Abstract
Introduction
We applied machine learning (ML) to routine bloods, then to advanced haematology data
from a full blood count (rawFBC) plus biochemistry, to build predictive models for heart
failure, which were then used at population scale.
Methods
Routine blood results from 8,031 patients with heart failure, with equal number of controls,
were used in ML training and testing datasets (Split 80:20). NT-proBNP was used for
diagnostic comparison. rawFBC metadata was used in a dataset of 698 patients, 314 of
whom had heart failure, to train and test ML models (Split 70:30) from rawFBC, rawFBC plus
biochemistry and routine bloods. The rawFBC model was used to predict heart failure in a
validation dataset of 69,492 FBCs (2.3% heart failure prevalence).
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2
Results
Heart failure was predicted from rawFBC and biochemistry versus rawFBC AUROC 0.93
versus 0.91, 95% CI -0.023 to 0.048, P = 0.5, and predicted from routine bloods and NT-
proBNP, AUROC 0.87 versus 0.81, 95% CI 0.004 to 0.097, P = 0.03. In the validation cohort
heart failure was predicted from rawFBC with AUROC 0.83, 95% CI 0.83 to 0.84, P < 0.001,
sensitivity 75%, specificity 76%, PPV 7%, NPV 99.2% (Figure 2). Elevated NT-proBNP (
≥ 34
pmol/L) was predicted from rawFBC with AUROC 0.97, 95% CI 0.93 to 0.99, P < 0.0001.
Common predictive features included markers of erythropoiesis (red cell distribution width,
haemoglobin, haematocrit).
Conclusion
Heart failure can be predicted from routine bloods with accuracy equivalent to NT-proBNP.
Predictive features included markers of erythropoiesis, with therapeutic monitoring
implications.
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Introduction
The term machine learning describes a range of pattern recognition tools which hold
considerable promise in the field of health care diagnostics, prognostics and therapeutics.
Machine learning has been applied to a number of imaging and diagnostic modalities,
including retinal photography (1), electrocardiography (2, 3), and echocardiography (4) to
enable cardiovascular disease prediction. Deep learning, a form of machine learning,
directed at echocardiography cine images has been shown to be highly accurate at
identifying cardiac amyloidosis (4). Integrating both ECG and echocardiography artificial
intelligence models provides an even more accurate prediction of the presence of cardiac
disease (5, 6). The greatest opportunity for the use of machine learning in healthcare is in its
application to low cost, readily available data which has imperceptible patterns hidden within
it, which answer unmet clinical needs in healthcare.
In heart failure several machine learning studies have been performed, using data extracted
from electronic healthcare records (7-9). Heart failure prognosis has been predicted with a
high degree of accuracy using machine learning applied to medical claims data (10). Whilst
intriguing, this method is dependent on adequate labelling of ICD10 case data,
completeness of clinical records and clinician behaviour, which may not be translatable to
other clinical systems or other countries (11). Whilst the potential for this type of bias is
considerable with black-box uninterpretable methods such as deep learning, there are
several machine learning methods that provide transparency and explainability but with
equivalent levels of accuracy.
Although laboratory testing is one of the most ubiquitous, high volume and low cost forms of
diagnostic information there is only a recently emerging literature on the use of machine
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learning applied to lab data (12). One of the most highly evolved tools available, based on
machine learning applied to longitudinal full blood count data is the ColonFlag™ Test,
designed to flag the presence of colorectal cancer (13). This predictive test has gone from a
research discovery to a clinically implemented electronic decision support tool (14). Many
studies have demonstrated the value of laboratory data to make not only an accurate
prediction of the presence of heart failure but also its prognosis (9, 10, 15).
Unsupervised machine learning, a method applied to unlabelled data to cluster similar
patient phenotypes, has been used to identify subtypes of both heart failure to preserved
ejection fraction (HFpEF) and heart failure with reduced ejection fraction (HFrEF) (16, 17).
Unsupervised machine learning holds the promise of personalising patient care, through the
use of targeted therapeutics (18, 19). This work has demonstrated the necessity of not only
including a wide breadth of multimodal data, but also standardised inputs, as again this field
is suffering from a reproducibility crisis (20). As occurred with genome wide association
studies the field of big data in medicine is crying out for a global pooled consortia to ensure
machine learning in health care is reproducible and translatable.
We and others have similarly shown the ability for machine learning applied to haematology
data to predict the presence of heart failure and biological age (21, 22). The study described
here had two parts. Firstly, we set out to integrate haematology and biochemistry data to
show the incremental value of adding other sources of laboratory information in the
discrimination of patients with heart failure. We then added further clinical metadata, such as
conventional ECG parameters and echocardiography measurements, into a more complete
holistic picture of patient phenotype. This global metadata was then used to validate
previously described HFpEF phenotypes. In the second part we used more granular
advanced haematology data to show an ability to identify heart failure at presentation to
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hospital and how this could be applied across an entire health care system. Lastly, we
demonstrate that explainability of machine learning models, a priori, points to potential uses
of this method, not only in diagnosis and prognosis, but also therapeutic interventions and
monitoring.
