Neural networks are increasingly used to infer hidden physical structure from dynamical observations, yet it remains unclear whether their out-of-distribution performance reflects transferable physical rule learning. We address this question in a controlled inverse problem: reconstructing interaction graphs of a kinetic Ising model from Glauber magnetization trajectories. Across convolutional, graph, Transformer, and hybrid architectures, we find that data-driven training produces distinct and reproducible statistical strategies under topology and temperature shifts. Edge-population diagnostics reveal that Transformer-based models tend to preserve the link density of the training ensemble, whereas convolutional models can collapse toward sparse- or no-link predictions that appear out-of-distribution stable by exploiting the majority no-link class. Thus, high in-distribution accuracy and apparent out-of-distribution robustness do not necessarily imply a learned dynamics-to-structure rule. Instead, neural reconstruction can be governed by architecture-dependent statistical priors. Our results identify a concrete failure mode of standard data-driven learning in physical inverse problems and motivate rule-guided principles for machine-learning-assisted scientific discovery.
Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood. We introduce GraphInfer-Bench, a benchmark for whether LLMs can perform this graph inference: producing an open-ended answer that no single node supports and no path retrieves. Existing graph-QA protocols cannot test this capability: algorithm simulation, node classification, single-node description, KG-QA, and GraphRAG all admit answers retrievable from one node or along a path. GraphInfer-Bench defines five tasks along Description (what a region is) and Comparison (how regions differ), each constructed so the ground truth lives in no single node. The release contains 42,000 samples across six real-world graphs, produced automatically and screened by a four-layer quality-control protocol. We evaluate four method families against the same tasks: graph-token alignment models, zero-shot frontier closed-source LLMs, Graph2Text supervised fine-tuning, and plain GNNs as a structural reference. No method family closes the gap. Graph-token alignment partially handles description tasks (relational, theme) but collapses on comparison tasks. Frontier LLMs lead on outlier detection and community partition among LLM-based methods but lag on masked-node prediction. Graph2Text SFT is the strongest LLM-based method on the description side yet falls behind frontier LLMs on comparison. Across every task, plain GNNs match or beat the strongest LLM-based row, with the largest margin on community detection. GraphInfer-Bench surfaces graph inference as an open capability gap rather than a property of any one architecture.