Overlap-Aware Sub-hypergraph Pattern Frequencies for Hypergraph-Level Classification

Self-supervised hypergraph representation learning can produce informative node embeddings, but existing methods often require deep encoders trained for hundreds of epochs, making embedding generation costly even for hypergraphs with a few thousand nodes. This limits applications requiring embeddings for many or evolving hypergraphs. We present HyperFuse, a label-free pipeline for fast hypergraph representation learning. HyperFuse (i) computes structural node coordinates by maximizing a spectral relaxation of hypergraph modularity using Banerjee's hypergraph adjacency and a matrix-free operator with cost linear in node-hyperedge incidences; (ii) constructs multi-scale feature summaries and assigns bounded utility weights to hyperedges based on member stability under feature and membership masking; and (iii) trains a lightweight utility-weighted hypergraph encoder for 100 epochs using an invariance-decorrelation objective. We compare HyperFuse with TriCL, SE-HSSL, VilLain, and HypeBoy on nine public hypergraphs using six downstream classifiers and k-means clustering. On the eight datasets where all methods completed, HyperFuse required 8.7 s per dataset on average, achieving 13-179x geometric-mean speed-ups over the baselines. It achieved the highest average accuracy with five of six classifiers, while classification and clustering performance was not significantly different from TriCL and SE-HSSL. Compared with HypeBoy, HyperFuse was 13x faster and 2.1-4.1 percentage points more accurate across all classifiers. HyperFuse provides a practical approach for fast, repeated hypergraph embedding generation.

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality: whether a higher-order relation is compositional, emergent, or inhibitory with respect to its observed or unobserved sets. In polypharmacy, the regime decides whether a drug should be dropped, kept, or excluded: a compositional drug triple can be safely simplified, an emergent triple requires all drugs jointly, and an inhibitory triple flags a drug that disrupts an existing interaction. However, existing hypergraph learning methods, which merely propagate messages over observed hyperedges, leave this compositional signal unmodeled, allowing dangerous drug combinations to slip through and be misclassified. To this end, we propose the Hypergraph Pattern Machine (HGPM), shifting the paradigm from message passing to learning the compositional pattern of subsets. It tokenizes compositional subsets, organizes them in an inclusion DAG, and trains an inclusion-aware Transformer under masked reconstruction. On ten hypergraph benchmarks, HGPM matches or exceeds state-of-the-art methods. Notably, in a real adverse-event prediction case, HGPM correctly identifies the drug addition that inhibits the side effect among feature-identical candidates, a discrimination existing methods cannot make. The code and data are in https://github.com/KryieZhao/HGPM.git.

Multi-label classification (MLC) requires predicting multiple relevant labels for each instance, where a central challenge is modeling complex label dependencies arising from co-occurrence patterns. Existing approaches are limited in capturing high-order label correlations, relying on implicit learning through contrastive objectives or pairwise attention mechanisms without structural guidance. We propose HyperLabel, an encoder-decoder framework that explicitly models label dependencies through hypergraph neural networks. Our contributions are twofold: (i) We construct a label hypergraph where sample-defined hyperedges naturally encode multi-way co-occurrence patterns, providing explicit structural prior knowledge that captures relationships beyond pairwise interactions. (ii) We propose a unified cross-modal learning approach where HGNN+ performs bidirectional message passing to integrate feature information with label structure, and a shared cross-attention decoder processes both modalities through complementary learning objectives. Extensive experiments on seven benchmark datasets demonstrate that HyperLabel achieves state-of-the-art performance, with particularly significant improvements on macro-F1 scores (+10.3% on Delicious, +8.2% on Bibtex), validating that explicit hypergraph structure effectively captures complex label relationships. The code is available at https://github.com/iZHpy/Multi-label_hypergraph .