Deep compressive autoencoder for action potential compression in large-scale neural recording

Objective. Understanding the coordinated activity underlying brain computations requires large-scale, simultaneous recordings from distributed neuronal structures at a cellular-level resolution. One major hurdle to design high-bandwidth, high-precision, large-scale neural interfaces lies in the formidable data streams (tens to hundreds of Gbps) that are generated by the recorder chip and need to be online transferred to a remote computer. The data rates can require hundreds to thousands of I/O pads on the recorder chip and power consumption on the order of Watts for data streaming alone. One of the solutions is to reduce the bandwidth of neural signals before transmission. Approach. We developed a deep learning-based compression model to reduce the data rate of multichannel action potentials. The proposed compression model is built upon a deep compressive autoencoder (CAE) with discrete latent embeddings. The encoder network of CAE is equipped with residual transformations to extract representative features from spikes, which are mapped into the latent embedding space and updated via vector quantization (VQ). The indexes of VQ codebook are further entropy coded as the compressed signals. The decoder network reconstructs spike waveforms with high quality from the quantized latent embeddings through stacked deconvolution. Main results. Extensive experimental results on both synthetic and in vivo datasets show that the proposed model consistently outperforms conventional methods that utilize hand-crafted features and/or signal-agnostic transformations and compressive sensing by achieving much higher compression ratios (20-500) and better or comparable reconstruction accuracies. Testing results also indicate that CAE is robust against a diverse range of imperfections, such as waveform variation and spike misalignment, and has minor influence on spike sorting accuracy. Furthermore, we have estimated the hardware cost and real-time performance of CAE and shown that it could support thousands of recording channels simultaneously without excessive power/heat dissipation. Significance. The proposed model can reduce the required data transmission bandwidth in large-scale recording experiments and maintain good signal qualities, which will be helpful to design power-efficient and lightweight wireless neural interfaces. We have open sourced the code implementation of the work at https://github.com/tong-wu-umn/spike-compression-autoencoder.