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2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

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Page 1: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Faculty of Health Sciences

R2-type Curves for Dynamic Predictions from

Joint Longitudinal-Survival Models

Inference & application to prediction of kidney graft failure

Paul Blanche

joint work with

M-C. Fournier & E. Dantan (Nantes, France)

July 2015

Slide 1/29

Page 2: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Context & Motivation

• Medical researchers hope to improve patient managementusing earlier diagnoses

• Statisticians can help by �tting prediction models

• The making of so-called "dynamic" predictions has recentlyreceived a lot of attention

• In order to be useful for medical practice, predictions shouldbe "accurate"

How should we evaluate dynamic prediction accuracy?

Slide 1/29 � P Blanche et al.

Page 3: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Data & Clinical goal

I Data:

DIVAT cohort dataof kidney transplant recipients(subsample, n = 4, 119)

I Clinical goal:

• Dynamic prediction of risk of kidneygraft failure (death or return to dialysis)

• Using repeated measurements ofserum creatinine

Slide 2/29 � P Blanche et al.

Page 4: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

DIVAT data sample (n=4,119)

• French cohort

• Adult recipients

• Transplanted after 2000

• Creatinine measured every year

• 6 centers

(www.divat.fr)

Slide 3/29 � P Blanche et al.

Page 5: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

DIVAT data sample (n=4,119)

• French cohort

• Adult recipients

• Transplanted after 2000

• Creatinine measured every year

• 6 centers

(www.divat.fr)

Slide 3/29 � P Blanche et al.

Page 6: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Statistical challenges discussed

How to evaluate and/or compare dynamic predictions?

I Using concepts of:

• Discrimination

• Calibration

I Accounting for:

• Dynamic setting

• Censoring issue

Slide 4/29 � P Blanche et al.

Page 7: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Basic idea & concepts for evaluating predictions

Basic idea: comparing predictions and observations

(simple!)

Concepts:

I Discrimination:A model has high discriminative power if the range of predicted risks iswide and subjects with low (high) predicted risk are more (less) likely toexperience the event.

I Calibration:

A model is calibrated if we can expect that x subjects out of 100

experience the event among all subjects that receive a predicted risk

of x% (�weak� de�nition).

Slide 5/29 � P Blanche et al.

Page 8: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Basic idea & concepts for evaluating predictions

Basic idea: comparing predictions and observations (simple!)

Concepts:

I Discrimination:A model has high discriminative power if the range of predicted risks iswide and subjects with low (high) predicted risk are more (less) likely toexperience the event.

I Calibration:

A model is calibrated if we can expect that x subjects out of 100

experience the event among all subjects that receive a predicted risk

of x% (�weak� de�nition).

Slide 5/29 � P Blanche et al.

Page 9: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Basic idea & concepts for evaluating predictions

Basic idea: comparing predictions and observations (simple!)

Concepts:

I Discrimination:

A model has high discriminative power if the range of predicted risks iswide and subjects with low (high) predicted risk are more (less) likely toexperience the event.

I Calibration:

A model is calibrated if we can expect that x subjects out of 100

experience the event among all subjects that receive a predicted risk

of x% (�weak� de�nition).

Slide 5/29 � P Blanche et al.

Page 10: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Basic idea & concepts for evaluating predictions

Basic idea: comparing predictions and observations (simple!)

Concepts:

I Discrimination:A model has high discriminative power if the range of predicted risks iswide and subjects with low (high) predicted risk are more (less) likely toexperience the event.

I Calibration:

A model is calibrated if we can expect that x subjects out of 100

experience the event among all subjects that receive a predicted risk

of x% (�weak� de�nition).

Slide 5/29 � P Blanche et al.

Page 11: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Basic idea & concepts for evaluating predictions

Basic idea: comparing predictions and observations (simple!)

Concepts:

I Discrimination:A model has high discriminative power if the range of predicted risks iswide and subjects with low (high) predicted risk are more (less) likely toexperience the event.

I Calibration:

A model is calibrated if we can expect that x subjects out of 100

experience the event among all subjects that receive a predicted risk

of x% (�weak� de�nition).

Slide 5/29 � P Blanche et al.

Page 12: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0

Slide 6/29 � P Blanche et al.

Page 13: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0

Slide 6/29 � P Blanche et al.

Page 14: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0

Slide 6/29 � P Blanche et al.

Page 15: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0

Slide 6/29 � P Blanche et al.

