Nikita I. Lytkin

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De-novo reverse-engineering of genome-scale regulatory networks is an increasingly important objective for biological and translational research. While many methods have been recently developed for this task, their absolute and relative performance remains poorly understood. The present study conducts a rigorous performance assessment of 32 computational(More)
A recent study reported that gene expression profiles from peripheral blood samples of healthy subjects prior to viral inoculation were indistinguishable from profiles of subjects who received viral challenge but remained asymptomatic and uninfected. If true, this implies that the host immune response does not have a molecular signature. Given the high(More)
BACKGROUND The promise of modern personalized medicine is to use molecular and clinical information to better diagnose, manage, and treat disease, on an individual patient basis. These functions are predominantly enabled by molecular signatures, which are computational models for predicting phenotypes and other responses of interest from high-throughput(More)
Traditional machine learning methods only consider relationships between feature values within individual data instances while disregarding the dependencies that link features across instances. In this work, we develop a general approach to supervised learning by leveraging higher-order dependencies between features. We introduce a novel Bayesian framework(More)
The discovery of molecular pathways is a challenging problem and its solution relies on the identification of causal molecular interactions in genomics data. Causal molecular interactions can be discovered using randomized experiments; however such experiments are often costly, infeasible, or unethical. Fortunately, algorithms that infer causal interactions(More)
GWAS owe their popularity to the expectation that they will make a major impact on diagnosis, prognosis and management of disease by uncovering genetics underlying clinical phenotypes. The dominant paradigm in GWAS data analysis so far consists of extensive reliance on methods that emphasize contribution of individual SNPs to statistical association with(More)
Discovery of causal relations from data is a fundamental objective of several scientific disciplines. Most causal discovery algorithms that use observational data can infer causality only up to a statistical equivalency class, thus leaving many causal relations undetermined. In general, complete identification of causal relations requires experimentation to(More)
Every year, millions of new students enter higher educational programs. Publicly available rankings of academic programs play a key role in prospective students' decisions regarding which universities to apply to and enroll in. While surveys indicate that majority of freshmen enter college to get good jobs after graduation, established methodologies for(More)
The problem of clustering is formulated as the problem of minimization of a certain objective function over the set of all possible clusterings. The objective function measures mathematically the quality of a clustering. According to a previously published theoretical result, if the objective function being minimized is strictly convex, then the(More)