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High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
We address binary classification using neural ordinary differential equations from the perspective of simultaneous control of $N$ data points. We consider a single-neuron architecture with parameters fixed as piecewise constant functions of…
This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…
Current research in clone detection suffers from poor ecosystems for evaluating precision of clone detection tools. Corpora of labeled clones are scarce and incomplete, making evaluation labor intensive and idiosyncratic, and limiting inter…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
Binarization of gene expression data is a \textbf{critical prerequisite} for the synthesis of Boolean gene regulatory network (GRN) models from omics datasets. Because Boolean networks encode gene activity as binary variables, the accuracy…
Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been limited. The main reason is that suitable data was not…
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…
A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…
Oligonucleotide arrays are used in a wide range of genomic analyses, such as gene expression profiling, comparative genomic hybridization, chromatin immunoprecipitation, SNP detection, etc. During fabrication, the sites of an…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
The method of Hol\'y, Sokol and \v{C}ern\'y (Applied Soft Computing, 2017, Vol. 60, p. 752-762) clusters objects based on their incidence in a large number of given sets. The idea is to minimize the occurrence of multiple objects from the…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
In recent years, with the development of microarray technique, discovery of useful knowledge from microarray data has become very important. Biclustering is a very useful data mining technique for discovering genes which have similar…
Software clone detection identifies similar code snippets. It has been an active research topic that attracts extensive attention over the last two decades. In recent years, machine learning (ML) based detectors, especially deep…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
The problem of hierarchical clustering items from pairwise similarities is found across various scientific disciplines, from biology to networking. Often, applications of clustering techniques are limited by the cost of obtaining…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
A code clone is a pair of code fragments, within or between software systems that are similar. Since code clones often negatively impact the maintainability of a software system, several code clone detection techniques and tools have been…
Atom probe tomography is commonly used to study solute clustering and precipitation in materials. However, standard techniques, such as the density based spatial clustering applications with noise (DBSCAN) perform poorly with respect to…