README.md

---
license: cc-by-4.0
---

# Protein Sequence Modelling with Bayesian Flow Networks

  Welcome to the model weights for the paper ["Protein Sequence Modelling with Bayesian Flow Networks"](https://www.biorxiv.org/content/10.1101/2024.09.24.614734v1). Using the [code on our GitHub page](https://github.com/instadeepai/protein-sequence-bfn), you can sample from our trained models ProtBFN, for general proteins, and AbBFN, for antibody VH chains. 

Bayesian Flow Networks are a new approach to generative modelling, and can be viewed as an extension of diffusion models to the parameter space of probability distributions. They define a continuous-time process that maps between a naive prior distribution and a psuedo-deterministic posterior distribution for each variable independently. By training our neural network to 'denoise' the current posterior, by taking into account mutual information between variables, we implicitly minimise a variational lower bound. We can then use our trained neural network to generate samples from the learned distribution.

One of the benefits of defining such a process in probability parameter space is that it can be applied to *any* family of distributions with continous-valued parameters. This means that BFNs can be directly applied to discrete data, allowing for diffusion-like generative modelling for sequences without restrictive left-to-right inductive biases or relying on discrete-time stochastic processes. The main focus of our work is to investigate the application of BFNs to *protein sequences*, as represented by a sequence of amino acids. The ProtBFN methodology is broadly summarised below:

![An overview of ProtBFN.](BFN_overview.png)

Having trained ProtBFN, we find that it is exceptionally performant at unconditional generation of de novo protein sequences. For example, we find that we are able to rediscover a variety of structural motifs, according to structures predicted by ESMFold, with high sequence novelty:

![Cath hits for ProtBFN.](cath_s40_proteins.png)


## Cite our work

If you have used ProtBFN or AbBFN in your work, you can cite us using the following bibtex entry:

```text
@article {Atkinson2024.09.24.614734,
	author = {Atkinson, Timothy and Barrett, Thomas D. and Cameron, Scott and Guloglu, Bora and Greenig, Matthew and Robinson, Louis and Graves, Alex and Copoiu, Liviu and Laterre, Alexandre},
	title = {Protein Sequence Modelling with Bayesian Flow Networks},
	elocation-id = {2024.09.24.614734},
	year = {2024},
	doi = {10.1101/2024.09.24.614734},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2024/09/26/2024.09.24.614734},
	eprint = {https://www.biorxiv.org/content/early/2024/09/26/2024.09.24.614734.full.pdf},
	journal = {bioRxiv}
}
```