PT  - JOURNAL ARTICLE
AU  - Ngoc Tran
AU  - Daniel Kepple
AU  - Sergey A. Shuvaev
AU  - Alexei A. Koulakov
TI  - DeepNose: Using artificial neural networks to represent the space of odorants
AID  - 10.1101/464735
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 464735
4099  - http://biorxiv.org/content/early/2018/11/07/464735.short
4100  - http://biorxiv.org/content/early/2018/11/07/464735.full
AB  - The olfactory system employs an ensemble of odorant receptors (ORs) to sense odorants and to derive olfactory percepts. We trained artificial neural networks to represent the chemical space of odorants and used that representation to predict human olfactory percepts. We hypothesized that ORs may be considered 3D spatial filters that extract molecular features and can be trained using conventional machine learning methods. First, we trained an autoencoder, called DeepNose, to deduce a low-dimensional representation of odorant molecules which were represented by their 3D spatial structure. Next, we tested the ability of DeepNose features in predicting physical properties and odorant percepts based on 3D molecular structure alone. We found that despite the lack of human expertise, DeepNose features led to perceptual predictions of comparable accuracy to molecular descriptors often used in computational chemistry. We propose that DeepNose network can extract de novo chemical features predictive of various bioactivities and can help understand the factors influencing the composition of ORs ensemble.