Related papers: AOC: Analysis of Orthologous Collections -- an app…
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…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
This paper presents eye2vec, an infrastructure for analyzing software developers' eye movements while reading source code. In common eye-tracking studies in program comprehension, researchers must preselect analysis targets such as control…
We compare the ability of a simulated annealing program and an evolutionary algorithm to find molecules with large molecular average hyperpolarizabilities. This property is an important component of nonlinear optical materials. Both…
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…
This paper introduces a new optimisation algorithm, called Adaptive Bacterial Colony Optimisation (ABCO), modelled after the foraging behaviour of E. coli bacteria. The algorithm follows three stages--explore, exploit and reproduce--and is…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
An ordinal classification (OC) problem corresponds to a special type of classification characterised by the presence of a natural order relationship among the classes. This type of problem can be found in a number of real-world…
Bias is an inherent threat to human decision-making, including in decisions made during software development. Extensive research has demonstrated the presence of biases at various stages of the software development life-cycle. Notably, code…
Automatic optical inspection (AOI) plays a pivotal role in the manufacturing process, predominantly leveraging high-resolution imaging instruments for scanning purposes. It detects anomalies by analyzing image textures or patterns, making…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
The paper addresses challenges in storing and retrieving sequences in contexts like anomaly detection, behavior prediction, and genetic information analysis. Associative Knowledge Graphs (AKGs) offer a promising approach by leveraging…
Classifying nodes in knowledge graphs is an important task, e.g., for predicting missing types of entities, predicting which molecules cause cancer, or predicting which drugs are promising treatment candidates. While black-box models often…
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
The World Wide Web Consortium (W3C) has published several recommendations for building and storing ontologies, including the most recent OWL 2 Web Ontology Language (OWL). These initiatives have been followed by practical implementations…
Biclustering has gained interest in gene expression data analysis due to its ability to identify groups of samples that exhibit similar behaviour in specific subsets of genes (or vice versa), in contrast to traditional clustering methods…
This chapter outlines how search engine technology can be used in online public access library catalogs (OPACs) to help improve users experiences, to identify users intentions, and to indicate how it can be applied in the library context,…
Compiler pass auto-tuning is critical for enhancing software performance, yet finding the optimal pass sequence for a specific program is an NP-hard problem. Traditional, general-purpose optimization flags like -O3 and -Oz adopt a…