LoGIC: Budgeted Context Construction for Node-Level Graph In-Context Learning with Tabular Foundation Models

Achieving strong performance with graph neural networks (GNNs) typically requires training and hyperparameter tuning for each dataset, incurring repeated costs and effort. Graph in-context learning (ICL) avoids this by using a single pretrained model to predict unknown node labels directly from labeled context nodes. Existing approaches, however, rely on dense attention across nodes, making inference increasingly expensive as graphs grow. In this work, we present Ephris, a new graph in-context learner built on sparse message passing, scaling linearly with the number of node-feature entries and graph edges. Ephris is pretrained entirely on synthetic graphs generated from structural causal models with diverse graph structures and relational dynamics, exposing the model to varied dependencies among topology, features, and labels. We evaluate Ephris on 51 node-classification datasets against 15 extensively tuned GNNs and existing graph ICL methods under both high- and low-label train/validation/test splits. Across both settings, Ephris ranks first on all four aggregate measures: Elo, improvability, average rank, and accuracy. Its inference cost remains comparable to training a single GNN once, while being over 10 times faster than previous graph ICL models. Together, these results advance the performance-runtime Pareto frontier, demonstrating that strong graph ICL does not require dense attention. Code and model weights are available at https://github.com/nums-ai/ephris.

Tabular foundation models perform in-context learning (ICL) by conditioning predictions on labeled training examples provided as context. Unlike traditional models that separate training from inference, these models must process all training examples in every forward pass, making each prediction expensive. Restricting the number of training examples reduces this cost but substantially degrades performance. Instead of discarding context, we propose activation alignment, a method that leverages the full context to teach a model how to behave when seeing only a subset. This is achieved by training a lightweight linear transformation on synthetic unlabeled data to map the intermediate activations of a data-constrained "student" (using partial context) toward those of a full-context "teacher" (using all data). Training the aligner requires no GPU and converges in seconds to minutes on commodity hardware. We evaluate on 38 classification datasets from the TabArena benchmark using the leading two tabular foundation models, TabPFN-3 and TabFM. Across all context budgets, the aligned student yields broad, statistically significant improvements over the unaligned baseline for both models. In low-data regimes, alignment recovers nearly half of the teacher's predictive advantage. The method provides a practical, low-overhead approach to achieving the inference speed of compact contexts while closing a significant fraction of the performance gap to the full-context teacher.

Graph foundation models face several fundamental challenges including transferability across diverse domains and data scarcity, which calls into question the very feasibility of creating such models. However, despite similar challenges, the tabular domain has recently witnessed the emergence of the first successful foundation models such as TabPFN. These models are based on the prior-data fitted networks (PFN) framework, in which models are pretrained on carefully designed synthetic datasets to make predictions in an in-context learning setting. Recently, G2T-FM, a framework that converts graph node-level tasks into tabular tasks, has made the first step towards adopting PFNs for graphs, yet it is limited to hand-crafted features and was never pretrained on graph data. In this work, we make the next step by proposing GraphPFN, a PFN-based model designed and pretrained specifically for graph node-level tasks. Following the PFN framework, we first design a prior distribution of synthetic attributed graphs by using a novel combination of multi-level stochastic block models and a preferential attachment process for structure generation and graph-aware structured causal models for attribute generation. Then, we augment the tabular foundation model LimiX with attention-based graph neighborhood aggregation layers and train it on millions of synthetic graphs sampled from our prior. On diverse real-world graph datasets with node-level tasks, GraphPFN achieves state-of-the-art results in both in-context learning and finetuning regimes, outperforming G2T-FM, prior GFMs, and task-specific GNNs trained from scratch. More broadly, GraphPFN shows the potential of PFN-based models for building graph foundation models.