risk prediction models: calibration, recalibration, and remodeling
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Risk Prediction Models: Calibration, Recalibration, and Remodeling. HST 951: Biomedical Decision Support 12/04/2006 – Lecture 23 Michael E. Matheny, MD, MS Brigham & Women’s Hospital Boston, MA. Lecture Outline. Review Risk Model Performance Measurements - PowerPoint PPT PresentationTRANSCRIPT
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Slide 1
Risk Prediction Models: Risk Prediction Models: Calibration, Recalibration, and Calibration, Recalibration, and
RemodelingRemodeling
HST 951: Biomedical Decision SupportHST 951: Biomedical Decision Support12/04/2006 – Lecture 2312/04/2006 – Lecture 23
Michael E. Matheny, MD, MSMichael E. Matheny, MD, MSBrigham & Women’s HospitalBrigham & Women’s Hospital
Boston, MABoston, MA
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Slide 2
Lecture OutlineLecture Outline
Review Risk Model Performance MeasurementsReview Risk Model Performance Measurements
Individual Risk Prediction for Binary OutcomesIndividual Risk Prediction for Binary Outcomes
Inadequate Calibration is “the rule not the Inadequate Calibration is “the rule not the exception”exception”
Addressing the problem with Recalibration and Addressing the problem with Recalibration and RemodelingRemodeling
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Model Performance MeasuresModel Performance Measures
DiscriminationDiscrimination– Ability to distinguish well between patients who Ability to distinguish well between patients who
will and will not experience an outcomewill and will not experience an outcome
CalibrationCalibration– Ability of a model to match expected and Ability of a model to match expected and
observed outcome rates across all of the dataobserved outcome rates across all of the data
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DiscriminationDiscriminationArea Under the Receiver Operating Characteristic CurveArea Under the Receiver Operating Characteristic Curve
PositiveFalseNegativeTrue
NegativeTrueSpec
__
_
NegativeFalsePositiveTrue
PositiveTrueSens
__
_
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DiscriminationDiscriminationROC Curve GenerationROC Curve Generation
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CalibrationCalibrationExample DataExample Data
Expected OutcomeExpected Outcome Observed OutcomeObserved Outcome0.050.05 000.100.10 000.150.15 000.200.20 000.250.25 110.300.30 000.350.35 000.400.40 110.450.45 110.500.50 112.752.75 44
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Standardized Outcomes RatioStandardized Outcomes Ratio
Most Aggregated (Crude) comparison of expected Most Aggregated (Crude) comparison of expected and observed valuesand observed values
1 Value for Entire Sample1 Value for Entire Sample
Risk-Adjusted by using a risk prediction model to Risk-Adjusted by using a risk prediction model to generate expected outcomesgenerate expected outcomes
45.175.2
4
_
_
OutcomesExpected
OutcomesObserved
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Standardized Mortality RatiosStandardized Mortality Ratios(SMR)(SMR)
CANCER MORTALITY ANALYSIS ALL MALES, SCRANTON CITY, 1975-1985
CAUSE OF DEATH(ICD CODES 140-204)
EXPECTEDDEATHS
OBSERVEDDEATHS SMR
All Cancer Deaths 1325.37 1516 1.14
Lip, Oral Cavity and Pharynx 33.81 47 1.39
Esophagus 36.84 45 1.22
Stomach 54.58 72 1.32
Colon, Rectum, Rectosigmoid 180.48 238 1.32
Pancreas 62.51 72 1.15
Trachea, Bronchus & Lung 430.98 481 1.12
Genitourinary 168.90 162 0.96
Bladder 45.02 50 1.11
Lymphomas 44.57 47 1.05
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Outcome RatiosOutcome Ratios
StrengthsStrengths
– SimpleSimple
– Frequently used in medical literatureFrequently used in medical literature
– Easily understood by clinical audiencesEasily understood by clinical audiences
WeaknessesWeaknesses
– Not a quantitative test of model calibrationNot a quantitative test of model calibration
– Unable to show variations in calibration in different risk Unable to show variations in calibration in different risk stratastrata
