Related papers: Sparse Long Blocks and the Micro-Structure of the …
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…
We present a new efficient method for approximate search in electronic lexica. Given an input string (the pattern) and a similarity threshold, the algorithm retrieves all entries of the lexicon that are sufficiently similar to the pattern.…
Let $X_1, X_2, ..., X_s$ and $Y_1, Y_2, ..., Y_t$ be strings over an alphabet $\Sigma$, where $s$ and $t$ are positive integers. The longest common subsequence and substring problem for multiple strings $X_1, X_2, ..., X_s$ and $Y_1, Y_2,…
In the Shortest Common Superstring problem, one needs to find the shortest superstring for a set of strings. This problem is APX-hard, and many approximation algorithms were proposed, with the current best approximation factor of 2.466.…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
In conventional sparse representations based dictionary learning algorithms, initial dictionaries are generally assumed to be proper representatives of the system at hand. However, this may not be the case, especially in some systems…
This paper gives new results for synchronization strings, a powerful combinatorial object that allows to efficiently deal with insertions and deletions in various communication settings: $\bullet$ We give a deterministic, linear time…
We consider the problem of sparse coding, where each sample consists of a sparse linear combination of a set of dictionary atoms, and the task is to learn both the dictionary elements and the mixing coefficients. Alternating minimization is…
Beginning with a review of the arguments leading to the so-called c=1 barrier in the continuum formulation of noncritical string theory, the pathology is then exhibited in a discretized version of the theory, formulated through dynamical…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
The length of the longest common subsequences (LCSs) is often used as a similarity measurement to compare two (or more) random words. Below we study its statistical behavior in mean and variance using a Monte-Carlo approach from which we…
Sparse coding is a crucial subroutine in algorithms for various signal processing, deep learning, and other machine learning applications. The central goal is to learn an overcomplete dictionary that can sparsely represent a given input…
We study a new generalization of palindromes and gapped palindromes called block palindromes. A block palindrome is a string that becomes a palindrome when identical substrings are replaced with a distinct character. We investigate several…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
We consider labeled directed graphs where each vertex is labeled with a non-empty string. Such labeled graphs are also known as non-linear texts in the literature. In this paper, we introduce a new problem of comparing two given labeled…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…
A weighted string, also known as a position weight matrix, is a sequence of probability distributions over some alphabet. We revisit the Weighted Shortest Common Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that is,…
In the Shortest-Superstring problem, we are given a set of strings S and want to find a string that contains all strings in S as substrings and has minimum length. This is a classical problem in approximation and the best known…
Efficient continual learning in humans is enabled by a rich set of neurophysiological mechanisms and interactions between multiple memory systems. The brain efficiently encodes information in non-overlapping sparse codes, which facilitates…