Unsupervised node representation learning aims to obtain meaningful node embeddings without relying on node labels. To achieve this, graph convolution, which aggregates information from neighboring nodes, is commonly employed to encode node features and graph topology. However, excessive reliance on graph convolution can be suboptimal—especially in non-homophilic graphs—since it may yield unduly similar embeddings for nodes that differ in their features or topological properties. As a result, adjusting the degree of graph convolution usage has been actively explored in supervised learning settings, whereas such approaches remain underexplored in unsupervised scenarios. To tackle this, we propose FUEL, which adaptively learns the adequate degree of graph convolution usage by aiming to enhance intra-class similarity and inter-class separability in the embedding space. Since classes are unknown, FUEL leverages node features to identify node clusters and treats these clusters as proxies for classes. Through extensive experiments using 15 baseline methods and 14 benchmark datasets, we demonstrate the effectiveness of FUEL in downstream tasks, achieving state-of-the-art performance across graphs with diverse levels of homophily.

Higher-order interactions (HOIs) in complex systems, such as scientific collaborations, multi-protein complexes, and multi-user communications, are commonly modeled as hypergraphs, where each hyperedge (i.e., a subset of nodes) represents an HOI among the nodes. Given a hypergraph, hyperedge prediction aims to identify hyperedges that are either missing or likely to form in the future, and it has broad applications, including recommending interest-based social groups, predicting collaborations, and uncovering functional complexes in biological systems. However, the vast search space of hyperedge candidates (i.e., all possible subsets of nodes) poses a significant computational challenge, making naïve exhaustive search infeasible. As a result, existing approaches rely on either heuristic sampling to obtain constrained candidate sets or ungrounded assumptions on hypergraph structure to select promising hyperedges. In this work, we propose HyperSearch, a search-based algorithm for hyperedge prediction that efficiently evaluates unconstrained candidate sets, by incorporating two key components: (1) an empirically grounded scoring function derived from observations in real-world hypergraphs and (2) an efficient search mechanism, where we derive and use an anti-monotonic upper bound of the original scoring function (which is not anti-monotonic) to prune the search space. This pruning comes with theoretical guarantees, ensuring that discarded candidates are never better than the kept ones w.r.t. the original scoring function. In extensive experiments on 10 real-world hypergraphs across five domains, HyperSearch consistently outperforms state-of-the-art baselines, achieving higher accuracy in predicting new (i.e., not in the training set) hyperedges.

Adversarial attacks are allegedly unnoticeable. Prior studies have designed attack noticeability measures on graphs, primarily using statistical tests to compare the topology of original and (possibly) attacked graphs. However, we observe two critical limitations in the existing measures. First, because the measures rely on simple rules, attackers can readily enhance their attacks to bypass them, reducing their attack ''noticeability'' and, yet, maintaining their attack performance. Second, because the measures naively leverage global statistics, such as degree distributions, they may entirely overlook attacks until severe perturbations occur, letting the attacks be almost ''totally unnoticeable.''

The performance of a deep learning model on a specific task and dataset depends heavily on its neural architecture, motivating considerable efforts to rapidly and accurately identify architectures suited to the target task and dataset. To achieve this, researchers use machine learning models—typically neural architecture encoders—to predict the performance of a neural architecture. Many state-of-the-art encoders aim to capture information flow within a neural architecture, which reflects how information moves through the forward pass and backpropagation, via a specialized model structure. However, due to their complicated structures, these flow-based encoders are significantly slower to process neural architectures compared to simpler encoders, presenting a notable practical challenge. To address this, we propose FGP, a novel pre-training method for neural architecture encoding that trains an encoder to capture the information flow without requiring specialized model structures. FGP trains an encoder to reconstruct a flow surrogate, our proposed representation of the neural architecture's information flow. Our experiments show that FGP boosts encoder performance by up to 106\% in Precision@1\%, compared to the same encoder trained solely with supervised learning.

Gene expression profiles can serve as proxies for cellular states and provide valuable insights into the discovery of functional connections across diverse cellular contexts. A cost-effective method called L1000 has been developed to generate gene expression profiles for over a million different conditions. Since gene expression inference of this method relies on linear regression, nonlinear regression methods, including deep learning models, have been assessed. However, these approaches process gene expression data as a vector structure, motivating us to investigate whether nonlinear models based on a graph structure are more effective in capturing the relationships between genes underlying gene expression profiles. In this work, we show that the graph neural network (GNN) model with genes as nodes outperforms both linear and nonlinear non-GNN models in predicting gene expression values and expression-based gene rankings. Importantly, our GNN model requires ~10-fold less information than other models to achieve comparable performance. A strategic selection of input features, or incorporating an organ feature, from which the gene expression data are derived, further improves gene expression inference performance of the GNN model. Additionally, we evaluate the cross-platform generality of gene expression inference. Our study demonstrates that the transformation of RNA expression data into a graph structure effectively captures nonlinear correlations between genes, thereby enabling highly accurate and efficient prediction of gene expression profiles.

Hypergraphs (i.e., sets of hyperedges) naturally represent group relations (e.g., researchers co-authoring a paper and ingredients used together in a recipe), each of which corresponds to a hyperedge (i.e., a subset of nodes). Predicting future or missing hyperedges bears significant implications for many applications (e.g., collaboration and recipe recommendation). What makes hyperedge prediction particularly challenging is the vast number of non-hyperedge subsets, which grows exponentially with the number of nodes. Since it is prohibitive to use all of them as negative examples for model training, it is inevitable to sample a very small portion of them, and to this end, heuristic sampling schemes have been employed. However, trained models suffer from poor generalization capability for examples of different natures. In this paper, we propose AHP, an adversarial training-based hyperedge-prediction method. It learns to sample negative examples without relying on any heuristic schemes. Using six real hypergraphs, we show that AHP generalizes better to negative examples of various natures. It yields up to 28.2% higher AUROC than the best existing methods and often even outperforms its variants with sampling schemes tailored to test sets.