Related papers: BGT: efficient and flexible genotype query across …
Transformers are ubiquitous in Natural Language Processing (NLP) tasks, but they are difficult to be deployed on hardware due to the intensive computation. To enable low-latency inference on resource-constrained hardware platforms, we…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
Software Testing is a process to identify the quality and reliability of software, which can be achieved through the help of proper test data. However, doing this manually is a difficult task due to the presence of number of predicate nodes…
Existing works on Binary Neural Network (BNN) mainly focus on model's weights and activations while discarding considerations on the input raw data. This article introduces Generic Learned Thermometer (GLT), an encoding technique to improve…
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts…
The Building Block Hypothesis (BBH) states that adaptive systems combine good partial solutions (so-called building blocks) to find increasingly better solutions. It is thought that Genetic Algorithms (GAs) implement the BBH. However, for…
In the UK, approximately 400,000 people with type 1 diabetes (T1D) rely on insulin delivery due to insufficient pancreatic insulin production. Managing blood glucose (BG) levels is crucial, with continuous glucose monitoring (CGM) playing a…
Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…
This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node…
The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…
3D color lookup tables (LUTs) enable precise color manipulation by mapping input RGB values to specific output RGB values. 3D LUTs are instrumental in various applications, including video editing, in-camera processing, photographic…
Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes…
In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…
The rapid advancements in Large Language Models (LLMs) have revolutionized natural language processing, with GPTs, customized versions of ChatGPT available on the GPT Store, emerging as a prominent technology for specific domains and tasks.…
Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype…
Event-driven genetic programming representations have been shown to outperform traditional imperative representations on interaction-intensive problems. The event-driven approach organizes genome content into modules that are triggered in…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of…
In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…
Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and…