Model Evaluation

效能評估

1 Reading List

"Model Evaluation, Model Selection, and Algorithm Selection in Machine Learning" by Sebastian Raschka, 2020. (https://arxiv.org/abs/1811.12808)
"Towards a guideline for evaluation metrics in medical image segmentation", Müller et al. BMC Research Notes (2022) 15:210 (https://doi.org/10.1186/s13104-022-06096-y)

2 AI 模型效能評估簡介

當我們建立人工智慧模型後，緊接而來的問題便是模型表現如何，由於表現的面相眾多，我們必須要掌握各種不同的衡量方式，才能使模型衡量面面俱到。在這一系列的影片中，我們將介紹各種面向的人工智慧模型效能評估方法。我們將會先介紹衡量分類模型的指標，並且利用其特性連結到衡量分割模型的指標。最後，我們也會針對模型的變化程度、拓展性，與合理性，介紹一些常見的評估方式。

Speaker｜張大衛

國立臺灣大學・MeDA Lab

Lecture |

Slides |

AI 模型效能評估.pdf [XYZ01]

3 多分類的效能評估

Speaker｜陳柔漪

國立臺灣大學・MeDA Lab

Lecture |

Performance Evaluation in Multi-Class Classification [14:33]

Hands-on |

程式碼講解 Code walkthrough [05:09]

Slides |

Performance Evaluation in Multi-Class Classification.pdf

Colab |

Colab: Multi-Class Classification (code)

Reference

Grandini, M., Bagli, E., & Visani, G. (2020). Metrics for multi-class classification: an overview. arXiv preprint arXiv:2008.05756.
- - - Mathematical formula basis
    - Explanation for micro-average & macro-average recall (sensitivity)
Galar, M., Fernández, A., Barrenechea, E., Bustince, H., & Herrera, F. (2011). An overview of ensemble methods for binary classifiers in multi-class problems: Experimental study on one-vs-one and one-vs-all schemes. Pattern Recognition, 44(8), 1761-1776.

4 Statistical Concepts

Statistics Fundamentals・StatQuest・[Playlist]

Confusion Matrix, Sensitivity, and Specificity

Machine Learning Fundamentals: The Confusion Matrix・StatQuest・[07:12]
Machine Learning Fundamentals: Sensitivity and Specificity・StatQuest・[11:46]

Sensitivity & Specificity Explained・Physiotutors・[07:57]
How to calculate Sensitivity and Specificity・Physiotutors・[05:44]

Sensitivity, Specificity, PPV, NPV・Dirty Medicine・[11:14]

The tradeoff between sensitivity and specificity・Rahul Patwari・[12:35]

PPV, NPV, and Prevalence

How to Calculate Positive (PPV) and Negative Predictive Values (NPV)・Physiotutors・[05:17]
Likelihood Ratios Explained・Physiotutors・[08:18]

Sensitivity, Specificity, PPV, NPV・Dirty Medicine・[11:14]

Positive predictive value - the role of prevalence・Medmastery・[05:12]
Positive Predictive Value - The role of specificity・Medmastery・[02:53]

ROC, AUC, pROC

ROC curve and AUC, Clearly Explained!・StatQuest・[16:16]

Precision–Recall Curve (PRC) for imbalanced datasets

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets・Takaya Saito and Marc Rehmsmeier・https://doi.org/10.1371%2Fjournal.pone.0118432

Likelihood Ratios

Likelihood ratios in diagnostic testing・Wikipedia
Diagnostic tests 4: likelihood ratios・Deeks and Altman・BMJ. 2004・https://doi.org/10.1136/bmj.329.7458.168

Cross Validation

A Guide to Cross-Validation for Artificial Intelligence in Medical Imaging ・ Bradshaw, Huemann, Hu, and Rahmim ・ https://doi.org/10.1148/ryai.220232
A Guide to Cross-Validation for AI (with Dr. Tyler Bradshaw) ・ Armam Rahmim ・ [49:19]
Cross-validation Colab Tutorial with examples using MNIST ・ Zach Huemann
Cross Validation in Medical AI・蔡欣翰・ [47:11]

How to Train a Final Machine Learning Model・Jason Brownlee・February 9, 2017

Complete Guide to Cross Validation・Rob Mulla・[29:48]

SHapley Additive exPlanations (SHAP)

A method in machine learning that explains individual predictions by quantifying the contribution of each feature to a model's output.

