Publication Date



Open access

Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Biomedical Engineering (Engineering)

Date of Defense


First Committee Member

Abhishek Prasad

Second Committee Member

Odelia Schwartz

Third Committee Member

Jorge Bohórquez

Fourth Committee Member

Suhrud M. Rajguru

Fifth Committee Member

Ozcan Ozdamar


Objective: Brain machine interface (BMI) or Brain Computer Interface (BCI) provides a direct pathway between the brain and an external device to help people suffering from severely impaired motor function by decoding brain activities and translating human intentions into control signals. Conventionally, the decoding pipeline for BMIs consists of chained different stages of feature extraction, time-frequency analysis and statistical learning models. Each of these stages uses a different algorithm trained in a sequential manner, which makes the whole system difficult to be adaptive. Our goal is to create differentiable signal processing modules and plug them together to build an adaptive online system. The system could be trained with a single objective function and a single learning algorithm so that each component can be updated in parallel to increase the performance in a robust manner. We use deep neural networks to address these needs. Main Results: We predicted the finger trajectory using Electrocorticography (ECoG) signals and compared results for the Least Angle Regression (LARS), Convolutional Long Short Term Memory Network (Conv-LSTM), Random Forest (RF), and a pipeline consisting of band-pass filtering, energy extraction, feature selection and linear regression. The results showed that the deep learning models performed better than the commonly used linear model. The deep learning models not only gave smoother and more realistic trajectories but also learned the transition between movement and rest state. We also estimated the source connectivity of the brain signals using a Recurrent Neural Network (RNN) and it correctly estimated the order and sparsity level of the underlying Multivariate Auto-regressive process (MVAR). The time course of the source connectivity was also recovered. Significance: We replace the conventional signal processing pipeline with differentiable modules so that the whole BMI system is adaptive. The study of the decoding system demonstrated a model for BMI that involved a convolutional and recurrent neural network. It integrated the feature extraction pipeline into the convolution and pooling layer and used Long Short Term Memory (LSTM) layer to capture the state transitions. The decoding network eliminated the need to separately train the model at each step in the decoding pipeline. The whole system can be jointly optimized using stochastic gradient descent and is capable of online learning. The study of the source connectivity estimation demonstrated a generative RNN model that can estimate the un-mixing matrix and the MVAR coefficients of the source activity at the same time. Our method addressed the issue of estimation and inference of the non-stationary MVAR coefficients and the un-mixing matrix in the presence of non-gaussian noise. More importantly, this model can be easily plugged into the BMI decoding system as a differentiable feature extraction module.


brain machine interface; signal processing; recurrent neural network; convolutional neural network; trajectory decoding; connectivity analysis