medpipe 0.0.1__tar.gz

medpipe-0.0.1/LICENSE

@@ -0,0 +1,201 @@
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medpipe-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: medpipe
+Version: 0.0.1
+Summary: A package for clinical AI pipeline development
+Author-email: Mathias Roesler <mathias.roesler@auckland.co.nz>
+License-Expression: Apache-2.0
+Project-URL: Repository, https://github.com/Surgical-Recovery-and-Safety-Lab/medpipe
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: imbalanced_learn==0.14.1
+Requires-Dist: imblearn==0.0
+Requires-Dist: matplotlib==3.10.8
+Requires-Dist: numpy==2.4.2
+Requires-Dist: pandas==2.3.3
+Requires-Dist: pytest==9.0.1
+Requires-Dist: scikit_learn==1.8.0
+Requires-Dist: scipy==1.17.0
+Requires-Dist: pyarrow==23.0.1
+Dynamic: license-file
+
+# medpipe
+
+![GitHub License](https://img.shields.io/github/license/Surgical-Recovery-and-Safety-Lab/medpipe)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12+-green.svg)](https://www.python.org/downloads/)
+[![tests](https://github.com/Surgical-Recovery-and-Safety-Lab/medpipe/actions/workflows/run_test.yml/badge.svg)](https://github.com/Surgical-Recovery-and-Safety-Lab/medpipe/actions/workflows/run_test.yml)
+## Table of content
+1. [Overview](#overview)
+2. [Installation](#installation)
+3. [Usage](#usage)
+	1. [Preprocessing operations](#preprocess)
+	2. [Models](#models)
+	3. [Recalibration](#recalibration)
+	4. [Metrics](#metrics)
+	5. [Plots](#plots)
+5. [Examples](#examples)
+
+## Overview
+The **medpipe** package is a layer to help create AI models for clinical applications from tabular data. It covers data loading and preprocessing, model creation and training, recalibration, and visualisation. 
+___
+## Installation
+
+To install **medpipe** clone the GitHub repository and install the package with pip: 
+```
+$ git clone git@github.com:Surgical-Recovery-and-Safety-Lab/medpipe.git
+$ cd medpipe
+$ pip install .
+```
+**NOTE**: It is recommended to use a virtual environment (venv) to install this package. 
+
+Ensure that the installation was succesfull and that all tests pass by running the following command in the medpipe directory:
+```
+$ pytest 
+```
+___
+
+## Usage
+This package was tested on a Linux distribution (Ubuntu 24.04) with Python v3.12.3. The [sckit-learn](https://scikit-learn.org/stable/index.html) was used as the base of most of the code. 
+
+A Pipeline contains the preprocessing operations, a model for each prediction label, and a recalibration model (if specified) for each label. Thus, with only a few lines of code, several models can be created from the same data and fitted. 
+
+### Preprocessing operations
+Currently four preprocessing operations are available:
+* **standarise**, this operation standardises the input features by removing the mean and scaling to unit variance;
+* **ordinal encoding**, this operation converts non-numerical categorical input features into ordinal ones;
+* **power transform**, this operation applies a power transform to make the data more Gaussian-like;
+* **binning**, this operation converts a continuous input feature into bins and caps the value. 
+
+### Models
+There is only one classifier available at the moment: the histogram boosted gradient classifier. 
+
+**NOTE:** Adding a new model only requires editing the **create_model** function in *models/core*. To work, it must have a fit and predict method. 
+
+### Recalibration
+Two recalibration models are available: logistic regression, and isotonic regression. 
+
+### Metrics
+The available metrics are divided into the score metrics and prediction metrics. The list of available metrics is the following:
+
+| Metric | Type | Description |
+| :--- | :--- | :--- |
+| Accuracy | Prediction | Proportion of all classifications that were correct. |
+| Recall | Prediction | Proportion of all actual positives that were classified correctly (true positive rate). |
+| Precision | Prediction | Proportion of all the  positive classifications that are actually positive. |
+| F1 score | Prediction | Harmonic mean of precision and recall. |
+| AUROC | Score | Area under the ROC curve. |
+| AP | Score | Area under the precision-recall curve. |
+| Log loss | Score | Logarithmic loss. |
+
+### Plots
+
+Three types of plots are available: bar graphs for the metrics, predicted probability distributions, and calibration curves. 
+
+The following graphs are from one pipeline with two models, one to predict complications and the other to predict 90-day mortality. The predictor and calibrator results are plotted on the same graphs to compare the effect of recalibration. 
+
+Plots of the AUROC and log loss metric values with confidence intervals for each outcome:
+
+| Any complication | 90-day mortality |
+| :---: | :---: |
+| ![AUROC_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_auroc.png) | ![AUROC_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_auroc.png) |
+| ![log_loss_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_log_loss.png) | ![log_loss_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_log_loss.png) |
+
+
+Predicted probability distributions for each outcome:
+
+| Any complication | 90-day mortality |
+| :---: | :---: |
+| ![proba_dist_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_proba_dist.png) | ![proba_dist_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_proba_dist.png) |
+
+
+Calibration curves for each outcome:
+
+| Any complication | 90-day mortality |
+| :---: | :---: |
+| ![calibration_curve_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_reliability_diagram.png) | ![proba_dist_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_reliability_diagram.png) |
+___
+## Example
+
+Here is a short example that shows how to load data, train the models, and plot the calibration curves:
+
+``` py linenums="1"
+from medpipe import (
+	Pipeline
+	read_toml_configuration,
+	load_data_from_csv,
+	get_positive_proba,
+	extract_labels,
+	plot_reliability_diagrams,
+)
+
+# Load configuration and data
+config = read_toml_configuration("config_file.toml")
+data = load_data_from_csv("data.csv")
+
+# Create pipeline
+pipeline = Pipeline(general_config)
+
+# Split data into sets and train model
+X_train, X_test = pipeline.get_test_data(data)
+pipeline.run(X_train)
+
+# Plot calibration curve
+X_test, y_test = extract_labels(X_test, pipeline.label_list)
+y_pred_proba = pipeline.predict_proba(X_test)
+plot_reliability_diagrams(y_test, get_positive_proba(y_pred_proba, display_kwargs={"n_bins": 10, "strategy": "quantile"})
+
+```

