An official website of the United States government
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.
more »
« less
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.
more »
« less
- PAR ID:
- 10411601
- Date Published:
- Journal Name:
- Chemical Science
- ISSN:
- 2041-6520
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
We present the OPEN GRAPH BENCHMARK (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple important graph ML tasks, and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, source code ASTs, and knowledge graphs. For each dataset, we provide a unified evaluation protocol using meaningful application-specific data splits and evaluation metrics. In addition to building the datasets, we also perform extensive benchmark experiments for each dataset. Our experiments suggest that OGB datasets present significant challenges of scalability to large-scale graphs and out-of-distribution generalization under realistic data splits, indicating fruitful opportunities for future research. Finally, OGB provides an automated end-to-end graph ML pipeline that simplifies and standardizes the process of graph data loading, experimental setup, and model evaluation. OGB will be regularly updated and welcomes inputs from the community. OGB datasets as well as data loaders, evaluation scripts, baseline code, and leaderboards are publicly available at https://ogb.stanford.edu.more » « less
-
Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. The test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.more » « less
-
IntroductionAdvancements in machine learning (ML) algorithms that make predictions from data without being explicitly programmed and the increased computational speeds of graphics processing units (GPUs) over the last decade have led to remarkable progress in the capabilities of ML. In many fields, including agriculture, this progress has outpaced the availability of sufficiently diverse and high-quality datasets, which now serve as a limiting factor. While many agricultural use cases appear feasible with current compute resources and ML algorithms, the lack of reusable hardware and software components, referred to as cyberinfrastructure (CI), for collecting, transmitting, cleaning, labeling, and training datasets is a major hindrance toward developing solutions to address agricultural use cases. This study focuses on addressing these challenges by exploring the collection, processing, and training of ML models using a multimodal dataset and providing a vision for agriculture-focused CI to accelerate innovation in the field. MethodsData were collected during the 2023 growing season from three agricultural research locations across Ohio. The dataset includes 1 terabyte (TB) of multimodal data, comprising Unmanned Aerial System (UAS) imagery (RGB and multispectral), as well as soil and weather sensor data. The two primary crops studied were corn and soybean, which are the state's most widely cultivated crops. The data collected and processed from this study were used to train ML models to make predictions of crop growth stage, soil moisture, and final yield. ResultsThe exercise of processing this dataset resulted in four CI components that can be used to provide higher accuracy predictions in the agricultural domain. These components included (1) a UAS imagery pipeline that reduced processing time and improved image quality over standard methods, (2) a tabular data pipeline that aggregated data from multiple sources and temporal resolutions and aligned it with a common temporal resolution, (3) an approach to adapting the model architecture for a vision transformer (ViT) that incorporates agricultural domain expertise, and (4) a data visualization prototype that was used to identify outliers and improve trust in the data. DiscussionFurther work will be aimed at maturing the CI components and implementing them on high performance computing (HPC). There are open questions as to how CI components like these can best be leveraged to serve the needs of the agricultural community to accelerate the development of ML applications in agriculture.more » « less
-
Accelerating the development of π-conjugated molecules for applications such as energy generation and storage, catalysis, sensing, pharmaceuticals, and (semi)conducting technologies requires rapid and accurate evaluation of the electronic, redox, or optical properties. While high-throughput computational screening has proven to be a tremendous aid in this regard, machine learning (ML) and other data-driven methods can further enable orders of magnitude reduction in time while at the same time providing dramatic increases in the chemical space that is explored. However, the lack of benchmark datasets containing the electronic, redox, and optical properties that characterize the diverse, known chemical space of organic π-conjugated molecules limits ML model development. Here, we present a curated dataset containing 25k molecules with density functional theory (DFT) and time-dependent DFT (TDDFT) evaluated properties that include frontier molecular orbitals, ionization energies, relaxation energies, and low-lying optical excitation energies. Using the dataset, we train a hierarchy of ML models, ranging from classical models such as ridge regression to sophisticated graph neural networks, with molecular SMILES representation as input. We observe that graph neural networks augmented with contextual information allow for significantly better predictions across a wide array of properties. Our best-performing models also provide an uncertainty quantification for the predictions. To democratize access to the data and trained models, an interactive web platform has been developed and deployed.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/d2sc06041h
