Thinking outside the graph: scholarly knowledge graph construction leveraging natural language processing

Despite improved digital access to scholarly knowledge in recent decades, scholarly communication remains exclusively document-based. The document-oriented workflows in science publication have reached the limits of adequacy as highlighted by recent discussions on the increasing proliferation of scientific literature, the deficiency of peer-review and the reproducibility crisis. In this form, scientific knowledge remains locked in representations that are inadequate for machine processing. As long as scholarly communication remains in this form, we cannot take advantage of all the advancements taking place in machine learning and natural language processing techniques. Such techniques would facilitate the transformation from pure text based into (semi-)structured semantic descriptions that are interlinked in a collection of big federated graphs. We are in dire need for a new age of semantically enabled infrastructure adept at storing, manipulating, and querying scholarly knowledge. Equally important is a suite of machine assistance tools designed to populate, curate, and explore the resulting scholarly knowledge graph. In this thesis, we address the issue of constructing a scholarly knowledge graph using natural language processing techniques. First, we tackle the issue of developing a scholarly knowledge graph for structured scholarly communication, that can be populated and constructed automatically. We co-design and co-implement the Open Research Knowledge Graph (ORKG), an infrastructure capable of modeling, storing, and automatically curating scholarly communications. Then, we propose a method to automatically extract information into knowledge graphs. With Plumber, we create a framework to dynamically compose open information extraction pipelines based on the input text. Such pipelines are composed from community-created information extraction components in an effort to consolidate individual research contributions under one umbrella. We further present MORTY as a more targeted approach that leverages automatic text summarization to create from the scholarly article's text structured summaries containing all required information. In contrast to the pipeline approach, MORTY only extracts the information it is instructed to, making it a more valuable tool for various curation and contribution use cases. Moreover, we study the problem of knowledge graph completion. exBERT is able to perform knowledge graph completion tasks such as relation and entity prediction tasks on scholarly knowledge graphs by means of textual triple classification. Lastly, we use the structured descriptions collected from manual and automated sources alike with a question answering approach that builds on the machine-actionable descriptions in the ORKG. We propose JarvisQA, a question answering interface operating on tabular views of scholarly knowledge graphs i.e., ORKG comparisons. JarvisQA is able to answer a variety of natural language questions, and retrieve complex answers on pre-selected sub-graphs. These contributions are key in the broader agenda of studying the feasibility of natural language processing methods on scholarly knowledge graphs, and lays the foundation of which methods can be used on which cases. Our work indicates what are the challenges and issues with automatically constructing scholarly knowledge graphs, and opens up future research directions

Architectural stability of self-adaptive software systems

This thesis studies the notion of stability in software engineering with the aim of understanding its dimensions, facets and aspects, as well as characterising it. The thesis further investigates the aspect of behavioural stability at the architectural level, as a property concerned with the architecture's capability in maintaining the achievement of expected quality of service and accommodating runtime changes, in order to delay the architecture drifting and phasing-out as a consequence of the continuous unsuccessful provision of quality requirements. The research aims to provide a systematic and methodological support for analysing, modelling, designing and evaluating architectural stability. The novelty of this research is the consideration of stability during runtime operation, by focusing on the stable provision of quality of service without violations. As the runtime dimension is associated with adaptations, the research investigates stability in the context of self-adaptive software architectures, where runtime stability is challenged by the quality of adaptation, which in turn affects the quality of service. The research evaluation focuses on the effectiveness, scale and accuracy in handling runtime dynamics, using the self-adaptive cloud architectures

Unravelling the molecular dynamics of c-MYC’s TAD domain: a journey from simulation optimisation to drug discovery

c-MYC, part of the MYC family of transcription factors, is often deregulated in cancer, and since the early 1980’s has been identified as a prime oncogenic factor. Despite much research interest, c-MYC’s structural dynamics remain largely uncharted due to its intrinsic structural disorder. Disordered proteins are challenging to study using solely structural experimental methods, thus lately attention has turned towards the development of reliable in-silico methods to get an accurate molecular description. Molecular Dynamics simulations, commonly and successfully used to study globular proteins, can also be optimised to correctly reproduce natural protein disorder. The simulation results were assessed for convergence and conformational equilibrium, achieved by comparing the c-MYC’s Molecular Dynamics conformational landscape to similar data derived from an abundantly sampled probabilistic distribution. After the preparatory and validation work, the efforts turned to the appraisal of c-MYC’s first 88 amino acids. The revelation of its conformational states and structural dynamics opened the door for drug discovery and proof-of-concept that c-MYC should not be considered ‘undruggable’. Further exploration into the protein first 150 residues, corresponding to its transactivation domain, uncovered important structural dynamics controlled by key phosphodegron residues. Phosphorylation and mutagenesis studies demonstrated how these control mechanisms, which serve to modulate accessibility to crucial regions, are facilitated by isomerisation events within the phosphodegron. Overarchingly, this study substantiates the robustness of well-parameterised computational simulations, and machine learning methods, in uncovering the workings of otherwise difficult to study disordered proteins.Open Acces

