Biology subjects

Pandarinath, C.

Publications and source records attributed to Pandarinath, C..

22 records · Page 2Linked to original sources

bioRxiv2021

Representation learning for neural population activity with Neural Data Transformers

Neural population activity is theorized to reflect an underlying dynamical structure. This structure can be accurately captured using state space models with explicit dynamics, such as those based on recurrent neural networks (RNNs). However, using recurrence to explicitly model dynamics necessitates sequential processing of data, slowing real-time applications such as brain-computer interfaces. Here we introduce the Neural Data Transformer (NDT), a non-recurrent alternative. We test the NDTs ability to capture autonomous dynamical systems by applying it to synthetic datasets with known dynamics and data from monkey motor cortex during a reaching task well-modeled by RNNs. The NDT models these datasets as well as state-of-the-art recurrent models. Further, its non-recurrence enables 3.9ms inference, well within the loop time of real-time applications and more than 6 times faster than recurrent baselines on the monkey reaching dataset. These results suggest that an explicit dynamics model is not necessary to model autonomous neural population dynamics. Codegithub.com/snel-repo/neural-data-transformers.

neuroscience↗

bioRxiv2021

A large-scale neural network training framework for generalized estimation of single-trial population dynamics

Recent technical advances have enabled recording of increasingly large populations of neural activity, even during natural, unstructured behavior. Deep sequential autoencoders are the current state-of-the-art for uncovering dynamics from these datasets. However, these highly complex models include many non-trainable hyperparameters (HPs) that are typically hand tuned with reference to supervisory information (e.g., behavioral data). This process is cumbersome and time consuming and biases model selection toward models with good representations of individual supervisory variables. Additionally, it cannot be applied to cognitive areas or unstructured tasks for which supervisory information is unavailable. Here we demonstrate AutoLFADS, an automated model-tuning framework that can characterize dynamics using only neural data, without the need for supervisory information. This enables inference of dynamics out-of-the-box in diverse brain areas and behaviors, which we demonstrate on several datasets: motor cortex during free-paced reaching, somatosensory cortex during reaching with perturbations, and dorsomedial frontal cortex during cognitive timing tasks. We also provide a cloud software package and comprehensive tutorials that enable new users to apply the method without dedicated computing resources.

neuroscience↗

bioRxiv2020

Distinct representations of finger movement and force in human motor and premotor cortices

The ability to grasp and manipulate objects requires controlling both finger movement kinematics and isometric force. Previous work suggests that these behavioral modes are controlled separately, but it is unknown whether the cerebral cortex represents them differently. Here, we investigated this question by recording high-density electrocorticography from the motor and premotor cortices of seven human subjects performing a sequential movement-force motor task. We decoded finger movement (0.7{+/-}0.3 fractional variance account for; FVAF) and force (0.7{+/-}0.2 FVAF) with high accuracy, yet found different spatial representations. We also found clear distinctions in electrocorticographic activity by using deep learning methods to uncover state-space representations, and by developing a new metric, the neural vector angle. Thus, state-space techniques can help to investigate broad cortical networks. Finally, we were able to classify the behavioral mode from neural signals with high accuracy (90{+/-}6%). Thus, finger movement and force have distinct representations in motor/premotor cortices. This will inform our understanding of the neural control of movement as well as the design of grasp brain-machine interfaces.

neuroscience↗

bioRxiv2017

Inferring single-trial neural population dynamics using sequential auto-encoders

Neuroscience is experiencing a data revolution in which simultaneous recording of many hundreds or thousands of neurons is revealing structure in population activity that is not apparent from single-neuron responses. This structure is typically extracted from trial-averaged data. Single-trial analyses are challenging due to incomplete sampling of the neural population, trial-to-trial variability, and fluctuations in action potential timing. Here we introduce Latent Factor Analysis via Dynamical Systems (LFADS), a deep learning method to infer latent dynamics from single-trial neural spiking data. LFADS uses a nonlinear dynamical system (a recurrent neural network) to infer the dynamics underlying observed population activity and to extract de-noised single-trial firing rates from neural spiking data. We apply LFADS to a variety of monkey and human motor cortical datasets, demonstrating its ability to predict observed behavioral variables with unprecedented accuracy, extract precise estimates of neural dynamics on single trials, infer perturbations to those dynamics that correlate with behavioral choices, and combine data from non-overlapping recording sessions (spanning months) to improve inference of underlying dynamics. In summary, LFADS leverages all observations of a neural populations activity to accurately model its dynamics on single trials, opening the door to a detailed understanding of the role of dynamics in performing computation and ultimately driving behavior.

neuroscience↗