chemical-language-models

[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models

The official codebase of the paper "Chemical language modeling with structured state space sequence models"

Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.

The official open-source repository for AutoMolDesigner, an easy-to-use Python application dedicated to automated molecular design.

InertDB, a resource of biologically inactive small molecules

A large language model for predicting membrane permeability of chemically modified peptides particularly for cyclic peptides. This method will help to discover novel orally deliverable peptide

Educational repo: building a tiny MolFormer-style encoder transformer from scratch for chemists. Sister course to GNNs-For-Chemists.

DL Pipeline for Antibiotic Discovery

Repository of artifacts for the BERTology manuscript

Code and data of "Lost in Translation: Chemical LMs and the Misunderstanding of Molecule Structures" paper

Controlled comparison of subword tokenizer vocabularies (BPE vs Unigram-LM) over chemistry SMILES

Parameter-efficient LoRA fine-tuning of Mistral-7B on USPTO reaction SMILES for reagent prediction and yield regression, with a chemistry-aware tokenizer extension and RDKit-backed data pipeline.

The official codebase for the reproducible experiments of the paper "Enhancing deep chemical reaction prediction with advanced chirality and fragment representation"

ModChemBERT: ModernBERT as a Chemical Language Model