Bias Reduction in Representation of Histopathology Images Using Deep Feature Selection
Bibliographic record
Abstract
Abstract Appearing traces of bias in deep networks is a serious issue that can play a significant role in ethics and generalization. Recent studies report that the deep features extracted from the histopathology images of The Cancer Genome Atlas (TCGA), the largest publicly available archive of 11,000 patients covering 25 organs and 32 cancer subtypes, are surprisingly able to accurately classify the whole slide images (WSIs) based on their acquisition site. This is clear evidence that the utilized Deep Neural Networks (DNNs) unexpectedly detect the specific patterns of the source site rather than histomorphologic patterns, biased behaviour resulting in degraded generalization. This observation motivated us to propose a method to alleviate the destructive impact of hospital bias through a novel feature selection process. To this effect, we have proposed an evolutionary strategy select a small set of optimal features to not only accurately represent the histological patterns of tissue samples but also to eliminate the features leading to internal bias toward the institution. The performance of the proposed method has been assessed using the features extracted from TCGA images made available by NIH (National Institute of Health). The selected features extracted by a state-of-the-art network trained on TCGA images (i.e., the KimiaNet), considerably decreased the institutional bias. The proposed scheme is not limited to DNNs and/or specific types of biases; it can be employed to reduce various kinds of bias in a much more comprehensive range of data-driven feature extraction models. The conducted experiments, the external validation in specific, clearly demonstrate that the bias cannot be fully controlled just during training a model. Therefore, a feature selection for downstream tasks plays a crucial role in significantly reducing the bias.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".