# Polyformer: a generative framework for thermodynamic modeling of polymeric molecules

arXiv: https://arxiv.org/abs/2604.14241 · HTML: https://mlsanity.com/paper/2604.14241/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 7 of its 27 references that are in the map.
- First posted on arXiv 15 Apr 2026.

## Builds on (most cited first, 7 of 7)

- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Efficient Diffusion Training via Min-SNR Weighting Strategy](https://mlsanity.com/paper/2303.09556/) (2023)
- [AlphaFold Meets Flow Matching for Generating Protein Ensembles](https://mlsanity.com/paper/2402.04845/) (2024)
- [Learnable Fourier Features for Multi-Dimensional Spatial Positional Encoding](https://mlsanity.com/paper/2106.02795/) (2021)
- [Unsupervised Generative Modeling Using Matrix Product States](https://mlsanity.com/paper/1709.01662/) (2017)
- [SimpleFold: Folding Proteins is Simpler than You Think](https://mlsanity.com/paper/2509.18480/) (2025)

## Abstract (arXiv)

The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold address this paradigm by predicting the single best conformation given a sequence that defines the molecule. However, biomolecules are not static structures, and their conformational ensemble determines their function. We present the Polyformer -- a generative framework for thermodynamic modeling of polymeric molecules. Given the sequence and temperature (or another thermodynamic variable), the Polyformer generates conformations faithful to the molecule's thermodynamic conformational ensemble. It is the first generative model that solves three problems simultaneously: how does a molecule fold, what is its conformational ensemble, and how does the conformational ensemble change as we change physical temperature. As a concrete test case, we apply Polyformer to protein domains with 50-111 residues and report good agreement of model predictions to Molecular Dynamics (MD) trajectories.