3. A B DC
Benign without atypia / Atypic / DCIS (ductal carcinoma in situ) / Invasive Carcinoma
Interpretation?
Elmore etl al. JAMA 2015
Diagnostic Concordance Among Pathologists
유방암 병리 데이터 판독하기
4. Figure 4. Participating Pathologists’ Interpretations of Each of the 240 Breast Biopsy Test Cases
0 25 50 75 100
Interpretations, %
2
4
6
8
10
12
14
16
18
20
22
24
26
28
30
32
34
36
38
40
42
44
46
48
50
52
54
56
58
60
62
64
66
68
70
72
Case
Benign without atypia
72 Cases
2070 Total interpretations
A
0 25 50 75 100
Interpretations, %
218
220
222
224
226
228
230
232
234
236
238
240
Case
Invasive carcinoma
23 Cases
663 Total interpretations
D
0 25 50 75 100
Interpretations, %
147
145
149
151
153
155
157
159
161
163
165
167
169
171
173
175
177
179
181
183
185
187
189
191
193
195
197
199
201
203
205
207
209
211
213
215
217
Case
DCIS
73 Cases
2097 Total interpretations
C
0 25 50 75 100
Interpretations, %
74
76
78
80
82
84
86
88
90
92
94
96
98
100
102
104
106
108
110
112
114
116
118
120
122
124
126
128
130
132
134
136
138
140
142
144
Case
Atypia
72 Cases
2070 Total interpretations
B
Benign without atypia
Atypia
DCIS
Invasive carcinoma
Pathologist interpretation
DCIS indicates ductal carcinoma in situ.
Diagnostic Concordance in Interpreting Breast Biopsies Original Investigation Research
Elmore etl al. JAMA 2015
유방암 판독에 대한 병리학과 전문의들의 불일치도
5. Elmore etl al. JAMA 2015
•정확도: 75.3%
(정답은 경험이 많은 세 명의 병리학과 전문의가 협의를 통해 정하였음)
spentonthisactivitywas16(95%CI,15-17);43participantswere
awarded the maximum 20 hours.
Pathologists’ Diagnoses Compared With Consensus-Derived
Reference Diagnoses
The 115 participants each interpreted 60 cases, providing 6900
total individual interpretations for comparison with the con-
sensus-derived reference diagnoses (Figure 3). Participants
agreed with the consensus-derived reference diagnosis for
75.3% of the interpretations (95% CI, 73.4%-77.0%). Partici-
pants (n = 94) who completed the CME activity reported that
Patient and Pathologist Characteristics Associated With
Overinterpretation and Underinterpretation
The association of breast density with overall pathologists’
concordance (as well as both overinterpretation and under-
interpretation rates) was statistically significant, as shown
in Table 3 when comparing mammographic density grouped
into 2 categories (low density vs high density). The overall
concordance estimates also decreased consistently with
increasing breast density across all 4 Breast Imaging-
Reporting and Data System (BI-RADS) density categories:
BI-RADS A, 81% (95% CI, 75%-86%); BI-RADS B, 77% (95%
Figure 3. Comparison of 115 Participating Pathologists’ Interpretations vs the Consensus-Derived Reference
Diagnosis for 6900 Total Case Interpretationsa
Participating Pathologists’ Interpretation
ConsensusReference
Diagnosisb
Benign
without atypia Atypia DCIS
Invasive
carcinoma Total
Benign without atypia 1803 200 46 21 2070
Atypia 719 990 353 8 2070
DCIS 133 146 1764 54 2097
Invasive carcinoma 3 0 23 637 663
Total 2658 1336 2186 720 6900
DCIS indicates ductal carcinoma
in situ.
a
Concordance noted in 5194 of
6900 case interpretations or
75.3%.
b
Reference diagnosis was obtained
from consensus of 3 experienced
breast pathologists.
Diagnostic Concordance in Interpreting Breast Biopsies Original Investigation Research
총 240개의 병리 샘플에 대해서,
115명의 병리학과 전문의들이 판독한 총 6,900건의 사례를 정답과 비교
유방암 판독에 대한 병리학과 전문의들의 불일치도
6. PERSPECTIVES
Diagnosis of malignant
from benign or
inflammation and/or
reactive changes
Pathologist
Detection of
intratumoural
heterogeneity by
analyzing variance
across the tissue block
Delineation or
annotation of
which area is
malignant or
suspicious of
pathology on
a whole slide
image
Detection of cells, cellular
subtypes and histologic
primitives (such as mitotic
figures, tubules or nuclei)
Quantification of
cells or objects (such
as types of blood cells
or haemoglobin)
Grading of the tissue
according to severity of
disease (for example, Gleason
grading in prostate cancer)
Low risk High risk
Identification of
novel prognostic
approaches beyond
visual identification
(such as spatial
architecture or
degree of
multinucleation)
Precision medicine
approaches: treatment
tailored to an
individual patient
Identification of unique
morphological features
associated with gene
alterations or signalling
pathways
Stratification of patients on the
basis of their risk of progression or
recurrence to guide intensification
or de-intensification therapy
Identification of patients who
are more likely to respond to
a particular therapeutic
regimen or treatment
As a companion diagnostic
assay to evaluate patient
prognosis to determine
optimum management plan
Early assessment
of response to a
specific drug or
treatment
Oncologist
Fig. 4 | Artificial intelligence (AI) and machine learning approaches complement the expertise and support the pathologist and oncologist.Some
AI and machine learning approaches
complement the expertise and support the pathologist and oncologist
Nat Rev Clin Onco 2019
Detection Quantification Grading
Detction Diagnosis
PrognosisAnnotation
7. (domain-inspired features) of pathologists of numerous hand-crafted feature-based These features were subsequently used in
PERSPECTIVES
Patient with suspected
malignancy has biopsy
and/or surgical resection
Deep learning
(deep neural
network)
approach
Hand-crafted
AI approach
Pathologist fixes and
sections the tissue
specimen, and makes
multiple whole slides
using several stains
Pathologist provides
reference comparison for
the region of interest
based on the problem
Pathologist digitizes
physical slide using
whole-slide scanner;
oncologist collates
adjoining database
of relevant clinical and/or
outcome information
AI-based approach
from both modalities
gives a prediction
based on input data
Prediction is compared
against the reference to
evaluate performance
of the model
Performance evaluation
is done by reporting
area under the curve as
well as survival analysis
using hazard models
Input
Convolution
Convolutional layer
Pooling layer
Output
Pooling Flattening
Construct a hand-crafted
model to build the
AI-based prediction;
classification approach
for the clinical problem
Pathologist, oncologist,
and AI expert use intrinsic
domain knowledge to
engineer features to be
analysed with AI
Fig. 2 | Workflow and general framework for artificial intelligence (AI) approaches in digital pathology. Typical steps involved in the use of two
popular categories of AI approaches: deep learning and hand-crafted feature engineering.
