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We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
This paper proposes a randomized optimization framework for constrained signal reconstruction, where the word "constrained" implies that data-fidelity is imposed as a hard constraint instead of adding a data-fidelity term to an objective…
Recently, sparsity-based algorithms are proposed for super-resolution spectrum estimation. However, to achieve adequately high resolution in real-world signal analysis, the dictionary atoms have to be close to each other in frequency,…
Spanning trees are an important primitive in many data analysis tasks, when a data set needs to be summarized in terms of its "skeleton", or when a tree-shaped graph over all observations is required for downstream processing. Popular…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
The closest string problem is an NP-hard problem, whose task is to find a string that minimizes maximum Hamming distance to a given set of strings. This can be reduced to an integer program (IP). However, to date, there exists no known…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
Establishing a low-dimensional representation of the data leads to efficient data learning strategies. In many cases, the reduced dimension needs to be explicitly stated and estimated from the data. We explore the estimation of dimension in…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
In this work, we study the problem of detecting periodic trends in strings. While detecting exact periodicity has been studied extensively, real-world data is often noisy, where small deviations or mismatches occur between repetitions. This…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
We propose the neural string edit distance model for string-pair matching and string transduction based on learnable string edit distance. We modify the original expectation-maximization learned edit distance algorithm into a differentiable…
A 'degenerate string' is a sequence of subsets of some alphabet; it represents any string obtainable by selecting one character from each set from left to right. Recently, Alanko et al. generalized the rank-select problem to degenerate…
This paper presents an evolutionary algorithm for modeling the arrival dates of document streams, which is any time-stamped collection of documents, such as newscasts, e-mails, IRC conversations, scientific journals archives and weblog…
Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…