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

Principal manifolds and graphs in practice: from molecular biology to dynamical systems

We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.Comment: 12 pages, 9 figure

Evolutionary Computation and QSAR Research

[Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P

Lung cancer EDA classification using the decision trees method in Python

Cancer is the second leading cause of death worldwide. In Indonesia, it is one of the diseases with a high mortality rate. Most patients are unaware of their lung cancer condition, resulting in delayed treatment. A prediction method with high accuracy is needed for early detection of lung cancer. This study aims to classify lung cancer using the Decision Trees method and perform Exploratory Data Analysis (EDA) using a dataset obtained from Kaggle. The research achieved a high recall value for the positive class (Yes class) but a low recall for the negative class (No class). The study utilized the Decision Trees algorithm known for its good performance. The dataset used includes clinical and demographic information of patients. By building a Decision Trees model, the research successfully classified lung cancer with good accuracy. The EDA results also provided insights into important factors in lung cancer classification. This study has the potential to contribute to the development of predictive models for lung cancer

Bioinformatics Applications Based On Machine Learning

The great advances in information technology (IT) have implications for many sectors, such as bioinformatics, and has considerably increased their possibilities. This book presents a collection of 11 original research papers, all of them related to the application of IT-related techniques within the bioinformatics sector: from new applications created from the adaptation and application of existing techniques to the creation of new methodologies to solve existing problems

Preface

DAMSS-2018 is the jubilee 10th international workshop on data analysis methods for software systems, organized in Druskininkai, Lithuania, at the end of the year. The same place and the same time every year. Ten years passed from the first workshop. History of the workshop starts from 2009 with 16 presentations. The idea of such workshop came up at the Institute of Mathematics and Informatics. Lithuanian Academy of Sciences and the Lithuanian Computer Society supported this idea. This idea got approval both in the Lithuanian research community and abroad. The number of this year presentations is 81. The number of registered participants is 113 from 13 countries. In 2010, the Institute of Mathematics and Informatics became a member of Vilnius University, the largest university of Lithuania. In 2017, the institute changes its name into the Institute of Data Science and Digital Technologies. This name reflects recent activities of the institute. The renewed institute has eight research groups: Cognitive Computing, Image and Signal Analysis, Cyber-Social Systems Engineering, Statistics and Probability, Global Optimization, Intelligent Technologies, Education Systems, Blockchain Technologies. The main goal of the workshop is to introduce the research undertaken at Lithuanian and foreign universities in the fields of data science and software engineering. Annual organization of the workshop allows the fast interchanging of new ideas among the research community. Even 11 companies supported the workshop this year. This means that the topics of the workshop are actual for business, too. Topics of the workshop cover big data, bioinformatics, data science, blockchain technologies, deep learning, digital technologies, high-performance computing, visualization methods for multidimensional data, machine learning, medical informatics, ontological engineering, optimization in data science, business rules, and software engineering. Seeking to facilitate relations between science and business, a special session and panel discussion is organized this year about topical business problems that may be solved together with the research community. This book gives an overview of all presentations of DAMSS-2018.DAMSS-2018 is the jubilee 10th international workshop on data analysis methods for software systems, organized in Druskininkai, Lithuania, at the end of the year. The same place and the same time every year. Ten years passed from the first workshop. History of the workshop starts from 2009 with 16 presentations. The idea of such workshop came up at the Institute of Mathematics and Informatics. Lithuanian Academy of Sciences and the Lithuanian Computer Society supported this idea. This idea got approval both in the Lithuanian research community and abroad. The number of this year presentations is 81. The number of registered participants is 113 from 13 countries. In 2010, the Institute of Mathematics and Informatics became a member of Vilnius University, the largest university of Lithuania. In 2017, the institute changes its name into the Institute of Data Science and Digital Technologies. This name reflects recent activities of the institute. The renewed institute has eight research groups: Cognitive Computing, Image and Signal Analysis, Cyber-Social Systems Engineering, Statistics and Probability, Global Optimization, Intelligent Technologies, Education Systems, Blockchain Technologies. The main goal of the workshop is to introduce the research undertaken at Lithuanian and foreign universities in the fields of data science and software engineering. Annual organization of the workshop allows the fast interchanging of new ideas among the research community. Even 11 companies supported the workshop this year. This means that the topics of the workshop are actual for business, too. Topics of the workshop cover big data, bioinformatics, data science, blockchain technologies, deep learning, digital technologies, high-performance computing, visualization methods for multidimensional data, machine learning, medical informatics, ontological engineering, optimization in data science, business rules, and software engineering. Seeking to facilitate relations between science and business, a special session and panel discussion is organized this year about topical business problems that may be solved together with the research community. This book gives an overview of all presentations of DAMSS-2018

An insight into imbalanced Big Data classification: outcomes and challenges

Big Data applications are emerging during the last years, and researchers from many disciplines are aware of the high advantages related to the knowledge extraction from this type of problem. However, traditional learning approaches cannot be directly applied due to scalability issues. To overcome this issue, the MapReduce framework has arisen as a “de facto” solution. Basically, it carries out a “divide-and-conquer” distributed procedure in a fault-tolerant way to adapt for commodity hardware. Being still a recent discipline, few research has been conducted on imbalanced classification for Big Data. The reasons behind this are mainly the difficulties in adapting standard techniques to the MapReduce programming style. Additionally, inner problems of imbalanced data, namely lack of data and small disjuncts, are accentuated during the data partitioning to fit the MapReduce programming style. This paper is designed under three main pillars. First, to present the first outcomes for imbalanced classification in Big Data problems, introducing the current research state of this area. Second, to analyze the behavior of standard pre-processing techniques in this particular framework. Finally, taking into account the experimental results obtained throughout this work, we will carry out a discussion on the challenges and future directions for the topic.This work has been partially supported by the Spanish Ministry of Science and Technology under Projects TIN2014-57251-P and TIN2015-68454-R, the Andalusian Research Plan P11-TIC-7765, the Foundation BBVA Project 75/2016 BigDaPTOOLS, and the National Science Foundation (NSF) Grant IIS-1447795

Applying Machine Learning Algorithms for the Analysis of Biological Sequences and Medical Records

The modern sequencing technology revolutionizes the genomic research and triggers explosive growth of DNA, RNA, and protein sequences. How to infer the structure and function from biological sequences is a fundamentally important task in genomics and proteomics fields. With the development of statistical and machine learning methods, an integrated and user-friendly tool containing the state-of-the-art data mining methods are needed. Here, we propose SeqFea-Learn, a comprehensive Python pipeline that integrating multiple steps: feature extraction, dimensionality reduction, feature selection, predicting model constructions based on machine learning and deep learning approaches to analyze sequences. We used enhancers, RNA N6- methyladenosine sites and protein-protein interactions datasets to evaluate the validation of the tool. The results show that the tool can effectively perform biological sequence analysis and classification tasks. Applying machine learning algorithms for Electronic medical record (EMR) data analysis is also included in this dissertation. Chronic kidney disease (CKD) is prevalent across the world and well defined by an estimated glomerular filtration rate (eGFR). The progression of kidney disease can be predicted if future eGFR can be accurately estimated using predictive analytics. Thus, I present a prediction model of eGFR that was built using Random Forest regression. The dataset includes demographic, clinical and laboratory information from a regional primary health care clinic. The final model included eGFR, age, gender, body mass index (BMI), obesity, hypertension, and diabetes, which achieved a mean coefficient of determination of 0.95. The estimated eGFRs were used to classify patients into CKD stages with high macro-averaged and micro-averaged metrics