An Introduction to SHAP Values and Machine Learning Interpretability・DataCamp・9 min read

SHapley Additive exPlanations (SHAP)・Conor O'Sullivan・Playlist [01:10:42]

SHAP values for beginners | What they mean and their applications・[7:07]
SHAP with Python (Code and Explanations)・[15:41]
The mathematics behind Shapley Values・[11:48]
Shapley Values for Machine Learning・[11:06]
4 Significant Limitations of SHAP・[6:35]
SHAP Violin and Heatmap Plots | Interpretations and New Insights・[5:26]
SHAP for Binary and Multiclass Target Variables | Code and Explanations for Classification Problems・[12:59]

Introduction to SHAP with Python・Conor O'Sullivan・10 min read

To Be Organized

Kappa Value Calculation | Reliability・Physiotutors・[03:28]
Reliability & Validity Explained・Physiotutors・[02:56]
Reliability (Reproducability) Explained | Statistics in Healthcare・Physiotutors・[06:09]
Agreement Explained | Statistics in Healthcare・Physiotutors・[09:10]

X XYZ

Classification

Hypothesis Testing
- Fisher's Exact Test [Slides, Video, Codes]
- Mann-Whitney U Test [Slides, Video, Codes]
- Paired DeLong's Method [Slides, Video, Codes]
- P-Value [Slides, Video, Codes]

Confusion Matrix
- Sensitivity [Slides, Video, Codes]
- Specificity [Slides, Video, Codes]
- Accuracy [Slides, Video, Codes]
- Balanced Accuracy [Slides, Video, Codes]

ROC Curve
- AUC [Slides, Video, Codes]
- pROC [Slides, Video, Codes]

Descriptive Statistics
- Mean [Slides, Video, Codes]
- Median [Slides, Video, Codes]
- IQR [Slides, Video, Codes]

Estimation
- Confidence Interval [Slides, Video, Codes]

Likelihood
- Likelihood ratio [Slides, Video, Codes]
- Positive likelihood ratio [Slides, Video, Codes]
- Negative likelihood ratio [Slides, Video, Codes]
- Likelihood ratio test [Slides, Video, Codes]

Segmentation

Hypothesis Testing
- Fisher's Exact Test [Slides, Video, Codes]
- Mann-Whitney U Test [Slides, Video, Codes]
- P-Value [Slides, Video, Codes]

Confusion Matrix
- Sensitivity [Slides, Video, Codes]
- Specificity [Slides, Video, Codes]
- Accuracy [Slides, Video, Codes]
- Positive predictive value [Slides, Video, Codes]
- Negative predictive value [Slides, Video, Codes]
- True positive rate [Slides, Video, Codes]
- False positive rate [Slides, Video, Codes]

ROC Curve
- AUC [Slides, Video, Codes]

Descriptive Statistics
- Mean [Slides, Video, Codes]
- Median [Slides, Video, Codes]
- IQR [Slides, Video, Codes]

Estimation
- Confidence Interval [Slides, Video, Codes]

Detection

A
- A1 [Slides, Video, Codes]
- A2 [Slides, Video, Codes]

B
- B1 [Slides, Video, Codes]
- B2 [Slides, Video, Codes]

C
- C1 [Slides, Video, Codes]
- C2 [Slides, Video, Codes]

Registration

A
- A1 [Slides, Video, Codes]
- A2 [Slides, Video, Codes]

B
- B1 [Slides, Video, Codes]
- B2 [Slides, Video, Codes]

C
- C1 [Slides, Video, Codes]
- C2 [Slides, Video, Codes]

Prognosis

Confusion Matrix
- Sensitivity [Slides, Video, Codes]
- Specificity [Slides, Video, Codes]
- Accuracy [Slides, Video, Codes]
- Positive predictive value [Slides, Video, Codes]
- Negative predictive value [Slides, Video, Codes]
- True positive rate [Slides, Video, Codes]
- False positive rate [Slides, Video, Codes]

