From c91dfc24c562d809d4c479d82dd8c1e99fd69f4e Mon Sep 17 00:00:00 2001 From: LINGLONGQIAN <15869023990@163.com> Date: Mon, 3 Mar 2025 17:17:21 +0000 Subject: [PATCH 1/2] fix TDS links --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index e1dbb55..4f55519 100644 --- a/README.md +++ b/README.md @@ -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 From 6c66e128abc9738dbfb20c340d244b5f5f9573db Mon Sep 17 00:00:00 2001 From: LinglongQian <38267728+LinglongQian@users.noreply.github.com> Date: Mon, 3 Mar 2025 18:09:02 +0000 Subject: [PATCH 2/2] Update requirements-dev.txt --- requirements-dev.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-dev.txt b/requirements-dev.txt index d6044f7..affc21e 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -7,3 +7,4 @@ nbconvert<6 jinja2<=3.0 matplotlib>=3.4.0,<3.8.0 seaborn +ipython<9.0.0