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Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Achieving faster execution with shorter compilation time can foster further diversity and innovation in neural networks. However, the current paradigm of executing neural networks either relies on hand-optimized libraries, traditional…
We develop an accelerated Genetic Algorithm (GA) system constructed by the cooperation of field-programmable gate array (FPGA) and optimized parameters of the GA. We found the enhanced decay of mutation rate makes convergence of the GA much…
We present tests of comparison between our versions of the Fast Multipole Algorithm (FMA) and ``classic'' tree-code to evaluate gravitational forces in particle systems. We have optimized the Greengard's original version of FMA allowing for…
Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…
How to model and encode the semantics of human-written text and select the type of neural network to process it are not settled issues in sentiment analysis. Accuracy and transferability are critical issues in machine learning in general.…
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm…
The design of DNN accelerators includes two key parts: HW resource configuration and mapping strategy. Intensive research has been conducted to optimize each of them independently. Unfortunately, optimizing for both together is extremely…
Training 1-bit deep convolutional neural networks (DCNNs) is one of the most challenging problems in computer vision, because it is much easier to get trapped into local minima than conventional DCNNs. The reason lies in that the binarized…
Despite significant medical advancements, cancer remains the second leading cause of death, with over 600,000 deaths per year in the US. One emerging field, pathway analysis, is promising but still relies on manually derived wet lab data,…
BACKGROUND: Breast cancer has emerged as one of the most prevalent cancers among women leading to a high mortality rate. Due to the heterogeneous nature of breast cancer, there is a need to identify differentially expressed genes associated…
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…
The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for…
This paper presents novel reconfigurable architectures for reducing the latency of recurrent neural networks (RNNs) that are used for detecting gravitational waves. Gravitational interferometers such as the LIGO detectors capture cosmic…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
Genetic algorithms have played an important role in engineering optimization. Traditional GAs treat each gene separately. However, biophysical studies of gene regulatory networks revealed direct associations between different genes. It…
Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
Breast cancer has long been a prominent cause of mortality among women. Diagnosis, therapy, and prognosis are now possible, thanks to the availability of RNA sequencing tools capable of recording gene expression data. Molecular subtyping…
Purpose: To develop a retrieval-augmented generation (RAG) system powered by LLaMA-4 109B for automated, protocol-aware, and interpretable evaluation of radiotherapy treatment plans. Methods and Materials: We curated a multi-protocol…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…