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Identifying change patterns of API misuses from code changes

Science China(Information Sciences) 2021年第3期64卷 69-87页

作者： Wenjian LIU bihuan chen Xin PENG Qinghao SUN Wenyun ZHAO School of Computer Science Fudan University Shanghai Key Laboratory of Data Science Fudan University Shanghai Institute of Intelligent Electronics & Systems

Library or framework APIs are difficult to learn and use, leading to unexpected software behaviors or bugs. Hence, various API mining techniques have been introduced to mine API usage patterns about the co-occurring of API calls or pre-conditions of API calls. However, they fail to mine patterns about an API call itself(e.g., whether the arguments of the API call are correctly set and whether the API is suitably chosen over other similar APIs). To bridge this gap, we propose Cpam to identify change patterns(in the form of a pair of APIs before and after code changes) to fix API misuses, using historical code changes. Given a set of target APIs and a corpus of open-source projects, Cpam first selects the commits that potentially fix API misuses from the corpus, then extracts changes to API misuses in each selected commit, and finally identifies change patterns of API misuses. We implement Cpam for Java, and conduct large-scale evaluation,targeting Java SE APIs and using a corpus of 1162 Java projects. Our experimental results demonstrate Cpam’s effectiveness and efficiency. By applying identified change patterns to bug detection, we find 44 new bugs, and 18 of them have been confirmed and fixed.

关键词： API misuses API mining AST differencing change patterns bug fixing

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BATON: symphony of random testing and concolic testing through machine learning and taint analysis

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Science China(Information Sciences) 2023年第3期66卷 97-117页

作者： bihuan chen Yang LIU Xin PENG Yijian WU Shengchao QIN School of Computer Science Fudan University Shanghai Key Laboratory of Data Science Fudan University School of Computer Science and Engineering Nanyang Technological University School of Computing Teesside University

Random testing is scalable but often fails to hit corner program behaviors,while systematic testing （e.g.,concolic execution） is promising to cover corner program behaviors but is not scalable to explore all program *** attempts to integrate random testing with systematic testing lack targeted *** this paper,we propose a guided hybrid testing approach,named BATON,to synergize random testing with concolic *** integrates the knowledge inside test cases and their executions into a conditional execution graph,and uses such knowledge to guide test case ***,we learn classification models for some conditionals in the conditional execution graph in a demand-driven *** models are used to guide random testing to reach and cover partially-covered *** further employ targeted concolic testing to cover conditionals that cannot be fully covered by guided random *** implemented BATONfor Java and evaluated it on three *** results show that BATONimproved branch coverage and mutation score over random testing by 16.2%–29.4%and 19.0%–30.0%,over adaptive random testing by 16.8%–33.8%and 19.4%–34.2%,over concolic testing by 2.3%–29.9%and 2.9%–30.1%,and over simple hybrid testing by 1.6%–14.5%and 1.4%–18.7%.

关键词： system testing random testing concolic testing

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Biochemical synthesis of taxanes from mevalonate

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Synthetic and Systems Biotechnology 2024年第4期9卷 694-700页

作者： Jing Li Xiaonan Liu Xiaoxi Zhu Jiayu Liu Lei Zhang Nida Ahmed Jian Qi bihuan chen Daliang Tang Jinsheng Yu Zhijin Fan Huifeng Jiang Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China State Key Laboratory of Elemento-Organic Chemistry College of ChemistryNankai UniversityTianjin300071China National Center of Technology Innovation for Synthetic Biology Tianjin300308China University of Chinese Academy of Sciences Beijing100049China Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai200062China

Taxanes are kinds of diterpenoids with important bioactivities,such as paclitaxel(taxol®)is an excellent natural broad-spectrum anticancer *** to biosynthesize taxanes have made with limited success,mainly due to the bottleneck of the low efficiency catalytic *** this study,we developed an artificial synthetic system to produce taxanes from mevalonate(MVA)by coupling biological and chemical methods,which comprises in vitro multi-enzyme catalytic module,chemical catalytic module and yeast cell catalytic *** optimizing in vitro multienzyme catalytic system,the yield of taxadiene was increased to 946.7 mg/L from MVA within 8 h and the productivity was 14.2-fold higher than microbial *** incorporating palladium catalysis,the conversion rate of Taxa-4(20),11(12)-dien-5α-yl acetate(T5α-AC)reached 48%,effectively addressing the product promiscuity and the low yield rate of T5α***,we optimized the expression of T10βOH in yeast resulting in the biosynthesis of Taxa-4(20),11(12)-dien-5α-acetoxy-10β-ol(T5α-AC-10β-ol)at a production of 15.8 mg/L,which displayed more than 2000-fold higher than that produced by co-culture fermentation *** technologies offered a promising new approach for efficient synthesis of taxanes.

