MD-HIT: Machine learning for materials property prediction with dataset redundancy control
Materials datasets are usually featured by the existence of many redundant
(highly similar) materials due to the tinkering material design practice over
the history of materials research. For example, the materials project database
has many perovskite cubic structure materials similar to SrTiO$_3$. This sample
redundancy within the dataset makes the random splitting of machine learning
model evaluation to fail so that the ML models tend to achieve over-estimated
predictive performance which is misleading for the materials science community.
This issue is well known in the field of bioinformatics for protein function
prediction, in which a redundancy reduction procedure (CD-Hit) is always
applied to reduce the sample redundancy by ensuring no pair of samples has a
sequence similarity greater than a given threshold. This paper surveys the
overestimated ML performance in the literature for both composition based and
structure based material property prediction. We then propose a material
dataset redundancy reduction algorithm called MD-HIT and evaluate it with
several composition and structure based distance threshold sfor reducing data
set sample redundancy. We show that with this control, the predicted
performance tends to better reflect their true prediction capability. Our
MD-hit code can be freely accessed at https://github.com/usccolumbia/MD-HIT