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1. Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

   https://doi.org/10.1039/D4DD00039K  

   Evans, Matthew L; Bergsma, Johan; Merkys, Andrius; Andersen, Casper W; Andersson, Oskar B; Beltrán, Daniel; Blokhin, Evgeny; Boland, Tara M; Castañeda_Balderas, Rubén; Choudhary, Kamal; et al (August 2024, Digital Discovery)

   The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development. 

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2. Design of the GraphBLAS API for C

   https://doi.org/10.1109/IPDPSW.2017.117  

   Buluc, Aydin; Mattson, Tim; McMillan, Scott; Moreira, Jose; Yang, Carl (May 2017, Graph Algorithms Building Blocks)

   The purpose of the GraphBLAS Forum is to standardize linear-algebraic building blocks for graph computations. An important part of this standardization effort is to translate the mathematical specification into an actual Application Programming Interface (API) that (i) is faithful to the mathematics and (ii) enables efficient implementations on modern hardware. This paper documents the approach taken by the C language specification subcommittee and presents the main concepts, constructs, and objects within the GraphBLAS API. Use of the API is illustrated by showing an implementation of the betweenness centrality algorithm. 

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3. The K-mer File Format: a standardized and compact disk representation of sets of k -mers

   https://doi.org/10.1093/bioinformatics/btac528  

   Dufresne, Yoann; Lemane, Teo; Marijon, Pierre; Peterlongo, Pierre; Rahman, Amatur; Kokot, Marek; Medvedev, Paul; Deorowicz, Sebastian; Chikhi, Rayan; Birol, ed., Inanc (July 2022, Bioinformatics)

   Abstract SummaryBioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3–5× compared to other formats, and bringing interoperability across tools. Availability and implementationFormat specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. Supplementary informationSupplementary data are available at Bioinformatics online. 

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4. LlamaRestTest: Effective REST API Testing with Small Language Models

   https://doi.org/10.1145/3715737  

   Kim, Myeongsoo; Sinha, Saurabh; Orso, Alessandro (June 2025, Proceedings of the ACM on Software Engineering)

   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. Finally, through an ablation study, we show that each component of LlamaRestTest contributes to its overall performance. 

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5. Verified sequential Malloc/Free

   https://doi.org/10.1145/3381898.3397211  

   Appel, Andrew W.; Naumann, David A. (June 2020, International Symposium on Memory Management)

   null (Ed.)

   We verify the functional correctness of an array-of-bins (segregated free-lists) single-thread malloc/free system with respect to a correctness specification written in separation logic. The memory allocator is written in standard C code compatible with the standard API; the specification is in the Verifiable C program logic, and the proof is done in the Verified Software Toolchain within the Coq proof assistant. Our "resource-aware" specification can guarantee when malloc will successfully return a block, unlike the standard Posix specification that allows malloc to return NULL whenever it wants to. We also prove subsumption (refinement): the resource-aware specification implies a resource-oblivious spec. 

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