In the space of only a few years, deep generative modeling has revolutionized how we think of artificial creativity, yielding autonomous systems which produce original images, music, and text. Inspired by these successes, researchers are now applying
deep generative modeling techniques to the generation and optimization of molecules - in our review we found 45 papers on the subject published in the past two years. These works point to a future where such systems will be used to generate lead molecules, greatly reducing resources spent downstream synthesizing and characterizing bad leads in the lab. In this review we survey the increasingly complex landscape of models and representation schemes that have been proposed. The four classes of techniques we describe are recursive neural networks, autoencoders, generative adversarial networks, and reinforcement learning. After first discussing some of the mathematical fundamentals of each technique, we draw high level connections and comparisons with other techniques and expose the pros and cons of each. Several important high level themes emerge as a result of this work, including the shift away from the SMILES string representation of molecules towards more sophisticated representations such as graph grammars and 3D representations, the importance of reward function design, the need for better standards for benchmarking and testing, and the benefits of adversarial training and reinforcement learning over maximum likelihood based training.
Due to its high computational speed and accuracy compared to ab-initio quantum chemistry and forcefield modeling, the prediction of molecular properties using machine learning has received great attention in the fields of materials design and drug di
scovery. A main ingredient required for machine learning is a training dataset consisting of molecular featurestextemdash for example fingerprint bits, chemical descriptors, etc. that adequately characterize the corresponding molecules. However, choosing features for any application is highly non-trivial. No universal method for feature selection exists. In this work, we propose a data fusion framework that uses Independent Vector Analysis to exploit underlying complementary information contained in different molecular featurization methods, bringing us a step closer to automated feature generation. Our approach takes an arbitrary number of individual feature vectors and automatically generates a single, compact (low dimensional) set of molecular features that can be used to enhance the prediction performance of regression models. At the same time our methodology retains the possibility of interpreting the generated features to discover relationships between molecular structures and properties. We demonstrate this on the QM7b dataset for the prediction of several properties such as atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity, and excitation energies. In addition, we show how our method helps improve the prediction of experimental binding affinities for a set of human BACE-1 inhibitors. To encourage more widespread use of IVA we have developed the PyIVA Python package, an open source code which is available for download on Github.
In this work, we discuss use of machine learning techniques for rapid prediction of detonation properties including explosive energy, detonation velocity, and detonation pressure. Further, analysis is applied to individual molecules in order to explo
re the contribution of bonding motifs to these properties. Feature descriptors evaluated include Morgan fingerprints, E-state vectors, a custom sum over bonds descriptor, and coulomb matrices. Algorithms discussed include kernel ridge regression, least absolute shrinkage and selection operator (LASSO) regression, Gaussian process regression, and the multi-layer perceptron (a neural network). Effects of regularization, kernel selection, network parameters, and dimensionality reduction are discussed. We determine that even when using a small training set, non-linear regression methods may create models within a useful error tolerance for screening of materials.
We present a proof of concept that machine learning techniques can be used to predict the properties of CNOHF energetic molecules from their molecular structures. We focus on a small but diverse dataset consisting of 109 molecular structures spread a
cross ten compound classes. Up until now, candidate molecules for energetic materials have been screened using predictions from expensive quantum simulations and thermochemical codes. We present a comprehensive comparison of machine learning models and several molecular featurization methods - sum over bonds, custom descriptors, Coulomb matrices, bag of bonds, and fingerprints. The best featurization was sum over bonds (bond counting), and the best model was kernel ridge regression. Despite having a small data set, we obtain acceptable errors and Pearson correlations for the prediction of detonation pressure, detonation velocity, explosive energy, heat of formation, density, and other properties out of sample. By including another dataset with 309 additional molecules in our training we show how the error can be pushed lower, although the convergence with number of molecules is slow. Our work paves the way for future applications of machine learning in this domain, including automated lead generation and interpreting machine learning models to obtain novel chemical insights.