Workflow and general framework
for AI approaches in digital pathology
Nat Rev Clin Onco 2019
8. PERSPECTIVES
a b c d
e f g h
Fig. 3 | Visual representations of hand-crafted features across cancer
types.a|Spatialarrangementofclustersoftissue-infiltratinglymphocytesin
a non-small-cell lung carcinoma (NSCLC) whole-slide image. b | Features
developedusingquantitativeimmunofluorescenceoftissue-infiltratinglym-
phocyte subpopulations (including detection of CD4+
and CD8+
T cells and
+
d | Features computing the relative orientation of the glands present in
prostate cancer tissue.e | Diversity of texture of cancer cell nuclei in an oral
cavitysquamouscellcarcinoma.f|Nuclearshapefeaturecomputedoncan-
cercellnucleiinahumanpapillomavirus-positiveoropharyngealcarcinoma.
g | Graph feature showing the spatial relationships of different cancer cell
Visual representations of hand-crafted features
across cancer types.
Nat Rev Clin Onco 2019
9. I M A G I N G
Systematic Analysis of Breast Cancer Morphology
Uncovers Stromal Features Associated with Survival
Andrew H. Beck,1,2
* Ankur R. Sangoi,1,3
Samuel Leung,4
Robert J. Marinelli,5
Torsten O. Nielsen,4
Marc J. van de Vijver,6
Robert B. West,1
Matt van de Rijn,1
Daphne Koller7†
The morphological interpretation of histologic sections forms the basis of diagnosis and prognostication for
cancer. In the diagnosis of carcinomas, pathologists perform a semiquantitative analysis of a small set of mor-
phological features to determine the cancer’s histologic grade. Physicians use histologic grade to inform their
assessment of a carcinoma’s aggressiveness and a patient’s prognosis. Nevertheless, the determination of grade
in breast cancer examines only a small set of morphological features of breast cancer epithelial cells, which has
been largely unchanged since the 1920s. A comprehensive analysis of automatically quantitated morphological
features could identify characteristics of prognostic relevance and provide an accurate and reproducible means
for assessing prognosis from microscopic image data. We developed the C-Path (Computational Pathologist)
system to measure a rich quantitative feature set from the breast cancer epithelium and stroma (6642 features),
including both standard morphometric descriptors of image objects and higher-level contextual, relational, and
global image features. These measurements were used to construct a prognostic model. We applied the C-Path
system to microscopic images from two independent cohorts of breast cancer patients [from the Netherlands
Cancer Institute (NKI) cohort, n = 248, and the Vancouver General Hospital (VGH) cohort, n = 328]. The prognostic
model score generated by our system was strongly associated with overall survival in both the NKI and the VGH
cohorts (both log-rank P ≤ 0.001). This association was independent of clinical, pathological, and molecular factors.
Three stromal features were significantly associated with survival, and this association was stronger than the
association of survival with epithelial characteristics in the model. These findings implicate stromal morpho-
logic structure as a previously unrecognized prognostic determinant for breast cancer.
INTRODUCTION
In the mid-19th century, it was first appreciated that the process of
carcinogenesis produces characteristic morphologic changes in can-
cer cells (1). Patey and Scarff showed in 1928 (2) that three histologic
features—tubule formation, epithelial nuclear atypia, and epithelial
mitotic activity—could each be scored qualitatively, and the assessments
could be combined to stratify breast cancer patients into three groups
that showed significant survival differences. This semiquantitative mor-
phological scoring scheme has been refined over the years (3–5) but
still remains the standard technique for histologic grading in invasive
breast cancer. Although considerable effort has been devoted recently
to molecular profiling for assessment of prognosis and prediction of
treatment response in cancer (6, 7), microscopic image assessment is
still the most commonly available (and in some places in the world,
the only) tool that is financially and logistically feasible.
Although the three epithelial features scored in current grading sys-
tems are useful in assessing cancer prognosis, valuable prognostic
information can also be derived from other factors, including proper-
ties of the cancer stroma such as its molecular characteristics (8–15)
and morphological features [such as stromal fibrotic focus, a scar-
like area in the center of a carcinoma (16)]. Thus, we sought to de-
velop a high-accuracy, image-based predictor to identify new clinically
predictive morphologic phenotypes of breast cancers, thereby pro-
viding new insights into the biological factors driving breast cancer
progression.
The development of such a system could also address other prob-
lems relevant to the clinical treatment of breast cancer. A limitation
to the current grading system is that there is considerable variability
in histologic grading among pathologists (17), with potentially neg-
ative consequences for determining treatment. An automated system
could provide an objective method for predicting patient prognosis
directly from image data. Moreover, once established, this system
could be used in breast cancer clinical trials to provide an accurate,
objective means for assessing breast cancer morphologic character-
istics, allowing objective stratification of breast cancer patients on the
basis of morphologic criteria and facilitating the discovery of mor-
phologic features associated with response to specific therapeutic
agents.
RESULTS
Experimental design overview
We developed the Computational Pathologist (C-Path), a machine
learning–based method for automatically analyzing cancer images
and predicting prognosis. To construct and evaluate the model, we
acquired hematoxylin and eosin (H&E)–stained histological images
from breast cancer tissue microarrays (TMAs) (figs. S4 and S5). The
1
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305,
USA. 2
Biomedical Informatics Training Program, Stanford University School of Medicine,
Stanford, CA 94305, USA. 3
Department of Pathology, El Camino Hospital, Mountain
View, CA 94040, USA. 4
Genetic Pathology Evaluation Centre, University of British Co-
lumbia, Vancouver, British Columbia V6H 3Z6, Canada. 5
Department of Biochemistry,
Stanford University, Stanford, CA 94305, USA. 6
Department of Pathology, Academic
Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands. 7
Department of Com-
puter Science, Stanford University, Stanford, CA 94305, USA.
*Present address: Department of Pathology, Beth Israel Deaconess Medical Center,
Harvard Medical School, Boston, MA 02115, USA.
