Web service composition: A survey of techniques and tools

Web services are a consolidated reality of the modern Web with tremendous, increasing impact on everyday computing tasks. They turned the Web into the largest, most accepted, and most vivid distributed computing platform ever. Yet, the use and integration of Web services into composite services or applications, which is a highly sensible and conceptually non-trivial task, is still not unleashing its full magnitude of power. A consolidated analysis framework that advances the fundamental understanding of Web service composition building blocks in terms of concepts, models, languages, productivity support techniques, and tools is required. This framework is necessary to enable effective exploration, understanding, assessing, comparing, and selecting service composition models, languages, techniques, platforms, and tools. This article establishes such a framework and reviews the state of the art in service composition from an unprecedented, holistic perspective

BPMN4sML: A BPMN Extension for Serverless Machine Learning. Technology Independent and Interoperable Modeling of Machine Learning Workflows and their Serverless Deployment Orchestration

Machine learning (ML) continues to permeate all layers of academia, industry and society. Despite its successes, mental frameworks to capture and represent machine learning workflows in a consistent and coherent manner are lacking. For instance, the de facto process modeling standard, Business Process Model and Notation (BPMN), managed by the Object Management Group, is widely accepted and applied. However, it is short of specific support to represent machine learning workflows. Further, the number of heterogeneous tools for deployment of machine learning solutions can easily overwhelm practitioners. Research is needed to align the process from modeling to deploying ML workflows. We analyze requirements for standard based conceptual modeling for machine learning workflows and their serverless deployment. Confronting the shortcomings with respect to consistent and coherent modeling of ML workflows in a technology independent and interoperable manner, we extend BPMN's Meta-Object Facility (MOF) metamodel and the corresponding notation and introduce BPMN4sML (BPMN for serverless machine learning). Our extension BPMN4sML follows the same outline referenced by the Object Management Group (OMG) for BPMN. We further address the heterogeneity in deployment by proposing a conceptual mapping to convert BPMN4sML models to corresponding deployment models using TOSCA. BPMN4sML allows technology-independent and interoperable modeling of machine learning workflows of various granularity and complexity across the entire machine learning lifecycle. It aids in arriving at a shared and standardized language to communicate ML solutions. Moreover, it takes the first steps toward enabling conversion of ML workflow model diagrams to corresponding deployment models for serverless deployment via TOSCA.Comment: 105 pages 3 tables 33 figure

Supporting Exploratory Search Tasks Through Alternative Representations of Information

Information seeking is a fundamental component of many of the complex tasks presented to us, and is often conducted through interactions with automated search systems such as Web search engines. Indeed, the ubiquity of Web search engines makes information so readily available that people now often turn to the Web for all manners of information seeking needs. Furthermore, as the range of online information seeking tasks grows, more complex and open-ended search activities have been identified. One type of complex search activities that is of increasing interest to researchers is exploratory search, where the goal involves "learning" or "investigating", rather than simply "looking-up". Given the massive increase in information availability and the use of online search for tasks beyond simply looking-up, researchers have noted that it becomes increasingly challenging for users to effectively leverage the available online information for complex and open-ended search activities. One of the main limitations of the current document retrieval paradigm offered by modern search engines is that it provides a ranked list of documents as a response to the searcher’s query with no further support for locating and synthesizing relevant information. Therefore, the searcher is left to find and make sense of useful information in a massive information space that lacks any overview or conceptual organization. This thesis explores the impact of alternative representations of search results on user behaviors and outcomes during exploratory search tasks. Our inquiry is inspired by the premise that exploratory search tasks require sensemaking, and that sensemaking involves constructing and interacting with representations of knowledge. As such, in order to provide the searchers with more support in performing exploratory activities, there is a need to move beyond the current document retrieval paradigm by extending the support for locating and externalizing semantic information from textual documents and by providing richer representations of the extracted information coupled with mechanisms for accessing and interacting with the information in ways that support exploration and sensemaking. This dissertation presents a series of discrete research endeavour to explore different aspects of providing information and presenting this information in ways that both extraction and assimilation of relevant information is supported. We first address the problem of extracting information – that is more granular than documents – as a response to a user's query by developing a novel information extraction system to represent documents as a series of entity-relationship tuples. Next, through a series of designing and evaluating alternative representations of search results, we examine how this extracted information can be represented such that it extends the document-based search framework's support for exploratory search tasks. Finally, we assess the ecological validity of this research by exploring error-prone representations of search results and how they impact a searcher's ability to leverage our representations to perform exploratory search tasks. Overall, this research contributes towards designing future search systems by providing insights into the efficacy of alternative representations of search results for supporting exploratory search activities, culminating in a novel hybrid representation called Hierarchical Knowledge Graphs (HKG). To this end we propose and develop a framework that enables a reliable investigation of the impact of different representations and how they are perceived and utilized by information seekers