Page 16: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0 s = 4 yearss = 4 years

Landmark time ''s''

Slide 6/29 � P Blanche et al.

Page 17: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0 s = 4 years

s = 4 years

Landmark time ''s''

Slide 6/29 � P Blanche et al.

Page 18: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0 s = 4 years

s = 4 years s+t = 9 years

Landmark time ''s''Horizon ''t''Horizon ''t''

Slide 6/29 � P Blanche et al.

Page 19: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Dynamic prediction

• s: Landmark time at which predictions are made (varies)

• t: prediction horizon (�xed)

follow−up time (years)

Cre

atin

ine

(mol

/L)

100

150

200

250

300

0 s = 4 years s+t = 9 years

0 %

100

%1−

Pr(

Gra

ft Fa

ilure

in (

s,s+

t])

Landmark time ''s''Horizon ''t''

1 − πi(s, t) = 64%

Slide 6/29 � P Blanche et al.

Page 20: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Right censoring issue

Landmark time s(when predictions are made)

Time s + t(end of prediction window)

time

: uncensored

: censored

For subject i censored within (s, s + t] the status

Di (s, t) = 11{event occurs in (s, s + t]}

is unknown.

Slide 7/29 � P Blanche et al.

Page 21: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Right censoring issue

Landmark time s(when predictions are made)

Time s + t(end of prediction window)

time

: uncensored

: censored

For subject i censored within (s, s + t] the status

Di (s, t) = 11{event occurs in (s, s + t]}

is unknown.

Slide 7/29 � P Blanche et al.

Page 22: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Right censoring issue

Landmark time s(when predictions are made)

Time s + t(end of prediction window)

time

: uncensored

: censored

For subject i censored within (s, s + t] the status

Di (s, t) = 11{event occurs in (s, s + t]}

is unknown.

Slide 7/29 � P Blanche et al.

Page 23: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Right censoring issue

Landmark time s(when predictions are made)

Time s + t(end of prediction window)

time

: uncensored

: censored

For subject i censored within (s, s + t] the status

Di (s, t) = 11{event occurs in (s, s + t]}

is unknown.

Slide 7/29 � P Blanche et al.

Page 24: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Notations for population parameters

I Indicator of event in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t}

where Ti is the time-to-event.

I Dynamic predictions:

πi (s, t)

= Pξ

(Di (s, t) = 1

∣∣∣Ti > s,Yi (s),Xi

)• ξ: previously estimated parameters (from independent training data)

• Yi (s): marker measurements observed before time s

• Xi : baseline covariates

Slide 8/29 � P Blanche et al.

Page 25: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Notations for population parameters

I Indicator of event in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t}

where Ti is the time-to-event.

I Dynamic predictions:

πi (s, t)

= Pξ

(Di (s, t) = 1

∣∣∣Ti > s,Yi (s),Xi

)• ξ: previously estimated parameters (from independent training data)

• Yi (s): marker measurements observed before time s

• Xi : baseline covariates

Slide 8/29 � P Blanche et al.

Page 26: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Notations for population parameters

I Indicator of event in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t}

where Ti is the time-to-event.

I Dynamic predictions:

πi (s, t) = Pξ

(

Di (s, t) = 1∣∣∣Ti > s,Yi (s),Xi

)• ξ: previously estimated parameters (from independent training data)

• Yi (s): marker measurements observed before time s

• Xi : baseline covariates

Slide 8/29 � P Blanche et al.

Page 27: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Notations for population parameters

I Indicator of event in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t}

where Ti is the time-to-event.

I Dynamic predictions:

πi (s, t) = Pξ

(Di (s, t) = 1

∣∣∣

Ti > s,Yi (s),Xi

)• ξ: previously estimated parameters (from independent training data)

• Yi (s): marker measurements observed before time s

• Xi : baseline covariates

Slide 8/29 � P Blanche et al.

Page 28: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Notations for population parameters

I Indicator of event in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t}

where Ti is the time-to-event.

I Dynamic predictions:

πi (s, t) = Pξ

(Di (s, t) = 1

∣∣∣Ti > s,Yi (s),

Xi

)• ξ: previously estimated parameters (from independent training data)

• Yi (s): marker measurements observed before time s

• Xi : baseline covariates

Slide 8/29 � P Blanche et al.

Page 29: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Notations for population parameters

I Indicator of event in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t}

where Ti is the time-to-event.