medpipe-0.0.1/README.md

@@ -0,0 +1,126 @@
+# medpipe
+
+![GitHub License](https://img.shields.io/github/license/Surgical-Recovery-and-Safety-Lab/medpipe)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12+-green.svg)](https://www.python.org/downloads/)
+[![tests](https://github.com/Surgical-Recovery-and-Safety-Lab/medpipe/actions/workflows/run_test.yml/badge.svg)](https://github.com/Surgical-Recovery-and-Safety-Lab/medpipe/actions/workflows/run_test.yml)
+## Table of content
+1. [Overview](#overview)
+2. [Installation](#installation)
+3. [Usage](#usage)
+	1. [Preprocessing operations](#preprocess)
+	2. [Models](#models)
+	3. [Recalibration](#recalibration)
+	4. [Metrics](#metrics)
+	5. [Plots](#plots)
+5. [Examples](#examples)
+
+## Overview
+The **medpipe** package is a layer to help create AI models for clinical applications from tabular data. It covers data loading and preprocessing, model creation and training, recalibration, and visualisation. 
+___
+## Installation
+
+To install **medpipe** clone the GitHub repository and install the package with pip: 
+```
+$ git clone git@github.com:Surgical-Recovery-and-Safety-Lab/medpipe.git
+$ cd medpipe
+$ pip install .
+```
+**NOTE**: It is recommended to use a virtual environment (venv) to install this package. 
+
+Ensure that the installation was succesfull and that all tests pass by running the following command in the medpipe directory:
+```
+$ pytest 
+```
+___
+
+## Usage
+This package was tested on a Linux distribution (Ubuntu 24.04) with Python v3.12.3. The [sckit-learn](https://scikit-learn.org/stable/index.html) was used as the base of most of the code. 
+
+A Pipeline contains the preprocessing operations, a model for each prediction label, and a recalibration model (if specified) for each label. Thus, with only a few lines of code, several models can be created from the same data and fitted. 
+
+### Preprocessing operations
+Currently four preprocessing operations are available:
+* **standarise**, this operation standardises the input features by removing the mean and scaling to unit variance;
+* **ordinal encoding**, this operation converts non-numerical categorical input features into ordinal ones;
+* **power transform**, this operation applies a power transform to make the data more Gaussian-like;
+* **binning**, this operation converts a continuous input feature into bins and caps the value. 
+
+### Models
+There is only one classifier available at the moment: the histogram boosted gradient classifier. 
+
+**NOTE:** Adding a new model only requires editing the **create_model** function in *models/core*. To work, it must have a fit and predict method. 
+
+### Recalibration
+Two recalibration models are available: logistic regression, and isotonic regression. 
+
+### Metrics
+The available metrics are divided into the score metrics and prediction metrics. The list of available metrics is the following:
+
+| Metric | Type | Description |
+| :--- | :--- | :--- |
+| Accuracy | Prediction | Proportion of all classifications that were correct. |
+| Recall | Prediction | Proportion of all actual positives that were classified correctly (true positive rate). |
+| Precision | Prediction | Proportion of all the  positive classifications that are actually positive. |
+| F1 score | Prediction | Harmonic mean of precision and recall. |
+| AUROC | Score | Area under the ROC curve. |
+| AP | Score | Area under the precision-recall curve. |
+| Log loss | Score | Logarithmic loss. |
+
+### Plots
+
+Three types of plots are available: bar graphs for the metrics, predicted probability distributions, and calibration curves. 
+
+The following graphs are from one pipeline with two models, one to predict complications and the other to predict 90-day mortality. The predictor and calibrator results are plotted on the same graphs to compare the effect of recalibration. 
+
+Plots of the AUROC and log loss metric values with confidence intervals for each outcome:
+
+| Any complication | 90-day mortality |
+| :---: | :---: |
+| ![AUROC_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_auroc.png) | ![AUROC_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_auroc.png) |
+| ![log_loss_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_log_loss.png) | ![log_loss_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_log_loss.png) |
+
+
+Predicted probability distributions for each outcome:
+
+| Any complication | 90-day mortality |
+| :---: | :---: |
+| ![proba_dist_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_proba_dist.png) | ![proba_dist_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_proba_dist.png) |
+
+
+Calibration curves for each outcome:
+
+| Any complication | 90-day mortality |
+| :---: | :---: |
+| ![calibration_curve_any_comp](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_ANY_COMP_reliability_diagram.png) | ![proba_dist_90d_mortality](docs/assets/ai_risk_HGBc_v0.4.1.4-d.1.3.2_MORTALITY_90D_reliability_diagram.png) |
+___
+## Example
+
+Here is a short example that shows how to load data, train the models, and plot the calibration curves:
+
+``` py linenums="1"
+from medpipe import (
+	Pipeline
+	read_toml_configuration,
+	load_data_from_csv,
+	get_positive_proba,
+	extract_labels,
+	plot_reliability_diagrams,
+)
+
+# Load configuration and data
+config = read_toml_configuration("config_file.toml")
+data = load_data_from_csv("data.csv")
+
+# Create pipeline
+pipeline = Pipeline(general_config)
+
+# Split data into sets and train model
+X_train, X_test = pipeline.get_test_data(data)
+pipeline.run(X_train)
+
+# Plot calibration curve
+X_test, y_test = extract_labels(X_test, pipeline.label_list)
+y_pred_proba = pipeline.predict_proba(X_test)
+plot_reliability_diagrams(y_test, get_positive_proba(y_pred_proba, display_kwargs={"n_bins": 10, "strategy": "quantile"})
+
+```