Methods
Hypothesis
That congestive heart failure (either heart failure with reduced ejection fraction (HFrEF), and
heart failure with preserved ejection fraction (HFpEF)) can be predicted from either routine
blood investigations e.g. full blood count (FBC) and biochemistry or raw haematology full
blood count (rawFBC) data extracted from a haematology analyser/flow cytometer.
Data collection
This study occurred in two parts. The first part involved the form of a retrospective
observational study using data collected as part of routine clinical care from 2008 until 2018
(Extracting Global Clinical Metadata from Large Patient DatabaSEs (ECLIPSE)). ECLIPSE
included extensive patient metadata inclusive of demographics, electrocardiography
conventional parameters, laboratory data, inpatient e-prescribing, coronary catheterisation
disease coding, CT angiography report extracts, echocardiography measurement data and
structured reporting, ICD10 coding, past and future admission and mortality coding.
Laboratory data was obtained at a time proximate to the first echocardiogram being
performed on a patient with a presumed cardiac diagnosis. This included patients who were
both inpatients and in outpatient ambulatory care. Patients with heart failure were identified
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by any ICD10 coding for heart failure. A matched number of randomly selected patients
without heart failure were taken from the ECLIPSE database.
The second part was also a retrospective observational study, (Pattern Recognition Of
Global Responses and Monitoring (PROGRAM), though instead this study used advanced
haematology raw data as well as biochemistry data. Haematology raw data came from full
blood counts (rawFBC) collected between July 1
st 2019 and June 8th 2020, some of which
occurred during the COVID-19 pandemic. Machine learning (ML) predictions for COVID-19,
other infectious diseases and heart failure have been presented previously (22). Apart from
COVID-19 these predictive models were developed using the first rawFBC performed during
an admission as input data and the primary ICD10 diagnosis as the objective. In this paper
we present new ML models for heart failure with the addition of biochemistry data.
Comparisons were then possible between each dataset, using each of the predictive
models. In addition, we also provide further validation of the same predictive haematology
ML model based on an independent dataset of all-comers, undergoing serial FBCs
throughout a hospitalisation (Figure 1).
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Figure 1. Machine learning application to ECLIPSE and PROGRAM
Ethics approval was obtained locally from the Research and Knowledge Centre (RM13732
for the ECLIPSE study for standard haematology and biochemistry data), and from the
regional HDEC ethics committee (20/CEN/162 for the PROGRAM study for haematology
raw data). Informed consent was waived, as the research was observational and used
secondary data.
Advanced haematology data
Whole blood collected in EDTA tubes were analysed using Sysmex XN-1000 and XN-3000
haematology analysers. The XN-3000 is made up of two XN-1000 modules and produces
the same haematology parameters. Advanced haematology data was exported from the
Information Process Unit (IPU) connected to both a Sysmex XN-1000 at Waitakere hospital
and XN-3000 at North shore hospital. This included data from both inpatients and
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outpatients within Waitemata District Health Board’s (WDHB) catchment. Data was
downloaded from the IPU in a comma separated value (CSV) data format, containing both
basic and advanced haematology parameters.
The Sysmex XN instrument uses fluorescence flow cytometry, impedance, hydrodynamic
focussing, SLS for haemoglobin and is capable of processing up to 100 samples/hour using
88 µL sample volume. Up to 38 clinical parameters and 50 research parameters, or
derivatives thereof are produced with up to 23 scattergrams and 4 histograms. The
instrument stores up to 100,000 records in a buffer. A glossary of haematology parameter
acronyms and explanations are available in a previously published supplemental (22).
Biochemistry data
Standard biochemical laboratory data from a Siemens Vista 1500 biochemistry analyser,
software version is 3.9_11.6-3t/1450, and sent to the laboratory information system (LIS)
Éclair and both entered into a national database (Testsafe) and hospital SQL data
warehouse. Biochemistry data was extracted from a SQL database using a Python script
and matched to either conventional FBC data or advanced haematology data by its closest
time point. Biochemistry data at the closest possible time point was matched to either the
standard FBC or advanced rawFBC data however as this data was collected as part of
clinical care there was significant degree of sparseness/missingness compared to the FBC
data. Machine learning models were developed inclusive and exclusive of missing numerics,
and with additional clinical data to demonstrate the utility of adding orthogonal multimodal
data. NT-proBNP (N-Terminal pro B-type Natriuretic Peptide) was measured using a
Siemens Dimension Vista assay and linked by closest time point to data in ECLIPSE. In
PROGRAM, NT-proBNP could be linked to a patient encounter but not by blood test date. A
ML model, using advanced haematology data, was trained on an abnormal NT-proBNP (
≥
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34 pmol/L) to provide corroboration of the features used to predict the coded ICD10 heart
failure endpoint.