– Likely to underestimate the lack of fitLikely to underestimate the lack of fit
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Outcome RatiosOutcome RatiosExample Calibration PlotExample Calibration Plot
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Global Performance MeasurementsGlobal Performance Measurementswith Calibration Componentswith Calibration Components
Methods that calculate a value for each data point Methods that calculate a value for each data point (most granular)(most granular)
– Pearson TestPearson Test
– Residual DevianceResidual Deviance
– Brier ScoreBrier Score
2)(*1
ii pyn
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Brier Score CalculationBrier Score Calculation
Expected Expected OutcomeOutcome
Observed Observed OutcomeOutcome
(Y(Yii – P – Pii))22
0.050.05 00 0.00250.00250.100.10 00 0.010.010.150.15 00 0.02250.02250.200.20 00 0.040.040.250.25 11 0.56250.56250.300.30 00 0.090.090.350.35 00 0.12250.12250.400.40 11 0.360.360.450.45 11 0.30250.30250.500.50 11 0.250.25
1.76251.7625
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Brier Score CalculationBrier Score Calculation
To assess the accuracy of the set of predictions, To assess the accuracy of the set of predictions, Spiegelhalter’s method is usedSpiegelhalter’s method is used
– Expected Brier (EBrier) = 0.18775Expected Brier (EBrier) = 0.18775– Variance of Brier (VBrier) = 0.003292Variance of Brier (VBrier) = 0.003292
17625.07625.1*10
1)(*
1 2 ii pyn
04357.0003292.0
)18775.017625.0()(5.05.0
VBrier
EBrierBrierZ
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Brier ScoreBrier Score
StrengthsStrengths
– Quantitative evaluationQuantitative evaluation
WeaknessesWeaknesses
– Sensitive to sample size (Sensitive to sample size (↑sample size more likely to fail ↑sample size more likely to fail test)test)
– Sensitive to outliers (large differences between expected Sensitive to outliers (large differences between expected and observed)and observed)
– Difficult to determine relative performance in risk Difficult to determine relative performance in risk subpopulationssubpopulations
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Hosmer-LemeshowHosmer-LemeshowGoodness of FitGoodness of Fit
Divide the data into subgroups and compare Divide the data into subgroups and compare observed to expected outcomes by subgroupobserved to expected outcomes by subgroup
C TestC Test– Divides the sample into 10 equal groups (by Divides the sample into 10 equal groups (by
number of samples)number of samples)
H TestH Test– Divides the sample into 10 groups (by deciles of Divides the sample into 10 groups (by deciles of
risk)risk)
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Hosmer-LemeshowHosmer-LemeshowGoodness of FitGoodness of Fit
10
1
28
22 ~
)/1(
)(
j jjj
jjHL x
nEE
EOG
group j in the cases ofnumber expected
group j in the cases ofnumber observed
group j in the nsobservatio ofnumber
th
th
th
j
j
j
E
O
n
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CALICO RegistryCALICO RegistryHosmer-Lemeshow Goodness of FitHosmer-Lemeshow Goodness of Fit
C Test
Predicted Mortality by Decile (%) Admissions Observed Expected H-L
Deaths Deaths Statistic
0.007 - .034 466 2 10.3 6.88
0.034 - 0.052 461 17 19.7 0.39
0.052 - 0.073 454 27 28.3 0.07
0.073 - 0.100 478 24 41.5 8.07
0.100 - 0.127 450 35 51.4 5.89
0.127 - 0.154 469 53 65.8 2.90
0.154 - 0.202 465 66 82.1 3.83
0.203 - 0.287 461 93 111.2 3.94
0.288 - 0.445 463 138 162.5 5.70
0.445 - 0.968 463 255 287.9 9.94
Total 4630 710 860.8 47.61
C= 47.61 df 8, p < 0.0001
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Calibration PlotCalibration PlotC Test DataC Test Data
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CALICO RegistryCALICO RegistryHosmer-Lemeshow Goodness of FitHosmer-Lemeshow Goodness of Fit
H Test
Predicted Mortality by Decile (%) Admissions Observed Expected H-L
Deaths Deaths Statistic
0.007 - 0.100 1859 70 99.9 9.46
0.100 - 0.200 1348 149 192.0 11.24
0.200 - 0.300 555 115 135.5 4.10
0.301 - 0.400 323 97 110.9 2.65
0.400 - 0.499 185 58 83.0 13.64
0.500 - 0.598 131 70 71.7 0.09
0.600 - 0.694 103 58 66.4 3.02
0.701 - 0.800 65 48 48.6 0.03
0.803 - 0.896 48 34 40.7 7.29
