Related papers: Fast computation of approximate weak common interv…
This short paper describes a simple coding technique, Sparse Sequential Dirichlet Coding, for multi-alphabet memoryless sources. It is appropriate in situations where only a small, unknown subset of the possible alphabet symbols can be…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
Regular expressions constitute a fundamental notion in formal language theory and are frequently used in computer science to define search patterns. A classic algorithm for these problems constructs and simulates a non-deterministic finite…
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…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
We give a strongly polynomial-time algorithm for integer linear programs defined by integer coefficient matrices whose subdeterminants are bounded by a constant and that contain at most two nonzero entries in each row. The core of our…
Cadences are structurally maximal arithmetic progressions of indices corresponding to equal characters in an underlying string. This paper provides a polynomial time detection algorithm for 3-cadences in grammar-compressed binary strings.…
A technique using a systolic array structure is proposed for solving the common approximate substring (CAS) problem. This approach extends the technique introduced in earlier work from the computation of the edit-distance between two…
Distributed algorithms are often beset by the straggler effect, where the slowest compute nodes in the system dictate the overall running time. Coding-theoretic techniques have been recently proposed to mitigate stragglers via algorithmic…
We consider the problem of finding a minimum common partition of two strings (MCSP). The problem has its application in genome comparison. MCSP problem is proved to be NP-hard. In this paper, we develop an Integer Programming (IP)…
We consider databases in which each attribute takes values from a partially ordered set (poset). This allows one to model a number of interesting scenarios arising in different applications, including quantitative databases, taxonomies, and…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
We show that confidence intervals in a variance component model, with asymptotically correct uniform coverage probability, can be obtained by inverting certain test-statistics based on the score for the restricted likelihood. The results…
Causal discovery, the task of inferring causal structure from data, has the potential to uncover mechanistic insights from biological experiments, especially those involving perturbations. However, causal discovery algorithms over larger…
We address the problem of constructing a fast lossless code in the case when the source alphabet is large. The main idea of the new scheme may be described as follows. We group letters with small probabilities in subsets (acting as super…
Synchronization strings are recently introduced by Haeupler and Shahrasbi [HS17a] in the study of codes for correcting insertion and deletion errors (insdel codes). A synchronization string is an encoding of the indices of the symbols in a…
We describe a method for fast approximation of sparse coding. The input space is subdivided by a binary decision tree, and we simultaneously learn a dictionary and assignment of allowed dictionary elements for each leaf of the tree. We…
Several recent works have considered the \emph{trace reconstruction problem}, in which an unknown source string $x\in\{0,1\}^n$ is transmitted through a probabilistic channel which may randomly delete coordinates or insert random bits,…
Integer programs (IPs) on constraint matrices with bounded subdeterminants are conjectured to be solvable in polynomial time. We give a strongly polynomial time algorithm to solve IPs where the constraint matrix has bounded subdeterminants…
In this paper we propose a new, more appropriate definition of regular and indeterminate strings. A regular string is one that is "isomorphic" to a string whose entries all consist of a single letter, but which nevertheless may itself…