Prerequisites for Affective Signal Processing (ASP)

Although emotions are embraced by science, their recognition has not reached a satisfying level. Through a concise overview of affect, its signals, features, and classification methods, we provide understanding for the problems encountered. Next, we identify the prerequisites for successful Affective Signal Processing: validation (e.g., mapping of constructs on signals), triangulation, a physiology-driven approach, and contributions of the signal processing community. Using these directives, a critical analysis of a real-world case is provided. This illustrates that the prerequisites can become a valuable guide for Affective Signal Processing (ASP)

Matching Biomedical Knowledge Graphs with Neural Embeddings

Tese de mestrado, Ciência de Dados, Universidade de Lisboa, Faculdade de Ciências, 2020Os grafos de conhecimento são estruturas que se tornaram fundamentais para a organização dos dados biomédicos que têm sido produzidos a um ritmo exponencial nos últimos anos. A abrangente adoção desta forma de estruturar e descrever dados levou ao desenvolvimento de abordagens de prospeção de dados que tirassem partido desta informação com o intuito de auxiliar o progresso do conhecimento científico. Porém, devido à impossibilidade de isolamento de domínios de conhecimento e à idiossincrasia humana, grafos de conhecimento construídos por diferentes indivíduos contêm muitas vezes conceitos equivalentes descritos de forma diferente, dificultando uma análise integrada de dados de diferentes grafos de conhecimento. Vários sistemas de alinhamento de grafos de conhecimento têm focado a resolução deste desafio. Contudo, o desempenho destes sistemas no alinhamento de grafos de conhecimento biomédicos estagnou nos últimos quatro anos com algoritmos e recursos externos bastante trabalhados para aprimorar os resultados. Nesta dissertação, apresentamos duas novas abordagens de alinhamento de grafos de conhecimento empregando Neural Embeddings: uma utilizando semelhança simples entre embeddings à base de palavras e de entidades de grafos; outra treinando um modelo mais complexo que refinasse a informação proveniente de embeddings baseados em palavras. A metodologia proposta visa integrar estas abordagens no processo regular de alinhamento, utilizando como infraestrutura o sistema AgreementMakerLight. Estas novas componentes permitem extender os algoritmos de alinhamento do sistema, descobrindo novos mapeamentos, e criar uma abordagem de alinhamento mais generalizável e menos dependente de ontologias biomédicas externas. Esta nova metodologia foi avaliada em três casos de teste de alinhamento de ontologias biomédicas, provenientes da Ontology Alignment Evaluation Initiative. Os resultados demonstraram que apesar de ambas as abordagens não excederem o estado da arte, estas obtiveram um desempenho benéfico nas tarefas de alinhamento, superando a performance de todos os sistemas que não usam ontologias externas e inclusive alguns que tiram proveito das mesmas, o que demonstra o valor das técnicas de Neural Embeddings na tarefa de alinhamento de grafos do conhecimento biomédicos.Knowledge graphs are data structures which became essential to organize biomedical data produced at an exponential rate in the last few years. The broad adoption of this method of structuring and describing data resulted in the increased interest to develop data mining approaches which took advantage of these information structures in order to improve scientific knowledge. However, due to human idiosyncrasy and also the impossibility to isolate knowledge domains in separate pieces, knowledge graphs constructed by different individuals often contain equivalent concepts described differently. This obstructs the path to an integrated analysis of data described by multiple knowledge graphs. Multiple knowledge graph matching systems have been developed to address this challenge. Nevertheless, the performance of these systems has stagnated in the last four years, despite the fact that they were provided with highly tailored algorithms and external resources to tackle this task. In this dissertation, we present two novel knowledge graph matching approaches employing neural embeddings: one using plain embedding similarity based on word and graph models; the other one using a more complex word-based model which requires training data to refine embeddings. The proposed methodology aims to integrate these approaches in the regular matching process, using the AgreementMakerLight system as a foundation. These new components enable the extension of the system’s current matching algorithms, discovering new mappings, and developing a more generalizable and less dependent on external biomedical ontologies matching procedure. This new methodology was evaluated on three biomedical ontology matching test cases provided by the Ontology Alignment Evaluation Initiative. The results showed that despite both embedding approaches don’t exceed state of the art results, they still produce better results than any other matching systems which do not make use of external ontologies and also surpass some that do benefit from them. This shows that Neural Embeddings are a valuable technique to tackle the challenge of biomedical knowledge graph matching

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research

Background: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? questions. Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. Results: We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information—a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. Conclusions: We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences

Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research

Background: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? questions. Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. Results: We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information—a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. Conclusions: We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences

A review of estimation of distribution algorithms in bioinformatics

Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain

Statistical Extraction of Multilingual Natural Language Patterns for RDF Predicates: Algorithms and Applications