关键词： Biochemical synthesis Taxanes Paclitaxel Modular synthesis

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Metabolic engineering of Yarrowia lipolytica for scutellarin production

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Synthetic and Systems Biotechnology 2022年第3期7卷 958-964页

作者： Yina Wang Xiaonan Liu bihuan chen Wei Liu Zhaokuan Guo Xiangyu Liu Xiaoxi Zhu Jiayu Liu Jin Zhang Jing Li Lei Zhang Yadi Gao Guanghui Zhang Yan Wang MIqbal Choudhary Shengchao Yang Huifeng Jiang National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China Yunnan Agricultural UniversityYunnanKunming650201China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan Agricultural UniversityYunnanKunming650201China Key Laboratory of Systems Microbial Biotechnology Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China University of Chinese Academy of Sciences Beijing100049China National Center of Technology Innovation for Synthetic Biology Tianjin300308China College of Life Science and Technology Wuhan Polytechnic UniversityWuhanHubei430023China H.E.J.Research Institute of Chemistry International Center for Chemical and Biological SciencesUniversity of KarachiKarachi75270Pakistan

Scutellarin related drugs have superior therapeutic effects on cerebrovascular and cardiovascular ***,an optimal biosynthetic pathway for scutellarin was constructed in Yarrowia lipolytica platform due to its excellent metabolic *** integrating multi-copies of core genes from different species,the production of scutellarin was increased from 15.11 mg/L to 94.79 mg/L and the ratio of scutellarin to the main by-product was improved about 110-fold in flask ***,the production of scutellarin was improved 23-fold and reached to 346 mg/L in fed-batch bioreactor,which was the highest reported titer for de novo production of scutellarin in *** results represent a solid basis for further production of natural products on unconventional yeasts and have a potential of industrial implementation.

关键词： Scutellarin Yarrowia lipolytica Metabolic engineering Combinatorial gene overexpression

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基于前馈和反馈控制运行时虚拟资源动态分配

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计算机研究与发展 2015年第4期52卷 889-897页

作者：俞岭谢奕陈碧欢彭鑫赵文耘复旦大学计算机科学技术学院上海201203

随着云计算的流行和发展,越来越多的应用系统被部署在云服务器上,以可伸缩的方式按需获取虚拟资源并按使用量付费.因此,如何在保证应用系统优化运行的同时以一种考虑成本效益的方式来分配和使用虚拟资源就成了一个重要的研究问题.传统... 详细信息

随着云计算的流行和发展,越来越多的应用系统被部署在云服务器上,以可伸缩的方式按需获取虚拟资源并按使用量付费.因此,如何在保证应用系统优化运行的同时以一种考虑成本效益的方式来分配和使用虚拟资源就成了一个重要的研究问题.传统的手工调整方法不但会增加系统管理员的负担,而且准确性较差并有一定的延迟.现有的虚拟资源动态分配方法大多是在发现系统运行时质量问题后进行资源动态调整的,因此具有一定的延迟性,而且还忽略了虚拟资源的异构性带来的影响.针对这些问题,提出了一种基于控制理论的虚拟资源动态分配方法.该方法使用一个前馈控制器来动态调整虚拟资源的数量,同时使用一个反馈控制器来动态调节各个虚拟资源处理的负载比例,从而实现应用系统的优化运行和虚拟资源的有效利用.与静态虚拟资源分配方法以及仅包括前馈控制方法的对比实验表明,所提出的方法能够在保证应用系统优化运行的同时提高虚拟资源利用的有效性.

关键词：云计算前馈控制反馈控制自适应虚拟资源资源分配

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