Related papers: Visualizing Gene Ontology annotations
Information system designers face many challenges w.r.t. selecting appropriate semantic technologies and deciding on a modelling approach for their system. However, there is no clear methodology yet to evaluate "semantically enriched"…
Recent advances in deep neuroevolution have demonstrated that evolutionary algorithms, such as evolution strategies (ES) and genetic algorithms (GA), can scale to train deep neural networks to solve difficult reinforcement learning (RL)…
This study presents a versatile ontology and a useful codification scheme for describing all kinds of engineered living materials (ELMs). The different components of the ontology, namely: families according to the taxonomy for ELMs,…
One of the challenges in analyzing high-dimensional expression data is the detection of important biological signals. A common approach is to apply a dimension reduction method, such as principal component analysis. Typically, after…
Conceptual Graphs (CGs) are a formalism to represent knowledge. However producing a CG database is complex. To the best of our knowledge, existing methods do not fully use the expressivity of CGs. It is particularly troublesome as it is…
Over the last decades, hand-crafted feature extractors have been used to encode image visual properties into feature vectors. Recently, data-driven feature learning approaches have been successfully explored as alternatives for producing…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
Testing provides means pertaining to assuring software performance. The total aim of software industry is actually to make a certain start associated with high quality software for the end user. However, associated with software testing has…
Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present…
Annotations are a critical component of visualizations, helping viewers interpret the visual representation and highlighting critical data insights. Despite their significant role, we lack an understanding of how annotations can be…
The Semantic Web is becoming a large scale framework that enables data to be published, shared, and reused in the form of ontologies. The ontology which is considered as basic building block of semantic web consists of two layers including…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
Periodically occurring accumulations of events or measured values are present in many time-dependent datasets and can be of interest for analyses. The frequency of such periodic behavior is often not known in advance, making it difficult to…
Explainable Artificial Intelligence (or xAI) has become an important research topic in the fields of Machine Learning and Deep Learning. In this paper, we propose a Genetic Programming (GP) based approach, named Genetic Programming…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
The primary aim of automated performance improvement is to reduce the running time of programs while maintaining (or improving on) functionality. In this paper, Genetic Programming is used to find performance improvements in regular…
Understanding the molecular processes that drive cellular life is a fundamental question in biological research. Ambitious programs have gathered a number of molecular datasets on large populations. To decipher the complex cellular…
Knowledge Graphs (KG) constitute a flexible representation of complex relationships between entities particularly useful for biomedical data. These KG, however, are very sparse with many missing edges (facts) and the visualisation of the…