# InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames

arXiv: https://arxiv.org/abs/2510.27497 · HTML: https://mlsanity.com/paper/2510.27497/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 37 of its 56 references that are in the map.
- First posted on arXiv 31 Oct 2025.

## Builds on (most cited first, 30 of 37)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [Taming Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2012.09841/) (2020)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [DeBERTa: Decoding-enhanced BERT with Disentangled Attention](https://mlsanity.com/paper/2006.03654/) (2020)
- [Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context](https://mlsanity.com/paper/1901.02860/) (2019)
- [Self-Attention with Relative Position Representations](https://mlsanity.com/paper/1803.02155/) (2018)
- [Visual Autoregressive Modeling: Scalable Image Generation via Next-Scale Prediction](https://mlsanity.com/paper/2404.02905/) (2024)
- [Autoregressive Model Beats Diffusion: Llama for Scalable Image Generation](https://mlsanity.com/paper/2406.06525/) (2024)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Autoregressive Image Generation without Vector Quantization](https://mlsanity.com/paper/2406.11838/) (2024)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [Frame Averaging for Invariant and Equivariant Network Design](https://mlsanity.com/paper/2110.03336/) (2021)
- [Diffusion-based Molecule Generation with Informative Prior Bridges](https://mlsanity.com/paper/2209.00865/) (2022)
- [MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation](https://mlsanity.com/paper/2302.09048/) (2023)
- [Benchmarking Graphormer on Large-Scale Molecular Modeling Datasets](https://mlsanity.com/paper/2203.04810/) (2022)
- [Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files](https://mlsanity.com/paper/2305.05708/) (2023)

## Built on by (most cited first, 3 of 3)

- [NEAT: Neighborhood-Guided, Efficient, Autoregressive Set Transformer for 3D Molecular Generation](https://mlsanity.com/paper/2512.05844/) (2025)
- [Autoregressive latent diffusion for 3D molecule generation](https://mlsanity.com/paper/2607.09277/) (2026)
- [Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles](https://mlsanity.com/paper/2603.02406/) (2026)

## Abstract (arXiv)

Transformer-based autoregressive models have emerged as a unifying paradigm across modalities such as text and images, but their extension to 3D molecule generation remains underexplored. The gap stems from two fundamental challenges: (1) how to tokenize molecules into a canonical 1D sequence of tokens that is invariant to both SE(3) transformations and atom index permutations, and (2) how to design an architecture capable of modeling hybrid atom-based tokens that couple discrete atom types with continuous 3D coordinates. To address these challenges, we introduce InertialAR. It first performs generation-oriented canonical tokenization by aligning each molecule to a canonical inertial frame and reordering atoms, thereby converting arbitrary 3D structures into a unique, SE(3)- and permutation-invariant sequence of tokens for autoregressive generation. Built upon this canonical tokenization, we propose geometric positional encoding (GeoPE), which endows Transformer attention with 3D geometric awareness. Finally, InertialAR utilizes a hierarchical autoregressive paradigm to decode the next atom, consecutively predicting the atom type and 3D coordinates via Diffusion Loss. Experimentally, InertialAR achieves state-of-the-art performance on 8 of the 10 evaluation metrics for unconditional generation across QM9, GEOM-Drugs, and B3LYP. Moreover, it significantly outperforms baselines in controllable generation for targeted chemical functionality, attaining state-of-the-art results across all 5 metrics. Code is available at github.com/HaoruiLi46/InertialAR.