DeepNCI: DFT Noncovalent Interaction Correction with Transferable Multimodal Three-Dimensional Convolutional Neural...

A multimodal deep learning model, DeepNCI, is proposed for improving noncovalent interactions (NCIs) calculated via density functional theory (DFT). DeepNCI is composed of a three-dimensional convolutional neural network (3D CNN) for abstracting critical and comprehensive features from 3D electron density, and a neural network for modeling one-dimensional quantum chemical properties. By merging features from two networks, DeepNCI is able to reduce the root-mean-square error of DFT-calculated NCI from 1.19 kcal/mol to ∼0.2 kcal/mol for a NCI molecular database (>1000 molecules). The representativeness of the joint features can be visualized by t-distributed stochastic neighbor embedding (t-SNE), where they can distinguish categorized NCI systems quite well. Therefore, the fused model performs better than its component networks. In addition, the 3D CNN takes electron density as inputs that are in the same range, despite the size of molecular systems, so it can promote model applicability and transferability. To clarify the applicability of DeepNCI, an application domain (AD) has been defined with merged features using the K-nearest-neighbor method. The calculations for external test sets are shown that AD can properly monitor the reliability for a prediction. The model transferability is tested with a small database of homolysis bond dissociation energy including only dozens of samples. With NCI database pretrained parameters, the same or better performance than the reported results is achieved by transfer learning. This suggests that the DeepNCI model is transferable and it may transfer to other relative tasks, which possibly can resolve some small sampling problems. The source code of DeepNCI can be freely accessed at https://github.com/wenzelee/DeepNCI.