Related papers: PHONI: Streamed Matching Statistics with Multi-Gen…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
The timed pattern matching problem is an actively studied topic because of its relevance in monitoring of real-time systems. There one is given a log $w$ and a specification $\mathcal{A}$ (given by a timed word and a timed automaton in this…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Due to the large data volume and number of distinct elements, space is often the bottleneck of many stream processing systems. The data structures used by these systems often consist of counters whose optimization yields significant memory…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Graph rewriting is a popular tool for the optimisation and modification of graph expressions in domains such as compilers, machine learning and quantum computing. The underlying data structures are often port graphs - graphs with labels at…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
We present new lower bounds that show that a polynomial number of passes are necessary for solving some fundamental graph problems in the streaming model of computation. For instance, we show that any streaming algorithm that finds a…
Frequency estimation of elements is an important task for summarizing data streams and machine learning applications. The problem is often addressed by using streaming algorithms with sublinear space data structures. These algorithms allow…
Pattern matching of streaming time series with lower latency under limited computing resource comes to a critical problem, especially as the growth of Industry 4.0 and Industry Internet of Things. However, against traditional single pattern…
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…
Search techniques make use of elementary information such as term frequencies and document lengths in computation of similarity weighting. They can also exploit richer statistics, in particular the number of documents in which any two terms…
Pattern matching of streaming time series with lower latency under limited computing resource comes to a critical problem, especially as the growth of Industry 4.0 and Industry Internet of Things. However, against traditional single pattern…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
We present a simple semi-streaming algorithm for $(1-\epsilon)$-approximation of bipartite matching in $O(\log{\!(n)}/\epsilon)$ passes. This matches the performance of state-of-the-art "$\epsilon$-efficient" algorithms -- the ones with…
One way of getting a better view of data is using frequent patterns. In this paper frequent patterns are subsets that occur a minimal number of times in a stream of itemsets. However, the discovery of frequent patterns in streams has always…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…