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Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU

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Abstract and Figures

Cardiac arrest is a rare but devastating event in critically ill children associated with death, disability and significant healthcare costs. When a cardiac arrest occurs, the limited interventions available to save patient lives are associated with poor patient outcomes. The most effective way of improving patient outcomes and decreasing the associated healthcare costs would be to prevent cardiac arrest from occurring. This observation highlights the importance of prediction models that consistently identify high risk individuals and assist health care providers in providing targeted care to the right patient at the right time. In this paper, we took advantage of the power of convolutional neural networks (CNN) to extract information from high resolution temporal data, and combine this with a recurrent network (LSTM) to model time dependencies that exist in these temporal signals. We trained this CNN+LSTM model on high-frequency physiological measurements that are recorded in the ICU to facilitate early detection of a potential cardiac arrest at the level of the individual patient. Our model results in an F1 value of .61 to .83 across six different physiological signals, the most predictive single signal being the heart rate. To address the issue of instances of missing data in the recorded physiological signals, we have also implemented an ensemble model that combines predictors for the signals that were collected for a given patient. The ensemble achieves .83 average F1 score on a held-out test set, on par with the best performing signal, even in the absence of a number of signals. The results of our model are clinically relevant. We intend to explore implementation of this model at the point of care as a means of providing precise, personalized, predictive care to an at-risk cohort of patients.
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Prediction of Cardiac Arrest from Physiological Signals in
the Pediatric ICU
Sana Tonekaboni1,2 stonekaboni@cs.toronto.edu
Mjaye Mazwi3mjaye.mazwi@sickkids.ca
Peter Laussen3peter.laussen@sickkids.ca
Danny Eytan3danny.eytan@sickkids.ca
Robert Greer3robert.greer@sickkids.ca
Sebastian D. Goodfellow2sebastian.goodfellow@sickkids.ca
Andrew Goodwin3andrew.goodwin@sickkids.ca
Michael Brudno1brudno@cs.toronto.edu
Anna Goldenberg1,2 anna.goldenberg@vectorinstitute.ai
1Department of Computer Science
University of Toronto
Toronto, Ontario, Canada
2Vector institute
Toronto, Ontario, Canada
3Department of Critical Care Medicine
The Hospital for Sick Children
Toronto, Ontario, Canada
Abstract
Cardiac arrest is a rare but devastating event in critically ill children associated with
death, disability and significant healthcare costs. When a cardiac arrest occurs, the limited
interventions available to save patient lives are associated with poor patient outcomes. The
most effective way of improving patient outcomes and decreasing the associated healthcare
costs would be to prevent cardiac arrest from occurring. This observation highlights the
importance of prediction models that consistently identify high risk individuals and assist
health care providers in providing targeted care to the right patient at the right time. In
this paper, we took advantage of the power of convolutional neural networks (CNN) to
extract information from high resolution temporal data, and combine this with a recurrent
network (LSTM) to model time dependencies that exist in these temporal signals. We
trained this CNN+LSTM model on high-frequency physiological measurements that are
recorded in the ICU to facilitate early detection of a potential cardiac arrest at the level of
1
the individual patient. Our model results in an F1 value of .61 to .83 across six different
physiological signals, the most predictive single signal being the heart rate. To address
the issue of instances of missing data in the recorded physiological signals, we have also
implemented an ensemble model that combines predictors for the signals that were collected
for a given patient. The ensemble achieves .83 average F1 score on a held-out test set, on
par with the best performing signal, even in the absence of a number of signals. The results
of our model are clinically relevant. We intend to explore implementation of this model at
the point of care as a means of providing precise, personalized, predictive care to an at-risk
cohort of patients.
1. Introduction
Critically ill patients in the Intensive Care Unit (ICU) undergo dynamic changes in state and
associated risk, requiring continuous, close monitoring to identify deterioration. Patient de-
terioration or clinical instability requires aggressive life-saving treatments or interventions
(Vincent, 2013). Early identification of patient instability allows proactive interventions
aimed at stabilization of the patients condition. To facilitate this earlier recognition mon-
itoring devices are utilized that record and keep track of patient vital sign behavior at all
times. This data is sampled at rates of up to 500Hz, creating massive amounts of infor-
mation that can be overwhelming for physicians attempting to evaluate patients. However,
this large and complex data is an ideal substrate for Machine Learning methods that have
the potential to learn patterns and trends that exist within these data (Henry et al., 2015;
Soleimani et al., 2017; Suresh et al., 2017).
Improved survival in critically ill patients relies on consistent identification and predic-
tion of states that precede instability and patient injury, as this allows proactive measures
to improve patient condition (Sandroni et al., 2006). This has motivated researchers to
develop methods that predict destabilizing insults like Septic Shock (Henry et al., 2015),
need for clinical interventions (Suresh et al., 2017), and disease severity (Ghassemi et al.,
2015) using data generated by patients in the process of care. Cardiac arrest is a devas-
tating complication of terminal clinical instability. It is classically defined as a requirement
for chest compressions or cardiac defibrillation. In-hospital cardiac arrest in pediatric pa-
tients is strongly associated with mortality (survival to discharge in only 28 - 37 percent
of patients), disability, cost and health care dependence (Ortmann et al., 2011). Effective
models of prediction would improve recognition of pediatric patients at risk of cardiac arrest
and enable medical and surgical interventions to avert impending arrest in select groups of
patients. This would improve patient disability-free survival. However, a wide variety of
physiological disturbances and clinical states can precede cardiac arrest making consistent,
reproducible prediction challenging. Earlier work focused on predicting patient conditions
of this sort have traditionally relied upon data elements available in the Electronic Health
Record (EHR)(Verplancke et al., 2008; Choi et al., 2017; Wellner et al., 2017). More recent
work has leveraged the density and continuity of physiological time series data for predic-
tion of this complex patient behavior. This data also has the temporal signature required
to support clinical decisions that arise in the dynamic process of care for the critically ill
child. For higher frequency physiological recordings, previous authors have taken advan-
tage of deep networks for learning relevant patterns in the signals that reflect on patient
condition (Rajpurkar et al. (2017), (Razavian et al., 2016), Aczon et al. (2017)). Recurrent
2
structures are also commonly used to incorporate the time-dependencies that exist in these
signals (Suresh et al., 2017; Razavian et al., 2016; Lipton et al., 2016; Choi et al., 2017)
as are probabilistic approaches. Ghassemi et al. (2015) Joseph Futoma (2017) that take
advantage of Gaussian Processes to estimate temporal clinical data. Survival analysis and
time to event estimation are also used for prediction tasks using health data (Soleimani
et al., 2017; Ranganath et al., 2016).
