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arXiv Machine Learning By Bum Chul Kwon, Ben Shapira, Moshiko Raboh, Shreyans Sethi, Shruti Murarka, Joseph A Morrone, Leili Zhang, Wendy Cornell, Jianying Hu, Parthasarathy Suryanarayanan

STAR-VAE: A Scalable Latent-Variable Transformer for Controllable Molecular Generation

Read the original on arXiv Machine Learning →

STAR-VAE is a Transformer-based variational autoencoder that uses SELFIES encoding and a bidirectional encoder with an autoregressive decoder pretrained on 79 million PubChem molecules. It incorporates a property signal to jointly condition the prior, posterior, and decoder, and employs LoRA adapters for fine‑tuning on small datasets without altering the backbone. The model achieves 100 % validity and near‑perfect novelty in MOSES sampling, low KL divergence on several GuacaMol descriptors, strong synthetic‑accessibility conditioning, and effective docking‑score control across multiple protein targets, while also enabling scaffold recovery and diverse label‑conditioned generation on ChEMBL targets.

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