Sukwon Yun

Sukwon Yun, Kibum Kim, Kanghoon Yoon et al.

Existing Graph Neural Networks (GNNs) usually assume a balanced situation where both the class distribution and the node degree distribution are balanced. However, in real-world situations, we often encounter cases where a few classes (i.e., head class) dominate other classes (i.e., tail class) as well as in the node degree perspective, and thus naively applying existing GNNs eventually fall short of generalizing to the tail cases. Although recent studies proposed methods to handle long-tail situations on graphs, they only focus on either the class long-tailedness or the degree long-tailedness. In this paper, we propose a novel framework for training GNNs, called Long-Tail Experts for Graphs (LTE4G), which jointly considers the class long-tailedness, and the degree long-tailedness for node classification. The core idea is to assign an expert GNN model to each subset of nodes that are split in a balanced manner considering both the class and degree long-tailedness. After having trained an expert for each balanced subset, we adopt knowledge distillation to obtain two class-wise students, i.e., Head class student and Tail class student, each of which is responsible for classifying nodes in the head classes and tail classes, respectively. We demonstrate that LTE4G outperforms a wide range of state-of-the-art methods in node classification evaluated on both manual and natural imbalanced graphs. The source code of LTE4G can be found at https://github.com/SukwonYun/LTE4G.

Junghurn Kim, Sukwon Yun, Chanyoung Park

Existing studies for applying the mixup technique on graphs mainly focus on graph classification tasks, while the research in node classification is still under-explored. In this paper, we propose a novel mixup augmentation for node classification called Structural Mixup (S-Mixup). The core idea is to take into account the structural information while mixing nodes. Specifically, S-Mixup obtains pseudo-labels for unlabeled nodes in a graph along with their prediction confidence via a Graph Neural Network (GNN) classifier. These serve as the criteria for the composition of the mixup pool for both inter and intra-class mixups. Furthermore, we utilize the edge gradient obtained from the GNN training and propose a gradient-based edge selection strategy for selecting edges to be attached to the nodes generated by the mixup. Through extensive experiments on real-world benchmark datasets, we demonstrate the effectiveness of S-Mixup evaluated on the node classification task. We observe that S-Mixup enhances the robustness and generalization performance of GNNs, especially in heterophilous situations. The source code of S-Mixup can be found at \url{https://github.com/SukwonYun/S-Mixup}

Kibum Kim, Dongmin Hyun, Sukwon Yun et al.

The long-tailed problem is a long-standing challenge in Sequential Recommender Systems (SRS) in which the problem exists in terms of both users and items. While many existing studies address the long-tailed problem in SRS, they only focus on either the user or item perspective. However, we discover that the long-tailed user and item problems exist at the same time, and considering only either one of them leads to sub-optimal performance of the other one. In this paper, we propose a novel framework for SRS, called Mutual Enhancement of Long-Tailed user and item (MELT), that jointly alleviates the long-tailed problem in the perspectives of both users and items. MELT consists of bilateral branches each of which is responsible for long-tailed users and items, respectively, and the branches are trained to mutually enhance each other, which is trained effectively by a curriculum learning-based training. MELT is model-agnostic in that it can be seamlessly integrated with existing SRS models. Extensive experiments on eight datasets demonstrate the benefit of alleviating the long-tailed problems in terms of both users and items even without sacrificing the performance of head users and items, which has not been achieved by existing methods. To the best of our knowledge, MELT is the first work that jointly alleviates the long-tailed user and item problems in SRS.

Chi-Jane Chen, Yuhang Chen, Sukwon Yun et al.

Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry's analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information: they struggle to generalize spatial coordinates and effectively encode spatial context as text, and (2) Treating each cell independently: they overlook cell-cell interactions, limiting their ability to capture biological relationships. To address these limitations, we propose Spatial2Sentence, a novel framework that integrates single-cell expression and spatial information into natural language using a multi-sentence approach. Spatial2Sentence constructs expression similarity and distance matrices, pairing spatially adjacent and expressionally similar cells as positive pairs while using distant and dissimilar cells as negatives. These multi-sentence representations enable LLMs to learn cellular interactions in both expression and spatial contexts. Equipped with multi-task learning, Spatial2Sentence outperforms existing single-cell LLMs on preprocessed IMC datasets, improving cell-type classification by 5.98% and clinical status prediction by 4.18% on the diabetes dataset while enhancing interpretability. The source code can be found here: https://github.com/UNITES-Lab/Spatial2Sentence.

Sukwon Yun, Xin Liu, Yunhak Oh et al.

