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Connecting time-dots for Outcomes Prediction
in LongitudinalHeterogeneous Multivariate healthcare
Big Data
mHealth meetup: Health Tech IP & Data Science
Robert Moskovitch, PhD
Complex Data Analytics Lab
Software and Information Systems Engineering
Ben Gurion University of the Negev
Monitoring for Modeling
Glucometer
Static:
Gender, Height, Weight,
socio economic status,
Blood type,..
Heart beat
Movements -> Activities
Applications
And more ..
Inpatient:
• Conditions
• Lab-tests
• Medications
• Procedures
Outpatientdata:
• Medications (continuous)
• Procedures
• Conditions
• Lab tests
Temporal Raw Data
From Time Points to Time Intervals Series
Time Intervals Related Patterns
Discovery – an illustration
Time Intervals Related Patterns
Discovery – an illustration
Allen’s (1983) Temporal Logic,
using Epsilon
Exploiting the Transitive Property
Ø Given three time intervals A, B and C and the
relations among A r1 B and B r2 C, the relation A
r3 C can be reasoned.
Time Intervals Related Pattern - TIRP
A TIRP is a conjunction of pairwise temporal relations
{A o B, A < C, A < D, A < E, B m C, B < D, B < E, C c D, C o E, D m E}
A k-sized TIRP includes k(k-1)/2 = (k2-k)/2 temporal relations
KarmaLego – Definitions 2
Ø Vertical Support(P) is the numberof entities |EP| (e.g., patients), in which
TIRP P was discovered atleast once, among the entire mined population
|E|. Ver_sup(P)= |EP| / |E|
Ø Horizontal Support (P) is the numberof instances hor_sup(P,ei)occurring in
each supporting entity.
Ø Mean Duration of the n supporting instances of the same k-sized TIRP P
within an entity e is defined by:
||
),sup(_
)sup(__
||
1
P
E
i
i
E
ePhor
Phormean
P
∑=
=
( )
n
IIMax
ePonMeanDurati
n
i
i
s
ji
e
k
j∑= = −
= 1
1,,
1
),(
Time Intervals Related Patterns
Discovery – an illustration
Procedures
Conditions
Drugs
Procedures
Conditions
Drugs
Procedures
Conditions
Drugs
HS = 2
HS = 2
HS = 3
HS = 1
HS = 1
HS = 1
K=1
K=4
K=3
K=5
K=2
NULL
+ A + B+ B
+ A
A B C
+ C+ B+ A + C+ A + C
A
B
B C
r1 r1
r2
A
B
B C
r1 r1
r1
A
B
B C
r1 r1
r3
A
B
B C
r1 r8
r7
A
B
B C
r1 r8
r8
+ B
+ A + A + B + C
+ B + C
+ C
B C A
A
B
r1 r1
r2
r1
r1
r1C
B C A
A
B
r1 r1
r3
r1
r1
r1C
B C B
A
B
r1 r1
r3
r1
r4
r5C
B C C
A
B
r1 r1
r3
r1
r1
r1C
B C C
A
B
r1 r1
r3
r1
r2
r8C
r5
r4
r1
B C B
A
B
r1 r1
r3
C
r3
r5
r2
r2B
C
r5
r4
r1
B C B
A
B
r1 r1
r3
C
r8
r4
r1
r2B
B
A
A
r1 A
A
r5 A
B
r1 A
B
r1 A
B
r7 A
C
r1 A
C
r5 A
C
r7
KarmaLego
Fast Time Intervals Mining
73 = 343 -> 3
Moskovitch et al, Outcomes Prediction via Time Intervals Related Patterns, IEEE
International Conference on Data Mining (ICDM), 2015
KarmaLego General Workflow
Moskovitch et al, Fast Time Intervals Mining by Exploiting the Transitivity of
Temporal Relations, Knowledge and Information Systems, 2015.
Use of TIRPs from KarmaLego
Diabetes Temporal Patterns
Example
0.26 0.18 0.22 0.28
0.25 0.23 0.33 0.42 0.29
KarmaLegoSification
Ø A major problem in multivariate time series classification is the
various types of raw temporal data
Ø TIRPs can be useful here as well, as classification features
Moskovitch et al, Classification of Multivariate Time Series via TemporalAbstraction
and Time-Intervals Mining, Knowledge and Information Systems, 2015
Unsupervised Discretization:
EWD and SAX
Ø EWD: the continuous values range is
divided into k equal bins (states)
Ø Symbolic Aggregate approXimation
Based on PAA, Piecewise Aggregate
Approximation, A time series segmenting
algorithm (Keogh et al.,2003).
