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README.md

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 license: cc-by-nc-4.0
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+---
+
+
+# FlashPPI: Linear-time prediction of proteome-scale microbial protein interactions
+
+
+FlashPPI is a contrastively trained model for protein-protein interaction (PPI) prediction, grounded in residue-level interactions, that enables full-proteome interaction prediction in minutes.
+
+By reframing PPI prediction as a dense retrieval task, FlashPPI circumvents the quadratic computational bottleneck of traditional all-vs-all structural screening.
+
+- **Scalable:** Reduces proteome-wide screening from days/months to minutes.
+- **Interpretable:** Predicts fine-grained, residue-level 2D contact maps for retrieved interaction candidates.
+- **Genomic Priors:** Leverages [gLM2](https://huggingface.co/tattabio/gLM2_650M) to capture cross-protein, multi-gene co-evolutionary signals.
+
+
+## Web Server
+FlashPPI is integrated into [seqhub.org](https://seqhub.org). You can upload a FASTA and interactively explore whole-proteome networks and contact maps. Explore an example network [here](https://seqhub.org/tattabio/mycobacterium_tb?ppi=true).
+
+
+## Usage
+
+See the github repo https://github.com/TattaBio/flashppi for usage and inference scripts.
+
+## License
+The model code and inference scripts in the GitHub repo are licensed under the Apache License 2.0.
+
+The FlashPPI model weights are hosted on Hugging Face and released under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license. The weights are freely available for academic and research purposes.
+
+## Citing 
+If you use FlashPPI or our datasets in your research, please cite:
+
+```
+@article {Cornman2026FlashPPI,
+	author = {Cornman, Andre and Tranzillo, Matt and Zulaybar, Nicolo G and Bouzit, Imane and Hwang, Yunha},
+	title = {Linear-time prediction of proteome-scale microbial protein interactions},
+	year = {2026},
+	doi = {10.64898/2026.03.01.708874},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2026/03/02/2026.03.01.708874},
+	journal = {bioRxiv}
+}
+```