Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

AUTOMATED META-ACTIONS DISCOVERY FOR PERSONALIZED MEDICAL TREATMENTS

Healthcare, among other domains, provides an attractive ground of work for knowl- edge discovery researchers. There exist several branches of health informatics and health data-mining from which we find actionable knowledge discovery is underserved. Actionable knowledge is best represented by patterns of structured actions that in- form decision makers about actions to take rather than providing static information that may or may not hint to actions. The Action rules model is a good example of active structured action patterns that informs us about the actions to perform to reach a desired outcome. It is augmented by the meta-actions model that rep- resents passive structured effects triggered by the application of an action. In this dissertation, we focus primarily on the meta-actions model that can be mapped to medical treatments and their effects in the healthcare arena. Our core contribution lies in structuring meta-actions and their effects (positive, neutral, negative, and side effects) along with mining techniques and evaluation metrics for meta-action effects. In addition to the mining techniques for treatment effects, this dissertation provides analysis and prediction of side effects, personalized action rules, alternatives for treat- ments with negative outcomes, evaluation for treatments success, and personalized recommendations for treatments. We used the tinnitus handicap dataset and the Healthcare Cost and Utilization Project (HCUP) Florida State Inpatient Databases (SID 2010) to validate our work. The results show the efficiency of our methods

Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

Explainable Patterns: Going from Findings to Insights to Support Data Analytics Democratization

In the past decades, massive efforts involving companies, non-profit organizations, governments, and others have been put into supporting the concept of data democratization, promoting initiatives to educate people to confront information with data. Although this represents one of the most critical advances in our free world, access to data without concrete facts to check or the lack of an expert to help on understanding the existing patterns hampers its intrinsic value and lessens its democratization. So the benefits of giving full access to data will only be impactful if we go a step further and support the Data Analytics Democratization, assisting users in transforming findings into insights without the need of domain experts to promote unconstrained access to data interpretation and verification. In this paper, we present Explainable Patterns (ExPatt), a new framework to support lay users in exploring and creating data storytellings, automatically generating plausible explanations for observed or selected findings using an external (textual) source of information, avoiding or reducing the need for domain experts. ExPatt applicability is confirmed via different use-cases involving world demographics indicators and Wikipedia as an external source of explanations, showing how it can be used in practice towards the data analytics democratization.Comment: 8 Figures, 10 pages, submitted to VIS 202

NASA JSC neural network survey results

A survey of Artificial Neural Systems in support of NASA's (Johnson Space Center) Automatic Perception for Mission Planning and Flight Control Research Program was conducted. Several of the world's leading researchers contributed papers containing their most recent results on artificial neural systems. These papers were broken into categories and descriptive accounts of the results make up a large part of this report. Also included is material on sources of information on artificial neural systems such as books, technical reports, software tools, etc

Comparing sentiment analysis tools on gitHub project discussions

Mestrado de dupla diplomação com a UTFPR - Universidade Tecnológica Federal do ParanáThe context of this work is situated in the rapidly evolving sphere of Natural Language Processing (NLP) within the scope of software engineering, focusing on sentiment analysis in software repositories. Sentiment analysis, a subfield of NLP, provides a potent method to parse, understand, and categorize these sentiments expressed in text. By applying sentiment analysis to software repositories, we can decode developers’ opinions and sentiments, providing key insights into team dynamics, project health, and potential areas of conflict or collaboration. However, the application of sentiment analysis in software engineering comes with its unique set of challenges. Technical jargon, code-specific ambiguities, and the brevity of software-related communications demand tailored NLP tools for effective analysis. The study unfolds in two primary phases. In the initial phase, we embarked on a meticulous investigation into the impacts of expanding the training sets of two prominent sentiment analysis tools, namely, SentiCR and SentiSW. The objective was to delineate the correlation between the size of the training set and the resulting tool performance, thereby revealing any potential enhancements in performance. The subsequent phase of the research encapsulates a practical application of the enhanced tools. We employed these tools to categorize discussions drawn from issue tickets within a varied array of Open-Source projects. These projects span an extensive range, from relatively small repositories to large, well-established repositories, thus providing a rich and diverse sampling ground.O contexto deste trabalho situa-se na esfera em rápida evolução do Processamento de Linguagem Natural (PLN) no âmbito da engenharia de software, com foco na análise de sentimentos em repositórios de software. A análise de sentimentos, um subcampo do PLN, fornece um método poderoso para analisar, compreender e categorizar os sentimentos expressos em texto. Ao aplicar a análise de sentimentos aos repositórios de software, podemos decifrar as opiniões e sentimentos dos desenvolvedores, fornecendo informações importantes sobre a dinâmica da equipe, a saúde do projeto e áreas potenciais de conflito ou colaboração. No entanto, a aplicação da análise de sentimentos na engenharia de software apresenta desafios únicos. Jargão técnico, ambiguidades específicas do código e a breviedade das comunicações relacionadas ao software exigem ferramentas de PLN personalizadas para uma análise eficaz. O estudo se desenvolve em duas fases principais. Na fase inicial, embarcamos em uma investigação meticulosa sobre os impactos da expansão dos conjuntos de treinamento de duas ferramentas proeminentes de análise de sentimentos, nomeadamente, SentiCR e SentiSW. O objetivo foi delinear a correlação entre o tamanho do conjunto de treinamento e o desempenho da ferramenta resultante, revelando assim possíveis aprimoramentos no desempenho. A fase subsequente da pesquisa engloba uma aplicação prática das ferramentas aprimoradas. Utilizamos essas ferramentas para categorizar discussões retiradas de bilhetes de problemas em uma variedade diversificada de projetos de código aberto. Esses projetos abrangem uma ampla gama, desde repositórios relativamente pequenos até repositórios grandes e bem estabelecidos, fornecendo assim um campo de amostragem rico e diversificado

