Multi-class confusion matrix library in Python
Maintainers
Project description
Table of contents
- Overview
- Installation
- Usage
- Document
- Issues & Bug Reports
- Todo
- Outputs
- Dependencies
- Contribution
- References
- Cite
- Authors
- License
- Donate
- Changelog
Overview
PyCM is a multi-class confusion matrix library written in Python that supports both input data vectors and direct matrix, and a proper tool for post-classification model evaluation that supports most classes and overall statistics parameters. PyCM is the swiss-army knife of confusion matrices, targeted mainly at data scientists that need a broad array of metrics for predictive models and an accurate evaluation of large variety of classifiers.
Fig1. PyCM Block Diagram
Installation
Source Code
- Download Version 0.9.5 or Latest Source
- Run
pip install -r requirements.txtorpip3 install -r requirements.txt(Need root access) - Run
python3 setup.py installorpython setup.py install(Need root access)
PyPI
- Check Python Packaging User Guide
- Run
pip install pycm --upgradeorpip3 install pycm --upgrade(Need root access)
Easy Install
- Run
easy_install --upgrade pycm(Need root access)
Usage
From Vector
>>> from pycm import * >>> y_actu = [2, 0, 2, 2, 0, 1, 1, 2, 2, 0, 1, 2] # or y_actu = numpy.array([2, 0, 2, 2, 0, 1, 1, 2, 2, 0, 1, 2]) >>> y_pred = [0, 0, 2, 1, 0, 2, 1, 0, 2, 0, 2, 2] # or y_pred = numpy.array([0, 0, 2, 1, 0, 2, 1, 0, 2, 0, 2, 2]) >>> cm = ConfusionMatrix(actual_vector=y_actu, predict_vector=y_pred) # Create CM From Data >>> cm.classes [0, 1, 2] >>> cm.table {0: {0: 3, 1: 0, 2: 0}, 1: {0: 0, 1: 1, 2: 2}, 2: {0: 2, 1: 1, 2: 3}} >>> print(cm) Predict 0 1 2 Actual 0 3 0 0 1 0 1 2 2 2 1 3 Overall Statistics : 95% CI (0.30439,0.86228) Bennett_S 0.375 Chi-Squared 6.6 Chi-Squared DF 4 Conditional Entropy 0.95915 Cramer_V 0.5244 Cross Entropy 1.59352 Gwet_AC1 0.38931 Joint Entropy 2.45915 KL Divergence 0.09352 Kappa 0.35484 Kappa 95% CI (-0.07708,0.78675) Kappa No Prevalence 0.16667 Kappa Standard Error 0.22036 Kappa Unbiased 0.34426 Lambda A 0.16667 Lambda B 0.42857 Mutual Information 0.52421 Overall_ACC 0.58333 Overall_J (1.225,0.40833) Overall_RACC 0.35417 Overall_RACCU 0.36458 PPV_Macro 0.56667 PPV_Micro 0.58333 Phi-Squared 0.55 Reference Entropy 1.5 Response Entropy 1.48336 Scott_PI 0.34426 Standard Error 0.14232 Strength_Of_Agreement(Altman) Fair Strength_Of_Agreement(Cicchetti) Poor Strength_Of_Agreement(Fleiss) Poor Strength_Of_Agreement(Landis and Koch) Fair TPR_Macro 0.61111 TPR_Micro 0.58333 Class Statistics : Classes 0 1 2 ACC(Accuracy) 0.83333 0.75 0.58333 BM(Informedness or bookmaker informedness) 0.77778 0.22222 0.16667 DOR(Diagnostic odds ratio) None 4.0 2.0 ERR(Error rate) 0.16667 0.25 0.41667 F0.5(F0.5 score) 0.65217 0.45455 0.57692 F1(F1 score - harmonic mean of precision and sensitivity) 0.75 0.4 0.54545 F2(F2 score) 0.88235 0.35714 0.51724 FDR(False discovery rate) 0.4 0.5 0.4 FN(False negative/miss/type 2 error) 0 2 3 FNR(Miss rate or false negative rate) 0.0 0.66667 0.5 FOR(False omission rate) 0.0 0.2 0.42857 FP(False positive/type 1 error/false alarm) 2 1 2 FPR(Fall-out or false positive rate) 0.22222 0.11111 0.33333 G(G-measure geometric mean of precision and sensitivity) 0.7746 0.40825 0.54772 J(Jaccard index) 0.6 0.25 0.375 LR+(Positive likelihood ratio) 4.5 3.0 1.5 LR-(Negative likelihood ratio) 0.0 0.75 0.75 MCC(Matthews correlation coefficient) 0.68313 0.2582 0.16903 MK(Markedness) 0.6 0.3 0.17143 