Cancer survival analysis with multimodal data is crucial for precise treatments and patient benefits. However, the following challenges prohibit integrating histopathology and genomics: (i) multimodal data is not always complete, especially for the more costly genomics data; (ii) intricate interactions between different modalities are difficult to capture and understand. To response, we propose an end-to-end framework (CIMA) that coordinates Cyclic modality generation and Multi-grained multimodal Alignment. Specifically, CIMA designs a cyclic modality reconstruction module to reciprocally impute missing modalities and infer the interactions between them. Next, it introduces the multi-grained alignment module over the imputed data and interactions to mine fine-grained alignments between histopathology (slide patches) and genomics (biological pathways). CIMA then constructs the adaptive fusion module to leverage multimodal data and alignments for survival prediction. Extensive experiments on cancer benchmark datasets demonstrate that CIMA outperforms existing methods and exhibits good interpretability, providing valuable insights into intricate relationships between pathological phenotypes and biological pathways.Our code is released in the supplementary materials.

Diagnosing cancer subtypes is a prerequisite for precise treatment. Existing multi-omics data fusion-based diagnostic solutions build on the requisite of sufficient samples with complete multi-omics data, which is challenging to obtain in clinical applications. To address the bottleneck of collecting sufficient samples with complete data in clinical applications, we proposed a flexible integrative model (CancerSD) to diagnose cancer subtype using limited samples with incomplete multi-omics data. CancerSD designs contrastive learning tasks and masking-and-reconstruction tasks to reliably impute missing omics, and fuses available omics data with the imputed ones to accurately diagnose cancer subtypes. To address the issue of limited clinical samples, it introduces a category-level contrastive loss to extend the meta-learning framework, effectively transferring knowledge from external datasets to pretrain the diagnostic model. Experiments on benchmark datasets show that CancerSD not only gives accurate diagnosis, but also maintains a high authenticity and good interpretability. In addition, CancerSD identifies important molecular characteristics associated with cancer subtypes, and it defines the Integrated CancerSD Score that can serve as an independent predictive factor for patient prognosis.