In this work, we designed a model that detects impending cardiac arrest in pediatric
patients by examining patient’s high-resolution longitudinal physiological recordings. This
is done by associating a cardiac arrest risk score to windows of recording, in order to
identify high-risk individuals. Taking advantage of the temporal nature of these signals, we
use a long short-term memory network (LSTM) to learn the existing trend in the signals
(Hochreiter and Schmidhuber, 1997).
Technical Significance Our method uses a combination of Convolutional and Recurrent
network for the analysis of longitudinal physiological data. Combining these two structures
allows us to take advantage of CNN’s power in extracting informative features from time-
series data and RNN’s capability of learning time dependencies in temporal data. Since
physiological signals can be densely packed with information, we use CNN to find a compact
latent representation, and use that representation for a recurrent network to learn the
existing pattern in signals prior to a cardiac arrest. We use an ensemble of models trained
on different signal types to assign a cardiac arrest risk score to windows of recordings. Also,
in order to tackle the problem of missing measurements within recordings, we use a low-pass
filtering method for sample imputation.
Clinical Relevance Even in experienced centers, in-hospital cardiac arrest in critically
ill pediatric patients is associated with survival to discharge in only 28 to 37% of patients.
Disability free survival is rare with the most relevant category of disability being neurological
injury (Ortmann et al., 2011). Limited treatments are available when cardiac arrest occurs
and include cardiopulmonary resuscitation (CPR) with or without surgical cannulation to
an extracorporeal pump. These both represent high-risk, necessary interventions aimed
at rescuing patients from certain death, but both contribute to the injury associated with
cardiac arrest. The most effective way of improving the dismal outlook for pediatric patients
at risk of cardiac arrest is proactive identification of the patient at risk and prevention of
cardiac arrest with the need for resuscitation. In addition to saving lives and decreasing
long-term disability, this would significantly reduce health care costs associated with the
complex needs of survivors (Dimick et al., 2004).
2. Cohort
For this study, we utilized high-resolution physiological signals collected and archived from
the Pediatric ICU at the Hospital for Sick Children in Toronto Ontario to predict the
onset of a cardiac arrest. These recordings are sampled at a frequency of every 5 seconds
pervasively for all patients throughout their ICU stay, and include measured vitals such as
heart rate, blood pressure, and respiratory rate, as well as other derived metrics created by
mathematical modification of measured vital signs, such as SDNN (a heart rate variability
metric). Inclusion criteria were any critically ill child admitted to the critical care unit
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during the period of review who experienced a cardiac arrest. This subset of patients
experienced either a single event or multiple cardiac arrests during their ICU course. All
data recordings are labeled with a verified time of the cardiac arrest event. For each subject,
we extracted the physiological signals that were collected in their medical record in the 24
hours prior to the arrest. The distribution of number of available signals for each individual
can be seen in Figure 1. In total, we had 228 instances of cardiac arrests across 208 patients.
Figure 1: The total count of unique physiological signals that are available for each patient
in the cohort.
2.1 Cohort Selection
Despite the large number of physiological signals that are able to be recorded for patients in
the ICU, not every individual has a comprehensive set of all of the measurements recorded
in the database due to variation in monitoring strategy based upon clinician preference or
patient characteristics. Typical ICU practice is to record vital signs based on perceived
patient need and presence of the relevant sensor as part of the patients care array. As an
example, no End Tidal Capnogram is recorded if the patient is not intubated at the time of
the arrest. As a result, we had to select a subset of the signals and patients for our analysis.
As shown in figure 2, among the 110 different types of signals available, many were only
present for a few patients. Therefore, our inclusion criteria for the signal types and subjects
were as follows:
1. Select vitals that are recorded for at least 100 subjects in the database
2. Select subject who have at least one of the selected vitals on their record.
Six physiological signal types were selected for the analysis of cardiac arrest. Table 1
lists the name of those signals along with the number of subjects in the database that had
these measures recorded. Also, for patients who experienced multiple arrests, we removed
the second arrest instance if this occurred too close to the first one. This was to avoid
having predictive windows that overlap with arrests.
2.2 Data Extraction and Preprocessing
After the inclusion criteria were applied there were 203 cardiac arrest instances from 171
unique patients. For each instance, we had a different number and combination of recorded
physiological variables available for review. There are two main sources of sparsity in the
data used for this study: 1) Missing measurements within a specific physiological signal
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Figure 2: Number of different signal types present in the entire dataset. As shown here,
some signals like heart rate are commonly collected for patients while others like end tidal
CO2(etCO2) are only collected for a subset of patients
Table 1: List of physiological signals used for the prediction and the number of cardiac
arrest instances for each recording
Signal Description Number of arrest instances
HR Heart rate 203
Resp Respiratory rate 203
Pulse Pulse rate 203
SpO2 Oxygen saturation level 203
ABP Arterial Blood Pressure 155
SDNN Standard deviation of R-R intervals 203
and 2) absence of an entire type of signal for some individuals if that was not part of the
monitoring strategy being employed at that bedside.
To deal with missing values that exist within signals, we have implemented a combination
of low-pass filtering and linear interpolation. The filter averages existing signal values over
a length lwindow of time ( l= 3 minutes in our implementation). As shown in Figure 3 in
the first step, the filter is able to smooth over missing values in blocks < len(l), and it also
helps to remove the high-frequency noise. For any remaining discontinuity, we used linear
interpolation for signal imputation. One advantage of the low-pass filtering method is that
it can easily be implemented for real-time processing of the signals. As new samples are
generated, if an individual value is missing, it will be replaced by the average of the other
samples of the filter window.
To handle the problem of missing entire signals for certain patients, we have implemented
an ensemble model, that is further explained in the Method section.
