Related papers: Estimating the Longest Increasing Subsequence in N…
We present the first $\mathrm{o}(n)$-space polynomial-time algorithm for computing the length of a longest common subsequence. Given two strings of length $n$, the algorithm runs in $\mathrm{O}(n^{3})$ time with $\mathrm{O}\left(\frac{n…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other…
In this paper, we investigate the complexity of one-dimensional dynamic programming, or more specifically, of the Least-Weight Subsequence (LWS) problem: Given a sequence of $n$ data items together with weights for every pair of the items,…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
We present an $O(1)$-round fully-scalable deterministic massively parallel algorithm for computing the min-plus matrix multiplication of unit-Monge matrices. We use this to derive a $O(\log n)$-round fully-scalable massively parallel…
The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
The Longest Common Subsequence (LCS) problem is a very important problem in math- ematics, which has a broad application in scheduling problems, physics and bioinformatics. It is known that the given two random sequences of infinite…
We consider the constrained Linear Inverse Problem (LIP), where a certain atomic norm (like the $\ell_1 $ norm) is minimized subject to a quadratic constraint. Typically, such cost functions are non-differentiable, which makes them not…
We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Estimating the density of a distribution from its samples is a fundamental problem in statistics. Hypothesis selection addresses the setting where, in addition to a sample set, we are given $n$ candidate distributions -- referred to as…
We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with…
Partitioning a sequence of length $n$ into $k$ coherent segments (Seg) is one of the classic optimization problems. As long as the optimization criterion is additive, Seg can be solved exactly in $O(n^2k)$ time using a classic dynamic…
Given a sequence $S$ of length $n$, a letter-duplicated subsequence is a subsequence of $S$ in the form of $x_1^{d_1}x_2^{d_2}\cdots x_k^{d_k}$ with $x_i\in\Sigma$, $x_j\neq x_{j+1}$ and $d_i\geq 2$ for all $i$ in $[k]$ and $j$ in $[k-1]$.…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
Monotonicity is a simple yet significant qualitative characteristic. We consider the problem of segmenting a sequence in up to K segments. We want segments to be as monotonic as possible and to alternate signs. We propose a quality metric…
We study computational aspects of a key problem in robust statistics -- the penalized least trimmed squares (LTS) regression problem, a robust estimator that mitigates the influence of outliers in data by capping residuals with large…