graph neural network engineers

Abstract: We look at a two-variable logic over finite graphs that allows Presburger quantifiers: linear arithmetic inequalities between the number of elements that satisfy subformulas. The prior literature shows that closing two-variable logic under Presburger quantification leads to undecidability, while closing under \emph{local quantification} -- the counts are always over neighbors of a given node -- preserves decidability. Here we show decidability of satisfiability for an intermediate logic that allows both local counts and global counts, but where the linear constraints do not mix the two. The proof requires a significant extension of the prior machinery developed for two-variable logic with counting. As a corollary we obtain decidability of satisfiability for an important family of Graph Neural Networks (GNNs). GNNs are a popular graph learning formalism. For example, in a variation of GNNs considered in the past literature, local aggregation is used in each layer to create modified values at each vertex of a graph, and then global aggregation is used in a final layer to obtain a single numerical value for the graph as a whole. Our logic is motivated by the fact that mixing of local counting and global aggregation in GNNs has been shown to lead to undecidability. Our results here show that if global and local aggregation are separated, one regains decidability. Decidability of other static analysis problems, like equivalence of GNNs, follows from the decidability of satisfiability.

Abstract: In a variety of multi-agent and physical environments, an element's update depends strongly on a few other elements and weakly on many, and both the identity and the number of the elements that matter change with the state of the system. Such graded sparse mechanisms are common, for instance, in flocks, crowds, learned particle simulators and the neighborhood aggregation of graph networks, yet they have received little systematic study as a class of functions with the grading given. In this paper we study the supervised learning of the mechanism when the grading is provided by the environment, as a weight on every element. First, we define the class by axioms, where each element's influence is capped by its weight, the dependence on the weights is regular, and no element is distinguished, and prove a representation theorem: the class is exactly the Lipschitz ball of a transport metric on weighted multisets, and the metric is forced by the axioms. Next, the geometry of the representation gives generalization bounds that depend on the data in two ways. One is via the sparsity profile of the data -- the law of how many elements matter and by how much -- which bounds the rate over all designs with that profile, with an exponent from the profile and no dependence on the number of elements. In a number of natural cases we also show matching lower bounds, up to constants in the exponent. The other is empirical: due to the representation result, classical empirical discrepancy bounds apply to the class as they stand, and the resulting bound is the transport distance between the two halves of the sample in the class's own metric, computed exactly by a matching, with an additional concentration term. Finally, we study a simulated Vicsek flock under four interaction rules at two noise levels, and show that the certificate is non-vacuous, a small fraction of the trivial value on every rule.

Abstract: Continuous random node features increase the expressivity of message-passing neural networks (MPNNs), but existing theoretical analyses are not fine-grained enough to capture their limitations, particularly in approximating functions across graph sizes or under a fixed number of random bits. We develop a population-level framework for size-uniform approximation. For MPNNs with a graph-size-independent Lipschitz bound in their initial features, including standard mean, max, and order-normalized sum architectures, we show that continuous random features can be quantized to finitely many colors with arbitrarily small uniform error in expected output. This reduction lets us transfer limitations on finite-color distinguishability to limitations on size-uniform approximation with continuous random features. We use this framework to prove that these MPNNs are not size-uniformly universal, analyze the expressivity gains from colors and independent trials, and establish incomparability between random-color MPNNs and higher-order Weisfeiler-Leman methods. We also give finite-color MPNN constructions for tree subgraph isomorphism via color coding and a local MST task.

Abstract: Scalable Graph Transformers are commonly trained and evaluated on static large graphs in a transductive setup. Many scalable Graph Transformer components can be formulated as a constant-size shared memory, similar to virtual nodes, providing compressed information about the whole graph. The counterpart of these models in language models and other domains is justified as the input changes, and this mechanism learns to compress some useful information about the input. In transductive learning on a single fixed graph, however, any shared memory can be seen as a constant at test time. This raises the question of what exactly this shared memory does in this static setup. We give preliminary evidence that optimizing a shared memory directly performs similarly to global communication methods, and so normal local message-passing models can embed similar information in their weights. Thus, these settings may be a poor fit for evaluating global communication in graph neural networks.

Abstract: Rotary position encodings make attention sensitive to relative position, but extending them to graphs requires choosing how graph structure enters the rotation. Previous works assign each node a rotation from spectral coordinates, so the rotary factor between two nodes depends only on their endpoints and cannot distinguish the routes connecting them. We introduce \textit{Analytic-Walk Rotary Positional Encodings} (AW-RoPE), which place the rotations on edges and sum the transported features over all walks, so contributions along different routes can reinforce or cancel. An exact variant evaluates the complete sum by a differentiable linear solve, and a sparse variant truncates it at a finite depth. We prove forward and parameter-derivative truncation bounds at fixed inputs and parameters. Both variants act on projected queries and keys, and the sparse recurrence also augments message-passing networks. Across five synthetic tasks both variants reduce nRMSE by $15$--$58\%$ relative to the strongest baseline, and on real superpixel, peptide and OGB benchmarks the sparse recurrence attains the best mean on every dataset with Performer kernels and on twelve of thirteen datasets with GIN. Analysis shows that AW-RoPE can distinguish routes whose only cue is how two endpoints are connected, while node-wise rotary encodings cannot.