2.3 Feature Choices
Along with the pre-processed signals, we also included patient’s age in the analysis, as it
is assumed to have a confounding effect on the arrest prediction task. No manual feature
selection was done on the temporal signals, as we used convolutional neural networks to
5
Figure 3: Preprocessing steps of high-resolution physiological signals. The first plot on the
top shows the normalized recording with the missing values replaced with zeros. The second
plot is the signal after passing through the low-pass filter. The third plot is the final signal
after linear imputation of missing values that weren’t resolved with filtering
extract the hidden information that exists within each recording. The implementation
details of the CNN are further discussed in the Methods section.
3. Methods
Our goal was to learn the underlying pattern that exists in patient’s physiological recordings,
prior to a cardiac arrest. The risk predictor model takes in a length Tminutes window of
a physiological signal, and assigns a risk score to it, based on how similar it is to pre-arrest
patterns. Looking into the trend of these scores during a patient’s stay at the hospital can
help clinicians identify individuals at high risk for a cardiac arrest by defining a patient
trajectory.
In the following section we describe the building blocks of the risk predictor model: 1)A
convolutional neural network that was used for feature extraction and for finding a compact
latent representation of the signal; 2) An LSTM network that captures the time-dependency
in the recordings; 3) The ensemble predictor that combines risk scores are evaluated from
different physiological signals. Following the section on network structure, we present our
method for generating training samples that makes the training process more robust and
prevents overfitting.
3.1 Convolutional Neural Network(CNN)
We use 1-dimensional CNN, in order to learn and extract features from the time series
signals. Without a fully-connected layer, the output of the network can be considered as a
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Figure 4: The CNN+LSTM network structure. A window of physiological signal is feed into
the convolutional network and the outputs of the CNN are used by the LSTM to generate
the Risk score
latent representation of the original signal in time. This method is used instead of hand-
picking features as it is expected to be more robust and to generalize well to different types
of recordings (as was also previously shown in (Razavian et al., 2016)). As demonstrated
in Figure 4, the network is composed of 2 convolutional layers. Each layer followed by tanh
activation and max-pooling. Also, dropout is applied to the elements of the final layer, to
prevent overfitting. All hyper-parameters are set by k-fold cross-validation. The output of
the network, f1:T0, is a condensed latent representation (f∈ RT0), of the original signal
(x∈ RT), where T0< T , and is the input to the LSTM that will generate the final risk
score.
3.2 Long Short-Term Memory Network(LSTM)
The extracted representation f1:T0goes into an LSTM network with n= 16 hidden units,
that generates 16 hidden states and 16 output states for every time step. We call the output
states h∈ Rn
Tand used the value of the hidden units of the final outputs to generate a
primary risk probability r(Figure 5). This score is calculated by feeding the final output to
a simple one layer network with Sigmoid activation (As shown in Figure 5). The recurrent
structure of the LSTMs encodes relative information of measurements across time and
provides a nonlinear improvement in model generalization.
h0
1, ..., h0
t0, ..., hn
1, ..., hn
t0=LST M (f1...ft0) (1)
r=Sigmoid(ht0W+b) (2)
In order to generate the final risk score, we took into account another confounding
factor: patient’s age. Specifically, we use patient’s age to generate a scaling factor for the
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Figure 5: The LSTM structure that accepts the latent representation of the physiological
signal and generates the primary risk score using the hidden layers of its output
final score. As shown in Eq. 3 this scale is calculated using a small neural network with
weights Wage and bias bage. The final risk score (risk) is then evaluated using Eq. 4 by
scaling the primary risk probability r.
agescale =RE LU (age Wage +bag e) (3)
risk =Sigmoid(ragescale) (4)
3.3 The Ensemble
There is a substantial discontinuity in our data where certain types of recordings for patients
during their stay at the hospital are not available due to interruption of a recording device,
movement of the patient within the unit or to a procedure or absence of a physiological
signal altogether as a result of that signal not being part of that patient’s monitoring
strategy. As a result, we trained separate risk predictor models for each physiological signal
independently. The final risk score is then the weighted aggregate of the risk predictions
generated from existing signals for an individual. The performance of the models across
signals vary, depending on the number of samples available for training and also the amount
of information each signal carries by nature. We assigned different weights to each of the
models Wi(where iis a given physiological signal), based on their prediction performance
during the training and validation process. This weight is the average F1 score calculated
on K different folds during the training. The ensemble generates the final risk score as the
weighted average of the predicted risks from the existing signals in a patient’s record (Eq.
5). The performance is then tested on held out samples that were not used at any point
during the training of any of the models.
Riskscore =Σn
i=1(Wiriski)1i
Σn
i=1(Wi)1i
(5)
Where 1i= 0 if signal iis missing and 1i= 1 otherwise
8
Figure 6: Risk score prediction using the ensemble model with existing physiological signals
3.4 Building Training Samples
For training, we needed to learn the pattern from windows of physiological recordings. We
extracted windows of length Tfrom the Dselected types of vital signals. We considered
recordings that are earlier than ∆ hours prior to the arrest (e.g. we used 5 hours prior
to the arrest), as normal signals, and recordings anywhere between 2 hours and 5 minutes
prior to the arrest as representing periods of risk. The learning task involved being able
to distinguish patterns that exist in normal signal versus signals in the ”pre-arrest range”
in order to flag the high risk patients earlier. To prevent overfitting to small sample size
for certain types of recordings and also to avoid dependance on reference time points, we
randomly pick windows of length Tfrom the pre-arrest and normal ranges every few epochs
during training (as shown in Figure 7) as we continue optimizing the network parameters.
Figure 7: Random selection of time windows from the pre-arrest and normal region of a
physiological recording. The normal region(colored in green), is part of the signal that is far
from the cardiac arrest, in our case more ∆ minutes earlier. The pre-arrest range (colored
in red) includes any window of recording that is closer than 5 minutes to the cardiac arrest.
