Update README.md

README.md

@@ -14,14 +14,14 @@ tags:
 
 ## Model Description
 
-This model is a fine-tuned version of ESMC-600M (ESM Cambrian) for paired antibody sequences (heavy and light chains).
+This model is a fine-tuned version of ESMC-600M (ESM Cambrian) for paired antibody variable-domain sequences containing heavy and light chains. It was trained using a CDR-focused masking strategy to improve representations for antibody binding affinity prediction.
 
 **Key Features:**
 - Trained on paired antibody sequences
-- 50% CDR fine-tuning
+- 50% CDR masking during fine-tuning
 - Input format: Heavy-Light chains separated by "-"
 - Output: 1152-dimensional embeddings
-- Optimized for antibody CDR region understanding
+- Designed to improve representation of antibody CDRs for downstream binding affinity prediction
 
 ### Preprocessing
 
@@ -194,18 +194,33 @@ sequence = "EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMS...-DIQMTQSPSSLSASVGDRVTITCRASQSI
 - **Format:** PyTorch tensor
 - **Dtype:** bfloat16
 
+## Publication
+
+**Preferential CDR masking in paired antibody language models improves binding affinity prediction**
+
+Mahtab Talaei, Kenji C. Walker, Boran Hao, Eliot Jolley, Yeping Jin, Dima Kozakov, John Misasi, Sandor Vajda, Ioannis Ch. Paschalidis, Diane Joseph-McCarthy.
+
+*Communications AI & Computing* **1**, 7 (2026).
+
+**DOI:** https://doi.org/10.1038/s44488-026-00010-2
+
+**Published:** August 13, 2026
+
+[Read the published article](https://www.nature.com/articles/s44488-026-00010-2)
 
 ## Citation
 
-If you use this model, please cite:
+If you use this model in your research, please cite the AbCDR paper and the underlying ESMC model:
 
 ```bibtex
-@article{talaei2025preferential,
-  title={Preferential CDR masking in paired antibody language models improves binding affinity prediction},
-  author={Talaei, Mahtab and Walker, Kenji C. and Hao, Boran and Jolley, Eliot and Jin, Yeping and Kozakov, Dima and Misasi, John and Vajda, Sandor and Paschalidis, Ioannis Ch. and Joseph-McCarthy, Diane},
-  journal={bioRxiv},
-  year={2025},
-  doi={10.1101/2025.10.31.685149}
+@article{Talaei2026,
+  author = {Talaei, Mahtab and Walker, Kenji C. and Hao, Boran and Jolley, Eliot and Jin, Yeping and Kozakov, Dima and Misasi, John and Vajda, Sandor and Paschalidis, Ioannis Ch. and Joseph-McCarthy, Diane},
+  title = {Preferential {CDR} masking in paired antibody language models improves binding affinity prediction},
+  journal = {Communications AI \& Computing},
+  volume = {1},
+  pages = {7},
+  year = {2026},
+  doi = {10.1038/s44488-026-00010-2}
 }
 
 @article{hayes2025simulating,
@@ -233,7 +248,7 @@ If you use this model, please cite:
 - **Maintainer:** Network Optimization & Control (NOC) Lab
 - **Email:** mtalaei@bu.edu
 - **GitHub:** [https://github.com/noc-lab/AbCDR-ESM](https://github.com/noc-lab/AbCDR-ESM)
-- **Paper:** [bioRxiv preprint](https://www.biorxiv.org/content/10.1101/2025.10.31.685149)
+- **Paper:** [Communications AI & Computing](https://doi.org/10.1038/s44488-026-00010-2)
 
 ## License