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In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…

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…

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:…

Various template-based and template-free approaches have been proposed for single-step retrosynthesis prediction in recent years. While these approaches demonstrate strong performance from a data-driven metrics standpoint, many model…

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…

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…

Recent advancements in computational chemistry have leveraged the power of trans-former-based language models, such as MoLFormer, pre-trained using a vast amount of simplified molecular-input line-entry system (SMILES) sequences, to…

Continual learning requires a model to adapt to ongoing changes in the data distribution, and often to the set of tasks to be performed. It is rare, however, that the data and task changes are completely unpredictable. Given a description…

In the computational prediction of chemical compound properties, molecular descriptors and fingerprints encoded to low dimensional vectors are used. The selection of proper molecular descriptors and fingerprints is both important and…

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional…

Retrosynthesis is the process of determining the set of reactant molecules that can react to form a desired product. Semi-template-based retrosynthesis methods, which imitate the reverse logic of synthesis reactions, first predict the…

The identification of synthetic routes that end with a desired product has been an inherently time-consuming process that is largely dependent on expert knowledge regarding a limited fraction of the entire reaction space. At present,…

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…

Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and…

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,…

We present an attention-based Transformer model for automatic retrosynthesis route planning. Our approach starts from reactants prediction of single-step organic reactions for given products, followed by Monte Carlo tree search-based…

Predicting the motion of multiple agents is necessary for planning in dynamic environments. This task is challenging for autonomous driving since agents (e.g. vehicles and pedestrians) and their associated behaviors may be diverse and…

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect…

Retrosynthesis planning, essential in organic synthesis and drug discovery, has greatly benefited from recent AI-driven advancements. Nevertheless, existing methods frequently face limitations in both applicability and explainability.…

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…