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Signal Type CNN LSTM CNN+LSTM
Heart rate (HR) 0.753 ±0.075 0.666 ±0.118 0.816 ±0.034
Respiratory rate (Resp) 0.739 ±0.043 N/A 0.67 ±0.05
Pulse rate (Pulse) 0.720 ±0.093 0.698 ±0.06 0.746 ±0.092
Oxygen Saturation level (SpO2) 0.714 ±0.078 0.617 ±0.101 0.723 ±0.055
Ambulatory Blood Pressure (ABP) 0.675 ±0.17 0.647 ±0.17 0.76 ±0.13
SDNN Heart Rate Variability Metric (SDNN) 0.663 ±0.080 N/A 0.692 ±0.07
Table 2: F1 scores for prediction, averaged over 5 cross-validation folds. Results for LSTM
training are not reported as they took longer than 48 hours to converge
4. Results
4.1 Evaluation Approach
We evaluated how well we could distinguish normal windows of physiological signals from
pre-arrest ones. Given the predicted risk scores and using a threshold of 0.5, predictions
are labeled and classified as ’pre-arrest’ and ’normal’. To evaluate the performance of our
classification based on this threshold, we use the F1 score (defined in Eq. 6) that combines
information about the sensitivity and specificity of the prediction. Both Recall and Precision
values are valuable in our model, as Recall determines the number of pre-arrest windows
we were able to identify, and Precision shows the accuracy of our positive predictions.
F1 = 2Recall P r ecision
Recall +P recision (6)
4.2 Results for individual Models
Table 2 shows the F1 prediction scores for models trained on each of the physiological signals
independently. The values are evaluated using a 5-fold cross validation and the scores are
compared across 3 different network structures: 1) CNN , 2) LSTM trained on raw signals
and 3) CNN+LSTM structure that uses the latent representation of the signals as input to
the LSTM network as described above.
From Table 2 we observe that the LSTM model, encoding the time dependence of
observations from raw data, performs considerably worse than the other two structures.
We attribute this performance to the noise intrinsic to the physiological data, illustrating
that identifying robust features from the raw data is of great importance in training LSTM
networks. We further show that the performance of CNN+LSTM improves on the CNN
performance across 5 out of 6 signals. This is not unexpected, given that our CNN+LSTM
architecture takes advantage of both robust feature selection of CNN and time dependence
encoding of LSTM.
Further, we tested the performance of CNN+LSTM models trained for each of the
signals, on a previously unseen test cohort, consisting of 20 patients (with at least one
cardiac arrest each). Our results shown in Table 3 are comparable and even slightly better
than our cross validation performance in Table 2. We attribute the slight improvement to
10
HR Resp Pulse SpO2 ABP SDNN
Recall 0.769 0.692 0.714 0.444 0.857 0.909
Precision 0.90 0.642 0.8333 1.0 0.6 0.714
F1 score 0.833 0.666 0.769 0.6153 0.705 0.8
Table 3: Performance of the models on the unobserved test set that includes 20 individuals
with one incident of cardiac arrest
the fact that we had more samples available for training of the final model since we used
the whole training set and not folds.
4.3 Results for the Ensemble Model
We also looked into how the ensemble can benefit the prediction results. Using subjects from
our test cohort, in Table 4 we showed how single models perform on their own compared to
the ensemble. Moving windows of signals were selected from these patients’ physiological
recordings, and for every window, each model generated a risk score. Note that in addition
to instances of signals missing entirely, even for some signals, a number of windows did
not have any observations. As seen in the scores from single models, missing windows can
dramatically impact the performance. However, for all of the individuals that we have
observed (4 are captured in Table 4), the ensemble is able to improve on the performance
over models based on the individual measurements. An interesting observation is how some
models perform better than others for different subjects. This is mainly because of the fact
explained in previous sections that there is no single pathway that leads to a cardiac arrest.
The arrest can be caused by respiratory failure, cardiac failure, or many other reasons, and
different models may be able to capture these signs.
To evaluate the performance of the model on non-cardiac arrest patients, we have used
another cohort of 20 subjects who have been in the ICU for at least 24 hours, but had
never experienced a cardiac arrest. In the test setting, risk scores were generated on sliding
windows in time, every 10 minutes, for 24 hours, and similar to previous sections, scores
higher than 0.5 generated an alarm. The false positive rate of our classifier was 0.012 on
these samples.
In Figure 8, we show the predicted risk score as a function of the difference between
the right boundary of the sliding window and the event for a random patient from the test
set. Figure 8(a) plots the generated score from models based on a single type of signal,
and we can see that it is highly volatile and very sensitive to the quality of the signal in
that window of time. Figure 8(b) shows the ensemble risk predictions that are less volatile.
Looking into the trend of risk scores, signs of an arrest building up can be observed as early
as 30 minutes prior to the event.
5. Discussion and Related Work
In this work, we presented a general architecture for early prediction of cardiac arrest, from
high-resolution physiological signals that is clinically relevant at the point of care. Previous
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(a) Predicted risk score from individual models (b) Final predicted risk score from the ensemble
Figure 8: Risk score prediction for a sliding window in time
Subject Ensemble HR Resp Pulse SpO2 ABP SDNN
1 0.857 0.8 0.5 0.3636 0.6 0.75 0.66
2 0.66 0.5 0.33 0.54 0.6 missing 0.33
3 0.857 0.66 0.33 0.85 0.22 missing 0.3
4 0.666 0.66 0.6 1. 0.57 0.2 0.3636
Table 4: F1 scores of single models and the ensemble model for subjects from the test cohort
with missing values
work has shown promising results using recurrent structures for learning and prediction from
time series health signals (Lipton et al. (2016)). In their work, (Razavian et al. (2016)) used
LSTM to model physiological signal at a much lower resolution, for prediction of disease
onset from patient lab results. Their work showed that using recurrent neural structure to
model low resolution physiological signal leads to good performance. Choi et al. (2017) also
uses an extension of the RNN framework, called gated recurrent units (GRU), for predicting
heart failure from EHR data such as diagnostic codes and medication prescription. These
EHR measures are also recorded less frequently than our 5-sec resolution physiological
measures and over long periods of time, which distinguishes their prediction task from ours,
as they look into months of observations to identify individuals with high risk of heart
failure. In temporal signals with more frequent measurements, such as the ones presented
in this work, the performance of the LSTM can be sensitive to the high-frequency noise
that might be present in the signal which results in lower performance as is shown in Table
2 in the Results section of the paper.
