Related papers: A Branch-and-Cut Algorithm for the 2-Species Dupli…
Reconstructing the evolutionary history of a set of species is a central task in computational biology. In real data, it is often the case that some information is missing: the Incomplete Directed Perfect Phylogeny (IDPP) problem asks,…
We give an improved branch-and-bound solver for the multiterminal cut problem, based on the recent work of Henzinger et al.. We contribute new, highly effective data reduction rules to transform the graph into a smaller equivalent instance.…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With…
Linear programming (LP) relaxation is a standard technique for solving hard combinatorial optimization (CO) problems. Here we present a gradient descent algorithm which exploits the special structure of some LP relaxations induced by CO…
The concept of data depth in non-parametric multivariate descriptive statistics is the generalization of the univariate rank method to multivariate data. Halfspace depth is a measure of data depth. Given a set S of points and a point p, the…
A major bottleneck in search-based program synthesis is the exponentially growing search space which makes learning large programs intractable. Humans mitigate this problem by leveraging the compositional nature of the real world: In…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
We tackle the problem of graph partitioning for image segmentation using correlation clustering (CC), which we treat as an integer linear program (ILP). We reformulate optimization in the ILP so as to admit efficient optimization via…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
When applying automatic analysis of fluorescence or histopathological images of cells, it is necessary to partition, or de-clump, partially overlapping cell nuclei. In this work, I describe a method of partitioning partially overlapping…
Practical optimization problems may contain different kinds of difficulties that are often not tractable if one relies on a particular optimization method. Different optimization approaches offer different strengths that are good at…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Model-based deep learning (MBDL) is a powerful methodology for designing deep models to solve imaging inverse problems. MBDL networks can be seen as iterative algorithms that estimate the desired image using a physical measurement model and…
We extend a primal-dual fixed point algorithm (PDFP) proposed in [5] to solve two kinds of separable multi-block minimization problems, arising in signal processing and imaging science. This work shows the flexibility of applying PDFP…
The length-constrained cycle partition problem (LCCP) is a graph optimization problem in which a set of nodes must be partitioned into a minimum number of cycles. Every node is associated with a critical time and the length of every cycle…
We consider the minimum cut problem in undirected, weighted graphs. We give a simple algorithm to find a minimum cut that $2$-respects (cuts two edges of) a spanning tree $T$ of a graph $G$. This procedure can be used in place of the…
The goal of branch length estimation in phylogenetic inference is to estimate the divergence time between a set of sequences based on compositional differences between them. A number of software is currently available facilitating branch…
Most combinatorial optimization problems can be formulated as mixed integer linear programming (MILP), in which branch-and-bound (B\&B) is a general and widely used method. Recently, learning to branch has become a hot research topic in the…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…