Related papers: MCUIUC -- A New Framework for Metagenomic Read Com…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Neural network weights are increasingly a bottleneck for deployment, yet most compression pipelines treat layers independently and overlook cross-layer redundancy induced by function-preserving symmetries. We propose Motion-Compensated…
Context-aware compression techniques have gained increasing attention as model sizes continue to grow, introducing computational bottlenecks that hinder efficient deployment. A structured encoding approach was proposed to selectively…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
Recent years have witnessed the prevailing progress of Generative Adversarial Networks (GANs) in image-to-image translation. However, the success of these GAN models hinges on ponderous computational costs and labor-expensive training data.…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of…
We introduce a cutting-edge video compression framework tailored for the age of ubiquitous video data, uniquely designed to serve machine learning applications. Unlike traditional compression methods that prioritize human visual perception,…
In this paper we present an end-to-end meta-learned system for image compression. Traditional machine learning based approaches to image compression train one or more neural network for generalization performance. However, at inference…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is…
The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats,…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
With the evolution of storage and communication protocols, ultra-low bitrate image compression has become a highly demanding topic. However, existing compression algorithms must sacrifice either consistency with the ground truth or…
Multispectral transmission imaging provides strong benefits for early breast cancer screening. The frame accumulation method addresses the challenge of low grayscale and signal-to-noise ratio resulting from the strong absorption and…
This study harnesses the embodied intelligence of mechanical metamaterials to sense and process environmental vibrations with minimal digital computation. Using physical reservoir computing (PRC), we turn the metamaterial and its nonlinear…
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…