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The in vitro clonogenic assay is a technique to study the ability of a cell to form a colony in a culture dish. By optical imaging, dishes with stained colonies can be scanned and assessed digitally. Identification, segmentation and…

Splice detection models are the need of the hour since splice manipulations can be used to mislead, spread rumors and create disharmony in society. However, there is a severe lack of image splicing datasets, which restricts the capabilities…

We study the problem of instance segmentation in biological images with crowded and compact cells. We formulate this task as an integer program where variables correspond to cells and constraints enforce that cells do not overlap. To solve…

In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…

Mapping the connectivity of neurons in the brain (i.e., connectomics) is a challenging problem due to both the number of connections in even the smallest organisms and the nanometer resolution required to resolve them. Because of this,…

Artificial intelligence is nowadays used for cell detection and classification in optical microscopy, during post-acquisition analysis. The microscopes are now fully automated and next expected to be smart, to make acquisition decisions…

Automated cellular instance segmentation is a process utilized for accelerating biological research for the past two decades, and recent advancements have produced higher quality results with less effort from the biologist. Most current…

Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…

In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…

In conventional clinical in-vitro fertilization practices embryos are transferred either at the cleavage or blastocyst stages of development. Cleavage stage transfers, particularly, are beneficial for patients with relatively poor prognosis…

To identify potential universal cellular automata, a method is developed to measure information processing capacity of elementary cellular automata. We consider two features of cellular automata: Ability to store information, and ability to…

A well-designed fine-grained categorization system usually has three contradictory requirements: accuracy (the ability to identify objects among subordinate categories); interpretability (the ability to provide human-understandable…

In the field of transmission electron microscopy, data interpretation often lags behind acquisition methods, as image processing methods often have to be manually tailored to individual datasets. Machine learning offers a promising approach…

Splicing systems are generative mechanisms introduced by Tom Head in 1987 to model the biological process of DNA recombination. The computational engine of a splicing system is the "splicing operation", a cut-and-paste binary string…

This work makes a substantial step in the field of split computing, i.e., how to split a deep neural network to host its early part on an embedded device and the rest on a server. So far, potential split locations have been identified…

Locating the promoter region in DNA sequences is of paramount importance in the field of bioinformatics. This is a problem widely studied in the literature, however, not yet fully resolved. Some researchers have presented remarkable results…

Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…

Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential…

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate…

Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its…