# ProFusion: 3D Reconstruction of Protein Complex Structures from Multi-view AFM Images

arXiv: https://arxiv.org/abs/2509.15242 · HTML: https://mlsanity.com/paper/2509.15242/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 70 references that are in the map.
- First posted on arXiv 17 Sep 2025.

## Builds on (most cited first, 19 of 19)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [The Unreasonable Effectiveness of Deep Features as a Perceptual Metric](https://mlsanity.com/paper/1801.03924/) (2018)
- [Adding Conditional Control to Text-to-Image Diffusion Models](https://mlsanity.com/paper/2302.05543/) (2023)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [Instant Neural Graphics Primitives with a Multiresolution Hash Encoding](https://mlsanity.com/paper/2201.05989/) (2022)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [DreamFusion: Text-to-3D using 2D Diffusion](https://mlsanity.com/paper/2209.14988/) (2022)
- [pixelNeRF: Neural Radiance Fields from One or Few Images](https://mlsanity.com/paper/2012.02190/) (2020)
- [MVSNet: Depth Inference for Unstructured Multi-view Stereo](https://mlsanity.com/paper/1804.02505/) (2018)
- [Accelerating 3D Deep Learning with PyTorch3D](https://mlsanity.com/paper/2007.08501/) (2020)
- [BARF: Bundle-Adjusting Neural Radiance Fields](https://mlsanity.com/paper/2104.06405/) (2021)
- [Generative Novel View Synthesis with 3D-Aware Diffusion Models](https://mlsanity.com/paper/2304.02602/) (2023)
- [Scene Representation Transformer: Geometry-Free Novel View Synthesis Through Set-Latent Scene Representations](https://mlsanity.com/paper/2111.13152/) (2021)
- [SparseFusion: Distilling View-conditioned Diffusion for 3D Reconstruction](https://mlsanity.com/paper/2212.00792/) (2022)
- [Fast-MVSNet: Sparse-to-Dense Multi-View Stereo With Learned Propagation and Gauss-Newton Refinement](https://mlsanity.com/paper/2003.13017/) (2020)
- [Differentiable Stereopsis: Meshes from multiple views using differentiable rendering](https://mlsanity.com/paper/2110.05472/) (2021)
- [UpFusion: Novel View Diffusion from Unposed Sparse View Observations](https://mlsanity.com/paper/2312.06661/) (2023)
- [Multi-View Neural 3D Reconstruction of Micro-/Nanostructures with Atomic Force Microscopy](https://mlsanity.com/paper/2401.11541/) (2024)

## Abstract (arXiv)

AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are accurate but costly and time-consuming. We present ProFusion, a hybrid framework that integrates a deep learning model with Atomic Force Microscopy (AFM), which provides high-resolution height maps from random orientations, naturally yielding multi-view data for 3D reconstruction. However, generating a large-scale AFM imaging data set sufficient to train deep learning models is impractical. Therefore, we developed a virtual AFM framework that simulates the imaging process and generated a dataset of ~542,000 proteins with multi-view synthetic AFM images. We train a conditional diffusion model to synthesize novel views from unposed inputs and an instance-specific Neural Radiance Field (NeRF) model to reconstruct 3D structures. Our reconstructed 3D protein structures achieve an average Chamfer Distance within the AFM imaging resolution, reflecting high structural fidelity. Our method is extensively validated on experimental AFM images of various PCs, demonstrating strong potential for accurate, cost-effective protein complex structure prediction and rapid iterative validation using AFM experiments.