| --- |
| 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). |
|
|
