Related papers: FastRemap: A Tool for Quickly Remapping Reads betw…
We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and…
We re-investigate a fundamental question: how effective is crossover in Genetic Algorithms in combining building blocks of good solutions? Although this has been discussed controversially for decades, we are still lacking a rigorous and…
Kernel approximation using randomized feature maps has recently gained a lot of interest. In this work, we identify that previous approaches for polynomial kernel approximation create maps that are rank deficient, and therefore do not…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
One of the important factors that make a search engine fast and accurate is a concise and duplicate free index. In order to remove duplicate and near-duplicate documents from the index, a search engine needs a swift and reliable duplicate…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
We designed a fast similarity search engine for large molecular libraries: FPScreen. We downloaded 100 million molecules' structure files in PubChem with SDF extension, then applied a computational chemistry tool RDKit to convert each…
Quantification of tissue parameters using MRI is emerging as a powerful tool in clinical diagnosis and research studies. The need for multiple long scans with different acquisition parameters prohibits quantitative MRI from reaching…
Audio classification models, particularly the Audio Spectrogram Transformer (AST), play a crucial role in efficient audio analysis. However, optimizing their efficiency without compromising accuracy remains a challenge. In this paper, we…
The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…
MapReduce is a technique used to vastly improve distributed processing of data and can massively speed up computation. Hadoop and its MapReduce relies on JVM and Java which is expensive on memory. High Performance Computing based MapReduce…
With the development of cheap image sensors, the amount of available image data have increased enormously, and the possibility of using crowdsourced collection methods has emerged. This calls for development of ways to handle all these…
Motivation: Storage of genomic data is a major cost for the Life Sciences, effectively addressed mostly via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen…
Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
Gene regulatory network reconstruction is a fundamental problem in computational biology. We recently developed an algorithm, called PANDA (Passing Attributes Between Networks for Data Assimilation), that integrates multiple sources of…
C++ code snippets from a multi-core parallel memory-efficient crossover for genetic programming are given. They may be adapted for separate generation evolutionary algorithms where large chromosomes or small RAM require no more than M + (2…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…