Related papers: Parallel DNA Sequence Alignment on High-Performanc…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
Enterprise software systems make complex interactions with other services in their environment. Developing and testing for production-like conditions is therefore a challenging task. Prior approaches include emulations of the dependency…
Motivated by the need for adaptive, secure and responsive scheduling in a great range of computing applications, including human-centered and time-critical applications, this paper proposes a scheduling framework that seamlessly adds…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
To train modern large DNN models, pipeline parallelism has recently emerged, which distributes the model across GPUs and enables different devices to process different microbatches in pipeline. Earlier pipeline designs allow multiple…
Splotch is a rendering algorithm for exploration and visual discovery in particle-based datasets coming from astronomical observations or numerical simulations. The strengths of the approach are production of high quality imagery and…
Genetic information is increasing exponentially, doubling every 18 months. Analyzing this information within a reasonable amount of time requires parallel computing resources. While considerable research has addressed DNA analysis using…
Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of…
The rapid growth of deep learning has driven exponential increases in model parameters and computational demands. NVIDIA GPUs and their CUDA-based software ecosystem provide robust support for parallel computing, significantly alleviating…
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
Existing Deep Learning frameworks exclusively use either Parameter Server(PS) approach or MPI parallelism. In this paper, we discuss the drawbacks of such approaches and propose a generic framework supporting both PS and MPI programming…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Support Vector Machine (SVM) algorithm requires a high computational cost (both in memory and time) to solve a complex quadratic programming (QP) optimization problem during the training process. Consequently, SVM necessitates high…
This paper addresses the problem of parallelizing computations to study non-linear dynamics in large networks of non-locally coupled oscillators using heterogeneous computing resources. The proposed approach can be applied to a variety of…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…
All-pairs similarity problem asks to find all vector pairs in a set of vectors the similarities of which surpass a given similarity threshold, and it is a computational kernel in data mining and information retrieval for several tasks. We…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
State-of-the-art multiple sequence alignment (MSA) algorithms are based on progressive approaches that rely on pairwise sequence alignment (PSA) to generate guide trees to align all sequences. Given an evidenced explosion in genomic data…