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From quantum chemical and experimental NMR data, a 3D graph neural network, CASCADE, has been developed to predict carbon and proton chemical shifts. Stereoisomers and conformers of organic molecules can be correctly distinguished.
In the last few years, we have seen the rise of deep learning applications in a broad range of computational chemistry research problems. Using human-engineered chemical features, such as molecular descriptors and fingerprints, deep learning models have shown similar, if not better performance that most traditional machine learning algorithms. Recently, we reported on the development of Chemception, a deep convolutional neural network (CNN) architecture for general-purpose small molecule property prediction. On average, Chemception matched the performance of expert-developed QSAR/QSPR models trained on chemical features (molecular fingerprints), despite that it was trained on just 2D images of molecular drawings with minimal chemical information. Here, we investigate the effects of systematically removing and adding basic chemical information to the image channels of the 2D images used to train Chemception. By augmenting our images with only 3 additional basic chemical information, we demonstrate the improvement of Chemception performance – that it is now more accurate than contemporary deep learning models trained on ECFP fingerprints for the prediction of toxicity, activity and solvation free energy, as well as physics-based free energy simulation methods for computing solvation properties. By altering the chemical information content in the image channels, and examining the resulting performance of Chemception, we also identify to two different “learning patterns” in toxicity/activity as compared to solvation free energy, and it parallels the fundamental differences in contemporary chemistry research for predicting toxicity/activity and solvation free energy.
While a molecular assessment of the perturbations and injury arising from diseases is essential in their diagnosis and treatment, understanding changes due to preventative strategies is also imperative. Currently, complex diseases such as cardiovascular disease (CVD), the leading cause of death worldwide, suffer from a limited understanding of how the molecular mechanisms taking place following preventive measures (e.g., exercise) differ from changes occurring due to the injuries caused from the disease (e.g., myocardial infarction (MI)). Therefore, this manuscript assesses lipidomic changes before and one hour after exercise treadmill testing (ETT) and before and one hour after a planned myocardial infarction (PMI) in two separate patient cohorts. Strikingly, unique lipidomic perturbations were observed for these events, as could be expected from their vastly different stresses on the body. The lipidomic results were then combined with previously published metabolomic characterizations of the same patients. This integration provides complementary insights into the exercise and PMI events, thereby giving a more holistic understanding of the molecular changes associated with each.
With access to large datasets, deep neural networks through representation learning have been able to identify patterns from raw data, achieving human-level accuracy in image and speech recognition tasks. However, in chemistry, availability of large standardized and labelled datasets is scarce, and with a multitude of chemical properties of interest, chemical data is inherently small and fragmented. In this work, we explore transfer learning techniques in conjunction with the existing Chemception CNN model, to create a transferable and generalizable deep neural network for small-molecule property prediction. Our latest model, ChemNet learns in a semi-supervised manner from inexpensive labels computed from the ChEMBL database. When fine-tuned to the Tox21, HIV and FreeSolv dataset, which are 3 separate chemical tasks that ChemNet was not originally trained on, we demonstrate that ChemNet exceeds the performance of existing Chemception models, contemporary MLP models that trains on molecular fingerprints, and it matches the performance of the ConvGraph algorithm, the current state-of-the-art. Furthermore, as ChemNet has been pre-trained on a large diverse chemical database, it can be used as a universal “plug-and-play” deep neural network, which accelerates the deployment of deep neural networks for the prediction of novel small-molecule chemical properties.
With access to large datasets, deep neural networks (DNN) have achieved human-level accuracy in image and speech recognition tasks. However, in chemistry, data is inherently small and fragmented. In this work, we develop an approach of integrating rule-based knowledge into the Chemception CNN model via transfer learning techniques. The resulting model, ChemNet, is a transferable and generalizable deep neural network for chemical property prediction that learns in a semi-supervised manner from large unlabeled chemical databases. When ChemNet is further fine-tuned on 3 smaller datasets to predict chemical properties that it was not originally trained on, we show that ChemNet exceeds the accuracy of existing Chemception CNN models and other contemporary DNN models that were trained using conventional supervised learning approaches. These results indicate that pre-training ChemNet on a large diverse chemical database while incorporating chemistry domain knowledge, enables the development of more generalizable deep neural networks for the prediction of novel chemical properties.