Generative deep learning has become pivotal in molecular design for drug discovery and materials science. A widely used paradigm is to pretrain neural networks on string representations of molecules and fine-tune them using reinforcement learning on specific objectives. However, string-based models face challenges in ensuring chemical validity and enforcing structural constraints like the presence of specific substructures. We propose to instead combine graph-based molecular representations, which can naturally ensure chemical validity, with transformer architectures, which are highly expressive and capable of modeling long-range dependencies between atoms. Our approach iteratively modifies a molecular graph by adding atoms and bonds, which ensures chemical validity and facilitates the incorporation of structural constraints. We present GraphXForm, a decoder-only graph transformer architecture, which is pretrained on existing compounds and then fine-tuned using a new training algorithm that combines elements of the deep cross-entropy method with self-improvement learning from language modeling, allowing stable fine-tuning of deep transformers with many layers. We evaluate GraphXForm on two solvent design tasks for liquid-liquid extraction, showing that it outperforms four state-of-the-art molecular design techniques, while it can flexibly enforce structural constraints or initiate the design from existing molecular structures.

In this work, we introduce a method: REINVENT-Transformer to fine-tune a Transformerbased generative model for molecular de novo design. Leveraging the superior sequence learning capacity of Transformers over Recurrent Neural Networks (RNNs), our model can generate molecular structures with desired properties effectively. In contrast to the traditional RNN-based models, our proposed method exhibits superior performance in generating compounds predicted to be active against various biological targets, capturing long-term dependencies in the molecular structure sequence. The model's efficacy is demonstrated across numerous tasks, including generating analogues to a query structure and producing compounds with particular attributes, outperforming the baseline RNN-based methods. Our approach can be used for scaffold hopping, library expansion starting from a single molecule, and generating compounds with high predicted activity against biological targets.