Towards Automating Precision Studies of Clone Detectors

Current research in clone detection suffers from poor ecosystems for evaluating precision of clone detection tools. Corpora of labeled clones are scarce and incomplete, making evaluation labor intensive and idiosyncratic, and limiting inter tool comparison. Precision-assessment tools are simply lacking. We present a semi-automated approach to facilitate precision studies of clone detection tools. The approach merges automatic mechanisms of clone classification with manual validation of clone pairs. We demonstrate that the proposed automatic approach has a very high precision and it significantly reduces the number of clone pairs that need human validation during precision experiments. Moreover, we aggregate the individual effort of multiple teams into a single evolving dataset of labeled clone pairs, creating an important asset for software clone research.Comment: Accepted to be published in the 41st ACM/IEEE International Conference on Software Engineerin

ASSESSING THE QUALITY OF SOFTWARE DEVELOPMENT TUTORIALS AVAILABLE ON THE WEB

Both expert and novice software developers frequently access software development resources available on the Web in order to lookup or learn new APIs, tools and techniques. Software quality is affected negatively when developers fail to find high-quality information relevant to their problem. While there is a substantial amount of freely available resources that can be accessed online, some of the available resources contain information that suffers from error proneness, copyright infringement, security concerns, and incompatible versions. Use of such toxic information can have a strong negative effect on developer’s efficacy. This dissertation focuses specifically on software tutorials, aiming to automatically evaluate the quality of such documents available on the Web. In order to achieve this goal, we present two contributions: 1) scalable detection of duplicated code snippets; 2) automatic identification of valid version ranges. Software tutorials consist of a combination of source code snippets and natural language text. The code snippets in a tutorial can originate from different sources, perhaps carrying stringent licensing requirements or known security vulnerabilities. Developers, typically unaware of this, can reuse these code snippets in their project. First, in this thesis, we present our work on a Web-scale code clone search technique that is able to detect duplicate code snippets between large scale document and source code corpora in order to trace toxic code snippets. As software libraries and APIs evolve over time, existing software development tutorials can become outdated. It is difficult for software developers and especially novices to determine the expected version of the software implicit in a specific tutorial in order to decide whether the tutorial is applicable to their software development environment. To overcome this challenge, in this thesis we present a novel technique for automatic identification of the valid version range of software development tutorials on the Web

Understanding Variability-Aware Analysis in Low-Maturity Variant-Rich Systems

Context: Software systems often exist in many variants to support varying stakeholder requirements, such as specific market segments or hardware constraints. Systems with many variants (a.k.a. variant-rich systems) are highly complex due to the variability introduced to support customization. As such, assuring the quality of these systems is also challenging since traditional single-system analysis techniques do not scale when applied. To tackle this complexity, several variability-aware analysis techniques have been conceived in the last two decades to assure the quality of a branch of variant-rich systems called software product lines. Unfortunately, these techniques find little application in practice since many organizations do use product-line engineering techniques, but instead rely on low-maturity \clo~strategies to manage their software variants. For instance, to perform an analysis that checks that all possible variants that can be configured by customers (or vendors) in a car personalization system conform to specified performance requirements, an organization needs to explicitly model system variability. However, in low-maturity variant-rich systems, this and similar kinds of analyses are challenging to perform due to (i) immature architectures that do not systematically account for variability, (ii) redundancy that is not exploited to reduce analysis effort, and (iii) missing essential meta-information, such as relationships between features and their implementation in source code.Objective: The overarching goal of the PhD is to facilitate quality assurance in low-maturity variant-rich systems. Consequently, in the first part of the PhD (comprising this thesis) we focus on gaining a better understanding of quality assurance needs in such systems and of their properties.Method: Our objectives are met by means of (i) knowledge-seeking research through case studies of open-source systems as well as surveys and interviews with practitioners; and (ii) solution-seeking research through the implementation and systematic evaluation of a recommender system that supports recording the information necessary for quality assurance in low-maturity variant-rich systems. With the former, we investigate, among other things, industrial needs and practices for analyzing variant-rich systems; and with the latter, we seek to understand how to obtain information necessary to leverage variability-aware analyses.Results: Four main results emerge from this thesis: first, we present the state-of-practice in assuring the quality of variant-rich systems, second, we present our empirical understanding of features and their characteristics, including information sources for locating them; third, we present our understanding of how best developers\u27 proactive feature location activities can be supported during development; and lastly, we present our understanding of how features are used in the code of non-modular variant-rich systems, taking the case of feature scattering in the Linux kernel.Future work: In the second part of the PhD, we will focus on processes for adapting variability-aware analyses to low-maturity variant-rich systems.Keywords:\ua0Variant-rich Systems, Quality Assurance, Low Maturity Software Systems, Recommender Syste

