Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Mining a Small Medical Data Set by Integrating the Decision Tree and t-test

[[abstract]]Although several researchers have used statistical methods to prove that aspiration followed by the injection of 95% ethanol left in situ (retention) is an effective treatment for ovarian endometriomas, very few discuss the different conditions that could generate different recovery rates for the patients. Therefore, this study adopts the statistical method and decision tree techniques together to analyze the postoperative status of ovarian endometriosis patients under different conditions. Since our collected data set is small, containing only 212 records, we use all of these data as the training data. Therefore, instead of using a resultant tree to generate rules directly, we use the value of each node as a cut point to generate all possible rules from the tree first. Then, using t-test, we verify the rules to discover some useful description rules after all possible rules from the tree have been generated. Experimental results show that our approach can find some new interesting knowledge about recurrent ovarian endometriomas under different conditions.[[journaltype]]國外[[incitationindex]]EI[[booktype]]紙本[[countrycodes]]FI

A Short Survey on Data Clustering Algorithms

With rapidly increasing data, clustering algorithms are important tools for data analytics in modern research. They have been successfully applied to a wide range of domains; for instance, bioinformatics, speech recognition, and financial analysis. Formally speaking, given a set of data instances, a clustering algorithm is expected to divide the set of data instances into the subsets which maximize the intra-subset similarity and inter-subset dissimilarity, where a similarity measure is defined beforehand. In this work, the state-of-the-arts clustering algorithms are reviewed from design concept to methodology; Different clustering paradigms are discussed. Advanced clustering algorithms are also discussed. After that, the existing clustering evaluation metrics are reviewed. A summary with future insights is provided at the end

A Multiobjective Evolutionary Conceptual Clustering Methodology for Gene Annotation Within Structural Databases: A Case of Study on the Gene Ontology Database

Current tools and techniques devoted to examine the content of large databases are often hampered by their inability to support searches based on criteria that are meaningful to their users. These shortcomings are particularly evident in data banks storing representations of structural data such as biological networks. Conceptual clustering techniques have demonstrated to be appropriate for uncovering relationships between features that characterize objects in structural data. However, typical con ceptual clustering approaches normally recover the most obvious relations, but fail to discover the lessfrequent but more informative underlying data associations. The combination of evolutionary algorithms with multiobjective and multimodal optimization techniques constitutes a suitable tool for solving this problem. We propose a novel conceptual clustering methodology termed evolutionary multiobjective conceptual clustering (EMO-CC), re lying on the NSGA-II multiobjective (MO) genetic algorithm. We apply this methodology to identify conceptual models in struc tural databases generated from gene ontologies. These models can explain and predict phenotypes in the immunoinflammatory response problem, similar to those provided by gene expression or other genetic markers. The analysis of these results reveals that our approach uncovers cohesive clusters, even those comprising a small number of observations explained by several features, which allows describing objects and their interactions from different perspectives and at different levels of detail.Ministerio de Ciencia y Tecnología TIC-2003-00877Ministerio de Ciencia y Tecnología BIO2004-0270EMinisterio de Ciencia y Tecnología TIN2006-1287

A review on the application of evolutionary computation to information retrieval

In this contribution, different proposals found in the specialized literature for the application of evolutionary computation to the field of information retrieval will be reviewed. To do so, different kinds of IR problems that have been solved by evolutionary algorithms are analyzed. Some of the specific existing approaches will be specifically described for some of these problems and the obtained results will be critically evaluated in order to give a clear view of the topic to the reader.CICYT under project TIC2002-03276University of Granada under project ‘‘Mejora de Metaheur ısticas mediante Hibridaci on y sus Aplicaciones

