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Optimal Transport (OT) provides a useful geometric framework to estimate the permutation matrix under unsupervised cross-lingual word embedding (CLWE) models that pose the alignment task as a Wasserstein-Procrustes problem. However, linear…
Dynamic time warping distance (DTW) is a widely used distance measure between time series. The best known algorithms for computing DTW run in near quadratic time, and conditional lower bounds prohibit the existence of significantly faster…
The weighted ancestor problem on a rooted node-weighted tree $T$ is a generalization of the classic predecessor problem: construct a data structure for a set of integers that supports fast predecessor queries. Both problems are known to…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
We investigate pseudo-polynomial time algorithms for Subset Sum. Given a multi-set $X$ of $n$ positive integers and a target $t$, Subset Sum asks whether some subset of $X$ sums to $t$. Bringmann proposes an $\tilde{O}(n + t)$-time…
For a nonlinear system (e.g. a robot) with its continuous state space trajectories constrained by a linear temporal logic specification, the synthesis of a low-level controller for mission execution often results in a non-convex…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…
We investigate various connections between the clustering for the Burrows-Wheeler transform, a lossless algorithm used in data compression, and languages of interval exchange transformations. We show that a primitive word $u$ clusters for a…
We introduce the first index that can be built in $o(n)$ time for a text of length $n$, and can also be queried in $o(q)$ time for a pattern of length $q$. On an alphabet of size $\sigma$, our index uses $O(n\sqrt{\log n\log\sigma})$ bits,…
Neural Machine Translation (NMT) is an open vocabulary problem. As a result, dealing with the words not occurring during training (a.k.a. out-of-vocabulary (OOV) words) have long been a fundamental challenge for NMT systems. The predominant…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…
The {\em maximum cardinality} and {\em maximum weight matching} problems can be solved in time $\tilde{O}(m\sqrt{n})$, a bound that has resisted improvement despite decades of research. (Here $m$ and $n$ are the number of edges and…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…