†To whom correspondence should be addressed. E-mail: koller@cs.stanford.edu
R E S E A R C H A R T I C L E
www.ScienceTranslationalMedicine.org 9 November 2011 Vol 3 Issue 108 108ra113 1
Sci Transl Med. 2011
10. n
all
Constructing higher-level
contextual/relational features:
Relationships between epithelial
nuclear neighbors
Relationships between morphologically
regular and irregular nuclei
Relationships between epithelial
and stromal objects
Relationships between epithelial
nuclei and cytoplasm
Characteristics of
stromal nuclei
Characteristics of
epithelial nuclei and
Building an epithelial/stromal classifier:
Epithelial vs.stroma
classifier
Epithelial vs.stroma
classifier
B
Basic image processing and feature construction:
H&E image Image broken into superpixels Nuclei identified within
each superpixel
A
Relationships of contiguous epithelial
regions with underlying nuclear objects
C
ne
sic
d-
es
es
nd
of
e-
els
a
al-
to
or
al/
al-
ed
nd
g-
ue;
en;
ed
ay;
nd
=
ch
D)
al.
er
er
g-
as
ot
gh
onNovember17,2011stm.sciencemag.orgfrom
TMAs contain 0.6-mm-diameter cores (median
of two cores per case) that represent only a small
sample of the full tumor. We acquired data from
two separate and independent cohorts: Nether-
lands Cancer Institute (NKI; 248 patients) and
Vancouver General Hospital (VGH; 328 patients).
Unlike previous work in cancer morphom-
etry (18–21), our image analysis pipeline was
not limited to a predefined set of morphometric
features selected by pathologists. Rather, C-Path
measures an extensive, quantitative feature set
from the breast cancer epithelium and the stro-
ma (Fig. 1). Our image processing system first
performed an automated, hierarchical scene seg-
mentation that generated thousands of measure-
ments, including both standard morphometric
descriptors of image objects and higher-level
contextual, relational, and global image features.
The pipeline consisted of three stages (Fig. 1, A
to C, and tables S8 and S9). First, we used a set of
processing steps to separate the tissue from the
background, partition the image into small regions
of coherent appearance known as superpixels,
find nuclei within the superpixels, and construct
Constructing higher-level
contextual/relational features:
Relationships between epithelial
nuclear neighbors
Relationships between morphologically
regular and irregular nuclei
Relationships between epithelial
and stromal objects
Relationships between epithelial
nuclei and cytoplasm
Characteristics of
stromal nuclei
and stromal matrix
Characteristics of
epithelial nuclei and
epithelial cytoplasm
Building an epithelial/stromal classifier:
Epithelial vs.stroma
classifier
Epithelial vs.stroma
classifier
B
Relationships of contiguous epithelial
regions with underlying nuclear objects
Learning an image-based model to predict survival
Processed images from patients
alive at 5 years
Processed images from patients
deceased at 5 years
L1-regularized
logisticregression
modelbuilding
5YS predictive model
Unlabeled images
Time
P(survival)
C
D
Identification of novel prognostically
important morphologic features
stroma. (C) Constructing higher-level contextual/
relational features. After application of the epithelial-
stromal classifier, all image objects are subclassified
and colored on the basis of their tissue region and
basic cellular morphologic properties (epithelial reg-
ular nuclei = red; epithelial atypical nuclei = pale blue;
epithelial cytoplasm = purple; stromal matrix = green;
stromal round nuclei = dark green; stromal spindled
nuclei = teal blue; unclassified regions = dark gray;
spindled nuclei in unclassified regions = yellow; round
nuclei in unclassified regions = gray; background =
white). (Left panel) After the classification of each
image object, a rich feature set is constructed. (D)
Learning an image-based model to predict survival.
Processed images from patients alive at 5 years after
surgery and from patients deceased at 5 years after
surgery were used to construct an image-based prog-
nostic model. After construction of the model, it was
applied to a test set of breast cancer images (not
used in model building) to classify patients as high
or low risk of death by 5 years.
Sci Transl Med. 2011
I M A G I N G
Systematic Analysis of Breast Cancer Morphology
Uncovers Stromal Features Associated with Survival
Andrew H. Beck,1,2
* Ankur R. Sangoi,1,3
Samuel Leung,4
Robert J. Marinelli,5
Torsten O. Nielsen,4
Marc J. van de Vijver,6
Robert B. West,1
Matt van de Rijn,1
Daphne Koller7†
The morphological interpretation of histologic sections forms the basis of diagnosis and prognostication for
cancer. In the diagnosis of carcinomas, pathologists perform a semiquantitative analysis of a small set of mor-
phological features to determine the cancer’s histologic grade. Physicians use histologic grade to inform their
assessment of a carcinoma’s aggressiveness and a patient’s prognosis. Nevertheless, the determination of grade
in breast cancer examines only a small set of morphological features of breast cancer epithelial cells, which has
been largely unchanged since the 1920s. A comprehensive analysis of automatically quantitated morphological
features could identify characteristics of prognostic relevance and provide an accurate and reproducible means
for assessing prognosis from microscopic image data. We developed the C-Path (Computational Pathologist)
system to measure a rich quantitative feature set from the breast cancer epithelium and stroma (6642 features),
including both standard morphometric descriptors of image objects and higher-level contextual, relational, and
global image features. These measurements were used to construct a prognostic model. We applied the C-Path
system to microscopic images from two independent cohorts of breast cancer patients [from the Netherlands
Cancer Institute (NKI) cohort, n = 248, and the Vancouver General Hospital (VGH) cohort, n = 328]. The prognostic
model score generated by our system was strongly associated with overall survival in both the NKI and the VGH
cohorts (both log-rank P ≤ 0.001). This association was independent of clinical, pathological, and molecular factors.
Three stromal features were significantly associated with survival, and this association was stronger than the
association of survival with epithelial characteristics in the model. These findings implicate stromal morpho-
logic structure as a previously unrecognized prognostic determinant for breast cancer.
INTRODUCTION
In the mid-19th century, it was first appreciated that the process of
carcinogenesis produces characteristic morphologic changes in can-
cer cells (1). Patey and Scarff showed in 1928 (2) that three histologic
features—tubule formation, epithelial nuclear atypia, and epithelial
mitotic activity—could each be scored qualitatively, and the assessments
could be combined to stratify breast cancer patients into three groups
that showed significant survival differences. This semiquantitative mor-
phological scoring scheme has been refined over the years (3–5) but
still remains the standard technique for histologic grading in invasive
breast cancer. Although considerable effort has been devoted recently
to molecular profiling for assessment of prognosis and prediction of
treatment response in cancer (6, 7), microscopic image assessment is
still the most commonly available (and in some places in the world,
the only) tool that is financially and logistically feasible.
