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1. Run-Time Prevention of Software Integration Failures of Machine Learning APIs

   https://doi.org/10.1145/3622806  

   Wan, Chengcheng; Liu, Yuhan; Du, Kuntai; Hoffmann, Henry; Jiang, Junchen; Maire, Michael; Lu, Shan (October 2023, Proceedings of the ACM on Programming Languages)

   Due to the under-specified interfaces, developers face challenges in correctly integrating machine learning (ML) APIs in software. Even when the ML API and the software are well designed on their own, the resulting application misbehaves when the API output is incompatible with the software. It is desirable to have an adapter that converts ML API output at runtime to better fit the software need and prevent integration failures. In this paper, we conduct an empirical study to understand ML API integration problems in real-world applications. Guided by this study, we present SmartGear, a tool that automatically detects and converts mismatching or incorrect ML API output at run time, serving as a middle layer between ML API and software. Our evaluation on a variety of open-source applications shows that SmartGear detects 70% incompatible API outputs and prevents 67% potential integration failures, outperforming alternative solutions. 

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2. Charting the sequence-activity landscape of peptide inhibitors of translation termination

   https://doi.org/10.1073/pnas.2026465118  

   Baliga, Chetana; Brown, Tyler J.; Florin, Tanja; Colon, Sarah; Shah, Vallari; Skowron, Kornelia J.; Kefi, Amira; Szal, Teresa; Klepacki, Dorota; Moore, Terry W.; et al (March 2021, Proceedings of the National Academy of Sciences)

   Apidaecin (Api), an unmodified 18-amino-acid-long proline-rich antibacterial peptide produced by bees, has been recently described as a specific inhibitor of translation termination. It invades the nascent peptide exit tunnel of the postrelease ribosome and traps the release factors preventing their recycling. Api binds in the exit tunnel in an extended conformation that matches the placement of a nascent polypeptide and establishes multiple contacts with ribosomal RNA (rRNA) and ribosomal proteins. Which of these interactions are critical for Api’s activity is unknown. We addressed this problem by analyzing the activity of all possible single-amino-acid substitutions of the Api variants synthesized in the bacterial cell. By conditionally expressing the engineeredapigene, we generated Api directly in the bacterial cytosol, thereby bypassing the need for importing the peptide from the medium. The endogenously expressed Api, as well as its N-terminally truncated mutants, retained the antibacterial properties and the mechanism of action of the native peptide. Taking advantage of the Api expression system and next-generation sequencing, we mapped in one experiment all the single-amino-acid substitutions that preserve or alleviate the on-target activity of the Api mutants. Analysis of the inactivating mutations made it possible to define the pharmacophore of Api involved in critical interactions with the ribosome, transfer RNA (tRNA), and release factors. We also identified the Api segment that tolerates a variety of amino acid substitutions; alterations in this segment could be used to improve the pharmacological properties of the antibacterial peptide. 

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3. OPTIMADE, an API for exchanging materials data

   https://doi.org/10.1038/s41597-021-00974-z  

   Andersen, Casper W.; Armiento, Rickard; Blokhin, Evgeny; Conduit, Gareth J.; Dwaraknath, Shyam; Evans, Matthew L.; Fekete, Ádám; Gopakumar, Abhijith; Gražulis, Saulius; Merkys, Andrius; et al (August 2021, Scientific Data)

   Abstract The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification. 

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4. A Large-scale Study on API Misuses in the Wild

   Li, Xia; Jiang, Jiajun; Benton, Samuel; Xiong, Yingfei; Zhang, Lingming (April 2021, IEEE International Conference on Software Testing, Verification and Validation)

   null (Ed.)

   API misuses are prevalent and extremely harmful. Despite various techniques have been proposed for API-misuse detection, it is not even clear how different types of API misuses distribute and whether existing techniques have covered all major types of API misuses. Therefore, in this paper, we conduct the first large-scale empirical study on API misuses based on 528,546 historical bug-fixing commits from GitHub (from 2011 to 2018). By leveraging a state-of-the-art fine-grained AST differencing tool, GumTree, we extract more than one million bug-fixing edit operations, 51.7% of which are API misuses. We further systematically classify API misuses into nine different categories according to the edit operations and context. We also extract various frequent API-misuse patterns based on the categories and corresponding operations, which can be complementary to existing API-misuse detection tools. Our study reveals various practical guidelines regarding the importance of different types of API misuses. Furthermore, based on our dataset, we perform a user study to manually analyze the usage constraints of 10 patterns to explore whether the mined patterns can guide the design of future API-misuse detection tools. Specifically, we find that 7,541 potential misuses still exist in latest Apache projects and 149 of them have been reported to developers. To date, 57 have already been confirmed and fixed (with 15 rejected misuses correspondingly). The results indicate the importance of studying historical API misuses and the promising future of employing our mined patterns for detecting unknown API misuses. 

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5. Self‐healing imidazolium‐based ionene‐polyamide membranes: an experimental study on physical and gas transport properties

   https://doi.org/10.1002/pi.5802  

   Kammakakam, Irshad; O'Harra, Kathryn_E; Dennis, Grayson_P; Jackson, Enrique_M; Bara, Jason_E (March 2019, Polymer International)

   ABSTRACT A new series of six imidazolium‐based ionenes containing aromatic amide linkages has been developed. These ionene‐polyamides are all constitutional isomers varying in the regiochemistry of the amide linkages (para, meta) and xylyl linkages (ortho, meta, para) along the polymer backbone. The physical properties as well as the gas separation behaviors of the corresponding membranes have been extensively studied. These ionene‐polyamide membranes show excellent thermal and mechanical stabilities, together with self‐healing and shape memory characteristics. Most importantly, [TC‐API(p)‐Xy][Tf₂N] and [IC‐API(m)‐Xy][Tf₂N] membranes (TC, terephthaloyl chloride; API, 1‐(3‐aminopropyl)imidazole; Xy, xylyl; Tf₂N, bis(trifluoromethylsulfonyl) imide; IC, isophthaloyl chloride), where the amide and xylyl linkages are attached at para and meta positions, exhibit superior selectivity for CO₂/CH₄and CO₂/N₂gas pairs. We also demonstrate the transport properties and diverse applicability of our newly developed ionene‐polyamides, particularly [TC‐API(p)‐Xy][Tf₂N], for various industrial applications. © 2019 Society of Chemical Industry 

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