Suresh et al. (2017) used physiological recordings from the ICU to predict different
clinical interventions. The authors have demonstrated that representing these signals with
discretized words (using a Z score measure) improves the performance of the LSTMs con-
siderably compared to training the LSTM on raw data. In general, training recurrent
structures on time series signal with high noise level, has a high risk for the network to
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only learn the naive solution Giles et al. (1999) and for the performance to be sensitive
to small fluctuations in input signal values. A number of work in speech recognition and
image processing, combine deep network structures with recurrent networks, in order to
take advantage of both the power of DNNs in reducing frequency variation and temporal
modeling in LSTMs (Sainath et al., 2015; Xu et al., 2016) as we have done in our paper.
In our work, we were able to improve the performance of LSTMs by using a latent rep-
resentation of the original signal as the input to the network. We use convolution networks
to extract a compact latent representation of the time series data, prior to using an LSTM
for the prediction task. This new structure not only improved prediction performance com-
pared to an LSTM network trained on raw recordings but also reduced the training time
considerably (by order 10). Looking into the results from Table 2, the ’CNN+LSTM’ model
outperforms LSTM on prediction for all physiological signals.
Figure 9: Evaluating the significance in the difference in F1 results for the Heart Rate model
using LSTM on raw signals and LSTM+CNN
In addition, using latent representation adds more stability to the model in most cases,
as can be inferred from standard deviation values reported in 2. We can also see that in
Figure 10, training LSTM on raw signals can be unstable and sensitive to variation in the
signal. Looking at Figure 10, we see sudden changes in the loss at regular intervals during
the training. These are epochs where we randomly select new windows of recordings. Using
the latent representation as inputs to the LSTM 10(b), gives the training process more
stability and robustness.
In this work, we were able to tackle two main challenges common to clinical data: 1)
sparsity and 2) complexity(Alistair E. W. Johnson, 2016). Our low-pass filtering method
handles short timescale discontinuities in temporal signals, while longer discontinuities were
addressed using linear interpolation. We showed that the ensemble method improves the
prediction performance by aggregating risk predictions from different models. Using a
mixture of experts makes the model robust to cases where certain physiological signals are
highly corrupted (due to issues with recording hardware) or missing entirely (not recorded
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(a) Training LSTM (b) Training LSTM+CNN
Figure 10: Comparing model performance during training for the LSTM model using ran
physiological data and LSTM+CNN structure that uses the latent representation of the
signal. Plots show the value of loss function on both test and training set.
at all). This means our model can generate a risk score for a window of recordings even
with a minimum of one existing signal, but as more recordings are available, the results will
be more confident and not sensitive to the noise likely present in a single recording.
A next step for this model will involve exploring how to deploy a model like this at the
point of care, as a predictive tool. As patients’ physiological signals are being recorded,
our model generates a cardiac arrest risk score for a sliding window in time. This score, is
independent of previous predictions. For calculating the personalized risk we will rely on the
output of the predictor model, as well as the trend of a patient’s clinical status during their
stay in the ICU. Ultimately, we expect our predictive model to be implemented in the ICU
and are exploring a translational framework. Translation will require better characterization
of the patient populations in whom the model performs particularly well as this cohort would
be the group who would most benefit from model deployment (i.e. maximization of true
positives). Implementation is a complex task for models that make frequent predictions
as an implementation plan has to define acceptable thresholds for false positives and true
negatives associated with model performance at the point of care. This is essential in order
to minimize the likelihood of compounding the well document problem of monitor alarm
fatigue amongst clinicians (Keller, 2012).
Approaches of the sort described here offer promising avenues for predictive rather
than reactive medicine provided in a highly personalized framework where clinical decision
support can be provided at the level of the individual patient.
References
Melissa Aczon, David Ledbetter, Long Van Ho, Alec M. Gunny, Albert Flynn, J. Williams,
and Randall C. Wetzel. Dynamic mortality risk predictions in pediatric critical care using
recurrent neural networks. CoRR, abs/1701.06675, 2017.
14
Shamim Nemati Katherine E. Niehaus David A. Clifton Gari D. Clifford Alistair E. W. John-
son, Mohammad M. Ghassemi. Machine learning and decision support in critical care.
In Proceedings of the IEEE, pages 444 – 466, 2016.
Edward Choi, Andy Schuetz, Walter F. Stewart, and Jimeng Sun. Using recurrent neural
network models for early detection of heart failure onset. In JAMIA, 2017.
Justin B. Dimick, Steven L. Chen, Paul A. Taheri, William G. Henderson, Shukri F. Khuri,
and Darrell A. Campbell. Hospital costs associated with surgical complications: A report
from the private-sector national surgical quality improvement program. Journal of the
American College of Surgeons, 199(4):531537, 2004. doi: 10.1016/j.jamcollsurg.2004.05.
276.
Marzyeh Ghassemi, Marco A. F. Pimentel, Tristan Naumann, Thomas Brennan, David A.
Clifton, Peter Szolovits, and Mengling Feng. A multivariate timeseries modeling approach
to severity of illness assessment and forecasting in icu with sparse, heterogeneous clinical
data. Proceedings of the ... AAAI Conference on Artificial Intelligence. AAAI Conference
on Artificial Intelligence, 2015:446–453, 2015.
C. Lee Giles, Steve Lawrence, A. C. Tsoi, and Ah Chung Tsoi. Noisy time series prediction
using a recurrent neural network and grammatical inference. 1999.
Katharine Henry, D. Hager, Peter J. Pronovost, and Suchi Saria. A targeted real-time
early warning score (trewscore) for septic shock. Science translational medicine, 7 299:
299ra122, 2015.
Sepp Hochreiter and J¨urgen Schmidhuber. Long short-term memory. Neural computation,
9 8:1735–80, 1997.
Katherine Heller Mark Sendak Nathan Brajer Meredith Clement Armando Bedoya
Cara OBrien Joseph Futoma, Sanjay Hariharan. An improved multi-output gaussian
process rnn with real-time validation for early sepsis detection. In Machine Learning for
Healthcare, 2017.
James P Keller. Clinical alarm hazards: a ”top ten” health technology safety concern.
Journal of electrocardiology, 45 6:588–91, 2012.
Zachary Chase Lipton, David C. Kale, Charles Elkan, and Randall C. Wetzel. Learning to
diagnose with lstm recurrent neural networks. ICLR, abs/1511.03677, 2016.
L. Ortmann, P. Prodhan, J. Gossett, S. Schexnayder, R. Berg, V. Nadkarni, and A. Bhutta.
Outcomes after in-hospital cardiac arrest in children with cardiac disease: A report from
get with the guidelines-resuscitation. Circulation, 124(21):23292337, 2011. doi: 10.1161/
circulationaha.110.013466.
Pranav Rajpurkar, Awni Y. Hannun, Masoumeh Haghpanahi, Codie Bourn, and Andrew Y.
Ng. Cardiologist-level arrhythmia detection with convolutional neural networks. CoRR,
abs/1707.01836, 2017.
15
Rajesh Ranganath, Adler J. Perotte, No´emie Elhadad, and David M. Blei. Deep survival
analysis. In MLHC, 2016.
Narges Razavian, Jake Marcus, and David Sontag. Multi-task prediction of disease onsets
from longitudinal lab tests. CoRR, abs/1608.00647, 2016.
Tara N. Sainath, Oriol Vinyals, Andrew W. Senior, and Hasim Sak. Convolutional, long
short-term memory, fully connected deep neural networks. 2015 IEEE International
Conference on Acoustics, Speech and Signal Processing (ICASSP), pages 4580–4584, 2015.
Claudio Sandroni, Jerry Nolan, Fabio Cavallaro, and Massimo Antonelli. In-hospital cardiac
arrest: incidence, prognosis and possible measures to improve survival. Intensive Care
Medicine, 33:237–245, 2006.
Hossein Soleimani, James Hensman, and Suchi Saria. Scalable joint models for reliable
uncertainty-aware event prediction. IEEE transactions on pattern analysis and machine
intelligence, 2017.
Harini Suresh, Nathan Hunt, Alistair Edward William Johnson, Leo Anthony Celi, Peter
Szolovits, and Marzyeh Ghassemi. Clinical intervention prediction and understanding
using deep networks. CoRR, abs/1705.08498, 2017.
Thierry Verplancke, Stijn Van Looy, Dominique D Benoit, Stijn Vansteelandt, Pieter
Depuydt, Filip De Turck, and Johan Decruyenaere. Support vector machine versus logis-
tic regression modeling for prediction of hospital mortality in critically ill patients with
haematological malignancies. BMC Medical Informatics and Decision Making, 8:56 – 56,
2008.
Jean-Louis Vincent. Critical care - where have we been and where are we going? In Critical
care, 2013.
Ben Wellner, Joan Grand, Elizabeth Canzone, Matt Coarr, Patrick W Brady, Jeffrey Sim-
mons, Eric S. Kirkendall, Nathan Dean, Monica Kleinman, and Peter Sylvester. Pre-
dicting unplanned transfers to the intensive care unit: A machine learning approach
leveraging diverse clinical elements. In JMIR medical informatics, 2017.
Zhenqi Xu, Shan Shan Li, and Weihong Deng. Learning temporal features using lstm-cnn
architecture for face anti-spoofing. IEEE Xplore, 2016.
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... In recent years, healthcare industry has been experiencing an increasing trend in the adoption of approaches like data-driven diagnostic methods [12,41], automated patient monitoring systems [21], and AI-assisted risk prediction models [2,19,43]. Advancements in the data collection technologies [14] and recent developments in fields like statistics and machine learning [30,45] are the major enabling factors for this shift from the traditional methods of healthcare practices. Hospitals collect and store hundreds of gigabytes of physiological data every day with the help of monitoring devices [39] attached to the patients in the intensive care units (ICUs) [7,15]. ...
... Moreover, statistical models are About to appear at ASPLOS '21, April 19-23, 2021, Virtual . shown to be capable of accurately predicting short and long term trends in the physiological data such as cardiac arrest [43] and sepsis risk [11]. Even though data analytics on physiological data shows great potential, there are several practical challenges that need to be addressed in order to unleash its full potential. ...
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Hospitals around the world collect massive amount of physiological data from their patients every day. Recently, there has been increasing research interest to subject this data into statistical analysis for gaining more insights and providing improved medical diagnoses. Enabling such advancements in healthcare require efficient data processing systems. In this paper, we show that currently available data processing solutions either fail to meet the performance requirements or lack simple and flexible programming interfaces. To address this problem, we propose LifeStream, a high performance stream processing engine for physiological data. LifeStream hits the sweet spot between ease of programming by providing a rich temporal query language support and performance by employing optimizations that exploit the constant frequency nature of physiological data. LifeStream demonstrates end-to-end performance up to $7.5\times$ higher than state-of-the-art streaming engines and $3.2\times$ than hand-optimized numerical libraries.
... PM has been revolutionized by the introduction of machine learning (ML) algorithms, which consider individual patient characteristics to predict specific outcomes or to highlight treatment plan modifications tailored to an individual patient's needs. For example, ML has been used for early prediction of cardiac arrests [8], onset of sepsis [9], and effectiveness of antibiotic prophylaxis in reflux [10]. The technology could be readily applied to pediatric urology patients with a history of UPJO by considering variables such as degree of HN, anteroposterior pelvic diameter (APD), patient weight [11], length of hospital stay post-surgery and operative time [4], and use them to help determine the risk of re-obstruction on a case-by-case basis. ...
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... Owing to the centrality of time series in the EHR, LSTMs have been by far the most popular model for predicting length of stay and have achieved state-of-the-art results [20,41,46]. This reflects the prominence of LSTMs in other clinical prediction tasks such as predicting in-hospital adverse events including cardiac arrest [54] and acute kidney injury [53], forecasting diagnoses and medication codes [6,31] and clinical interventions [51], missing-data imputation [4], and the classic task of mortality prediction [5,20,47]. The Transformer model [56] was originally designed for natural language processing (NLP), but it has marginally outperformed the LSTM on LoS [48]. ...
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The pressure of ever-increasing patient demand and budget restrictions make hospital bed management a daily challenge for clinical staff. Most critical is the efficient allocation of resource-heavy Intensive Care Unit (ICU) beds to the patients who need life support. Central to solving this problem is knowing for how long the current set of ICU patients are likely to stay in the unit. In this work, we propose a new deep learning model based on the combination of temporal convolution and pointwise (1x1) convolution, to solve the length of stay prediction task on the eICU critical care dataset. The model - which we refer to as Temporal Pointwise Convolution (TPC) - is specifically designed to mitigate for common challenges with Electronic Health Records, such as skewness, irregular sampling and missing data. In doing so, we have achieved significant performance benefits of 18-51% (metric dependent) over the commonly used Long-Short Term Memory (LSTM) network, and the multi-head self-attention network known as the Transformer.
... As machine learning algorithms have become on par or even superior to humans in a number of decision making problems (Rajpurkar et al., 2017;Silver et al., 2018), the idea that humans might be assisted by computer programs across a large variety of tasks has gained momentum. Already today, automated decision making systems are being used to predict cardiac arrests, credit scores, and recidivism (Tonekaboni et al., 2018;Board of Governors, 2007;Angwin et al., 2016). An emerging literature asks how humans, who often remain the final decision makers, can and should interact with such systems (Tonekaboni et al., 2019;Lucic et al., 2020). ...
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... The home environment is where many of these applications are used. Examples include virtual reality (VR) and augmented reality (AR) [18,29], activity detection for smart home [21,31] and health applications [20,30]. Such applications have also emerged in retail environments such as "cashierless" stores where users can checkout items by simply walking out with them and have a computer vision system detect and process the purchase [1], and AR smart mirrors that let users try on clothes, accessories or make-up. ...
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Purpose of review Machine learning (ML), a branch of artificial intelligence, is influencing all fields in medicine, with an abundance of work describing its application to adult practice. ML in pediatrics is distinctly unique with clinical, technical, and ethical nuances limiting the direct translation of ML tools developed for adults to pediatric populations. To our knowledge, no work has yet focused on outlining the unique considerations that need to be taken into account when designing and implementing ML in pediatrics. Recent findings The nature of varying developmental stages and the prominence of family-centered care lead to vastly different data-generating processes in pediatrics. Data heterogeneity and a lack of high-quality pediatric databases further complicate ML research. In order to address some of these nuances, we provide a common pipeline for clinicians and computer scientists to use as a foundation for structuring ML projects, and a framework for the translation of a developed model into clinical practice in pediatrics. Throughout these pathways, we also highlight ethical and legal considerations that must be taken into account when working with pediatric populations and data. Summary Here, we describe a comprehensive outline of special considerations required of ML in pediatrics from project ideation to implementation. We hope this review can serve as a high-level guideline for ML scientists and clinicians alike to identify applications in the pediatric setting, generate effective ML solutions, and subsequently deliver them to patients, families, and providers.
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Early diagnosis of critically ill patients depends on the attention and observation of medical staff about different variables, as vital signs, results of laboratory tests, among other. Seriously ill patients usually have changes in their vital signs before worsening. Monitoring these changes is important to anticipate the diagnosis in order to initiate patients’ care. Prognostic indexes play a fundamental role in this context since they allow to estimate the patients’ health status. Besides, the adoption of electronic health records improved the availability of data, which can be processed by machine learning techniques for information extraction to support clinical decisions. In this context, this work aims to create a computational model able to predict the deterioration of patients’ health status in such a way that it is possible to start the appropriate treatment as soon as possible. The model was developed based on Deep Learning technique, a Recurrent Neural Networks, the Long Short-Term Memory, for the prediction of patient’s vital signs and subsequent evaluation of the patient’s health status severity through Prognostic Indexes commonly used in the health area. Experiments showed that it is possible to predict vital signs with good precision (accuracy > 80%) and, consequently, predict the Prognostic Indexes in advance to treat the patients before deterioration. Predicting the patient’s vital signs for the future and use them for the Prognostic Index’ calculation allows clinical times to predict future severe diagnoses that would not be possible applying the current patient’s vital signs (50%–60% of cases would not be identified).
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Background: Early warning scores aid in the detection of pediatric clinical deteriorations but include limited data inputs, rarely include data trends over time, and have limited validation. Objective: Machine learning methods that make use of large numbers of predictor variables are now commonplace. This work examines how different types of predictor variables derived from the electronic health record affect the performance of predicting unplanned transfers to the intensive care unit (ICU) at three large children's hospitals. Methods: We trained separate models with data from three different institutions from 2011 through 2013 and evaluated models with 2014 data. Cases consisted of patients who transferred from the floor to the ICU and met one or more of 5 different priori defined criteria for suspected unplanned transfers. Controls were patients who were never transferred to the ICU. Predictor variables for the models were derived from vitals, labs, acuity scores, and nursing assessments. Classification models consisted of L1 and L2 regularized logistic regression and neural network models. We evaluated model performance over prediction horizons ranging from 1 to 16 hours. Results: Across the three institutions, the c-statistic values for our best models were 0.892 (95% CI 0.875-0.904), 0.902 (95% CI 0.880-0.923), and 0.899 (95% CI 0.879-0.919) for the task of identifying unplanned ICU transfer 6 hours before its occurrence and achieved 0.871 (95% CI 0.855-0.888), 0.872 (95% CI 0.850-0.895), and 0.850 (95% CI 0.825-0.875) for a prediction horizon of 16 hours. For our first model at 80% sensitivity, this resulted in a specificity of 80.5% (95% CI 77.4-83.7) and a positive predictive value of 5.2% (95% CI 4.5-6.2). Conclusions: Feature-rich models with many predictor variables allow for patient deterioration to be predicted accurately, even up to 16 hours in advance.
