Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes

Comparison analysis between standard polysomnographic data and in-ear-electroencephalography signals: a preliminary study

Study Objectives

Polysomnography (PSG) currently serves as the benchmark for evaluating sleep disorders. Its discomfort makes long-term monitoring unfeasible, leading to bias in sleep quality assessment. Hence, less invasive, cost-effective, and portable alternatives need to be explored. One promising contender is the in-ear-electroencephalography (EEG) sensor. This study aims to establish a methodology to assess the similarity between the single-channel in-ear-EEG and standard PSG derivations.

Methods

The study involves 4-hour signals recorded from 10 healthy subjects aged 18-60 years. Recordings are analyzed following two complementary approaches: (1) a hypnogram-based analysis aimed at assessing the agreement between PSG and in-ear-EEG-derived hypnograms; and (2) a feature- and analysis-based on time- and frequency-domain feature extraction, unsupervised feature selection, and definition of Feature-based Similarity Index via Jensen-Shannon Divergence (JSD-FSI).

Results

We find large variability between PSG and in-ear-EEG hypnograms scored by the same sleep expert according to Cohen's kappa metric, with significantly greater agreements for PSG scorers than for in-ear-EEG scorers (p < .001) based on Fleiss' kappa metric. On average, we demonstrate a high similarity between PSG and in-ear-EEG signals in terms of JSD-FSI-0.79 ± 0.06-awake, 0.77 ± 0.07-nonrapid eye movement, and 0.67 ± 0.10-rapid eye movement-and in line with the similarity values computed independently on standard PSG channel combinations.

Conclusions

In-ear-EEG is a valuable solution for home-based sleep monitoring; however, further studies with a larger and more heterogeneous dataset are needed.

Deep model predictive control of gene expression in thousands of single cells

Gene expression is inherently dynamic, due to complex regulation and stochastic biochemical events. However, the effects of these dynamics on cell phenotypes can be difficult to determine. Researchers have historically been limited to passive observations of natural dynamics, which can preclude studies of elusive and noisy cellular events where large amounts of data are required to reveal statistically significant effects. Here, using recent advances in the fields of machine learning and control theory, we train a deep neural network to accurately predict the response of an optogenetic system in Escherichia coli cells. We then use the network in a deep model predictive control framework to impose arbitrary and cell-specific gene expression dynamics on thousands of single cells in real time, applying the framework to generate complex time-varying patterns. We also showcase the framework's ability to link expression patterns to dynamic functional outcomes by controlling expression of the tetA antibiotic resistance gene. This study highlights how deep learning-enabled feedback control can be used to tailor distributions of gene expression dynamics with high accuracy and throughput without expert knowledge of the biological system.