Related papers: Computing maximal palindromes in non-standard matc…
Symmetric positive semidefinite (SPSD) matrix approximation is an important problem with applications in kernel methods. However, existing SPSD matrix approximation methods such as the Nystr\"om method only have weak error bounds. In this…
We study the statistics of height and balanced height in the binary search tree problem in computer science. The search tree problem is first mapped to a fragmentation problem which is then further mapped to a modified directed polymer…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
Computing a Single-Linkage Dendrogram (SLD) is a key step in the classic single-linkage hierarchical clustering algorithm. Given an input edge-weighted tree $T$, the SLD of $T$ is a binary dendrogram that summarizes the $n-1$ clusterings…
We study infinite words u over an alphabet A satisfying the property P : P(n)+ P(n+1) = 1+ #A for any n in N, where P(n) denotes the number of palindromic factors of length n occurring in the language of u. We study also infinite words…
Term unification plays an important role in many areas of computer science, especially in those related to logic. The universal mechanism of grammar-based compression for terms, in particular the so-called Singleton Tree Grammars (STG),…
We reconsider randomized algorithms for the low-rank approximation of symmetric positive semi-definite (SPSD) matrices such as Laplacian and kernel matrices that arise in data analysis and machine learning applications. Our main results…
The palindromic fingerprint of a string $S[1\ldots n]$ is the set $PF(S) = \{(i,j)~|~ S[i\ldots j] \textit{ is a maximal }\\ \textit{palindrome substring of } S\}$. In this work, we consider the problem of string reconstruction from a…
We perform a reverse engineering from the ``extended Spellman data'', consisting of 6178 mRNA levels measured by microarrays at 73 instances in four time series during the cell cycle of the yeast Saccharomyces cerevisae. By assuming a…
We present fast algorithms for approximate shortest paths in the massively parallel computation (MPC) model. We provide randomized algorithms that take $poly(\log{\log{n}})$ rounds in the near-linear memory MPC model. Our results are for…
Grammar based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. In this paper, we present a novel…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…
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…
Over the last two decades, the Latent Position Model (LPM) has become a prominent tool to obtain model-based visualizations of networks. However, the geometric structure of the LPM is inherently symmetric, in the sense that outgoing and…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. In this work, we present sublinear time quantum algorithms…
Non-parametric entropy estimation on sequential data is a fundamental tool in signal processing, capturing information flow within or between processes to measure predictability, redundancy, or similarity. Methods based on longest common…
Logically constrained term rewriting is a relatively new rewriting formalism that naturally supports built-in data structures, such as integers and bit vectors. In the analysis of logically constrained term rewrite systems (LCTRSs),…
Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of…