professor chris williams et al - healthcare condition monitoring using icu data
TRANSCRIPT
Healthcare condition monitoring using ICUdata
Chris Williamsjoint work with Yvonne Freer, Konstantinos Georgatzis, ChrisHawthorne, Partha Lal, Neil McIntosh, Ian Piper, John Quinn,
Martin Shaw, Ioan Stanculescu
School of Informatics, University of Edinburgh,and Alan Turing Institute, London
November 2017
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My main research interests:
I Time series understandingI Computer vision, especially object recognition, shape and
texture modellingI Semi-automation of data cleaning and preparationI Unsupervised learningI Gaussian processes
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Time Series UnderstandingI Explain the multivariate time series in terms of an
underlying set of discrete factorsI Make inferences for underlying variables when
observations are corrupted by artifactI We will address such problems with various switching
linear dynamical systems (SLDS) models
BS
Time (s)
BR0 200 400 600 800
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HR (bp
m)
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Sys. BP
(mmH
g)
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Dia. BP
(mmH
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ICU Condition Monitoring
I Population: patients receiving intensive careI Data: physiological vital signs recordingsI Problems: artifact corruption, false alarms, amount of dataI Goal: Determine the state of health of the patient,
uncorrupted vital signs
Image source: Wikipedia Intensive Care Unit page
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Overview
I Factorial Switching Linear Dynamical SystemI Inference and LearningI FSLDS and DSLDSI Novel RegimesI DataI ResultsI Summary
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Factors Affecting MeasurementsI The physiological observations are affected by different
factors.I Factors can be artifactual or physiological.
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Sys
. BP
(m
mH
g)
0 200 400 600 800 10000
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Dia
. BP
(m
mH
g)
Time (s)0 20 40 60 80 100
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HR
(bp
m)
Time (s)
Arterial blood sample Bradycardia
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Factorial Switching Linear Dynamical System
Artifactual state
Physiological state
Observations
Physiological factors
Artifactual factors
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FSLDS notation
I st is the switch variable, which indexes factor settings, e.g.‘blood sample occurring and first stage of TCPrecalibration’.
I xt is the hidden continuous state at time t . This containsinformation on the true physiology of the baby, and on thelevels of artifactual processes.
I y1:t are the observations.
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Kalman filtering
I Continuous hidden state affects some observations:
xt ∼ N (Axt−1,Q)
yt ∼ N (Cxt ,R)
I Kalman filter equations can be used to work computep(x1:t |y1:t)
I Done iteratively by predicting and updating
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Switching dynamics
I The switch variable st selects the dynamics for a particularcombination of factor settings:
xt ∼ N (A(st )xt−1,Q(st ))
yt ∼ N (C(st )xt ,R(st ))
I For each setting of st , the Kalman filter equations give apredictive distribution for xt .
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Factor interactions
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Related work
I Switching linear dynamical models have been studied bymany authors, e.g. Alspach and Sorenson (1972),Ghahramani and Hinton (1996).
I Applications include fault detection in mobile robots (deFreitas et al., 2004), speech recognition (Droppo andAcero, 2004), industrial monitoring (Morales-Menedez etal., 2002).
I A two-factor FSLDS was used for speech recognition byMa and Deng (2004). Factorised SLDS also used formusical transcription (Cemgil et al., 2006).
I There has been previous work on condition monitoring inthe ICU, though we are unaware of any previous studiesthat use a FSLDS.
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Inference and Learning
I For this application, we are interested in filtering, inferringp(st ,xt |y1:t)
I Exact inference is intractable (Lerner and Parr, 2001)I We use the Gaussian sum approximation (e.g. Murphy,
1998)I Learning uses labelled data for different regimes, and
overwriting order of factors
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Example inference results
I Can examine variance of estimates of true physiology x̂t ,e.g. for blood sample (left) and temperature probedisconnection (right):
Time (s)
BS0 50 100 150 200 250
Sys
. BP
(m
mH
g)
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40
45
50
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Dia
. BP
(m
mH
g)
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Time (s)
TD0 500 1000
Cor
e te
mp.
(°C
)35
35.5
36
36.5
37
37.5
38
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Models: FSLDS, DSLDS
DSLDS (Georgatzis and Williams, UAI 2015)
I st is predicted with a classifierI Inference for xt is similar to FSLDSI α-mixture combines FSLDS and DSLDS
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FSLDS and DSLDS: pros and cons
+ Knowledge engineering tells us how the factors interactgeneratively
+ There is not very much labelled data+ Normality varies per patient (multi-task learning)- In the DSLDS discrete state distributions are predicted
directly, rather than inferred. Can encode knowledge withinformative features.
- Some events (esp. artifactual) might be easier to identifywith a discriminative approach. Harder to come up with agenerative model.
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Novel RegimesI There are many other factors influencing the data: drugs,
sepsis, neurological problems...
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Heart rate
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Dia. BP
0 200 400 600 800 1000 12000
50
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SpO2
?
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Known UnknownsI Add a factor to represent abnormal dynamics
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Known UnknownsI Add a factor to represent abnormal dynamics
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X-factor for static 1-D data
I For static data, we can use a modelM∗ representing‘abnormal’ data points.
y
p(y|
s)
I The high-variance model wins when the data is not wellexplained by the original model
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X-factor with known factors
I The X-factor can be applied to the static data inconjunction with known factors (green):
y
p(y|
s)
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X-factor for dynamic data
xt ∼ N (Axt−1,Q)
yt ∼ N (Cxt ,R)
I Can construct an ‘abnormal’ dynamic regime analogously:
Normal dynamics: {A,Q,C,R}
X-factor dynamics: {A,ξQ,C,R}, ξ > 1.