Although the three epithelial features scored in current grading sys-
tems are useful in assessing cancer prognosis, valuable prognostic
information can also be derived from other factors, including proper-
ties of the cancer stroma such as its molecular characteristics (8–15)
and morphological features [such as stromal fibrotic focus, a scar-
like area in the center of a carcinoma (16)]. Thus, we sought to de-
velop a high-accuracy, image-based predictor to identify new clinically
predictive morphologic phenotypes of breast cancers, thereby pro-
viding new insights into the biological factors driving breast cancer
progression.
The development of such a system could also address other prob-
lems relevant to the clinical treatment of breast cancer. A limitation
to the current grading system is that there is considerable variability
in histologic grading among pathologists (17), with potentially neg-
ative consequences for determining treatment. An automated system
could provide an objective method for predicting patient prognosis
directly from image data. Moreover, once established, this system
could be used in breast cancer clinical trials to provide an accurate,
objective means for assessing breast cancer morphologic character-
istics, allowing objective stratification of breast cancer patients on the
basis of morphologic criteria and facilitating the discovery of mor-
phologic features associated with response to specific therapeutic
agents.
RESULTS
Experimental design overview
We developed the Computational Pathologist (C-Path), a machine
learning–based method for automatically analyzing cancer images
and predicting prognosis. To construct and evaluate the model, we
acquired hematoxylin and eosin (H&E)–stained histological images
from breast cancer tissue microarrays (TMAs) (figs. S4 and S5). The
1
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305,
USA. 2
Biomedical Informatics Training Program, Stanford University School of Medicine,
Stanford, CA 94305, USA. 3
Department of Pathology, El Camino Hospital, Mountain
View, CA 94040, USA. 4
Genetic Pathology Evaluation Centre, University of British Co-
lumbia, Vancouver, British Columbia V6H 3Z6, Canada. 5
Department of Biochemistry,
Stanford University, Stanford, CA 94305, USA. 6
Department of Pathology, Academic
Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands. 7
Department of Com-
puter Science, Stanford University, Stanford, CA 94305, USA.
*Present address: Department of Pathology, Beth Israel Deaconess Medical Center,
Harvard Medical School, Boston, MA 02115, USA.
†To whom correspondence should be addressed. E-mail: koller@cs.stanford.edu
R E S E A R C H A R T I C L E
www.ScienceTranslationalMedicine.org 9 November 2011 Vol 3 Issue 108 108ra113 1
11. Sci Transl Med. 2011
patients; 192 of 328 VGH patients), these statistics were summarized
as their mean across the images (Supplementary Material).
The NKI images were used to build an image feature–based prognos-
tic model to predict the binary outcome of 5-year survival (5YS model)
(Fig. 1D) using L1-regularized logistic regression, implemented in the
R package glmnet (22). Model performance on the NKI data set was
assessed by eightfold cross-validation, where the data set is split into
allowing each case to be classifi
cancer molecular signatures: the
the genomic grade index score
(26), the hypoxia gene signatu
type (28). The subtype classific
the original publications or fr
prevalidation C-Path scores we
su
cli
tro
siz
ch
tu
sig
sic
1A
ass
sig
gr
ca
tat
by
pa
tem
sam
pa
im
A
0 5 10 15 20 25
0.00.20.40.60.81.0
181 153 100 27 4 Low-risk (black)
67 46 29 10 1 High-risk (red)
P < 0.001
B
C-Path 5YS model on the NKI cohort (n = 248)
0 5 10 15 20 25 30
0.00.20.40.60.81.0
223 174 139 90 22 7
63 39 27 16 3 1
Low-risk (black)
High-risk (red)
P = 0.001
C-Path 5YS model on the VGH cohort (n = 286)
Fig. 2. Kaplan-Meier survival curves of the 5YS model predictions and overall survival on the NKI and VGH
data sets. Cases classified as high risk are plotted on the red dotted line and cases classified as low risk on
the black solid line. The error bars represent 95% CIs. The y axis is probability of overall survival, and the x
I M A G I N G
Systematic Analysis of Breast Cancer Morphology
Uncovers Stromal Features Associated with Survival
Andrew H. Beck,1,2
* Ankur R. Sangoi,1,3
Samuel Leung,4
Robert J. Marinelli,5
Torsten O. Nielsen,4
Marc J. van de Vijver,6
Robert B. West,1
Matt van de Rijn,1
Daphne Koller7†
The morphological interpretation of histologic sections forms the basis of diagnosis and prognostication for
cancer. In the diagnosis of carcinomas, pathologists perform a semiquantitative analysis of a small set of mor-
phological features to determine the cancer’s histologic grade. Physicians use histologic grade to inform their
assessment of a carcinoma’s aggressiveness and a patient’s prognosis. Nevertheless, the determination of grade
in breast cancer examines only a small set of morphological features of breast cancer epithelial cells, which has
been largely unchanged since the 1920s. A comprehensive analysis of automatically quantitated morphological
features could identify characteristics of prognostic relevance and provide an accurate and reproducible means
for assessing prognosis from microscopic image data. We developed the C-Path (Computational Pathologist)
system to measure a rich quantitative feature set from the breast cancer epithelium and stroma (6642 features),
including both standard morphometric descriptors of image objects and higher-level contextual, relational, and
global image features. These measurements were used to construct a prognostic model. We applied the C-Path
system to microscopic images from two independent cohorts of breast cancer patients [from the Netherlands
Cancer Institute (NKI) cohort, n = 248, and the Vancouver General Hospital (VGH) cohort, n = 328]. The prognostic
model score generated by our system was strongly associated with overall survival in both the NKI and the VGH
cohorts (both log-rank P ≤ 0.001). This association was independent of clinical, pathological, and molecular factors.
Three stromal features were significantly associated with survival, and this association was stronger than the
association of survival with epithelial characteristics in the model. These findings implicate stromal morpho-
logic structure as a previously unrecognized prognostic determinant for breast cancer.
INTRODUCTION
In the mid-19th century, it was first appreciated that the process of
carcinogenesis produces characteristic morphologic changes in can-
cer cells (1). Patey and Scarff showed in 1928 (2) that three histologic
features—tubule formation, epithelial nuclear atypia, and epithelial
mitotic activity—could each be scored qualitatively, and the assessments
could be combined to stratify breast cancer patients into three groups
that showed significant survival differences. This semiquantitative mor-
phological scoring scheme has been refined over the years (3–5) but
still remains the standard technique for histologic grading in invasive
breast cancer. Although considerable effort has been devoted recently
to molecular profiling for assessment of prognosis and prediction of
treatment response in cancer (6, 7), microscopic image assessment is
still the most commonly available (and in some places in the world,
the only) tool that is financially and logistically feasible.
