Related papers: On the Approximability of Comparing Genomes with D…
We consider the problem of breakpoint detection in a regression modeling framework. To that end, we introduce a novel method, the max-EM algorithm which combines a constrained Hidden Markov Model with the Classification-EM (CEM) algorithm.…
Changepoint detection methods are used in many areas of science and engineering, e.g., in the analysis of copy number variation data, to detect abnormalities in copy numbers along the genome. Despite the broad array of available tools,…
The growing amount of applications that generate vast amount of data in short time scales render the problem of partial monitoring, coupled with prediction, a rather fundamental one. We study the aforementioned canonical problem under the…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Tolerance graphs model interval relations in such a way that intervals can tolerate a certain amount of overlap without being in conflict. In one of the most natural generalizations of tolerance graphs with direct applications in the…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Equivalence testing, a fundamental problem in the field of distribution testing, seeks to infer if two unknown distributions on $[n]$ are the same or far apart in the total variation distance. Conditional sampling has emerged as a powerful…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
We consider the problem of hypothesis testing for discrete distributions. In the standard model, where we have sample access to an underlying distribution $p$, extensive research has established optimal bounds for uniformity testing,…
In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance…
Changepoint detection is commonly formulated by minimizing the sum of in-sample losses to quantify the model's overall fit. However, for flexible modeling procedures -- especially those involving high-dimensional parameter spaces or…
The graph is one of the most widely used mathematical structures in engineering and science because of its representational power and inherent ability to demonstrate the relationship between objects. The objective of this work is to…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…
Finding correspondences between shapes is a fundamental problem in computer vision and graphics, which is relevant for many applications, including 3D reconstruction, object tracking, and style transfer. The vast majority of correspondence…
This paper introduces the \emph{$d$-distance $b$-matching problem}, in which we are given a bipartite graph $G=(S,T;E)$ with $S=\{s_1,\dots,s_n\}$, a weight function on the edges, an integer $d\in\mathbb{Z}_+$ and a degree bound function…
Diagnostic accuracy studies assess sensitivity and specificity of a new index test in relation to an established comparator or the reference standard. The development and selection of the index test is usually assumed to be conducted prior…
Multiple kernel learning algorithms are proposed to combine kernels in order to obtain a better similarity measure or to integrate feature representations coming from different data sources. Most of the previous research on such methods is…