The ECLIPSE heart failure model was also validated in the PROGRAM test dataset for
comparison. The PROGRAM model was validated in an independent dataset inclusive of
rawFBC values taken throughout multiple hospitalisations.
Outcomes
ICD10 primary diagnoses, age, ethnicity and sex were obtained from specific hospital
encounter numbers using a SQL query along with mortality data. Congestive heart failure
was defined as an ICD10 code within a patient’s entire list of diagnoses. A list of specific
ICD10 codes of interest included I509, I500, I130, I110, I132, I42, I25. This also included
readmission outcome data. Heart failure with reduced ejection fraction (HFrEF) was defined
as an ejection fraction by Simpson biplane < 50% and heart failure with preserved ejection
fraction (HFpEF)
≥ 50%. Heart failure machine learning and biological age probability scores
(22), were generated for patients in the PROGRAM validation group where there were ≥ two
serial blood tests within the same admission encounter. Scores from these two time points
(last and first within an admission and discharge) were compared for changes related to
disease progression and therapeutic response.
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Statistics and machine learning
Univariate analysis was performed using the student t-test for continuous parametric
variables and receiver-operating characteristic curve (ROC) analysis was used to assess
performance of diagnostic biomarkers by c-statistic. Z scores were used for proportional
values of missingness. All tests were two-tailed and P<0.05 deemed statistically significant,
except where Bonferroni correction for multiplicity was applied. Medcalc software version
16.8.4 was used to analyse the data. BigML https://bigml.com/
was used for applying
machine learning models, using decision trees, and ensembles, logistic regression and deep
neural networks with transparency
(https://static.bigml.com/pdf/BigML_Classification_and_Regression.pdf?ver=c306567#page=
250). Model development involved splitting data 80:20 into training and test sets. OptiML, an
automated BigML optimization process for model selection and parametrization was used to
find the best supervised model for sex classification and predicting age using regression.
OptiML uses Bayesian parameter optimization and Mote Carlo cross-validation
(https://static.bigml.com/pdf/BigML_OptiML.pdf?ver=c306567). An interactive network was
generated to compare the rawFBC metadata using a Javascript D3 Force layout and a
Pearson correlation matrix. K-nearest neighbour clustering was used for unsupervised
machine learning. Uniform Manifold Approximation and Projection (UMAP) was used to
visualise clusters in the advanced haematology and biochemistry data from PROGRAM.
Data availability
The materials, data, code, and associated protocols are available to readers with application
to the corresponding author and Waitemata Privacy, Security and Governance (PSGG)
group with a limited data sharing agreement. BigML models will be shared without
limitations.
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Results
Machine learning applied to routine laboratory data
ECLIPSE includes data from 75,619 patients who had undergone an echocardiogram.
Baseline patient characteristics are in Table 1 and clinical results in Table 2. In patients
without heart failure (n = 67,588) the mean (SD) interval between the echocardiogram and
the most recent haemoglobin was – 60 (+/-342) days, and between the haemoglobin and
creatinine was – 2 (+/-313) days. In patients with heart failure (n = 8,031) the mean (SD)
interval between the echocardiogram and the most recent haemoglobin was – 7 (+/- 77)
days, and between the haemoglobin and creatinine was + 1 (+/- 72 days). There were 8,031
controls.
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Table 1. ECLIPSE baseline patient characteristics for heart failure and control groups. Total
number of patients with each variable displayed, as well as proportion to total number of
patients (%). Age displayed as mean (SD).
