Related papers: PHONI: Streamed Matching Statistics with Multi-Gen…
Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any)…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
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…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
Businesses, governmental bodies and NGO's have an ever-increasing amount of data at their disposal from which they try to extract valuable information. Often, this needs to be done not only accurately but also within a short time frame.…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
Data streaming, in which a large dataset is received as a "stream" of updates, is an important model in the study of space-bounded computation. Starting with the work of Le Gall [SPAA `06], it has been known that quantum streaming…
Common clustering algorithms require multiple scans of all the data to achieve convergence, and this is prohibitive when large databases, with data arriving in streams, must be processed. Some algorithms to extend the popular K-means method…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Sequential probabilistic inference from streaming observations requires modeling distributions over future trajectories as new observations arrive. Although diffusion and flow-matching models are effective at capturing high-dimensional,…
We address the problem of counting the number of strings in a collection where a given pattern appears, which has applications in information retrieval and data mining. Existing solutions are in a theoretical stage. We implement these…
Given a pattern $w$ and a text $t$, the speed of a pattern matching algorithm over $t$ with regard to $w$, is the ratio of the length of $t$ to the number of text accesses performed to search $w$ into $t$. We first propose a general method…
This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…
High-speed research networks are built to meet the ever-increasing needs of data-intensive distributed workflows. However, data transfers in these networks often fail to attain the promised transfer rates for several reasons, including I/O…
In recent years, the management and processing of data streams has become a topic of active research in several fields of computer science such as, distributed systems, database systems, and data mining. A data stream can be thought of as a…
The number of triangles in a graph is a fundamental metric, used in social network analysis, link classification and recommendation, and more. Driven by these applications and the trend that modern graph datasets are both large and dynamic,…
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches…
Sampling over joins is a fundamental task in large-scale data analytics. Instead of computing the full join results, which could be massive, a uniform sample of the join results would suffice for many purposes, such as answering analytical…
While Internet of Things (IoT) devices and sensors create continuous streams of information, Big Data infrastructures are deemed to handle the influx of data in real-time. One type of such a continuous stream of information is time series…