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This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Citation graphs can be helpful in generating high-quality summaries of scientific papers, where references of a scientific paper and their correlations can provide additional knowledge for contextualising its background and main…
We present bundled references, a new building block to provide linearizable range query operations for highly concurrent linked data structures. Bundled references allow range queries to traverse a path through the data structure that is…
In this paper, we address the problem of searching for semantically similar images from a large database. We present a compact coding approach, supervised quantization. Our approach simultaneously learns feature selection that linearly…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
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…
Learning scientific document representations can be substantially improved through contrastive learning objectives, where the challenge lies in creating positive and negative training samples that encode the desired similarity semantics.…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Building robust natural language understanding systems will require a clear characterization of whether and how various linguistic meaning representations complement each other. To perform a systematic comparative analysis, we evaluate the…
The clustering of data into physically meaningful subsets often requires assumptions regarding the number, size, or shape of the subgroups. Here, we present a new method, simultaneous coherent structure coloring (sCSC), which accomplishes…
Identifying influential nodes in complex networks is a fundamental task in network analysis with wide-ranging applications across domains. While deep learning has advanced node influence detection, existing supervised approaches remain…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
We present QCAM, a quantum analogue of Content-Addressable Memory (CAM), useful for finding matches in two sequences of bit-strings. Our QCAM implementation takes advantage of Grover's search algorithm and proposes a highly-optimized…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…