I Dynamic predictions:

πi (s, t) = Pξ

(Di (s, t) = 1

∣∣∣Ti > s,Yi (s),Xi

)• ξ: previously estimated parameters (from independent training data)

• Yi (s): marker measurements observed before time s

• Xi : baseline covariates

Slide 8/29 � P Blanche et al.

Page 30: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Predictive accuracy

How close are the predicted risks πi (s, t) to the �true underlying�risk P

(event occurs in (s,s+t]

∣∣information at s)?

I Prediction Error:

PEπ(s, t) = E[{

D(s, t)− π(s, t)}2∣∣∣T > s

]

• the lower the better

• PE ≈ Bias2 + Variance

• evaluates both Calibration and Discrimination

• depends on P(event occurs in (s,s+t]

∣∣at risk at s)

• often called "Expected Brier Score"

Slide 9/29 � P Blanche et al.

Page 31: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Predictive accuracy

How close are the predicted risks πi (s, t) to the �true underlying�risk P

(event occurs in (s,s+t]

∣∣information at s)?

I Prediction Error:

PEπ(s, t) = E[{

D(s, t)− π(s, t)}2∣∣∣T > s

]

• the lower the better

• PE ≈ Bias2 + Variance

• evaluates both Calibration and Discrimination

• depends on P(event occurs in (s,s+t]

∣∣at risk at s)

• often called "Expected Brier Score"

Slide 9/29 � P Blanche et al.

Page 32: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

Predictive accuracy

How close are the predicted risks πi (s, t) to the �true underlying�risk P

(event occurs in (s,s+t]

∣∣information at s)?

I Prediction Error:

PEπ(s, t) = E[{

D(s, t)− π(s, t)}2∣∣∣T > s

]

• the lower the better

• PE ≈ Bias2 + Variance

• evaluates both Calibration and Discrimination

• depends on P(event occurs in (s,s+t]

∣∣at risk at s)

• often called "Expected Brier Score"

Slide 9/29 � P Blanche et al.

Page 33: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[{

D(s, t)− π(s, t)}2∣∣∣T > s

]E[{

D(s, t)+ E[D(s, t)

∣∣Hπ(s)]︸ ︷︷ ︸

�true underlying� risk

−π(s, t)∣∣∣T > s

]

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

Page 34: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[{

D(s, t)− E[D(s, t)

∣∣Hπ(s)]}2

E[{

D(s, t) + E[D(s, t)

∣∣Hπ(s)]︸ ︷︷ ︸

�true underlying� risk

− π(s, t)}2∣∣∣T > s

]

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

Page 35: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[{

D(s, t)− E[D(s, t)

∣∣Hπ(s)]}2∣∣∣T > s

]+ E

[{E[D(s, t)

∣∣Hπ(s)]︸ ︷︷ ︸

�true underlying� risk

− π(s, t)}2∣∣∣T > s

]

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

Page 36: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[{

D(s, t)− E[D(s, t)

∣∣Hπ(s)]}2∣∣∣T > s

]︸ ︷︷ ︸

Inseparability

+ E[{

E[D(s, t)

∣∣Hπ(s)]− π(s, t)

}2∣∣∣T > s]

︸ ︷︷ ︸Bias/Calibration

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

Page 37: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[Var{D(s, t)

∣∣Hπ(s)}∣∣∣T > s

]︸ ︷︷ ︸

Discrimination

+ E[{

E[D(s, t)

∣∣Hπ(s)]− π(s, t)

}2∣∣∣T > s]

︸ ︷︷ ︸Calibration

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

Page 38: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[Var{D(s, t)

∣∣Hπ(s)}∣∣∣T > s

]︸ ︷︷ ︸

Discrimination

+ E[{

E[D(s, t)

∣∣Hπ(s)]− π(s, t)

}2∣∣∣T > s]

︸ ︷︷ ︸Calibration

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

Page 39: 2 -type Curves for Dynamic Predictions from Joint ... · R 2-type Curves for Dynamic Predictions from Joint Longitudinal-Survival Models Inference & application to prediction of kidney

un iver s i ty of copenhagen department of b io stat i s t i c s

How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[Var{D(s, t)

∣∣Hπ(s)}∣∣∣T > s

]︸ ︷︷ ︸

Discrimination

+ E[{

E[D(s, t)

∣∣Hπ(s)]− π(s, t)

}2∣∣∣T > s]

︸ ︷︷ ︸Calibration

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

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How does the PE relate to calibration and

discrimination?

