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Title: Classification and Disease Localization in Histopathology Using Only Global Labels: A Weakly-Supervised Approach

Paper content:
Analysis of histopathology slides is a critical step for many diagnoses, and in particular in oncology where it defines the gold standard.
In the case of digital histopathological analysis, highly trained pathologists must review vast whole-slide-images of extreme digital resolution (100,000^2 pixels) across multiple zoom levels in order to locate abnormal regions of cells, or in some cases single cells, out of millions.
The application of deep learning to this problem is hampered not only by small sample sizes, as typical datasets contain only a few hundred samples, but also by the generation of ground-truth localized annotations for training interpretable classification and segmentation models.
We propose a method for disease available during training.
Even without pixel-level annotations, we are able to demonstrate performance comparable with models trained with strong annotations on the Camelyon-16 lymph node metastases detection challenge.
We accomplish this through the use of pre-trained deep convolutional networks, feature embedding, as well as learning via top instances and negative evidence, a multiple instance learning technique fromatp the field of semantic segmentation and object detection.
Histopathological image analysis (HIA) is a critical element of diagnosis in many areas of medicine, and especially in oncology, where it defines the gold standard metric.
Recent works have sought to leverage modern developments in machine learning (ML) to aid pathologists in disease detection tasks, but the majority of these techniques require localized annotation masks as training data.
These annotations are even more costly to obtain than the original diagnosis, as pathologists must spend time to assemble pixel-by-pixel segmentation maps of diseased tissue at extreme resolution, thus HIA datasets with annotations are very limited in size.
Additionally, such localized annotations may not be available when facing new problems in HIA, such as new disease subtybe classification, prognosis estimation, or drug response prediction.
Thus, the critical question for HIA is: can one design a learning architecture which achieves accurate classification with no additional localized annotation?
A successful technique would be able train algorithms to assist pathologists during analysis, and could also be used to identify previously unknown structures and regions of interest.Indeed, while histopathology is the gold standard diagnostic in oncology, it is extremely costly, requiring many hours of focus from pathologists to make a single diagnosis BID21 BID30 .
Additionally, as correct diagnosis for certain diseases requires pathologists to identify a few cells out of millions, these tasks are akin to "finding a needle in a haystack."
Hard numbers on diagnostic error rates in histopathology are difficult to obtain, being dependent upon the disease and tissue in question as well as self-reporting by pathologists of diagnostic errors.
However, as reported in the review of BID25 , false negatives in cancer diagnosis can lead not only to catastrophic consequences for the patient, but also to incredible financial risk to the pathologist.
Any tool which can aid pathologists to focus their attention and effort to the must suspect regions can help reduce false-negatives and improve patient outcomes through more accurate diagnoses BID8 .
Medical researchers have looked to computer-aided diagnosis for decades, but the lack of computational resources and data have prevented wide-spread implementa-tion and usage of such tools BID11 .
Since the advent of automated digital WSI capture in the 1990s, researchers have sought approaches for easing the pathologist's workload and improve patient outcomes through image processing algorithms BID11 BID22 .
Rather than predicting final diagnosis, many of these procedures focused instead on segmentation, either for cell-counting, or for the detection of suspect regions in the WSI.
Historical methods have focused on the use of hand-crafted texture or morphological BID5 features used in conjunction with unsupervised techniques such as K-means clustering or other dimensionality reduction techniques prior to classification via k-Nearest Neighbor or a support vector machine.Over the past decade, fruitful developments in deep learning BID19 have lead to an explosion of research into the automation of image processing tasks.
While the application of such advanced ML techniques to image tasks has been successful for many consumer applications, the adoption of such approaches within the field of medical imaging has been more gradual.
However, these techniques demonstrate remarkable promise in the field of HIA.
Specifically, in digital pathology with whole-slide-imaging (WSI) BID33 BID26 , highly trained and skilled pathologists review digitally captured microscopy images from prepared and stained tissue samples in order to make diagnoses.
Digital WSI are massive datasets, consisting of images captured at multiple zoom levels.
At the greatest magnification levels, a WSI may have a digital resolution upwards of 100 thousand pixels in both dimensions.
However, since localized annotations are very difficult to obtain, datasets may only contain WSI-level diagnosis labels, falling into the category of weakly-supervised learning.The use of DCNNs was first proposed for HIA in BID3 , where the authors were able to train a model for mitosis detection in H&E stained images.
A similar technique was applied for WSI for the detection of invasive ductal carcinoma in BID4 .
These approaches demonstrated the usefulness of learned features as an effective replacement for hand-crafted image features.