Semantic discovery and reuse of business process patterns

Patterns currently play an important role in modern information systems (IS) development and their use has mainly been restricted to the design and implementation phases of the development lifecycle. Given the increasing significance of business modelling in IS development, patterns have the potential of providing a viable solution for promoting reusability of recurrent generalized models in the very early stages of development. As a statement of research-in-progress this paper focuses on business process patterns and proposes an initial methodological framework for the discovery and reuse of business process patterns within the IS development lifecycle. The framework borrows ideas from the domain engineering literature and proposes the use of semantics to drive both the discovery of patterns as well as their reuse

Pristup integraciji tehničkih prostora zasnovan na preslikavanjima iinženjerstvu vođenom modelima

In order to automate development of integration adapters in industrial settings, a model-driven approach to adapter specification is devised. In this approach, a domain-specific modeling language is created to allow specification of mappings between integrated technical spaces. Also proposed is the mapping automation engine that comprises reuse and alignment algorithms. Based on mapping specifications, executable adapters are automatically generated and executed. Results of approach evaluations indicate that it is possible to use a model-driven approach to successfully integrate technical spaces and increase the automation by reusing domainspecific mappings from previously created adapters.За потребе повећања степена аутоматизације развоја адаптера за интеграцију у индустријском окружењу, осмишљен је моделом вођен приступ развоју адаптера. У оквиру овог приступа развијен је наменски језик за спецификацију пресликавања између техничких простора који су предмет интеграције. Приступ обухвата и алгоритме за поравнање и поновно искориштење претходно креираних пресликавања са циљем аутоматизације процеса спецификације. На основу креираних пресликавања, могуће je аутоматски генерисати извршиви код адаптера. У испитивањима приступа, показано је да је могуће успешно применити моделом вођен приступ у интеграцији техничких простора као и да је могуће успешно повећати степен аутоматизације поновним искоришћењем претходно креираних пресликавања.Za potrebe povećanja stepena automatizacije razvoja adaptera za integraciju u industrijskom okruženju, osmišljen je modelom vođen pristup razvoju adaptera. U okviru ovog pristupa razvijen je namenski jezik za specifikaciju preslikavanja između tehničkih prostora koji su predmet integracije. Pristup obuhvata i algoritme za poravnanje i ponovno iskorištenje prethodno kreiranih preslikavanja sa ciljem automatizacije procesa specifikacije. Na osnovu kreiranih preslikavanja, moguće je automatski generisati izvršivi kod adaptera. U ispitivanjima pristupa, pokazano je da je moguće uspešno primeniti modelom vođen pristup u integraciji tehničkih prostora kao i da je moguće uspešno povećati stepen automatizacije ponovnim iskorišćenjem prethodno kreiranih preslikavanja

