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Advances in life sciences over the last few decades have lead to the generation of a huge amount of biological data. Computing research has become a vital part in driving biological discovery where analysis and categorization of biological…
This document presents a vision for a novel AI infrastructure design that has been initially validated through inference simulations on state-of-the-art large language models. Advancements in deep learning and specialized hardware have…
In this paper, we present FLiMS, a highly-efficient and simple parallel algorithm for merging two sorted lists residing in banked and/or wide memory. On FPGAs, its implementation uses fewer hardware resources than the state-of-the-art…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…
Hardware-firmware integration is becoming a productivity bottleneck due to the increasing complexity of accelerators, characterized by intricate memory hierarchies and firmware-intensive execution. While numerous verification techniques…
Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary…
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…
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…
Advances in sensor technology and automation have ushered in an era of data abundance, where the ability to identify and extract relevant information in real time has become increasingly critical. Traditional filtering approaches, which…
Finding the convex hull is a fundamental problem in computational geometry. Quickhull is a fast algorithm for finding convex hulls. In this paper, we present VQhull, a fast parallel implementation of Quickhull that exploits vector…
We propose HAMSI (Hessian Approximated Multiple Subsets Iteration), which is a provably convergent, second order incremental algorithm for solving large-scale partially separable optimization problems. The algorithm is based on a local…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Recent hardware acceleration advances have enabled powerful specialized accelerators for finite element computations, spiking neural network inference, and sparse tensor operations. However, existing approaches face fundamental limitations:…
As quantum computers continue to improve and support larger, more complex computations, smart control hardware and compilers are needed to efficiently leverage the capabilities of these systems. This paper introduces a novel approach to…
Hardware accelerators, such as those based on GPUs and FPGAs, offer an excellent opportunity to efficiently parallelize functionalities. Recently, modern embedded platforms started being equipped with such accelerators, resulting in a…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
FM-index is an efficient data structure for string search and is widely used in next-generation sequencing (NGS) applications such as sequence alignment and de novo assembly. Recently, FM-indexing is even performed down to the read level,…
An efficient hardware implementation for Simultaneous Localization and Mapping (SLAM) methods is of necessity for mobile autonomous robots with limited computational resources. In this paper, we propose a resource-efficient FPGA…
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…