Although the three epithelial features scored in current grading sys-
tems are useful in assessing cancer prognosis, valuable prognostic
information can also be derived from other factors, including proper-
ties of the cancer stroma such as its molecular characteristics (8–15)
and morphological features [such as stromal fibrotic focus, a scar-
like area in the center of a carcinoma (16)]. Thus, we sought to de-
velop a high-accuracy, image-based predictor to identify new clinically
predictive morphologic phenotypes of breast cancers, thereby pro-
viding new insights into the biological factors driving breast cancer
progression.
The development of such a system could also address other prob-
lems relevant to the clinical treatment of breast cancer. A limitation
to the current grading system is that there is considerable variability
in histologic grading among pathologists (17), with potentially neg-
ative consequences for determining treatment. An automated system
could provide an objective method for predicting patient prognosis
directly from image data. Moreover, once established, this system
could be used in breast cancer clinical trials to provide an accurate,
objective means for assessing breast cancer morphologic character-
istics, allowing objective stratification of breast cancer patients on the
basis of morphologic criteria and facilitating the discovery of mor-
phologic features associated with response to specific therapeutic
agents.
RESULTS
Experimental design overview
We developed the Computational Pathologist (C-Path), a machine
learning–based method for automatically analyzing cancer images
and predicting prognosis. To construct and evaluate the model, we
acquired hematoxylin and eosin (H&E)–stained histological images
from breast cancer tissue microarrays (TMAs) (figs. S4 and S5). The
1
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305,
USA. 2
Biomedical Informatics Training Program, Stanford University School of Medicine,
Stanford, CA 94305, USA. 3
Department of Pathology, El Camino Hospital, Mountain
View, CA 94040, USA. 4
Genetic Pathology Evaluation Centre, University of British Co-
lumbia, Vancouver, British Columbia V6H 3Z6, Canada. 5
Department of Biochemistry,
Stanford University, Stanford, CA 94305, USA. 6
Department of Pathology, Academic
Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands. 7
Department of Com-
puter Science, Stanford University, Stanford, CA 94305, USA.
*Present address: Department of Pathology, Beth Israel Deaconess Medical Center,
Harvard Medical School, Boston, MA 02115, USA.
†To whom correspondence should be addressed. E-mail: koller@cs.stanford.edu
R E S E A R C H A R T I C L E
www.ScienceTranslationalMedicine.org 9 November 2011 Vol 3 Issue 108 108ra113 1
12. I M A G I N G
Systematic Analysis of Breast Cancer Morphology
Uncovers Stromal Features Associated with Survival
Andrew H. Beck,1,2
* Ankur R. Sangoi,1,3
Samuel Leung,4
Robert J. Marinelli,5
Torsten O. Nielsen,4
Marc J. van de Vijver,6
Robert B. West,1
Matt van de Rijn,1
Daphne Koller7†
The morphological interpretation of histologic sections forms the basis of diagnosis and prognostication for
cancer. In the diagnosis of carcinomas, pathologists perform a semiquantitative analysis of a small set of mor-
phological features to determine the cancer’s histologic grade. Physicians use histologic grade to inform their
assessment of a carcinoma’s aggressiveness and a patient’s prognosis. Nevertheless, the determination of grade
in breast cancer examines only a small set of morphological features of breast cancer epithelial cells, which has
been largely unchanged since the 1920s. A comprehensive analysis of automatically quantitated morphological
features could identify characteristics of prognostic relevance and provide an accurate and reproducible means
for assessing prognosis from microscopic image data. We developed the C-Path (Computational Pathologist)
system to measure a rich quantitative feature set from the breast cancer epithelium and stroma (6642 features),
including both standard morphometric descriptors of image objects and higher-level contextual, relational, and
global image features. These measurements were used to construct a prognostic model. We applied the C-Path
system to microscopic images from two independent cohorts of breast cancer patients [from the Netherlands
Cancer Institute (NKI) cohort, n = 248, and the Vancouver General Hospital (VGH) cohort, n = 328]. The prognostic
model score generated by our system was strongly associated with overall survival in both the NKI and the VGH
cohorts (both log-rank P ≤ 0.001). This association was independent of clinical, pathological, and molecular factors.
Three stromal features were significantly associated with survival, and this association was stronger than the
association of survival with epithelial characteristics in the model. These findings implicate stromal morpho-
logic structure as a previously unrecognized prognostic determinant for breast cancer.
INTRODUCTION
In the mid-19th century, it was first appreciated that the process of
carcinogenesis produces characteristic morphologic changes in can-
cer cells (1). Patey and Scarff showed in 1928 (2) that three histologic
features—tubule formation, epithelial nuclear atypia, and epithelial
mitotic activity—could each be scored qualitatively, and the assessments
could be combined to stratify breast cancer patients into three groups
that showed significant survival differences. This semiquantitative mor-
phological scoring scheme has been refined over the years (3–5) but
still remains the standard technique for histologic grading in invasive
breast cancer. Although considerable effort has been devoted recently
to molecular profiling for assessment of prognosis and prediction of
treatment response in cancer (6, 7), microscopic image assessment is
still the most commonly available (and in some places in the world,
the only) tool that is financially and logistically feasible.
Although the three epithelial features scored in current grading sys-
tems are useful in assessing cancer prognosis, valuable prognostic
information can also be derived from other factors, including proper-
ties of the cancer stroma such as its molecular characteristics (8–15)
and morphological features [such as stromal fibrotic focus, a scar-
like area in the center of a carcinoma (16)]. Thus, we sought to de-
velop a high-accuracy, image-based predictor to identify new clinically
predictive morphologic phenotypes of breast cancers, thereby pro-
viding new insights into the biological factors driving breast cancer
progression.
The development of such a system could also address other prob-
lems relevant to the clinical treatment of breast cancer. A limitation
to the current grading system is that there is considerable variability
in histologic grading among pathologists (17), with potentially neg-
ative consequences for determining treatment. An automated system
could provide an objective method for predicting patient prognosis
directly from image data. Moreover, once established, this system
could be used in breast cancer clinical trials to provide an accurate,
objective means for assessing breast cancer morphologic character-
istics, allowing objective stratification of breast cancer patients on the
basis of morphologic criteria and facilitating the discovery of mor-
phologic features associated with response to specific therapeutic
agents.
RESULTS
Experimental design overview
We developed the Computational Pathologist (C-Path), a machine
learning–based method for automatically analyzing cancer images
and predicting prognosis. To construct and evaluate the model, we
acquired hematoxylin and eosin (H&E)–stained histological images
from breast cancer tissue microarrays (TMAs) (figs. S4 and S5). The
1
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305,
USA. 2
Biomedical Informatics Training Program, Stanford University School of Medicine,
Stanford, CA 94305, USA. 3
Department of Pathology, El Camino Hospital, Mountain
View, CA 94040, USA. 4
Genetic Pathology Evaluation Centre, University of British Co-
lumbia, Vancouver, British Columbia V6H 3Z6, Canada. 5
Department of Biochemistry,
Stanford University, Stanford, CA 94305, USA. 6
Department of Pathology, Academic
Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands. 7
Department of Com-
puter Science, Stanford University, Stanford, CA 94305, USA.
*Present address: Department of Pathology, Beth Israel Deaconess Medical Center,
Harvard Medical School, Boston, MA 02115, USA.
†To whom correspondence should be addressed. E-mail: koller@cs.stanford.edu
R E S E A R C H A R T I C L E
www.ScienceTranslationalMedicine.org 9 November 2011 Vol 3 Issue 108 108ra113 1
Sci Transl Med. 2011
Top stromal features associated with survival.
laborious image object identification by skilled pathologists, followed
by the measurement of a small number of expert predefined features,
primarily characterizing epithelial nuclear characteristics, such as
size, color, and texture (21, 36). In contrast, after initial filtering of im-
ages to ensure high-quality TMA images and training of the C-Path
models using expert-derived image annotations (epithelium and
stroma labels to build the epithelial-stromal classifier and survival
time and survival status to build the prognostic model), our image
analysis system is automated with no manual steps, which greatly in-
creases its scalability. Additionally, in contrast to previous approaches,
our system measures thousands of morphologic descriptors of diverse
elements of the microscopic cancer image, including many relational
features from both the cancer epithelium and the stroma, allowing
identification of prognostic features whose significance was not pre-
viously recognized.
Using our system, we built an image-based prognostic model on
the NKI data set and showed that in this patient cohort the model
was a strong predictor of survival and provided significant additional
prognostic information to clinical, molecular, and pathological prog-
nostic factors in a multivariate model. We also demonstrated that the
image-based prognostic model, built using the NKI data set, is a strong
prognostic factor on another, independent data set with very different
SD of the ratio of the pixel intensity SD to the mean intensity
for pixels within a ring of the center of epithelial nuclei
A
The sum of the number of unclassified objects
SD of the maximum blue pixel value for atypical epithelial nuclei
Maximum distance between atypical epithelial nuclei
B
C
D
Maximum value of the minimum green pixel intensity value in
epithelial contiguous regions
Minimum elliptic fit of epithelial contiguous regions
SD of distance between epithelial cytoplasmic and nuclear objects
Average border between epithelial cytoplasmic objects
E
F
G
H
Fig. 5. Top epithelial features. The eight panels in the figure (A to H) each
shows one of the top-ranking epithelial features from the bootstrap anal-
ysis. Left panels, improved prognosis; right panels, worse prognosis. (A) SD
of the (SD of intensity/mean intensity) for pixels within a ring of the center
of epithelial nuclei. Left, relatively consistent nuclear intensity pattern (low
score); right, great nuclear intensity diversity (high score). (B) Sum of the
number of unclassified objects. Red, epithelial regions; green, stromal re-
score; right, low score. (D) Maximum distance between atypical epithe-
lial nuclei. Left, high score; right, low score. (Insets) Red, atypical epithelial
nuclei; black, typical epithelial nuclei. (E) Minimum elliptic fit of epithelial
contiguous regions. Left, high score; right, low score. (F) SD of distance
between epithelial cytoplasmic and nuclear objects. Left, high score; right,
low score. (G) Average border between epithelial cytoplasmic objects. Left,
high score; right, low score. (H) Maximum value of the minimum green
onNovember17,2011stm.sciencemag.orgDownloadedfrom
and stromal matrix throughout the image, with thin cords of epithe-
lial cells infiltrating through stroma across the image, so that each
stromal matrix region borders a relatively constant proportion of ep-
ithelial and stromal regions. The stromal feature with the second
largest coefficient (Fig. 4B) was the sum of the minimum green in-
tensity value of stromal-contiguous regions. This feature received a
value of zero when stromal regions contained dark pixels (such as
inflammatory nuclei). The feature received a positive value when
stromal objects were devoid of dark pixels. This feature provided in-
formation about the relationship between stromal cellular composi-
tion and prognosis and suggested that the presence of inflammatory
cells in the stroma is associated with poor prognosis, a finding con-
sistent with previous observations (32). The third most significant
stromal feature (Fig. 4C) was a measure of the relative border between
spindled stromal nuclei to round stromal nuclei, with an increased rel-
ative border of spindled stromal nuclei to round stromal nuclei asso-
ciated with worse overall survival. Although the biological underpinning
of this morphologic feature is currently not known, this analysis sug-
gested that spatial relationships between different populations of stro-
mal cell types are associated with breast cancer progression.
Reproducibility of C-Path 5YS model predictions on
samples with multiple TMA cores
For the C-Path 5YS model (which was trained on the full NKI data
set), we assessed the intrapatient agreement of model predictions when
predictions were made separately on each image contributed by pa-
tients in the VGH data set. For the 190 VGH patients who contributed
two images with complete image data, the binary predictions (high
or low risk) on the individual images agreed with each other for 69%
(131 of 190) of the cases and agreed with the prediction on the aver-
aged data for 84% (319 of 380) of the images. Using the continuous
prediction score (which ranged from 0 to 100), the median of the ab-
solute difference in prediction score among the patients with replicate
images was 5%, and the Spearman correlation among replicates was
0.27 (P = 0.0002) (fig. S3). This degree of intrapatient agreement is
only moderate, and these findings suggest significant intrapatient tumor
heterogeneity, which is a cardinal feature of breast carcinomas (33–35).
Qualitative visual inspection of images receiving discordant scores
suggested that intrapatient variability in both the epithelial and the
stromal components is likely to contribute to discordant scores for
the individual images. These differences appeared to relate both to
the proportions of the epithelium and stroma and to the appearance
of the epithelium and stroma. Last, we sought to analyze whether sur-
vival predictions were more accurate on the VGH cases that contributed
multiple cores compared to the cases that contributed only a single
core. This analysis showed that the C-Path 5YS model showed signif-
icantly improved prognostic prediction accuracy on the VGH cases
for which we had multiple images compared to the cases that con-
tributed only a single image (Fig. 7). Together, these findings show
a significant degree of intrapatient variability and indicate that increased
Heat map of stromal matrix
objects mean abs.diff
to neighbors
H&E image separated
into epithelial and
stromal objects
A
B
C
Worse
prognosis
Improved
prognosis
Improved
prognosis
Improved
prognosis
Worse
prognosis
Worse
prognosis
Fig. 4. Top stromal features associated with survival. (A) Variability in ab-
solute difference in intensity between stromal matrix regions and neigh-
R E S E A R C H A R T I C L E
onNovember17,2011stm.sciencemag.orgDownloadedfrom
Top epithelial features.The eight panels in the figure (A to H) each
shows one of the top-ranking epithelial features from the bootstrap
analysis. Left panels, improved prognosis; right panels, worse prognosis.
13. (domain-inspired features) of pathologists of numerous hand-crafted feature-based These features were subsequently used in
PERSPECTIVES
Patient with suspected
malignancy has biopsy
and/or surgical resection
Deep learning
(deep neural
network)
approach
Hand-crafted
AI approach
Pathologist fixes and
sections the tissue
specimen, and makes
multiple whole slides
using several stains
Pathologist provides
reference comparison for
the region of interest
based on the problem
Pathologist digitizes
physical slide using
whole-slide scanner;
oncologist collates
adjoining database
of relevant clinical and/or
outcome information
AI-based approach
from both modalities
gives a prediction
based on input data
Prediction is compared
against the reference to
evaluate performance
of the model
Performance evaluation
is done by reporting
area under the curve as
well as survival analysis
using hazard models
Input
Convolution
Convolutional layer
Pooling layer
Output
Pooling Flattening
Construct a hand-crafted
model to build the
AI-based prediction;
classification approach
for the clinical problem
Pathologist, oncologist,
and AI expert use intrinsic
domain knowledge to
engineer features to be
analysed with AI
Fig. 2 | Workflow and general framework for artificial intelligence (AI) approaches in digital pathology. Typical steps involved in the use of two
popular categories of AI approaches: deep learning and hand-crafted feature engineering.
Workflow and general framework
for AI approaches in digital pathology
Nat Rev Clin Onco 2019
14. interoperative tumor diagnosis
of surgical specimen
cancer immunotherapy
response assessment
augmentation of pathologists’
manual assessment
analytical
validity
additive effect
with pathologist
Prediction of
genetic characteristic
AI in Pathology
15. interoperative tumor diagnosis
of surgical specimen
cancer immunotherapy
response assessment
augmentation of pathologists’
manual assessment
analytical
validity
additive effect
with pathologist
Prediction of
genetic characteristic
AI in Pathology
24. 구글의 유방 병리 판독 인공지능
• The localization score(FROC) for the algorithm reached 89%, which significantly
exceeded the score of 73% for a pathologist with no time constraint.
Yun Liu et al. Detecting Cancer Metastases on Gigapixel Pathology Images (2017)
25. 인공지능의 민감도 + 인간의 특이도
Yun Liu et al. Detecting Cancer Metastases on Gigapixel Pathology Images (2017)
• 구글의 인공지능은 민감도에서 큰 개선 (92.9%, 88.5%)
•@8FP: FP를 8개까지 봐주면서, 달성할 수 있는 민감도
•FROC: FP를 슬라이드당 1/4, 1/2, 1, 2, 4, 8개를 허용한 민감도의 평균
•즉, FP를 조금 봐준다면, 인공지능은 매우 높은 민감도를 달성 가능
• 인간 병리학자는 민감도 73%에 반해, 특이도는 거의 100% 달성
•인간 병리학자와 인공지능 병리학자는 서로 잘하는 것이 다름
•양쪽이 협력하면 판독 효율성, 일관성, 민감도 등에서 개선 기대 가능
26. ARTICLES
https://doi.org/10.1038/s41591-018-0177-5
1
Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA. 2
Skirball Institute, Department of Cell Biology,
New York University School of Medicine, New York, NY, USA. 3
Department of Pathology, New York University School of Medicine, New York, NY, USA.
4
School of Mechanical Engineering, National Technical University of Athens, Zografou, Greece. 5
Institute for Systems Genetics, New York University School
of Medicine, New York, NY, USA. 6
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY,
USA. 7
Center for Biospecimen Research and Development, New York University, New York, NY, USA. 8
Department of Population Health and the Center for
Healthcare Innovation and Delivery Science, New York University School of Medicine, New York, NY, USA. 9
These authors contributed equally to this work:
Nicolas Coudray, Paolo Santiago Ocampo. *e-mail: narges.razavian@nyumc.org; aristotelis.tsirigos@nyumc.org
A
ccording to the American Cancer Society and the Cancer
Statistics Center (see URLs), over 150,000 patients with lung
cancer succumb to the disease each year (154,050 expected
for 2018), while another 200,000 new cases are diagnosed on a
yearly basis (234,030 expected for 2018). It is one of the most widely
spread cancers in the world because of not only smoking, but also
exposure to toxic chemicals like radon, asbestos and arsenic. LUAD
and LUSC are the two most prevalent types of non–small cell lung
cancer1
, and each is associated with discrete treatment guidelines. In
the absence of definitive histologic features, this important distinc-
tion can be challenging and time-consuming, and requires confir-
matory immunohistochemical stains.
Classification of lung cancer type is a key diagnostic process
because the available treatment options, including conventional
chemotherapy and, more recently, targeted therapies, differ for
LUAD and LUSC2
. Also, a LUAD diagnosis will prompt the search
for molecular biomarkers and sensitizing mutations and thus has
a great impact on treatment options3,4
. For example, epidermal
growth factor receptor (EGFR) mutations, present in about 20% of
LUAD, and anaplastic lymphoma receptor tyrosine kinase (ALK)
rearrangements, present in<5% of LUAD5
, currently have tar-
geted therapies approved by the Food and Drug Administration
(FDA)6,7
. Mutations in other genes, such as KRAS and tumor pro-
tein P53 (TP53) are very common (about 25% and 50%, respec-
tively) but have proven to be particularly challenging drug targets
so far5,8
. Lung biopsies are typically used to diagnose lung cancer
type and stage. Virtual microscopy of stained images of tissues is
typically acquired at magnifications of 20×to 40×, generating very
large two-dimensional images (10,000 to>100,000 pixels in each
dimension) that are oftentimes challenging to visually inspect in
an exhaustive manner. Furthermore, accurate interpretation can be
difficult, and the distinction between LUAD and LUSC is not always
clear, particularly in poorly differentiated tumors; in this case, ancil-
lary studies are recommended for accurate classification9,10
. To assist
experts, automatic analysis of lung cancer whole-slide images has
been recently studied to predict survival outcomes11
and classifica-
tion12
. For the latter, Yu et al.12
combined conventional thresholding
and image processing techniques with machine-learning methods,
such as random forest classifiers, support vector machines (SVM) or
Naive Bayes classifiers, achieving an AUC of ~0.85 in distinguishing
normal from tumor slides, and ~0.75 in distinguishing LUAD from
LUSC slides. More recently, deep learning was used for the classi-
fication of breast, bladder and lung tumors, achieving an AUC of
0.83 in classification of lung tumor types on tumor slides from The
Cancer Genome Atlas (TCGA)13
. Analysis of plasma DNA values
was also shown to be a good predictor of the presence of non–small
cell cancer, with an AUC of ~0.94 (ref. 14
) in distinguishing LUAD
from LUSC, whereas the use of immunochemical markers yields an
AUC of ~0.94115
.