Report on a Strategic Approach to Research Publishing in South Africa

Cite: Academy of Science of South Africa (ASSAf), (2006). Report on a Strategic Approach to Research Publishing in South Africa. [Online] Available at: DOI http://dx.doi.org/10.17159/assaf/0038Two strands of influence have affected the publication of local scholarly journals in South Africa in the recent past. The first of these was the establishment of the Bureau of Scientific Publications that subsidized the publication of a number of journals that had been established during the 20th century. The ‘Bureau journals’ were an attempt to foster academic publication in South Africa and to make their products available to an international readership – quality of material was to be coupled to quality of production. In this respect the establishment of the Bureau was mimicking a similar development in Australia and could be seen as a mechanism for fostering home-grown talent. The second influence was a new mechanism of funding universities, which rewarded them directly for the academic publications that they produced. Both of these influences had a significant impact on the development of local journals, the behaviour of individuals, the financial sustainability of learned societies that produced the journals, and the institutions that received the ‘output’ subsidy. The Bureau was recently closed, with only one journal, The South Africa Journal of Science, continuing to receive support through the Academy of Science of South Africa on the basis of its international impact. The funding for ‘outputs’ of the tertiary institutions has continued, although in a modified form that includes a reward for completed masters and doctoral degrees. These developments raised two related questions. The first was whether it was appropriate for the state to support the publication of (some) learned journals in the interest of fostering intellectual exchange. The second question was whether all of the articles, published in journals recognized for the output subsidy of universities, deserved to receive recognition, in view of the wide variation in quality of the material produced. The Academy was commissioned in 2001 in this context by the Department of Arts, Culture, Science and Technology (now the Department of Science and Technology) to undertake a study to address these two questions, with a view to making recommendations for the optimal development of policy in the future. The effect of globalization on knowledge exchange, which is mediated very largely through scientific journals being published in English, and having their origins in Europe and North America, has resulted in the neglect of regional journals. It has also led to the development of benchmarks based on bibliometric analysis of publication patterns that has resulted in global ranking of tertiary institutions. These trends are being countered in the African context, with its relatively neglected tertiary sector, by a need that is expressed by the African Academies of Science that are members of the Network of African Scientific Academies (NASAC), to consider the publication of high-quality journals that report work of significance to African scientists. The degree to which such a project is feasible, and whether it could be successfully implemented both in South Africa and elsewhere on the continent, needs to be explored after the release of this report. Although the report was prepared at the request of, and with funding from the Department of Science and Technology, in order amongst other matters to address specific questions that had been raised about the subsidy for scholarly outputs, its potential impact both in understanding international trends in scholarly knowledge production and in giving guidance to those who would like to foster the publication of indigenous journals, will be great if careful attention is given to the recommendations that are contained in this study. The report was developed and has been guided to a successful conclusion by Prof Wieland Gevers who initiated it during his tenure as President of the Academy and has now brought it to fruition as the Academy’s Executive Officer, with the invaluable assistance of Dr Xola Mati as study director. He and the authors of the various chapters are thanked for the care and attention with which they have produced a seminal analysis of South African publication patterns. They will receive their reward in full measure through the impact that this report will have on the further development of the National System of Innovation.Department of Science and Technolog

Guideline-based decision support in medicine : modeling guidelines for the development and application of clinical decision support systems

Guideline-based Decision Support in Medicine Modeling Guidelines for the Development and Application of Clinical Decision Support Systems The number and use of decision support systems that incorporate guidelines with the goal of improving care is rapidly increasing. Although developing systems that are both effective in supporting clinicians and accepted by them has proven to be a difficult task, of the systems that were evaluated by a controlled trial, the majority showed impact. The work, described in this thesis, aims at developing a methodology and framework that facilitates all stages in the guideline development process, ranging from the definition of models that represent guidelines to the implementation of run-time systems that provide decision support, based on the guidelines that were developed during the previous stages. The framework consists of 1) a guideline representation formalism that uses the concepts of primitives, Problem-Solving Methods (PSMs) and ontologies to represent guidelines of various complexity and granularity and different application domains, 2) a guideline authoring environment that enables guideline authors to define guidelines, based on the newly developed guideline representation formalism, and 3) a guideline execution environment that translates defined guidelines into a more efficient symbol-level representation, which can be read in and processed by an execution-time engine. The described methodology and framework were used to develop and validate a number of guidelines and decision support systems in various clinical domains such as Intensive Care, Family Practice, Psychiatry and the areas of Diabetes and Hypertension control

Performance Optimization Strategies for Transactional Memory Applications

This thesis presents tools for Transactional Memory (TM) applications that cover multiple TM systems (Software, Hardware, and hybrid TM) and use information of all different layers of the TM software stack. Therefore, this thesis addresses a number of challenges to extract static information, information about the run time behavior, and expert-level knowledge to develop these new methods and strategies for the optimization of TM applications

A computational framework for structure-based drug discovery with GPU acceleration.

