Related papers: ProSt: computing, storing and visualizing attribut…
Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
An effective and efficient encoding of the source code of a computer program is critical to the success of sequence-to-sequence deep neural network models for tasks in computer program comprehension, such as automated code summarization and…
Emerging technologies present opportunities for system designers to meet the challenges presented by competing trends of big data analytics and limitations on CMOS scaling. Specifically, memristors are an emerging high-density technology…
Clustering consists of grouping together samples giving their similar properties. The problem of modeling simultaneously groups of samples and features is known as Co-Clustering. This paper introduces ROCCO - a Robust Continuous…
The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…
We propose a special-purpose class of compression algorithms for efficient compression of Prolog programs. It is a dictionary-based compression method, specially designed for the compression of Prolog code, and therefore we name it PCA…
Convolutional neural networks (CNNs) are crucial for computer vision tasks on resource-constrained devices. Quantization effectively compresses these models, reducing storage size and energy cost. However, in modern depthwise-separable…
We present Propulate, an evolutionary optimization algorithm and software package for global optimization and in particular hyperparameter search. For efficient use of HPC resources, Propulate omits the synchronization after each generation…
The Progressive-X algorithm, Prog-X in short, is proposed for geometric multi-model fitting. The method interleaves sampling and consolidation of the current data interpretation via repetitive hypothesis proposal, fast rejection, and…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Protein design has become a critical method in advancing significant potential for various applications such as drug development and enzyme engineering. However, protein design methods utilizing large language models with solely pretraining…
This paper presents Bancroft, a computational genomics acceleration platform that provides the illusion of practically infinite on-device memory capacity by compressing genomic data movement over PCIe. Bancroft introduces novel…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
In many applications of evolutionary algorithms the computational cost of applying operators and storing populations is comparable to the cost of fitness evaluation. Furthermore, by knowing what exactly has changed in an individual by an…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Proton computed tomography (pCT) is a novel medical imaging modality for mapping the distribution of proton relative stopping power (RSP) in medical objects of interest. Compared to conventional X-ray computed tomography, where range…