PEπ(s, t) =E[Var{D(s, t)

∣∣Hπ(s)}∣∣∣T > s

]︸ ︷︷ ︸

Does NOT depend on π(s,t)

+ E[{

E[D(s, t)

∣∣Hπ(s)]− π(s, t)

}2∣∣∣T > s]

︸ ︷︷ ︸Depends on π(s,t)

Hπ(s) = {X π(s),T > s} denotes the subject-speci�c history attime s.

I the more discriminating Hπ(s) the smaller Var{D(s, t)

∣∣Hπ(s)}

I E[D(s, t)

∣∣Hπ(s)]− π(s, t) ≡ 0 de�nes "strong" calibration.

Slide 10/29 � P Blanche et al.

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R2π-type criterion

I Benchmark PE0

The best "null" prediction tool, which gives the same (marginal)predicted risk

S(s + t|s) = E[D(s, t)

∣∣H0(s)], H0(s) = {T > s}

to all subjects leads to

PE0(s, t) = Var{D(s, t)|T > s} = S(s + t|s){1− S(s + t|s)

}.

I Simple idea

R2π(s, t) = 1− PEπ(s, t)

PE0(s, t)

Slide 11/29 � P Blanche et al.

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R2π-type criterion

I Benchmark PE0

The best "null" prediction tool, which gives the same (marginal)predicted risk

S(s + t|s) = E[D(s, t)

∣∣H0(s)], H0(s) = {T > s}

to all subjects leads to

PE0(s, t) = Var{D(s, t)|T > s} = S(s + t|s){1− S(s + t|s)

}.

I Simple idea

R2π(s, t) = 1− PEπ(s, t)

PE0(s, t)

Slide 11/29 � P Blanche et al.

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Why bother?

I R2π(s, t) aims to circumvent the di�cult interpretation of:

• the scale on which PE (s, t) is measured

• interpretation for trend of PE (s, t) vs s

I Because the meaning of the scale on which PE(s,t) ismeasured changes with s, an increasing/decreasing trend can bedue to changes in:

• the quality of the predictions

and/or • the at risk population

Slide 12/29 � P Blanche et al.

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Why bother?

I R2π(s, t) aims to circumvent the di�cult interpretation of:

• the scale on which PE (s, t) is measured

• interpretation for trend of PE (s, t) vs s

I Because the meaning of the scale on which PE(s,t) ismeasured changes with s, an increasing/decreasing trend can bedue to changes in:

• the quality of the predictions

and/or • the at risk population

Slide 12/29 � P Blanche et al.

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Changes in the quality of the predictions

"Essentially, all models are wrong, but someare useful.", G. Box

I The prediction model from which we have obtained thepredictions can be �more wrong� for some s than for some others.

• Calibration term of PE (s, t) changes with s

• We can work on it!

Slide 13/29 � P Blanche et al.

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Changes in the quality of the predictions

"Essentially, all models are wrong, but someare useful.", G. Box

I The prediction model from which we have obtained thepredictions can be �more wrong� for some s than for some others.

• Calibration term of PE (s, t) changes with s

• We can work on it!

Slide 13/29 � P Blanche et al.

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Changes in the at risk population

An example:

• Patients with cardiovascular history (CV) all die early.

• Only those without CV remain at risk for late s.

• Then:

• the earlier s the more homogeneous the at risk population• CV is useful for prediction for early s but useless for late s.

I The available information can be more informative for some sthan for some others.

• Discriminating term of PE (s, t) changes with s

• This is just how it is, there is nothing we can do!

(we can only work with the data we have)

Slide 14/29 � P Blanche et al.

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Changes in the at risk population

An example:

• Patients with cardiovascular history (CV) all die early.

• Only those without CV remain at risk for late s.

• Then:

• the earlier s the more homogeneous the at risk population• CV is useful for prediction for early s but useless for late s.

I The available information can be more informative for some sthan for some others.

• Discriminating term of PE (s, t) changes with s

• This is just how it is, there is nothing we can do!

(we can only work with the data we have)

Slide 14/29 � P Blanche et al.

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R2π(s, t) interpretation

I Always true:Measure of how the prediction tool π(s, t) performs compared to the

benchmark null prediction tool, which gives the same predicted risk to

all subjects (marginal risk).