0.904 - 0.968 13 11 12.1 1.59
Total 4630 710 860.8 53.10
H= 53.10 df 8, p < 0.0001
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Calibration PlotCalibration PlotH Test DataH Test Data
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Hosmer-LemeshowHosmer-LemeshowGoodness of FitGoodness of Fit
StrengthsStrengths
– Quantitative evaluationQuantitative evaluation
– Assesses calibration in risk subgroupsAssesses calibration in risk subgroups
WeaknessesWeaknesses
– Disagreement with how to generate subgroups (C versus H)Disagreement with how to generate subgroups (C versus H)
– Even among the same method (C or H), different statistical Even among the same method (C or H), different statistical packages generate different results due to rounding rule differencespackages generate different results due to rounding rule differences
– Sensitive to sample size (Sensitive to sample size (↑sample size more likely to fail test)↑sample size more likely to fail test)
– Sensitive to outliers (but to a lesser degree than Brier Score)Sensitive to outliers (but to a lesser degree than Brier Score)
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Risk Prediction ModelsRisk Prediction Modelsfor Binary Outcomesfor Binary Outcomes
Case Data (Variables XCase Data (Variables X11..X..Xii) ) -> Predictive Model for Outcome Y (Yes/No)-> Predictive Model for Outcome Y (Yes/No)-> Case Outcome Prediction (0 – 1)-> Case Outcome Prediction (0 – 1)
Logistic RegressionLogistic Regression Bayesian NetworksBayesian Networks Artificial Neural NetworksArtificial Neural Networks Support Vector Machine RegressionSupport Vector Machine Regression
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Risk Prediction ModelsRisk Prediction ModelsClinical UtilityClinical Utility
Risk Stratification for Research and Clinical Risk Stratification for Research and Clinical PracticePractice
Risk-Adjusted Assessment of Providers and Risk-Adjusted Assessment of Providers and InstitutionsInstitutions
Individual risk predictionIndividual risk prediction
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Individual Risk PredictionIndividual Risk Prediction
Good discrimination is necessary but not Good discrimination is necessary but not sufficient for individual risk predictionsufficient for individual risk prediction
Calibration is the key index for individual risk Calibration is the key index for individual risk predictionprediction
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Inadequate CalibrationInadequate CalibrationWhy?Why?
Models require external validation to be generally Models require external validation to be generally accepted, and in those studies the general trend is:accepted, and in those studies the general trend is:
– Discrimination retainedDiscrimination retained– Calibration failsCalibration fails
Factors that contribute to inadequate model Factors that contribute to inadequate model calibration in clinical practicecalibration in clinical practice
– Regional VariationRegional Variation• Different Clinical Practice StandardsDifferent Clinical Practice Standards• Different Patient Case MixesDifferent Patient Case Mixes
– Temporal VariationTemporal Variation• Changes in Clinical Practice Changes in Clinical Practice • New diagnostic tools availableNew diagnostic tools available• Changes in Disease Incidence and PrevalenceChanges in Disease Incidence and Prevalence
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Individual Risk PredictionIndividual Risk PredictionClinical ExamplesClinical Examples
10 year “Hard” Coronary 10 year “Hard” Coronary heart disease risk heart disease risk estimationestimation
Logistic RegressionLogistic Regression– Framingham Heart StudyFramingham Heart Study
Calibration ProblemsCalibration Problems– Low SESLow SES– Young ageYoung age– FemaleFemale– Non-US populationsNon-US populations
Kannel et al. Am J Cardiol, 1976Kannel et al. Am J Cardiol, 1976
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Individual Risk PredictionIndividual Risk PredictionClinical ExamplesClinical Examples
Lifetime Invasive Breast Lifetime Invasive Breast Cancer Risk EstimationCancer Risk Estimation
