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arxiv preprint

Cancer diagnosis, prognosis, and therapeutic response predictions are based on morphological information from histology slides and molecular profiles from genomic data. However, most deep learning-based objective outcome prediction and grading paradigms are based on histology or genomics alone and do not make use of the complementary information in an intuitive manner. In this work, we propose Pathomic Fusion, a strategy for end-to-end multimodal fusion of histology image and genomic (mutations, CNV, mRNAseq) features for survival outcome prediction. Our approach models pairwise feature interactions across modalities by taking the Kronecker product of gated feature representations and controls the expressiveness of each representation via a gating-based attention mechanism. The proposed framework is able to model pairwise interactions across features in different modalities and control their relative importance. We validate our approach using glioma datasets from the Cancer Genome Atlas (TCGA), which contains paired whole-slide image, genotype, and transcriptome data with ground truth survival and histologic grade labels. Based on a rigorous 15-fold cross-validation, our results demonstrate that the proposed multimodal fusion paradigm improves prognostic determinations from grading and molecular subtyping as well as unimodal deep networks trained on histology and genomic data alone. The proposed method establishes insight and theory on how to train deep networks on multimodal biomedical data in an intuitive manner, which will be useful for other problems in medicine that seek to combine heterogeneous data streams for understanding diseases and predicting response and resistance to treatment.

Richard J. Chen, Ming Y. Lu, Jingwen Wang, Drew F. K. Williamson, Scott J. Rodig, Neal I. Lindeman, Faisal Mahmood