Hear t failu re n = 803 1 Cont rol s n = 67, 588 P Valu e
Gend er Mal e (%) 4 ,368 (54) 21,66 7 (32) < 0.0001
Age mean (S D) 76 (13) 60 (19) < 0.0001
Hyperte nsi on (%) 5 ,363 (67) 11,99 6 (18) < 0.0001
Ty pe II di abe te s (% ) 2 ,450 (31) 5,24 0 (8) < 0.0001
Fa mily h is to ry of C A D (% ) 93 (1) 550 (1) 0.7 5
Chronic r enal fa ilur e (%) 2 ,617 (33) 2,42 0 (4) < 0.0001
Dyslipid a emia (% ) 1 ,807 (23) 4,21 4 (6) < 0.0001
ACE i nhibit or (%) 5 ,568 (69) 12,60 0 (19) < 0.0001
Beta b l ocke r (%) 6 ,142 (76) 14,80 5 (22) < 0.0001
Cal cium c hanne l bloc ke r (%) 4 ,755 (59) 10,00 0 (15) < 0.0001
Statin ( % ) 5 ,469 (68) 16,32 3 (24) 50% (% ) 1 ,280 (16) 3,93 0 (6) 50% (%) 1 ,528 (19) 4,82 4 (7) 50% (%) 1 ,201 (15) 3,47 5 (5) < 0.0001
Coron ary artery bypa s s s u rge r y (%) 82 (1) 118 (0.1) < 0.0001
Prior a tri al fi br i l lati on (% ) 3 ,974 (49) 5,35 9 (8) < 0.0001
Future a t ri a l fibr illati on (%) 521 (6) 855 (1) < 0.0001
Prior myo cardi al inf arctio n (% ) 2 ,637 (33) 6,16 4 (9) < 0.0001
Future my oca r di a l inf arc t i o n (%) 339 (4) 340 (1) < 0.0001
Morta lity (% ) 4 ,024 (50) 4,60 1 (7) < 0.0001
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Table 2. ECLIPSE patient clinical results for both heart failure and control groups. Mean
(SD) displayed for each variable and corresponding student t-test P Values.
Hear t fail u r e n = 80 31 Cont rol s n = 67 ,588 P Valu e
Albumin (g/L) 33. 9 (5.9 ) 37. 8 (5) < 0.0001
ALP (U/L) 105.9 (72 ) 83. 9 (66) < 0.0001
ALT (U /L) 38 (138) 30. 7 (73) < 0.0001
AST (U /L ) 42.3 (150 ) 30.8 (116) < 0.0001
Bili r ubi n (umol /L) 13.3 (13 ) 10. 6 (12) < 0.0001
Cal cium a lbumin a dju sted (mmol/L ) 2.3 (0.1 ) 2.3 (0.1 ) < 0.0001
Chole ster ol: HDL r atio 3.6 (1) 3.8 (1.2 ) < 0.0001
Chole ster ol (mmol/L ) 4.1 (1.2 ) 4. 6 (1) < 0.0001
Cre atinin e (umol /L) 125.3 (10 0) 99.4 (104) < 0.0001
CRP (mg / L ) 41.1 (53 ) 42. 9 (59) 0. 04
eGFR (ml / min /1.73 m2) 53.1 (20 ) 64. 8 (19) < 0.0001
Fe r ri tin (ug / L ) 230 (523) 205. 2 (438) < 0.0001
Fol ate (nmol /L) 21.6 (10 ) 22. 1 (10) 0.0 01
GG T (U/L) 76.5 (105 ) 52. 8 (92) < 0.0001
Gluco se (mmo l / L ) 7.2 (3) 6. 5 (3) < 0.0001
Haema toc rit (L /L) 0.4 (0.1 ) 0.4 (0.1 ) < 0.0001
Haemog lobin (g /L ) 125.6 (20 ) 134 .7 (18) < 0.0001
HbA1c (mm ol/ mo l ) 45.6 (13 ) 42. 9 (12) < 0.0001
Iron (umo l/L) 10. 9 (8.3 ) 14 (7) < 0.0001
LDL (mmol/L) 2.1 (8.3 ) 2. 5 (1) < 0.000 1
Magn e s iu m (mmol/L ) 0.8 (0.1 ) 0.8 (0.1 0.00 02
NT-pr oBNP ( p mol / L ) 8 91.7 (106 7) 266. 7 (600) < 0.0001
Pla te le t s (x 10E9) 240.9 (97 ) 255 .7 (87) < 0.0001
Pot as s i um (mmol/L) 4.1 (0.5 ) 4.3 (0.5 ) < 0.0001
Red c ell di s tri bution w id th (%) 15.1 (2) 14 (2) < 0.000 1
Sod ium (mmol/L) 13 8 (4) 139 .4 (3) < 0.0001
T4 ( p mol/ L ) 15.7 (3) 14. 4 (3) < 0.0001
Trigl yce r ide s (mmo l/ L ) 1.5 (1) 1. 7 (1) < 0.0001
Troponin I ( ng/L) 973 (4,44 2) 9 44.7 (4,5 13) 0. 6
TS H (mU/L) 2.6 (3) 2. 1 (3) < 0.0001
Ur e a (mg/dL) 10.4 (8) 7. 3 (5) < 0.0001
WBC (x10 E9) 8.4 (4) 7. 8 (5) < 0.0001
PR i nte r v al (m s) 114.4 (93 ) 149 .2 (66) < 0.0001
LV ejec t io n fr a c tion (% ) 40 (14) 53. 6 (11) < 0.0001
ECG he a r t r at e (bpm ) 81.5 (23 ) 77. 6 (22) < 0.0001
P w ave axis (d eg r e e s) 132.7 (29 7) 61.2 (141) < 0.000 1
QRS du rati on (m s) 113.2 (29 ) 100 .3 (21) < 0.0001
QT int erval (m s ) 402.7 (54 ) 397 .5 (48) < 0.0001
QTc i nte r v al (m s) 446.2 (46 ) 436 .5 (40) < 0.0001
T w ave axis (deg r e e s ) 69.4 (74 ) 51. 3 (55) < 0.0001
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Only 3,644 (23%) patients of the total 16,062 had an ejection fraction measured by Simpson
biplane (EF bp), 2,058 (26%) within the heart failure group. Of those with heart failure and a
measured Simpsons ejection fraction the EF bp was < 50% in 1,550 (75%), and < 40% in
1,072 (52%). Despite having no ICD10 code for heart failure within the control group n = 535
(7%) had an EF bp < 50%. These patients were retained within the control group with the
presumption that there had been no hospital admission with congestive heart failure.