Ø TD4C
Moskovitch et al, Data Mining and Knowledge Discovery, 2015
TD4C
Temporal Discretization for Classification
Ø TD4C performs supervised temporal abstraction to increase the
expected accuracy.
Ø TD4C: search set of cut-offs to abstract later each temporal
variable into meaningfully different states for each class.
Ø Having different states for each class -> will discover different
frequent TIRPs for each class -> expected to increase the
accuracy.
Moskovitch et al, Classification-driven temporaldiscretization of multivariate time
series, Data Mining and Knowledge Discovery,2015
TD4C Formulation
Ø Given C = {c1, c2,.. cn} classes, E entities divided into {E1, E2,.. Ec}
sets of entities per class and T = {t1, t2,.. tm} temporal variables, and
A – a TD4C abstraction method.
Ø The problem is to find the set of cutoffs for each temporal variable ti
that increases the difference in the dominant states in each class.
Ø Thus, we want to measure the distribution of the states in each class
entities, and to measure when these are most different.
Ø For that three measure were determined:
l Entropy
l Cosinus
l Kullback-Leibler
Generalization of Allen’s
Temporal Relations
Ø KarmaLegoS enables to mine TIRPs with 7 (Allen’s original)
or 3 abstract temporal relations and various epsilon values
BEFORE
TIRPs as Features
ClassTirpn..…Tirp4Tirp3Tirp2Tirp1entity
0???????P1
1???????P2
0???????P3
0???????P4
1???????P5
1???????P6
1???????Pm
ClassTirpn..…Tirp4Tirp3Tirp2Tirp1entity
00001110P1
11111100P2
00011100P3
00001111P4
11000011P5
11001011P6
10001001Pm
ClassTirpn..…Tirp4Tirp3Tirp2Tirp1entity
00001320P1
13123100P2
00013200P3
00002131P4
12000022P5
11001021P6
10002001Pm
ClassTirpn..…Tirp4Tirp3Tirp2Tirp1entity
00001.23.42.30P1
13.31.232.543.561.2300P2
00013.342.5600P3
00002.71.453.341.6P4
12.400002.342.2P5
11.34001.5602.51.2P6
10002.23001.8Pm
Binary
(default)
Horizontal
Support
Mean
Duration
Datasets
Ø ICU Dataset - 645 patients who underwent cardiac surgery at
the AMC in Amsterdam (2002-2004). Includes over 12 hours
of High and Low frequency.
196 patients were mechanically ventilated for more than 24
hours (70%), and the rest were 449.
Ø Diabetes - Contains 2038 diabetic patients data along 5 years
(2002-2007) from Israeli HMO, measured monthly HA1c, Glucose,
Cholesterol values and medication purchased.
992 males and 1012 females, having a quite balanced (~50%)
dataset.
Ø Hepatitis – Laboratory measurements of Hepatitis B and C patients,
admitted in Japan. Eleven temporal variables, having the top vertical
support.
204 Hepatitis B patients and 294 Hepatitis C patients (~60%).
KarmaLegoS Evaluation Setup
Moskovitch and Shahar, Classification of Multivariate Time Series via Temporal
Abstraction and Time-Intervals Mining, Knowledge and Information Systems,2015
Class 1
data
Class 2
data
Class n
data
KarmaLego
KarmaLego
KarmaLego U
KarmaLego
TIRPs
TrainingTest
Single
Entity data
Signle
KarmaLego
Training Matrix
(EntitiesTIRPs and
labels)
Vector of TIRPs
Induced
Classifier
Feature
Selection
TIRPs
TIRPs
TIRPs
Class
KarmaLegoS - Parameters
Ø To evaluate KarmaLegoS 5 experiments were designed for the
various parameters in the KarmaLegoS framework, including:
l Abstraction method (KB, EWD, SAX, TD4Cs)
l Number of bins (3, 4)
l Temporal relations set (3, 7)
l TIRP Representation (Binary, HS, MeanD)
Ø For that experiments we designed and ran on three real datasets
using 10 fold cross validation and RandomForest, compared
according to the Accuracy measure.
