Related papers: A Fast Randomized Algorithm for Finding the Maxima…
We study the maximum likelihood model in emission tomography and propose a new family of algorithms for its solution, called String-Averaging Expectation-Maximization (SAEM). In the String-Averaging algorithmic regime, the index set of all…
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…
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 $S$…
Given a sequence of n numbers, the Maximum Consecutive Subsums Problem (MCSP) asks for the maximum consecutive sum of lengths l for each l = 1,...,n. No algorithm is known for this problem which is significantly better than the naive…
Variable Length Memory Chains (VLMC), which are generalizations of finite order Markov chains, turn out to be an essential tool to modelize random sequences in many domains, as well as an interesting object in contemporary probability…
The problem of identification of statistically significant patterns in a sequence of data has been applied to many domains such as intrusion detection systems, financial models, web-click records, automated monitoring systems, computational…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Random linear codes (RLCs) are well known to have nice combinatorial properties and near-optimal parameters in many different settings. However, getting explicit constructions matching the parameters of RLCs is challenging, and RLCs are…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
The distributions of the $m$-th longest runs of multivariate random sequences are considered. For random sequences made up of $k$ kinds of letters, the lengths of the runs are sorted in two ways to give two definitions of run length…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
Given two {0,1}-sequences X and Y of lengths m and n, respectively, we write L(X,Y) to denote the length of the longest common subsequence (LCS) of X and Y, and write L(m,n) to denote the expected value of L(X,Y) when X and Y are random…
The Longest Common Increasing Subsequence (LCIS) is a variant of the classical Longest Common Subsequence (LCS), in which we additionally require the common subsequence to be strictly increasing. While the well-known "Four Russians"…
We consider the problem of recovering a single or multiple frequency-sparse signals, which share the same frequency components, from a subset of regularly spaced samples. The problem is referred to as continuous compressed sensing (CCS) in…
Linear mixed models (LMMs), which incorporate fixed and random effects, are key tools for analyzing heterogeneous data, such as in personalized medicine. Nowadays, this type of data is increasingly wide, sometimes containing thousands of…
In this paper we address the problem of discovering a small set of frequent serial episodes from sequential data so as to adequately characterize or summarize the data. We discuss an algorithm based on the Minimum Description Length (MDL)…
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…
The longest run subsequence (LRS) problem is an NP-hard combinatorial optimization problem belonging to the class of subsequence problems from bioinformatics. In particular, the problem plays a role in genome reassembly. In this paper, we…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…