A Large Encoder-Decoder Family of Foundation Models For Chemical
  Language
Authors: name: Eduardo Soares; name: Victor Shirasuna; name: Emilio Vital Brazil; name: Renato Cerqueira; name: Dmitry Zubarev; name: Kristin Schmidt
Published: 2024-07-24 20:30:39

Abstract: Large-scale pre-training methodologies for chemical language models represent
a breakthrough in cheminformatics. These methods excel in tasks such as
property prediction and molecule generation by learning contextualized
representations of input tokens through self-supervised learning on large
unlabeled corpora. Typically, this involves pre-training on unlabeled data
followed by fine-tuning on specific tasks, reducing dependence on annotated
datasets and broadening chemical language representation understanding. This
paper introduces a large encoder-decoder chemical foundation models pre-trained
on a curated dataset of 91 million SMILES samples sourced from PubChem, which
is equivalent to 4 billion of molecular tokens. The proposed foundation model
supports different complex tasks, including quantum property prediction, and
offer flexibility with two main variants (289M and 8times289M). Our
experiments across multiple benchmark datasets validate the capacity of the
proposed model in providing state-of-the-art results for different tasks. We
also provide a preliminary assessment of the compositionality of the embedding
space as a prerequisite for the reasoning tasks. We demonstrate that the
produced latent space is separable compared to the state-of-the-art with
few-shot learning capabilities.