# Data-Dependent Smoothing for Protein Discovery with Walk-Jump Sampling

arXiv: https://arxiv.org/abs/2509.02069 · HTML: https://mlsanity.com/paper/2509.02069/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 7 of its 10 references that are in the map.
- First posted on arXiv 2 Sep 2025.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

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

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Video Diffusion Models](https://mlsanity.com/paper/2204.03458/) (2022)
- [Sliced Score Matching: A Scalable Approach to Density and Score Estimation](https://mlsanity.com/paper/1905.07088/) (2019)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Neural Empirical Bayes](https://mlsanity.com/paper/1903.02334/) (2019)
- [Protein Discovery with Discrete Walk-Jump Sampling](https://mlsanity.com/paper/2306.12360/) (2023)

## Abstract (arXiv)

Diffusion models have emerged as a powerful class of generative models by learning to iteratively reverse the noising process. Their ability to generate high-quality samples has extended beyond high-dimensional image data to other complex domains such as proteins, where data distributions are typically sparse and unevenly spread. Importantly, the sparsity itself is uneven. Empirically, we observed that while a small fraction of samples lie in dense clusters, the majority occupy regions of varying sparsity across the data space. Existing approaches largely ignore this data-dependent variability. In this work, we introduce a Data-Dependent Smoothing Walk-Jump framework that employs kernel density estimation (KDE) as a preprocessing step to estimate the noise scale σ for each data point, followed by training a score model with these data-dependent σ values. By incorporating local data geometry into the denoising process, our method accounts for the heterogeneous distribution of protein data. Empirical evaluations demonstrate that our approach yields consistent improvements across multiple metrics, highlighting the importance of data-aware sigma prediction for generative modeling in sparse, high-dimensional settings.