Logistic RegressionLogistic Regression– Gail ModelGail Model
Calibration ProblemsCalibration Problems– Age <35Age <35– Prior Hx Breast CAPrior Hx Breast CA– Strong Family HxStrong Family Hx– Lack of regular Lack of regular
mammogramsmammograms
Gail et al. JNCI, 1989Gail et al. JNCI, 1989
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Individual Risk PredictionIndividual Risk PredictionClinical ExamplesClinical Examples
Intensive Care Unit Mortality PredictionIntensive Care Unit Mortality Prediction
– APACHE-IIAPACHE-II– APACHE-IIIAPACHE-III– MPMMPM00– MPMMPM00-II-II– SAPSSAPS– SAPS-IISAPS-II
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Individual Risk PredictionIndividual Risk PredictionClinical ExamplesClinical Examples
Ohno-Machado, et al. Annu Rev Biomed Eng. 2006;8:567-99Ohno-Machado, et al. Annu Rev Biomed Eng. 2006;8:567-99
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Individual Risk PredictionIndividual Risk PredictionClinical ExamplesClinical Examples
Ohno-Machado, et al. Annu Rev Biomed Eng. 2006;8:567-99Ohno-Machado, et al. Annu Rev Biomed Eng. 2006;8:567-99
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Individual Risk Prediction Individual Risk Prediction Clinical ExamplesClinical Examples
Model Dates Location Sample
NY 1992 1991 NY 5827
NY 1997 1991 – 1994 NY 62670
CC 1997 1993 – 1994 Cleveland, OH 12985
NNE 1999 1994 – 1996 NH, ME, MA, VT 15331
MI 2001 1999 – 2000 Detroit, MI 10796
BWH 2001 1997 – 1999 Boston, MA 2804
ACC 2002 1998 – 2000 National 100253
Matheny, et al. J Biomed Inform. 2005 Oct;38(5):367-75Matheny, et al. J Biomed Inform. 2005 Oct;38(5):367-75
Interventional Cardiology Mortality PredictionInterventional Cardiology Mortality Prediction
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Individual Risk Prediction Individual Risk Prediction Clinical ExamplesClinical Examples
Model Deaths AUC HL χ2 HL (p)
NY 1992 96.7 0.82 31.1 <0.001
NY 1997 61.6 0.88 32.2 <0.001
CC 1997 78.8 0.88 27.8 <0.001
NNE 1999 56.2 0.89 45.9 <0.001
MI 2001 61.8 0.86 30.4 <0.001
BWH 2001 136.1 0.89 39.7 <0.001
ACC 2002 49.9 0.90 42.0 <0.001
BWH 2004 70.5 0.93 7.61 0.473
Observed Deaths = 71Observed Deaths = 71
Matheny, et al. J Biomed Inform. 2005 Oct;38(5):367-75Matheny, et al. J Biomed Inform. 2005 Oct;38(5):367-75
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Inadequate CalibrationInadequate CalibrationWhat to do?What to do?
In most cases, risk prediction models are In most cases, risk prediction models are developed on much larger data sets than are developed on much larger data sets than are available for local model generation.available for local model generation.
– Decreased variance and increased stability of model Decreased variance and increased stability of model covariate valuescovariate values
– Large, external models (especially those that have been Large, external models (especially those that have been externally validated) are generally accepted by domain externally validated) are generally accepted by domain expertsexperts
Goal is to ‘throw out’ as little prior model Goal is to ‘throw out’ as little prior model information as possible while improving information as possible while improving performanceperformance
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Recalibration and RemodelingRecalibration and RemodelingGeneral Evaluation RulesGeneral Evaluation Rules
Model recalibration or remodeling follows the same Model recalibration or remodeling follows the same rules of evaluation as model building in generalrules of evaluation as model building in general
– Separate training and test data, orSeparate training and test data, or– Cross-Validation, etcCross-Validation, etc
If temporal issues are central to that domain’s If temporal issues are central to that domain’s calibration problems, training data should be both calibration problems, training data should be both before (in time) and separate from testing databefore (in time) and separate from testing data
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Discrimination versus CalibrationDiscrimination versus Calibration
Model AModel AExpected OutcomeExpected Outcome
