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[PDSM] Medical Testcases for benchmarking #157

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merged 98 commits into from
Jul 18, 2024
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ytehran
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@ytehran ytehran commented May 24, 2024

Please note, that this PR is still in work

What does this PR do?

  • Creation of test cases split into medical fields and languages (German & English)
  • Analyzing those results and classifying their failure groups

Notes

For the analysis:
Adaption of benchmark_utils for the failure_groups and added new methods
To test for synonyms, “nltk” is used, which must

  1. be installed e.g. pip install nltk
  2. Downloaded by commenting line 26 in our test.py

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ytehran commented Jun 16, 2024

@slobentanzer Wir haben jetzt einen Teil der SW Engineering umgesetzt und die Fragen anpasst. Wir wären ready um den großen Durchlauf zu machen

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Hi @ytehran and all,
could you kindly address the open issues and anything else you may want to fix before we merge into main? I'd like to do this soon to be able to proceed with the manuscript. :)

@@ -1,29 +1,28 @@
import os

import requests
from dotenv import load_dotenv
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@ytehran could you or another team member address this? prevents me from merging.

@@ -387,6 +386,9 @@ def evaluation_conversation():
prompts={},
correct=False,
)
# delete first dots if venv is in project env
cus_path = os.getcwd() + "../../venv/bin/.env"
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@ytehran please someone remove this so we can merge this PR.

openAIKey.py Outdated
@@ -0,0 +1,9 @@
import os
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@ytehran please address this (remove) in order to be able to merge into main :)

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ytehran commented Jul 16, 2024

@slobentanzer We changed our code in order to get the PR ready. Even some updates and improvements for our stats. If something is missing, please let me know

@slobentanzer slobentanzer changed the base branch from main to dev July 18, 2024 08:59
@slobentanzer slobentanzer merged commit 161d9fa into biocypher:dev Jul 18, 2024
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