Yaorui Shi
2024
ReactXT: Understanding Molecular “Reaction-ship” via Reaction-Contextualized Molecule-Text Pretraining
Zhiyuan Liu
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Yaorui Shi
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An Zhang
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Sihang Li
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Enzhi Zhang
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Xiang Wang
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Kenji Kawaguchi
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Tat-Seng Chua
Findings of the Association for Computational Linguistics: ACL 2024
Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling – experimental procedure prediction – is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.
2023
ReLM: Leveraging Language Models for Enhanced Chemical Reaction Prediction
Yaorui Shi
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An Zhang
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Enzhi Zhang
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Zhiyuan Liu
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Xiang Wang
Findings of the Association for Computational Linguistics: EMNLP 2023
Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited by insufficient training data and their inability to utilize textual information, undermining their applicability in real-world applications. In this work, we propose **ReLM**, a novel framework that leverages the chemical knowledge encoded in language models (LMs) to assist GNNs, thereby enhancing the accuracy of real-world chemical reaction predictions. To further enhance the model’s robustness and interpretability, we incorporate the confidence score strategy, enabling the LMs to self-assess the reliability of their predictions. Our experimental results demonstrate that ReLM improves the performance of state-of-the-art GNN-based methods across various chemical reaction datasets, especially in out-of-distribution settings. Codes are available at https://github.com/syr-cn/ReLM.
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Co-authors
- An Zhang 2
- Enzhi Zhang 2
- Zhiyuan Liu 2
- Xiang Wang 2
- Sihang Li 1
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