This paper is concerned with a molecular optimization framework using variational autoencoders (VAEs). In this paradigm, VAE allows us to convert a molecular graph into from its latent continuous vector, and therefore, the molecular optimization problem can be solved by continuous optimization techniques. One of the longstanding issues in this area is that it is difficult to always generate valid molecules. The very recent work called the junction tree variational autoencoder (JT-VAE) successfully solved this issue by generating a molecule fragment-by-fragment. While it achieves the state-of-the-art performance, it requires several neural networks to be trained, which predict which atoms are used to connect fragments and stereochemistry of each bond. In this paper, we present a molecular hypergraph grammar variational autoencoder (MHG-VAE), which uses a single VAE to address the issue. Our idea is to develop a novel graph grammar for molecular graphs called molecular hypergraph grammar (MHG), which can specify the connections between fragments and the stereochemistry on behalf of neural networks. This capability allows us to address the issue using only a single VAE. We empirically demonstrate the effectiveness of MHG-VAE over existing methods.
There are two complementary approaches to molecular optimization. One is the combination of VAE and Bayesian optimization, originally developed by , and the other is reinforcement learning, where the construction of a molecule is modeled as a Markov decision process @cite_16 @cite_3 @cite_2 . These two approaches cover complementary application areas, and therefore, they are not conflicting with each other. The key difference is the assumption on function evaluation cost. The former assumes that the cost is so high that the number of function evaluations should be kept at a minimum, while the latter assumes that the cost is negligible and a number of trial-and-errors are allowed. Therefore, the former is more favorable when the evaluation requires wet-lab experiments or computationally heavy first-principles calculation, and the latter is more favorable when the evaluation can be carried out by light-weight computer simulation. Since our paper focuses on the former setting, in the following, we will discuss its literature.
@cite_16 @cite_3 @cite_2
2898000008 2755801529 2408019865 2027638447
We present a framework, which we call Molecule Deep @math -Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (prioritized experience replay, double @math -learning, and randomized value functions). We directly define modifications on molecules, thereby ensuring 100 chemical validity. Further, we operate without pre-training on any dataset to avoid possible bias from the choice of that set. As a result, our model outperforms several other state-of-the-art algorithms by having a higher success rate of acquiring molecules with better properties. Inspired by problems faced during medicinal chemistry lead optimization, we extend our model with multi-objective reinforcement learning, which maximizes drug-likeness while maintaining similarity to the original molecule. We further show the path through chemical space to achieve optimization for a molecule to understand how the model works. Automatic Chemical Design leverages recent advances in deep generative modelling to provide a framework for performing continuous optimization of molecular properties. Although the provision of a continuous representation for prospective lead drug candidates has opened the door to hitherto inaccessible tools of mathematical optimization, some challenges remain for the design process. One known pathology is the model's tendency to decode invalid molecular structures. The goal of this thesis is to test the hypothesis that the origin of this pathology is rooted in the current formulation of Bayesian optimization. Recasting the optimization procedure as a constrained Bayesian optimization problem results in novel drug compounds produced by the model consistently ranking in the 100th percentile of the distribution over training set scores. Bayesian optimization has become a successful tool for hyperparameter optimization of machine learning algorithms, such as support vector machines or deep neural networks. Despite its success, for large datasets, training and validating a single configuration often takes hours, days, or even weeks, which limits the achievable performance. To accelerate hyperparameter optimization, we propose a generative model for the validation error as a function of training set size, which is learned during the optimization process and allows exploration of preliminary configurations on small subsets, by extrapolating to the full dataset. We construct a Bayesian optimization procedure, dubbed Fabolas, which models loss and training time as a function of dataset size and automatically trades off high information gain about the global optimum against computational cost. Experiments optimizing support vector machines and deep neural networks show that Fabolas often finds high-quality solutions 10 to 100 times faster than other state-of-the-art Bayesian optimization methods or the recently proposed bandit strategy Hyperband. Abstract Two major components are required for a successful prediction of the three-dimensional structure of peptides and proteins: an efficient global optimization procedure which is capable of finding an appropriate local minimum for the strongly anisotropic function of hundreds of variables, and a set of free energy components for a protein molecule in solution which are computationally inexpensive enough to be used in the search procedure, yet sufficiently accurate to ensure the uniqueness of the native conformation. We here found an efficient way to make a random step in a Monte Carlo procedure given knowledge of the energy or statistical properties of conformational subspaces (e.g. φ-ψ zones or side-chain torsion angles). This biased probability Monte Carlo (BPMC) procedure randomly selects the subspace first, then makes a step to a new random position independent of the previous position, but according to the predefined continuous probability distribution. The random step is followed by a local minimization in torsion angle space. The positions, sizes and preferences for high-probability zones on φ-ψ maps and χ-angle maps were calculated for different residue types from the representative set of 191 and 161 protein 3D-structures, respectively. A fast and precise method to evaluate the electrostatic energy of a protein in solution is developed and combined with the BPMC procedure. The method is based on the modified spherical image charge approximation, efficiently projected onto a molecule of arbitrary shape. Comparison with the finite-difference solutions of the Poisson-Boltzmann equation shows high accuracy for our approach. The BPMC procedure is applied successfully to the structure prediction of 12- and 16-residue synthetic peptides and the determination of protein structure from NMR data, with the immunoglobulin binding domain of streptococcal protein G as an example. The BPMC runs display much better convergence properties than the non-biased simulations. The advantage of a true global optimization procedure for NMR structure determination is its ability to cope with local minima originating from data errors and ambiguities in NMR data.