In real-world graphs, we often encounter missing feature situations where a few or the majority of node features, e.g., sensitive information, are missed. In such scenarios, directly utilizing Graph Neural Networks (GNNs) would yield sub-optimal results in downstream tasks such as node classification. Despite the emergence of a few GNN-based methods attempting to mitigate its missing situation, when only a few features are available, they rather perform worse than traditional structure-based models. To this end, we propose a novel framework that further illuminates the potential of classical Label Propagation (Oldie), taking advantage of Feature Propagation, especially when only a partial feature is available. Now called by GOODIE, it takes a hybrid approach to obtain embeddings from the Label Propagation branch and Feature Propagation branch. To do so, we first design a GNN-based decoder that enables the Label Propagation branch to output hidden embeddings that align with those of the FP branch. Then, GOODIE automatically captures the significance of structure and feature information thanks to the newly designed Structure-Feature Attention. Followed by a novel Pseudo-Label contrastive learning that differentiates the contribution of each positive pair within pseudo-labels originating from the LP branch, GOODIE outputs the final prediction for the unlabeled nodes. Through extensive experiments, we demonstrate that our proposed model, GOODIE, outperforms the existing state-of-the-art methods not only when only a few features are available but also in abundantly available situations. Source code of GOODIE is available at: https://github.com/SukwonYun/GOODIE.

Yeonjun In, Kanghoon Yoon, Sukwon Yun et al.

In real-world applications, node features in graphs often contain noise from various sources, leading to significant performance degradation in GNNs. Although several methods have been developed to enhance robustness, they rely on the unrealistic assumption that noise in node features is independent of the graph structure and node labels, thereby limiting their applicability. To this end, we introduce a more realistic noise scenario, dependency-aware noise on graphs (DANG), where noise in node features create a chain of noise dependencies that propagates to the graph structure and node labels. We propose a novel robust GNN, DA-GNN, which captures the causal relationships among variables in the data generating process (DGP) of DANG using variational inference. In addition, we present new benchmark datasets that simulate DANG in real-world applications, enabling more practical research on robust GNNs. Extensive experiments demonstrate that DA-GNN consistently outperforms existing baselines across various noise scenarios, including both DANG and conventional noise models commonly considered in this field. Our code is available at https://github.com/yeonjun-in/torch-DA-GNN.

Zhenglun Kong, Mufan Qiu, John Boesen et al.

Understanding how cellular morphology, gene expression, and spatial organization jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but machine learning methods typically analyze these modalities in isolation or at limited resolution. We address the problem of learning unified, spatially aware representations that integrate cell morphology, gene expression, and spatial context across biological scales. This requires models that can operate at single-cell resolution, reason across spatial neighborhoods, and generalize to whole-slide tissue organization. Here, we introduce SPATIA, a multi-scale generative and predictive model for spatial transcriptomics. SPATIA learns cell-level embeddings by fusing image-derived morphological tokens and transcriptomic vector tokens using cross-attention and then aggregates them at niche and tissue levels using transformer modules to capture spatial dependencies. SPATIA incorporates token merging in its generative diffusion decoder to synthesize high-resolution cell images conditioned on gene expression. We assembled a multi-scale dataset consisting of 17 million cell-gene pairs, 1 million niche-gene pairs, and 10,000 tissue-gene pairs across 49 donors, 17 tissue types, and 12 disease states. We benchmark SPATIA against 13 existing models across 12 individual tasks, which span several categories including cell annotation, cell clustering, gene imputation, cross-modal prediction, and image generation. SPATIA achieves improved performance over all baselines and generates realistic cell morphologies that reflect transcriptomic perturbations.

Tai Hasegawa, Sukwon Yun, Xin Liu et al.

Graph Neural Networks (GNNs) have achieved notable success in various applications over graph data. However, recent research has revealed that real-world graphs often contain noise, and GNNs are susceptible to noise in the graph. To address this issue, several Graph Structure Learning (GSL) models have been introduced. While GSL models are tailored to enhance robustness against edge noise through edge reconstruction, a significant limitation surfaces: their high reliance on node features. This inherent dependence amplifies their susceptibility to noise within node features. Recognizing this vulnerability, we present DEGNN, a novel GNN model designed to adeptly mitigate noise in both edges and node features. The core idea of DEGNN is to design two separate experts: an edge expert and a node feature expert. These experts utilize self-supervised learning techniques to produce modified edges and node features. Leveraging these modified representations, DEGNN subsequently addresses downstream tasks, ensuring robustness against noise present in both edges and node features of real-world graphs. Notably, the modification process can be trained end-to-end, empowering DEGNN to adjust dynamically and achieves optimal edge and node representations for specific tasks. Comprehensive experiments demonstrate DEGNN's efficacy in managing noise, both in original real-world graphs and in graphs with synthetic noise.