ECLIPSE included NT-proBNP results for 4,485 patients, 3,913 (56%) of the heart failure
group and 572 (7%) of the group without heart failure. Similarly high sensitivity troponin I
values were available for 13,081 patients, 7,768 (96%) with heart failure and 5,313 (66%)
without heart failure.
12,849 individual patient laboratory results were available for training and 3,213 for testing
ML models. A deep learning model applied to just age + conventional bloods including
missing numerics had the highest accuracy predicting heart failure (Table 3), with highest
ranked features being haematocrit (32%), age (24%), red cell distribution width (RDW)
(18%), T4 thyroxine (4%) and troponin I (4%). However incremental gains were
demonstrated with the addition of further demographics (ethnicity), orthogonal information
(conventional ECG parameters: PR interval, QRS duration and T wave axis) and longer
training time. Model performance reduced substantially with the exclusion of missing
numerics, suggesting a possible role of bias. Three (14%) of the 22 laboratory variables had
statistically greater proportions of missingness in the control group (red cell distribution
width, cholesterol HDL ratio and HbA1c) compared to those with heart failure. Various
machine learning methods e.g. decision tree ensemble, deep learning and logistic
regression provided the most accurate model, based on phi score and this was not limited to
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just deep learning. Even in the absence of key variables, e.g. RDW, reasonable predictions
were still possible.
Table 3. Accuracy of ECLIPSE machine learning models
Machine learning models AUC SE a 95% CI b
(1) Conventional bloods + ethnicity + ECG + long train time 0.929 0.00436 0.919 to 0.938
(2) Conventional bloods + ethnicity + ECG + short train time 0.925 0.00451 0.915 to 0.934
(3) Conventional bloods, including missing numerics 0.921 0.00466 0.911 to 0.930
(4) Conventional bloods + ethnicity, excluding missing numerics 0.870 0.00612 0.858 to 0.882
(5) Conventional bloods, excluding missing numerics 0.851 0.00662 0.838 to 0.863
a DeLong et al., 1988
b Binomial exact
Figure 2. Receiver operator curves comparing ECLIPSE models
Conventional blood ML model accuracy was compared with NT-proBNP with comparable
results, though the ML model including missing numerics exceeded NT-proBNP’s accuracy
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in identifying heart failure, AUROC 0.87 versus 0.81, 95% CI 0.004 to 0.0974 P = 0.03
(Figure 3).
Figure 3. Receiver operator curves comparing ECLIPSE models with NT-proBNP
678 (21%) of patients in the test set had EF bp measured, 294 with HfpEF and 383 with
HfrEF. Applying both the conventional bloods ML models, including and excluding missing
numerics, demonstrated similar accuracy for identifying both HfrEF AUROC 0.88 to 0.79
(95% CI 0.05 to 0.13, P < 0.0001) and HfpEF AUROC 0.91 to 0.83 (95% CI 0.04 to 0.11, P =
0.0001). Including NT-proBNP in the HfpEF ML model increased the AUROC to 0.93, with
sensitivity 86% and specificity 85%, 95% CI 0.89 to 0.95, P < 0.0001. Using the entire
ECLIPSE dataset, both past and future HfpEF (n = 416) compared to controls (n = 6,800
controls; EF bp
≥ 50%, no heart failure) was predicted with AUROC 0.997, 95% CI 0.992 to
0.999, P < 0.0001. Highest ranked features were two chamber stroke volume (SV) (17%),
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HbA1c (5%), left ventricular end diastolic dimension indexed to height (4%), Teicholz SV
(4%), potassium (4%). Other predictive models with similar accuracy included ejection
fraction, QTc, and other variables. Echocardiography variables dominated the highest
ranked features for HfpEF prediction in most models.
k-nearest neighbour unsupervised machine learning was applied to conventional bloods,
ECG and echocardiography parameters in 400 patients with HfpEF. Three phenoclusters
(Figure 4 and Table 4) were identified with variable longitudinal mortality outcomes,
replicating work by Shah et al and others (16, 17).
