Path-GPTOmic: A Balanced Multi-modal Learning Framework for Survival Outcome Prediction
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arXiv
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| Autori principali: | , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866913269437956096 |
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| author | Wang, Hongxiao Yang, Yang Zhao, Zhuo Gu, Pengfei Sapkota, Nishchal Chen, Danny Z. |
| author_facet | Wang, Hongxiao Yang, Yang Zhao, Zhuo Gu, Pengfei Sapkota, Nishchal Chen, Danny Z. |
| contents | For predicting cancer survival outcomes, standard approaches in clinical research are often based on two main modalities: pathology images for observing cell morphology features, and genomic (e.g., bulk RNA-seq) for quantifying gene expressions. However, existing pathology-genomic multi-modal algorithms face significant challenges: (1) Valuable biological insights regarding genes and gene-gene interactions are frequently overlooked; (2) one modality often dominates the optimization process, causing inadequate training for the other modality. In this paper, we introduce a new multi-modal ``Path-GPTOmic" framework for cancer survival outcome prediction. First, to extract valuable biological insights, we regulate the embedding space of a foundation model, scGPT, initially trained on single-cell RNA-seq data, making it adaptable for bulk RNA-seq data. Second, to address the imbalance-between-modalities problem, we propose a gradient modulation mechanism tailored to the Cox partial likelihood loss for survival prediction. The contributions of the modalities are dynamically monitored and adjusted during the training process, encouraging that both modalities are sufficiently trained. Evaluated on two TCGA(The Cancer Genome Atlas) datasets, our model achieves substantially improved survival prediction accuracy. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_11375 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Path-GPTOmic: A Balanced Multi-modal Learning Framework for Survival Outcome Prediction Wang, Hongxiao Yang, Yang Zhao, Zhuo Gu, Pengfei Sapkota, Nishchal Chen, Danny Z. Computer Vision and Pattern Recognition Machine Learning Genomics For predicting cancer survival outcomes, standard approaches in clinical research are often based on two main modalities: pathology images for observing cell morphology features, and genomic (e.g., bulk RNA-seq) for quantifying gene expressions. However, existing pathology-genomic multi-modal algorithms face significant challenges: (1) Valuable biological insights regarding genes and gene-gene interactions are frequently overlooked; (2) one modality often dominates the optimization process, causing inadequate training for the other modality. In this paper, we introduce a new multi-modal ``Path-GPTOmic" framework for cancer survival outcome prediction. First, to extract valuable biological insights, we regulate the embedding space of a foundation model, scGPT, initially trained on single-cell RNA-seq data, making it adaptable for bulk RNA-seq data. Second, to address the imbalance-between-modalities problem, we propose a gradient modulation mechanism tailored to the Cox partial likelihood loss for survival prediction. The contributions of the modalities are dynamically monitored and adjusted during the training process, encouraging that both modalities are sufficiently trained. Evaluated on two TCGA(The Cancer Genome Atlas) datasets, our model achieves substantially improved survival prediction accuracy. |
| title | Path-GPTOmic: A Balanced Multi-modal Learning Framework for Survival Outcome Prediction |
| topic | Computer Vision and Pattern Recognition Machine Learning Genomics |
| url | https://arxiv.org/abs/2403.11375 |