A5043977099- Advanced Data Storage Technologies
- Cloud Computing and Resource Management
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Parallel Computing and Optimization Techniques
- Gut microbiota and health
- Advanced Neural Network Applications
- Natural Language Processing Techniques
- Graph Theory and Algorithms
- Machine Learning in Bioinformatics
- Tryptophan and brain disorders
- Plant and fungal interactions
- Advanced Image and Video Retrieval Techniques
- Algorithms and Data Compression
- Topic Modeling
- Distributed systems and fault tolerance
National Energy Research Scientific Computing Center
2024
University of Utah
2023-2024
Lawrence Berkeley National Laboratory
2022-2024
Summary Disaggregated memory is a promising approach that addresses the limitations of traditional architectures by enabling to be decoupled from compute nodes and shared across data center. Cloud platforms have deployed such systems improve overall system utilization, but performance can vary workloads. High‐performance computing (HPC) crucial in scientific engineering applications, where HPC machines also face issue underutilized memory. As result, improving utilization while understanding...
Tightly-coupled HPC systems have rigid memory allocation and can result in expensive resource underutilization. As novel network technologies mature, disaggregated are becoming a promising solution for future systems. It allows workloads to use the available of entire system. In this paper, we propose design framework explore system space. The incorporates capacity, bandwidth, local remote access ratio, provides an intuitive approach guide machine configurations based on technology trends...
Sequence alignment algorithms play a central role in most bioinformatics software. However, porting these to GPUs can be challenging due their reliance on irregular memory access patterns and integer-heavy operations. Here we present TANGO, an optimized GPU implementation of the Smith-Waterman (SW) algorithm with focus traceback phase. We leverage stacked diagonal-major indexing compressed binary representation for efficient adaptation phase GPUs. Our proposed achieves speedups 12.6 × 9.9...
Genomic language models have recently emerged as powerful tools to decode and interpret genetic sequences. Existing genomic utilized various tokenization methods including character tokenization, overlapping non-overlapping k-mer byte-pair encoding, a method widely used in natural models. significant differences from protein because of their low variability, complex features, inconsistent directionality. These make sub-word significantly different traditional This study explores the impact...
Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations two species woodrat (Neotoma lepida and bryanti) that have independently converged feed on same toxic diet (creosote bush; Larrea tridentata) compared them do not creosote bush. Leveraging this natural experiment, collected...
Disaggregated memory is a promising approach that addresses the limitations of traditional architectures by enabling to be decoupled from compute nodes and shared across data center. Cloud platforms have deployed such systems improve overall system utilization, but performance can vary workloads. High-performance computing (HPC) crucial in scientific engineering applications, where HPC machines also face issue underutilized memory. As result, improving utilization while understanding...
Abstract Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which often toxic, influence these symbiotic partners. Using 16S rRNA gene and shotgun metagenomic sequencing, we investigated the possibility of a unique taxonomic functional core microbiome in populations two species woodrats ( Neotoma lepida bryanti ) that have independently converged feed on same toxic diet (creosote bush; Larrea tridentata ). In each...