medpipe-0.0.1/pyproject.toml

@@ -0,0 +1,29 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [ "setuptools>=80.9" ]
+
+[project]
+name = "medpipe"
+version = "0.0.1"
+description = "A package for clinical AI pipeline development"
+readme = "README.md"
+license = "Apache-2.0"
+license-files = [ "LICEN[CS]E*" ]
+authors = [
+  { name = "Mathias Roesler", email = "mathias.roesler@auckland.co.nz" },
+]
+requires-python = ">=3.12"
+classifiers = [
+  "Operating System :: Unix",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+]
+dynamic = [ "dependencies" ]
+urls.Repository = "https://github.com/Surgical-Recovery-and-Safety-Lab/medpipe"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+packages = [ "medpipe", "medpipe.data", "medpipe.models", "medpipe.metrics", "medpipe.pipeline", "medpipe.utils" ]
+dynamic.dependencies = { file = [ "requirements.txt" ] }

medpipe-0.0.1/requirements.txt

@@ -0,0 +1,9 @@
+imbalanced_learn==0.14.1
+imblearn==0.0
+matplotlib==3.10.8
+numpy==2.4.2
+pandas==2.3.3
+pytest==9.0.1
+scikit_learn==1.8.0
+scipy==1.17.0
+pyarrow==23.0.1

medpipe-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

medpipe-0.0.1/src/medpipe/__init__.py

@@ -0,0 +1,54 @@
+"""
+medpipe module
+
+submodules:
+- data: contains data related functions
+- metrics: contains model metric functions
+- models: contains model creation functions
+- pipeline: contains pipeline functions
+- utils: contains utility functions
+"""
+
+from .data import db, extract_data_from_db, extract_labels, preprocessing
+from .metrics import (
+    compute_all_CI,
+    compute_pred_metrics,
+    compute_score_metrics,
+    plot_metrics_CI,
+    plot_prediction_distribution,
+    plot_reliability_diagrams,
+    print_metrics,
+    print_metrics_CI,
+)
+from .models import get_full_proba, get_positive_proba, load_pipeline, save_pipeline
+from .pipeline.Pipeline import Pipeline
+from .utils import (
+    exception_handler,
+    load_data_from_csv,
+    print_message,
+    read_toml_configuration,
+    setup_logger,
+)
+
+__all__ = [
+    "Pipeline",
+    "exception_handler",
+    "load_data_from_csv",
+    "print_message",
+    "read_toml_configuration",
+    "setup_logger",
+    "get_full_proba",
+    "get_positive_proba",
+    "load_pipeline",
+    "save_pipeline",
+    "compute_all_CI",
+    "compute_pred_metrics",
+    "compute_score_metrics",
+    "plot_metrics_CI",
+    "plot_prediction_distribution",
+    "plot_reliability_diagrams",
+    "print_metrics",
+    "print_metrics_CI",
+    "extract_data_from_db",
+    "extract_labels",
+]