Temporal Relations and TIRP representation
Abstraction Methods vs Bins Number
ε=0, 3 temporal relations, MeanD and NoFS
Thank You!
Dr. Robert Moskovitch
Head, Complex Data Analytics Lab
Software and Information Systems Engineering
Ben Gurion University
Israel
robertmo@bgu.ac.il
Backup
KarmaLegoV
KarmaLegoV
KarmaLegoV – Search Results

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mHealth Israel_Connecting time-dots for Outcomes Prediction in Healthcare Big Data_Robert Moskovitch, PhD, Ben Gurion University of the Negev

  • 1. Connecting time-dots for Outcomes Prediction in LongitudinalHeterogeneous Multivariate healthcare Big Data mHealth meetup: Health Tech IP & Data Science Robert Moskovitch, PhD Complex Data Analytics Lab Software and Information Systems Engineering Ben Gurion University of the Negev
  • 2. Monitoring for Modeling Glucometer Static: Gender, Height, Weight, socio economic status, Blood type,.. Heart beat Movements -> Activities Applications And more .. Inpatient: • Conditions • Lab-tests • Medications • Procedures Outpatientdata: • Medications (continuous) • Procedures • Conditions • Lab tests
  • 4. From Time Points to Time Intervals Series
  • 5. Time Intervals Related Patterns Discovery – an illustration
  • 6. Time Intervals Related Patterns Discovery – an illustration
  • 7. Allen’s (1983) Temporal Logic, using Epsilon
  • 8. Exploiting the Transitive Property Ø Given three time intervals A, B and C and the relations among A r1 B and B r2 C, the relation A r3 C can be reasoned.
  • 9. Time Intervals Related Pattern - TIRP A TIRP is a conjunction of pairwise temporal relations {A o B, A < C, A < D, A < E, B m C, B < D, B < E, C c D, C o E, D m E} A k-sized TIRP includes k(k-1)/2 = (k2-k)/2 temporal relations
  • 10. KarmaLego – Definitions 2 Ø Vertical Support(P) is the numberof entities |EP| (e.g., patients), in which TIRP P was discovered atleast once, among the entire mined population |E|. Ver_sup(P)= |EP| / |E| Ø Horizontal Support (P) is the numberof instances hor_sup(P,ei)occurring in each supporting entity. Ø Mean Duration of the n supporting instances of the same k-sized TIRP P within an entity e is defined by: || ),sup(_ )sup(__ || 1 P E i i E ePhor Phormean P ∑= = ( ) n IIMax ePonMeanDurati n i i s ji e k j∑= = − = 1 1,, 1 ),(
  • 11. Time Intervals Related Patterns Discovery – an illustration Procedures Conditions Drugs Procedures Conditions Drugs Procedures Conditions Drugs HS = 2 HS = 2 HS = 3 HS = 1 HS = 1 HS = 1
  • 12. K=1 K=4 K=3 K=5 K=2 NULL + A + B+ B + A A B C + C+ B+ A + C+ A + C A B B C r1 r1 r2 A B B C r1 r1 r1 A B B C r1 r1 r3 A B B C r1 r8 r7 A B B C r1 r8 r8 + B + A + A + B + C + B + C + C B C A A B r1 r1 r2 r1 r1 r1C B C A A B r1 r1 r3 r1 r1 r1C B C B A B r1 r1 r3 r1 r4 r5C B C C A B r1 r1 r3 r1 r1 r1C B C C A B r1 r1 r3 r1 r2 r8C r5 r4 r1 B C B A B r1 r1 r3 C r3 r5 r2 r2B C r5 r4 r1 B C B A B r1 r1 r3 C r8 r4 r1 r2B B A A r1 A A r5 A B r1 A B r1 A B r7 A C r1 A C r5 A C r7 KarmaLego Fast Time Intervals Mining 73 = 343 -> 3 Moskovitch et al, Outcomes Prediction via Time Intervals Related Patterns, IEEE International Conference on Data Mining (ICDM), 2015
  • 13. KarmaLego General Workflow Moskovitch et al, Fast Time Intervals Mining by Exploiting the Transitivity of Temporal Relations, Knowledge and Information Systems, 2015.