I When predictions are calibrated (strongly):

R2π(s, t) =

Var{π(s, t)|T > s}Var{D(s, t)|T > s}

explained variation

= Corr2{D(s, t), π(s, t)

∣∣T > s}

correlation

= E{π(s, t)

∣∣∣D(s, t) = 1,T > s}

mean risk di�erence

− E{π(s, t)

∣∣∣D(s, t) = 0,T > s}.

(after little algebra)

Slide 15/29 � P Blanche et al.

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R2π(s, t) interpretation

I Always true:Measure of how the prediction tool π(s, t) performs compared to the

benchmark null prediction tool, which gives the same predicted risk to

all subjects (marginal risk).

I When predictions are calibrated (strongly):

R2π(s, t) =

Var{π(s, t)|T > s}Var{D(s, t)|T > s}

explained variation

= Corr2{D(s, t), π(s, t)

∣∣T > s}

correlation

= E{π(s, t)

∣∣∣D(s, t) = 1,T > s}

mean risk di�erence

− E{π(s, t)

∣∣∣D(s, t) = 0,T > s}.

(after little algebra)

Slide 15/29 � P Blanche et al.

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R2π(s, t) interpretation

I Always true:Measure of how the prediction tool π(s, t) performs compared to the

benchmark null prediction tool, which gives the same predicted risk to

all subjects (marginal risk).

I When predictions are calibrated (strongly):

R2π(s, t) =

Var{π(s, t)|T > s}Var{D(s, t)|T > s}

explained variation

= Corr2{D(s, t), π(s, t)

∣∣T > s}

correlation

= E{π(s, t)

∣∣∣D(s, t) = 1,T > s}

mean risk di�erence

− E{π(s, t)

∣∣∣D(s, t) = 0,T > s}.

(after little algebra)

Slide 15/29 � P Blanche et al.

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R2π(s, t) interpretation

I Always true:Measure of how the prediction tool π(s, t) performs compared to the

benchmark null prediction tool, which gives the same predicted risk to

all subjects (marginal risk).

I When predictions are calibrated (strongly):

R2π(s, t) =

Var{π(s, t)|T > s}Var{D(s, t)|T > s}

explained variation

= Corr2{D(s, t), π(s, t)

∣∣T > s}

correlation

= E{π(s, t)

∣∣∣D(s, t) = 1,T > s}

mean risk di�erence

− E{π(s, t)

∣∣∣D(s, t) = 0,T > s}.

(after little algebra)

Slide 15/29 � P Blanche et al.

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Observations & IPCW PE estimatorI Observations (i.i.d.){(

Ti ,∆i , πi (·, ·)), i = 1, . . . , n

}where Ti = Ti ∧ Ci , ∆i = 11{Ti ≤ Ci}

I Indicator of �observed event occurrence� in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t,∆i = 1} =

1 : event occurred

0 : event did not occur

or censored obs.

I Inverse Probability of Censoring Weighting (IPCW) estimator:

PEπ(s, t) =1

n

n∑i=1

Wi (s, t)

{Di (s, t)− πi (s, t)

}2

and

R2

π(s, t) = 1− PEπ(s, t)

PE 0(s, t)

Slide 16/29 � P Blanche et al.

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Observations & IPCW PE estimatorI Observations (i.i.d.){(

Ti ,∆i , πi (·, ·)), i = 1, . . . , n

}where Ti = Ti ∧ Ci , ∆i = 11{Ti ≤ Ci}

I Indicator of �observed event occurrence� in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t,∆i = 1} =

1 : event occurred

0 : event did not occur

or censored obs.

I Inverse Probability of Censoring Weighting (IPCW) estimator:

PEπ(s, t) =1

n

n∑i=1

Wi (s, t)

{Di (s, t)− πi (s, t)

}2

and

R2

π(s, t) = 1− PEπ(s, t)

PE 0(s, t)

Slide 16/29 � P Blanche et al.

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Observations & IPCW PE estimatorI Observations (i.i.d.){(

Ti ,∆i , πi (·, ·)), i = 1, . . . , n

}where Ti = Ti ∧ Ci , ∆i = 11{Ti ≤ Ci}

I Indicator of �observed event occurrence� in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t,∆i = 1} =

1 : event occurred

0 : event did not occur

or censored obs.

I Inverse Probability of Censoring Weighting (IPCW) estimator:

PEπ(s, t) =1

n

n∑i=1

Wi (s, t)

{Di (s, t)− πi (s, t)

}2

and

R2

π(s, t) = 1− PEπ(s, t)

PE 0(s, t)

Slide 16/29 � P Blanche et al.

