Modeling non-uniform uncertainty in Reaction Prediction via Boosting and Dropout

• URL: http://arxiv.org/abs/2310.04674v1
• Date: Sat, 7 Oct 2023 03:18:26 GMT
• Title: Modeling non-uniform uncertainty in Reaction Prediction via Boosting and Dropout
• Authors: Taicheng Guo, Changsheng Ma, Xiuying Chen, Bozhao Nan, Kehan Guo, Shichao Pei, Nitesh V. Chawla, Olaf Wiest, Xiangliang Zhang
• Abstract summary: Variational Autoencoder(VAE) framework has typically been employed to tackle challenges in reaction prediction. We introduce randomness into product generation via boosting to ensemble diverse models and cover the range of potential outcomes. We design a ranking method to union the predictions from boosting and dropout, prioritizing the most plausible products.
• Score: 44.5946975612778
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Reaction prediction has been recognized as a critical task in synthetic chemistry, where the goal is to predict the outcome of a reaction based on the given reactants. With the widespread adoption of generative models, the Variational Autoencoder(VAE) framework has typically been employed to tackle challenges in reaction prediction, where the reactants are encoded as a condition for the decoder, which then generates the product. Despite effectiveness, these conditional VAE (CVAE) models still fail to adequately account for the inherent uncertainty in reaction prediction, which primarily stems from the stochastic reaction process. The principal limitations are twofold. Firstly, in these CVAE models, the prior is independent of the reactants, leading to a default wide and assumed uniform distribution variance of the generated product. Secondly, reactants with analogous molecular representations are presumed to undergo similar electronic transition processes, thereby producing similar products. This hinders the ability to model diverse reaction mechanisms effectively. Since the variance in outcomes is inherently non-uniform, we are thus motivated to develop a framework that generates reaction products with non-uniform uncertainty. Firstly, we eliminate the latent variable in previous CVAE models to mitigate uncontrol-label noise. Instead, we introduce randomness into product generation via boosting to ensemble diverse models and cover the range of potential outcomes, and through dropout to secure models with minor variations. Additionally, we design a ranking method to union the predictions from boosting and dropout, prioritizing the most plausible products. Experimental results on the largest reaction prediction benchmark USPTO-MIT show the superior performance of our proposed method in modeling the non-uniform uncertainty compared to baselines.

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