Figure 4. Kaplan Meier plot of HfpEF clusters
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Table 4. Cluster phenotype patterns
Clu ste r 1 La r g er hea rt Highe r S V Obe se , le s s H TN, dy s l ip id, y ounger, l ow e st NT-p roBN P
Clu ste r 2 Sma ller hea r t L ower SV L ong PR i nt e r v al
Clu ste r 3 Dia stol ic dysfun ction L arges t LA Older , renal failu re, L ow ra te T 2DM, longes t p w ave
Machine learning applied to advanced haematology and biochemistry data
314 heart failure patients and 384 controls were used for training and testing machine
learning models using age + advanced haematology (rawFBC) and conventional
biochemistry data. Incremental gains were demonstrated with both the use of advanced
haematology data and biochemistry data Table 4, compared to the ECLIPSE model (95% CI
0.03 to 0.15, P = 0.002) Figure 5. Although there appeared to be some gain adding
biochemistry data to advanced haematology this comparison was not statistically significant,
possibly due to underpowering. Highest ranked features in the ML model including advanced
haematology data were age (18%), RDW-SD(fL) (10%), RDW-CV(%) (7%), MacroR(%) (5%)
and NEUT#(10^9/L) (4%) demonstrating similar features to ECLIPSE, e.g. RDW, and
pathophysiological features of heart failure consistent with prior literature. Highest ranked
features in the combined advanced haematology and biochemistry model included creatinine
(9%) but highest ranked features were still dominated by haematology variables.
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Table 4. Accuracy of PROGRAM machine learning models
Variable AUC SE a 95% CI b
(1) Advanced haematology + biochemistry 0.925 0.0234 0.868 to 0.963
(2) Advanced haematology 0.913 0.0233 0.853 to 0.954
(3) Conventional bloods, including missing numerics 0.832 0.0366 0.759 to 0.889
a DeLong et al., 1988
b Binomial exact
Figure 5. Receiver operator curves for PROGRAM and validation of ECLIPSE n = 140
In the PROGRAM validation set there were 69,492 FBCs, 2.3% of which had an ICD10
primary diagnosis of heart failure. Heart failure was predicted with a sensitivity 75%,
specificity 76% (Figure 5), positive predictive value 7%, negative predictive value 99.2%
(AUROC 0.83, 95% CI 0.83 to 0.84, P < 0.001) in validation (Figure 6).
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Figure 6. Validation of PROGRAM, machine learning heart failure model
1,028 rawFBC results had an associated NT-proBNP ≥ 34 pmol/L during the same hospital
encounter 452 (44%). A decision tree ensemble predicted an NT-proBNP ≥ 34 pmol/L with
AUROC 0.97 (95% CI 0.93 to 0.99, P < 0.0001). Red blood cell agglutination (9%),
haemoglobin (g/L) (8%), haematocrit (7%), RDW-CV(%) (6%), haemoglobin defect (4%)
were the highest ranked features consistent with models predicting ICD10 codes for heart
failure.
Network analysis
Visualisations of the advanced haematology and biochemistry data from PROGRAM is
available as an interactive network here https://projects.interacta.io/theranostics-covid/
.
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21
UMAP clustering of combined rawFBC and biochemistry data showed distinct separation of
patients with heart failure with controls (Figure 7).
Figure 7. UMAP clustering of PROGRAM data
Global and Individual patient responses to treatment
We calculated a heart failure disease probability score and biological age score for each
blood result to compare an admission and discharge result. Although there was considerable
individual heterogeneity in haematology heart failure patterns over time, the mean global
difference between these two time points was not statistically significant (Figure 8a and 8b).
The individual response to dapagliflozin in a single patient was demonstrated using only two
haematology parameters (Figure 9).
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Figure 8a and 8b. Machine learning scores for biological age and heart failure over time for
individual patients, during single hospitalisation
Mac hine le a rning bi ologic al a ge scor e s (2 2) ove r t i me , during s ing le ho spit ali sati o n.
0
10
20
30
40
50
60
70
80
90
10 0
A d m i ssi o n D i sc h a r g e
Biological Age Scores
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Mac hine le a rning prob a bility o f h ear t fa il ure dia gno si s over time, d ur i ng single ho s pi ta li s a ti on
0%
10 %
20 %
30 %
40 %
50 %
60 %
70 %
80 %
90 %
10 0%
F irs t He a rt Fai l ure La s t He art F ai lu re
Heart Failure Probability
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Figure 9. Individual response to dapagliflozin, started at timepoint 2.
