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Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity
Byron M Yu · John P Cunningham · Gopal Santhanam · Stephen I Ryu · Krishna V Shenoy · Maneesh Sahani

Mon Dec 08 08:45 PM -- 12:00 AM (PST) @

We consider the problem of extracting smooth low-dimensional neural trajectories'' that summarize the activity recorded simultaneously from tens to hundreds of neurons on individual experimental trials. Beyond the benefit of visualizing the high-dimensional noisy spiking activity in a compact denoised form, such trajectories can offer insight into the dynamics of the neural circuitry underlying the recorded activity. Current methods for extracting neural trajectories involve a two-stage process: the data are firstdenoised'' by smoothing over time, then a static dimensionality reduction technique is applied. We first describe extensions of the two-stage methods that allow the degree of smoothing to be chosen in a principled way, and account for spiking variability that may vary both across neurons and across time. We then present a novel method for extracting neural trajectories, Gaussian-process factor analysis (GPFA), which unifies the smoothing and dimensionality reduction operations in a common probabilistic framework. We applied these methods to the activity of 61 neurons recorded simultaneously in macaque premotor and motor cortices during reach planning and execution. By adopting a goodness-of-fit metric that measures how well the activity of each neuron can be predicted by all other recorded neurons, we found that GPFA provided a better characterization of the population activity than the two-stage methods. From the extracted single-trial neural trajectories, we directly observed a convergence in neural state during motor planning, an effect suggestive of attractor dynamics that was shown indirectly by previous studies.

Author Information

Byron M Yu (Carnegie Mellon University)
John P Cunningham (Columbia University)
Gopal Santhanam
Stephen I Ryu (Dept Electrical Eng., Stanford University)
Krishna V Shenoy (Stanford University)
Maneesh Sahani (Gatsby Unit, UCL)

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