jhnwu3 · Oct 19, 2026 · Oct 18, 2026 · Oct 18, 2026
diff --git a/examples/tutorials/series/00_quickstart.ipynb b/examples/tutorials/series/00_quickstart.ipynb
diff --git a/examples/tutorials/series/01_datasets.ipynb b/examples/tutorials/series/01_datasets.ipynb
diff --git a/examples/tutorials/series/02_tasks_and_processors.ipynb b/examples/tutorials/series/02_tasks_and_processors.ipynb
diff --git a/examples/tutorials/series/03_training_and_evaluation.ipynb b/examples/tutorials/series/03_training_and_evaluation.ipynb
diff --git a/examples/tutorials/series/04_choosing_a_model.ipynb b/examples/tutorials/series/04_choosing_a_model.ipynb
diff --git a/examples/tutorials/series/05_interpreting_predictions.ipynb b/examples/tutorials/series/05_interpreting_predictions.ipynb
diff --git a/examples/tutorials/series/06_medical_codes.ipynb b/examples/tutorials/series/06_medical_codes.ipynb
diff --git a/examples/tutorials/series/07_clinical_text.ipynb b/examples/tutorials/series/07_clinical_text.ipynb
diff --git a/examples/tutorials/series/08_contributing.ipynb b/examples/tutorials/series/08_contributing.ipynb
diff --git a/examples/tutorials/series/README.md b/examples/tutorials/series/README.md
@@ -1,33 +1,47 @@
 # PyHealth tutorial series
 
-Nine Colab-ready notebooks, from a first model to contributing a dataset. Each
-runs on a free Colab CPU runtime with public or synthetic data, so no
-credentials are needed.
+Colab notebooks for PyHealth 2.1, from a first model to contributing a
+dataset, plus three short notebooks on what changed in 2.1. Each one installs
+`pyhealth==2.1.0` and uses public or synthetic data, so no credentials are
+needed. The saved outputs come from a full run on Colab, so you can read the
+results here before running anything.
+
+## Tutorial series
 
 | # | Notebook | Covers |
 |---|---|---|
-| 00 | [Quickstart](00_quickstart.ipynb) | The five steps: dataset, task, split, model, evaluation |
+| 00 | [Quickstart](00_quickstart.ipynb) | A complete in-hospital mortality study: data figures, Table 1, three models with CIs and calibration, SHAP, subgroups, exported results (T4 GPU) |
 | 01 | [Datasets](01_datasets.ipynb) | Patients and events, YAML configs, caching, loading your own CSVs |
 | 02 | [Tasks and processors](02_tasks_and_processors.ipynb) | Writing tasks, what each processor produces |
 | 03 | [Training and evaluation](03_training_and_evaluation.ipynb) | Leakage-free splits, early stopping, class imbalance, calibration, bootstrap CIs |
-| 04 | [Choosing a model](04_choosing_a_model.ipynb) | Logistic regression to Transformer, plus an XGBoost baseline, on one split |
+| 04 | [Choosing a model](04_choosing_a_model.ipynb) | Logistic regression, MLP, RNN, Transformer, RETAIN and XGBoost on one split (T4 GPU) |
 | 05 | [Interpreting predictions](05_interpreting_predictions.ipynb) | TreeSHAP, Integrated Gradients, checking faithfulness |
 | 06 | [Medical codes](06_medical_codes.ipynb) | Lookups, ICD-9/ICD-10 translation, CCS/ATC groupers, `code_mapping` |
-| 07 | [Clinical text](07_clinical_text.ipynb) | Fine-tuning language models; specialty classification and ICD coding |
+| 07 | [Clinical text](07_clinical_text.ipynb) | Fine-tuning language models; specialty classification and ICD coding; label distributions and baselines (T4 GPU) |
 | 08 | [Contributing](08_contributing.ipynb) | Dataset classes, file-based data, tests, PR checklist |
 
-Open one in Colab from
-`https://colab.research.google.com/github/sunlabuiuc/PyHealth/blob/master/examples/tutorials/series/<notebook>.ipynb`.
+Most notebooks run on a free Colab CPU runtime. Tutorials 00, 04 and 07 open on
+a free T4 GPU runtime and also run on a CPU (04 and 07 with smaller settings).
 
-## Editing
+## What's new in PyHealth 2.1
 
-The notebooks are generated from `_source/tutorials/tNN_*.py`; edit those, then
-rebuild (and optionally execute) with:
+| # | Notebook | Covers |
+|---|---|---|
+| 1 | [Splits and reproducibility](whats_new_1_splits_and_reproducibility.ipynb) | `PatientSplit`, four-way splits with a calibration set, reproducible training |
+| 2 | [Calibration and confidence intervals](whats_new_2_calibration_and_intervals.ipynb) | Calibration metrics, patient-level bootstrap intervals, `set_pos_weight` |
+| 3 | [XGBoost and code mapping](whats_new_3_xgboost_and_code_mapping.ipynb) | `XGBoostModel` with exact TreeSHAP, ICD-9/ICD-10 and CCSR mapping, `nested_multihot` |
 
-```bash
-python examples/tutorials/series/_source/build.py            # all notebooks
-python examples/tutorials/series/_source/build.py t04 --run   # rebuild and execute one
-```
+## Opening in Colab
+
+Open a notebook from this folder with
+`https://colab.research.google.com/github/sunlabuiuc/PyHealth/blob/master/examples/tutorials/series/<notebook>.ipynb`,
+or use the maintained Colab copies listed on
+[pyhealth.dev](https://pyhealth.dev/tutorials.html) and in the
+[documentation](https://pyhealth.readthedocs.io/en/latest/tutorials.html).
+
+## Editing
 
-`--run` needs `nbclient` and a Jupyter kernel with PyHealth installed; it skips
-the install cell and stops at the first failing cell.
+The Colab copies are the working versions; the notebooks here are exported
+from them after a full run. To change a tutorial, edit it in Colab (or here),
+run it end to end with **Runtime > Run all**, and commit the notebook with its
+outputs.
diff --git a/examples/tutorials/series/_source/build.py b/examples/tutorials/series/_source/build.py
diff --git a/examples/tutorials/series/_source/nbkit.py b/examples/tutorials/series/_source/nbkit.py
diff --git a/examples/tutorials/series/_source/tutorials/__init__.py b/examples/tutorials/series/_source/tutorials/__init__.py