Related papers: FermiKit: assembly-based variant calling for Illum…
Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and…
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…
With the booming of next generation sequencing technology and its implementation in clinical practice and life science research, the need for faster and more efficient data analysis methods becomes pressing in the field of sequencing. Here…
Foundation models (FMs) have opened new avenues for machine learning applications due to their ability to adapt to new and unseen tasks with minimal or no further training. Time-series foundation models (TSFMs) -- FMs trained on time-series…
We present FedKit, a federated learning (FL) system tailored for cross-platform FL research on Android and iOS devices. FedKit pipelines cross-platform FL development by enabling model conversion, hardware-accelerated training, and…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Dr$.$Jit is a new just-in-time compiler for physically based rendering and its derivative. Dr$.$Jit expedites research on these topics in two ways: first, it traces high-level simulation code (e.g., written in Python) and aggressively…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix…
Recommender systems are a long-standing research problem in data mining and machine learning. They are incremental in nature, as new user-item interaction logs arrive. In real-world applications, we need to periodically train a…
Compiler optimization decisions are often based on hand-crafted heuristics centered around a few established benchmark suites. Alternatively, they can be learned from feature and performance data produced during compilation. However,…
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…
MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing…
Highly parallelized workloads like machine learning training, inferences and general HPC tasks are greatly accelerated using GPU devices. In a cloud computing cluster, serving a GPU's computation power through multi-tasks sharing is highly…
The Real-Time Systems Engineering Department of the Scientific Computing Division at Fermilab is developing a flexible, scalable, and powerful data-acquisition (DAQ) toolkit which serves the needs of experiments from bench-top hardware…
Kernel methods are a highly effective and widely used collection of modern machine learning algorithms. A fundamental limitation of virtually all such methods are computations involving the kernel matrix that naively scale quadratically…
We present a parallel algorithm for computing the approximate factorization of an $N$-by-$N$ kernel matrix. Once this factorization has been constructed (with $N \log^2 N $ work), we can solve linear systems with this matrix with $N \log N…