Related papers: FermiKit: assembly-based variant calling for Illum…
DerivKit is a Python package for derivative-based statistical inference. It implements stable numerical differentiation and derivative assembly utilities for Fisher-matrix forecasting and higher-order likelihood approximations in scientific…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
Achieving an accurate description of fermionic systems typically requires considerably many more orbitals than fermions. Previous resource analyses of quantum chemistry simulation often failed to exploit this low fermionic number…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
Accurate and reproducible disease risk prediction remains challenging due to heterogeneous features, limited samples, and severe class imbalance. This study introduces yvsoucom-iterkit, a deterministic and log-driven automated machine…
The role of inferencing with uncertainty is becoming more important in rule-based expert systems (ES), since knowledge given by a human expert is often uncertain or imprecise. We have succeeded in designing a VLSI chip which can perform an…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Simulating fermionic systems on a quantum computer requires representing fermionic states using qubits. The complexity of many simulation algorithms depends on the complexity of implementing rotations generated by fermionic…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…
Modern processors are equipped with single instruction multiple data (SIMD) instructions for fine-grained data parallelism. Compiler auto-vectorization techniques that target SIMD instructions face performance limitations due to…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction…
DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…
FEMSIM, a Fortran code, has been developed to simulate the fluctuation electron microscopy signal, the variance, V(k), from a model atomic structure. FEMSIM has been incorporated into a hybrid-reverse Monte Carlo code that combines an…
The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or…
Many modern virtual machines, such as JVMs, .NET Framework, and V8, employ a just-in-time (JIT) compiler to achieve their high-performance. There are two major compilation strategies; trace-based compilation and method-based compilation.…
Freely Long-Thinking Transformer (FraiLT) is an improved transformer model designed to enhance processing capabilities without scaling up size. It utilizes a recursive approach, iterating over a subset of layers multiple times, and…
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic sequencing and in turn the amount of data that needs to be processed, requiring highly efficient computation for its analysis. In this…
A remote data acquisition chassis, called a HOTLink Rack Monitor, HRM, has been developed for use in the Fermilab control system. This chassis provides for 64 analog input channels, 8 analog output channels, and 8 bytes of digital I/O. The…