Spike rate estimation using Bayesian Adaptive Kernel Smoother (BAKS) and its application to brain machine interfaces

Brain Machine Interfaces (BMIs) mostly utilise spike rate as an input feature for decoding a desired motor output as it conveys a useful measure to the underlying neuronal activity. The spike rate is typically estimated by a using non-overlap binning method that yields a coarse estimate. There exist several methods that can produce a smooth estimate which could potentially improve the decoding performance. However, these methods are relatively computationally heavy for real-time BMIs. To address this issue, we propose a new method for estimating spike rate that is able to yield a smooth estimate and also amenable to real-time BMIs. The proposed method, referred to as Bayesian adaptive kernel smoother (BAKS), employs kernel smoothing technique that considers the bandwidth as a random variable with prior distribution which is adaptively updated through a Bayesian framework. With appropriate selection of prior distribution and kernel function, an analytical expression can be achieved for the kernel bandwidth. We apply BAKS and evaluate its impact on of fline BMI decoding performance using Kalman filter. The results show that overlap BAKS improved the decoding performance up to 3.33% and 12.93% compared to overlap and non-overlap binning methods, respectively, depending on the window size. This suggests the feasibility and the potential use of BAKS method for real-time BMIs

Nonhuman Primate Reaching with Multichannel Sensorimotor Cortex Electrophysiology

