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Pattern Matching Based on Object Graphs

IEEE ACCESS 2021年 9卷 159313-159325页

作者： Ke, Wei Chan, Ka-Hou Macao Polytech Inst Sch Appl Sci Macau Peoples R China Macao Polytech Inst Engn Res Ctr Appl Technol Machine Translat & Arti Minist Educ Macau Peoples R China

Pattern matching has been widely adopted in functional programming languages, and is gradually getting popular in OO languages, from Scala to Python. The structural pattern matching currently in use has its foundation on algebraic data types from functional languages. To better reflect the pointer structures of OO programs, we propose a pattern matching extension to general statically typed OO languages based on object graphs. By this extension, we support patterns having aliasing and circular referencing, that are typically found in pointer structures. With the requirement of only an abstract subtyping preorder on types, our extension is not restricted to a particular hierarchical class model. We give the formal base of the graph model, that is able to handle aliases and cycles in patterns, together with the abstract syntax to construct the object graphs. More complex cases of conjunction and disjunction of multiple patterns are explored with resolution. We present the type checking rules and operational semantics to reason about the soundness by proving the type safety. We also discuss the design decisions, applicability and limitation of our pattern matching extension.

关键词： Pattern matching Semantics Syntactics Safety Libraries C plus plus languages Writing Pattern matching object graph subtyping type system operational semantics programming language

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MSCCD: Grammar Pluggable Clone Detection Based on ANTLR Parser Generation 30

MSCCD: Grammar Pluggable Clone Detection Based on ANTLR Pars...

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30th IEEE/ACM International Conference on Program Comprehension (ICPC)

作者： Zhu, Wenqing Yoshida, Norihiro Kamiya, Toshihiro Choi, Eunjong Takada, Hiroaki Nagoya Univ Nagoya Aichi Japan Shimane Univ Matsue Shimane Japan Kyoto Inst Technol Kyoto Kyoto Japan

ISBN: (纸本)9781450392983

For various reasons, programming languages continue to multiply and evolve. It has become necessary to have a multilingual clone detection tool that can easily expand supported programming languages and detect various code clones is needed. However, research on multilingual code clone detection has not received sufficient attention. In this study, we propose MSCCD (Multilingual Syntactic Code Clone Detector), a grammar pluggable code clone detection tool that uses a parser generator to generate a code block extractor for the target language. The extractor then extracts the semantic code blocks from a parse tree. MSCCD can detect Type-3 clones at various granularities. We evaluated MSCCD's language extensibility by applying MSCCD to 20 modern languages. Sixteen languages were perfectly supported, and the remaining four were provided with the same detection capabilities at the expense of execution time. We evaluated MSCCD's recall by using BigCloneEval and conducted a manual experiment to evaluate precision. MSCCD achieved equivalent detection performance equivalent to state-of-the-art tools.

关键词： Code Clone Parser Generator Clone Detection Syntactic Analysis programming language

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Level up your coding: a systematic review of personalized, cognitive, and gamified learning in programming education

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PEERJ COMPUTER SCIENCE 2024年 10卷 e2310-e2310页

作者： Ishaq, Kashif Alvi, Atif ul Haq, Muhammad Ikram Rosdi, Fadhilah Choudhry, Abubakar Nazeer Anjum, Arslan Khan, Fawad Ali Univ Management & Technol Sch Syst & Technol Lahore Pakistan Super Univ Dept Comp Sci Lahore Pakistan Univ Kebangsaan Malaysia Fac Informat Sci & Technol Bangi Malaysia Univ Sargodha Res Innovat & Commercializat Sargodha Pakistan

programming courses in computer science play a crucial role as they often serve as students' initial exposure to computer programming. Many university students fi nd introductory courses overwhelming due to the vast amount of information they need to grasp. The traditional teacher-lecturer model used in university lecture halls frequently leads to low motivation and student participation. Personalized gamification, a pedagogical approach that blends gamification and personalized learning, offers a solution to this challenge. This approach integrates gaming elements and personalized learning strategies to motivate and engage students while addressing their individual learning needs and differences. A comprehensive literature review analyzes 101 studies based on research design, intervention, outcome measures, and quality assessment. The fi ndings suggest that personalized gamification can enhance student cognition in programming courses by boosting motivation, engagement, and learning outcomes. However, the effectiveness of personalized gamification depends on various factors, including the types of gaming elements used, the level of personalization, and learner characteristics. This article offers insights into designing and implementing effective personalized gamification interventions in programming courses. The fi ndings may inform educators and researchers in programming education about the potential benefits of personalized gamification and its implications for educational practice.

