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Chemical reaction prediction is pivotal for accelerating drug discovery and synthesis planning. Despite advances in data-driven models, current approaches are hindered by an overemphasis on parameter and dataset scaling. Some methods…

Retrosynthesis, which aims to identify viable synthetic pathways for target molecules by decomposing them into simpler precursors, is often treated as a search problem. However, its complexity arises from multi-branched tree-structured…

Retrosynthetic planning is a fundamental problem in chemistry for finding a pathway of reactions to synthesize a target molecule. Recently, search algorithms have shown promising results for solving this problem by using deep neural…

The accurate prediction of chemical reaction outcomes is a major challenge in computational chemistry. Current models rely heavily on either highly specific reaction templates or template-free methods, both of which present limitations. To…

Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance remains limited. Existing benchmarks and metrics typically…

This paper proposes a machine learning (ML) method to predict stable molecular geometries from their chemical composition. The method is useful for generating molecular conformations which may serve as initial geometries for saving time…

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…

Organic synthesis is one of the key stumbling blocks in medicinal chemistry. A necessary yet unsolved step in planning synthesis is solving the forward problem: given reactants and reagents, predict the products. Similar to other work, we…

Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges:…

We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state…

A fundamental problem in organic chemistry is identifying and predicting the series of reactions that synthesize a desired target product molecule. Due to the combinatorial nature of the chemical search space, single-step reactant…

Identification and verification of molecular properties such as side effects is one of the most important and time-consuming steps in the process of molecule synthesis. For example, failure to identify side effects before submission to…

We demonstrate a machine learning based approach which can learn the time-dependent electronic excitation dynamics of small molecules subjected to ion irradiation. Ensembles of recurrent neural networks are trained on data generated by…

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…

Synthesizability in generative molecular design remains a pressing challenge. Existing methods to assess synthesizability span heuristics-based methods, retrosynthesis models, and synthesizability-constrained molecular generation. The…

There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic…

Is there a unified framework for graph-based retrosynthesis prediction? Through analysis of full-, semi-, and non-template retrosynthesis methods, we discovered that they strive to strike an optimal balance between combinability and…

The synthesis of complex natural products remains one of the grand challenges of organic chemistry. We present DeepRetro, a major advancement in computational retrosynthesis that enables the discovery of viable synthetic routes for complex…

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…

Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner.…