The paper introduces UAE-3D, a multi-modal VAE for 3D molecule generation that compresses molecules into a unified latent space, maintaining near-zero reconstruction error. This approach simplifies latent diffusion modeling by eliminating the need to handle multi-modality and equivariance separately. Experiments on GEOM-Drugs and QM9 datasets show UAE-3D establishes new benchmarks in de novo and conditional 3D molecule generation, with significant improvements in efficiency and quality.
MBZUAI researchers have developed MorphDiff, a diffusion model that predicts cell morphology from gene expression data. MorphDiff uses the transcriptome to generate realistic post-perturbation images, either from scratch or by transforming a control image. The model combines a Morphology Variational Autoencoder (MVAE) with a Latent Diffusion Model, enabling both gene-to-image generation and image-to-image transformation. Why it matters: This could significantly accelerate drug discovery and biological research by allowing scientists to preview cellular changes before conducting experiments.
This paper introduces Diffusion-BBO, a new online black-box optimization (BBO) framework that uses a conditional diffusion model as an inverse surrogate model. The framework employs an Uncertainty-aware Exploration (UaE) acquisition function to propose scores in the objective space for conditional sampling. The approach is shown theoretically to achieve a near-optimal solution and empirically outperforms existing online BBO baselines across 6 scientific discovery tasks.
Ahmed Elhag, a PhD student at the University of Oxford, presented a new training procedure that approximates equivariance in unconstrained machine learning models via a multitask objective. The approach adds an equivariance loss to unconstrained models, allowing them to learn approximate symmetries without the computational cost of fully equivariant methods. Formulating equivariance as a flexible learning objective allows control over the extent of symmetry enforced, matching the performance of strictly equivariant baselines at a lower cost. Why it matters: This research from a speaker at MBZUAI balances rigorous theory and practical scalability in geometric deep learning, potentially accelerating drug discovery and design.
Daisuke Kihara from Purdue University presented a seminar at MBZUAI on using deep learning for biomolecular structure modeling. His lab is developing 3D structure modeling methods, especially for cryo-electron microscopy (cryo-EM) data. They are also working on RNA structure prediction and peptide docking using deep neural networks inspired by AlphaFold2. Why it matters: Applying advanced deep learning techniques to biomolecular structure prediction can accelerate drug discovery and our understanding of molecular functions.