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The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…
The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…
The Burrows-Wheeler transform (BWT) is a string transformation that enhances string indexing and compressibility. Cotumaccio and Prezza [SODA '21] extended this transformation to nondeterministic finite automata (NFAs) through…
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…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
Subgraph representation learning has been effective in solving various real-world problems. However, current graph neural networks (GNNs) produce suboptimal results for subgraph-level tasks due to their inability to capture complex…
In this paper we study variants of the widely used spectral clustering that partitions a graph into k clusters by (1) embedding the vertices of a graph into a low-dimensional space using the bottom eigenvectors of the Laplacian matrix, and…
One of the most natural optimization problems is the k-Set Packing problem, where given a family of sets of size at most k one should select a maximum size subfamily of pairwise disjoint sets. A special case of 3-Set Packing is the well…
Given an undirected $n$-vertex graph and $k$ pairs of terminal vertices $(s_1,t_1), \ldots, (s_k,t_k)$, the $k$-Disjoint Shortest Paths ($k$-DSP)-problem asks whether there are $k$ pairwise vertex-disjoint paths $P_1,\ldots, P_k$ such that…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
Spectral clustering is a well-known technique which identifies $k$ clusters in an undirected graph with weight matrix $W\in\mathbb{R}^{n\times n}$ by exploiting its graph Laplacian $L(W)$, whose eigenvalues $0=\lambda_1\leq \lambda_2 \leq…
The Longest Common Substring (LCS) and Longest Palindromic Substring (LPS) are classical problems in computer science, representing fundamental challenges in string processing. Both problems can be solved in linear time using a classical…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
We consider the problem of finding repetitive structures and inherent patterns in a given string $\s{s}$ of length $n$ over a finite totally ordered alphabet. A border $\s{u}$ of a string $\s{s}$ is both a prefix and a suffix of $\s{s}$…
We present the first sample-optimal sublinear time algorithms for the sparse Discrete Fourier Transform over a two-dimensional sqrt{n} x sqrt{n} grid. Our algorithms are analyzed for /average case/ signals. For signals whose spectrum is…
Palindromes are non-empty strings that read the same forward and backward. The problem of recognizing strings that can be represented as the concatenation of even-length palindromes, the concatenation of palindromes of length at least two,…