Hypothesis Testing
- Student t test [Slides, Video, Codes]
- Log rank test [Slides, Video, Codes]
- P-Value [Slides, Video, Codes]

Survival analysis
- Kaplan-Meier analysis [Slides, Video, Codes]
- Survival curve [Slides, Video, Codes]
- C-index [Slides, Video, Codes]

Odds
- Odds ratio [Slides, Video, Codes]

Estimation
- Confidence interval [Slides, Video, Codes]

Descriptive Statistics
- Median [Slides, Video, Codes]

ROC Curve
- AUC [Slides, Video, Codes]

XGBoost
- SHAP [Slides, Video, Codes]

4 Case Study

Segmentation
Classification

Deep Learning to Distinguish Pancreatic Cancer Tissue From Non-cancerous Pancreatic Tissue: a Retrospective Study With Cross-racial External Validation
The Lancet Digital Health, Vol. 2, Iss. 6, pp. 303-313, 2020
https://doi.org/10.1016/S2589-7500(20)30078-9

Hypothesis Testing
- Fisher's Exact Test
- Mann-Whitney U Test
- P-Value

Confusion Matrix
- Sensitivity
- Specificity
- Accuracy
- Balanced Accuracy

ROC Curve
- AUC

Descriptive Statistics
- Mean
- Median
- IQR

Estimation
- Confidence Interval

Classification

Detection of Pancreatic Cancer With Two- and Three-dimensional Radiomic Analysis in a Nationwide Population-based Real-world Dataset
BMC Cancer, 23:58, 2023
https://doi.org/10.1186/s12885-023-10536-8

Likelihood
- Likelihood ratio
- Positive likelihood ratio
- Negative likelihood ratio
- Likelihood ratio test

Confusion Matrix
- Sensitivity
- Specificity
- Accuracy

ROC Curve
- AUC
- pROC

Hypothesis Testing
- Fisher's Exact Test
- Mann-Whitney U Test
- Paired DeLong's Method

Prognosis prediction

Radiomic Analysis of Magnetic Resonance Imaging Predicts Brain Metastases Velocity and Clinical Outcome After Upfront Radiosurgery
Neuro-Oncology Advances, vdaa100, 2020
https://doi.org/10.1093/noajnl/vdaa100

Confusion Matrix
- Sensitivity
- Specificity
- Accuracy
- Positive predictive value
- Negative predictive value
- True positive rate
- False positive rate

Hypothesis Testing
- Student t test
- Log rank test
- P-Value

Survival analysis
- Kaplan-Meier analysis
- Survival curve
- C-index

Odds
- Odds ratio

Estimation
- Confidence interval

Descriptive Statistics
- Median

ROC curve

XGBoost
- SHAP

Classification

Radiomic Features Distinguish Pancreatic Cancer from Non-cancerous Pancreas.
Radiology: Imaging Cancer, Vol. 3, No. 4, 2021.
https://doi.org/10.1148/rycan.2021210010

Confusion Matrix
- Sensitivity
- Specificity
- Accuracy

Descriptive Statistics
- Median
- IQR
- Mean
- Standard deviation

ROC Curve
- AUC

Hypothesis Testing
- DeLong Test
- Fisher's Exact Test
- Mann-Whitney U Test
- P-value
- Inflated type I error

Estimation
- Confidence Interval

Probability Distribution
- Binomial distribution
- Student t distribution

XGboost

Segmentation
Classification

Pancreatic cancer detection on CT scans with deep learning: a nationwide population-based study
Radiology, Vol. 306, No.1, pp. 172-182, 2023.
https://pubs.rsna.org/doi/full/10.1148/radiol.220152

Confusion Matrix
- Sensitivity
- Specificity
- Accuracy

Hypothesis Testing
- McNemar Test
- Fisher's Exact Test
- Mann-Whitney U Test
- P-value

ROC Curve
- AUC

Estimation
- Confidence interval
- Likelihood
- Likelihood ratio

Descriptive Statistics
- IQR

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