Designing for Cross-Device Interactions

Driven by technological advancements, we now own and operate an ever-growing number of digital devices, leading to an increased amount of digital data we produce, use, and maintain. However, while there is a substantial increase in computing power and availability of devices and data, many tasks we conduct with our devices are not well connected across multiple devices. We conduct our tasks sequentially instead of in parallel, while collaborative work across multiple devices is cumbersome to set up or simply not possible. To address these limitations, this thesis is concerned with cross-device computing. In particular it aims to conceptualise, prototype, and study interactions in cross-device computing. This thesis contributes to the field of Human-Computer Interaction (HCI)—and more specifically to the area of cross-device computing—in three ways: first, this work conceptualises previous work through a taxonomy of cross-device computing resulting in an in-depth understanding of the field, that identifies underexplored research areas, enabling the transfer of key insights into the design of interaction techniques. Second, three case studies were conducted that show how cross-device interactions can support curation work as well as augment users’ existing devices for individual and collaborative work. These case studies incorporate novel interaction techniques for supporting cross-device work. Third, through studying cross-device interactions and group collaboration, this thesis provides insights into how researchers can understand and evaluate multi- and cross-device interactions for individual and collaborative work. We provide a visualization and querying tool that facilitates interaction analysis of spatial measures and video recordings to facilitate such evaluations of cross-device work. Overall, the work in this thesis advances the field of cross-device computing with its taxonomy guiding research directions, novel interaction techniques and case studies demonstrating cross-device interactions for curation, and insights into and tools for effective evaluation of cross-device systems

Mobiilse värkvõrgu protsessihaldus

Värkvõrk, ehk Asjade Internet (Internet of Things, lüh IoT) edendab lahendusi nagu nn tark linn, kus meid igapäevaselt ümbritsevad objektid on ühendatud infosüsteemidega ja ka üksteisega. Selliseks näiteks võib olla teekatete seisukorra monitoorimissüsteem. Võrku ühendatud sõidukitelt (nt bussidelt) kogutakse videomaterjali, mida seejärel töödeldakse, et tuvastada löökauke või lume kogunemist. Tavaliselt hõlmab selline lahendus keeruka tsentraalse süsteemi ehitamist. Otsuste langetamiseks (nt milliseid sõidukeid parasjagu protsessi kaasata) vajab keskne süsteem pidevat ühendust kõigi IoT seadmetega. Seadmete hulga kasvades võib keskne lahendus aga muutuda pudelikaelaks. Selliste protsesside disaini, haldust, automatiseerimist ja seiret hõlbustavad märkimisväärselt äriprotsesside halduse (Business Process Management, lüh BPM) valdkonna standardid ja tööriistad. Paraku ei ole BPM tehnoloogiad koheselt kasutatavad uute paradigmadega nagu Udu- ja Servaarvutus, mis tuleviku värkvõrgu jaoks vajalikud on. Nende puhul liigub suur osa otsustustest ja arvutustest üksikutest andmekeskustest servavõrgu seadmetele, mis asuvad lõppkasutajatele ja IoT seadmetele lähemal. Videotöötlust võiks teostada mini-andmekeskustes, mis on paigaldatud üle linna, näiteks bussipeatustesse. Arvestades IoT seadmete üha suurenevat hulka, vähendab selline koormuse jaotamine vähendab riski, et tsentraalne andmekeskust ülekoormamist. Doktoritöö uurib, kuidas mobiilsusega seonduvaid IoT protsesse taoliselt ümber korraldada, kohanedes pidevalt muutlikule, liikuvate seadmetega täidetud servavõrgule. Nimelt on ühendused katkendlikud, mistõttu otsuste langetus ja planeerimine peavad arvestama muuhulgas mobiilseadmete liikumistrajektoore. Töö raames valminud prototüüpe testiti Android seadmetel ja simulatsioonides. Lisaks valmis tööriistakomplekt STEP-ONE, mis võimaldab teadlastel hõlpsalt simuleerida ja analüüsida taolisi probleeme erinevais realistlikes stsenaariumites nagu seda on tark linn.The Internet of Things (IoT) promotes solutions such as a smart city, where everyday objects connect with info systems and each other. One example is a road condition monitoring system, where connected vehicles, such as buses, capture video, which is then processed to detect potholes and snow build-up. Building such a solution typically involves establishing a complex centralised system. The centralised approach may become a bottleneck as the number of IoT devices keeps growing. It relies on constant connectivity to all involved devices to make decisions, such as which vehicles to involve in the process. Designing, automating, managing, and monitoring such processes can greatly be supported using the standards and software systems provided by the field of Business Process Management (BPM). However, BPM techniques are not directly applicable to new computing paradigms, such as Fog Computing and Edge Computing, on which the future of IoT relies. Here, a lot of decision-making and processing is moved from central data-centers to devices in the network edge, near the end-users and IoT sensors. For example, video could be processed in mini-datacenters deployed throughout the city, e.g., at bus stops. This load distribution reduces the risk of the ever-growing number of IoT devices overloading the data center. This thesis studies how to reorganise the process execution in this decentralised fashion, where processes must dynamically adapt to the volatile edge environment filled with moving devices. Namely, connectivity is intermittent, so decision-making and planning need to involve factors such as the movement trajectories of mobile devices. We examined this issue in simulations and with a prototype for Android smartphones. We also showcase the STEP-ONE toolset, allowing researchers to conveniently simulate and analyse these issues in different realistic scenarios, such as those in a smart city.  https://www.ester.ee/record=b552551

