A Generative Shape Compositional Framework to Synthesize Populations of Virtual Chimeras

Haoran Dou, Seppo Virtanen, Nishant Ravikumar, Alejandro F Frangi

Research output: Contribution to journalArticlepeer-review


Generating virtual organ populations that capture sufficient variability while remaining plausible is essential to conduct in silico trials (ISTs) of medical devices. However, not all anatomical shapes of interest are always available for each individual in a population. The imaging examinations and modalities used can vary between subjects depending on their individualized clinical pathways. Different imaging modalities may have various fields of view and are sensitive to signals from other tissues/organs, or both. Hence, missing/partially overlapping anatomical information is often available across individuals. We introduce a generative shape model for multipart anatomical structures, learnable from sets of unpaired datasets, i.e., where each substructure in the shape assembly comes from datasets with missing or partially overlapping substructures from disjoint subjects of the same population. The proposed generative model can synthesize complete multipart shape assemblies coined virtual chimeras (VCs). We applied this framework to build VCs from databases of whole-heart shape assemblies that each contribute samples for heart substructures. Specifically, we propose a graph neural network-based generative shape compositional framework, which comprises two components, a part-aware generative shape model that captures the variability in shape observed for each structure of interest in the training population and a spatial composition network that assembles/composes the structures synthesized by the former into multipart shape assemblies (i.e., VCs). We also propose a novel self-supervised learning scheme that enables the spatial composition network to be trained with partially overlapping data and weak labels. We trained and validated our approach using shapes of cardiac structures derived from cardiac magnetic resonance (MR) images in the UK Biobank (UKBB). When trained with complete and partially overlapping data, our approach significantly outperforms a principal component analysis (PCA)-based shape model (trained with complete data) in terms of generalizability and specificity. This demonstrates the superiority of the proposed method, as the synthesized cardiac virtual populations are more plausible and capture a greater degree of shape variability than those generated by the PCA-based shape model.

Original languageEnglish
Pages (from-to)1-15
Number of pages15
JournalIEEE Transactions on NEural Networks and Learning Systems
Publication statusE-pub ahead of print - 19 Mar 2024


  • Generative model
  • Graph neural network
  • In silico trials (ISTs)
  • Virtual populations
  • in silico trials (ISTs)
  • Shape
  • Computational modeling
  • Anatomical structure
  • Statistics
  • Training
  • Sociology
  • virtual populations
  • graph neural network
  • Biomedical imaging


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