Discussion
In these studies (ECLIPSE and PROGAM) we have demonstrated it is possible to use
machine learning to predict the presence of heart failure from both conventional bloods and
advanced haematology data. We used an automated Cloud-based machine learning,
software as a service platform, which required no coding experience. The machine learning
Methods
varied between decision tree ensemble, logistic regression and deep learning
however, no particular method exceeded others in predictive accuracy. What was apparent
is that by increasing compute time and the addition of orthogonal data (e.g. ethnicity and
ECG data) incrementally improved model predictions, though with diminishing returns.
Although the machine learning models were transparent and explainable, with ranked
identifiable features, these did not aid in making causal inferences with each predictive
model. For instance, although ethnicity provided incremental value in predictions it cannot be
assumed that specific at risk ethnicities carry a higher risk due to genetic variants (such as
titin truncations, which increase the risk of heart failure) or if socioeconomic confounding is
having an influence (23). Another concern with including non-biologically causal predictive
features is the risk of dataset shift and bias (24).
12 0
13 0
14 0
15 0
16 0
17 0
1234
Haemoglobin (g/L)
0.3 5
0.4
0.4 5
0.5
0.5 5
1 234
Haematocrit (Ratio)
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25
A note of caution must be made in placing excessive confidence in ECLIPSE predictions
combining haematology and biochemistry, for the reason that whilst some bloods are
ordered almost universally, such as an FBC, others e.g. iron studies are only ordered on the
basis of a preconceived diagnostic notion or concurrent condition. Therefore, the presence
or absence of data in itself represents a source of self-fulfilling bias (25, 26). Furthermore,
health care data collected in a real-world setting is plagued with not only missing data but
also time variance, meaning training data may not always be collected prior to the
confirmation of a diagnosis. These encoded hidden biases in the data could easily have
skewed test results into demonstrating predictions of much higher accuracy, as possibly
demonstrated with the removal of missing numerics from the predictive model. The control
group from which the ECLIPSE data was randomly selected had a far higher frequency of
missing data, possibly due to being ambulatory patients rather than inpatients. However
even after accounting for this bias, by excluding missing numerics, the model still performed
well on an independent inpatient dataset within PROGRAM and when compared with NT-
proBNP within a subset of the ECLIPSE patients.
In PROGRAM, machine learning models discriminated heart failure from both rawFBC and
rawFBC plus biochemistry with similar accuracy to the ECLIPSE models. The results were
underpowered to demonstrate improved accuracy with the addition of biochemistry data,
however the results from just the rawFBC are interesting for a number of reasons. Firstly, the
ability to discriminate heart failure with an approximate AUROC 0.83 has now been validated
internally twice (22) and independently (21). Secondly, since the data exported from the
Sysmex analyser is complete, for each sample, missing values and bias is minimised.
Thirdly, Sysmex haematology analysers are in widespread use, in over 85% of clinical
laboratories, and produce highly consistent results independent of geographic location etc.
Others have indicated that machine learning predictions, based on haematology data, could
be used for adjudicating endpoints for more encompassing machine learning applications, or
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26
by institutions or payers to monitor population level data (21). We would concur with that,
with the addition that such technology could be useful at both an individual level in predicting
risk (27), particularly in resource constrained settings but also a population scale for the
surveillance and monitoring of not only noncommunicable cardiovascular disease but also
infectious diseases and pandemics (22).
Two factors increase the confidence in the validity and clinical utility of both the results from
PROGRAM and ECLIPSE. Firstly, the data in PROGRAM was collected from a single
snapshot in time at the first point of contact in an admission, unlike ECLIPSE. Further work
will be required to demonstrate incremental diagnostic gains from the use of machine
learning predictions applied to haematology data, however since heart failure, particularly
HFpEF, is often undifferentiated at presentation the likelihood of this adding value either in
the emergency department or primary care is high. Secondly, when interrogating the highest
ranked features of the predictive models in both ECLIPSE and PROGRAM some
commonalities are clearly seen. Markers of erythropoiesis, such as red cell distribution width
(RDW), haemoglobin concentration and haematocrit, clearly dominate the statistical models,
explaining why haematology data on its own is capable of making fairly accurate predictions.
Whilst anaemia in heart failure has been well documented, its causes are multifactorial in
part due to co-existent renal disease, iron storage and transport and failure of erythropoietin
production (28). Similarly altered haematocrit, commonly seen in heart failure and presumed
due to haemodilution, has been identified as both a predictor (29) and risk factor in heart
failure (30). Paradoxically in a population setting a higher haematocrit is associated with an
increased risk of heart failure (29). This may be related to causal ABO genetic variants,
themselves associated with lipid traits identified through genome wide association studies
(GWAS) of haematological quantitative traits (31-33). Therapeutic targeting of erythropoiesis
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in heart failure has had mixed results, though not for iron replacement therapy (28, 34).
