LINGO Profiles Fingerprint and Association Rule Mining for drug-target interaction prediction
Abstract
The prediction of drug-target interactions (DTIs) using machine learning techniques together with the proper representation of compounds can speed up the time-consuming experimental work in predicting DTIs especially when a large dataset is used. Hence, in this paper, we have proposed a new molecular descriptor based on LINGO Profiles known as LINGO Profiles Fingerprint (LPFP). LPFP is used together with machine learning to predict DTIs on a ChEMBL dataset. Dimensionality reduction using Association Rule Mining (ARM) is also introduced to overcome the high dimensionality suffered by LPFP. LPFP managed to reach an equal accuracy reading to the state-of-the-art descriptor called ECFP4 (Δ0.18%), but it suffers in the time taken (Δ27 mins) due to the dimensionality problem mentioned. Hence, three new smaller size LPFPs (s = 60%, s = 70%, s = 80%) were constructed by only extracting the important fragments using ARM and then a benchmark analysis with the original LPFP and ECFP4 fingerprints was done. This study not only solved the dimensionality problem, but also managed to excel in both the accuracy and time taken when predicting DTIs. An increase in the accuracy of over 250 times faster than the original LPFP was observed after the benchmark analysis is performed. Furthermore, an accuracy of over 80% was achieved in three new activity classes that are acquired from ChEMBL, further proving the promising performance of ARM which has made it favourable for LPFPs to be used in DTI prediction and in other drug discovery problems.
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