Here, we demonstrate how the field can further benefit from deep
learning by presenting a strategy based on convolutional neural
networks (CNNs) that not only outperforms methods in previously
Classification and mutation prediction from
non–small cell lung cancer histopathology
images using deep learning
Nicolas Coudray 1,2,9
, Paolo Santiago Ocampo3,9
, Theodore Sakellaropoulos4
, Navneet Narula3
,
Matija Snuderl3
, David Fenyö5,6
, Andre L. Moreira3,7
, Narges Razavian 8
* and Aristotelis Tsirigos 1,3
*
Visual inspection of histopathology slides is one of the main methods used by pathologists to assess the stage, type and sub-
type of lung tumors. Adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) are the most prevalent subtypes of lung
cancer, and their distinction requires visual inspection by an experienced pathologist. In this study, we trained a deep con-
volutional neural network (inception v3) on whole-slide images obtained from The Cancer Genome Atlas to accurately and
automatically classify them into LUAD, LUSC or normal lung tissue. The performance of our method is comparable to that of
pathologists, with an average area under the curve (AUC) of 0.97. Our model was validated on independent datasets of frozen
tissues, formalin-fixed paraffin-embedded tissues and biopsies. Furthermore, we trained the network to predict the ten most
commonly mutated genes in LUAD. We found that six of them—STK11, EGFR, FAT1, SETBP1, KRAS and TP53—can be pre-
dicted from pathology images, with AUCs from 0.733 to 0.856 as measured on a held-out population. These findings suggest
that deep-learning models can assist pathologists in the detection of cancer subtype or gene mutations. Our approach can be
applied to any cancer type, and the code is available at https://github.com/ncoudray/DeepPATH.
NATURE MEDICINE | www.nature.com/naturemedicine
• TCGA의 병리 이미지(whole-slide image)를 구글넷(Inception v3)으로 학습
• 정상, adenocarcinoma(LUAD), squamous cell carcinoma(LUSC) 정확하게 구분
• Tumor vs. normal, LUAD vs. LUSC 의 구분에 AUC 0.99, 0.95 이상
• Normal, LUAD, LUSC 중 하나를 다른 두 가지와 구분하는 것도 5x 20x 모두 AUC 0.9 이상
• 이 정확도는 세 명의 병리과 전문의와 동등한 수준
• 딥러닝이 틀린 것 중에 50%는, 병리과 전문의 세 명 중 적어도 한 명이 틀렸고,
• 병리과 전문의 세 명 중 적어도 한 명이 틀린 케이스 중, 83%는 딥러닝이 정확히 분류했다.
Nat Med 2018
27. • 더 나아가서 TCGA를 바탕으로 개발된 인공지능을,
• 완전히 독립적인 데이터셋, 특히 fresh frozen, FFPE, biopsy 의 세 가지 방식으로 얻은
• LUAD, LUSC 데이터에 적용해보았을 때에도 대부분 AUC 0.9 이상으로 정확하게 판독
fibrosis, inflammation or blood was also present, but also in very
poorly differentiated tumors. Sections obtained from biopsies are
usually much smaller, which reduces the number of tiles per slide,
but the performance of our model remains consistent for the 102
samples tested (AUC ~0.834–0.861 using 20×magnification and
0.871–0.928 using 5×magnification; Fig. 2c), and the accuracy
the tumor area on the frozen and FFPE samples, then applied this
model to the biopsies and finally applied the TCGA-trained three-
way classifier on the tumor area selected by the automatic tumor
selection model. The per-tile AUC of the automatic tumor selection
model (using the pathologist’s tumor selection as reference) was
0.886 (CI, 0.880–0.891) for the biopsies, 0.797 (CI, 0.795–0.800)
LUAD at 5×
AUC = 0.919, CI = 0.861–0.949
1
a
b
c
0.5
Truepositive
0
0 0.5
False positive
1
1
0.5
Truepositive
0
0 0.5
False positive
1
1
0.5
Truepositive
0
0 0.5
False positive
1
Frozen
FFPE
Biopsies
LUSC at 5×
AUC = 0.977, CI = 0.949–0.995
LUAD at 20×
AUC = 0.913, CI = 0.849–0.963
LUSC at 20×
AUC = 0.941, CI = 0.894–0.977
LUAD at 5×
AUC = 0.861, CI = 0.792–0.919
LUSC at 5×
AUC = 0.975, CI = 0.945–0.996
LUAD at 20×
AUC = 0.833, CI = 0.762–0.894
LUSC at 20×
AUC = 0.932, CI = 0.884–0.971
LUAD at 5×
AUC = 0.871, CI = 0.784–0.938
LUSC at 5×
AUC = 0.928, CIs = 0.871–0.972
LUAD at 20×
AUC = 0.834, CI = 0.743–0.909
LUSC at 20×
AUC = 0.861, CI = 0.780–0.928
Fig. 2 | Classification of presence and type of tumor on alternative cohorts. a–c, Receiver operating characteristic (ROC) curves (left) from tests on
frozen sections (n=98 biologically independent slides) (a), FFPE sections (n=140 biologically independent slides) (b) and biopsies (n=102 biologically
independent slides) from NYU Langone Medical Center (c). On the right of each plot, we show examples of raw images with an overlap in light gray of the
mask generated by a pathologist and the corresponding heatmaps obtained with the three-way classifier. Scale bars, 1mm.
Frozen
FFPE
Biopsy
28. interoperative tumor diagnosis
of surgical specimen
cancer immunotherapy
response assessment
augmentation of pathologists’
manual assessment
analytical
validity
additive effect
with pathologist
Prediction of
genetic characteristic
AI in Pathology