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Real-time prediction of clinical interventions remains a challenge within intensive care units (ICUs). This task is complicated by data sources that are noisy, sparse, heterogeneous and outcomes that are imbalanced. In this paper, we integrate data from all available ICU sources (vitals, labs, notes, demographics) and focus on learning rich representations of this data to predict onset and weaning of multiple invasive interventions. In particular, we compare both long short-term memory networks (LSTM) and convolutional neural networks (CNN) for prediction of five intervention tasks: invasive ventilation, non-invasive ventilation, vasopressors, colloid boluses, and crystalloid boluses. Our predictions are done in a forward-facing manner to enable "real-time" performance, and predictions are made with a six hour gap time to support clinically actionable planning. We achieve state-of-the-art results on our predictive tasks using deep architectures. We explore the use of feature occlusion to interpret LSTM models, and compare this to the interpretability gained from examining inputs that maximally activate CNN outputs. We show that our models are able to significantly outperform baselines in intervention prediction, and provide insight into model learning, which is crucial for the adoption of such models in practice.
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Viewing the trajectory of a patient as a dynamical system, a recurrent neural network was developed to learn the course of patient encounters in the Pediatric Intensive Care Unit (PICU) of a major tertiary care center. Data extracted from Electronic Medical Records (EMR) of about 12000 patients who were admitted to the PICU over a period of more than 10 years were leveraged. The RNN model ingests a sequence of measurements which include physiologic observations, laboratory results, administered drugs and interventions, and generates temporally dynamic predictions for in-ICU mortality at user-specified times. The RNN's ICU mortality predictions offer significant improvements over those from two clinically-used scores and static machine learning algorithms.
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Objective We explored whether use of deep learning to model temporal relations among events in electronic health records (EHRs) would improve model performance in predicting initial diagnosis of heart failure (HF) compared to conventional methods that ignore temporality. Materials and Methods Data were from a health system’s EHR on 3884 incident HF cases and 28 903 controls, identified as primary care patients, between May 16, 2000, and May 23, 2013. Recurrent neural network (RNN) models using gated recurrent units (GRUs) were adapted to detect relations among time-stamped events (eg, disease diagnosis, medication orders, procedure orders, etc.) with a 12- to 18-month observation window of cases and controls. Model performance metrics were compared to regularized logistic regression, neural network, support vector machine, and K-nearest neighbor classifier approaches. Results Using a 12-month observation window, the area under the curve (AUC) for the RNN model was 0.777, compared to AUCs for logistic regression (0.747), multilayer perceptron (MLP) with 1 hidden layer (0.765), support vector machine (SVM) (0.743), and K-nearest neighbor (KNN) (0.730). When using an 18-month observation window, the AUC for the RNN model increased to 0.883 and was significantly higher than the 0.834 AUC for the best of the baseline methods (MLP). Conclusion Deep learning models adapted to leverage temporal relations appear to improve performance of models for detection of incident heart failure with a short observation window of 12–18 months.
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Clinical medical data, especially in the intensive care unit (ICU), consists of multivariate time series of observations. For each patient visit (or episode), sensor data and lab test results are recorded in the patient's Electronic Health Record (EHR). While potentially containing a wealth of insights, the data is difficult to mine effectively, owing to varying length, irregular sampling and missing data. Recurrent Neural Networks (RNNs), particularly those using Long Short-Term Memory (LSTM) hidden units, are powerful and increasingly popular models for learning from sequence data. They adeptly model varying length sequences and capture long range dependencies. We present the first study to empirically evaluate the ability of LSTMs to recognize patterns in multivariate time series of clinical measurements. Specifically, we consider multilabel classification of diagnoses, training a model to classify 128 diagnoses given 13 frequently but irregularly sampled clinical measurements. First, we establish the effectiveness of a simple LSTM network for modeling clinical data. Then we demonstrate a straightforward and effective deep supervision strategy in which we replicate targets at each sequence step. Trained only on raw time series, our models outperforms several strong baselines on a wide variety of metrics, and nearly matches the performance of a multilayer perceptron trained on carefully hand-engineered features, establishing the usefulness of LSTMs for modeling medical data. The best LSTM model accurately classifies many diagnoses, including diabetic ketoacidosis (F1 score of .714), scoliosis (.677), and status asthmaticus (.632).
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Missing data and noisy observations pose significant challenges for reliably predicting events from irregularly sampled multivariate time series (longitudinal) data. Imputation methods, which are typically used for completing the data prior to event prediction, lack a principled mechanism to account for the uncertainty due to missingness. Alternatively, state-of-the-art joint modeling techniques can be used for jointly modeling the longitudinal and event data and compute event probabilities conditioned on the longitudinal observations. These approaches, however, make strong parametric assumptions and do not easily scale to multivariate signals with many observations. Our proposed approach consists of several key innovations. First, we develop a flexible and scalable joint model based upon sparse multiple-output Gaussian processes. Unlike state-of-the-art joint models, the proposed model can explain highly challenging structure including non-Gaussian noise while scaling to large data. Second, we derive an optimal policy for predicting events using the distribution of the event occurrence estimated by the joint model. The derived policy trades-off the cost of a delayed detection versus incorrect assessments and abstains from making decisions when the estimated event probability does not satisfy the derived confidence criteria. Experiments on a large dataset show that the proposed framework significantly outperforms state-of-the-art techniques in event prediction.
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We develop an algorithm which exceeds the performance of board certified cardiologists in detecting a wide range of heart arrhythmias from electrocardiograms recorded with a single-lead wearable monitor. We build a dataset with more than 500 times the number of unique patients than previously studied corpora. On this dataset, we train a 34-layer convolutional neural network which maps a sequence of ECG samples to a sequence of rhythm classes. Committees of board-certified cardiologists annotate a gold standard test set on which we compare the performance of our model to that of 6 other individual cardiologists. We exceed the average cardiologist performance in both recall (sensitivity) and precision (positive predictive value).
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Disparate areas of machine learning have benefited from models that can take raw data with little preprocessing as input and learn rich representations of that raw data in order to perform well on a given prediction task. We evaluate this approach in healthcare by using longitudinal measurements of lab tests, one of the more raw signals of a patient's health state widely available in clinical data, to predict disease onsets. In particular, we train a Long-Short Term Memory (LSTM) network and two novel convolutional neural networks for multi-task prediction of disease onset for 133 conditions based on 18 common lab tests measured over time in a cohort of 298K patients derived from 8 years of administrative claims data. We compare the neural networks to a logistic regression with several hand-engineered, clinically relevant features. We find that the representation-based learning approaches significantly outperform this baseline. We believe that our work suggests a new avenue of patient risk stratification based solely on lab results.