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Spectral view of the X-factor
f
S y(f)
0 1/2
I Plot shows the spectrum of a hidden AR(5) process, andaccompanying X-factor
I More power at every frequencyI Dynamical analogue of the static 1-D case
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Data
I 27 patients from Neuro ICU in the Southern GeneralHospital, Glasgow (15 TBI, 12 SAH)
I Channels:I arterial blood pressure (ABP)I electrocardiogram (ECG)I pulse oximetryI intracranial pressure (ICP)I end tidal CO2 (EtCO2)I respiratory signal (Resp)
I Downsampled to 1 Hz
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Annotation
I 46 event-types labelled, including blood sample, dampedtrace, patient turning and suctioning
I Damped trace events have a mean duration of over 8hours per patient
I Other significant events: blood sample, patient turning andsuctioning, noisy channels, preparation for or return fromtransfer
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Processing pipeline
Extraction from
ICU databasePreprocessing FSLDS
Stabilitydetection
I Made to work all together on ICU serverI System operates at ∼ 10× realtimeI Stability detection: need to estimate AR/ARMA parameters
for every patient individually for the stability regimeI This is done by predicting intervals that are stable vs
non-stable, and using these to learn the stability regimeI Software available at https://datashare.is.ed.ac.uk/handle/10283/855
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Results
0 0.2 0.4 0.6 0.8 10
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False positive rate
Tru
e po
sitiv
e ra
te
Blood sample
FSLDSDSLDSalpha−combination
0 0.2 0.4 0.6 0.8 10
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False positive rate
Tru
e po
sitiv
e ra
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Damped
FSLDSDSLDSalpha−combination
0 0.2 0.4 0.6 0.8 10
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False positive rate
Tru
e po
sitiv
e ra
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Suction
FSLDSDSLDSalpha−combination
0 0.2 0.4 0.6 0.8 10
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False positive rate
Tru
e po
sitiv
e ra
te
X−factor
FSLDSDSLDSalpha−combination
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AUC BS DT SC X
DSLDS 0.94 0.78 0.64 0.56FSLDS 0.86 0.77 0.60 0.60α-mixture 0.95(0.9) 0.79(0.9) 0.64(−∞) 0.61(1.4)
I Blood sample performance is very good, and is potentiallyuseful for silencing false alarms
I Damped trace is particularly interesting as it has significantduration and is not an event caused by nursinginterventions; it is therefore particularly helpful to flag up
I Suction events are complex and have a variable timecourse. Also suction and position change events can havesimilar effects on the patient. Position change was notmodelled with a factor in our experiments, thus it may notbe surprising if these two event types are confused
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Damped Trace Example
True X
True SC
True BS
True DT
00:13:00 00:13:45 00:14:30 00:15:15 00:16:00 00:16:45 00:17:30 00:18:15 00:19:00 00:19:44 00:20:29 00:21:14 00:21:59 00:22:44 00:23:29 00:24:14 00:24:590
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250
ABP
(mm
Hg)
Patient damped_trace_demo
Dia.MeanSys.
X −− DSLDS
X −− FSLDS
X −− alpha
SC −− DSLDS
SC −− FSLDS
SC −− alpha
BS −− DSLDS
BS −− FSLDS
BS −− alpha
DT −− DSLDS
DT −− FSLDS
DT −− alpha
0.2
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1
I Note imputed x-stateI Our clinicians believe that showing imputed state and
flagging up artifact would be helpful
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Blood Sample Example
True X
True SC
True BS
True DT
00:09:00 00:09:41 00:10:22 00:11:04 00:11:45 00:12:26 00:13:07 00:13:48 00:14:30 00:15:11 00:15:52 00:16:33 00:17:14 00:17:55 00:18:37 00:19:180
50
100
150
200
250
ABP
(mm
Hg)
Patient blood_sample_demo
Dia.MeanSys.
X −− DSLDS
X −− FSLDS
X −− alpha
SC −− DSLDS
SC −− FSLDS
SC −− alpha
BS −− DSLDS
BS −− FSLDS
BS −− alpha
DT −− DSLDS
DT −− FSLDS
DT −− alpha
0.2
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0.6
0.8
1
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Summary
I Quantification of the amount of artifact in this dataset,importance of damped trace events
I AUC scores are very high for blood samples (0.95), goodfor damped trace (0.79), and poor for suction (0.64) andX-factor (0.61) events
I Successful implementation of a real-time system carryingout FSLDS analysis on the raw data coming from the ICU
I FSLDS/DSLDS models can be applied to other ICUmonitoring tasks (e.g. identifying sepsis) and moregenerally
I We are also developing models for the effect ofinterventions (e.g. drug administration)
Funding: Chief Scientist Office (Scotland) CHZ/4/801
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References
I Factorial Switching Linear Dynamical Systems applied toPhysiological Condition Monitoring.John A. Quinn, Christopher K.I. Williams, Neil McIntosh. IEEETrans. on Pattern Analysis and Machine Intelligence 31(9) pp1537-1551 (2009).
I Discriminative Switching Linear Dynamical Systems applied toPhysiological Condition Monitoring. Konstantinos Georgatzis,Christopher K. I. Williams, Proc UAI 2015.
I Detecting Artifactual Events in Vital Signs Monitoring Data.Partha Lal, Christopher K. I. Williams, Konstantinos Georgatzis,Christopher Hawthorne, Paul McMonagle, Ian Piper, MartinShaw. Tech report, September 2015.
I Available from http://homepages.inf.ed.ac.uk/ckiw/
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