Related papers: Minimum Segmentation for Pan-genomic Founder Recon…
For an undirected edge-weighted graph $G$ and a set $R$ of pairs of vertices called pairs of terminals, a multicut is a set of edges such that removing these edges from $G$ disconnects each pair in $R$. We provide an algorithm computing a…
The low-rank matrix factorization as a L1 norm minimization problem has recently attracted much attention due to its intrinsic robustness to the presence of outliers and missing data. In this paper, we propose a new method, called the…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
We present $k^{O(k^2)} m$ time algorithms for various problems about decomposing a given undirected graph by edge cuts or vertex separators of size $<k$ into parts that are ``well-connected'' with respect to cuts or separators of size $<k$;…
We give sublinear-time approximation algorithms for some optimization problems arising in machine learning, such as training linear classifiers and finding minimum enclosing balls. Our algorithms can be extended to some kernelized versions…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a scenario where the sender transmits a codeword from some codebook, and the receiver obtains $N$ noisy outputs of the codeword. We study the problem of…
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…
Distributed optimization algorithms are frequently faced with solving sub-problems on disjoint connected parts of a network. Unfortunately, the diameter of these parts can be significantly larger than the diameter of the underlying network,…
We design a sublinear-time approximation algorithm for quadratic function minimization problems with a better error bound than the previous algorithm by Hayashi and Yoshida (NIPS'16). Our approximation algorithm can be modified to handle…
The goal of the trace reconstruction problem is to recover a string $x\in\{0,1\}^n$ given many independent {\em traces} of $x$, where a trace is a subsequence obtained from deleting bits of $x$ independently with some given probability…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
We study the problem of finding a minimum homology basis, that is, a lightest set of cycles that generates the $1$-dimensional homology classes with $\mathbb{Z}_2$ coefficients in a given simplicial complex $K$. This problem has been…
We consider the problem of finding a sparse solution for an underdetermined linear system of equations when the known parameters on both sides of the system are subject to perturbation. This problem is particularly relevant to…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
We present a method for reducing the treewidth of a graph while preserving all of its minimal $s-t$ separators up to a certain fixed size $k$. This technique allows us to solve $s-t$ Cut and Multicut problems with various additional…
We study the parameterized complexity of the Cograph Deletion problem, which asks whether one can delete at most $k$ edges from a graph to make it $P_4$-free. This is a well-known graph modification problem with applications in computation…
We define a notion called leftmost separator of size at most $k$. A leftmost separator of size $k$ is a minimal separator $S$ that separates two given sets of vertices $X$ and $Y$ such that we "cannot move $S$ more towards $X$" such that…
The problem of finding the degeneracy of a graph is a subproblem of the k-core decomposition problem. In this paper, we present a (1 + epsilon)-approximate solution to the degeneracy problem which runs in O(n log n) time, sublinear in the…
In this paper, we introduce a variant of spectral sparsification, called probabilistic $(\varepsilon,\delta)$-spectral sparsification. Roughly speaking, it preserves the cut value of any cut $(S,S^{c})$ with an $1\pm\varepsilon$…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…