Identifying drug-target and drug-disease associations using computational intelligence

Background: Traditional drug development is an expensive process that typically requires the investment of a large number of resources in terms of finances, equipment, and time. However, sometimes these efforts do not result in a pharmaceutical product in the market. To overcome the limitations of this process, complementary—or in some cases, alternative—methods with high-throughput results are necessary. Computational drug discovery is a shortcut that can reduce the difficulties of traditional methods because of its flexible nature. Drug repositioning, which aims to find new applications for existing drugs, is one of the promising approaches in computational drug discovery. Considering the availability of different types of data in various public databases, drug-disease association identification and drug repositioning can be performed based on the interaction of drugs and biomolecules. Moreover, drug repositioning mainly focuses on the similarity of drugs and the similarity of agents interacting with drugs. It is assumed that if drug D is associated or interacts with target T, then drugs similar to drug D can be associated or interact with target T or targets similar to target T. Therefore, similarity-based approaches are widely used for drug repositioning. Research Objectives: Develop novel computational methods for drug-target and drug-disease association prediction to be used for drug repositioning. Results: In this thesis, the problem of drug-disease association identification and drug repositioning is divided into sub-problems. These sub-problems include drug-target interaction prediction and using targets as intermediaries for drug-disease association identification. Addressing these subproblems results in the development of three new computational models for drug-target interaction and drug-disease association prediction: MDIPA, NMTF-DTI, and NTD-DR. MDIPA is a nonnegative matrix factorization-based method to predict interaction scores of drug-microRNA pairs, where the interaction scores can effectively be used for drug repositioning. This method uses the functional similarity of microRNAs and structural similarity of drugs to make predictions. To include more biomolecules (e.g., proteins) in the study as well as achieve a more flexible model, we develop NMTF-DTI. This nonnegative matrix tri- factorization method uses multiple types of similarities for drugs and proteins to predict the associations between drugs and targets and their interaction score. To take another step towards drug repositioning, we identify the associations between drugs and disease. In this step, we develop NTD-DR, a nonnegative tensor decomposition approach where multiple similarities for drugs, targets, and diseases are used to identify the associations between drugs and diseases to be used for drug repositioning. The detail of each method is discussed in Chapters 3, 4, 5, respectively. Future work will focus on considering additional biomolecules as the drug target to identify drug-disease associations for drug repositioning. In summary, using nonnegative matrix factorization, nonnegative matrix tri-factorization, and nonnegative tensor decomposition, as well as applying different types of association information and multiple types of similarities, improve the performance of proposed methods over those methods that use single association or similarity information

Adapting Community Detection Approaches to Large, Multilayer, and Attributed Networks

Networks have become a common data mining tool to encode relational definitions between a set of entities. Whether studying biological correlations, or communication between individuals in a social network, network analysis tools enable interpretation, prediction, and visualization of patterns in the data. Community detection is a well-developed subfield of network analysis, where the objective is to cluster nodes into 'communities' based on their connectivity patterns. There are many useful and robust approaches for identifying communities in a single, moderately-sized network, but the ability to work with more complicated types of networks containing extra or a large amount of information poses challenges. In this thesis, we address three types of challenging network data and how to adapt standard community detection approaches to handle these situations. In particular, we focus on networks that are large, attributed, and multilayer. First, we present a method for identifying communities in multilayer networks, where there exist multiple relational definitions between a set of nodes. Next, we provide a pre-processing technique for reducing the size of large networks, where standard community detection approaches might have inconsistent results or be prohibitively slow. We then introduce an extension to a probabilistic model for community structure to take into account node attribute information and develop a test to quantify the extent to which connectivity and attribute information align. Finally, we demonstrate example applications of these methods in biological and social networks. This work helps to advance the understand of network clustering, network compression, and the joint modeling of node attributes and network connectivity.Doctor of Philosoph

Generalized averaged Gaussian quadrature and applications

A simple numerical method for constructing the optimal generalized averaged Gaussian quadrature formulas will be presented. These formulas exist in many cases in which real positive GaussKronrod formulas do not exist, and can be used as an adequate alternative in order to estimate the error of a Gaussian rule. We also investigate the conditions under which the optimal averaged Gaussian quadrature formulas and their truncated variants are internal

MS FT-2-2 7 Orthogonal polynomials and quadrature: Theory, computation, and applications

Quadrature rules find many applications in science and engineering. Their analysis is a classical area of applied mathematics and continues to attract considerable attention. This seminar brings together speakers with expertise in a large variety of quadrature rules. It is the aim of the seminar to provide an overview of recent developments in the analysis of quadrature rules. The computation of error estimates and novel applications also are described

Pacific Symposium on Biocomputing 2023

The Pacific Symposium on Biocomputing (PSB) 2023 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2023 will be held on January 3-7, 2023 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2023 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field

Recent Advances in Social Data and Artificial Intelligence 2019

The importance and usefulness of subjects and topics involving social data and artificial intelligence are becoming widely recognized. This book contains invited review, expository, and original research articles dealing with, and presenting state-of-the-art accounts pf, the recent advances in the subjects of social data and artificial intelligence, and potentially their links to Cyberspace

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods