Color Fundus Photography and Deep Learning Applica
Color Fundus Photography and Deep Learning Applica
Abstract
Objective: To report the development and performance of 2 distinct deep learning models trained
exclusively on retinal color fundus photographs to classify Alzheimer disease (AD).
Patients and Methods: Two independent datasets (UK Biobank and our tertiary academic institution) of
good-quality retinal photographs derived from patients with AD and controls were used to build 2 deep
learning models, between April 1, 2021, and January 30, 2024. ADVAS is a U-Netebased architecture that
uses retinal vessel segmentation. ADRET is a bidirectional encoder representations from transformers style
self-supervised learning convolutional neural network pretrained on a large data set of retinal color
photographs from UK Biobank. The models’ performance to distinguish AD from non-AD was determined
using mean accuracy, sensitivity, specificity, and receiving operating curves. The generated attention
heatmaps were analyzed for distinctive features.
Results: The self-supervised ADRET model had superior accuracy when compared with ADVAS, in both
UK Biobank (98.27% vs 77.20%; P<.001) and our institutional testing data sets (98.90% vs 94.17%;
P¼.04). No major differences were noted between the original and binary vessel segmentation and be-
tween both eyes vs single-eye models. Attention heatmaps obtained from patients with AD highlighted
regions surrounding small vascular branches as areas of highest relevance to the model decision making.
Conclusion: A bidirectional encoder representations from transformers style self-supervised convolutional
neural network pretrained on a large data set of retinal color photographs alone can screen symptomatic
AD with high accuracy, better than U-Netepretrained models. To be translated in clinical practice, this
methodology requires further validation in larger and diverse populations and integrated techniques to
harmonize fundus photographs and attenuate the imaging-associated noise.
ª 2024 THE AUTHORS. Published by Elsevier Inc on behalf of Mayo Foundation for Medical Education and Research. This is an open access article under
the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) n Mayo Clin Proc Digital Health 2024;2(4):548-558
W
ithout new advancements in Alz-
heimer disease (AD) care, the revealed pathologic alterations in the neuro-
From the Department of cost associated with AD and sensory retina that precede and correlate
Neurology (O.M.D., B.K.W.,
S.N., J.S., A.Y., S.S., J.A., R.J.C.),
other dementias’ care is projected to reach with brain AD changes.5,12 Retina accumulates
and Department of Ophthal- nearly $1 trillion in 2050.1 Accurate and amyloid b-protein plaques and abnormal tau
mology (O.M.D.), Mayo widely accessible AD screening tools are proteins13e15 and exhibits neurodegeneration,
Clinic, Scottsdale, AZ; School
of Computed and
crucial in this emerging global health crisis.2 vascular amyloidosis, and increased
Augmented Intelligence, Ari- Current AD biomarkers’ availability is limited inflammation.5,10e12,16,17 Retinal changes can
zona State University, Tempe, by their prohibitive cost, invasiveness, or be captured via color fundus photography, a
AZ (X.L., W.Z., Y.W.); and
Department of Ophthal-
need for additional validation.3,4 The retina widely accessible technology in eye care, pri-
mology (J.J.C.), and Depart- is an unshielded extension of the brain that of- mary care, and underresourced community
ment of Neurology (J.J.C.), fers the opportunity to investigate multiple settings, carrying the promise of a noninvasive
Mayo Clinic Rochester, MN.
central nervous system disorders.5e7 Postmor- and cost-effective biomarker for AD.17e20 Ma-
tem histopathologic investigations of eyes and chine learning tools were developed to over-
brains from patients with AD8,9 and clinical come the subjectivity and low efficiency
associated with manual retinal photographs 86,069 patients). During the ADRET model
analysis for disease and biomarker identifica- pretraining on these images, we first randomly
tion and to automate their interpretation in masked 60% of the input image, where the
multiple ocular disorders.21e23 Moreover, ma- size of each mask is equal to the (mask’s height
chine learning applications using retinal imag- [H] adjusted by the downsampling ratio [D],
ing alone demonstrate good prediction mask’s width [W] adjusted by the down-
accuracy of the individuals’ biological sex, sampling ratio [D] of the network) (HD, WD).
blood pressure, and smoking status.24,25 Then, we processed only the unmasked visible
Given the retinal changes in Alzheimer’s mir- regions of the input image. The size of the
rors the Alzheimer’s brain pathology,5,12,25,26 output image was (224, 224), and the down-
deep learning applications have been sampling ratio was 32, making our mask size
expanded27e31 to enable the automatic classi- (7, 7). We used the feature maps learned from
fication of AD and identification of retinal AD the pretraining module for classification
biomarkers that are not visible to the human studies. For quality control, 2 trained graders
eye.29,30,32 Although promising, we noted (A.Y. and S.S.) excluded the retinal images
certain limitations of the traditional convolu- exhibiting blur, low contrast, poor illumina-
tional neural networks (CNNs) that rely on tion, or artifacts (Supplemental Figure 1,
large numbers of images and expert labeling. available online at https://www.
Modern technologies, such as vision trans- mcpdigitalhealth.org/). After the quality con-
formers and self-supervised learning, provide trol, we selected 362 good-quality images (169
a pretraining strategy that uses easier attain- left eyes and 193 right eyes) from 230 patients
able unlabeled data, overcoming the challenge with AD. The reference group included 389
of label acquisition and expanding the span of good-quality images (170 left eyes and 219
images utilization. These are based on the right eyes) from 282 patients without AD. The
advancement of natural language processing, AD label was based on International Classifi-
in the form of self-supervised learning models cation of Diseases (ICD) codes from hospital
of bidirectional encoder representations from admission and death records, indicating a
transformers (BERT)33 and generative pre- definitive clinical diagnosis of dementia caused
trained transformers.34 Here, we evaluate the by AD (Data-field 42021).37 The non-AD label
value of both traditional CNNs and the mod- was based on absent neurodegenerative con-
ern generative self-supervised learning. We ditions and other dementias. We excluded
report the technological development and patients with Parkinson disease (G20), sec-
clinical application of ADVAS, a U-Netebased ondary parkinsonism (G21), other parkin-
architecture employing retinal vessel segmen- sonism (G22), other degenerative disorders of
tation35 and ADRET, a BERT-style self-super- nervous system (G32), vascular syndromes in
vised learning CNN pretrained on retinal cerebrovascular disease (G46), vascular de-
color photographs from UK Biobank.36 We mentia (F01), dementia associated with other
determined the 2 models’ performance to clas- diseases (F02), unspecified dementia (F03),
sify AD in 2 real-world patient populations and organic amnestic syndrome (F04). We
and attempted to identify the retinal regions also excluded patients with ocular conditions,
that were highlighted as AD discriminators including age-related macular degeneration,
by the models’ decision making. glaucoma, and diabetic retinopathy. For each
input image, we first detected the retina using
PATIENTS AND METHODS the Hough circle transform and then cropped
the mask region to minimize the effect of the
Participants and Retinal Color Photograph black background. Afterward, the images were
Acquisition resized to 224 224 and normalized to
UK Biobank Data Set. We used 178,803 (1, 1).38
unlabeled color fundus images from the UK
Biobank (http://www.ukbiobank.ac.uk/about- Institutional Data Set. The study received
biobank-uk)36 involving 87,245 participants, exempt approval from our institutional review
including patients with AD (1136 images, 553 board, with waiver of informed consent owing
patients) and without AD (176,392 images, to exclusive use of retrospective and
n n
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MAYO CLINIC PROCEEDINGS: DIGITAL HEALTH
0
U-net (encoder) classifier
50
AD
100 U-net Fully connected Softmax
(encoder) layer function
150 Non-
AD
200
Dataset of retinal 0
fundus photographs U-net (encoder) classifier
50
AD
100 U-net Fully connected Softmax
150 (encoder) layer function
Non-
200 AD
deidentified data (Protocol #21-013272). We single batch and the computational efficiency
collected 45 digital color fundus photographs were lower.40,41
from 118 patients with a clinical diagnosis of
AD from our academic multisite tertiary insti- Deep Learning Models Training and Testing
tution. The patients were retrospectively iden- (April 1, 2021, Through January 30, 2024)
tified through an electronic medical record ADVAS Model. The framework consisted of 2
search using ICD9 (331) and ICD10 (G30) main steps. In the first step, we used a U-
codes from January 1, 2011, to June 30, Netebased architecture42 with 2 parts,
2021; 129 patients from the EyePACS data- encoder (downsampling) and decoder
base created the control data set.39 After im- (upsampling). We first segmented the retinal
age quality control, the ADVAS model vasculature in the retinal images from the UK
included 318 binary vessel segmentation im- Biobank and our institutional data set and
ages from 113 patients with AD and 338 then inputted the segmented vessel results into
original vessel segmentation images from 116 the U-Net encoder for feature extraction. For
patients with AD. The control group vessel segmentation, we used the Digital
comprised 259 vessel segmentation images Retinal Images for Vessel Extraction database43
(original and binary) from 129 participants. to train the model and obtain its optimized
ADRET used 283 images from 76 patients weight parameters. Two outputs were gener-
with AD. We detected the retina using the ated: the original vessel segmentation image,
Hough circle transform and cropped the mask with detailed vessel structure (model 1); and
region to minimize the effect of the black binary vessel segmentation (denoted either
background. The images were then resized to 0 or 1), which enhanced the clear parts of the
512 512 and normalized to (1, 1).38 This vessel and ignored the faint parts, facilitating
resolution was chosen to increase the attention further analyses (model 2). Subsequently,
to detail in this small data set because the re- these segmentation results were used as inputs
quirements for the number of images in a for further extraction of vascular features using
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RETINAL IMAGING-BASED DEEP LEARNING IN ALZHEIMER’S
Pretrain process
Random
mask
Patches (60%)
Encoder Decoder
Feature maps
AD classification
AD
Pre-trained Fully connected Softmax
encoder layer function
Non-
AD
U-Net encoders,44 which performed initiali- heatmaps were generated in the last layer of
zation using weight from the first segmenta- the U-Net classifier using Gradient-weighted
tion stage. This process focused on extracting Class Activation Mapping (GRAD-CAM).46,47
key information from the segmented images
that could help with the disease diagnosis. ADRET Model. The backbone was our
Finally, the extracted features were fed to a recently developed nn-MobileNet48 that re-
new linear classifier, a fully connected layer, ported improved network performance by the
and a Softmax function (pipeline illustrated in following: (1) adjusting the order of channel
Figure 1). A fully connected layer is a neural configurations for the inverted linear residual
network layer in which every neuron is con- bottleneck in the MobileNetV2 network49; (2)
nected to all activation units from the pre- using a heavy data augmentation strategy
ceding layer. This layer typically resides at the through Mixup,50 CutMix51 image cropping,
network’s end and maps the learned nonlinear flipping, contrast adjustment, brightness
features to the sample’s output space. The adjustment, and sharpening; and (3) adding
Softmax function is an activation function spatial-dropout52 modules at various locations
widely used for multiclass classification prob- within the network to identify their optimal
lems.45 It transforms a real-value vector into a placement in an attempt to address the over-
probability distribution where each element’s fitting. We adopted a BERT-style self-super-
value is between 0 and 1, and the sum of all vised learning53 method (Figure 2), masking
elements equals 1. The output from the Soft- the image and then reducing it to pretrain the
max function can be interpreted as the prob- encoder to obtain the representative features.54
ability distribution over various classes, To improve the computational efficiency, we
representing the likelihood that the sample resized the input image to 224 224. This
belongs to each class. The classifier predicted image resolution was chosen given ADRET
whether the individual represented by the was pretrained on many fundus images, to
image is an AD or control patient. The ensure computational efficiency and the
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MAYO CLINIC PROCEEDINGS: DIGITAL HEALTH
Both vs L
P¼.97 Next, we performed random masking with a
P¼.12
masking rate of 60%. We adopted the hierar-
Binary
Binary
Accuracy ¼ 0.9017
Accuracy ¼ 0.9070
Accuracy ¼ 0.9767
nn-MobileNet48 to generate feature maps with
169 training
169 training
43 testing
43 testing
different resolutions. Then, the feature maps
Institutional data set
Left eye
Both vs L
P¼.34
P¼.08
Original
Processor.
476 training
Original vessel
120 testing
segmentation
Accuracy ¼ 0.9773
Accuracy ¼ 0.8636
Statistical Analyses
175 training
271 training
44 testing
68 testing
Left eye
Both vs L
P¼.73
Binary
Accuracy ¼ 0.7373
Accuracy ¼ 0.7941
329 training
271 training
83 testing
68 testing
Both vs L
P¼.17
P¼.22
Original
150 testing
segmentation
Accuracy ¼ 0.7229
Accuracy ¼ 0.8676
271 training
83 testing
68 testing
Left eye
Institutional dataset
ROC curve ROC curve ROC curve
1.0 1.0 1.0
0.8 0.8 0.8
Sensitivity
Sensitivity
Sensitivity
0.6 0.6 0.6
0.4 0.4 0.4
0.2 0.2 0.2
0.0 0.0 0.0
0.0 0.2
0.4 0.6 0.8 1.0 0.0 0.20.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0
1-Specificity 1-Specificity 1-Specificity
ADVAS original vessel segmentation ADVAS binary vessel segmentation ADRET
AUROC=0.991 AUROC=0.9801 AUROC=1.0000
UK biobank dataset
ROC curve ROC curve ROC curve
1.0 1.0 1.0
0.8 0.8 0.8
Sensitivity
Sensitivity
Sensitivity
FIGURE 3. Graphs illustrating the performance of the ADVAS and ADRET models in both data sets and the corresponding receiver
operating characteristic (ROC) curves.
TABLE 2. ADRET and ADVAS Models Performance for Alzheimer Disease Prediction in the UK Biobank and Our Institutional Data Set
ADVAS ADVAS
Original vessel segmentation Binary vessel segmentation ADRET
UK Biobank testing Institutional testing UK Biobank testing Institutional testing UK Biobank testing Institutional testing
data set (n¼150) data set (n¼120) data set (n¼150) data set (n¼116) data set (n¼150) data set (n¼109)
Accuracy 0.772 (0.0179) 0.9417 (0.0243) 0.7373 (0.0278) 0.9017 (0.0326) 0.9827 (0.0059) 0.989 (0.0077)
k score 0.5377 (0.0376) 0.8785 (0.0412) 0.4691 (0.0635) 0.7984 (0.0618) 0.9652 (0.012) 0.9777 (0.0157)
AUROC 0.8137 (0.0189) 0.9800 (0.0077) 0.7809 (0.0372) 0.9588 (0.0177) 0.9967 (0.0022) 0.9978 (0.0019)
Sensitivity 0.6554 (0.0906) 0.9549 (0.0310) 0.6823 (0.0683) 0.9065 (0.0540) 0.9827 (0.0059) 0.989 (0.0077)
Specificity 0.8775 (0.0517) 0.9176 (0.0393) 0.7839 (0.0719) 0.8992 (0.0797) 0.9817 (0.0122) 0.9805 (0.0137)
The data are mean (SD). Five-fold cross-validation method was applied in each testing data set.
AUROC, area under the receiver operating characteristic curve.
0.9652, and an AUROC of 0.9967 for AD clas- may be chosen for optimization in future
sification. In our institutional data set, the studies. The fact that multiple distinctive
model achieved 98.90% accuracy, a k score groups had similarly high performance rein-
of 0.9777, and an AUROC of 0.9978 for AD forces our findings accuracy and applicability.
classification (Table 2, Figure 3). Our framework identified regions surrounding
All models generated attention heatmaps smaller retinal vessels in AD-derived heat-
using GRAD-CAM. The AD-derived attention maps, which was similarly highlighted in AD
maps highlighted areas surrounding retinal imaging and pathologic studies.10,15,16,60e62
small vascular branches as regions of highest These hypothesis-generating findings will
relevance to the model decision making require confirmation in future machine
(Supplemental Figure 2, available online at learning studies. ADVAS reported different
https://www.mcpdigitalhealth.org/). performance metrics in the 2 data sets. Previ-
ous literature similarly reports considerable
DISCUSSION differences between UK Biobank and other
We report 2 different CNNs trained exclu- data sets (such as EyePACS) when performing
sively on 45 retinal color photographs, which the same task.63,64 This effect is explained by
reached good performance to discriminate AD several factors impacting diverse data sets,
from non-AD in 2 different populations. We such as different sampling equipment, sample
trained and tested these automated models diversity, data quality, or condition severity
to overcome the subjectivity and inefficiency and is particularly pronounced in large-scale
of retinal photographs manual analysis. First, data sets.
we aimed to further investigate the potential Our novel BERT-style self-supervised
of a formerly reported AD classification tool ADRET model had superior accuracy when
based on retinal vessel segmentation.30 In compared with ADVAS, in both UK Biobank
this scope, we developed ADVAS, a novel U- (98.27% vs 77.20%; P<.001) and our institu-
Netebased CNN using original retinal vessel tional testing data sets (98.90% vs 94.17%;
segmentation. We also explored binary vessel P¼.04). This underscores the increased preci-
segmentation, which pays more attention to sion of modern self-supervised techniques for
clearly delineated vessels and less attention disease classification. ADRET was imple-
to the faint vessels. All ADVAS models mented through a lightweight CNN architec-
achieved a classifying accuracy of at least ture, nn-MobileNet.48 This method fully
69.8%, without notable differences between leverages the advantages of CNNs in medical
both eyes vs single-eye models. The highest image processing and incorporates the pre-
accuracy (97%) was reached when images training mechanism of self-supervised
from right eye and original vessel segmenta- learning, aiming to efficiently process large-
tion, and left eye and binary vessel segmenta- scale unlabeled medical image data sets. The
tion, were used, suggesting that any of them performance of the model in data
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RETINAL IMAGING-BASED DEEP LEARNING IN ALZHEIMER’S
also investigate deep learningeassisted retinal Grant Support: This work has been partially supported by
imaging tools in AD clinical trials. the NIH (R01EY032125, R01DE030286, R01AG069453,
and P30AG072980) and the state of Arizona via the Ari-
zona Alzheimer’s Consortium.
CONCLUSION
Data Previously Presented: A subaim of this work was
A BERT-style self-supervised neural network presented at the American Academy of Neurology Annual
pretrained on a large data set of retinal color Meeting, April 2024, Denver, CO.
photographs alone can screen symptomatic
Correspondence: Address to Oana M. Dumitrascu, MD,
AD with high accuracy, better than U-Nete
Mayo Clinic College of Medicine and Science, 13400 East
pretrained models. With further validation in Shea Boulevard, Scottsdale, AZ 85259 (dumitrascu.oana@
diverse populations, as well as integrated mayo.edu; Twitter: @OanaDumitrascu5).
methods to attenuate imaging-associated
ORCID
noise, this methodology has the potential for
Oana M. Dumitrascu: https://orcid.org/0000-0003-2033-
application in clinical practice for point-of- 449X
care AD screening.
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