Neurocognitive Informatics Manifesto.

Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given

Theory and Applications for Advanced Text Mining

Due to the growth of computer technologies and web technologies, we can easily collect and store large amounts of text data. We can believe that the data include useful knowledge. Text mining techniques have been studied aggressively in order to extract the knowledge from the data since late 1990s. Even if many important techniques have been developed, the text mining research field continues to expand for the needs arising from various application fields. This book is composed of 9 chapters introducing advanced text mining techniques. They are various techniques from relation extraction to under or less resourced language. I believe that this book will give new knowledge in the text mining field and help many readers open their new research fields

Doctor of Philosophy

dissertationBiomedical data are a rich source of information and knowledge. Not only are they useful for direct patient care, but they may also offer answers to important population-based questions. Creating an environment where advanced analytics can be performed against biomedical data is nontrivial, however. Biomedical data are currently scattered across multiple systems with heterogeneous data, and integrating these data is a bigger task than humans can realistically do by hand; therefore, automatic biomedical data integration is highly desirable but has never been fully achieved. This dissertation introduces new algorithms that were devised to support automatic and semiautomatic integration of heterogeneous biomedical data. The new algorithms incorporate both data mining and biomedical informatics techniques to create "concept bags" that are used to compute similarity between data elements in the same way that "word bags" are compared in data mining. Concept bags are composed of controlled medical vocabulary concept codes that are extracted from text using named-entity recognition software. To test the new algorithm, three biomedical text similarity use cases were examined: automatically aligning data elements between heterogeneous data sets, determining degrees of similarity between medical terms using a published benchmark, and determining similarity between ICU discharge summaries. The method is highly configurable and 5 different versions were tested. The concept bag method performed particularly well aligning data elements and outperformed the compared algorithms by iv more than 5%. Another configuration that included hierarchical semantics performed particularly well at matching medical terms, meeting or exceeding 30 of 31 other published results using the same benchmark. Results for the third scenario of computing ICU discharge summary similarity were less successful. Correlations between multiple methods were low, including between terminologists. The concept bag algorithms performed consistently and comparatively well and appear to be viable options for multiple scenarios. New applications of the method and ideas for improving the algorithm are being discussed for future work, including several performance enhancements, configuration-based enhancements, and concept vector weighting using the TF-IDF formulas

Automated extension of biomedical ontologies

Developing and extending a biomedical ontology is a very demanding process, particularly because biomedical knowledge is diverse, complex and continuously changing and growing. Existing automated and semi-automated techniques are not tailored to handling the issues in extending biomedical ontologies. This thesis advances the state of the art in semi-automated ontology extension by presenting a framework as well as methods and methodologies for automating ontology extension specifically designed to address the features of biomedical ontologies.The overall strategy is based on first predicting the areas of the ontology that are in need of extension and then applying ontology learning and ontology matching techniques to extend them. A novel machine learning approach for predicting these areas based on features of past ontology versions was developed and successfully applied to the Gene Ontology. Methods and techniques were also specifically designed for matching biomedical ontologies and retrieving relevant biomedical concepts from text, which were shown to be successful in several applications.O desenvolvimento e extensão de uma ontologia biomédica é um processo muito exigente, dada a diversidade, complexidade e crescimento contínuo do conhecimento biomédico. As técnicas existentes nesta área não estão preparadas para lidar com os desafios da extensão de uma ontologia biomédica. Esta tese avança o estado da arte na extensão semi-automática de ontologias, apresentando uma framework assim como métodos e metodologias para a automação da extensão de ontologias especificamente desenhados tendo em conta as características das ontologias biomédicas. A estratégia global é baseada em primeiro prever quais as áreas da ontologia que necessitam extensão, e depois usá-las como enfoque para técnicas de alinhamento e aprendizagem de ontologias, com o objectivo de as estender. Uma nova estratégia de aprendizagem automática para prever estas áreas baseada em atributos de antigas versões de ontologias foi desenvolvida e testada com sucesso na Gene Ontology. Foram também especificamente desenvolvidos métodos e técnicas para o alinhamento de ontologias biomédicas e extracção de conceitos relevantes de texto, cujo sucesso foi demonstrado em várias aplicações.Fundação para a Ciência e a Tecnologi

Hybrid fuzzy multi-objective particle swarm optimization for taxonomy extraction

Ontology learning refers to an automatic extraction of ontology to produce the ontology learning layer cake which consists of five kinds of output: terms, concepts, taxonomy relations, non-taxonomy relations and axioms. Term extraction is a prerequisite for all aspects of ontology learning. It is the automatic mining of complete terms from the input document. Another important part of ontology is taxonomy, or the hierarchy of concepts. It presents a tree view of the ontology and shows the inheritance between subconcepts and superconcepts. In this research, two methods were proposed for improving the performance of the extraction result. The first method uses particle swarm optimization in order to optimize the weights of features. The advantage of particle swarm optimization is that it can calculate and adjust the weight of each feature according to the appropriate value, and here it is used to improve the performance of term and taxonomy extraction. The second method uses a hybrid technique that uses multi-objective particle swarm optimization and fuzzy systems that ensures that the membership functions and fuzzy system rule sets are optimized. The advantage of using a fuzzy system is that the imprecise and uncertain values of feature weights can be tolerated during the extraction process. This method is used to improve the performance of taxonomy extraction. In the term extraction experiment, five extracted features were used for each term from the document. These features were represented by feature vectors consisting of domain relevance, domain consensus, term cohesion, first occurrence and length of noun phrase. For taxonomy extraction, matching Hearst lexico-syntactic patterns in documents and the web, and hypernym information form WordNet were used as the features that represent each pair of terms from the texts. These two proposed methods are evaluated using a dataset that contains documents about tourism. For term extraction, the proposed method is compared with benchmark algorithms such as Term Frequency Inverse Document Frequency, Weirdness, Glossary Extraction and Term Extractor, using the precision performance evaluation measurement. For taxonomy extraction, the proposed methods are compared with benchmark methods of Feature-based and weighting by Support Vector Machine using the f-measure, precision and recall performance evaluation measurements. For the first method, the experiment results concluded that implementing particle swarm optimization in order to optimize the feature weights in terms and taxonomy extraction leads to improved accuracy of extraction result compared to the benchmark algorithms. For the second method, the results concluded that the hybrid technique that uses multi-objective particle swarm optimization and fuzzy systems leads to improved performance of taxonomy extraction results when compared to the benchmark methods, while adjusting the fuzzy membership function and keeping the number of fuzzy rules to a minimum number with a high degree of accuracy

