Related papers: AliBI: An Alignment-Based Index for Genomic Datase…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
The human microbiome plays an important role in human health and disease status. Next generating sequencing technologies allow for quantifying the composition of the human microbiome. Clustering these microbiome data can provide valuable…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
Many existing data mining algorithms use feature values directly in their model, making them sensitive to units/scales used to measure/represent data. Pre-processing of data based on rank transformation has been suggested as a potential…
We develop a scalable algorithm to learn binary hash codes for indexing large-scale datasets. Near-isometric binary hashing (NIBH) is a data-dependent hashing scheme that quantizes the output of a learned low-dimensional embedding to obtain…
Longest prefix matching has long been the bottleneck of the Bloom filter-based solutions for packet forwarding implemented in software. We propose a search algorithm to match a destination IP address against a compact representation of the…
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Recent advances in AI agents for software engineering and scientific discovery have demonstrated remarkable capabilities, yet their application to developing novel ranking models in commercial search engines remains unexplored. In this…
With declining sequencing costs a promising and affordable tool is emerging in cancer diagnostics: genomics. By using association studies, genomic variants that predispose patients to specific cancers can be identified, while by using tumor…
Alzheimer's Disease Analysis Model (ADAM) is a multi-agent reasoning large language model (LLM) framework designed to integrate and analyze multimodal data, including microbiome profiles, clinical datasets, and external knowledge bases, to…
This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected task-aligned dataset can match or even…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Medical Informatics and the application of modern signal processing in the assistance of the diagnostic process in medical imaging is one of the more recent and active research areas today. This thesis addresses a variety of issues related…
We present a genetic algorithm for the atomistic design and global optimisation of substitutionally disordered bulk materials and surfaces. Premature convergence which hamper conventional genetic algorithms due to problems with…
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…
Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall properties, could…
Medical data collected for diagnostic decisions are typically multimodal, providing comprehensive information on a subject. While computer-aided diagnosis systems can benefit from multimodal inputs, effectively fusing such data remains a…
Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…