Reducing self-supervised learning complexity improves weakly-supervised classification performance in computational pathology
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866916156738109440 |
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| author | Lenz, Tim Nahhas, Omar S. M. El Ligero, Marta Kather, Jakob Nikolas |
| author_facet | Lenz, Tim Nahhas, Omar S. M. El Ligero, Marta Kather, Jakob Nikolas |
| contents | Deep Learning models have been successfully utilized to extract clinically actionable insights from routinely available histology data. Generally, these models require annotations performed by clinicians, which are scarce and costly to generate. The emergence of self-supervised learning (SSL) methods remove this barrier, allowing for large-scale analyses on non-annotated data. However, recent SSL approaches apply increasingly expansive model architectures and larger datasets, causing the rapid escalation of data volumes, hardware prerequisites, and overall expenses, limiting access to these resources to few institutions. Therefore, we investigated the complexity of contrastive SSL in computational pathology in relation to classification performance with the utilization of consumer-grade hardware. Specifically, we analyzed the effects of adaptations in data volume, architecture, and algorithms on downstream classification tasks, emphasizing their impact on computational resources. We trained breast cancer foundation models on a large public patient cohort and validated them on various downstream classification tasks in a weakly supervised manner on two external public patient cohorts. Our experiments demonstrate that we can improve downstream classification performance whilst reducing SSL training duration by 90%. In summary, we propose a set of adaptations which enable the utilization of SSL in computational pathology in non-resource abundant environments. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_04558 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Reducing self-supervised learning complexity improves weakly-supervised classification performance in computational pathology Lenz, Tim Nahhas, Omar S. M. El Ligero, Marta Kather, Jakob Nikolas Machine Learning Artificial Intelligence Computer Vision and Pattern Recognition Deep Learning models have been successfully utilized to extract clinically actionable insights from routinely available histology data. Generally, these models require annotations performed by clinicians, which are scarce and costly to generate. The emergence of self-supervised learning (SSL) methods remove this barrier, allowing for large-scale analyses on non-annotated data. However, recent SSL approaches apply increasingly expansive model architectures and larger datasets, causing the rapid escalation of data volumes, hardware prerequisites, and overall expenses, limiting access to these resources to few institutions. Therefore, we investigated the complexity of contrastive SSL in computational pathology in relation to classification performance with the utilization of consumer-grade hardware. Specifically, we analyzed the effects of adaptations in data volume, architecture, and algorithms on downstream classification tasks, emphasizing their impact on computational resources. We trained breast cancer foundation models on a large public patient cohort and validated them on various downstream classification tasks in a weakly supervised manner on two external public patient cohorts. Our experiments demonstrate that we can improve downstream classification performance whilst reducing SSL training duration by 90%. In summary, we propose a set of adaptations which enable the utilization of SSL in computational pathology in non-resource abundant environments. |
| title | Reducing self-supervised learning complexity improves weakly-supervised classification performance in computational pathology |
| topic | Machine Learning Artificial Intelligence Computer Vision and Pattern Recognition |
| url | https://arxiv.org/abs/2403.04558 |