Agriculture 4.0 and beyond: Evaluating cyber threat intelligence sources and techniques in smart farming ecosystems

The digitisation of agriculture, integral to Agriculture 4.0, has brought significant benefits while simultaneously escalating cybersecurity risks. With the rapid adoption of smart farming technologies and infrastructure, the agricultural sector has become an attractive target for cyberattacks. This paper presents a systematic literature review that assesses the applicability of existing cyber threat intelligence (CTI) techniques within smart farming infrastructures (SFIs). We develop a comprehensive taxonomy of CTI techniques and sources, specifically tailored to the SFI context, addressing the unique cyber threat challenges in this domain. A crucial finding of our review is the identified need for a virtual Chief Information Security Officer (vCISO) in smart agriculture. While the concept of a vCISO is not yet established in the agricultural sector, our study highlights its potential significance. The implementation of a vCISO could play a pivotal role in enhancing cybersecurity measures by offering strategic guidance, developing robust security protocols, and facilitating real-time threat analysis and response strategies. This approach is critical for safeguarding the food supply chain against the evolving landscape of cyber threats. Our research underscores the importance of integrating a vCISO framework into smart farming practices as a vital step towards strengthening cybersecurity. This is essential for protecting the agriculture sector in the era of digital transformation, ensuring the resilience and sustainability of the food supply chain against emerging cyber risks

Towards Collaborative Scientific Workflow Management System

The big data explosion phenomenon has impacted several domains, starting from research areas to divergent of business models in recent years. As this intensive amount of data opens up the possibilities of several interesting knowledge discoveries, over the past few years divergent of research domains have undergone the shift of trend towards analyzing those massive amount data. Scientific Workflow Management System (SWfMS) has gained much popularity in recent years in accelerating those data-intensive analyses, visualization, and discoveries of important information. Data-intensive tasks are often significantly time-consuming and complex in nature and hence SWfMSs are designed to efficiently support the specification, modification, execution, failure handling, and monitoring of the tasks in a scientific workflow. As far as the complexity, dimension, and volume of data are concerned, their effective analysis or management often become challenging for an individual and requires collaboration of multiple scientists instead. Hence, the notion of 'Collaborative SWfMS' was coined - which gained significant interest among researchers in recent years as none of the existing SWfMSs directly support real-time collaboration among scientists. In terms of collaborative SWfMSs, consistency management in the face of conflicting concurrent operations of the collaborators is a major challenge for its highly interconnected document structure among the computational modules - where any minor change in a part of the workflow can highly impact the other part of the collaborative workflow for the datalink relation among them. In addition to the consistency management, studies show several other challenges that need to be addressed towards a successful design of collaborative SWfMSs, such as sub-workflow composition and execution by different sub-groups, relationship between scientific workflows and collaboration models, sub-workflow monitoring, seamless integration and access control of the workflow components among collaborators and so on. In this thesis, we propose a locking scheme to facilitate consistency management in collaborative SWfMSs. The proposed method works by locking workflow components at a granular attribute level in addition to supporting locks on a targeted part of the collaborative workflow. We conducted several experiments to analyze the performance of the proposed method in comparison to related existing methods. Our studies show that the proposed method can reduce the average waiting time of a collaborator by up to 36% while increasing the average workflow update rate by up to 15% in comparison to existing descendent modular level locking techniques for collaborative SWfMSs. We also propose a role-based access control technique for the management of collaborative SWfMSs. We leverage the Collaborative Interactive Application Methodology (CIAM) for the investigation of role-based access control in the context of collaborative SWfMSs. We present our proposed method with a use-case of Plant Phenotyping and Genotyping research domain. Recent study shows that the collaborative SWfMSs often different sets of opportunities and challenges. From our investigations on existing research works towards collaborative SWfMSs and findings of our prior two studies, we propose an architecture of collaborative SWfMSs. We propose - SciWorCS - a Collaborative Scientific Workflow Management System as a proof of concept of the proposed architecture; which is the first of its kind to the best of our knowledge. We present several real-world use-cases of scientific workflows using SciWorCS. Finally, we conduct several user studies using SciWorCS comprising different real-world scientific workflows (i.e., from myExperiment) to understand the user behavior and styles of work in the context of collaborative SWfMSs. In addition to evaluating SciWorCS, the user studies reveal several interesting facts which can significantly contribute in the research domain, as none of the existing methods considered such empirical studies, and rather relied only on computer generated simulated studies for evaluation

