Assessing Foundation Models' Transferability to Physiological Signals in Precision Medicine
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arXiv
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| Auteurs principaux: | , , , , |
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| Format: | Preprint |
| Publié: |
2024
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| _version_ | 1866916507370389504 |
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| author | Christenson, Matthias Geary, Cove Locke, Brian Koirala, Pranav Pettine, Warren Woodrich |
| author_facet | Christenson, Matthias Geary, Cove Locke, Brian Koirala, Pranav Pettine, Warren Woodrich |
| contents | The success of precision medicine requires computational models that can effectively process and interpret diverse physiological signals across heterogeneous patient populations. While foundation models have demonstrated remarkable transfer capabilities across various domains, their effectiveness in handling individual-specific physiological signals - crucial for precision medicine - remains largely unexplored. This work introduces a systematic pipeline for rapidly and efficiently evaluating foundation models' transfer capabilities in medical contexts. Our pipeline employs a three-stage approach. First, it leverages physiological simulation software to generate diverse, clinically relevant scenarios, particularly focusing on data-scarce medical conditions. This simulation-based approach enables both targeted capability assessment and subsequent model fine-tuning. Second, the pipeline projects these simulated signals through the foundation model to obtain embeddings, which are then evaluated using linear methods. This evaluation quantifies the model's ability to capture three critical aspects: physiological feature independence, temporal dynamics preservation, and medical scenario differentiation. Finally, the pipeline validates these representations through specific downstream medical tasks. Initial testing of our pipeline on the Moirai time series foundation model revealed significant limitations in physiological signal processing, including feature entanglement, temporal dynamics distortion, and reduced scenario discrimination. These findings suggest that current foundation models may require substantial architectural modifications or targeted fine-tuning before deployment in clinical settings. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2412_03427 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Assessing Foundation Models' Transferability to Physiological Signals in Precision Medicine Christenson, Matthias Geary, Cove Locke, Brian Koirala, Pranav Pettine, Warren Woodrich Machine Learning The success of precision medicine requires computational models that can effectively process and interpret diverse physiological signals across heterogeneous patient populations. While foundation models have demonstrated remarkable transfer capabilities across various domains, their effectiveness in handling individual-specific physiological signals - crucial for precision medicine - remains largely unexplored. This work introduces a systematic pipeline for rapidly and efficiently evaluating foundation models' transfer capabilities in medical contexts. Our pipeline employs a three-stage approach. First, it leverages physiological simulation software to generate diverse, clinically relevant scenarios, particularly focusing on data-scarce medical conditions. This simulation-based approach enables both targeted capability assessment and subsequent model fine-tuning. Second, the pipeline projects these simulated signals through the foundation model to obtain embeddings, which are then evaluated using linear methods. This evaluation quantifies the model's ability to capture three critical aspects: physiological feature independence, temporal dynamics preservation, and medical scenario differentiation. Finally, the pipeline validates these representations through specific downstream medical tasks. Initial testing of our pipeline on the Moirai time series foundation model revealed significant limitations in physiological signal processing, including feature entanglement, temporal dynamics distortion, and reduced scenario discrimination. These findings suggest that current foundation models may require substantial architectural modifications or targeted fine-tuning before deployment in clinical settings. |
| title | Assessing Foundation Models' Transferability to Physiological Signals in Precision Medicine |
| topic | Machine Learning |
| url | https://arxiv.org/abs/2412.03427 |