GRACE-VAE couples a graph neural network encoder with a causal discrepancy VAE decoder so that known pathway and protein networks improve learning of latent causal programs and prediction of CRISPR perturbation effects.
Concept-free Causal Disentanglement with Variational Graph Auto-Encoder
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abstract
In disentangled representation learning, the goal is to achieve a compact representation that consists of all interpretable generative factors in the observational data. Learning disentangled representations for graphs becomes increasingly important as graph data rapidly grows. Existing approaches often rely on Variational Auto-Encoder (VAE) or its causal structure learning-based refinement, which suffer from sub-optimality in VAEs due to the independence factor assumption and unavailability of concept labels, respectively. In this paper, we propose an unsupervised solution, dubbed concept-free causal disentanglement, built on a theoretically provable tight upper bound approximating the optimal factor. This results in an SCM-like causal structure modeling that directly learns concept structures from data. Based on this idea, we propose Concept-free Causal VGAE (CCVGAE) by incorporating a novel causal disentanglement layer into Variational Graph Auto-Encoder. Furthermore, we prove concept consistency under our concept-free causal disentanglement framework, hence employing it to enhance the meta-learning framework, called concept-free causal Meta-Graph (CC-Meta-Graph). We conduct extensive experiments to demonstrate the superiority of the proposed models: CCVGAE and CC-Meta-Graph, reaching up to $29\%$ and $11\%$ absolute improvements over baselines in terms of AUC, respectively.
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Causal Representation Learning from Network Data
GRACE-VAE couples a graph neural network encoder with a causal discrepancy VAE decoder so that known pathway and protein networks improve learning of latent causal programs and prediction of CRISPR perturbation effects.