GV
G. Vogel
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Online databases contain extensive collections of (bio)chemical reactions serving as valuable resources for a variety of applications. However, these large datasets often suffer from incomplete reaction data missing, for example, co-reactants and by-products. Machine learning can help to predict these missing molecules in partial reactions. In this study, we adapt an existing transformer model to enhance its capability in completing these incomplete reactions. We retrain the model using a more diverse dataset of atom-balanced ground truth reactions and introduce both soft and hard atom-balance constraints to improve the completeness and chemical validity of the predictions. Our findings indicate that models trained with soft constraints in their loss function do not demonstrate improved balancing performance and require further tuning. Conversely, the implementation of hard atom-balance constraints during constrained beam search, where we restrict predicting tokens that violate the atom-balance of the prediction, effectively improves the performance of transformer-based models in reaction completion tasks. However, this approach also presents the risk of inaccurately balancing reactions; a limitation that is difficult to identify without chemical expertise, underscoring the necessity for reliable ground truth data to evaluate the predictions.
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Online databases contain extensive collections of (bio)chemical reactions serving as valuable resources for a variety of applications. However, these large datasets often suffer from incomplete reaction data missing, for example, co-reactants and by-products. Machine learning can help to predict these missing molecules in partial reactions. In this study, we adapt an existing transformer model to enhance its capability in completing these incomplete reactions. We retrain the model using a more diverse dataset of atom-balanced ground truth reactions and introduce both soft and hard atom-balance constraints to improve the completeness and chemical validity of the predictions. Our findings indicate that models trained with soft constraints in their loss function do not demonstrate improved balancing performance and require further tuning. Conversely, the implementation of hard atom-balance constraints during constrained beam search, where we restrict predicting tokens that violate the atom-balance of the prediction, effectively improves the performance of transformer-based models in reaction completion tasks. However, this approach also presents the risk of inaccurately balancing reactions; a limitation that is difficult to identify without chemical expertise, underscoring the necessity for reliable ground truth data to evaluate the predictions.
Synthetic polymers are crucial in diverse industries, but current AI-driven design methodologies primarily target linear homopolymers, with limited emphasis on developing customized approaches for copolymers. To address this gap, we introduce a generative model for goal-directed synthetic copolymer design using reinforcement learning. Our model operates in a graph generation environment, facilitating efficient monomer unit design while incorporating domain-specific constraints to ensure high validity rates. In a case study optimizing for Hydrogen Evolution Rate (HER) and synthetic accessibility, our approach showcases the efficacy of reinforcement learning in advancing copolymer design. Furthermore, experimental results underscore the challenges in designing effective scoring functions due to the sparse nature of polymer datasets, emphasizing the need for robust property predictors in polymer design methodologies before integrating more complex generative models into the design process.
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Synthetic polymers are crucial in diverse industries, but current AI-driven design methodologies primarily target linear homopolymers, with limited emphasis on developing customized approaches for copolymers. To address this gap, we introduce a generative model for goal-directed synthetic copolymer design using reinforcement learning. Our model operates in a graph generation environment, facilitating efficient monomer unit design while incorporating domain-specific constraints to ensure high validity rates. In a case study optimizing for Hydrogen Evolution Rate (HER) and synthetic accessibility, our approach showcases the efficacy of reinforcement learning in advancing copolymer design. Furthermore, experimental results underscore the challenges in designing effective scoring functions due to the sparse nature of polymer datasets, emphasizing the need for robust property predictors in polymer design methodologies before integrating more complex generative models into the design process.
Recent advancements in machine learning (ML) have shown promise in accelerating polymer discovery by aiding in tasks such as virtual screening via property prediction, and the design of new polymer materials with desired chemical properties. However, progress in polymer ML is hampered by the scarcity of high-quality, labelled datasets, which are necessary for training supervised ML models. In this work, we study the use of the very recent ’Joint Embedding Predictive Architecture’ (JEPA) type for self-supervised learning (SSL) on polymer molecular graphs, to understand whether pretraining with the proposed SSL strategy improves downstream performance when labelled data is scarce. By doing so, this study aims to shed light on this new family of architectures in the molecular graph domain and provide insights and directions for future research on JEPAs. Our experimental results indicate that JEPA self-supervised pretraining enhances downstream performance, particularly when labelled data is very scarce, achieving improvements across all tested datasets.
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Recent advancements in machine learning (ML) have shown promise in accelerating polymer discovery by aiding in tasks such as virtual screening via property prediction, and the design of new polymer materials with desired chemical properties. However, progress in polymer ML is hampered by the scarcity of high-quality, labelled datasets, which are necessary for training supervised ML models. In this work, we study the use of the very recent ’Joint Embedding Predictive Architecture’ (JEPA) type for self-supervised learning (SSL) on polymer molecular graphs, to understand whether pretraining with the proposed SSL strategy improves downstream performance when labelled data is scarce. By doing so, this study aims to shed light on this new family of architectures in the molecular graph domain and provide insights and directions for future research on JEPAs. Our experimental results indicate that JEPA self-supervised pretraining enhances downstream performance, particularly when labelled data is very scarce, achieving improvements across all tested datasets.
Large chemical reaction databases often suffer from incompleteness, such as missing molecules or stoichiometric information. Concurrently, numerous computational models are being developed in predictive chemistry that rely on reaction databases and would hugely benefit from complete reaction equations. Also, research in sustainable chemistry often focuses on automated mass balance tasks, which require a full reaction to properly evaluate. In this work, we present a hybrid approach for computational completion of reaction equations. Specifically, we combine a rule-based method and a machine learning (ML) model to complete reactions. The rule-based approach constructs a balance of atoms and charge on either side of the reaction in an attempt to find missing molecules. We tailor the pre-trained transformer model on the chemical language domain to take partial reactions as inputs and predict missing molecules. Furthermore, we present a novel approach to measure the correctness of our model, which is useful when we apply it to the uncurated dataset and the ground-truth is unknown.
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Large chemical reaction databases often suffer from incompleteness, such as missing molecules or stoichiometric information. Concurrently, numerous computational models are being developed in predictive chemistry that rely on reaction databases and would hugely benefit from complete reaction equations. Also, research in sustainable chemistry often focuses on automated mass balance tasks, which require a full reaction to properly evaluate. In this work, we present a hybrid approach for computational completion of reaction equations. Specifically, we combine a rule-based method and a machine learning (ML) model to complete reactions. The rule-based approach constructs a balance of atoms and charge on either side of the reaction in an attempt to find missing molecules. We tailor the pre-trained transformer model on the chemical language domain to take partial reactions as inputs and predict missing molecules. Furthermore, we present a novel approach to measure the correctness of our model, which is useful when we apply it to the uncurated dataset and the ground-truth is unknown.