 2023)

Code translation aims to convert source code from one programming language (PL) to another. Given the promising abilities of large language models (LLMs) in code synthesis, researchers are exploring their potential to automate code translation. The prerequisite for advancing the state of LLM-based code translation is to understand their promises and limitations over existing techniques. To that end, we present a large-scale empirical study to investigate the ability of general LLMs and code LLMs for code translation across pairs of different languages, including C, C++, Go, Java, and Python. Our study, which involves the translation of 1,700 code samples from three benchmarks and two real-world projects, reveals that LLMs are yet to be reliably used to automate code translation -- with correct translations ranging from 2.1% to 47.3% for the studied LLMs. Further manual investigation of unsuccessful translations identifies 15 categories of translation bugs. We also compare LLM-based code translation with traditional non-LLM-based approaches. Our analysis shows that these two classes of techniques have their own strengths and weaknesses. Finally, insights from our study suggest that providing more context to LLMs during translation can help them produce better results. To that end, we propose a prompt-crafting approach based on the symptoms of erroneous translations; this improves the performance of LLM-based code translation by 5.5% on average. Our study is the first of its kind, in terms of scale and breadth, that provides insights into the current limitations of LLMs in code translation and opportunities for improving them. Our dataset -- consisting of 1,700 code samples in five PLs with 10K+ tests, 43K+ translated code, 1,748 manually labeled bugs, and 1,365 bug-fix pairs -- can help drive research in this area., Comment: Published in ICSE 2024

Modern web applications make extensive use of API calls to update the UI state in response to user events or server-side changes. For such applications, API-level testing can play an important role, in-between unit-level testing and UI-level (or end-to-end) testing. Existing API testing tools require API specifications (e.g., OpenAPI), which often may not be available or, when available, be inconsistent with the API implementation, thus limiting the applicability of automated API testing to web applications. In this paper, we present an approach that leverages UI testing to enable API-level testing for web applications. Our technique navigates the web application under test and automatically generates an API-level test suite, along with an OpenAPI specification that describes the application's server-side APIs (for REST-based web applications). A key element of our solution is a dynamic approach for inferring API endpoints with path parameters via UI navigation and directed API probing. We evaluated the technique for its accuracy in inferring API specifications and the effectiveness of the "carved" API tests. Our results on seven open-source web applications show that the technique achieves 98% precision and 56% recall in inferring endpoints. The carved API tests, when added to test suites generated by two automated REST API testing tools, increase statement coverage by 52% and 29% and branch coverage by 99% and 75%, on average. The main benefits of our technique are: (1) it enables API-level testing of web applications in cases where existing API testing tools are inapplicable and (2) it creates API-level test suites that cover server-side code efficiently while exercising APIs as they would be invoked from an application's web UI, and that can augment existing API test suites.

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.

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.

Modern web services routinely provide REST APIs for clients to access their functionality. These APIs present unique challenges and opportunities for automated testing, driving the recent development of many techniques and tools that generate test cases for API endpoints using various strategies. Understanding how these techniques compare to one another is difficult, as they have been evaluated on different benchmarks and using different metrics. To fill this gap, we performed an empirical study aimed to understand the landscape in automated testing of REST APIs and guide future research in this area. We first identified, through a systematic selection process, a set of 10 state-of-the-art REST API testing tools that included tools developed by both researchers and practitioners. We then applied these tools to a benchmark of 20 real-world open-source RESTful services and analyzed their performance in terms of code coverage achieved and unique failures triggered. This analysis allowed us to identify strengths, weaknesses, and limitations of the tools considered and of their underlying strategies, as well as implications of our findings for future research in this area., Comment: 13 pages, 6 figures, In Proceedings of the 31st ACM SIGSOFT International Symposium on Software Testing and Analysis (ISSTA) 2022

We present a DevIce-to-System Performance EvaLuation (DISPEL) workflow that integrates transistor and interconnect modeling, parasitic extraction, standard cell library characterization, logic synthesis, cell placement and routing, and timing analysis to evaluate system-level performance of new CMOS technologies. As the impact of parasitic resistances and capacitances continues to increase with dimensional downscaling, component-level optimization alone becomes insufficient, calling for a holistic assessment and optimization methodology across the boundaries between devices, interconnects, circuits, and systems. The physical implementation flow in DISPEL enables realistic analysis of complex wires and vias in VLSI systems and their impact on the chip power, speed, and area, which simple circuit simulations cannot capture. To demonstrate the use of DISPEL, a 32-bit commercial processor core is implemented using theoretical n-type MoS2 and p-type Black Phosphorous (BP) planar FETs at a projected 5-nm node, and the performance is benchmarked against Si FinFETs. While the superior gate control of the MoS2/BP FETs can theoretically provide 51% reduction in the iso-frequency energy consumption, the actual performance can be greatly limited by the source/drain contact resistances. With the large amount of data generated by DISPEL, a neural-network is trained to predict the key performance metrics of the 32-bit processor core using the characteristics of transistors and interconnects as the input features without the need to go through the time-consuming physical implementation flow. The machine learning algorithms show great potentials as a means for evaluation and optimization of new CMOS technologies and identifying the most significant technology design parameters., Comment: 12 pages, 23 figures

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.