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Observations & IPCW PE estimatorI Observations (i.i.d.){(

Ti ,∆i , πi (·, ·)), i = 1, . . . , n

}where Ti = Ti ∧ Ci , ∆i = 11{Ti ≤ Ci}

I Indicator of �observed event occurrence� in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t,∆i = 1} =

1 : event occurred

0 : event did not occur

or censored obs.

I Inverse Probability of Censoring Weighting (IPCW) estimator:

PEπ(s, t) =1

n

n∑i=1

Wi (s, t){Di (s, t)− πi (s, t)

}2

and

R2

π(s, t) = 1− PEπ(s, t)

PE 0(s, t)

Slide 16/29 � P Blanche et al.

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Observations & IPCW PE estimatorI Observations (i.i.d.){(

Ti ,∆i , πi (·, ·)), i = 1, . . . , n

}where Ti = Ti ∧ Ci , ∆i = 11{Ti ≤ Ci}

I Indicator of �observed event occurrence� in (s, s + t]:

Di (s, t) = 11{s < Ti ≤ s + t,∆i = 1} =

1 : event occurred

0 : event did not occur

or censored obs.

I Inverse Probability of Censoring Weighting (IPCW) estimator:

PEπ(s, t) =1

n

n∑i=1

Wi (s, t){Di (s, t)− πi (s, t)

}2

and

R2

π(s, t) = 1− PEπ(s, t)

PE 0(s, t)

Slide 16/29 � P Blanche et al.

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Inverse Probability of Censoring Weights

Wi (s, t) =

11{s < Ti ≤ s + t}∆i

G (Ti |s)

+

11{Ti > s + t}G (s + t|s)

+

0

with G(u|s) the Kaplan-Meier estimator of P(C > u|C > s).

Landmark time s Time s + t

time

: uncensored

: censored

Slide 17/29 � P Blanche et al.

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Inverse Probability of Censoring Weights

Wi (s, t) =11{s < Ti ≤ s + t}∆i

G (Ti |s)+

11{Ti > s + t}G (s + t|s)

+

0

with G(u|s) the Kaplan-Meier estimator of P(C > u|C > s).

Landmark time s Time s + t

time

: uncensored

: censored

Slide 17/29 � P Blanche et al.

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Inverse Probability of Censoring Weights

Wi (s, t) =11{s < Ti ≤ s + t}∆i

G (Ti |s)+

11{Ti > s + t}G (s + t|s)

+

0

with G(u|s) the Kaplan-Meier estimator of P(C > u|C > s).

Landmark time s Time s + t

time

: uncensored

: censored

Slide 17/29 � P Blanche et al.

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Inverse Probability of Censoring Weights

Wi (s, t) =11{s < Ti ≤ s + t}∆i

G (Ti |s)+

11{Ti > s + t}G (s + t|s)

+ 0

with G(u|s) the Kaplan-Meier estimator of P(C > u|C > s).

Landmark time s Time s + t

time

: uncensored

: censored

Slide 17/29 � P Blanche et al.

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Asymptotic i.i.d. representation

Lemma: Assume that the censoring time C is independent of(T , η, π(·, ·)) and let θ denote either PEπ, R

2π or a di�erence in PE

or R2π, then

√n(θ(s, t)− θ(s, t)

)=

1√n

n∑i=1

IFθ(Ti ,∆i , πi (s, t), s, t) + op (1)

where IFθ(Ti ,∆i , πi (s, t), s, t) being :

I zero-mean i.i.d. terms

I easy to estimate (using Nelson-Aalen & Kaplan-Meier)

Slide 18/29 � P Blanche et al.

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Pointwise con�dence interval (�xed s)

• Asymptotic normality:

√n(θ(s, t)− θ(s, t)

)D−→ N

(0, σ2s,t

)• 95% con�dence interval:{

θ(s, t)± z1−α/2σs,t√n

}

where z1−α/2 is the 1− α/2 quantile of N (0, 1).

