Related papers: AMGC: Adaptive match-based genomic compression alg…
Artificial Intelligence Generated Content (AIGC) is leading a new technical revolution for the acquisition of digital content and impelling the progress of visual compression towards competitive performance gains and diverse functionalities…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
Compressed sensing (CS) leverages the sparsity prior to provide the foundation for fast magnetic resonance imaging (fastMRI). However, iterative solvers for ill-posed problems hinder their adaption to time-critical applications. Moreover,…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…
Graph Neural Networks (GNNs) are effective for processing graph-structured data but face challenges with large graphs due to high memory requirements and inefficient sparse matrix operations on GPUs. Quantum Computing (QC) offers a…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
The application of machine learning(ML) and genetic programming(GP) to the image compression domain has produced promising results in many cases. The need for compression arises due to the exorbitant size of data shared on the internet.…
Retrieval-Augmented Generation (RAG) helps LLMs stay accurate, but feeding long documents into a prompt makes the model slow and expensive. This has motivated context compression, ranging from token pruning and summarization to…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
As large language models (LLMs) continue to be deployed and utilized across domains, the volume of LLM-generated data is growing rapidly. This trend highlights the increasing importance of effective and lossless compression for such data in…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
Generative Adversarial Networks (GANs) have shown remarkable success in modeling complex data distributions for image-to-image translation. Still, their high computational demands prohibit their deployment in practical scenarios like edge…
Effective search methods are crucial for improving the performance of deep generative models at test time. In this paper, we introduce a novel test-time search method, Neural Genetic Search (NGS), which incorporates the evolutionary…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…