Invariant Conditional Molecular Generation Under Distribution Shift

Conditional molecular generation, aiming to generate 2D and 3D molecules that satisfy given properties, has achieved remarkable progress, thanks to the advances in deep generative models such as graph diffusion. However, existing methods generally assume that the given conditions for training and testing are consistent, failing to handle the realistic challenge when there exist distribution shifts between training and testing conditions. Invariant learning is a mainstream paradigm for addressing distribution shifts, but fusing invariant learning principles with conditional molecular generation faces three core challenges: (1) existing invariant learning methods focus on discriminative tasks and cannot be directly adapted to molecule generative tasks; (2) how to distinguish between invariant subgraph and variant subgraph of a molecule graph, which is treated as an integrated input; (3) how to fuse invariant subgraphs, variant subgraphs, and property conditions for effective generation. To tackle these challenges, we propose Invariant Conditional MOLecular generation (IC-MOL), a framework that combines invariant learning with graph diffusion to improve the generalization ability of conditional molecular generation under distribution shifts. Specifically, we first disentangle molecular graphs into invariant and variant subgraphs while maintaining SE(3) equivariance, an important inductive bias for molecular generation. On this basis, we further design a two-phase graph diffusion generation model. In the first phase, we generate an invariant molecular consistent with the target property. In the second phase, we propose a cross-attention mechanism to fuse variant subgraph representations and property conditions to guide the generation of complete molecules while maintaining property alignment. Extensive experiments on the benchmark dataset show that IC-MOL consistently outperforms state-of-the-art baselines across six property conditions under distribution shifts.