Energetic electrons inside Earth's outer Van Allen belt pose a major radiation threat to space-borne electronics that often play vital roles in our modern society. Ultra-relativistic electrons with energies greater than or equal to two Megaelectron-volt (MeV) are of particular interest due to their high penetrating ability, and thus forecasting these >=2 MeV electron levels has significant meaning to all space sectors. Here we update the latest development of the predictive model for MeV electrons inside the Earth's outer radiation belt. The new version, called PreMevE-2E, focuses on forecasting ultra-relativistic electron flux distributions across the outer radiation belt, with no need of in-situ measurements except for at the geosynchronous (GEO) orbit. Model inputs include precipitating electrons observed in low-Earth-orbits by NOAA satellites, upstream solar wind conditions (speeds and densities) from solar wind monitors, as well as ultra-relativistic electrons measured by one Los Alamos GEO satellite. We evaluated a total of 32 supervised machine learning models that fall into four different classes of linear and neural network architectures, and also successfully tested ensemble forecasting by using groups of top-performing models. All models are individually trained, validated, and tested by in-situ electron data from NASA's Van Allen Probes mission. It is shown that the final ensemble model generally outperforms individual models overs L-shells, and this PreMevE-2E model provides reliable and high-fidelity 25-hr (~1-day) and 50-hr (~2-day) forecasts with high mean performance efficiency values. Our results also suggest this new model is dominated by non-linear components at low L-shells (< ~4) for ultra-relativistic electrons, which is different from the dominance of linear components at all L-shells for 1 MeV electrons as previously discovered., Comment: manuscript submitted to Space Weather journal

3D integration technologies are seeing widespread adoption in the semiconductor industry to offset the limitations and slowdown of two-dimensional scaling. High-density 3D integration techniques such as face-to-face wafer bonding with sub-10 $\mu$m pitch can enable new ways of designing SoCs using all 3 dimensions, like folding a microprocessor design across multiple 3D tiers. However, overlapping thermal hotspots can be a challenge in such 3D stacked designs due to a general increase in power density. In this work, we perform a thorough thermal simulation study on sign-off quality physical design implementation of a state-of-the-art, high-performance, out-of-order microprocessor on a 7nm process technology. The physical design of the microprocessor is partitioned and implemented in a 2-tier, 3D stacked configuration with logic blocks and memory instances in separate tiers (logic-over-memory 3D). The thermal simulation model was calibrated to temperature measurement data from a high-performance, CPU-based 2D SoC chip fabricated on the same 7nm process technology. Thermal profiles of different 3D configurations under various workload conditions are simulated and compared. We find that stacking microprocessor designs in 3D without considering thermal implications can result in maximum die temperature up to 12{\deg}C higher than their 2D counterparts under the worst-case power-indicative workload. This increase in temperature would reduce the amount of time for which a power-intensive workload can be run before throttling is required. However, logic-over-memory partitioned 3D CPU implementation can mitigate this temperature increase by half, which makes the temperature of the 3D design only 6$^\circ$C higher than the 2D baseline. We conclude that using thermal aware design partitioning and improved cooling techniques can overcome the thermal challenges associated with 3D stacking.

3D integration, i.e., stacking of integrated circuit layers using parallel or sequential processing is gaining rapid industry adoption with the slowdown of Moore's law scaling. 3D stacking promises potential gains in performance, power and cost but the actual magnitude of gains varies depending on end-application, technology choices and design. In this talk, we will discuss some key challenges associated with 3D design and how design-for-3D will require us to break traditional silos of micro-architecture, circuit/physical design and manufacturing technology to work across abstractions to enable the gains promised by 3D technologies., Comment: 5 pages, 6 Figures, invited talk at S3S conference held in San Jose, October 2019

Standard cell libraries are the foundation for the entire backend design and optimization flow in modern application-specific integrated circuit designs. At 7nm technology node and beyond, standard cell library design and optimization is becoming increasingly difficult due to extremely complex design constraints, as described in the ASAP7 process design kit (PDK). Notable complexities include discrete transistor sizing due to FinFETs, complicated design rules from lithography and restrictive layout space from modern standard cell architectures. The design methodology presented in this paper enables efficient and high-quality standard cell library design and optimization with the ASAP7 PDK. The key techniques include exhaustive transistor sizing for cell timing optimization, transistor placement with generalized Euler paths and back-end design prototyping for library-level explorations., Comment: 6 papes, ICCAD 2017

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., Comment: SIGIR 2018 Full Paper

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".

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., Comment: Seventh International Workshop on Statistical Relational AI, 2017