John Bradshaw

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  • A Model to Search for Synthesizable Molecules

    Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees that the molecules can actually be synthesized in practice. We propose a new molecule generation model, mirroring a more realistic real-world process, where (a) reactants are selected, and (b) combined to form more complex molecules. More specifically, our generative model proposes a bag of initial reactants (selected from a pool of commercially-available molecules) and uses a reaction model to predict how they react together to generate new molecules. We first show that the model can generate diverse, valid and unique molecules due to the useful inductive biases of modeling reactions. Furthermore, our model allows chemists to interrogate not only the properties of the generated molecules but also the feasibility of the synthesis routes. We conclude by using our model to solve retrosynthesis problems, predicting a set of reactants that can produce a target product.

    06/12/2019 ∙ by John Bradshaw, et al. ∙ 7 share

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  • Adversarial Examples, Uncertainty, and Transfer Testing Robustness in Gaussian Process Hybrid Deep Networks

    Deep neural networks (DNNs) have excellent representative power and are state of the art classifiers on many tasks. However, they often do not capture their own uncertainties well making them less robust in the real world as they overconfidently extrapolate and do not notice domain shift. Gaussian processes (GPs) with RBF kernels on the other hand have better calibrated uncertainties and do not overconfidently extrapolate far from data in their training set. However, GPs have poor representational power and do not perform as well as DNNs on complex domains. In this paper we show that GP hybrid deep networks, GPDNNs, (GPs on top of DNNs and trained end-to-end) inherit the nice properties of both GPs and DNNs and are much more robust to adversarial examples. When extrapolating to adversarial examples and testing in domain shift settings, GPDNNs frequently output high entropy class probabilities corresponding to essentially "don't know". GPDNNs are therefore promising as deep architectures that know when they don't know.

    07/08/2017 ∙ by John Bradshaw, et al. ∙ 0 share

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  • Predicting Electron Paths

    Chemical reactions can be described as the stepwise redistribution of electrons in molecules. As such, reactions are often depicted using "arrow-pushing" diagrams which show this movement as a sequence of arrows. We propose an electron path prediction model (ELECTRO) to learn these sequences directly from raw reaction data. Instead of predicting product molecules directly from reactant molecules in one shot, learning a model of electron movement has the benefits of (a) being easy for chemists to interpret, (b) incorporating constraints of chemistry, such as balanced atom counts before and after the reaction, and (c) naturally encoding the sparsity of chemical reactions, which usually involve changes in only a small number of atoms in the reactants. We design a method to extract approximate reaction paths from any dataset of atom-mapped reaction SMILES strings. Our model achieves state-of-the-art results on a subset of the UPSTO reaction dataset. Furthermore, we show that our model recovers a basic knowledge of chemistry without being explicitly trained to do so.

    05/23/2018 ∙ by John Bradshaw, et al. ∙ 0 share

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