Related papers: copMEM: Finding maximal exact matches via sampling…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Conformance checking encompasses a body of process mining techniques which aim to find and describe the differences between a process model capturing the expected process behavior and a corresponding event log recording the observed…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
Since data is often stored in different sources, it needs to be integrated to gather a global view that is required in order to create value and derive knowledge from it. A critical step in data integration is schema matching which aims to…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
In this paper, we describe the implementation and performance of GreeM, a massively parallel TreePM code for large-scale cosmological N-body simulations. GreeM uses a recursive multi-section algorithm for domain decomposition. The size of…
Coreset selection is powerful in reducing computational costs and accelerating data processing for deep learning algorithms. It strives to identify a small subset from large-scale data, so that training only on the subset practically…
The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…
Robots have the potential to improve health monitoring outcomes for the elderly by providing doctors, and caregivers with information about the person's behavior, health activities and their surrounding environment. Over the years, less…
Maximum entropy principle (MEP) offers an effective and unbiased approach to inferring unknown probability distributions when faced with incomplete information, while neural networks provide the flexibility to learn complex distributions…