Related papers: Cutting an alignment with Ockham's razor
In the computational-mechanics structural analysis of one-dimensional cellular automata the following automata-theoretic analogue of the \emph{change-point problem} from time series analysis arises: \emph{Given a string $\sigma$ and a…
Readout multiplexing is a promising solution to overcome hardware limitations and data bottlenecks in imaging with single-photon detectors. Conventional multiplexed readout processing creates an upper bound on photon counts at a very fine…
The maximum clique problem (MCP) is a fundamental problem in graph theory and in computational complexity. Given a graph G, the problem is that of finding the largest clique (complete subgraph) in G. The MCP has many important applications…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. A standard approach to speed up this task is to compute "sketches" of the DNA reads (typically via…
Balancing assembly lines, a family of optimization problems commonly known as Assembly Line Balancing Problem, is notoriously NP-Hard. They comprise a set of problems of enormous practical interest to manufacturing industry due to the…
Permutation Pattern Matching (or PPM) is a decision problem whose input is a pair of permutations $\pi$ and $\tau$, represented as sequences of integers, and the task is to determine whether $\tau$ contains a subsequence order-isomorphic to…
In this paper, we consider approximability issues of the following four problems: triangle packing, full sibling reconstruction, maximum profit coverage and 2-coverage. All of them are generalized or specialized versions of set-cover and…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
We introduce an evolutionary algorithm called recombinator-$k$-means for optimizing the highly non-convex kmeans problem. Its defining feature is that its crossover step involves all the members of the current generation, stochastically…
Given a set of $n$ points $P$ in the plane, each colored with one of the $t$ given colors, a color-spanning set $S\subset P$ is a subset of $t$ points with distinct colors. The minimum diameter color-spanning set (MDCS) is a color-spanning…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
The most established method of reconstructing neural circuits from animals involves slicing tissue very thin, then taking mosaics of electron microscope (EM) images. To trace neurons across different images and through different sections,…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
We discuss a technique that allows blind recovery of signals or blind identification of mixtures in instances where such recovery or identification were previously thought to be impossible: (i) closely located or highly correlated sources…
Dermoscopy image detection stays a tough task due to the weak distinguishable property of the object.Although the deep convolution neural network signifigantly boosted the performance on prevelance computer vision tasks in recent…
We propose new primal-dual decomposition algorithms for solving systems of inclusions involving sums of linearly composed maximally monotone operators. The principal innovation in these algorithms is that they are block-iterative in the…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
The {\sc $c$-Balanced Separator} problem is a graph-partitioning problem in which given a graph $G$, one aims to find a cut of minimum size such that both the sides of the cut have at least $cn$ vertices. In this paper, we present new…