Related papers: kruX: Matrix-based non-parametric eQTL discovery
Cross-graph Relational Learning (CGRL) refers to the problem of predicting the strengths or labels of multi-relational tuples of heterogeneous object types, through the joint inference over multiple graphs which specify the internal…
We consider the problem of estimating the number of clusters (k) in a dataset. We propose a non-parametric approach to the problem that utilizes similarity graphs to construct a robust statistic that effectively captures similarity…
In the recent past, automatic selection or combination of kernels (or features) based on multiple kernel learning (MKL) approaches has been receiving significant attention from various research communities. Though MKL has been extensively…
This paper proposes a new deep-learning method to construct test statistics by computer vision and metrics learning. The application highlighted in this paper is applying computer vision on Q-Q plot to construct a new test statistic for…
We present a new computational scheme that enables efficient and reliable Quantitative Trait Loci (QTL) scans for experimental populations. Using a standard brute-force exhaustive search effectively prohibits accurate QTL scans involving…
Admixture mapping is a popular tool to identify regions of the genome associated with traits in a recently admixed population. Existing methods have been developed primarily for identification of a single locus influencing a dichotomous…
Transcriptome-wide association studies (TWAS) are powerful tools for identifying gene-level associations by integrating genome-wide association studies and gene expression data. However, most TWAS methods focus on linear associations…
Most statistical methods for QTL mapping focus on a single phenotype. However, multiple phenotypes are commonly measured, and recent technological advances have greatly simplified the automated acquisition of numerous phenotypes, including…
We apply our statistically deterministic machine learning/clustering algorithm *K-means (recently developed in https://ssrn.com/abstract=2908286) to 10,656 published exome samples for 32 cancer types. A majority of cancer types exhibit…
Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression…
Adaptive Random Testing (ART) has faced criticism, particularly for its computational inefficiency, as highlighted by Arcuri and Briand. Their analysis clarified how ART requires a quadratic number of distance computations as the number of…
A genome-wide association study (GWAS) correlates marker variation with trait variation in a sample of individuals. Each study subject is genotyped at a multitude of SNPs (single nucleotide polymorphisms) spanning the genome. Here we assume…
Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the…
Genetic association study is an essential step to discover genetic factors that are associated with a complex trait of interest. In this paper we present a novel generalized quasi-likelihood score (GQLS) test that is suitable for a study…
Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population-genetic test for…
In this paper we propose a Multiple kernel testing procedure to infer survival data when several factors (e.g. different treatment groups, gender, medical history) and their interaction are of interest simultaneously. Our method is able to…
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…
The Genotype-Tissue Expression (GTEx) project collects samples from multiple human tissues to study the relationship between genetic variation or single nucleotide polymorphisms (SNPs) and gene expression in each tissue. However, most…
Nonparametric tests for functional data are a challenging class of tests to work with because of the potentially high dimensional nature of the data. One of the main challenges for considering rank-based tests, like the Mann-Whitney or…
Principled nonparametric tests for regression curvature in $\mathbb{R}^{d}$ are often statistically and computationally challenging. This paper introduces the stratified incomplete local simplex (SILS) tests for joint concavity of…