Model BModel BExpected OutcomeExpected Outcome
ObservedObservedOutcomeOutcome
0.050.05 0.330.33 000.100.10 0.450.45 000.150.15 0.470.47 000.200.20 0.530.53 000.250.25 0.680.68 110.300.30 0.770.77 000.350.35 0.810.81 000.400.40 0.930.93 110.450.45 0.950.95 110.500.50 0.960.96 112.752.75 6.886.88 44
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Logistic RegressionLogistic RegressionGeneral EquationGeneral Equation
BB00 is the intercept of the equation, which represents is the intercept of the equation, which represents the outcome probability in the absence of all other the outcome probability in the absence of all other risk factors (baseline risk)risk factors (baseline risk)
The model assumes each covariate is independent The model assumes each covariate is independent of each other, and Bof each other, and Bxx is the natural log of the odds is the natural log of the odds ratio of the risk attributable to that risk factorratio of the risk attributable to that risk factor
)( 1101
1)]1[(
iixBxBBeYP
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Logistic RegressionLogistic Regression”Original” Model and Cases”Original” Model and Cases
ModelModel
VariableVariable ββ coeff coeff Case 1Case 1 Case 2Case 2 Case 3Case 3 Case 4*Case 4*
InterceptIntercept -3-3 11 11 11 11
Variable 1Variable 1 0.20.2 00 11 11 11
Variable 2Variable 2 0.50.5 00 00 11 11
Variable 3Variable 3 1.01.0 00 00 00 11
Case Case ProbabilityProbability
0.0470.047 0.0570.057 0.0910.091 0.3100.310
Minimum predicted risk for each case is intercept Minimum predicted risk for each case is intercept onlyonly
Adjusting intercept scales all resultsAdjusting intercept scales all results
* Case 4 is Outcome = 1, Case 1 -3 are Outcome = 0* Case 4 is Outcome = 1, Case 1 -3 are Outcome = 0
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LR Intercept RecalibrationLR Intercept Recalibration
The proportion of risk contributed by the intercept The proportion of risk contributed by the intercept (baseline) can be calculated for a data set by:(baseline) can be calculated for a data set by:
nobsxBxBB
nobsB
iie
eRiskInt
)(
)(
110
0
11
11
(%)
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LR Intercept Recalibration LR Intercept Recalibration
The intercept contribution to risk (RiskInt(%)) is The intercept contribution to risk (RiskInt(%)) is multiplied by the observed event rate, and multiplied by the observed event rate, and converted back to a Beta Coefficient from a converted back to a Beta Coefficient from a probability:probability:
1
*(%)
1ln)(0 teObsEventRaRiskInt
NewB
A relative weakness of the method is that values A relative weakness of the method is that values can exceed 1, and must be truncatedcan exceed 1, and must be truncated
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LR Intercept RecalibrationLR Intercept RecalibrationExample Model and CasesExample Model and Cases
OldOld NewNew
VariableVariable ββ coeff coeff ββ coeff coeff Case 1Case 1 Case 2Case 2 Case 3Case 3 Case 4*Case 4*
InterceptIntercept -3.0-3.0 -2.2-2.2 11 11 11 11
Variable 1Variable 1 0.20.2 0.20.2 00 11 11 11
Variable 2Variable 2 0.50.5 0.50.5 00 00 11 11
Variable 3Variable 3 1.01.0 1.01.0 00 00 00 11
New Prob.New Prob. 0.0990.099 0.1190.119 0.1820.182 0.5000.500
Orig Prob.Orig Prob. 0.0470.047 0.0570.057 0.0910.091 0.3100.310
Original Expected = 0.51Original Expected = 0.51 Intercept Recalibration Expected = 0.90Intercept Recalibration Expected = 0.90
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LR Slope RecalibrationLR Slope Recalibration
In this method, the output probability of the original In this method, the output probability of the original LR equation is used to model a new LR equation LR equation is used to model a new LR equation with that output as the only covariate:with that output as the only covariate:
)])([( 101
1)( OldPBBe
NewP
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LR Slope RecalibrationLR Slope RecalibrationExample Model and CasesExample Model and Cases
New ModelNew Model
VariableVariable ββ coeff coeff Case 1Case 1 Case 2Case 2 Case 3Case 3 Case 4*Case 4*
New Model InterceptNew Model Intercept -3.0-3.0 11 11 11 11
