# OmegAMP: Targeted AMP Discovery via Biologically Informed Generation

arXiv: https://arxiv.org/abs/2504.17247 · HTML: https://mlsanity.com/paper/2504.17247/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 61 references that are in the map.
- First posted on arXiv 24 Apr 2025.

## Builds on (most cited first, 11 of 11)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning](https://mlsanity.com/paper/2208.04202/) (2022)
- [Why do tree-based models still outperform deep learning on tabular data?](https://mlsanity.com/paper/2207.08815/) (2022)
- [CADS: Unleashing the Diversity of Diffusion Models through Condition-Annealed Sampling](https://mlsanity.com/paper/2310.17347/) (2023)
- [Artificial intelligence-driven antimicrobial peptide discovery](https://mlsanity.com/paper/2308.10921/) (2023)

## Abstract (arXiv)

Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as limited controllability, lack of representations that efficiently model antimicrobial properties, and low experimental hit rates. To address these challenges, we introduce OmegAMP, a framework designed for reliable AMP generation with increased controllability. Its diffusion-based generative model leverages a novel conditioning mechanism to achieve fine-grained control over desired physicochemical properties and to direct generation towards specific activity profiles, including species-specific effectiveness. This is further enhanced by a biologically informed encoding space that significantly improves overall generative performance. Complementing these generative capabilities, OmegAMP leverages a novel synthetic data augmentation strategy to train classifiers for AMP filtering, drastically reducing false positive rates and thereby increasing the likelihood of experimental success. Our in silico experiments demonstrate that OmegAMP delivers state-of-the-art performance across key stages of the AMP discovery pipeline, enabling us to achieve an unprecedented success rate in wet lab experiments. We tested 25 candidate peptides, 24 of them (96%) demonstrated antimicrobial activity, proving effective even against multi-drug resistant strains. Our findings underscore OmegAMP's potential to significantly advance computational frameworks in the fight against antimicrobial resistance.