Predicting chemical reaction yields is pivotal for efficient chemical synthesis, an area that focuses on the creation of novel compounds for diverse uses. Yield prediction demands accurate representations of reactions for forecasting practical transformation rates. Yet, the uncertainty issues broadcasting in real-world situations prohibit current models to excel in this task owing to the high sensitivity of yield activities and the uncertainty in yield measurements. Existing models often utilize single-modal feature representations, such as molecular
fingerprints, SMILES sequences, or molecular graphs, which is not sufficient to capture the complex interactions
and dynamic behavior of molecules in reactions. In this paper, we present an advanced Uncertainty-Aware Multimodal model (UAM) to tackle these challenges. Our approach seamlessly integrates data sources from multiple modalities by encompassing sequence representations, molecular graphs, and expert-defined chemical reaction features for a comprehensive representation of reactions. Additionally, we address both the model and data-based uncertainty, refining the model’s predictive capability. Extensive experiments on three datasets, including two high throughput experiment (HTE) datasets and one chemist-constructed Amide coupling reaction
dataset, demonstrate that UAM outperforms the stateof-the-art methods. The code and used datasets are available at https://github.com/jychen229/Multimodal-reaction-yieldprediction.
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On the use of real-world datasets for reaction yield prediction
The lack of publicly available, large, and unbiased datasets is a key bottleneck for the application of machine learning (ML) methods in synthetic chemistry. Data from electronic laboratory notebooks (ELNs) could provide less biased, large datasets, but no such datasets have been made publicly available. The first real-world dataset from the ELNs of a large pharmaceutical company is disclosed and its relationship to high-throughput experimentation (HTE) datasets is described. For chemical yield predictions, a key task in chemical synthesis, an attributed graph neural network (AGNN) performs as well as or better than the best previous models on two HTE datasets for the Suzuki–Miyaura and Buchwald–Hartwig reactions. However, training the AGNN on an ELN dataset does not lead to a predictive model. The implications of using ELN data for training ML-based models are discussed in the context of yield predictions.
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- NSF-PAR ID:
- 10411601
- Date Published:
- Journal Name:
- Chemical Science
- ISSN:
- 2041-6520
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/d2sc06041h