It is possible to train deep architectures from scratch for the classification of tile images BID29 BID13 .
However, training such DCNN architectures can be extremely resource intensive.
For this reason, many recent approaches applying DCNNs to HIA make use of large pre-trained networks to act as rich feature extractors for tiles BID15 BID17 BID21 BID32 BID27 .
Such approaches have found success as aggregation of rich representations from pre-trained DCNNs has proven to be quite effective, even without from-scratch training on WSI tiles.In this paper, we propose CHOWDER 1 , an approach for the interpretable prediction of general localized diseases in WSI with only weak, whole-image disease labels and without any additional expert-produced localized annotations, i.e. per-pixel segmentation maps, of diseased areas within the WSI.
To accomplish this, we modify an existing architecture from the field of multiple instance learning and object region detection BID9 to WSI diagnosis prediction.
By modifying the pre-trained DCNN model BID12 , introducing an additional set of fully-connected layers for context-aware classification from tile instances, developing a random tile sampling scheme for efficient training over massive WSI, and enforcing a strict set of regualrizations, we are able to demonstrate performance equivalent to the best human pathologists .
Notably, while the approach we propose makes use of a pre-trained DCNN as a feature extractor, the entire procedure is a true end-to-end classification technique, and therefore the transferred pre-trained layers can be fine-tuned to the context of H&E WSI.
We demonstrate, using only whole-slide labels, performance comparable to top-10 ranked methods trained with strong, pixel-level labels on the Camelyon-16 challenge dataset, while also producing disease segmentation that closely matches ground-truth annotations.
We also present results for diagnosis prediction on WSI obtained from The Cancer Genome Atlas (TCGA), where strong annotations are not available and diseases may not be strongly localized within the tissue sample.
We have shown that using state-of-the-art techniques from MIL in computer vision, such as the top instance and negative evidence approach of BID9 , one can construct an effective technique for diagnosis prediction and disease location for WSI in histopathology without the need Table 2 : Final leader boards for Camelyon-16 competition.
All competition methods had access to the full set of strong annotations for training their models.
In contrast, our proposed approach only utilizes image-wide diagnosis levels and obtains comparable performance as top-10 methods.
for expensive localized annotations produced by expert pathologists.
By removing this requirement, we hope to accelerate the production of computer-assistance tools for pathologists to greatly improve the turn-around time in pathology labs and help surgeons and oncologists make rapid and effective patient care decisions.
This also opens the way to tackle problems where expert pathologists may not know precisely where relevant tissue is located within the slide image, for instance for prognosis estimation or prediction of drug response tasks.
The ability of our approach to discover associated regions of interest without prior localized annotations hence appears as a novel discovery approach for the field of pathology.
Moreover, using the suggested localization from CHOWDER, one may considerably speed up the process of obtaining ground-truth localized annotations.A number of improvements can be made in the CHOWDER method, especially in the production of disease localization maps.
As presented, we use the raw values from convolutional embedding layer, which means that the resolution of the produced disease localization map is fixed to that of the sampled tiles.
However, one could also sample overlapping tiles and then use a data fusion technique to generate a final localization map.
Additionally, as a variety of annotations may be available, CHOWDER could be extended to the case of heterogenous annotation, e.g. some slides with expert-produced localized annotations and those with only whole-slide annotations.A FURTHER RESULTS Figure 5 : Visualization of metastasis detection on test image 2 of the Camelyon-16 dataset using our proposed approach.
Left: Full WSI at zoom level 6 with ground truth annotation of metastases shown via black border.
Tiles with positive feature embeddings are colored from white to red according to their magnitude, with red representing the largest magnitude.
Right: Detail of metastases at zoom level 2 overlaid with classification output of our proposed approach.
Here, the output of all tested tiles are shown and colored according to their value, from blue to white to red, with blue representing the most negative values, and red the most positive.
Tiles without color were not included when randomly selecting tiles for inference.
Figure 6 : Visualization of metastasis detection on test image 92 of the Camelyon-16 dataset using our proposed approach.
Left: Full WSI at zoom level 6 with ground truth annotation of metastases shown via black border.
Tiles with positive feature embeddings are colored from white to red according to their magnitude, with red representing the largest magnitude.
Right: Detail of metastases at zoom level 2 overlaid with classification output of our proposed approach.
Here, the output of all tested tiles are shown and colored according to their value, from blue to white to red, with blue representing the most negative values, and red the most positive.
Tiles without color were not included when randomly selecting tiles for inference.

assistant: text: We propose a weakly supervised learning method for the classification and localization of cancers in extremely high resolution histopathology whole slide images using only image-wide labels.