Structural variation in Parkinson’s disease: Focusing on the role of Transposable elements in disease predisposition and pathogenesis

Parkinson’s disease (PD) is a neurodegenerative disorder with a complex aetiology including genetic risk factors, environmental exposure and aging. Recent genome wide association studies have been successful at identifying genetic variation that confers a risk for PD, yet despite this it is predicted that the large majority of the genetic attribution to the disease is still unknown. It is also noted that much of the identified risk loci lie within poorly annotated regions of the genome such as those containing repetitive sequences and transposable elements (TE)s, highlighting the importance of further investigation into such regions. Despite many reports that associate TE insertions with PD no study has comprehensively analysed the role of these elements in the disease. The work presented in this thesis sought to ask three main questions; first, are TE overrepresented at PD risk loci using a haplotype block based genome-wide analysis, second are non-reference TE associated with risk of PD using a newly developed TE detection tool and PD WGS data; and third, are TE differentially regulated in the blood or skin of individuals with PD. This work leveraged genetic and expression datasets to comprehensively address the role of TE in PD. Along with identifying that specific TE are overrepresented at PD risk loci we also show that in the blood, specific repetitive elements (satellite) are differentially expression in PD. Most significantly, we characterised known non-reference TE presence/absence polymorphisms in collaboration with the International Parkinson’s Disease Genomic Consortium (IPDGC) in PD whole genome sequencing data (WGS) from the Parkinson’s Progression Markers Initiative (PPMI) cohort using the TE detection tool MELT. We identify that TE insertions are a heritable and common form of genetic variation that lie within potentially important functional domains of the genome. Not only do many non-reference TE map to PD risk loci, but from our initial study we have identified that non-reference TE’s are in moderate linkage disequilibrium with PD risk variants, and thus a candidate causal variant that warrant further study at these loci. In summary, TE insertions are a major source and often overlooked form of genetic variation in the human genome. Collectively the research presented in this thesis suggests that not only could integrating TE variants be a valuable and critical step forward for furthering our understanding of existing risk PD variants, but it could also be valuable for establishing new risk factors

IN SILICO METHODS FOR DRUG DESIGN AND DISCOVERY

Computer-aided drug design (CADD) methodologies are playing an ever-increasing role in drug discovery that are critical in the cost-effective identification of promising drug candidates. These computational methods are relevant in limiting the use of animal models in pharmacological research, for aiding the rational design of novel and safe drug candidates, and for repositioning marketed drugs, supporting medicinal chemists and pharmacologists during the drug discovery trajectory.Within this field of research, we launched a Research Topic in Frontiers in Chemistry in March 2019 entitled “In silico Methods for Drug Design and Discovery,” which involved two sections of the journal: Medicinal and Pharmaceutical Chemistry and Theoretical and Computational Chemistry. For the reasons mentioned, this Research Topic attracted the attention of scientists and received a large number of submitted manuscripts. Among them 27 Original Research articles, five Review articles, and two Perspective articles have been published within the Research Topic. The Original Research articles cover most of the topics in CADD, reporting advanced in silico methods in drug discovery, while the Review articles offer a point of view of some computer-driven techniques applied to drug research. Finally, the Perspective articles provide a vision of specific computational approaches with an outlook in the modern era of CADD