Related papers: Sequence Searching Allowing for Non-Overlapping Ad…
We define a new problem in comparative genomics, denoted PQ-Tree Search, that takes as input a PQ-tree $T$ representing the known gene orders of a gene cluster of interest, a gene-to-gene substitution scoring function $h$, integer…
In Gapped String Indexing, the goal is to compactly represent a string $S$ of length $n$ such that for any query consisting of two strings $P_1$ and $P_2$, called patterns, and an integer interval $[\alpha, \beta]$, called gap range, we can…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Emergent misalignment, where fine-tuning on narrow, non-harmful tasks induces harmful behaviors, poses a key challenge for AI safety in LLMs. Despite growing empirical evidence, its underlying mechanism remains unclear. To uncover the…
We study the communication complexity and streaming complexity of approximating unweighted semi-matchings. A semi-matching in a bipartite graph G = (A, B, E), with n = |A|, is a subset of edges S that matches all A vertices to B vertices…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
A border of a string is a non-empty proper prefix of the string that is also a suffix. A string is unbordered if it has no border. The longest unbordered factor is a fundamental notion in stringology, closely related to string periodicity.…
We consider the sensitivity of algorithms for the maximum matching problem against edge and vertex modifications. Algorithms with low sensitivity are desirable because they are robust to edge failure or attack. In this work, we show a…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…
Dual decomposition is widely utilized in distributed optimization of multi-agent systems. In practice, the dual decomposition algorithm is desired to admit an asynchronous implementation due to imperfect communication, such as time delay…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…
We design a generic method for reducing the task of finding weighted matchings to that of finding short augmenting paths in unweighted graphs. This method enables us to provide efficient implementations for approximating weighted matchings…
The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
We consider the classic Set Cover problem in the data stream model. For $n$ elements and $m$ sets ($m\geq n$) we give a $O(1/\delta)$-pass algorithm with a strongly sub-linear $\tilde{O}(mn^{\delta})$ space and logarithmic approximation…
In the Longest Common Factor with $k$ Mismatches (LCF$_k$) problem, we are given two strings $X$ and $Y$ of total length $n$, and we are asked to find a pair of maximal-length factors, one of $X$ and the other of $Y$, such that their…