LASSO – an observatorium for the dynamic selection, analysis and comparison of software

Mining software repositories at the scale of 'big code' (i.e., big data) is a challenging activity. As well as finding a suitable software corpus and making it programmatically accessible through an index or database, researchers and practitioners have to establish an efficient analysis infrastructure and precisely define the metrics and data extraction approaches to be applied. Moreover, for analysis results to be generalisable, these tasks have to be applied at a large enough scale to have statistical significance, and if they are to be repeatable, the artefacts need to be carefully maintained and curated over time. Today, however, a lot of this work is still performed by human beings on a case-by-case basis, with the level of effort involved often having a significant negative impact on the generalisability and repeatability of studies, and thus on their overall scientific value. The general purpose, 'code mining' repositories and infrastructures that have emerged in recent years represent a significant step forward because they automate many software mining tasks at an ultra-large scale and allow researchers and practitioners to focus on defining the questions they would like to explore at an abstract level. However, they are currently limited to static analysis and data extraction techniques, and thus cannot support (i.e., help automate) any studies which involve the execution of software systems. This includes experimental validations of techniques and tools that hypothesise about the behaviour (i.e., semantics) of software, or data analysis and extraction techniques that aim to measure dynamic properties of software. In this thesis a platform called LASSO (Large-Scale Software Observatorium) is introduced that overcomes this limitation by automating the collection of dynamic (i.e., execution-based) information about software alongside static information. It features a single, ultra-large scale corpus of executable software systems created by amalgamating existing Open Source software repositories and a dedicated DSL for defining abstract selection and analysis pipelines. Its key innovations are integrated capabilities for searching for selecting software systems based on their exhibited behaviour and an 'arena' that allows their responses to software tests to be compared in a purely data-driven way. We call the platform a 'software observatorium' since it is a place where the behaviour of large numbers of software systems can be observed, analysed and compared

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch.

As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones

Computational Methods for the Analysis of Genomic Data and Biological Processes

In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality

Data-driven learning how oncogenic gene expression locally alters heterocellular networks

Developing drugs increasingly relies on mechanistic modeling and simulation. Models that capture causal relations among genetic drivers of oncogenesis, functional plasticity, and host immunity complement wet experiments. Unfortunately, formulating such mechanistic cell-level models currently relies on hand curation, which can bias how data is interpreted or the priority of drug targets. In modeling molecular-level networks, rules and algorithms are employed to limit a priori biases in formulating mechanistic models. Here we combine digital cytometry with Bayesian network inference to generate causal models of cell-level networks linking an increase in gene expression associated with oncogenesis with alterations in stromal and immune cell subsets from bulk transcriptomic datasets. We predict how increased Cell Communication Network factor 4, a secreted matricellular protein, alters the tumor microenvironment using data from patients diagnosed with breast cancer and melanoma. Predictions are then tested using two immunocompetent mouse models for melanoma, which provide consistent experimental results