N(Condition negative) 9 9 6 NPV(Negative predictive value) 1.0 0.8 0.57143 P(Condition positive) 3 3 6 POP(Population) 12 12 12 PPV(Precision or positive predictive value) 0.6 0.5 0.6 PRE(Prevalence) 0.25 0.25 0.5 RACC(Random accuracy) 0.10417 0.04167 0.20833 RACCU(Random accuracy unbiased) 0.11111 0.0434 0.21007 TN(True negative/correct rejection) 7 8 4 TNR(Specificity or true negative rate) 0.77778 0.88889 0.66667 TON(Test outcome negative) 7 10 7 TOP(Test outcome positive) 5 2 5 TP(True positive/hit) 3 1 3 TPR(Sensitivity, recall, hit rate, or true positive rate) 1.0 0.33333 0.5 >>> cm.matrix() Predict 0 1 2 Actual 0 3 0 0 1 0 1 2 2 2 1 3 >>> cm.normalized_matrix() Predict 0 1 2 Actual 0 1.0 0.0 0.0 1 0.0 0.33333 0.66667 2 0.33333 0.16667 0.5
Direct CM
>>> from pycm import * >>> cm2 = ConfusionMatrix(matrix={"Class1": {"Class1": 1, "Class2":2}, "Class2": {"Class1": 0, "Class2": 5}}) # Create CM Directly >>> cm2 pycm.ConfusionMatrix(classes: ['Class1', 'Class2']) >>> print(cm2) Predict Class1 Class2 Actual Class1 1 2 Class2 0 5 Overall Statistics : 95% CI (0.44994,1.05006) Bennett_S 0.5 Chi-Squared None Chi-Squared DF 1 Conditional Entropy None Cramer_V None Cross Entropy 1.2454 Gwet_AC1 0.6 Joint Entropy None KL Divergence 0.29097 Kappa 0.38462 Kappa 95% CI (-0.354,1.12323) Kappa No Prevalence 0.5 Kappa Standard Error 0.37684 Kappa Unbiased 0.33333 Lambda A None Lambda B None Mutual Information None Overall_ACC 0.75 Overall_J (1.04762,0.52381) Overall_RACC 0.59375 Overall_RACCU 0.625 PPV_Macro 0.85714 PPV_Micro 0.75 Phi-Squared None Reference Entropy 0.95443 Response Entropy 0.54356 Scott_PI 0.33333 Standard Error 0.15309 Strength_Of_Agreement(Altman) Fair Strength_Of_Agreement(Cicchetti) Poor Strength_Of_Agreement(Fleiss) Poor Strength_Of_Agreement(Landis and Koch) Fair TPR_Macro 0.66667 TPR_Micro 0.75 Class Statistics : Classes Class1 Class2 ACC(Accuracy) 0.75 0.75 BM(Informedness or bookmaker informedness) 0.33333 0.33333 DOR(Diagnostic odds ratio) None None ERR(Error rate) 0.25 0.25 F0.5(F0.5 score) 0.71429 0.75758 F1(F1 score - harmonic mean of precision and sensitivity) 0.5 0.83333 F2(F2 score) 0.38462 0.92593 FDR(False discovery rate) 0.0 0.28571 FN(False negative/miss/type 2 error) 2 0 FNR(Miss rate or false negative rate) 0.66667 0.0 FOR(False omission rate) 0.28571 0.0 FP(False positive/type 1 error/false alarm) 0 2 FPR(Fall-out or false positive rate) 0.0 0.66667 G(G-measure geometric mean of precision and sensitivity) 0.57735 0.84515 J(Jaccard index) 0.33333 0.71429 LR+(Positive likelihood ratio) None 1.5 LR-(Negative likelihood ratio) 0.66667 0.0 MCC(Matthews correlation coefficient) 0.48795 0.48795 MK(Markedness) 0.71429 0.71429 N(Condition negative) 5 3 NPV(Negative predictive value) 0.71429 1.0 P(Condition positive) 3 5 POP(Population) 8 8 PPV(Precision or positive predictive value) 1.0 0.71429 PRE(Prevalence) 0.375 0.625 RACC(Random accuracy) 0.04688 0.54688 RACCU(Random accuracy unbiased) 0.0625 0.5625 TN(True negative/correct rejection) 5 1 TNR(Specificity or true negative rate) 1.0 0.33333 TON(Test outcome negative) 7 1 TOP(Test outcome positive) 1 7 TP(True positive/hit) 1 5 TPR(Sensitivity, recall, hit rate, or true positive rate) 0.33333 1.0
Activation Threshold
threshold is added in Version 0.9 for real value prediction.
For more information visit Example3
Load From File
file is added in Version 0.9.5 in order to load saved confusion matrix with .obj format generated by save_obj method.
