Search bioRxivSearch

Biology subjects

Sorokin, J.

Publications and source records attributed to Sorokin, J..

2 recordsLinked to original sources

An Evolving-Dynamic Network Activity Approach toEpileptic Seizure Prediction using Machine Learning

Absence epilepsy is a neurological condition characterized by abnormally synchronous electrical activity within two mutually connected brain regions, the thalamus and cortex, that results in seizures and affects more than 6.5 million people. Epilepsy is commonly studied through the use of the electroencephalogram (EEG), a device that monitors brain waves over time. In this study, we introduced machine learning models to predict epileptic seizures in two ways, one to train logistic regression models to provide an accurate decision boundary to predict based off frequency features, and second to train convolutional neural networks to predict based off spectral power images from EEG. This pipeline employed a two model approach, using logistic regression and convolutional neural networks to predict seizures. The evaluation, performed on data from 9 mice, achieved prediction accuracies of 98%. The proposed methodology introduces a novel aspect of looking at predicting absence seizures, which are known to be short events, in addition to the comparison between a time-dependent and time-agnostic seizure prediction classifier. The overall goal of these experiments were to build a model that can accurately predict whether or not a seizure will occur.

neuroscience

Optimization and scaling of patient-derived brain organoids uncovers deep phenotypes of disease

Cerebral organoids provide unparalleled access to human brain development in vitro. However, variability induced by current culture methodologies precludes using organoids as robust disease models. To address this, we developed an automated Organoid Culture and Assay (ORCA) system to support longitudinal unbiased phenotyping of organoids at scale across multiple patient lines. We then characterized organoid variability using novel machine learning methods and found that the contribution of donor, clone, and batch is significant and remarkably consistent over gene expression, morphology, and cell-type composition. Next, we performed multi-factorial protocol optimization, producing a directed forebrain protocol compatible with 96-well culture that exhibits low variability while preserving tissue complexity. Finally, we used ORCA to study tuberous sclerosis, a disease with known genetics but poorly representative animal models. For the first time, we report highly reproducible early morphological and molecular signatures of disease in heterozygous TSC+/- forebrain organoids, demonstrating the benefit of a scaled organoid system for phenotype discovery in human disease models.

neuroscience