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}

Sukwon Yun, Jie Peng, Pingzhi Li et al.

With an ever-growing zoo of LLMs and benchmarks, the need to orchestrate multiple models for improved task performance has never been more pressing. While frameworks like Mixture-of-Agents (MoA) attempt to coordinate LLMs, they often fall short in terms of (1) selecting relevant agents, (2) facilitating effective intra-agent communication, and (3) integrating responses efficiently. In this work, we propose Graph-of-Agents (GoA), a new graph-based framework for modeling multi-agent LLM communication. Our approach begins with node sampling, selecting only the most relevant agents by leveraging model cards that summarize each model's domain, task specialization, and other characteristics. Next, we construct edges between the selected agents by evaluating their responses against one another to determine relevance ordering. Directed message passing is then performed from highly relevant agents to less relevant ones to enhance their responses, followed by reverse message passing to refine the original responses of the more relevant agents. Finally, the updated responses are aggregated via graph-based pooling (e.g., max or mean pooling) to produce a single, unified answer. We evaluate GoA on diverse multi-domain benchmarks (MMLU, MMLU-Pro, GPQA) and domain-specific benchmarks (MATH, HumanEval, MedMCQA), with an agent pool of 6 LLMs spanning multiple domains. Surprisingly, GoA achieves superior performance using only 3 selected agents, outperforming recent multi-agent LLM baselines that utilize all 6 agents simultaneously. By adopting a graph structure, GoA offers both scalability and effectiveness through structured message passing-positioning it as a strong candidate for navigating the challenges of the ever-growing LLM zoo. Code is available at: https://github.com/UNITES-Lab/GoA.

Sukwon Yun, Jie Peng, Alexandro E. Trevino et al.

Recent advancements in graph-based approaches for multiplexed immunofluorescence (mIF) images have significantly propelled the field forward, offering deeper insights into patient-level phenotyping. However, current graph-based methodologies encounter two primary challenges: (1) Cellular Heterogeneity, where existing approaches fail to adequately address the inductive biases inherent in graphs, particularly the homophily characteristic observed in cellular connectivity and; (2) Scalability, where handling cellular graphs from high-dimensional images faces difficulties in managing a high number of cells. To overcome these limitations, we introduce Mew, a novel framework designed to efficiently process mIF images through the lens of multiplex network. Mew innovatively constructs a multiplex network comprising two distinct layers: a Voronoi network for geometric information and a Cell-type network for capturing cell-wise homogeneity. This framework equips a scalable and efficient Graph Neural Network (GNN), capable of processing the entire graph during training. Furthermore, Mew integrates an interpretable attention module that autonomously identifies relevant layers for image classification. Extensive experiments on a real-world patient dataset from various institutions highlight Mew's remarkable efficacy and efficiency, marking a significant advancement in mIF image analysis. The source code of Mew can be found here: \url{https://github.com/UNITES-Lab/Mew}

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.

Dawei Li, Shu Yang, Zhen Tan et al.

Recent advancements in large language models (LLMs) have achieved promising performances across various applications. Nonetheless, the ongoing challenge of integrating long-tail knowledge continues to impede the seamless adoption of LLMs in specialized domains. In this work, we introduce DALK, a.k.a. Dynamic Co-Augmentation of LLMs and KG, to address this limitation and demonstrate its ability on studying Alzheimer's Disease (AD), a specialized sub-field in biomedicine and a global health priority. With a synergized framework of LLM and KG mutually enhancing each other, we first leverage LLM to construct an evolving AD-specific knowledge graph (KG) sourced from AD-related scientific literature, and then we utilize a coarse-to-fine sampling method with a novel self-aware knowledge retrieval approach to select appropriate knowledge from the KG to augment LLM inference capabilities. The experimental results, conducted on our constructed AD question answering (ADQA) benchmark, underscore the efficacy of DALK. Additionally, we perform a series of detailed analyses that can offer valuable insights and guidelines for the emerging topic of mutually enhancing KG and LLM. We will release the code and data at https://github.com/David-Li0406/DALK.