For more information visit Example4
Acceptable Data Types
actual_vector: pythonlistor numpyarrayof any stringable objectspredict_vector: pythonlistor numpyarrayof any stringable objectsmatrix:dictdigit:intthreshold:FunctionType (function or lambda)file:File object
- run
help(ConfusionMatrix)forConfusionMatrixobject details
For more information visit here
Issues & Bug Reports
Just fill an issue and describe it. We'll check it ASAP! or send an email to shaghighi@ce.sharif.edu.
Todo
- [x] Basic
- [x] TP
- [x] FP
- [x] FN
- [x] TN
- [x] Population
- [x] Condition positive
- [x] Condition negative
- [x] Test outcome positive
- [x] Test outcome negative
- [x] Class Statistics
- [x] ACC
- [x] ERR
- [x] BM
- [x] DOR
- [x] F1-Score
- [x] FDR
- [x] FNR
- [x] FOR
- [x] FPR
- [x] LR+
- [x] LR-
- [x] MCC
- [x] MK
- [x] NPV
- [x] PPV
- [x] TNR
- [x] TPR
- [x] Prevalence
- [x] G-measure
- [x] RACC
- [x] Outputs
- [x] CSV File
- [x] HTML File
- [x] Output File
- [x] Table
- [x] Normalized Table
- [x] Overall Statistics
- [x] CI
- [x] Chi-Squared
- [x] Phi-Squared
- [x] Cramer's V
- [x] Kappa
- [x] Kappa Unbiased
- [x] Kappa No Prevalence
- [ ] Aickin's alpha
- [x] Bennett S score
- [x] Gwet's AC1
- [x] Scott's pi
- [ ] Krippendorff's alpha
- [x] Goodman and Kruskal's lambda A
- [x] Goodman and Kruskal's lambda B
- [x] Kullback-Liebler divergence
- [x] Entropy
- [x] Overall ACC
- [x] Strength of Agreement
- [x] Landis and Koch
- [x] Fleiss
- [x] Altman
- [x] Cicchetti
- [x] TPR Micro/Macro
- [x] PPV Micro/Macro
- [x] Jaccard Index
Outputs
Dependencies
Contribution
Changes and improvements are more than welcome! ❤️ Feel free to fork and open a pull request. Please make your changes in a specific branch and request to pull into dev
Remember to write a few tests for your code before sending pull requests.
References
1- J. R. Landis, G. G. Koch, “The measurement of observer agreement for categorical data. Biometrics,” in International Biometric Society, pp. 159–174, 1977.
2- D. M. W. Powers, “Evaluation: from precision, recall and f-measure to roc, informedness, markedness & correlation,” in Journal of Machine Learning Technologies, pp.37-63, 2011.
3- C. Sammut, G. Webb, “Encyclopedia of Machine Learning” in Springer, 2011.
4- J. L. Fleiss, “Measuring nominal scale agreement among many raters,” in Psychological Bulletin, pp. 378-382.
5- D.G. Altman, “Practical Statistics for Medical Research,” in Chapman and Hall, 1990.
6- K. L. Gwet, “Computing inter-rater reliability and its variance in the presence of high agreement,” in The British Journal of Mathematical and Statistical Psychology, pp. 29–48, 2008.”
7- W. A. Scott, “Reliability of content analysis: The case of nominal scaling,” in Public Opinion Quarterly, pp. 321–325, 1955.
8- E. M. Bennett, R. Alpert, and A. C. Goldstein, “Communication through limited response questioning,” in The Public Opinion Quarterly, pp. 303–308, 1954.
9- D. V. Cicchetti, "Guidelines, criteria, and rules of thumb for evaluating normed and standardized assessment instruments in psychology," in Psychological Assessment, pp. 284–290, 1994.
10- R.B. Davies, "Algorithm AS155: The Distributions of a Linear Combination of χ2 Random Variables," in Journal of the Royal Statistical Society, pp. 323–333, 1980.
11- S. Kullback, R. A. Leibler "On information and sufficiency," in Annals of Mathematical Statistics, pp. 79–86, 1951.
12- L. A. Goodman, W. H. Kruskal, "Measures of Association for Cross Classifications, IV: Simplification of Asymptotic Variances," in Journal of the American Statistical Association, pp. 415–421, 1972.
13- L. A. Goodman, W. H. Kruskal, "Measures of Association for Cross Classifications III: Approximate Sampling Theory," in Journal of the American Statistical Association, pp. 310–364, 1963.
14- T. Byrt, J. Bishop and J. B. Carlin, “Bias, prevalence, and kappa,” in Journal of Clinical Epidemiology pp. 423-429, 1993.
