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Home Technology peripherals AI The accuracy rate reaches 60.8%. Zhejiang University's chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

The accuracy rate reaches 60.8%. Zhejiang University's chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

Aug 06, 2024 pm 07:34 PM
theory

The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

Editor | KX

Retrosynthesis is a critical task in drug discovery and organic synthesis, and AI is increasingly used to speed up the process.

Existing AI methods have unsatisfactory performance and limited diversity. In practice, chemical reactions often cause local molecular changes, with considerable overlap between reactants and products.

Inspired by this, Hou Tingjun’s team at Zhejiang University proposed to redefine single-step retrosynthetic prediction as a molecular string editing task, and iteratively refine the target molecular string to generate precursor compounds. And an edit-based retrosynthesis model EditRetro is proposed, which can achieve high-quality and diverse predictions.

Extensive experiments show that the model achieves excellent performance on the standard benchmark data set USPTO-50 K, with a top-1 accuracy of 60.8%.

The results show that EditRetro exhibits good generalization capabilities and robustness, highlighting its potential in the field of AI-driven chemical synthesis planning.

Related research titled "Retrosynthesis prediction with an iterative string editing model" was published in "Nature Communications" on July 30.

The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

Paper link: https://www.nature.com/articles/s41467-024-50617-1

Molecular synthesis path design is an important task in organic synthesis, which is important for biomedicine, pharmaceuticals and It is of great significance in various fields such as materials industry.

Retrosynthetic analysis is the most widely used method for developing synthetic routes. It involves using established reactions to iteratively break down molecules into simpler, easier-to-synthesize precursors.

In recent years, AI-driven retrosynthesis has facilitated the exploration of more complex molecules, greatly reducing the time and effort required to design synthetic experiments. Single-step retrosynthesis prediction is an important part of retrosynthesis planning. There are currently several deep learning-based methods with excellent results. These methods can be roughly divided into three categories: template-based methods, template-free methods, and semi-template-based methods.

Here, researchers focus on template-free retrosynthetic prediction. propose to redefine the problem as a molecular string editing task and propose EditRetro, an editing-based retrosynthetic model that can achieve high-quality and diverse predictions.

The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

Illustration: Schematic diagram of the proposed EditRetro method based on molecular string retrosynthesis. (Source: Paper)

The core concept of this research is to generate reactant strings through an iterative editing process using Levenshtein operations. The approach draws inspiration from recent advances in edit-based sequence generation models. Specifically, operations from EDITOR, an editing-based Transformer designed for neural machine translation, are employed.

EditRetro Overview

The EditRetro model contains three editing operations, namely sequence relocation, placeholder insertion and marker insertion, to generate reactant strings. It is implemented by a Transformer model, which consists of an encoder and three decoders, both consisting of stacked Transformer blocks.

  • Relocation decoder: Relocation operations include basic token editing operations such as retain, delete, and reorder. It can be compared to the process of identifying reaction centers, including reordering and deleting atoms or groups to obtain synthons.
  • Placeholder decoder: The placeholder insertion strategy (classifier) ??predicts the number of placeholders to insert between adjacent tokens. It plays a crucial role in determining the structure of reactants, similar to identifying the positions of added atoms or groups in intermediate synthons obtained from the sequence repositioning stage.
  • Token decoder: token insertion strategy (classifier), responsible for generating candidate tokens for each placeholder. This is crucial to determine the actual reactants that can be used to synthesize the target product. This process can be viewed as a similar process done by synthons, combined with placeholder insertion operations.

EditRetro model improves generation efficiency through its non-autoregressive decoder. Although incorporating additional decoders to iteratively predict editing operations, EditRetro performs editing operations in parallel within each decoder (i.e., non-autoregressive generation).

When given a target molecule, the encoder takes its string as input and generates the corresponding hidden representation, which is then used as input to the decoder’s cross-attention module. Similarly, the decoder also takes the product string as input on the first iteration. During each decoding iteration, the three decoders are executed sequentially.

Better than baseline, generate accurate reactants

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The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

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The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

?? ??? USPTO-FULL ??? ???? ?? 1?? ??? ?? ???? 52.2%? ?? ?? ???? ???? ?? ????? ? ??? ???????.

The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

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The accuracy rate reaches 60.8%. Zhejiang Universitys chemical retrosynthesis prediction model based on Transformer was published in the Nature sub-journal

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? ?? ?? ?? ??? ??? ?? ?? ???? ??? ??? ????? ???? ??? ?? 2?? ?????. ??? 16?? ?? ?? ? 10?? ?? ???? 1?????. ??? ??? ?? ??? ???? EditRetro? ???? ???? ?????.

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