Search Results for author: John Bradshaw

Found 9 papers, 5 papers with code

Beyond Major Product Prediction: Reproducing Reaction Mechanisms with Machine Learning Models Trained on a Large-Scale Mechanistic Dataset

no code implementations7 Mar 2024 Joonyoung F. Joung, Mun Hong Fong, Jihye Roh, Zhengkai Tu, John Bradshaw, Connor W. Coley

Mechanistic understanding of organic reactions can facilitate reaction development, impurity prediction, and in principle, reaction discovery.

Prefix-Tree Decoding for Predicting Mass Spectra from Molecules

1 code implementation NeurIPS 2023 Samuel Goldman, John Bradshaw, Jiayi Xin, Connor W. Coley

Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites.

Local Latent Space Bayesian Optimization over Structured Inputs

1 code implementation28 Jan 2022 Natalie Maus, Haydn T. Jones, Juston S. Moore, Matt J. Kusner, John Bradshaw, Jacob R. Gardner

By reformulating the encoder to function as both an encoder for the DAE globally and as a deep kernel for the surrogate model within a trust region, we better align the notion of local optimization in the latent space with local optimization in the input space.

Bayesian Optimization

Barking up the right tree: an approach to search over molecule synthesis DAGs

1 code implementation NeurIPS 2020 John Bradshaw, Brooks Paige, Matt J. Kusner, Marwin H. S. Segler, José Miguel Hernández-Lobato

When designing new molecules with particular properties, it is not only important what to make but crucially how to make it.

A Model to Search for Synthesizable Molecules

1 code implementation NeurIPS 2019 John Bradshaw, Brooks Paige, Matt J. Kusner, Marwin H. S. Segler, José Miguel Hernández-Lobato

Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure.

Retrosynthesis valid

Generating Molecules via Chemical Reactions

no code implementations ICLR Workshop DeepGenStruct 2019 John Bradshaw, Matt J. Kusner, Brooks Paige, Marwin H. S. Segler, José Miguel Hernández-Lobato

We therefore propose a new molecule generation model, mirroring a more realistic real-world process, where reactants are selected and combined to form more complex molecules.

Retrosynthesis valid

Are Generative Classifiers More Robust to Adversarial Attacks?

1 code implementation19 Feb 2018 Yingzhen Li, John Bradshaw, Yash Sharma

There is a rising interest in studying the robustness of deep neural network classifiers against adversaries, with both advanced attack and defence techniques being actively developed.

Adversarial Defense Adversarial Robustness

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

no code implementations8 Jul 2017 John Bradshaw, Alexander G. de G. Matthews, Zoubin Ghahramani

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

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