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All cognitive agents are composite beings. Specifically, complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behavior science, evolutionary developmental biology,…
Chromosome classification is critical for karyotyping in abnormality diagnosis. To expedite the diagnosis, we present a novel method named Varifocal-Net for simultaneous classification of chromosome's type and polarity using deep…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
This paper introduces a novel toolbox named BIDEAL for the generation of biclusters, their analysis, visualization, and validation. The objective is to facilitate researchers to use forefront biclustering algorithms embedded on a single…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse…
In this paper, we will show that the recently introduced graphical model: Conditional Random Fields (CRF) provides a template to integrate micro-level information about biological entities into a mathematical model to understand their…
Background: To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding…
Representing distributions over permutations can be a daunting task due to the fact that the number of permutations of $n$ objects scales factorially in $n$. One recent way that has been used to reduce storage complexity has been to exploit…
Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate…
Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Clustering is an unsupervised learning method that constitutes a cornerstone of an intelligent data analysis process. It is used for the exploration of inter-relationships among a collection of patterns, by organizing them into homogeneous…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Slot filling is a crucial component in task-oriented dialog systems that is used to parse (user) utterances into semantic concepts called slots. An ontology is defined by the collection of slots and the values that each slot can take. The…
Recently, evolutionary multitasking (EMT) has been successfully used in the field of high-dimensional classification. However, the generation of multiple tasks in the existing EMT-based feature selection (FS) methods is relatively simple,…
Federated learning is generally used in tasks where labels are readily available (e.g., next word prediction). Relaxing this constraint requires design of unsupervised learning techniques that can support desirable properties for federated…
Responsible for many complex human diseases including cancers, disrupted or abnormal gene interactions can be identified through their expression changes correlating with the progression of a disease. However, the examination of all…