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drawing

About

The repository consists of information assosicated with the research on uncertainity quantification for graph neural network architectures. This work was part of an internship at ANL in the Mathematics and Computer Sciences (MCS) division. The repository has 5 directories:

  • data/ - The directory that consists of the datasets in the form of pickled files
  • literature/ - Summaries of all the scholarly articles that are read through the course of the project.
  • src/ - Code, documentation, and essential information about the models built for the project.
  • scripts/ - Essential scripts necessary for setting up the project.
  • tests/ - Deterministic unit tests for better replication of the results.
  • notebooks/ - Jupyter notebook(s) with sample code showcasing how to utilize the resources of the project.

Installation

Install the appropriate python packages

pip install -r requirements.txt

Data

We have used two datasets. The idea was to perform uncertainty quantification on Fully Connected Networks, and Graph Neural Networks. So, for the Fully Connected Networks we generated a sin dataset of sample size 1201 with gaussian noise given by, y = 10 sin(x) + ε. The dataset looks like this:

data

For the Graph Neural Networks, we have used the Quantum Chemistry dataset, QM7.

Both of the datasets have single output and would be mapped as regression problems.

Experiments

We built simple deep neural networks for predicting the response variable. We then estimated the uncertainties in the models predicting the response values. We tried different approaches and as a result some of the methods that we used supported quantification of both aleatoric, and epistemic uncertainties, while the remaining weren't equipped for the same. The approaches we have tried could potentially be categorized into ones that are capable of estimating both aleatoric, and epistemic uncertainties, and others that can only estimate epistemic uncertainties.

Methods that can approximate both aleatoric and epistemic uncertainty :


Methods that can approximate only epistemic uncertainty :

For the models predicting the y values of the sin dataset, we have used a simple one hidden layer fully connected neural network. The following are the architectural details:

Model Optimum hyper parameters
Epochs 200,
1500 for BNN
Batch size 128
Loss Function MSE,
Gaussian Loss for DeepEnsemble,
Negative log likelihood for BNN,
Pinball Loss for SQR+ONC
Hidden Layers 1 layer with 256 neurons
Optimization function Adam with 0.001 learning rate
Activation function(s) ReLU for the hidden layer,
Linear for the o/p layer

Results

Linear regression on the sin dataset:

Model MSE MAE RMSE R2 Training time Inference Time
Fully Connected Network (FCN) 1.0053 0.8078 1.0026 0.9813 33.4 s 246 ms
FCN with MC Dropout 1.4041 0.9555 1.1849 0.9740 15.7 s 54.7 s
FCN with Ensemble MC Dropout 1.4430 0.9697 1.2012 0.9733 5min 56s 32min 19s
FCN with DeepEnsembles 0.9531 0.7767 0.9763 0.9820 10min 25s 1min 50s
FCN with SQR, and ONC 1.0929 0.8318 1.0454 0.9793 43s 10.2s
Bayesian Neural Network 3.3879 1.4489 1.9418 0.953 8min 39s 44s

Linear regression on the QM7 dataset :

On the test set,

Model MSE MAE RMSE R2 Training Time Inference Time
Graph Convolutional Network (GCN) 15498.9595 75.9521 124.4948 0.6830 2min 30s 444 ms
GCN with MC Dropout 23116.5562 119.5583 152.0412 0.5272 1min 51s 8.46 s
GCN with Ensemble MC Dropout 23382.3769 121.7387 152.9129 0.5218 1h 45s 6min 46s
GCN with DeepEnsembles 15726.9933 76.9819 125.3840 0.6783 1h 3min 15s 2min 59s
GCN with SQR, and ONC 21182.1737 99.7401 145.5409 0.5668 2min 30s 579 ms
Bayesian Graph Neural Network - - - -

On the validation set,

Model MSE MAE RMSE R2 Inference Time
Graph Convolutional Network (GCN) 10658.5007 68.3195 103.2400 0.7811 153 ms
GCN with MC Dropout 17058.3652 106.2512 130.6076 0.6497 7.99 s
GCN with Ensemble MC Dropout 18296.0994 112.2832 135.2630 0.6243s 3min 36s
GCN with DeepEnsembles 10529.2807 67.4484 102.5716 0.7838 4.01 s
GCN with SQR, and ONC 17238.2398 94.7970 131.2944 0.6460 427 ms
Bayesian Graph Neural Network - - - -

Author

Akhil Pandey

Mentor

Prasanna Balaprakash