Orig Model ResultOrig Model Result 11.011.0 0.0470.047 0.0570.057 0.0910.091 0.3100.310
New ProbabilityNew Probability 0.0770.077 0.0860.086 0.1190.119 0.6010.601
Intercept ProbabilityIntercept Probability 0.0990.099 0.1190.119 0.1820.182 0.5000.500
Original Expected = 0.51Original Expected = 0.51 Slope Recalibration Expected = 0.88Slope Recalibration Expected = 0.88
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LR Covariate RecalibrationLR Covariate Recalibration
OldOld NewNew
VariableVariable ββ coeff coeff ββ coeff coeff Case 1Case 1 Case 2Case 2 Case 3Case 3 Case 4*Case 4*
InterceptIntercept -3-3 -2.5-2.5 11 11 11 11
Variable 1Variable 1 0.20.2 0.10.1 00 11 11 11
Variable 2Variable 2 0.50.5 0.30.3 00 00 11 11
Variable 3Variable 3 1.01.0 3.03.0 00 00 00 11
New ProbNew Prob 0.0760.076 0.0830.083 0.1090.109 0.7110.711
Orig ProbOrig Prob 0.0470.047 0.0570.057 0.0910.091 0.3100.310
Original Expected = 0.51Original Expected = 0.51 Covariate Recalibration Expected = 0.97Covariate Recalibration Expected = 0.97
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Recalibration ExampleRecalibration ExampleLocal Institutional DataLocal Institutional Data
Year Cases Mortality (%)2002 1947 15 (0.8%)
2003 1841 33 (1.8%)
2004 1767 33 (1.9%)
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Recalibration ExampleRecalibration ExampleExternal Risk Prediction ModelsExternal Risk Prediction Models
Year Abbrev Outcomes Sample %
National ACC ACC 707 50123 1.4
Northern New England NNE 165 15331 1.1
University of Michigan MIC 169 10796 1.6
Cleveland Clinic CCL 169 2985 1.3
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ResultsResultsNo RecalibrationNo Recalibration
Model Observed Expected HL χ2
2003
ACC 33 414 634
NNE 33 39.0 24.3
MIC 33 27.2 6.6
CCL 33 56.3 14.0
2004
ACC 33 418 641
NNE 33 36.6 51.0
MIC 33 23.3 22.9
CCL 33 60.3 21.2
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ResultsResultsLR Intercept RecalibrationLR Intercept Recalibration
Model Observed Expected HL χ2
2003
ACC 33 45.1 10.0
NNE 33 26.0 43.6
MIC 33 22.1 12.7
CCL 33 24.8 10.5
2004
ACC 33 34.1 14.6
NNE 33 28.9 69.8
MIC 33 26.5 17.6
CCL 33 33.5 14.2
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ResultsResultsLR Slope RecalibrationLR Slope Recalibration
Model Observed Expected HL χ2
2003
ACC 33 24.0 12.7
NNE 33 18.6 32.9
MIC 33 20.1 24.0
CCL 33 25.5 15.2
2004
ACC 33 32.0 35.7
NNE 33 31.2 21.7
MIC 33 31.0 23.6
CCL 33 31.6 13.2
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Clinical ApplicationsClinical ApplicationsCALICOCALICO
California Intensive Care Outcomes (CALICO) California Intensive Care Outcomes (CALICO) ProjectProject
– 23 Volunteer Hospitals beginning in 200223 Volunteer Hospitals beginning in 2002
– Compare hospital outcomes for selected conditions, Compare hospital outcomes for selected conditions, procedures, and intensive care unit typesprocedures, and intensive care unit types
– Identified popular, well-validated modelsIdentified popular, well-validated models• MPMMPMoo-II, SAPS-II, APACHE-II, APACHE-III-II, SAPS-II, APACHE-II, APACHE-III
– Evaluated the models on CALICO data, after determining Evaluated the models on CALICO data, after determining they were inadequately calibrated, conducted they were inadequately calibrated, conducted recalibration of each of the models using the LR recalibration of each of the models using the LR Covariate Recalibration methodCovariate Recalibration method
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Clinical ApplicationsClinical ApplicationsCALICOCALICO
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Examples on WebsiteExamples on Website
Most of the calculations from this Most of the calculations from this presentation are available on the website in presentation are available on the website in an Excel workbookan Excel workbook
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Slide 52
Michael Matheny, MD, MSMichael Matheny, MD, MS [email protected]@dsg.harvard.edu
Brigham & Women’s HospitalBrigham & Women’s HospitalThorn 309Thorn 309
75 Francis Street75 Francis StreetBoston, MA 02115Boston, MA 02115
The EndThe End