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HIV dynamical models are often based on non-linear systems of ordinary differential equations (ODE), which do not have analytical solution. Introducing random effects in such models leads to very challenging non-linear mixed-effects models.…
Anomaly detection is a fundamental problem in domains such as healthcare, manufacturing, and cybersecurity. This thesis proposes new unsupervised methods for anomaly detection in both structured and streaming data settings. In the first…
The probability-scale residual (PSR) is well defined across a wide variety of variable types and models, making it useful for studies of HIV/AIDS. In this manuscript, we highlight some of the properties of the PSR and illustrate its…
Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…
Weakly-supervised classification of histopathology slides is a computationally intensive task, with a typical whole slide image (WSI) containing billions of pixels to process. We propose Discriminative Region Active Sampling for Multiple…
Spatial transcriptomics offers spatially resolved gene expression profiling within tissue sections, but its cost and limited throughput hinder large-scale deployment. To extend this capability to routine practice, recent computational…
Definitive cancer diagnosis and management depend upon the extraction of information from microscopy images by pathologists. These images contain complex information requiring time-consuming expert human interpretation that is prone to…
Lung adenocarcinoma (LUAD) is characterized by substantial genetic heterogeneity, posing challenges in identifying reliable biomarkers for improved diagnosis and treatment. Tumor Mutational Burden (TMB) has traditionally been regarded as a…
Modeling viral dynamics in HIV/AIDS studies has resulted in a deep understanding of pathogenesis of HIV infection from which novel antiviral treatment guidance and strategies have been derived. Viral dynamics models based on nonlinear…
The primary goal of public health efforts to control HIV epidemics is to diagnose and treat people with HIV infection as soon as possible after seroconversion. The timing of initiation of antiretroviral therapy (ART) treatment after HIV…
We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic…
Network surveys of key populations at risk for HIV are an essential part of the effort to understand how the epidemic spreads and how it can be prevented. Estimation of population values from the sample data has been probematical, however,…
We study Eigen's model of quasi-species, characterized by sequences that replicate with a specified fitness and mutate independently at single sites. The evolution of the population vector in time is then closely related to that of quantum…
In recent years the importance of finding a meaningful pattern from huge datasets has become more challenging. Data miners try to adopt innovative methods to face this problem by applying feature selection methods. In this paper we propose…
Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…
With an increasing focus on precision medicine in medical research, numerous studies have been conducted in recent years to clarify the relationship between treatment effects and patient characteristics. The treatment effects for patients…
During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Chromosomal DNA is characterized by variation between individuals at the level of entire chromosomes (e.g., aneuploidy in which the chromosome copy number is altered), segmental changes (including insertions, deletions, inversions, and…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…