MattStammers commited on
Commit
7f92684
·
1 Parent(s): 1605bd6

readme updated

Browse files
Files changed (1) hide show
  1. app.py +14 -7
app.py CHANGED
@@ -282,13 +282,15 @@ def redact_and_visualize(text: str, model_name: str):
282
 
283
 
284
  hint = """
285
- ![SETT Logo](./assets/img/SETT_Logo.jpg)
 
 
286
 
287
  ## Pteredactyl Gradio Webapp and API
288
 
289
- Clinical patient identifiable information (cPII) presents a significant challenge in natural language processing (NLP) that has yet to be fully resolved but significant progress is being made [1,2].
290
 
291
- This is why we created [Pteredactyl](https://pypi.org/project/pteredactyl/) - a python module to help with redaction of clinical free text.
292
 
293
  ## Tool Usage Instructions
294
 
@@ -305,10 +307,15 @@ docker build -t pteredactyl:latest .
305
  docker run -d -p 7860:7860 --name pteredactyl-app pteredactyl:latest
306
  ```
307
 
308
- ## Information
309
 
310
- A lot of work and experimentation has gone into the development of this tool. Because we believe in being fully transparent further details are given below.
 
 
311
 
 
 
 
312
 
313
  ### Methods:
314
 
@@ -347,8 +354,8 @@ The validation cohort introduced in this study proves to be a highly effective t
347
  We invite the open-source community to collaborate to improve the present results and enhance the robustness of cPII redaction methods by building on the work we have begun [here](https://github.com/SETT-Centre-Data-and-AI/PteRedactyl).
348
 
349
  ### References:
350
- 1. Chambon PJ, Wu C, Steinkamp JM, Adleberg J, Cook TS, Langlotz CP. Automated deidentification of radiology reports combining transformer and “hide in plain sight” rule-based methods. J Am Med Inform Assoc. 2023 Feb 1;30(2):318–28.
351
- 2. Kotevski DP, Smee RI, Field M, Nemes YN, Broadley K, Vajdic CM. Evaluation of an automated Presidio anonymisation model for unstructured radiation oncology electronic medical records in an Australian setting. Int J Med Inf. 2022 Dec 1;168:104880.
352
  """
353
 
354
  description = """
 
282
 
283
 
284
  hint = """
285
+ <p align="center">
286
+ <img src="https://github.com/MattStammers/Pteredactyl/blob/main/src/pteredactyl_webapp/assets/img/SETT_Logo.jpg" alt="SETT Logo" />
287
+ </p>
288
 
289
  ## Pteredactyl Gradio Webapp and API
290
 
291
+ Clinical patient identifiable information (cPII) presents a significant challenge in natural language processing (NLP) that has yet to be fully resolved but significant progress is being made [1,2].
292
 
293
+ This is why we created [Pteredactyl](https://pypi.org/project/pteredactyl/) - a python module to help with redaction of clinical free text.
294
 
295
  ## Tool Usage Instructions
296
 
 
307
  docker run -d -p 7860:7860 --name pteredactyl-app pteredactyl:latest
308
  ```
309
 
310
+ ## Logo
311
 
312
+ <p align="center">
313
+ <img src="https://github.com/MattStammers/Pteredactyl/blob/main/src/pteredactyl_webapp/assets/img/Pteredactyl_Logo.jpg" alt="SETT Logo" />
314
+ </p>
315
 
316
+ ## Background
317
+
318
+ We introduce a concentrated validation battery to the open-source OHDSI community, a Python module for cPII redaction on free text, and a web application that compares various models against the battery. This setup, which allows simultaneous production API deployment using Gradio, is remarkably efficient and can operate on a single CPU core.
319
 
320
  ### Methods:
321
 
 
354
  We invite the open-source community to collaborate to improve the present results and enhance the robustness of cPII redaction methods by building on the work we have begun [here](https://github.com/SETT-Centre-Data-and-AI/PteRedactyl).
355
 
356
  ### References:
357
+ 1. Chambon PJ, Wu C, Steinkamp JM, Adleberg J, Cook TS, Langlotz CP. Automated deidentification of radiology reports combining transformer and “hide in plain sight” rule-based methods. J Am Med Inform Assoc. 2023 Feb 1;30(2):318–28.
358
+ 2. Kotevski DP, Smee RI, Field M, Nemes YN, Broadley K, Vajdic CM. Evaluation of an automated Presidio anonymisation model for unstructured radiation oncology electronic medical records in an Australian setting. Int J Med Inf. 2022 Dec 1;168:104880.
359
  """
360
 
361
  description = """