Creating Persian-like music using computational intelligence

Dastgāh are modal systems in traditional Persian music. Each Dastgāh consists of a group of melodies called Gushé, classified in twelve groups about a century ago (Farhat, 1990). Prior to that time, musical pieces were transferred through oral tradition. The traditional music productions revolve around the existing Dastgāh, and Gushe pieces. In this thesis computational intelligence tools are employed in creating novel Dastgāh-like music.There are three types of creativity: combinational, exploratory, and transformational (Boden, 2000). In exploratory creativity, a conceptual space is navigated for discovering new forms. Sometimes the exploration results in transformational creativity. This is due to meaningful alterations happening on one or more of the governing dimensions of an item. In combinational creativity new links are established between items not previously connected. Boden stated that all these types of creativity can be implemented using artificial intelligence.Various tools, and techniques are employed, in the research reported in this thesis, for generating Dastgāh-like music. Evolutionary algorithms are responsible for navigating the space of sequences of musical motives. Aesthetical critics are employed for constraining the search space in exploratory (and hopefully transformational) type of creativity. Boltzmann machine models are applied for assimilating some of the mechanisms involved in combinational creativity. The creative processes involved are guided by aesthetical critics, some of which are derived from a traditional Persian music database.In this project, Cellular Automata (CA) are the main pattern generators employed to produce raw creative materials. Various methodologies are suggested for extracting features from CA progressions and mapping them to musical space, and input to audio synthesizers. The evaluation of the results of this thesis are assisted by publishing surveys which targeted both public and professional audiences. The generated audio samples are evaluated regarding their Dastgāh-likeness, and the level of creativity of the systems involved

The development of a fuzzy expert system to help top decision makers in political and investment domains

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel UniversityThe world’s increasing interconnectedness and the recent increase in the number of notable regional and international events pose greater and greater challenges for political decision-making, especially the decision to strengthen bilateral economic relationships between friendly nations. Typically, such critical decisions are influenced by certain factors and variables that are based on heterogeneous and vague information that exists in different domains. A serious problem that the decision-maker faces is the difficulty in building efficient political decision support systems (DSS) with heterogeneous factors. One must take many factors into account, for example, language (natural or human language), the availability, or lack thereof, of precise data (vague information), and possible consequences (rule conclusions). The basic concept is a linguistic variable whose values are words rather than numbers and are therefore closer to human intuition. A common language is thus needed to describe such information which requires human knowledge for interpretation. To achieve robustness and efficiency of interpretation, we need to apply a method that can be used to generate high-level knowledge and information integration. Fuzzy logic is based on natural language and is tolerant of imprecise data. Fuzzy logic’s greatest strength lies in its ability to handle imprecise data, and it is perfectly suited for this situation. In this thesis, we propose to use ontology to integrate the scattered information resources from the political and investment domains. The process started with understanding each concept and extracting key ideas and relationships between sets of information by constructing object paradigm ontology. Re-engineering according to the object-paradigm (OP) provided quality for the developed ontology where conceptualization can provide more expressive, reusable object and temporal ontology. Then fuzzy logic has been integrated with ontology. And a fuzzy ontology membership value that reflects the strength of an inter-concept relationship to represent pairs of concepts across ontology has been consistently used. Each concept is assigned a fixed numerical value representing the concept consistency. Concept consistency is computed as a function of strength of all the relationships associated with the concept. Fuzzy expert systems enable one to weigh the consequences (rule conclusions) of certain choices based on vague information. Rule conclusions follow from rules composed of two parts, the if antecedent (input) and the then consequent (output). With fuzzy expert systems, one uses fuzzy logic toolbox graphical user interface (GUI) tools to build up a fuzzy inference system (FIS) to aid in decision-making. This research includes four main phases to develop a prototype architecture for an intelligent DSS that can help top political decision makers