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Local field potentials (LFPs) sampled with extracellular electrodes are frequently used as a measure of population neuronal activity. However, relating such measurements to underlying neuronal behaviour and connectivity is non-trivial. To…
A fundamental problem in neuroscience is understanding how a network's properties dictate its function. Connectomics provides one avenue to predict nervous system function. To test this explicitly, we systematically measure signal…
Electromagnetic Navigation Systems (eMNS) can be used to control a variety of multiscale devices within the human body for remote surgery. Accurate modeling of the magnetic fields generated by the electromagnets of an eMNS is crucial for…
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data…
Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic,…
Meta-learning traditionally relies on backpropagation through entire tasks to iteratively improve a model's learning dynamics. However, this approach is computationally intractable when scaled to complex tasks. We propose a distributed…
Metagenomic taxonomic annotation aims to identify the microbial origins of DNA fragments in environmental samples. Traditional methods that rely on sequence similarity are often constrained by the high microbial diversity and the…
Electroencephalograph (EEG) is a crucial tool for studying brain activity. Recently, self-supervised learning methods leveraging large unlabeled datasets have emerged as a potential solution to the scarcity of widely available annotated EEG…
Many evolutionary algorithms (EAs) take advantage of parallel evaluation of candidates. However, if evaluation times vary significantly, many worker nodes (i.e.,\ compute clients) are idle much of the time, waiting for the next generation…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We develop an artificial neural circuit for contour tracking and navigation inspired by the chemotaxis of the nematode Caenorhabditis elegans. In order to harness the computational advantages spiking neural networks promise over their…
Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
We introduce a simple, easy to implement, and computationally efficient tropical convolutional neural network architecture that is robust against adversarial attacks. We exploit the tropical nature of piece-wise linear neural networks by…
Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design…
Despite recent interest in reconstructing neuronal networks, complete wiring diagrams on the level of individual synapses remain scarce and the insights into function they can provide remain unclear. Even for Caenorhabditis elegans, whose…
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees…
Neuron segmentation from electron microscopy (EM) volumes is crucial for understanding brain circuits, yet the complex neuronal structures in high-resolution EM images present significant challenges. EM data exhibits unique characteristics…
This work tackles the problem of characterizing and understanding the decision boundaries of neural networks with piecewise linear non-linearity activations. We use tropical geometry, a new development in the area of algebraic geometry, to…