• Variance estimator:

σ2s,t =1

n

n∑i=1

{IFθ(Ti ,∆i , πi (s, t), s, t)

}2

Slide 19/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm

(≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}

(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}

(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣ 1√n

n∑i=1

ωbiIFθ(Ti ,∆i , πi (s, t), s, t)

σs,t

∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}

(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣ 1√n

n∑i=1

ωbiIFθ(Ti ,∆i , πi (s, t), s, t)

σs,t

∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}

(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣ 1√n

n∑i=1

ωbiIFθ(Ti ,∆i , πi (s, t), s, t)

σs,t

∣∣∣∣∣

2 Compute q(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}

(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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Simultaneous con�dence band over s ∈ S

{θ(s, t)± q

(S,t)1−α

σs,t√n

}, s ∈ S

Computation of q(S,t)1−α by the simulation algorithm (≈ Wild Bootstrap):

1 For b = 1, . . . ,B, say B = 4000, do:

1 Generate {ωb1 , . . . , ω

bn} from n i.i.d. N (0, 1).

2 Using the plug-in estimator IFθ(·), compute:

Υb = sups∈S

∣∣∣∣∣ 1√n

n∑i=1

ωbiIFθ(Ti ,∆i , πi (s, t), s, t)

σs,t

∣∣∣∣∣2 Compute q

(S,t)1−α as the 100(1− α)th percentile of

{Υ1, . . . ,ΥB

}(Conditional multiplier central limit theorem)

Slide 20/29 � P Blanche et al.

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DIVAT sample

• Population based study of kidney recipients (n=4,119)

• Split the data into training (2/3) and validation (1/3) samples

• T : time from 1-year after transplantation to graft failure which is:

Death Return to dialysis

OR

• Censoring due to:

• delayed entries: 2000-2013• end of follow-up: 2014

• Baseline covariates: age, sex, cardiovascular history

• Longitudinal biomarker (yearly): serum creatinine

Slide 21/29 � P Blanche et al.

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DIVAT sample

• Population based study of kidney recipients (n=4,119)

• Split the data into training (2/3) and validation (1/3) samples

• T : time from 1-year after transplantation to graft failure which is:

Death Return to dialysis

OR

• Censoring due to:

• delayed entries: 2000-2013• end of follow-up: 2014

• Baseline covariates: age, sex, cardiovascular history

• Longitudinal biomarker (yearly): serum creatinine

Slide 21/29 � P Blanche et al.

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DIVAT sample

• Population based study of kidney recipients (n=4,119)

• Split the data into training (2/3) and validation (1/3) samples

• T : time from 1-year after transplantation to graft failure which is:

Death Return to dialysis

OR

• Censoring due to:

• delayed entries: 2000-2013• end of follow-up: 2014

• Baseline covariates: age, sex, cardiovascular history

• Longitudinal biomarker (yearly): serum creatinine

Slide 21/29 � P Blanche et al.

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Descriptive statistics & censoring issue

• s ∈ S = {0, 0.5, . . . , 5}• t = 5 years

s=0 s=1 s=2 s=3 s=4 s=5

Censored in (s,s+5]Known as event−free at s+5Observed failure in (s,s+5]

landmark time (year)

No.

of s

ubje

cts

020

060

010

0014

00

Slide 22/29 � P Blanche et al.

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Joint model

I Longitudinal

log[Yi (tij)

]= (β0 + b0i ) + β0,ageAGEi + β0,sexSEXi

+(β1 + b1i + β1,ageAGEi

)× tij + εij

= mi (t) + εij

I Survival (hazard)

hi (t) = h0(t) exp

{γageAGEi + γCVCVi

+ α1mi (t) + α2dmi (t)

dt

}

(�tted using package JM)

Slide 23/29 � P Blanche et al.

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Joint model

I Longitudinal

log[Yi (tij)

]= (β0 + b0i ) + β0,ageAGEi + β0,sexSEXi

+(β1 + b1i + β1,ageAGEi

)× tij + εij

= mi (t) + εij

I Survival (hazard)

hi (t) = h0(t) exp

{γageAGEi + γCVCVi

+ α1mi (t) + α2dmi (t)

dt

}(�tted using package JM)

Slide 23/29 � P Blanche et al.

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R2π(s, t) vs s (t=5 years)

Landmark time s (years)

Rπ2 (s

, t)

0 1 2 3 4 5

0 %

10 %

20 %

30 %

95% pointwise CI95% simultaneous CB

Slide 24/29 � P Blanche et al.

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Comparing R2π(s, t) vs s for di�erent π(s, t)

Landmark time s (years)

Rπ2 (s

, t)

0 1 2 3 4 5

0 %

10 %

20 %

30 %

T ~ Age + CV + m(t) + m'(t) (JM)

Slide 25/29 � P Blanche et al.

