Related papers: PCA and K-Means decipher genome

An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…

A general asymptotic framework is developed for studying consis- tency properties of principal component analysis (PCA). Our frame- work includes several previously studied domains of asymptotics as special cases and allows one to…

We consider the problem of learning a mixture of Random Utility Models (RUMs). Despite the success of RUMs in various domains and the versatility of mixture RUMs to capture the heterogeneity in preferences, there has been only limited…

Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…

We propose a spectral clustering method based on local principal components analysis (PCA). After performing local PCA in selected neighborhoods, the algorithm builds a nearest neighbor graph weighted according to a discrepancy between the…

Kernel methods have been proven to be a powerful tool for the integration and analysis of highthroughput technologies generated data. Kernels offer a nonlinear version of any linear algorithm solely based on dot products. The kernelized…

Segmentation of Prostate Cancer (PCa) tissues from Gleason graded histopathology images is vital for accurate diagnosis. Although deep learning (DL) based segmentation methods achieve state-of-the-art accuracy, they rely on large datasets…

This paper presents a new statistical method for clustering step data, a popular form of health record data easily obtained from wearable devices. Since step data are high-dimensional and zero-inflated, classical methods such as K-means and…

We present quasicyclic principal component analysis (QPCA), a generalization of principal component analysis (PCA), that determines an optimized basis for a dataset in terms of families of shift-orthogonal principal vectors. This is of…

High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…

Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…

We introduce a variant of (sparse) PCA in which the set of feasible support sets is determined by a graph. In particular, we consider the following setting: given a directed acyclic graph $G$ on $p$ vertices corresponding to variables, the…

Principal Component Analysis (PCA) is an important tool of dimension reduction especially when the dimension (or the number of variables) is very high. Asymptotic studies where the sample size is fixed, and the dimension grows [i.e., High…

We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…

Clustering, a fundamental activity in unsupervised learning, is notoriously difficult when the feature space is high-dimensional. Fortunately, in many realistic scenarios, only a handful of features are relevant in distinguishing clusters.…

To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis. We show that the…

Random walks can reveal communities or clusters in networks, because they are more likely to stay within a cluster than leave it. Thus, one family of community detection algorithms uses random walks to measure distance between pairs of…

Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…

In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…

Graph-based subspace clustering methods have exhibited promising performance. However, they still suffer some of these drawbacks: encounter the expensive time overhead, fail in exploring the explicit clusters, and cannot generalize to…