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Apr 23, 2025
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Fix Broken Links #29

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c91dfc2
fix TDS links
LinglongQian Mar 3, 2025
6c66e12
Update requirements-dev.txt
LinglongQian Mar 3, 2025
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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -8,16 +8,16 @@ In this tutorial, we will walk you through each stage of a basic MedCAT project.

| Part | Title | Google Colab | Blog Post |
| ---- |-----------------------------------------------------------------------------|------------------------------------------------------------------------------------|-----------|
| 1 | Introduction | - | [TDS](https://towardsdatascience.com/medcat-introduction-analyzing-electronic-health-records-e1c420afa13a) |
| 1 | Introduction | - | [TDS](https://medium.com/@w_is_h/medcat-introduction-analyzing-electronic-health-records-e1c420afa13a) |
| 1.1 | [\[OPTIONAL\] Logging With MedCAT](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb) | -
| 2 | [Data set Preparation and Basic Statistics](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_2_Dataset_Analysis_and_Preparation.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_2_Dataset_Analysis_and_Preparation.ipynb) | [TDS](https://towardsdatascience.com/medcat-dataset-analysis-and-preparation-be8bc910bd6d) |
| 3.1 | [Building a new Concept Database (CDB) and Vocabulary (Vocab)](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb) | [TDS](https://towardsdatascience.com/medcat-extracting-diseases-from-electronic-health-records-f53c45b3d1c1) |
| 3.2 | [Unsupervised training and NER+L](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.ipynb) | [TDS](https://towardsdatascience.com/medcat-extracting-diseases-from-electronic-health-records-f53c45b3d1c1) |
| 2 | [Data set Preparation and Basic Statistics](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_2_Dataset_Analysis_and_Preparation.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_2_Dataset_Analysis_and_Preparation.ipynb) | [TDS](https://medium.com/towards-data-science/medcat-dataset-analysis-and-preparation-be8bc910bd6d) |
| 3.1 | [Building a new Concept Database (CDB) and Vocabulary (Vocab)](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb) | [TDS](https://medium.com/towards-data-science/medcat-extracting-diseases-from-electronic-health-records-f53c45b3d1c1) |
| 3.2 | [Unsupervised training and NER+L](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.ipynb) | [TDS](https://medium.com/towards-data-science/medcat-extracting-diseases-from-electronic-health-records-f53c45b3d1c1) |
| 3.3 | [Technical model optimisations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_3_Model_technical_optimisations.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_3_3_Model_technical_optimisations.ipynb) | - |
| 4.1 | [Creating a tokenizer model (huggingface) and embeddings for MetaAnnotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_1_ByteLevelBPETokenizer_and_Embeddings.ipynb) | - |
| 4.2 | [Supervised training and fine-tuning + Meta-annotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.ipynb) | - |
| 4.3 | [Annotating documents with the full MedCAT pipeline with MetaAnnotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.ipynb) | - |
| 5 | [Analysing the results](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.ipynb) | [TDS](https://towardsdatascience.com/prevalence-of-physical-and-mental-diseases-450c0f4f5851) |
| 5 | [Analysing the results](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.ipynb) | [TDS](https://medium.com/@w_is_h/prevalence-of-physical-and-mental-diseases-450c0f4f5851) |


## Specialised tutorials
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1 change: 1 addition & 0 deletions requirements-dev.txt
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Expand Up @@ -7,3 +7,4 @@ nbconvert<6
jinja2<=3.0
matplotlib>=3.4.0,<3.8.0
seaborn
ipython<9.0.0