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+## SciSpacy
+
+In this tutorial, we will use [scispacy](https://allenai.github.io/scispacy/) for various extraction tasks on MIMIC notes. Here we use named entity extraction as a detailed example.
+##### Named Entities
+```get_named_entities.py```
+
+Arguments:
+- ```--mimic_dir```: directory to mimic data that includes NOTEEVENTS.csv, default to data/mimic\_data in the tutorials directory
+- ```--model```: spaCy model to use, default to en_core_sci_sm
+- ```--row_id```: the row_id of the row whose NOTE field will be processed, default to 178
+- ```--output_file```: output file to save identified named entities default to ./output_named_entities.txt
+
+Commands:
+```sh
+python get_named_entities.py
+python get_named_entities.py --model en_core_sci_scibert --row_id 174
+```
+*Remark: if running with custom model, need to download the corresponding model using ```pip install <model url>``` where model urls can be found [here](https://allenai.github.io/scispacy/).
+
+A list of named entities will be written to the file specified by --ouput_file. 
+
+##### Abbreviations
+```get_abbreviations.py```
+##### Hyponyms
+```get_hyponyms.py```
+##### Linked Entities
+```get_linked_entities.py ```
+
+The arguments for these 3 tasks are the same as get_named_entities.py. Use the following commands to run in default values.
+
+```sh
+python get_abbreviations.py 
+python get_hyponyms.py
+python get_linked_entities.py 
+```
+
+## Translation with MarianMT
+We use [MarianMT](https://huggingface.co/transformers/model_doc/marian.html) to translate clinical notes to another language.
+
+```get_translation.py```
+
+Arguments:
+- ```--mimic_dir```: directory to mimic data that includes NOTEEVENTS.csv, default to data/mimic\_data in the tutorials directory
+- ```--target_language```: supported languages are {Spanish, French, Portuguese, Italian, Romanian, Malay_written_with_Latin, Mauritian_Creole, Haitian, Papiamento, Asturian, Catalan, Indonesian, Galician, Walloon, Occitan, Aragonese, Minangkabau}, default to Spanish
+- ```--row_id```: the row_id of the row whose NOTE field will be processed, default to 178
+- ```--output_file```: output file to save original and translated notes, default to ./output_translation.txt
+
+Commands:
+```sh
+python get_translation.py
+python get_translation.py --target_language French --row_id 2000 --output_file ./output_French.txt
+```