Related papers: Genetic Sequence Matching Using D4M Big Data Appro…

RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions,…

Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for…

Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…

Design space exploration (DSE) is critical for developing optimized hardware architectures, especially for AI workloads such as deep neural networks (DNNs) and large language models (LLMs), which require specialized acceleration. As model…

The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many…

Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work…

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…

The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…

Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to…

Discrete mixture models provide a well-known basis for effective clustering algorithms, although technical challenges have limited their scope. In the context of gene-expression data analysis, a model is presented that mixes over a finite…

The recent development of artificial intelligence (AI) technology, especially the advance of deep neural network (DNN) technology, has revolutionized many fields. While DNN plays a central role in modern AI technology, it has been rarely…

Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…

The increasing penetration of distributed energy resources into active distribution networks (ADNs) has made effective ADN dispatch imperative. However, the numerous newly-integrated ADN operators, such as distribution system aggregators,…

We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…

We propose a stochastic optimization method for minimizing loss functions, expressed as an expected value, that adaptively controls the batch size used in the computation of gradient approximations and the step size used to move along such…

Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…

This paper introduces DLM-One, a score-distillation-based framework for one-step sequence generation with continuous diffusion language models (DLMs). DLM-One eliminates the need for iterative refinement by aligning the scores of a student…

Despite the proliferation of generative models, achieving fast sampling during inference without compromising sample diversity and quality remains challenging. Existing models such as Denoising Diffusion Probabilistic Models (DDPM) deliver…

The increasing adoption of large language models (LLMs) necessitates inference serving systems that can deliver both high throughput and low latency. Deploying LLMs with hundreds of billions of parameters on memory-constrained GPUs exposes…