Enrichment of ontologies using machine learning and summarization

Biomedical ontologies are structured knowledge systems in biomedicine. They play a major role in enabling precise communications in support of healthcare applications, e.g., Electronic Healthcare Records (EHR) systems. Biomedical ontologies are used in many different contexts to facilitate information and knowledge management. The most widely used clinical ontology is the SNOMED CT. Placing a new concept into its proper position in an ontology is a fundamental task in its lifecycle of curation and enrichment. A large biomedical ontology, which typically consists of many tens of thousands of concepts and relationships, can be viewed as a complex network with concepts as nodes and relationships as links. This large-size node-link diagram can easily become overwhelming for humans to understand or work with. Adding concepts is a challenging and time-consuming task that requires domain knowledge and ontology skills. IS-A links (aka subclass links) are the most important relationships of an ontology, enabling the inheritance of other relationships. The position of a concept, represented by its IS-A links to other concepts, determines how accurately it is modeled. Therefore, considering as many parent candidate concepts as possible leads to better modeling of this concept. Traditionally, curators rely on classifiers to place concepts into ontologies. However, this assumes the accurate relationship modeling of the new concept as well as the existing concepts. Since many concepts in existing ontologies, are underspecified in terms of their relationships, the placement by classifiers may be wrong. In cases where the curator does not manually check the automatic placement by classifier programs, concepts may end up in wrong positions in the IS-A hierarchy. A user searching for a concept, without knowing its precise name, would not find it in its expected location. Automated or semi-automated techniques that can place a concept or narrow down the places where to insert it, are highly desirable. Hence, this dissertation is addressing the problem of concept placement by automatically identifying IS-A links and potential parent concepts correctly and effectively for new concepts, with the assistance of two powerful techniques, Machine Learning (ML) and Abstraction Networks (AbNs). Modern neural networks have revolutionized Machine Learning in vision and Natural Language Processing (NLP). They also show great promise for ontology-related tasks, including ontology enrichment, i.e., insertion of new concepts. This dissertation presents research using ML and AbNs to achieve knowledge enrichment of ontologies. Abstraction networks (AbNs), are compact summary networks that preserve a significant amount of the semantics and structure of the underlying ontologies. An Abstraction Network is automatically derived from the ontology itself. It consists of nodes, where each node represents a set of concepts that are similar in their structure and semantics. Various kinds of AbNs have been previously developed by the Structural Analysis of Biomedical Ontologies Center (SABOC) to support the summarization, visualization, and quality assurance (QA) of biomedical ontologies. Two basic kinds of AbNs are the Area Taxonomy and the Partial-area Taxonomy, which have been developed for various biomedical ontologies (e.g., SNOMED CT of SNOMED International and NCIt of the National Cancer Institute). This dissertation presents four enrichment studies of SNOMED CT, utilizing both ML and AbN-based techniques

The Gene Ontology Handbook

bioinformatics; biotechnolog

HESML: A scalable ontology-based semantic similarity measures library with a set of reproducible experiments and a replication dataset

This work is a detailed companion reproducibility paper of the methods and experiments proposed by Lastra-Díaz and García-Serrano in (2015, 2016) [56–58], which introduces the following contributions: (1) a new and efficient representation model for taxonomies, called PosetHERep, which is an adaptation of the half-edge data structure commonly used to represent discrete manifolds and planar graphs; (2) a new Java software library called the Half-Edge Semantic Measures Library (HESML) based on PosetHERep, which implements most ontology-based semantic similarity measures and Information Content (IC) models reported in the literature; (3) a set of reproducible experiments on word similarity based on HESML and ReproZip with the aim of exactly reproducing the experimental surveys in the three aforementioned works; (4) a replication framework and dataset, called WNSimRep v1, whose aim is to assist the exact replication of most methods reported in the literature; and finally, (5) a set of scalability and performance benchmarks for semantic measures libraries. PosetHERep and HESML are motivated by several drawbacks in the current semantic measures libraries, especially the performance and scalability, as well as the evaluation of new methods and the replication of most previous methods. The reproducible experiments introduced herein are encouraged by the lack of a set of large, self-contained and easily reproducible experiments with the aim of replicating and confirming previously reported results. Likewise, the WNSimRep v1 dataset is motivated by the discovery of several contradictory results and difficulties in reproducing previously reported methods and experiments. PosetHERep proposes a memory-efficient representation for taxonomies which linearly scales with the size of the taxonomy and provides an efficient implementation of most taxonomy-based algorithms used by the semantic measures and IC models, whilst HESML provides an open framework to aid research into the area by providing a simpler and more efficient software architecture than the current software libraries. Finally, we prove the outperformance of HESML on the state-of-the-art libraries, as well as the possibility of significantly improving their performance and scalability without caching using PosetHERep