Training-Free Cross-Architecture Merging for Graph Neural Networks

Graph Neural Networks (GNNs) have revolutionized Neural Force Fields for atomistic simulations, achieving near-quantum accuracy at reduced cost, yet adapting these models to new chemical systems requires expensive retraining of foundation models. Inspired by model merging in vision and language processing, we introduce GFFMERGE, the first principled framework for closed-form model merging in GNNs. We exploit the linear structure of message-passing layers and formulate merging as a convex embedding-alignment problem with an analytical solution. Through the first systematic benchmarking of model merging for GNNs, we show that existing methods designed for vision and language catastrophically fail on force field regression, while GFFMERGE recovers performance approaching gold standard joint training. Across molecular (MD17, MD22), solid-state (LiPS20), and large-scale graph benchmarks, GFFMERGE and GNNMERGE (its generic GNN counterpart) achieve 5-27$\times$ speedups while enabling modular composition of specialized models. Remarkably, our closed-form solution alone outperforms all baseline methods before fine-tuning and provides superior initialization for faster, data-efficient convergence.

Weight-space networks operate directly on parameters of other neural networks, enabling tasks such as predicting model properties, editing trained models, and generating weights. Weight-space symmetries such as neuron permutations make equivariance a key design principle. However, existing equivariant weight-space architectures have primarily been studied for transformations that preserve the network architecture. In contrast, many practical transformations, including model compression and upscaling, map a trained source network into a target network with a different architecture. In this setting, the source and target permutation symmetries act on different parameter spaces, making equivariance less straightforward to formulate. Our key idea for addressing this mismatch is to reformulate cross-architecture operators with two inputs: a trained source network and an initialization of the target network. This lets us define equivariant cross-architecture operators that refine the initialization of the target network using information from the source network, while being invariant to source-network permutations and equivariant to target-network permutations. Based on this formulation, we introduce CrossGMN, a graph metanetwork that jointly processes both networks through symmetry-preserving cross-network message passing. We prove CrossGMN is universal for continuous cross-architecture operators on compact sets under a general-position assumption. We evaluate CrossGMN for model compression, predicting a smaller network's parameters to accelerate subsequent knowledge distillation. Across 2-D and 3-D INRs and image classification with MLPs, CNNs, and Vision Transformers, CrossGMN speeds up distillation by up to 8.89x, transfers across datasets without retraining (3.78x), and a single model can accelerate compression from heterogeneous source architectures into a common target architecture.

Model merging consolidates fine-tuned experts into one multi-task model without retraining. All existing data-free methods approach this problem entirely in weight space. Restricted to arithmetic on parameters, these methods never observe how each expert behaves, a signal that only emerges through forward evaluation. Accessing this behavioral signal requires inputs to evaluate on, which the data-free setting prohibits. We propose Merge++, a post-hoc method that addresses this by inverting the expert checkpoints to synthesize task-representative images, then distilling expert knowledge into the merged model using those images. Merge++ requires no additional data beyond the checkpoints themselves. It applies universally across merging algorithms and operates as a complementary refinement stage independent of the underlying weight-space method. The method consistently improves merging algorithms ranging from simple task arithmetic to state-of-the-art spectral methods, with average gains of +2 to +8 points and up to +25.9 on individual configurations.