Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference

El documento solamente contiene el resumen de la ponenciaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET)UCR::Vicerrectoría de Docencia::Salud::Facultad de Microbiologí

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested

Big data analytics for preventive medicine

© 2019, Springer-Verlag London Ltd., part of Springer Nature. Medical data is one of the most rewarding and yet most complicated data to analyze. How can healthcare providers use modern data analytics tools and technologies to analyze and create value from complex data? Data analytics, with its promise to efficiently discover valuable pattern by analyzing large amount of unstructured, heterogeneous, non-standard and incomplete healthcare data. It does not only forecast but also helps in decision making and is increasingly noticed as breakthrough in ongoing advancement with the goal is to improve the quality of patient care and reduces the healthcare cost. The aim of this study is to provide a comprehensive and structured overview of extensive research on the advancement of data analytics methods for disease prevention. This review first introduces disease prevention and its challenges followed by traditional prevention methodologies. We summarize state-of-the-art data analytics algorithms used for classification of disease, clustering (unusually high incidence of a particular disease), anomalies detection (detection of disease) and association as well as their respective advantages, drawbacks and guidelines for selection of specific model followed by discussion on recent development and successful application of disease prevention methods. The article concludes with open research challenges and recommendations

Big data analytics in computational biology and bioinformatics

Big data analytics in computational biology and bioinformatics refers to an array of operations including biological pattern discovery, classification, prediction, inference, clustering as well as data mining in the cloud, among others. This dissertation addresses big data analytics by investigating two important operations, namely pattern discovery and network inference. The dissertation starts by focusing on biological pattern discovery at a genomic scale. Research reveals that the secondary structure in non-coding RNA (ncRNA) is more conserved during evolution than its primary nucleotide sequence. Using a covariance model approach, the stems and loops of an ncRNA secondary structure are represented as a statistical image against which an entire genome can be efficiently scanned for matching patterns. The covariance model approach is then further extended, in combination with a structural clustering algorithm and a random forests classifier, to perform genome-wide search for similarities in ncRNA tertiary structures. The dissertation then presents methods for gene network inference. Vast bodies of genomic data containing gene and protein expression patterns are now available for analysis. One challenge is to apply efficient methodologies to uncover more knowledge about the cellular functions. Very little is known concerning how genes regulate cellular activities. A gene regulatory network (GRN) can be represented by a directed graph in which each node is a gene and each edge or link is a regulatory effect that one gene has on another gene. By evaluating gene expression patterns, researchers perform in silico data analyses in systems biology, in particular GRN inference, where the “reverse engineering” is involved in predicting how a system works by looking at the system output alone. Many algorithmic and statistical approaches have been developed to computationally reverse engineer biological systems. However, there are no known bioin-formatics tools capable of performing perfect GRN inference. Here, extensive experiments are conducted to evaluate and compare recent bioinformatics tools for inferring GRNs from time-series gene expression data. Standard performance metrics for these tools based on both simulated and real data sets are generally low, suggesting that further efforts are needed to develop more reliable GRN inference tools. It is also observed that using multiple tools together can help identify true regulatory interactions between genes, a finding consistent with those reported in the literature. Finally, the dissertation discusses and presents a framework for parallelizing GRN inference methods using Apache Hadoop in a cloud environment

Identification and characterization of diseases on social web

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CREATE: Concept Representation and Extraction from Heterogeneous Evidence

Traditional information retrieval methodology is guided by document retrieval paradigm, where relevant documents are returned in response to user queries. This paradigm faces serious drawback if the desired result is not explicitly present in a single document. The problem becomes more obvious when a user tries to obtain complete information about a real world entity, such as person, company, location etc. In such cases, various facts about the target entity or concept need to be gathered from multiple document sources. In this work, we present a method to extract information about a target entity based on the concept retrieval paradigm that focuses on extracting and blending information related to a concept from multiple sources if necessary. The paradigm is built around a generic notion of concept which is defined as any item that can be thought of as a topic of interest. Concepts may correspond to any real world entity such as restaurant, person, city, organization, etc, or any abstract item such as news topic, event, theory, etc. Web is a heterogeneous collection of data in different forms such as facts, news, opinions etc. We propose different models for different forms of data, all of which work towards the same goal of concept centric retrieval. We motivate our work based on studies about current trends and demands for information seeking. The framework helps in understanding the intent of content, i.e. opinion versus fact. Our work has been conducted on free text data in English. Nevertheless, our framework can be easily transferred to other languages

Aggregation of biological knowledge for immunological and virological applications

Ph.DDOCTOR OF PHILOSOPH

Open Data

Open data is freely usable, reusable, or redistributable by anybody, provided there are safeguards in place that protect the data’s integrity and transparency. This book describes how data retrieved from public open data repositories can improve the learning qualities of digital networking, particularly performance and reliability. Chapters address such topics as knowledge extraction, Open Government Data (OGD), public dashboards, intrusion detection, and artificial intelligence in healthcare