Related papers: PHONI: Streamed Matching Statistics with Multi-Gen…
We present two novel approaches for the computation of the exact distribution of a pattern in a long sequence. Both approaches take into account the sparse structure of the problem and are two-part algorithms. The first approach relies on a…
We consider the problem of monotone, submodular maximization over a ground set of size $n$ subject to cardinality constraint $k$. For this problem, we introduce the first deterministic algorithms with linear time complexity; these…
Exploring statistics of locally connected subgraph patterns (also known as network motifs) has helped researchers better understand the structure and function of biological and online social networks (OSNs). Nowadays the massive size of…
We define the Streaming Communication model that combines the main aspects of communication complexity and streaming. We consider two agents that want to compute some function that depends on inputs that are distributed to each agent. The…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
MONI (Rossi et al., {\it JCB} 2022) is a BWT-based compressed index for computing the matching statistics and maximal exact matches (MEMs) of a pattern (usually a DNA read) with respect to a highly repetitive text (usually a database of…
Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
As a representative sequential pattern mining problem, counting the frequency of serial episodes from a streaming sequence has drawn continuous attention in academia due to its wide application in practice, e.g., telecommunication alarms,…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
Finding dense subgraphs is a fundamental algorithmic tool in data mining, community detection, and clustering. In this problem, one aims to find an induced subgraph whose edge-to-vertex ratio is maximized. We study the directed case of this…
Multi-pass streaming algorithm for Maximum Matching have been studied since more than 15 years and various algorithmic results are known today, including $2$-pass streaming algorithms that break the $1/2$-approximation barrier, and…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
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…
In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…
We study two-pass streaming algorithms for Maximum Bipartite Matching (MBM). All known two-pass streaming algorithms for MBM operate in a similar fashion: They compute a maximal matching in the first pass and find 3-augmenting paths in the…
We propose scalable methods to execute counting queries in machine learning applications. To achieve memory and computational efficiency, we abstract counting queries and their context such that the counts can be aggregated as a stream. We…
We propose two one-pass streaming algorithms for the $\mathcal{NP}$-hard hypergraph matching problem. The first algorithm stores a small subset of potential matching edges in a stack using dual variables to select edges. It has an…
An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable…
We introduce the poly-streaming model, a generalization of streaming models of computation in which $k$ processors process $k$ data streams containing a total of $N$ items. The algorithm is allowed $O\left(f(k)\cdot M_1\right)$ space, where…