# ASTEROID: A Spatiotemporal Information Transformer for Forecasting Multi-Step Time Series of Molecular Dynamics

arXiv: https://arxiv.org/abs/2606.17668 · HTML: https://mlsanity.com/paper/2606.17668/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 32 references that are in the map.
- First posted on arXiv 16 Jun 2026.

## Builds on (most cited first, 9 of 9)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [A Time Series is Worth 64 Words: Long-term Forecasting with Transformers](https://mlsanity.com/paper/2211.14730/) (2022)
- [iTransformer: Inverted Transformers Are Effective for Time Series Forecasting](https://mlsanity.com/paper/2310.06625/) (2023)
- [Transformers in Time Series: A Survey](https://mlsanity.com/paper/2202.07125/) (2022)
- [AlphaFold Meets Flow Matching for Generating Protein Ensembles](https://mlsanity.com/paper/2402.04845/) (2024)
- [TorchMD: A deep learning framework for molecular simulations](https://mlsanity.com/paper/2012.12106/) (2020)
- [Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling](https://mlsanity.com/paper/2306.03117/) (2023)
- [Deep Reinforcement Learning of Transition States](https://mlsanity.com/paper/2011.06700/) (2020)
- [Spatiotemporal information conversion machine for time-series prediction](https://mlsanity.com/paper/2107.01353/) (2021)

## Abstract (arXiv)

Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis. Accurate forecast of the outcomes of a MD simulation is not only an attractive scientific challenge but also has substantial practical value. In this work, we developed a data-driven framework, termed ASTEROID (Advanced Spatiotemporal TransformER fOr Inferring Dynamics), that can directly predict multi-step atomic coordinates, avoiding conventional iterative integration. For this purpose, our ASTEROID reformulates MD trajectories as high-dimensional spatiotemporal sequences and integrates the Spatiotemporal Information (STI) Transformation equation into a Transformer architecture. The core innovation of ASTEROID lies in its ability to model multiscale spatiotemporal dependencies. In particular, for spatial dependencies, a local-global self-attention mechanism captures both short- and long-range interactions. For temporal dependencies, an encoder-decoder structure integrates global context with autoregressive forecasting. ASTEROID was evaluated on several quantum-mechanics derived molecular datasets. Our results indicate that ASTEROID achieved not only a higher level of accuracy in multi-step prediction than existing methods on various benchmarks, but also significantly reduced computational cost of conventional MD simulation. Moreover, the model supports iterative multi-step forecasting over an extended time scale. This work establishes a robust and generalizable data-driven paradigm for accelerating MD simulations.