Xinyu Dai

MOL-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective

The paper introduces a 3D molecular auto-encoder with a new training objective, achieving better performance than existing methods.

ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling

This paper introduces ESM-AA, a protein language model that operates at both atom and residue scales, outperforming previous methods in protein-molecule tasks.

Boosting Gene Expression Clustering with System-Wide Biological Information: A Robust Autoencoder Approach

This paper introduces a deep learning-based clustering method for gene expression data that integrates biological information, outperforming existing methods on yeast and human datasets.