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README.md

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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).