Dataset Information

Generative Models for Extrapolation Prediction in Materials Informatics.

ABSTRACT: We report a deep generative model for regression tasks in materials informatics. The model is introduced as a component of a data imputer and predicts more than 20 diverse experimental properties of organic molecules. The imputer is designed to predict material properties by "imagining" the missing data in the database, enabling the use of incomplete material data. Even removing 60% of the data does not diminish the prediction accuracy in a model task. Moreover, the model excels at extrapolation prediction, where target values of the test data are out of the range of the training data. Such an extrapolation has been regarded as an essential technique for exploring novel materials but has hardly been studied to date due to its difficulty. We demonstrate that the prediction performance can be improved by >30% by using the imputer compared with traditional linear regression and boosting models. The benefit becomes especially pronounced with few records for an experimental property (<100 cases) when prediction would be difficult by conventional methods. The presented approach can be used to more efficiently explore functional materials and break through previous performance limits.

SUBMITTER: Hatakeyama-Sato K

PROVIDER: S-EPMC8190893 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Generative Models for Extrapolation Prediction in Materials Informatics.

Hatakeyama-Sato Kan K Oyaizu Kenichi K

ACS omega 20210525 22

We report a deep generative model for regression tasks in materials informatics. The model is introduced as a component of a data imputer and predicts more than 20 diverse experimental properties of organic molecules. The imputer is designed to predict material properties by "imagining" the missing data in the database, enabling the use of incomplete material data. Even removing 60% of the data does not diminish the prediction accuracy in a model task. Moreover, the model excels at extrapolation ...[more]

PMID: 34124480

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Project description:Predicting changes in protein thermostability due to amino acid substitutions is essential for understanding human diseases and engineering useful proteins for clinical and industrial applications. While recent advances in protein generative models, which learn probability distributions over amino acids conditioned on structural or evolutionary sequence contexts, have shown impressive performance in predicting various protein properties without task-specific training, their strong unsupervised prediction ability does not extend to all protein functions. In particular, their potential to improve protein stability prediction remains underexplored. In this work, we present SPURS, a novel deep learning framework that adapts and integrates two general-purpose protein generative models-a protein language model (ESM) and an inverse folding model (ProteinMPNN)-into an effective stability predictor. SPURS employs a lightweight neural network module to rewire per-residue structure representations learned by ProteinMPNN into the attention layers of ESM, thereby informing and enhancing ESM's sequence representation learning. This rewiring strategy enables SPURS to harness evolutionary patterns from both sequence and structure data, where the sequence likelihood distribution learned by ESM is conditioned on structure priors encoded by ProteinMPNN to predict mutation effects. We steer this integrated framework to a stability prediction model through supervised training on a recently released mega-scale thermostability dataset. Evaluations across 12 benchmark datasets showed that SPURS delivers accurate, rapid, scalable, and generalizable stability predictions, consistently outperforming current state-of-the-art methods. Notably, SPURS demonstrates remarkable versatility in protein stability and function analyses: when combined with a protein language model, it accurately identifies protein functional sites in an unsupervised manner. Additionally, it enhances current low-N protein fitness prediction models by serving as a stability prior model to improve accuracy. These results highlight SPURS as a powerful tool to advance current protein stability prediction and machine learning-guided protein engineering workflows. The source code of SPURS is available at https://github.com/luo-group/SPURS.

Dataset Information

Generative Models for Extrapolation Prediction in Materials Informatics.

Publications

Generative Models for Extrapolation Prediction in Materials Informatics.

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