Saturday, August 28, 2021

Evidential Deep Learning for Guided Molecular Property Prediction and Discovery

Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, and Connor W. Coley 2021
Highlighted by Jan Jensen

TOC figure from the paper. (c) 2021 The authors. Reproduced under the CC BY NC ND license

While knowing the uncertainty of a ML-predicted value is valuable, it is really only the Gaussian process method that delivers a rigorous estimate of this. If you want to use other ML methods such as NN you have to use more ad hoc methods like the ensemble or dropout methods and these only report of the uncertainty in the model parameters (if you retrain your model you'll get slightly different answers) and not on the uncertainty in the data (if you remeasure your data you'll get slightly different answers).

This paper presents a way to quantify both types of uncertainty for NN models (evidential learning). To apply it you change your output layer to output 4 values instead of 1 and you use a special loss function. One of the four output values is your prediction while the remaining 3 output values are plugged into a formula that gives you the uncertainty.

The paper compares this approach to the ensemble and dropout methods and shows that the evidential learning approach usually works better, i.e. there's a better correlation between the predicted uncertainty and the deviation from the ground truth. Note that it's a little tricky to quantify this correlation: if the error is random (which is the basic assumption behind all this) then the error can, by chance, be very small for a point with large uncertainty; it's just less likely compared to a point with low uncertainty. 

The code is available here (note the link in the paper is wrong)

This work is licensed under a Creative Commons Attribution 4.0 International License.