Transfer Learning and Machine Learning for Training Five Year Survival Prognostic Models in Early Breast Cancer
Abstract
Prognostic information is essential for decision-making in breast cancer management. Recently trials have predominantly focused on genomic prognostication tools, even though clinicopathological prognostication is less costly and more widely accessible. Machine learning (ML), transfer learning and ensemble integration offer opportunities to build robust prognostication frameworks. We evaluate this potential to improve survival prognostication in breast cancer by comparing de-novo ML, transfer learning from a pre-trained prognostic tool and ensemble integration. Data from the MA.27 trial was used for model training, with external validation on the TEAM trial and a SEER cohort. Transfer learning was applied by fine-tuning the pre-trained prognostic tool PREDICT v3, de-novo ML included Random Survival Forests and Extreme Gradient Boosting, and ensemble integration was realized through a weighted sum of model predictions. Transfer learning, de-novo RSF, and ensemble integration improved calibration in MA.27 over the pre-trained model (ICI reduced from 0.042 in PREDICT v3 to <=0.007) while discrimination remained comparable (AUC increased from 0.738 in PREDICT v3 to 0.744-0.799). Invalid PREDICT v3 predictions were observed in 23.8-25.8% of MA.27 individuals due to missing information. In contrast, ML models and ensemble integration could predict survival regardless of missing information. Across all models, patient age, nodal status, pathological grading and tumor size had the highest SHAP values, indicating their importance for survival prognostication. External validation in SEER, but not in TEAM, confirmed the benefits of transfer learning, RSF and ensemble integration. This study demonstrates that transfer learning, de-novo RSF, and ensemble integration can improve prognostication in situations where relevant information for PREDICT v3 is lacking or where a dataset shift is likely.
Authors 23
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University of Ottawa · Children's Hospital of Eastern Ontario
Affiliation as printed
Children's Hospital of Eastern Ontario Research Institute , Ontario , Canada
School of Epidemiology and Public Health , University of Ottawa , Ontario , Canada
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Affiliation as printed
Division of Medical Oncology , Department of Medicine , The University of Ottawa , Ontario , Ottawa , Canada
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Affiliation as printed
Department of Oncology , McMaster University , Hamilton , Ontario , Canada
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Ottawa Hospital Research Institute
Affiliation as printed
Cancer Therapeutics Program , The Ottawa Hospital Research Institute , Ottawa , Ontario , Canada
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Ottawa Hospital · Ottawa Hospital Research Institute
Affiliation as printed
Ottawa Hospital Cancer Center , The Ottawa Hospital Research Institute , Ottawa , Ontario , Canada
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Affiliation as printed
Division of Medical Oncology , Department of Medicine , The University of Ottawa , Ontario , Ottawa , Canada
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Centre Hospitalier de l’Université de Montréal · Université de Montréal
Affiliation as printed
CHUM , Division of Medical Oncology and Hematology , Université de Montréal , Montreal , Quebec , Canada
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Queen's University · Canadian Cancer Trials Group
Affiliation as printed
Canadian Canadian Cancer Trials Group , Queen's University , Kingston , Ontario , Canada
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Queen's University · Canadian Cancer Trials Group
Affiliation as printed
Canadian Canadian Cancer Trials Group , Queen's University , Kingston , Ontario , Canada
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Edinburgh Cancer Research · Institute of Genetics and Cancer · University of Edinburgh
Affiliation as printed
Edinburgh Cancer Research , Institute of Genetics and Cancer , University of Edinburgh , Edinburgh , United Kingdom
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Edinburgh Cancer Research · Institute of Genetics and Cancer · University of Edinburgh
Affiliation as printed
Edinburgh Cancer Research , Institute of Genetics and Cancer , University of Edinburgh , Edinburgh , United Kingdom
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Ontario Institute for Cancer Research · University of Toronto
Affiliation as printed
Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
Diagnostic Development , Ontario Institute for Cancer Research , Toronto , Ontario , Canada
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Ontario Institute for Cancer Research
Affiliation as printed
Diagnostic Development , Ontario Institute for Cancer Research , Toronto , Ontario , Canada
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Ontario Institute for Cancer Research · University of Toronto
Affiliation as printed
Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
Diagnostic Development , Ontario Institute for Cancer Research , Toronto , Ontario , Canada
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Leiden University Medical Center
Affiliation as printed
Department of Surgery , Leiden University Medical Center , Leiden , the Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Surgery , Leiden University Medical Center , Leiden , the Netherlands
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Affiliation as printed
St. Augustinus Hospital , Antwerp , Belgium
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Glasgow Life · Royal College of Physicians and Surgeons of Glasgow · University of Glasgow
Affiliation as printed
Department of Pathology , Glasgow , United Kingdom
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University Medical Center of the Johannes Gutenberg University Mainz
Affiliation as printed
Department of Gynecology and Obstetrics , University Center Mainz , Mainz , Germany
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Children's Hospital of Eastern Ontario
Affiliation as printed
Children's Hospital of Eastern Ontario Research Institute , Ontario , Canada
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Affiliation as printed
Division of Medical Oncology , Department of Medicine , The University of Ottawa , Ontario , Ottawa , Canada
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University of Ottawa · Children's Hospital of Eastern Ontario
Affiliation as printed
Children's Hospital of Eastern Ontario Research Institute , Ontario , Canada
School of Epidemiology and Public Health , University of Ottawa , Ontario , Canada
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