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AAMFM

protein
antibody
antibody-design
multimodal
biological-sequence-modeling
structure-aware
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AAMFM
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---
arxiv: 2607.20057
license: mit
tags:
  - protein
  - antibody
  - antibody-design
  - multimodal
  - biological-sequence-modeling
  - structure-aware
---

# AAMFM: Antigen-specific Antibody Multi-modal Foundation Model

**AAMFM** is a multi-modal foundation model for antigen-specific functional
antibody design. It jointly models antibody sequence and structure, conditioned
on antigen geometry and epitope annotations.

[[Paper]](https://arxiv.org/abs/2607.20057)
[[Code]](https://github.com/XL-S224/AAMFM)

<p align="center">
  <img src="https://raw.githubusercontent.com/XL-S224/AAMFM/main/assets/aamfm-overview.png" alt="Overview of AAMFM" width="100%">
</p>
<p align="center"><em>Hierarchical training and inference pipeline of AAMFM.</em></p>

## Model description

AAMFM follows a hierarchical training strategy:

1. **Antibody-domain adaptation:** continual pre-training on paired antibody
   sequence--structure data.
2. **Antigen-specific supervised fine-tuning:** a lightweight adapter fuses
   antigen geometric features with epitope information.
3. **Preference alignment:** calibrated DPO aligns the model with
   structure-based functional preferences and sequence plausibility.

At inference time, the model is conditioned on an antigen, epitope-site
annotations, and antibody framework sequences to generate CDR sequences and a
complete antibody structure.

## Checkpoint

| File | Description |
| --- | --- |
| **AAMFM.pt** | AAMFM model checkpoint. |

## Usage

Use this checkpoint with the official
[AAMFM code repository](https://github.com/XL-S224/AAMFM). The repository
contains the training, generation, evaluation, and pseudo-log-likelihood
utilities, together with instructions for the required external assets.

Generation requires a compatible base-model backend, its externally supplied
weights, antigen geometric features, and antigen/epitope inputs. See the
[repository README](https://github.com/XL-S224/AAMFM#readme) for the complete
environment and runtime setup.

## Intended use and limitations

This checkpoint is intended for research in computational antibody design. Its
outputs are computational candidates, not experimentally validated antibodies,
and must not be used for clinical, diagnostic, or therapeutic decisions without
appropriate experimental validation and expert review.

## Citation

If you use AAMFM, please cite:

    @article{shi2026aamfm,
      title={Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design},
      author={Shi, Xiaoliang and Wang, Zichen and Ma, Runze and Zhang, Zhongyue and Zheng, Shuangjia},
      journal={arXiv preprint arXiv:2607.20057},
      year={2026}
    }

## License

The AAMFM checkpoint and the accompanying
[source-code repository](https://github.com/XL-S224/AAMFM) are released under
the [MIT License](https://opensource.org/license/mit).