General Description. This dataset consists of: The threshold crossing times of extracellularly and simultaneously recorded spikes, sorted into units (up to five, including a "hash" unit), along with sorted waveform snippets, and, The x,y position of the fingertip of the reaching hand and the x,y position of reaching targets (both sampled at 250 Hz). The behavioral task was to make self-paced reaches to targets arranged in a grid (e.g. 8x8) without gaps or pre-movement delay intervals. One monkey reached with the right arm (recordings made in the left hemisphere); The other reached with the left arm (right hemisphere). In some sessions recordings were made from both M1 and S1 arrays (192 channels); in most sessions M1 recordings were made alone (96 channels). Data from two primate subjects are included: 37 sessions from monkey 1 ("Indy", spanning about 10 months) and 10 sessions from monkey 2 ("Loco", spanning about 1 month), for a total of ~ 20,000 reaches and 6,500 reaches from monkeys 1 and 2, respectively. Possible uses. These data are ideal for training BCI decoders, in particular because they are not segmented into trials. We expect that the dataset will be valuable for researchers who wish to design improved models of sensorimotor cortical spiking or provide an equal footing for comparing different BCI decoders. Other uses could include analyses of the statistics of arm kinematics, spike noise-correlations or signal-correlations, or for exploring the stability or variability of extracellular recording over sessions. Variable names. Each file contains data in the following format. In the below, n refers to the number of recording channels, u refers to the number of sorted units, and k refers to the number of samples. chan_names - n x 1 A cell array of channel identifier strings, e.g. "M1 001". cursor_pos - k x 2 The position of the cursor in Cartesian coordinates (x, y), mm. finger_pos - k x 3 or k x 6 The position of the working fingertip in Cartesian coordinates (z, -x, -y), as reported by the hand tracker in cm. Thus the cursor position is an affine transformation of fingertip position using the following matrix: $\begin{pmatrix} 0 & 0 \\ -10 & 0 \\ 0 & -10 \end{pmatrix}$ Note that for some sessions finger_pos includes the orientation of the sensor as well; the full state is thus: (z, -x, -y, azimuth, elevation, roll). target_pos - k x 2 The position of the target in Cartesian coordinates (x, y), mm. t - k x 1 The timestamp corresponding to each sample of the cursor_pos, finger_pos, and target_pos, seconds. spikes - n x u A cell array of spike event vectors. Each element in the cell array is a vector of spike event timestamps, in seconds. The first unit (u1) is the "unsorted" unit, meaning it contains the threshold crossings which remained after the spikes on that channel were sorted into other units (u2, u3, etc.) For some sessions spikes were sorted into up to 2 units (i.e. u=3); for others, 4 units (u=5). wf - n x u A cell array of spike event waveform "snippets". Each element in the cell array is a matrix of spike event waveforms. Each waveform corresponds to a timestamp in "spikes". Waveform samples are in microvolts. Videos. For some sessions, we recorded screencasts of the stimulus presentation display using a dedicated hardware video grabber. These screencasts are thus a faithful representation of the stimuli and feedback presented to the monkey and are available for the following sessions: indy_20160921_01 indy_20160930_02 indy_20160930_05 indy_20161005_06 indy_20161006_02 indy_20161007_02 indy_20161011_03 indy_20161013_03 indy_20161014_04 indy_20161017_02 Supplements. The raw broadband neural recordings that the spike trains in this dataset were extracted from are available for the following sessions: indy_20160622_01: doi:10.5281/zenodo.1488440 indy_20160624_03: doi:10.5281/zenodo.1486147 indy_20160627_01: doi:10.5281/zenodo.1484824 indy_20160630_01: doi:10.5281/zenodo.1473703 indy_20160915_01: doi:10.5281/zenodo.1467953 indy_20160916_01: doi:10.5281/zenodo.1467050 indy_20160921_01: doi:10.5281/zenodo.1451793 indy_20160927_04: doi:10.5281/zenodo.1433942 indy_20160927_06: doi:10.5281/zenodo.1432818 indy_20160930_02: doi:10.5281/zenodo.1421880 indy_20160930_05: doi:10.5281/zenodo.1421310 indy_20161005_06: doi:10.5281/zenodo.1419774 indy_20161006_02: doi:10.5281/zenodo.1419172 indy_20161007_02: doi:10.5281/zenodo.1413592 indy_20161011_03: doi:10.5281/zenodo.1412635 indy_20161013_03: doi:10.5281/zenodo.1412094 indy_20161014_04: doi:10.5281/zenodo.1411978 indy_20161017_02: doi:10.5281/zenodo.1411882 indy_20161024_03: doi:10.5281/zenodo.1411474 indy_20161025_04: doi:10.5281/zenodo.1410423 indy_20161026_03: doi:10.5281/zenodo.1321264 indy_20161027_03: doi:10.5281/zenodo.1321256 indy_20161206_02: doi:10.5281/zenodo.1303720 indy_20161207_02: doi:10.5281/zenodo.1302866 indy_20161212_02: doi:10.5281/zenodo.1302832 indy_20161220_02: doi:10.5281/zenodo.1301045 indy_20170123_02: doi:10.5281/zenodo.1167965 indy_20170124_01: doi:10.5281/zenodo.1163026 indy_20170127_03: doi:10.5281/zenodo.1161225 indy_20170131_02: doi:10.5281/zenodo.854733 Contact Information. We would be delighted to hear from you if you find this dataset valuable, especially if it leads to publication. Corresponding author: J. E. O'Doherty <[email protected]>. Publications making use of this dataset. Makin, J. G., O'Doherty, J. E., Cardoso, M. M. B. & Sabes, P. N. (2018). Superior arm-movement decoding from cortex with a new, unsupervised-learning algorithm. J Neural Eng 15(2): 026010. doi:10.1088/1741-2552/aa9e95 Ahmadi, N., Constandinou, T. G., & Bouganis, C. S. (2018). Spike Rate Estimation Using Bayesian Adaptive Kernel Smoother (BAKS) and Its Application to Brain Machine Interfaces. 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Honolulu, HI, USA, 2018, pp. 2547-2550. doi:10.1109/EMBC.2018.8512830 Balasubramanian, M., Ruiz, T., Cook, B., Bhattacharyya, S., Prabhat, Shrivastava, A. & Bouchard K. (2018). Optimizing the Union of Intersections LASSO (UoILASSO) and Vector Autoregressive (UoIVAR) Algorithms for Improved Statistical Estimation at Scale. arXiv preprint arXiv:1808.06992 Ahmadi, N., Constandinou, T. G., & Bouganis, C. S. (2019). Decoding Hand Kinematics from Local Field Potentials Using Long Short-Term Memory (LSTM) Network. arXiv preprint arXiv:1901.00708 Clark, D. G., Livezey, J. A., & Bouchard, K. E. (2019). Unsupervised Discovery of Temporal Structure in Noisy Data with Dynamical Components Analysis. arXiv preprint arXiv:1905.0994