arXiv:2509.21886v1 Announce Type: new Abstract: Learning to compute, the ability to model the functional behavior of a computational graph, is a fundamental challenge for graph representation learning. Yet, the dominant paradigm is architecturally mismatched for this task. This flawed assumption, central to mainstream message passing neural networks (MPNNs) and their conventional Transformer-based counterparts, prevents models from capturing the position-aware, hierarchical nature of computation. To resolve this, we introduce \textbf{TRACE}, a new paradigm built on an architecturally sound backbone and a principled learning objective. First, TRACE employs a Hierarchical Transformer that mirrors the step-by-step flow of computation, providing a faithful architectural backbone that replaces the flawed permutation-invariant aggregation. Second, we introduce \textbf{function shift learning}, a novel objective that decouples the learning problem. Instead of predicting the complex global function directly, our model is trained to predict only the \textit{function shift}, the discrepancy between the true global function and a simple local approximation that assumes input independence. We validate this paradigm on electronic circuits, one of the most complex and economically critical classes of computational graphs. Across a comprehensive suite of benchmarks, TRACE substantially outperforms all prior architectures. These results demonstrate that our architecturally-aligned backbone and decoupled learning objective form a more robust paradigm for the fundamental challenge of learning to compute on graphs.
