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Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…

Coronavirus disease (Covid-19) has been the main agenda of the whole world since it came in sight in December 2019. It has already caused thousands of causalities and infected several millions worldwide. Any technological tool that can be…

Kernel embeddings have emerged as a powerful tool for representing probability measures in a variety of statistical inference problems. By mapping probability measures into a reproducing kernel Hilbert space (RKHS), kernel embeddings enable…

Novel Coronavirus disease (COVID-19) is an extremely contagious and quickly spreading Coronavirus infestation. Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), which outbreak in 2002 and 2011, and the…

Efficient categorization of historical documents is crucial for fields such as genealogy, legal research, and historical scholarship, where manual classification is impractical for large collections due to its labor-intensive and…

This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity…

Hawkes stochastic point process models have emerged as valuable statistical tools for analyzing viral contagion. The spatiotemporal Hawkes process characterizes the speeds at which viruses spread within human populations. Unfortunately,…

Surges that have been observed at different periods in the number of COVID-19 cases are associated with the emergence of multiple SARS-CoV-2 (Severe Acute Respiratory Virus) variants. The design of methods to support laboratory detection…

Information retrieval with compact binary embeddings, also referred to as hashing, is crucial for scalable fast search applications, yet state-of-the-art hashing methods require expensive, scenario-specific training. In this work, we…

Future SARS-CoV-2 virus outbreak COVID-XX might possibly occur during the next years. However the pathology in humans is so recent that many clinical aspects, like early detection of complications, side effects after recovery or early…

Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…

The new Coronavirus is spreading rapidly, and it has taken the lives of many people so far. The virus has destructive effects on the human lung, and early detection is very important. Deep Convolution neural networks are such powerful tools…

In supervised learning with distributional inputs in the two-stage sampling setup, relevant to applications like learning-based medical screening or causal learning, the inputs (which are probability distributions) are not accessible in the…

With the ongoing global pandemic of coronavirus disease 2019 (COVID-19), there is an increasing quest for more accessible, easy-to-use, rapid, inexpensive, and high accuracy diagnostic tools. Traditional disease diagnostic methods such as…

Network embedding approaches are gaining momentum to analyse a large variety of networks. Indeed, these approaches have demonstrated their efficiency for tasks such as community detection, node classification, and link prediction. However,…

Given the severity of the SARS-CoV-2 pandemic, a major challenge is to rapidly repurpose existing approved drugs for clinical interventions. While a number of data-driven and experimental approaches have been suggested in the context of…

Vector data is prevalent across business and scientific applications, and its popularity is growing with the proliferation of learned embeddings. Vector data collections often reach billions of vectors with thousands of dimensions, thus,…

Machine learning and deep learning play vital roles in predicting diseases in the medical field. Machine learning algorithms are widely classified as supervised, unsupervised, and reinforcement learning. This paper contains a detailed…

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…