Updated heart tutorial #23

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ repos:
     rev: 1.3.10
     hooks:
       - id: databooks-meta
-        args: ["--cell-meta-keep=tags", "--nb-meta-keep=kernelspec"]
+        args: ["--cell-meta-keep=tags", "--cell-fields-keep=id", "--nb-meta-keep=kernelspec"]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0

_toc.yml

@@ -35,7 +35,7 @@ parts:
       title: Helper Functions
     - file: tutorials/brain-disorder-diagnosis/extend-reading/data-config
       title: Data & Config
-  - file: tutorials/drug-target-interaction/tutorial
+  - file: tutorials/drug-target-interaction/tutorial-drug
   - file: tutorials/multiomics-cancer-classification/tutorial-cancer
     sections:
     - file: tutorials/multiomics-cancer-classification/extend-reading/data

overview.md

@@ -68,28 +68,6 @@ This repository uses pre-commit hooks to ensure code quality and consistency. To
    pre-commit run --all-files
    ```
 
-[//]: # (### Part 2: Group Work)
-
-[//]: # (Participants will form small groups and select **one of the four domains** (Brain, Heart, Cancer, or Drug) to explore deeper:)
-
-[//]: # ()
-[//]: # (- Identify specific challenges (e.g., data integration, model generalisation, interpretability))
-
-[//]: # (- Extend existing tutorial pipelines or propose alternative solutions)
-
-[//]: # (- Present findings and ideas to the group for discussion)
-
-[//]: # ()
-[//]: # (Facilitators and demonstrators will provide support throughout, encouraging **open sharing, creativity, and peer learning**.)
-
-[//]: # ()
-[//]: # (---)
-
-[//]: # ()
-[//]: # (This tutorial forms a **launchpad for open, collaborative, and impactful biomedical AI research**, aligning with the broader vision of EMBC and the global scientific community.)
-
-[//]: # ()
-
 ## Contributors
 
 This workshop is made possible by contributions from:

tutorials/brain-disorder-diagnosis/extend-reading/data-config.md

@@ -44,7 +44,7 @@ It returns four values, including:
 
 - **`coords`** (`np.ndarray`): ROI coordinates for visualization purposes.
 
-[Back to the main tutorial](../tutorial.ipynb#data-loading)
+[Back to the main tutorial](https://pykale.github.io/mmai-tutorials/tutorials/brain-disorder-diagnosis/tutorial.html#data-loading)
 
 ## Categorical Variables from Phenotypic Data
 
@@ -135,7 +135,7 @@ The function returns the following:
     - `HANDEDNESS_CATEGORY`
     - `EYE_STATUS_AT_SCAN`
 
-[Back to the main tutorial](../tutorial.ipynb#data-preprocessing)
+[Back to the main tutorial](https://pykale.github.io/mmai-tutorials/tutorials/brain-disorder-diagnosis/tutorial.html#data-preprocessing)
 
 ## Configuration Arguments for Cross-Validation
 
@@ -155,7 +155,7 @@ In this tutorial, we specify the following arguments for cross-validation:
 - **`random_state`**: Seed for random number generators for reproducibility.
   - *Default:* `None`
 
-[Back to the main tutorial](../tutorial.ipynb#cross-validation-split)
+[Back to the main tutorial](https://pykale.github.io/mmai-tutorials/tutorials/brain-disorder-diagnosis/tutorial.html#cross-validation-split)
 
 ## Hyperparameter Grid
 
@@ -220,4 +220,4 @@ We also specify the hyperparameter search strategy and other training parameters
 - **`random_state`**: Seed for random number generators for reproducibility.
   - *Default:* `None`
 
-[Back to the main tutorial](../tutorial.ipynb#baseline-and-proposed-model)
+[Back to the main tutorial](https://pykale.github.io/mmai-tutorials/tutorials/brain-disorder-diagnosis/tutorial.html#baseline-and-proposed-model)

tutorials/brain-disorder-diagnosis/extend-reading/helper-functions.md

@@ -3,11 +3,11 @@
 Several helper scripts are provided to modularize the code and streamline the workflow. These scripts are located in the [current working directory](https://github.com/pykale/mmai-tutorials/tree/main/tutorials/brain-disorder-diagnosis) of the notebook and can be inspected directly as `.py` files. The helper scripts include:
 
 - [**`config.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/config.py): Defines base configuration settings, which can be customized or overridden using external `.yml` files.
-- [**`data.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/data.py): Provides data loading functions and utilities for automatically downloading required datasets.
-- [**`parsing.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/parsing.py): Contains utilities for compiling and summarizing evaluation results, as well as parsing the hyperparameter grid defined in the configuration.
-- [**`preprocess.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/preprocess.py): Handles phenotype preprocessing, including missing value imputation, categorical variable encoding, and FC extraction from the brain signals.
-- [**`visualization.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/visualization.py): Provides functions to visualize functional connectivity (FC) examples and the distribution of phenotypic variables.
+- [**`data.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/helpers/data.py): Provides data loading functions and utilities for automatically downloading required datasets.
+- [**`parsing.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/helpers/parsing.py): Contains utilities for compiling and summarizing evaluation results, as well as parsing the hyperparameter grid defined in the configuration.
+- [**`preprocess.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/helpers/preprocess.py): Handles phenotype preprocessing, including missing value imputation, categorical variable encoding, and FC extraction from the brain signals.
+- [**`visualization.py`**](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/brain-disorder-diagnosis/helpers/visualization.py): Provides functions to visualize functional connectivity (FC) examples and the distribution of phenotypic variables.
 
 Throughout the tutorial, we will provide further explanations on the contents and roles of these helper scripts as they are used.
 
-[Back to the main tutorial](../tutorial.ipynb)
+[Back to the main tutorial](https://pykale.github.io/mmai-tutorials/tutorials/brain-disorder-diagnosis/tutorial.html#step-0-environment-preparation)