关键词： Cognition Gamification Motivation Personalization programming language

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Can AI Fix Buggy Code? Exploring the Use of Large language Models in Automated Program Repair

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Computer 2025年第7期58卷 122-128页

作者： Lan Zhang Anoop Singhal Qingtian Zou Xiaoyan Sun Peng Liu Hsiao-Ying Lin Northern Arizona University Flagstaff AZ USA National Institute of Standards and Technology Gaithersburg MD USA University of Texas Southwestern Medical Center Dallas TX USA Department of Computer Science Worcester Polytechnic Institute Worcester MA USA The Pennsylvania State University State College PA USA Huawei France France

This article reviews the current human–large language models collaboration approach to bug fixing and points out the research directions toward (the development of) autonomous program repair artificial intelligence a... 详细信息

关键词： Software Development language Model Intelligence Agencies Software Engineering Human Experts Complete Coding Artificial Intelligence Systems Autonomous Agents Software Defect Complex Software Code Review Bug Fixes programming language Application programming Interface Understanding Of Context Debugging Artificial Intelligence Models Part Of Code Memory Management programming Tasks

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Mechanized Reasoning about "How" Using Functional Programs and Embeddings

Mechanized Reasoning about "How" Using Functional Programs a...

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作者： Li, Yao University of Pennsylvania

学位级别：Ph.D., Doctor of Philosophy

Embedding describes the process of encoding a program's syntax and/or semantics in another language—typically a theorem prover in the context of mechanized reasoning. Among different embedding styles, deep embeddings are generally preferred as they enable the most faithful modeling of the original language. However, deep embeddings are also the most complex, and working with them requires additional effort. In light of that, this dissertation aims to draw more attention to alternative styles, namely shallow and mixed embeddings, by studying their use in mechanized reasoning about programs' properties that are related to "how". More specifically, I present a simple shallow embedding for reasoning about computation costs of lazy programs, and a class of mixed embeddings that are useful for reasoning about properties of general computation patterns in effectful programs. I show the usefulness of these embedding styles with examples based on real-world applications.

关键词： Coq Embedding Formal verification Functional programming Mechanized reasoning programming language

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Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

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NATURE METHODS 2021年第10期18卷 1161-1168页

作者： Wratten, Laura Wilm, Andreas Goke, Jonathan Genome Inst Singapore Singapore Singapore ImmunoScape Singapore Singapore

The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not just for experiments, but also for computational analysis. However, transforming data into information involves running a large number of tools, optimizing parameters, and integrating dynamically changing reference data. Workflow managers were developed in response to such challenges. They simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing. In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational users. We outline community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows. In sum, we illustrate how workflow managers contribute to making computational analysis in biomedical research shareable, scalable, and reproducible. This Perspective highlights workflow managers, which are useful for developing and managing complex bioinformatics pipelines.

关键词： Computational platforms and environments programming language Software Life Sciences general Biological Techniques Biological Microscopy Biomedical Engineering/Biotechnology Bioinformatics Proteomics

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Benefits, challenges, and usability evaluation of DeloreanJS: a back-in-time debugger for JavaScript

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PEERJ COMPUTER SCIENCE 2023年 9卷 e1238页

作者： Leger, Paul Ruiz, Felipe Fukuda, Hiroaki Cardozo, Nicolas Univ Catolica Norte Escuela Ingn Coquimbo Elqui Chile Shibaura Inst Technol Tokyo Japan Univ Los Andes Bogota Colombia

JavaScript Web applications are a common product in industry. As with most applica-tions, Web applications can acquire software flaws (known as bugs), whose symptoms are seen during the development stage and, even worse, in production. The use of debuggers is beneficial for detecting bugs. Unfortunately, most JavaScript debuggers (1) only support the "step into/through"feature in an execution program to detect a bug, and (2) do not allow developers to go back-in-time at the application execution to take actions to detect the bug accurately. For example, the second limitation does not allow developers to modify the value of a variable to fix a bug while the application is running or test if the same bug is triggered with other values of that variable. Using concepts such as continuations and static analysis, this article presents a usable debugger for JavaScript, named DeloreanJS, which enables developers to go back-in-time in different execution points and resume the execution of a Web application to improve the understanding of a bug, or even experiment with hypothetical scenarios around the bug. Using an online and available version, we illustrate the benefits of DeloreanJS through five examples of bugs in JavaScript. Although DeloreanJS is developed for JavaScript, a dynamic prototype-based object model with side effects (mutable variables), we discuss our proposal with the state-of-art/practice of debuggers in terms of features. For example, modern browsers like Mozilla Firefox include a debugger in their distribution that only support for the breakpoint feature. However DeloreanJS uses a graphical user interface that considers back-in-time features. The aim of this study is to evaluate and compare the usability of DeloreanJS and Mozilla Firefox's debugger using the system usability scale approach. We requested 30 undergraduate students from two computer science programs to solve five tasks. Among the findings, we highlight two results. First, we found that 100%

关键词： programming languages Engineering Web applications programming language Software engineering Usability evaluation JavaScript Debugger

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Execution Mechanisms of Oragent-an Organisation-based programming language

Execution Mechanisms of Oragent-an Organisation-based Progra...

