Related papers: Indexing large genome collections on a PC
Today, very large amounts of data are produced and stored in all branches of society including science. Mining these data meaningfully has become a considerable challenge and is of the broadest possible interest. The size, both in numbers…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
High-throughput technologies such as next generation sequencing allow biologists to observe cell function with unprecedented resolution, but the resulting datasets are too large and complicated for humans to understand without the aid of…
Large-scale source-code clone detection is a challenging task. In our previous work, we proposed an approach (SSCD) that leverages artificial neural networks and approximates nearest neighbour search to effectively and efficiently locate…
Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…
In a dynamic retrieval system, documents must be ingested as they arrive, and be immediately findable by queries. Our purpose in this paper is to describe an index structure and processing regime that accommodates that requirement for…
Matrix multiplication is a foundational operation in scientific computing and machine learning, yet its computational complexity makes it a significant bottleneck for large-scale applications. The shift to parallel architectures, primarily…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
Detailed models of observed interacting galaxies suffer from the extended parameter space. Here, we present results from our code MINGA which couples an evolutionary optimization strategy (a genetic algorithm) with a fast N-body method.…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…
The use of brain images as markers for diseases or behavioral differences is challenged by the small effects size and the ensuing lack of power, an issue that has incited researchers to rely more systematically on large cohorts. Coupled…
The Beagle framework, through GPU-based Genetic Programming, enables population dynamics previously unattainable (within practical time frames) by CPU-constrained Genetic Programming systems. This work explores how GPU-enabled population…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…
Blini is a tool for quick lookup of nucleotide sequences in databases, and for quick dereplication of sequence collections. It is meant to help clean and characterize large collections of assembled contigs or long sequences that would…
Computational models have become one of the prevalent methods to model complex phenomena. To accurately model complex interactions, such as detailed biomolecular interactions, scientists often rely on multiscale models comprised of several…
Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…