Related papers: $\mathsf{G^2Retro}$ as a Two-Step Graph Generative…

In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…

Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…

We address a fundamental problem in chemistry known as chemical reaction product prediction. Our main insight is that the input reactant and reagent molecules can be jointly represented as a graph, and the process of generating product…

Retrosynthesis prediction aims to infer the reactant molecule based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing models rely on static pattern-matching paradigm, which limits their…

Computer-assisted methods have emerged as valuable tools for retrosynthesis analysis. However, quantifying the plausibility of generated retrosynthesis routes remains a challenging task. We introduce Retro-BLEU, a statistical metric adapted…

We cast retrosynthesis as a machine translation problem by introducing a special Tensor2Tensor, an entire attention-based and fully data-driven model. Given a data set comprising about 50,000 diverse reactions extracted from USPTO patents,…

Finding synthesis routes for molecules of interest is an essential step in the discovery of new drugs and materials. To find such routes, computer-assisted synthesis planning (CASP) methods are employed which rely on a model of chemical…

Chemical synthesis remains a critical bottleneck in the discovery and manufacture of functional small molecules. AI-based synthesis planning models could be a potential remedy to find effective syntheses, and have made progress in recent…

Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization. We address this gap with a…

Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate…

Single-step retrosynthesis (SSR) in organic chemistry is increasingly benefiting from deep learning (DL) techniques in computer-aided synthesis design. While template-free DL models are flexible and promising for retrosynthesis prediction,…

Retrosynthesis plays a crucial role in the fields of organic synthesis and drug development, where the goal is to identify suitable reactants that can yield a target product molecule. Although existing methods have achieved notable success,…

Traditional computer-aided synthesis planning (CASP) methods rely on iterative single-step predictions, leading to exponential search space growth that limits efficiency and scalability. We introduce a series of transformer-based models,…

Retrosynthesis planning remains a central challenge in molecular discovery due to the vast and complex chemical reaction space. While traditional template-based methods offer tractability, they suffer from poor scalability and limited…

A significant challenge in wet lab experiments with current drug design generative models is the trade-off between pharmacological properties and synthesizability. Molecules predicted to have highly desirable properties are often difficult…

The field of computer-aided synthesis planning (CASP) has seen rapid advancements in recent years, achieving significant progress across various algorithmic benchmarks. However, chemists often encounter numerous infeasible reactions when…

We have developed an end-to-end, retrosynthesis system, named ChemiRise, that can propose complete retrosynthesis routes for organic compounds rapidly and reliably. The system was trained on a processed patent database of over 3 million…

In retrosynthetic planning, the huge number of possible routes to synthesize a complex molecule using simple building blocks leads to a combinatorial explosion of possibilities. Even experienced chemists often have difficulty to select the…

We introduce a mathematical framework for retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules and their interaction using string diagrams in layered props - a recently introduced…

Graph Neural Network (GNN) resembles the diffusion process, leading to the over-smoothing of learned representations when stacking many layers. Hence, the reverse process of message passing can produce the distinguishable node…