Alignment Matters Inside and Out in Equivariant Graph Flow Matching

Equivariance is central to graph generative models, as it ensures the model respects the permutation symmetry of graphs. However, strict equivariance can increase computational cost due to added architectural constraints, and can slow down convergence because the model must be consistent across a large space of possible node permutations. We study this trade-off for graph generative models. Specifically, we start from an equivariant discrete flow-matching model, and relax its equivariance during training via a controllable symmetry modulation scheme based on sinusoidal positional encodings and node permutations. Experiments first show that symmetry-breaking can accelerate early training by providing an easier learning signal, but at the expense of encouraging shortcut solutions that can cause overfitting, where the model repeatedly generates graphs that are duplicates of the training set. On the contrary, properly modulating the symmetry signal can delay overfitting while accelerating convergence, allowing the model to reach stronger performance with $19\%$ of the baseline training epochs.

We study generative modeling of graphs with recurring subgraph motifs. We propose Flowette, a continuous flow matching framework that employs a graph neural network-based transformer to learn a velocity field over graph representations with node and edge attributes. Our model promotes topology-aware alignment through optimal transport-based coupling and preserves structural fidelity through endpoint- and chemistry-aware regularisation. To incorporate domain-driven structural priors, we introduce graphettes, a new probabilistic family of graph structure models that generalize graphons via controlled structural edits for motifs such as rings, stars, and trees. We theoretically analyze the coupling, invariance, and structural properties of the framework, evaluate it on synthetic and molecular benchmarks, and isolate the contributions of the structural prior, the optimal-transport coupling, and the regularisation terms through controlled ablations. Flowette achieves competitive performance overall, attaining state-of-the-art results on several metrics across multiple benchmarks, highlighting the effectiveness of combining structural priors with flow-based training for modeling complex graph distributions.

Flow matching models learn to transport samples from a simple prior distribution to a complex data distribution. When prior-data pairs are coupled via optimal transport (OT), the learned trajectories are straight and non-crossing, enabling fast, even single-step, generation. However, computing the OT coupling in high dimensions is intractable, and existing methods attempt to solve the OT problem, at the cost of persistent bias or significant overhead. Rather than solving for the OT coupling, we reformulate the problem. Once the prior is treated as a design choice rather than a fixed input, the OT coupling between prior and data is no longer unique. Many priors admit an OT-optimal identity coupling to the data, leaving us free to choose one that is also tractable to sample. We identify low-frequency projection of natural images as such a choice. The identity coupling between data and its low-frequency representation is empirically OT-optimal, the prior is structured enough to be sampled by a lightweight model at inference, and the remaining flow-matching task reduces to synthesizing high-frequency detail. Interpolating the prior with Gaussian noise further improves generation quality while preserving the OT coupling. The approach requires no modifications to the flow model itself, and integrates naturally with latent-space models, classifier-free guidance, and one-step generation frameworks. Across all benchmarks, our method reduces trajectory curvature by more than $2\times$ compared to existing flow matching methods, yielding better generation quality in the few-step regime.