Cooperative Metaheuristics for Exploring Proteomic Data

Most combinatorial optimization problems cannotbe solved exactly. A class of methods, calledmetaheuristics, has proved its efficiency togive good approximated solutions in areasonable time. Cooperative metaheuristics area sub-set of metaheuristics, which implies aparallel exploration of the search space byseveral entities with information exchangebetween them. The importance of informationexchange in the optimization process is relatedto the building block hypothesis ofevolutionary algorithms, which is based onthese two questions: what is the pertinentinformation of a given potential solution andhow this information can be shared? Aclassification of cooperative metaheuristicsmethods depending on the nature of cooperationinvolved is presented and the specificproperties of each class, as well as a way tocombine them, is discussed. Severalimprovements in the field of metaheuristics arealso given. In particular, a method to regulatethe use of classical genetic operators and todefine new more pertinent ones is proposed,taking advantage of a building block structuredrepresentation of the explored space. Ahierarchical approach resting on multiplelevels of cooperative metaheuristics is finallypresented, leading to the definition of acomplete concerted cooperation strategy. Someapplications of these concepts to difficultproteomics problems, including automaticprotein identification, biological motifinference and multiple sequence alignment arepresented. For each application, an innovativemethod based on the cooperation concept isgiven and compared with classical approaches.In the protein identification problem, a firstlevel of cooperation using swarm intelligenceis applied to the comparison of massspectrometric data with biological sequencedatabase, followed by a genetic programmingmethod to discover an optimal scoring function.The multiple sequence alignment problem isdecomposed in three steps involving severalevolutionary processes to infer different kindof biological motifs and a concertedcooperation strategy to build the sequencealignment according to their motif conten

