Related papers: AOC: Analysis of Orthologous Collections -- an app…
Code retrieval helps developers reuse the code snippet in the open-source projects. Given a natural language description, code retrieval aims to search for the most relevant code among a set of code. Existing state-of-the-art approaches…
Searching, filtering and analysing scientific literature are time-consuming tasks when performing a systematic literature review. With the rise of artificial intelligence, some steps in the review process are progressively being automated.…
The Software Development Life Cycle (SDLC) starts with eliciting requirements of the customers in the form of Software Requirement Specification (SRS). SRS document needed for software development is mostly written in Natural Language(NL)…
Self-organized criticality (SOC) is a popular concept that has been the subject of more than 3000 articles in the last 25 years. Here we show that SOC may enable theory to connect standard Web-based (BLAST) short-range amino acid (aa)…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
Deep neural network predictions are notoriously difficult to interpret. Feature attribution methods aim to explain these predictions by identifying the contribution of each input feature. Faithfulness, often evaluated using the area over…
Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of…
One-class classification (OCC) algorithms aim to build classification models when the negative class is either absent, poorly sampled or not well defined. This unique situation constrains the learning of efficient classifiers by defining…
Public repositories for genome and proteome annotations, such as the Gene Ontology (GO), rarely stores negative annotations, i.e. proteins not possessing a given function. This leaves undefined or ill defined the set of negative examples,…
Through discovery of meso-scale structures, community detection methods contribute to the understanding of complex networks. Many community finding methods, however, rely on disjoint clustering techniques, in which node membership is…
Pseudocode in a scholarly paper provides a concise way to express the algorithms implemented therein. Pseudocode can also be thought of as an intermediary representation that helps bridge the gap between programming languages and natural…
Motivation: The size of available omics datasets is steadily increasing with technological advancement in recent years. While this increase in sample size can be used to improve the performance of relevant prediction tasks in healthcare,…
Existing object detectors often struggle to generalize across domains while adapting to emerging novel categories. Adaptive open-set object detection (AOOD) addresses this challenge by training on base categories in the source domain and…
Accurate screening of cancer types is crucial for effective cancer detection and precise treatment selection. However, the association between gene expression profiles and tumors is often limited to a small number of biomarker genes. While…
Use case specifications have successfully been used for requirements description. They allow joining, in the same modeling space, the expectations of the stakeholders as well as the needs of the software engineer and analyst involved in the…
Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
Adaptive categorization of visual scenes is essential for AI agents to handle changing tasks. Unlike fixed common categories for plants or animals, ad-hoc categories are created dynamically to serve specific goals. We study open ad-hoc…
The SemanticWeb emerged as an extension to the traditional Web, towards adding meaning to a distributed Web of structured and linked data. At its core, the concept of ontology provides the means to semantically describe and structure…
In the evolutionary computation research community, the performance of most evolutionary algorithms (EAs) depends strongly on their implemented coordinate system. However, the commonly used coordinate system is fixed and not well suited for…