Recently SGLT2 inhibitors have been shown to have significant benefits in both HFrEF and
HFpEF (35), with effects predicted by erythropoietic responses and their ability to alleviate
cellular stress (36, 37). These effects seem to operate at the level of aging related pathways
such as SIRT1 and AMPK (38, 39) possibly indicating a role beyond heart failure and
diabetes. Abnormal red cell distribution width (RDW), a marker of loss of control of
homeostasis otherwise known as anisocytosis, was identified here as a key feature in heart
failure prediction models. RDW has been well described as a predictor of heart failure
outcomes (40) and a GWAS has similarly demonstrated its ability to predict a range of
negative health outcomes is similarly influenced by fundamental pathways of aging (41). We
and others have previously demonstrated RDW’s role in the prediction of biological age
using ML applied to blood results (22, 42). Although we were not able to show serial
changes in either the prediction scores for heart failure or biological age at a population
level, this does not rule out the possibility of these being useful at an individual level
particularly in monitoring therapeutic responses to heart failure therapies, such as SGLT2
inhibitors (Figures 8 and 9). We have previously shown an ability to monitor LV systolic
dysfunction over time, using personalised trajectories, using ML applied to ECG (2), and
integrated this with multiomics, to provide a more holistic overview of HFrEF (3).
With the expanded global metadata also available in ECLIPSE we have shown added value
of incorporating heterogenous clinical data into machine learning models to predict certain
diagnoses, such as HFpEF with higher accuracy. Although ML applied to conventional
bloods predicted both HFrEF and HFpEF with reasonable accuracy, blanket application of
such a tool at population scale would result in a larger number of false positives, more so
than true positives due to the low prevalence of heart failure (2.3%) in hospital blood results,
shown in our validation set of 69,492 FBCs. Targeting this technology in a sequential
manner, possibly starting with a standard clinical history but then adding in more costly
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28
investigations such as NT-proBNP, electrocardiography and echocardiography could result
in better use of resources, as recently shown by a Mayo group investigating the use of deep
learning applied to ECG (43, 44). A predictive model for HFpEF in ECLIPSE was dominated
by echocardiography variables, notably stroke volume and others indicating that
echocardiography is an essential component to the identification of HFpEF. Global clinical
metadata was also useful in validating prior work done in subtyping HFpEF into various
phenogroups, using unsupervised machine learning (16, 17). Unsupervised machine
learning holds significant promise in extracting latent space from high dimensional clinical
data to reclassify the taxonomy of disease. This may have particular utility in circumstances
where clinician driven diagnostic coding does not capture the full nuance or longitudinal
spectrum of a complex condition, such as HFpEF. With the removal of key features from
machine learning models, reasonable predictions were still possible using global clinical
metadata suggesting a self-healing, almost holographic quality of broad clinical data.
Conclusion
We have demonstrated in this study an ability to discriminate heart failure, both HFpEF and
HFrEF using machine learning applied to both routine bloods as well as advanced
haematology data, extracted from a commonly used flow cytometer. The predictions
obtained from the haematology flow cytometer have been validated independently and due
to their underlying predictive features might have value in predicting and monitoring
responses to heart failure therapies in near real-time. The use of machine learning applied to
abundant, low-cost laboratory data may have particular value in low to middle income
countries where access to high level, expensive diagnostic testing is limited.
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Limitations
As with most machine learning studies the results from this project may not be transferable
into other settings, due to differences in regional practices, disease presentation and
prevalence etc. However transferable machine learning models are preferably generated
from data which comes from a similar source, is complete and is resilient to clinician biases.
Haematology and to a lesser degree biochemistry data fulfils that requirement. Over-fitting is
always a possibility when using data from a single source and preferably we would have
applied our ML models to external data to validate. The use of matched cases and controls
over-estimates the accuracy of predictive models when using AUROC (45), however we also
validated our models in a real world dataset to demonstrate what implementation might look
like. Clinical utility cannot be assumed until predictive models of heart failure are able to
identify missed cases of heart failure or alert to the diagnosis of heart failure earlier, whereby
patient outcomes can be improved. Although algorithms applied to existing clinical data may
be low-cost to implement the downstream human and societal cost implications of false
positives and negatives needs to be studied during an implementation program.
Conflicts of interest
Dr. P. A. Gladding is founder of Theranostics Laboratory, a molecular diagnostics company,
and HeartLab, an echocardiography artificial intelligence company.
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30
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