Li, Hongjian.Thesis (M.Phil.)--Chinese University of Hong Kong, 2011.Includes bibliographical references (p. 132-156).Abstracts in English and Chinese.Abstract --- p.iAbstract in Chinese --- p.iiiAcknowledgement --- p.ivChapter 1 --- Introduction --- p.1Chapter 1.1 --- Motivation --- p.2Chapter 1.2 --- Objective --- p.2Chapter 1.3 --- Method --- p.3Chapter 1.4 --- Outline --- p.4Chapter 2 --- Background --- p.7Chapter 2.1 --- Overview of the Pharmaceutical Industry --- p.7Chapter 2.2 --- The Process of Modern Drug Discovery --- p.10Chapter 2.2.1 --- Development of an Innovative Idea --- p.10Chapter 2.2.2 --- Establishment of a Project Team --- p.11Chapter 2.2.3 --- Target Identification --- p.11Chapter 2.2.4 --- Hit Identification --- p.12Chapter 2.2.5 --- Lead Identification --- p.13Chapter 2.2.6 --- Lead Optimization --- p.14Chapter 2.2.7 --- Clinical Trials --- p.14Chapter 2.3 --- Drug Discovery via Computational Means --- p.15Chapter 2.3.1 --- Structure-Based Virtual Screening --- p.16Chapter 2.3.2 --- Computational Synthesis of Potent Ligands --- p.20Chapter 2.3.3 --- General-Purpose Computing on GPU --- p.23Chapter 3 --- Approximate Matching of DNA Patterns --- p.26Chapter 3.1 --- Problem Definition --- p.27Chapter 3.2 --- Motivation --- p.28Chapter 3.3 --- Background --- p.30Chapter 3.4 --- Method --- p.32Chapter 3.4.1 --- Binary Representation --- p.32Chapter 3.4.2 --- Agrep Algorithm --- p.32Chapter 3.4.3 --- CUDA Implementation --- p.34Chapter 3.5 --- Experiments and Results --- p.39Chapter 3.6 --- Discussion --- p.44Chapter 3.7 --- Availability --- p.45Chapter 3.8 --- Conclusion --- p.47Chapter 4 --- Structure-Based Virtual Screening --- p.50Chapter 4.1 --- Problem Definition --- p.51Chapter 4.2 --- Motivation --- p.52Chapter 4.3 --- Medicinal Background --- p.52Chapter 4.4 --- Computational Background --- p.59Chapter 4.4.1 --- Scoring Function --- p.59Chapter 4.4.2 --- Optimization Algorithm --- p.65Chapter 4.5 --- Method --- p.68Chapter 4.5.1 --- Scoring Function --- p.69Chapter 4.5.2 --- Inactive Torsions --- p.72Chapter 4.5.3 --- Optimization Algorithm --- p.73Chapter 4.5.4 --- C++ Implementation Tricks --- p.74Chapter 4.6 --- Data --- p.75Chapter 4.6.1 --- Proteins --- p.75Chapter 4.6.2 --- Ligands --- p.76Chapter 4.7 --- Experiments and Results --- p.77Chapter 4.7.1 --- Program Validation --- p.77Chapter 4.7.2 --- Virtual Screening --- p.81Chapter 4.8 --- Discussion --- p.89Chapter 4.9 --- Availability --- p.90Chapter 4.10 --- Conclusion --- p.91Chapter 5 --- Computational Synthesis of Ligands --- p.92Chapter 5.1 --- Problem Definition --- p.93Chapter 5.2 --- Motivation --- p.93Chapter 5.3 --- Background --- p.94Chapter 5.4 --- Method --- p.97Chapter 5.4.1 --- Selection --- p.99Chapter 5.4.2 --- Mutation --- p.102Chapter 5.4.3 --- Crossover --- p.102Chapter 5.4.4 --- Split --- p.103Chapter 5.4.5 --- Merging --- p.104Chapter 5.4.6 --- Drug Likeness Testing --- p.104Chapter 5.5 --- Data --- p.105Chapter 5.5.1 --- Proteins --- p.105Chapter 5.5.2 --- Initial Ligands --- p.107Chapter 5.5.3 --- Fragments --- p.107Chapter 5.6 --- Experiments and Results --- p.109Chapter 5.6.1 --- Binding Conformation --- p.112Chapter 5.6.2 --- Free Energy and Molecule Weight --- p.115Chapter 5.6.3 --- Execution Time --- p.116Chapter 5.6.4 --- Support for Phosphorus --- p.116Chapter 5.7 --- Discussion --- p.120Chapter 5.8 --- Availability --- p.123Chapter 5.9 --- Conclusion --- p.123Chapter 5.10 --- Personal Contribution --- p.124Chapter 6 --- Conclusion --- p.125Chapter 6.1 --- Conclusion --- p.125Chapter 6.2 --- Future Work --- p.128Chapter A --- Publications --- p.130Chapter A.1 --- Conference Papers --- p.130Chapter A.2 --- Journal Papers --- p.131Bibliography --- p.13

Computer Science & Technology Series : XXI Argentine Congress of Computer Science. Selected papers

CACIC’15 was the 21thCongress in the CACIC series. It was organized by the School of Technology at the UNNOBA (North-West of Buenos Aires National University) in Junín, Buenos Aires. The Congress included 13 Workshops with 131 accepted papers, 4 Conferences, 2 invited tutorials, different meetings related with Computer Science Education (Professors, PhD students, Curricula) and an International School with 6 courses. CACIC 2015 was organized following the traditional Congress format, with 13 Workshops covering a diversity of dimensions of Computer Science Research. Each topic was supervised by a committee of 3-5 chairs of different Universities. The call for papers attracted a total of 202 submissions. An average of 2.5 review reports werecollected for each paper, for a grand total of 495 review reports that involved about 191 different reviewers. A total of 131 full papers, involving 404 authors and 75 Universities, were accepted and 24 of them were selected for this book.Red de Universidades con Carreras en Informática (RedUNCI