Related papers: Cutting an alignment with Ockham's razor
The insertion-deletion channel takes as input a bit string ${\bf x}\in\{0,1\}^{n}$, and outputs a string where bits have been deleted and inserted independently at random. The trace reconstruction problem is to recover $\bf x$ from many…
Sparse optimization is a central problem in machine learning and computer vision. However, this problem is inherently NP-hard and thus difficult to solve in general. Combinatorial search methods find the global optimal solution but are…
Piecewise linearization is a key technique for solving nonlinear problems in transportation network design and other optimization fields, in which generating breakpoints is a fundamental task. This paper proposes an optimal breakpoint…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
Protein/Peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and highthroughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having…
In the multiple changepoint setting, various search methods have been proposed which involve optimising either a constrained or penalised cost function over possible numbers and locations of changepoints using dynamic programming. Such…
Proximal splitting algorithms for monotone inclusions (and convex optimization problems) in Hilbert spaces share the common feature to guarantee for the generated sequences in general weak convergence to a solution. In order to achieve…
V. Levenshtein first proposed the sequence reconstruction problem in 2001. This problem studies the model where the same sequence from some set is transmitted over multiple channels, and the decoder receives the different outputs. Assume…
The longest arc-preserving common subsequence problem is an NP-hard combinatorial optimization problem from the field of computational biology. This problem finds applications, in particular, in the comparison of arc-annotated Ribonucleic…
In the Minimum Bisection problem, input is a graph $G$ and the goal is to partition the vertex set into two parts $A$ and $B$, such that $||A|-|B|| \le 1$ and the number $k$ of edges between $A$ and $B$ is minimized. This problem can be…
Meaningful comparison between sets of observations often necessitates alignment or registration between them, and the resulting optimization problems range in complexity from those admitting simple closed-form solutions to those requiring…
We consider the Minimum Convex Partition problem: Given a set P of n points in the plane, draw a plane graph G on P, with positive minimum degree, such that G partitions the convex hull of P into a minimum number of convex faces. We show…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
In the Minimum Common String Partition Problem (MCSP), we are given two strings on input, and we want to partition both into the same collection of substrings, minimizing the number of the substrings in the partition. This combinatorial…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
Polynomial systems occur in many areas of science and engineering. Unlike general nonlinear systems, the algebraic structure enables to compute all solutions of a polynomial system. We describe our massive parallel predictor-corrector…
Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
In several multiobjective decision problems Pairwise Comparison Matrices (PCM) are applied to evaluate the decision variants. The problem that arises very often is the inconsistency of a given PCM. In such a situation it is important to…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…