Related papers: From Best Hits to Best Matches
This paper concerns the construction of tests for universal hypothesis testing problems, in which the alternate hypothesis is poorly modeled and the observation space is large. The mismatched universal test is a feature-based technique for…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
Consider a finite set of sources, each producing i.i.d. observations that follow a unique probability distribution on a finite alphabet. We study the problem of matching a finite set of observed sequences to the set of sources under the…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
We consider the problem of search through comparisons, where a user is presented with two candidate objects and reveals which is closer to her intended target. We study adaptive strategies for finding the target, that require knowledge of…
In this paper we deal with contour detection based on the recent image analogy principle which has been successfully used for super-resolution, texture and curves synthesis and interactive editing. Hand-drawn outlines are initially as…
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
We present a method for extracting depth information from a rectified image pair. Our approach focuses on the first stage of many stereo algorithms: the matching cost computation. We approach the problem by learning a similarity measure on…
A novel combination of established data analysis techniques for reconstructing all charged-particle tracks in high energy collisions is proposed. It uses all information available in a collision event while keeping competing choices open as…
Classifier evasion consists in finding for a given instance $x$ the nearest instance $x'$ such that the classifier predictions of $x$ and $x'$ are different. We present two novel algorithms for systematically computing evasions for tree…
Ontology-based approaches for predicting gene-disease associations include the more classical semantic similarity methods and more recently knowledge graph embeddings. While semantic similarity is typically restricted to hierarchical…
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running…
Recognizing symmetries in data allows for significant boosts in neural network training. In many cases, however, the underlying symmetry is present only in an idealized dataset, and is broken in the training data, due to effects such as…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…
Shallow seismic sources excite Rayleigh wave ground motion with azimuthally dependent radiation patterns. We place binary hypothesis tests on theoretical models of such radiation patterns to screen cylindrically symmetric sources (like…
Community detection is one of the most important problems in network analysis. Among many algorithms proposed for this task, methods based on statistical inference are of particular interest: they are mathematically sound and were shown to…
Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This has led to the development of…