PathologyGAN: Learning Deep Representations of Cancer Tissue
Bibliographic record
Abstract
Histopathological images of tumours contain abundant information about how tumours grow and how they interact with their micro-environment. Better understanding of tissue phenotypes in these images could reveal novel determinants of pathological processes underlying cancer, and in turn improve diagnosis and treatment options. Advances of Deep learning makes it ideal to achieve those goals, however, its application is limited by the cost of high quality labels from patients data. Unsupervised learning, in particular, deep generative models with representation learning properties provides an alternative path to further understand cancer tissue phenotypes, capturing tissue morphologies. \n \nIn this paper, we develop a framework which allows Generative Adversarial Networks (GANs) to capture key tissue features and uses these characteristics to give structure to its latent space. To this end, we trained our model on two different datasets, an H and E colorectal cancer tissue from the National Center for Tumor diseases (NCT, Germany) and an H and E breast cancer tissue from the Netherlands Cancer Institute (NKI, Netherlands) and Vancouver General Hospital (VGH, Canada). Composed of 86 slide images and 576 tissue micro-arrays (TMAs) respectively. \n \nWe show that our model generates high quality images, with a Frechet Inception Distance (FID) of 16.65 (breast cancer) and 32.05 (colorectal cancer). We further assess the quality of the images with cancer tissue characteristics (e.g. count of cancer, lymphocytes, or stromal cells), using quantitative information to calculate the FID and showing consistent performance of 9.86. Additionally, the latent space of our model shows an interpretable structure and allows semantic vector operations that translate into tissue feature transformations. Furthermore, ratings from two expert pathologists found no significant difference between our generated tissue images from real ones. \n \nThe code, generated images, and pretrained model are available at https://github.com/AdalbertoCq/Pathology-GAN
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".