Decoupled Prune-and-Reconstruct: Training on a Compact Core with Double-Layer Sparsification

Siqi Gu, Gaozhen Ma, Liheng Huang, Weiqi He, Jiawen Luo +2

On million-node graphs, the memory wall arrives before the compute wall: a GNN that never fits in VRAM cannot deliver the all-node inference its accuracy promises. The standard remedy, pruning, has always been an accuracy tax - paid once and never refunded. DPR refuses this framing. Its central insight is that the mask that shrinks training can also scaffold recovery: one compact node set bounds both computations of graph learning, serving as the encoder's training graph and, at inference, as the anchor from which a sparse structure-aware decoder rebuilds every pruned node (double-layer sparsification). The order is inverted - prune for efficiency, then reconstruct for accuracy - and the tax is repaid: the deployed 30%-budget model trains in 1,450 MiB of peak memory on one 6 GB GPU and recovers 96.9% of its dense-reconstruction reference, beating a same-GPU rerun of the edge-sparsification baseline DSpar by +1.36 pp at 50.1% lower peak training memory; against the same-protocol full-batch no-prune encoder the deployed point pays a measured 2.64 pp accuracy tax for a 2.8x smaller training footprint. Pruning without reconstruction leaves the encoder at 0.378 within the same…