Related papers: Minimum Segmentation for Pan-genomic Founder Recon…

In this paper, we consider a class of structured nonsmooth fractional minimization, where the first part of the objective is the ratio of a nonnegative nonsmooth nonconvex function to a nonnegative nonsmooth convex function, while the…

In this work, we develop a fast hierarchical solver for solving large, sparse least squares problems. We build upon the algorithm, spaQR (sparsified QR), that was developed by the authors to solve large sparse linear systems. Our algorithm…

he segment minimization problem consists of finding the smallest set of integer matrices that sum to a given intensity matrix, such that each summand has only one non-zero value, and the non-zeroes in each row are consecutive. This has…

We give the first almost-linear time algorithms for several problems in incremental graphs including cycle detection, strongly connected component maintenance, $s$-$t$ shortest path, maximum flow, and minimum-cost flow. To solve these…

In this paper, we propose a unified energy minimization model for the segmentation of non-smooth image structures. The energy of piecewise linear patch reconstruction is considered as an objective measure of the quality of the segmentation…

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…

For a given $n$, what is the smallest number $k$ such that every sequence of length $n$ is determined by the multiset of all its $k$-subsequences? This is called the $k$-deck problem for sequence reconstruction, and has been generalized to…

In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…

Consider a set $P$ of $n$ points in $\mathbb{R}^d$. In the discrete median line segment problem, the objective is to find a line segment bounded by a pair of points in $P$ such that the sum of the Euclidean distances from $P$ to the line…

A spanner of a graph is a subgraph that preserves lengths of shortest paths up to a multiplicative distortion. For every $k$, a spanner with size $O(n^{1+1/k})$ and stretch $(2k+1)$ can be constructed by a simple centralized greedy…

We present a nearly-linear time algorithm for finding a minimum-cost flow in planar graphs with polynomially bounded integer costs and capacities. The previous fastest algorithm for this problem is based on interior point methods (IPMs) and…

We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…

Let $G = (V,E,w)$ be a weighted undirected graph on $|V| = n$ vertices and $|E| = m$ edges, let $k \ge 1$ be any integer, and let $\epsilon < 1$ be any parameter. We present the following results on fast constructions of spanners with…

In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…

Given a financial time series data, one of the most fundamental and interesting challenges is the need to learn the stock dynamics signals in a financial time series data. A good example is to represent the time series in line segments…

Balanced partitioning is often a crucial first step in solving large-scale graph optimization problems, e.g., in some cases, a big graph can be chopped into pieces that fit on one machine to be processed independently before stitching the…

This paper proposes an algorithmic framework for various reconfiguration problems using zero-suppressed binary decision diagrams (ZDDs), a data structure for families of sets. In general, a reconfiguration problem checks if there is a…

Phase retrieval is the problem of reconstructing images from magnitude-only measurements. In many real-world applications the problem is underdetermined. When training data is available, generative models allow optimization in a…

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…