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12th IEEE/WIC/ACM International Joint Conference on Intelligent Agent Technology (IAT)

作者： Chen, Yin Mao, Xinjun Hu, Cuiyun Natl Univ Def Technol Coll Comp Changsha Hunan Peoples R China

ISBN: (纸本)9781479929023

the adoption of organisation-based agent-oriented programming has been quite limited, due to the lack of programming languages which are expressive enough to tackle the complexity brought by the dynamism of multi-agent systems. Oragent is an organisation-based agent-oriented programming language which provides explicit language primitives to program organisational concepts such as agents and groups as first-class entities, and to realise adaptation of multi-agent systems via role enactment and role-based interaction. In this paper, we present the execution mechanisms for Oragent language, which support adaptation of agent behaviour via role enactment, and role-based interaction among agents. A case study is presented to demonstrate the viability of these mechanisms.

关键词： organisation agent multi-agent system execution mechanisms programming language

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Julia for biologists (vol 20, pg 655, 2023)

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NATURE METHODS 2023年第5期20卷 771-771页

作者： Roesch, Elisabeth Greener, Joe G. MacLean, Adam L. Nassar, Huda Rackauckas, Christopher Holy, Timothy E. Stumpf, Michael P. H. School of Mathematics and Statistics University of Melbourne Melbourne Victoria Australia Melbourne Integrative Genomics University of Melbourne Melbourne Victoria Australia JuliaHub Somerville MA USA Medical Research Council Laboratory of Molecular Biology Cambridge UK Department of Quantitative and Computational Biology University of Southern California Los Angeles CA USA RelationalAI Berkeley CA USA Department of Mathematics Massachusetts Institute of Technology Cambridge MA USA Pumas-AI Centreville VA USA Departments of Neuroscience and Biomedical Engineering Washington University in St. Louis St. Louis MO USA School of BioSciences The University of Melbourne Melbourne Victoria Australia ARC Centre of Excellence for the Mathematical Analysis of Cellular Systems Melbourne Victoria Australia

Major computational challenges exist in relation to the collection, curation, processing and analysis of large genomic and imaging datasets, as well as the simulation of larger and more realistic models in systems biology. Here we discuss how a relative newcomer among programming languages—Julia—is poised to meet the current and emerging demands in the computational biosciences and beyond. Speed, flexibility, a thriving package ecosystem and readability are major factors that make high-performance computing and data analysis available to an unprecedented degree. We highlight how Julia’s design is already enabling new ways of analyzing biological data and systems, and we provide a list of resources that can facilitate the transition into Julian computing.

关键词： Biochemical reaction networks Computational biophysics Computational models programming language

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Common Assays in Mammalian Golgi Studies

Common Assays in Mammalian Golgi Studies

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作者： Jie Li Jianchao Zhang Sarah Bui Erpan Ahat Divya Kolli Whitney Reid Lijuan Xing Yanzhuang Wang

The Golgi is a complex structure characterized by stacks of tightly aligned flat cisternae. In mammalian cells, Golgi stacks often concentrate in the perinuclear region and link together to form a ribbon. This structure is dynamic to accommodate continuous cargo flow in and out of the Golgi in both directions and undergoes morphological changes under physiological and pathological conditions. The fine, stacked Golgi structure makes it difficult to study by conventional light or even super-resolution microscopySuper-resolution microscopy. Furthermore, efforts to understand how Golgi structural dynamics impact cellular processes have been slow because of the knowledge gap in the protein machinery that maintains the complex and dynamic Golgi structure. In this method article, we list the common assays used in our research to help new and established researchers select the most appropriate method to properly address their questions. less

关键词： Transfection RNA Interference Microscopy Fractionation Proteomics RNA-seq Recombinant Protein Expression Imaging Techniques Subcellular Fractionation Transient Transfection Western Blot Electroporation Gene Knockdown Autoradiography Cell And Tissue Culture Electrophoresis Immunofluorescence Microscopy FRAP FRET Electron Microscopy (EM) Electron Tomography Cryo-electron Tomography Flow Cytometry SDS-PAGE Differential Centrifugation Low Speed Centrifugation Homogenization Density-gradient Centrifugation Spectroscopy Data analysis Bradford Protein Assay Transcriptomics Microarray Illumina Sequencing Bowtie programming language Cell Lysis Differential Expression Analysis Immunofluorescence Isobaric Mass Labeling Cutadapt Trimmomatic FastP TopHat HISAT RNA-Seq Analysis Database Search Bos taurus HeLa S3 Glycosylation Trafficking Proximity labeling Functions Secretomics Golgi biology Morphologies Viral systems In Vitro techniques

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