  • 14. Use of TIRPs from KarmaLego
  • 15. Diabetes Temporal Patterns Example 0.26 0.18 0.22 0.28 0.25 0.23 0.33 0.42 0.29
  • 16. KarmaLegoSification Ø A major problem in multivariate time series classification is the various types of raw temporal data Ø TIRPs can be useful here as well, as classification features Moskovitch et al, Classification of Multivariate Time Series via TemporalAbstraction and Time-Intervals Mining, Knowledge and Information Systems, 2015
  • 17. Unsupervised Discretization: EWD and SAX Ø EWD: the continuous values range is divided into k equal bins (states) Ø Symbolic Aggregate approXimation Based on PAA, Piecewise Aggregate Approximation, A time series segmenting algorithm (Keogh et al.,2003). Ø TD4C Moskovitch et al, Data Mining and Knowledge Discovery, 2015
  • 18. TD4C Temporal Discretization for Classification Ø TD4C performs supervised temporal abstraction to increase the expected accuracy. Ø TD4C: search set of cut-offs to abstract later each temporal variable into meaningfully different states for each class. Ø Having different states for each class -> will discover different frequent TIRPs for each class -> expected to increase the accuracy. Moskovitch et al, Classification-driven temporaldiscretization of multivariate time series, Data Mining and Knowledge Discovery,2015
  • 19. TD4C Formulation Ø Given C = {c1, c2,.. cn} classes, E entities divided into {E1, E2,.. Ec} sets of entities per class and T = {t1, t2,.. tm} temporal variables, and A – a TD4C abstraction method. Ø The problem is to find the set of cutoffs for each temporal variable ti that increases the difference in the dominant states in each class. Ø Thus, we want to measure the distribution of the states in each class entities, and to measure when these are most different. Ø For that three measure were determined: l Entropy l Cosinus l Kullback-Leibler
  • 20. Generalization of Allen’s Temporal Relations Ø KarmaLegoS enables to mine TIRPs with 7 (Allen’s original) or 3 abstract temporal relations and various epsilon values BEFORE
  • 22. Datasets Ø ICU Dataset - 645 patients who underwent cardiac surgery at the AMC in Amsterdam (2002-2004). Includes over 12 hours of High and Low frequency. 196 patients were mechanically ventilated for more than 24 hours (70%), and the rest were 449. Ø Diabetes - Contains 2038 diabetic patients data along 5 years (2002-2007) from Israeli HMO, measured monthly HA1c, Glucose, Cholesterol values and medication purchased. 992 males and 1012 females, having a quite balanced (~50%) dataset. Ø Hepatitis – Laboratory measurements of Hepatitis B and C patients, admitted in Japan. Eleven temporal variables, having the top vertical support. 204 Hepatitis B patients and 294 Hepatitis C patients (~60%).
  • 23. KarmaLegoS Evaluation Setup Moskovitch and Shahar, Classification of Multivariate Time Series via Temporal Abstraction and Time-Intervals Mining, Knowledge and Information Systems,2015 Class 1 data Class 2 data Class n data KarmaLego KarmaLego KarmaLego U KarmaLego TIRPs TrainingTest Single Entity data Signle KarmaLego Training Matrix (EntitiesTIRPs and labels) Vector of TIRPs Induced Classifier Feature Selection TIRPs TIRPs TIRPs Class
  • 24. KarmaLegoS - Parameters Ø To evaluate KarmaLegoS 5 experiments were designed for the various parameters in the KarmaLegoS framework, including: l Abstraction method (KB, EWD, SAX, TD4Cs) l Number of bins (3, 4) l Temporal relations set (3, 7) l TIRP Representation (Binary, HS, MeanD) Ø For that experiments we designed and ran on three real datasets using 10 fold cross validation and RandomForest, compared according to the Accuracy measure.
  • 25. Temporal Relations and TIRP representation
  • 26. Abstraction Methods vs Bins Number ε=0, 3 temporal relations, MeanD and NoFS
  • 27. Thank You! Dr. Robert Moskovitch Head, Complex Data Analytics Lab Software and Information Systems Engineering Ben Gurion University Israel robertmo@bgu.ac.il