Abstract PO-080: Predicting relapse in patients with triple negative breast cancer (TNBC) using a deep-learning approach
Bibliographic record
Abstract
Abstract The abundance and/or precise location of tumor infiltrating lymphocytes (TILs), especially CD8+ T cells, can serve as a prognostic indicator in various types of solid tumors. However, it is often difficult to select an appropriate algorithm in order to stratify patients into well-defined risk groups. More importantly, patient stratification results often depends on the selection of tumor regions, where subjective judgement could affect the final results. On the other hand, machine-learning approaches can help to stratify patients in an objective and automatic fashion. Based on immunofluorescence (IF) images of CD8+ T lymphocytes and cancer cells, we develop a machine-learning approach which can predict the risk of relapse for patients with Triple Negative Breast Cancer (TNBC). Tumor-section images from 9 patients with poor outcome and 15 patients with good outcome were used as a training set. Tumor-section images of 29 patients in an independent cohort were used to test the predictive power of our algorithm. One of the key innovations is dissecting the section images into patches in a size of 640 µm x 640 µm for training and test, which allows one to make use of the information in the section images despite the small number of patients. In the test cohort, 6 (out of 29) patients who belong to the poor-outcome group were all correctly identified by our algorithm; for the 23 (out of 29) patients who belong to the good-outcome group, 17 were correctly predicted with some evidence that improvement is possible if other measures, such as the grade of tumors, are factored in. Our approach does not involve arbitrarily defined metrics and can be applied to other types of cancer in which the abundance/location of CD8+ T lymphocytes/other types of cells is an indicator of prognosis. Furthermore, we showed that using limited parts of the tumor section image for predictions would give rise to inaccurate results, which suggests that tumor heterogeneity should be carefully taken into account for a rigorous evaluation of the outcome. In summary, despite the limited number of patients, we demonstrated that the deep-learning approach can make good use information in the infiltration pattern of CD8+ T lymphocytes and thereby enable prognosis. Additional data collection efforts should be made to eventually enable a more rigorous analysis. Citation Format: Guangyuan Yu, Xuefei Li, Ting-Fang He, Tina Gruosso, Dongmei Zuo, Margarita Souleimanova, Valentina Muñoz Ramos, Atilla Omeroglu, Sarkis Meterissian, Marie-Christine Guiot, Li Yang, Yuan Yuan, Morag Park, Peter P. Lee, Herbert Levine. Predicting relapse in patients with triple negative breast cancer (TNBC) using a deep-learning approach [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-080.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| 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".