Related papers: Mean-Field Approximations to the Longest Common Su…
Given a set of $t$ words of length $n$ over a $k$-letter alphabet, it is proved that there exists a common subsequence among two of them of length at least $\frac{n}{k}+cn^{1-1/(t-k-2)}$, for some $c>0$ depending on $k$ and $t$. This is…
The Longest Common Weakly Increasing Subsequence problem (LCWIS) is a variant of the classic Longest Common Subsequence problem (LCS). Both problems can be solved with simple quadratic time algorithms. A recent line of research led to a…
We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…
The Mallows measure is measure on permutations which was introduced by Mallows in connection with ranking problems in statistics. Under this measure, the probability of a permutation $\pi$ is proportional to $q^{Inv(\pi)}$ where $q$ is a…
Graph similarity measurement, which computes the distance/similarity between two graphs, arises in various graph-related tasks. Recent learning-based methods lack interpretability, as they directly transform interaction information between…
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…
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 $P=\{P_1,\cdots,P_d\}$…
In this paper we address the longest common extension (LCE) problem: to compute the length $\ell$ of the longest common prefix between any two suffixes of $T\in \Sigma^n$ with $ \Sigma = \{0, \ldots \sigma-1\} $. We present two fast and…
A mean field feedback artificial neural network algorithm is developed and explored for the set covering problem. A convenient encoding of the inequality constraints is achieved by means of a multilinear penalty function. An approximate…
Large language models (LLMs) have exhibited impressive performance and surprising emergent properties. However, their effectiveness remains limited by the fixed context window of the transformer architecture, posing challenges for…
This thesis presents two similarity-based approaches to sparse data problems. The first approach is to build soft, hierarchical clusters: soft, because each event belongs to each cluster with some probability; hierarchical, because cluster…
The Chord Length Sampling (CLS) algorithm is a powerful Monte Carlo method that models the effects of stochastic media on particle transport by generating on-the-fly the material interfaces seen by the random walkers during their…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
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"…
In this paper we propose a general framework for topic-specific summarization of large text corpora and illustrate how it can be used for the analysis of news databases. Our framework, concise comparative summarization (CCS), is built on…
We consider the learning and communication complexity of subsequence containment. In the learning problem, we seek to learn a classifier that positively labels a binary string $x$ if it contains a fixed binary string $y$ as a subsequence.…
We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized…
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…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…