The Data Web has undergone a tremendous growth period. It currently consists of more then 3300 publicly available knowledge bases describing millions of resources from various domains, such as life sciences, government or geography, with over 89 billion facts. In the same way, the Document Web grew to the state where approximately 4.55 billion websites exist, 300 million photos are uploaded on Facebook as well as 3.5 billion Google searches are performed on average every day. However, there is a gap between the Document Web and the Data Web, since for example knowledge bases available on the Data Web are most commonly extracted from structured or semi-structured sources, but the majority of information available on the Web is contained in unstructured sources such as news articles, blog post, photos, forum discussions, etc. As a result, data on the Data Web not only misses a significant fragment of information but also suffers from a lack of actuality since typical extraction methods are time-consuming and can only be carried out periodically. Furthermore, provenance information is rarely taken into consideration and therefore gets lost in the transformation process. In addition, users are accustomed to entering keyword queries to satisfy their information needs. With the availability of machine-readable knowledge bases, lay users could be empowered to issue more specific questions and get more precise answers. In this thesis, we address the problem of Relation Extraction, one of the key challenges pertaining to closing the gap between the Document Web and the Data Web by four means. First, we present a distant supervision approach that allows finding multilingual natural language representations of formal relations already contained in the Data Web. We use these natural language representations to find sentences on the Document Web that contain unseen instances of this relation between two entities. Second, we address the problem of data actuality by presenting a real-time data stream RDF extraction framework and utilize this framework to extract RDF from RSS news feeds. Third, we present a novel fact validation algorithm, based on natural language representations, able to not only verify or falsify a given triple, but also to find trustworthy sources for it on the Web and estimating a time scope in which the triple holds true. The features used by this algorithm to determine if a website is indeed trustworthy are used as provenance information and therewith help to create metadata for facts in the Data Web. Finally, we present a question answering system that uses the natural language representations to map natural language question to formal SPARQL queries, allowing lay users to make use of the large amounts of data available on the Data Web to satisfy their information need

Development of a web-based platform for Biomedical Text Mining

Dissertação de mestrado em Engenharia InformáticaBiomedical Text Mining (BTM) seeks to derive high-quality information from literature in the biomedical domain, by creating tools/methodologies that can automate time-consuming tasks when searching for new information. This encompasses both Information Retrieval, the discovery and recovery of relevant documents, and Information Extraction, the capability to extract knowledge from text. In the last years, SilicoLife, with the collaboration of the University of Minho, has been developing @Note2, an open-source Java-based multiplatform BTM workbench, including libraries to perform the main BTM tasks, also provid ing user-friendly interfaces through a stand-alone application. This work addressed the development of a web-based software platform that is able to address some of the main tasks within BTM, supported by the existing core libraries from the @Note project. This included the improvement of the available RESTful server, providing some new methods and APIs, and improving others, while also developing a web-based application through calls to the API provided by the server and providing a functional user-friendly web-based interface. This work focused on the development of tasks related with Information Retrieval, addressing the efficient search of relevant documents through an integrated interface. Also, at this stage the aim was to have interfaces to visualize and explore the main entities involved in BTM: queries, documents, corpora, annotation processes entities and resources.A mineração de Literatura Biomédica (BioLM) pretende extrair informação de alta qualidade da área biomédica, através da criação de ferramentas/metodologias que consigam automatizar tarefas com elevado dispêndio de tempo. As tarefas subjacentes vão desde recuperação de informação, descoberta e recuperação de documentos relevantes para a extração de informação pertinente e a capacidade de extrair conhecimento de texto. Nos últimos anos a SilicoLife tem vindo a desenvolver uma ferramenta, o @Note2, uma BioLM Workbench multiplataforma baseada em JAVA, que executa as principais tarefas inerentes a BioLM. Também possui uma versão autónoma com uma interface amigável para o utilizador. Esta tese desenvolveu uma plataforma de software baseada na web, que é capaz de executar algumas das tarefas de BioLM, com suporte num núcleo de bibliotecas do projeto @Note. Para tal foi necessário melhorar o servidor RESTfid atual, criando novos métodos e APIs, como também desenvolver a aplicação baseada na web, com uma interface amigável para o utilizador, que comunicará com o servidor através de chamadas à sua APL Este trabalho focou o seu desenvolvimento em tarefas relacionadas com recuperação de informação, focando na pesquisa eficiente de documentos de interesse através de uma interface integrada. Nesta fase, o objetivo foi também ter um conjunto de interfaces capazes de visualizar e explorar as principais entidades envolvidas em BioLM: pesquisas, documentos, corpora, entidades relacionadas com processos de anotações e recursos