Update README.md

README.md

@@ -4,7 +4,7 @@ license: apache-2.0
 
 <h2>GatorTron-Medium overview </h2>
 
-Developed by a joint effort between the University of Florida and NVIDIA, GatorTron-Medium is a large language model of 3.9 billiom parameters, pre-trained using a BERT architecure implemented in the Megatron package (https://github.com/NVIDIA/Megatron-LM). 
+Developed by a joint effort between the University of Florida and NVIDIA, GatorTron-Medium is a clinical language model of 3.9 billion parameters, pre-trained using a BERT architecure implemented in the Megatron package (https://github.com/NVIDIA/Megatron-LM). 
 
 GatorTron-Medium is pre-trained using a dataset consisting of:
 
@@ -13,6 +13,25 @@ GatorTron-Medium is pre-trained using a dataset consisting of:
 - 2.5B words from WikiText,
 - 0.5B words of de-identified clinical notes from MIMIC-III
 
+The Github for GatorTron is at : https://github.com/uf-hobi-informatics-lab/GatorTron
+
+
+<h2>Model variations</h2>
+
+Model | Parameter 
+--- | --- 
+[gatortron-base](https://huggingface.co/UFNLP/gatortron-base)| 345 million 
+[gatortronS](https://huggingface.co/UFNLP/gatortronS) | 345 million
+[gatortron-medium (this model)](https://huggingface.co/UFNLP/gatortron-medium) | 3.9 billion 
+gatortron-large | 8.9 billion
+
+<h2>How to use</h2>
+
+
+- An NLP pacakge using GatorTron for clinical concept extraction (Named Entity Recognition): https://github.com/uf-hobi-informatics-lab/ClinicalTransformerNER
+- An NLP pacakge using GatorTron for Relation Extraction: https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction
+- An NLP pacakge using GatorTron for extraction of social determinants of health (SDoH) from clinical narratives: https://github.com/uf-hobi-informatics-lab/SDoH_SODA
+
 <h2>De-identification</h2>
 
 We applied a de-identification system to remove protected health information (PHI) from clinical text. We adopted the safe-harbor method to identify 18 PHI categories defined in the Health Insurance Portability and Accountability Act (HIPAA) and replaced them with dummy strings (e.g., replace people’s names into [\*\*NAME\*\*]). 
@@ -25,6 +44,20 @@ Yang X, Lyu T, Li Q, Lee C-Y, Bian J, Hogan WR, Wu Y†. A study of deep learnin
 
 Yang X, Chen A, PourNejatian N, Shin HC, Smith KE, Parisien C, Compas C, Martin C, Costa AB, Flores MG, Zhang Y, Magoc T, Harle CA, Lipori G, Mitchell DA, Hogan WR, Shenkman EA, Bian J, Wu Y†. A large language model for electronic health records. Npj Digit Med. Nature Publishing Group; . 2022 Dec 26;5(1):1–9. https://www.nature.com/articles/s41746-022-00742-2
 
+- BibTeX entry
+```
+@article{yang2022large,
+  title={A large language model for electronic health records},
+  author={Yang, Xi and Chen, Aokun and PourNejatian, Nima and Shin, Hoo Chang and Smith, Kaleb E and Parisien, Christopher and Compas, Colin and Martin, Cheryl and Costa, Anthony B and Flores, Mona G and Zhang, Ying and Magoc, Tanja and Harle, Christopher A and Lipori, Gloria and Mitchell, Duane A and Hogan, William R and Shenkman, Elizabeth A and Bian, Jiang and Wu, Yonghui },
+  journal={npj Digital Medicine},
+  volume={5},
+  number={1},
+  pages={194},
+  year={2022},
+  publisher={Nature Publishing Group UK London}
+} 
+```
+
 <h2>Contact</h2>
 
 - Yonghui Wu: yonghui.wu 'at' ufl.edu