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All-atom Diffusion Transformers: Unified generative modelling of molecules and materials

2025-03-05 · Chaitanya K. Joshi, Xiang Fu, Yi-Lun Liao, Vahe Gharakhanyan, Benjamin Kurt Miller, Anuroop Sriram, Zachary W. Ulissi

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems - such as molecules and materials - the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on QM9 and MP20 datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, exceeding state-of-the-art results from molecule and crystal-specific models. ADiT uses standard Transformers for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

📄 PDF Abstract BibTeX arXiv:2503.03965

Code (1)

facebookresearch/all-atom-diffusion-transformer 공식 구현 pytorch

Tasks

AllUnconditional Crystal GenerationUnconditional Molecule Generation

Methods 이 논문이 사용한 방법론

Attention 설명 없음
Linear Layer A Linear Layer is a projection $\mathbf{XW + b}$.
Multi-Head Attention 설명 없음
Dense Connections Dense Connections, or Fully Connected Connections, are a type of layer in a deep neural network that use a linear operation where every input is connected to every output…
Adam 설명 없음
Dropout Dropout is a regularization technique for neural networks that drops a unit (along with connections) at training time with a specified probability $p$ (a common value is…
Diffusion Diffusion models generate samples by gradually removing noise from a signal, and their training objective can be expressed as a reweighted variational lower-bound…
Layer Normalization Unlike batch normalization, Layer Normalization directly estimates the normalization statistics from the summed inputs…

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