Rezaei, M. R. | bioRxiv Science

bioRxiv2020

Deep Recurrent Neural Network and Point Process Filter Approaches in Multidimensional Neural Decoding Problems

Recent technological and experimental advances in recording from neural systems have led to a significant increase in the type and volume of data being collected in neuroscience experiments. This brings an increasing demand for development of appropriate analytical tools to analyze large scale neuroscience data. Simultaneously, advancement in deep neural networks (DNNs) and statistical modeling frameworks have provided new techniques for analysis of diverse forms of neuroscience data. DNNs like Long short-term memory (LSTM) or statistical modeling approaches like state-space point-process (SSPP) are widely used in the analysis of neural data including neural coding and inference analysis. Despite wide utilization of these techniques, there is a lack of comprehensive studies which systematically assess attributes of LSTM and SSPP approaches on a common neuroscience data analysis problem. As a result, this occasionally leads to inconsistent and divergent conclusions on the strength or weakness of either of the methodologies and also statistical significance of the analytical outcomes. In this research, we focus on providing a more systematic and multifaceted assessment of LSTM and SSPP techniques in a neural decoding problem. We examine different settings and modeling specifications to attain the optimal modeling solutions. We propose new LSTM network topologies and approximate filter solution to estimate a rat movement trajectory in a 2-D spaces using an ensemble of place cells spiking activity. For each technique; we then study performance, computational efficiency, and generalizability of each technique in this decoding problem. By utilizing these results, we provided a succinct picture of the strength and weakness of each modeling approach and suggest who each of these techniques can be properly utilized in neural decoding problems.

bioinformatics↗

bioRxiv2018

Real-Time Point Process Filter for Multidimensional Decoding Problems Using Mixture Models

There is an increasing demand for a computationally efficient and accurate point process filter solution for real-time decoding of population spiking activity in multidimensional spaces. Real-time tools for neural data analysis, specifically real-time neural decoding solutions open doors for developing experiments in a closed-loop setting and more versatile brain-machine interfaces. Over the past decade, the point process filter has been successfully applied in the decoding of behavioral and biological signals using spiking activity of an ensemble of cells; however, the filter solution is computationally expensive in multi-dimensional filtering problems. Here, we propose an approximate filter solution for a general point-process filter problem when the conditional intensity of a cells spiking activity is characterized using a Mixture of Gaussians. We propose the filter solution for a broader class of point process observation called marked point-process, which encompasses both clustered - mainly, called sorted - and clusterless - generally called unsorted or raw- spiking activity. We assume that the posterior distribution on each filtering time-step can be approximated using a Gaussian Mixture Model and propose a computationally efficient algorithm to estimate the optimal number of mixture components and their corresponding weights, mean, and covariance estimates. This algorithm provides a real-time solution for multi-dimensional point-process filter problem and attains accuracy comparable to the exact solution. Our solution takes advantage of mixture dropping and merging algorithms, which collectively control the growth of mixture components on each filtering time-step. We apply this methodology in decoding a rats position in both 1-D and 2-D spaces using clusterless spiking data of an ensemble of rat hippocampus place cells. The approximate solution in 1-D and 2-D decoding is more than 20 and 4,000 times faster than the exact solution, while their accuracy in decoding a rat position only drops by less than 9% and 4% in RMSE and 95% HPD coverage performance metrics. Though the marked-point filter solution is better suited for real-time decoding problems, we discuss how the filter solution can be applied to sorted spike data to better reflect the proposed methodology versatility.

bioinformatics↗