Upload 32 files

README.md

@@ -0,0 +1,43 @@
+# ACI-BENCH
+
+##  Introduction 
+
+This repository contains the data and source code for:
+
+**Aci-bench: a Novel Ambient Clinical Intelligence Dataset for Benchmarking Automatic Visit Note Generation". Wen-wai Yim, Yujuan Fu, Asma Ben Abacha, Neal Snider, Thomas Lin, Meliha Yetisgen. Submitted to Nature Scientific Data, 2023.**
+https://www.nature.com/articles/s41597-023-02487-3
+
+```
+@article{aci-bench,
+  author = {Wen{-}wai Yim and
+                Yujuan Fu and
+                Asma {Ben Abacha} and
+                Neal Snider and Thomas Lin and Meliha Yetisgen},
+  title = {ACI-BENCH: a Novel Ambient Clinical Intelligence Dataset for Benchmarking Automatic Visit Note Generation},
+  journal = {Nature Scientific Data},
+  year = {2023}
+}
+```
+
+## Data statistics
+
+The ACI-BENCH collection consists of full doctor-patient conversations and associated clinical notes and includes the data splits from the [MEDIQA-CHAT 2023](https://sites.google.com/view/mediqa2023/clinicalnlp-mediqa-chat-2023) and [MEDIQA-SUM 2023](https://www.imageclef.org/2023/medical/mediqa) challenges: 
+```
+TRAIN: 67
+VALID: 20
+TEST1: 40 ( MEDIQA-CHAT TASK B test set )
+TEST2: 40 ( MEDIQA-CHAT TASK C test set )
+TEST3: 40 ( MEDIQA-SUM TASK C test set )
+```
+
+## License
+
+The data here is published under a Creative Commons Attribution 4.0 International Licence (CC BY).
+https://creativecommons.org/licenses/by/4.0/
+
+
+## Contact
+
+    -  Asma Ben abacha (abenabacha at microsoft dot com)
+     - Wen-wai Yim (yimwenwai at microsoft dot com)
+

requirements.txt

@@ -0,0 +1,16 @@
+quickumls
+evaluate==0.4.0
+nltk==3.8.1
+rouge-score==0.1.2
+bert-score==0.3.12
+git+https://github.com/google-research/bleurt.git
+spacy==3.4.4
+scispacy==0.5.1
+https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_lg-0.5.1.tar.gz
+https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_ner_bc5cdr_md-0.5.1.tar.gz
+https://github.com/explosion/spacy-models/releases/download/en_core_web_md-3.5.0/en_core_web_md-3.5.0-py3-none-any.whl
+chardet
+cchardet
+accelerate==0.15.0
+datasets==2.9.0
+nlp