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Comparing R2π(s, t) vs s for di�erent π(s, t)

Landmark time s (years)

Rπ2 (s

, t)

0 1 2 3 4 5

0 %

10 %

20 %

30 %

●● ●

●● ●

●●

T ~ Age + CV + m(t) + m'(t) (JM)

T ~ Age + CV

Slide 25/29 � P Blanche et al.

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Comparing R2π(s, t) vs s for di�erent π(s, t)

Landmark time s (years)

Rπ2 (s

, t)

0 1 2 3 4 5

0 %

10 %

20 %

30 %

●● ●

●● ●

●●●

●●

● ●

● ●

T ~ Age + CV + m(t) + m'(t) (JM)T ~ Age + CV + Y(t=0)T ~ Age + CV

Slide 25/29 � P Blanche et al.

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Comparing R2π(s, t) vs s for di�erent π(s, t)

Landmark time s (years)

Rπ2 (s

, t)

0 1 2 3 4 5

0 %

10 %

20 %

30 %

●●

●●

T ~ Age + CV + m(t) + m'(t) (JM)T ~ Age + CV + Y(t=0)

Slide 25/29 � P Blanche et al.

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Comparing R2π(s, t) vs s for di�erent π(s, t)

Landmark time s

Diff

eren

ce in

Rπ2 (s

,t)

●●

●●

−5

%5

%10

%20

%0

%

0 1 2 3 4 5

Slide 25/29 � P Blanche et al.

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Comparing R2π(s, t) vs s for di�erent π(s, t)

Landmark time s

Diff

eren

ce in

Rπ2 (s

,t)

●●

●●

● ●

−5

%5

%10

%20

%0

%

0 1 2 3 4 5

Slide 25/29 � P Blanche et al.

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Calibration plot (example for s = 3 years)

(0,10) (0;3.5]

(10,20) (3.5;5.3]

(20,30) (5.3;8]

(30,40) (8;10.4]

(40,50) (10.4;13.1]

(50,60) (13.1;16.5]

(60,70) (16.5;22.3]

(70,80) (22.3;33]

(80,90) (33;55.1]

(90,100) (55.1;100]

PredictedObserved

Risk groups (quantile groups, in %)

5−ye

ar r

isk

(%)

020

4060

8010

0

2%

8(4)%4%

15(6)%

7%

15(5)%

9%13(5)% 12%

16(6)% 15%

21(7)%19%

26(6)% 27%29(7)%

42%

36(9)%

77%74(8)%

Slide 26/29 � P Blanche et al.

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Area under the ROC(s, t) curve vs s

Landmark time s (years)

AU

Cπ(s

, t)

0 1 2 3 4 5

50%

60%

70%

80%

100%

●●

●● ● ●

●●

● ●●

●●

●●

●●

●●

T ~ Age + CV + m(t) + m'(t) (JM)T ~ Age + CV + Y(t=0)T ~ Age + CV

Slide 27/29 � P Blanche et al.

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Summing up

I R2-type curve

• summarizes calibration and discriminating simultaneously

• has an understandable trend

I Simple model free inference

• predictions can be obtained from any model

• we do not assume any model to hold

• allows fair comparisons of di�erent predictions

I The method accounts for:

• Censoring

• Dynamic setting (the at risk population changes)

Slide 28/29 � P Blanche et al.

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Discussion

I The strong calibration assumption allows di�erent interestinginterpretations:

• Explained variation• Correlation• Mean risk di�erence

I Unfortunately

• the strong calibration cannot be checked(curse of dimensionality)

I However• weak and strong de�nitions are closely related:

• strong calibration implies weak calibration• weak calibration can �often� be seen as a reasonable

approximation of strong calibration in practice

• weak calibration can be assessed (plots)

Thank you for your attention!

Slide 29/29 � P Blanche et al.

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Discussion

I The strong calibration assumption allows di�erent interestinginterpretations:

• Explained variation• Correlation• Mean risk di�erence

I Unfortunately

• the strong calibration cannot be checked(curse of dimensionality)

I However• weak and strong de�nitions are closely related:

• strong calibration implies weak calibration• weak calibration can �often� be seen as a reasonable

approximation of strong calibration in practice

• weak calibration can be assessed (plots)

Thank you for your attention!

Slide 29/29 � P Blanche et al.