Related papers: Blini: lightweight nucleotide sequence search and …
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
Indexing is an effective way to support efficient query processing in large databases. Recently the concept of learned index, which replaces or complements traditional index structures with machine learning models, has been actively…
When faced with new data, we often conduct a cluster analysis to obtain a better understanding of the data's structure and the archetypical samples present in the data. This process often includes visualization of the data, either as a way…
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these…
Blockchain is an enabler of many emerging decentralized applications in areas of cryptocurrency, Internet of Things, smart healthcare, among many others. Although various open-source blockchain frameworks are available, the infrastructure…
While clustering is one of the most popular methods for data mining, analysts lack adequate tools for quick, iterative clustering analysis, which is essential for hypothesis generation and data reasoning. We introduce Clustrophile, an…
One of the main challenges in data mining is choosing the optimal number of clusters without prior information. Notably, existing methods are usually in the philosophy of cluster validation and hence have underlying assumptions on data…
Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" become a verb, describing the act of performing sequence search and alignment. However, if one needs…
Recent successes in virtual screening have been made possible by large models and extensive chemical libraries. However, combining these elements is challenging: the larger the model, the more expensive it is to run, making ultra-large…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
For binary neural networks (BNNs) to become the mainstream on-device computer vision algorithm, they must achieve a superior speed-vs-accuracy tradeoff than 8-bit quantization and establish a similar degree of general applicability in…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…
The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a…
Substructure search in chemical compound databases is a fundamental task in cheminformatics with critical implications for fields such as drug discovery, materials science, and toxicology. However, the increasing size and complexity of…
Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infectious diseases. In this paper, we…
A significantly faster algorithm is presented for the original kNN mode seeking procedure. It has the advantages over the well-known mean shift algorithm that it is feasible in high-dimensional vector spaces and results in uniquely, well…
Model parameter synchronization across GPUs introduces high overheads for data-parallel training at scale. Existing parameter synchronization protocols cannot effectively leverage available network resources in the face of ever increasing…
We present an open source Python library for simulating overlapping (i.e., blended) images of galaxies and performing self-consistent comparisons of detection and deblending algorithms based on a suite of metrics. The package, named…
A novel non-linear approach to fast and effective comparison of sequences is presented, compared to the traditional cross-correlation operator, and illustrated with respect to DNA sequences.