15- M. Shepperd, D. Bowes, and T. Hall, “Researcher Bias: The Use of Machine Learning in Software Defect Prediction,” in IEEE Transactions on Software Engineering, pp. 603-616, 2014.
16- X. Deng, Q. Liu, Y. Deng, and S. Mahadevan, “An improved method to construct basic probability assignment based on the confusion matrix for classification problem, ” in Information Sciences, pp.250-261, 2016.
Cite
If you use PyCM in your research , please cite this paper :
Haghighi, S., Jasemi, M., Hessabi, S. and Zolanvari, A. (2018). PyCM: Multiclass confusion matrix library in Python. Journal of Open Source Software, 3(25), p.729.
@article{Haghighi2018,
doi = {10.21105/joss.00729},
url = {https://doi.org/10.21105/joss.00729},
year = {2018},
month = {may},
publisher = {The Open Journal},
volume = {3},
number = {25},
pages = {729},
author = {Sepand Haghighi and Masoomeh Jasemi and Shaahin Hessabi and Alireza Zolanvari},
title = {{PyCM}: Multiclass confusion matrix library in Python},
journal = {Journal of Open Source Software}
}
Download PyCM.bib
License
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Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Unreleased
0.9.5 - 2018-07-08
Added
- Obj load
- Obj save
- Example-4
Changed
README.mdmodified- Block diagram updated
0.9 - 2018-06-28
Added
- Activation Threshold
- Example-3
- Jaccard index
- Overall Jaccard index
Changed
README.mdmodifiedsetup.pymodified
0.8.6 - 2018-05-31
Added
- Example section in document
- Python 2.7 CI
- JOSS paper pdf
Changed
- Cite section
- ConfusionMatrix docstring
- round function changed to numpy.around
README.mdmodified
0.8.5 - 2018-05-21
Added
- Example-1 (Comparison of three different classifiers)
- Example-2 (How to plot via matplotlib)
- JOSS paper
- ConfusionMatrix docstring
Changed
- Table size in HTML report
- Test system
README.mdmodified
0.8.1 - 2018-03-22
Added
- Goodman and Kruskal's lambda B
- Goodman and Kruskal's lambda A
- Cross Entropy
- Conditional Entropy
- Joint Entropy
- Reference Entropy
- Response Entropy
- Kullback-Liebler divergence
- Direct ConfusionMatrix
- Kappa Unbiased
- Kappa No Prevalence
- Random Accuracy Unbiased
pycmVectorErrorclasspycmMatrixErrorclass- Mutual Information
- Support
numpyarrays
Changed
- Notebook file updated
Removed
pycmErrorclass
0.7 - 2018-02-26
Added
- Cramer's V
- 95% Confidence interval
- Chi-Squared
- Phi-Squared
- Chi-Squared DF
- Standard error
- Kappa standard error
- Kappa 95% confidence interval
- Cicchetti benchmark
Changed
- Overall statistics color in HTML report
- Parameters description link in HTML report
0.6 - 2018-02-21
Added
- CSV report
- Changelog
- Output files
digitparameter toConfusionMatrixobject
Changed
- Confusion matrix color in HTML report
- Parameters description link in HTML report
- Capitalize descriptions
0.5 - 2018-02-17
Added
- Scott's pi
- Gwet's AC1
- Bennett S score
- HTML report
0.4 - 2018-02-05
Added
- TPR Micro/Macro
- PPV Micro/Macro
- RACC overall
- ERR(Error rate)
- FBeta-Score
- F0.5
- F2
- Fleiss benchmark
- Altman benchmark
- Output file(.pycm)
Changed
- Class with zero item
- Normalized matrix
Removed
- Kappa and SOA for each class
0.3 - 2018-01-27
Added
- Kappa
- Random accuracy
- Landis and Koch benchmark
overall_stat
0.2 - 2018-01-24
Added
- Population
- Condition positive
- Condition negative
- Test outcome positive
- Test outcome negative
- Prevalence
- G-measure
- Matrix method
- Normalized matrix method
- Params method
Changed
statistic_resulttoclass_statparamstostat
0.1 - 2018-01-22
Added
- ACC
- BM
- DOR
- F1-Score
- FDR
- FNR
- FOR
- FPR
- LR+
- LR-
- MCC
- MK
- NPV
- PPV
- TNR
- TPR
- documents and
README.md
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
| Filename, size & hash SHA256 hash help | File type | Python version | Upload date |
|---|---|---|---|
| pycm-0.9.5-py2.py3-none-any.whl (27.7 kB) Copy SHA256 hash SHA256 | Wheel | py2.py3 | Jul 8, 2018 |
| pycm-0.9.5.tar.gz (348.3 kB) Copy SHA256 hash SHA256 | Source | None | Jul 8, 2018 |
