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Sorting is one of the most basic algorithms, and developing highly parallel sorting programs is becoming increasingly important in high-performance computing because the number of CPU cores per node in modern supercomputers tends to…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
Nearest Neighbor Search (NNS) has recently drawn a rapid increase of interest due to its core role in managing high-dimensional vector data in data science and AI applications. The interest is fueled by the success of neural embedding,…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
In recent years, the rapidly increasing number of reads produced by next-generation sequencing (NGS) technologies has driven the demand for efficient implementations of sequence alignments in bioinformatics. However, current…
In this paper, a contrastive evaluation of massively parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU. Besides…
Sequence alignment is one of the oldest and the most famous problems in bioinformatics. Even after 45 years, for one reason or another, this problem is still actual; current solutions are trade-offs between execution time, memory…
Addressing the growing demands of artificial intelligence (AI) and data analytics requires new computing approaches. In this paper, we propose a reconfigurable hardware accelerator designed specifically for AI and data-intensive…
Near-term quantum computers are noisy and have limited connectivity between qubits. Compilers are required to introduce SWAP operations in order to perform two-qubit gates between non-adjacent qubits. SWAPs increase the number of gates and…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Similarity search is a key to a variety of applications including content-based search for images and video, recommendation systems, data deduplication, natural language processing, computer vision, databases, computational biology, and…
In many engineering applications, processes must be followed precisely, making conformance checking between event logs and declarative process models crucial for ensuring adherence to desired behaviors. This is a critical area where…
Spiking Neural Networks (SNNs) hold promise for energy-efficient, biologically inspired computing. We identify substantial informatio loss during spike transmission, linked to temporal dependencies in traditional Leaky Integrate-and-Fire…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…
The vast majority of successful deep neural networks are trained using variants of stochastic gradient descent (SGD) algorithms. Recent attempts to improve SGD can be broadly categorized into two approaches: (1) adaptive learning rate…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…