Related papers: GPU-Accelerated BWT Construction for Large Collect…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
Binary code analysis is widely used to assess a program's correctness, performance, and provenance. Binary analysis applications often construct control flow graphs, analyze data flow, and use debugging information to understand how machine…
In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
Benefitting from large-scale training datasets and the complex training network, Convolutional Neural Networks (CNNs) are widely applied in various fields with high accuracy. However, the training process of CNNs is very time-consuming,…
Probabilistic breadth-first traversals (BPTs) are used in many network science and graph machine learning applications. In this paper, we are motivated by the application of BPTs in stochastic diffusion-based graph problems such as…
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…
Convolutional neural networks have gained a remarkable success in computer vision. However, most usable network architectures are hand-crafted and usually require expertise and elaborate design. In this paper, we provide a block-wise…
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
Betweenness Centrality (BC) is steadily growing in popularity as a metrics of the influence of a vertex in a graph. The BC score of a vertex is proportional to the number of all-pairs-shortest-paths passing through it. However, complete and…
Capacitive coupling wireless power transfer (CCWPT) is one of the pervasive methods to transfer power in the reactive near-field zone. In this paper, a flexible design methodology based on Binary Particle Swarm Optimization (BPSO) algorithm…
The Transformer architecture has shown significant success in many language processing and visual tasks. However, the method faces challenges in efficiently scaling to long sequences because the self-attention computation is quadratic with…
Graph Convolutional Networks (GCNs) are recently getting much attention in bioinformatics and chemoinformatics as a state-of-the-art machine learning approach with high accuracy. GCNs process convolutional operations along with graph…
Conventional neural accelerators rely on isolated self-sufficient functional units that perform an atomic operation while communicating the results through an operand delivery-aggregation logic. Each single unit processes all the bits of…
Reading a qubit is a fundamental operation in quantum computing. It translates quantum information into classical information enabling subsequent classification to assign the qubit states `0' or `1'. Unfortunately, qubit readout is one of…
Structural clustering is one of the most popular graph clustering methods, which has achieved great performance improvement by utilizing GPUs. Even though, the state-of-the-art GPU-based structural clustering algorithm, GPUSCAN, still…
The rapid advancement of GPU technology has unlocked powerful parallel processing capabilities, creating new opportunities to enhance classic search algorithms. This hardware has been exploited in best-first search algorithms with neural…