Recuperação multimodal e interativa de informação orientada por diversidade

Orientador: Ricardo da Silva TorresTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Os métodos de Recuperação da Informação, especialmente considerando-se dados multimídia, evoluíram para a integração de múltiplas fontes de evidência na análise de relevância de itens em uma tarefa de busca. Neste contexto, para atenuar a distância semântica entre as propriedades de baixo nível extraídas do conteúdo dos objetos digitais e os conceitos semânticos de alto nível (objetos, categorias, etc.) e tornar estes sistemas adaptativos às diferentes necessidades dos usuários, modelos interativos que consideram o usuário mais próximo do processo de recuperação têm sido propostos, permitindo a sua interação com o sistema, principalmente por meio da realimentação de relevância implícita ou explícita. Analogamente, a promoção de diversidade surgiu como uma alternativa para lidar com consultas ambíguas ou incompletas. Adicionalmente, muitos trabalhos têm tratado a ideia de minimização do esforço requerido do usuário em fornecer julgamentos de relevância, à medida que mantém níveis aceitáveis de eficácia. Esta tese aborda, propõe e analisa experimentalmente métodos de recuperação da informação interativos e multimodais orientados por diversidade. Este trabalho aborda de forma abrangente a literatura acerca da recuperação interativa da informação e discute sobre os avanços recentes, os grandes desafios de pesquisa e oportunidades promissoras de trabalho. Nós propusemos e avaliamos dois métodos de aprimoramento do balanço entre relevância e diversidade, os quais integram múltiplas informações de imagens, tais como: propriedades visuais, metadados textuais, informação geográfica e descritores de credibilidade dos usuários. Por sua vez, como integração de técnicas de recuperação interativa e de promoção de diversidade, visando maximizar a cobertura de múltiplas interpretações/aspectos de busca e acelerar a transferência de informação entre o usuário e o sistema, nós propusemos e avaliamos um método multimodal de aprendizado para ranqueamento utilizando realimentação de relevância sobre resultados diversificados. Nossa análise experimental mostra que o uso conjunto de múltiplas fontes de informação teve impacto positivo nos algoritmos de balanceamento entre relevância e diversidade. Estes resultados sugerem que a integração de filtragem e re-ranqueamento multimodais é eficaz para o aumento da relevância dos resultados e também como mecanismo de potencialização dos métodos de diversificação. Além disso, com uma análise experimental minuciosa, nós investigamos várias questões de pesquisa relacionadas à possibilidade de aumento da diversidade dos resultados e a manutenção ou até mesmo melhoria da sua relevância em sessões interativas. Adicionalmente, nós analisamos como o esforço em diversificar afeta os resultados gerais de uma sessão de busca e como diferentes abordagens de diversificação se comportam para diferentes modalidades de dados. Analisando a eficácia geral e também em cada iteração de realimentação de relevância, nós mostramos que introduzir diversidade nos resultados pode prejudicar resultados iniciais, enquanto que aumenta significativamente a eficácia geral em uma sessão de busca, considerando-se não apenas a relevância e diversidade geral, mas também o quão cedo o usuário é exposto ao mesmo montante de itens relevantes e nível de diversidadeAbstract: Information retrieval methods, especially considering multimedia data, have evolved towards the integration of multiple sources of evidence in the analysis of the relevance of items considering a given user search task. In this context, for attenuating the semantic gap between low-level features extracted from the content of the digital objects and high-level semantic concepts (objects, categories, etc.) and making the systems adaptive to different user needs, interactive models have brought the user closer to the retrieval loop allowing user-system interaction mainly through implicit or explicit relevance feedback. Analogously, diversity promotion has emerged as an alternative for tackling ambiguous or underspecified queries. Additionally, several works have addressed the issue of minimizing the required user effort on providing relevance assessments while keeping an acceptable overall effectiveness. This thesis discusses, proposes, and experimentally analyzes multimodal and interactive diversity-oriented information retrieval methods. This work, comprehensively covers the interactive information retrieval literature and also discusses about recent advances, the great research challenges, and promising research opportunities. We have proposed and evaluated two relevance-diversity trade-off enhancement work-flows, which integrate multiple information from images, such as: visual features, textual metadata, geographic information, and user credibility descriptors. In turn, as an integration of interactive retrieval and diversity promotion techniques, for maximizing the coverage of multiple query interpretations/aspects and speeding up the information transfer between the user and the system, we have proposed and evaluated a multimodal learning-to-rank method trained with relevance feedback over diversified results. Our experimental analysis shows that the joint usage of multiple information sources positively impacted the relevance-diversity balancing algorithms. Our results also suggest that the integration of multimodal-relevance-based filtering and reranking was effective on improving result relevance and also boosted diversity promotion methods. Beyond it, with a thorough experimental analysis we have investigated several research questions related to the possibility of improving result diversity and keeping or even improving relevance in interactive search sessions. Moreover, we analyze how much the diversification effort affects overall search session results and how different diversification approaches behave for the different data modalities. By analyzing the overall and per feedback iteration effectiveness, we show that introducing diversity may harm initial results whereas it significantly enhances the overall session effectiveness not only considering the relevance and diversity, but also how early the user is exposed to the same amount of relevant items and diversityDoutoradoCiência da ComputaçãoDoutor em Ciência da ComputaçãoP-4388/2010140977/2012-0CAPESCNP

A Review on Advanced Decision Trees for Efficient & Effective k-NN Classification

K Nearest Neighbor (KNN) strategy is a notable classification strategy in data mining and estimations in light of its direct execution and colossal arrangement execution. In any case, it is outlandish for ordinary KNN strategies to select settled k esteem to all tests. Past courses of action assign different k esteems to different test tests by the cross endorsement strategy however are typically tedious. This work proposes new KNN strategies, first is a KTree strategy to learn unique k esteems for different test or new cases, by including a training arrange in the KNN classification. This work additionally proposes a change rendition of KTree technique called K*Tree to speed its test organize by putting additional data of the training tests in the leaf node of KTree, for example, the training tests situated in the leaf node, their KNNs, and the closest neighbor of these KNNs. K*Tree, which empowers to lead KNN arrangement utilizing a subset of the training tests in the leaf node instead of all training tests utilized in the recently KNN techniques. This really reduces the cost of test organize