Benchmarking Unsupervised Clustering Algorithms for Atomic Force Microscopy Data on Polyhydroxyalkanoate Films

Abstract

Surface of polyhydroxyalkanoate (PHA) films of varying monomer compositions are analyzed using atomic force microscopy (AFM) and unsupervised machine learning (ML) algorithms to investigate and classify films based on global attributes such as the scan size, film thickness, and monomer type. The experiment provides benchmarked results for 12 of the most widely used clustering algorithms via a hybrid investigation approach while highlighting the impact of using the Fourier transform (FT) on high-dimensional vectorized data for classification on various pools of data. Our findings indicate that the use of a one-dimensional (1D) FT of vectorized data produces the most accurate outcome. The experiment also provides insights into case-by-case investigations of algorithm performances and the impact of various data pools. Lastly, we show an early version of our tool aimed at investigating surfaces using ML approaches and discuss the results of our current experiment to configure future improvements.