Huaizhi Qu, Inyoung Choi, Zhen Tan et al.

LLM ensembles are widely used for LLM judges. However, how to estimate their accuracy, especially in an efficient way, is unknown. In this paper, we present a principled maximum a posteriori (MAP) framework for an economical and precise estimation of the performance of LLM ensemble judgment. We first propose a mixture of Beta-Binomial distributions to model the judgment distribution, revising from the vanilla Binomial distribution. Next, we introduce a conformal prediction-driven approach that enables adaptive stopping during iterative sampling to balance accuracy with efficiency. Furthermore, we design a prior transfer mechanism that utilizes learned distributions on open-source datasets to improve estimation on a target dataset when only scarce annotations are available. Finally, we present BetaConform, a framework that integrates our distribution assumption, adaptive stopping, and the prior transfer mechanism to deliver a theoretically guaranteed distribution estimation of LLM ensemble judgment with minimum labeled samples. BetaConform is also validated empirically. For instance, with only 10 samples from the TruthfulQA dataset, for a Llama ensembled judge, BetaConform gauges its performance with error margin as small as 3.37%.

Sungwon Kim, Yoonho Lee, Yunhak Oh et al.

Federated Learning (FL) on graphs enables collaborative model training to enhance performance without compromising the privacy of each client. However, existing methods often overlook the mutable nature of graph data, which frequently introduces new nodes and leads to shifts in label distribution. Since they focus solely on performing well on each client's local data, they are prone to overfitting to their local distributions (i.e., local overfitting), which hinders their ability to generalize to unseen data with diverse label distributions. In contrast, our proposed method, FedLoG, effectively tackles this issue by mitigating local overfitting. Our model generates global synthetic data by condensing the reliable information from each class representation and its structural information across clients. Using these synthetic data as a training set, we alleviate the local overfitting problem by adaptively generalizing the absent knowledge within each local dataset. This enhances the generalization capabilities of local models, enabling them to handle unseen data effectively. Our model outperforms baselines in our proposed experimental settings, which are designed to measure generalization power to unseen data in practical scenarios. Our code is available at https://github.com/sung-won-kim/FedLoG

Jiayi Xin, Sukwon Yun, Jie Peng et al.

Modality fusion is a cornerstone of multimodal learning, enabling information integration from diverse data sources. However, vanilla fusion methods are limited by (1) inability to account for heterogeneous interactions between modalities and (2) lack of interpretability in uncovering the multimodal interactions inherent in the data. To this end, we propose I2MoE (Interpretable Multimodal Interaction-aware Mixture of Experts), an end-to-end MoE framework designed to enhance modality fusion by explicitly modeling diverse multimodal interactions, as well as providing interpretation on a local and global level. First, I2MoE utilizes different interaction experts with weakly supervised interaction losses to learn multimodal interactions in a data-driven way. Second, I2MoE deploys a reweighting model that assigns importance scores for the output of each interaction expert, which offers sample-level and dataset-level interpretation. Extensive evaluation of medical and general multimodal datasets shows that I2MoE is flexible enough to be combined with different fusion techniques, consistently improves task performance, and provides interpretation across various real-world scenarios. Code is available at https://github.com/Raina-Xin/I2MoE.

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.

Justin Chih-Yao Chen, Sukwon Yun, Elias Stengel-Eskin et al.

Combining existing pre-trained expert LLMs is a promising avenue for scalably tackling large-scale and diverse tasks. However, selecting task-level experts is often too coarse-grained, as heterogeneous tasks may require different expertise per instance. To enable adaptive instance-level mixing of pre-trained LLM experts, we propose Symbolic-MoE, a symbolic, text-based, and gradient-free Mixture-of-Experts framework. Symbolic-MoE takes a fine-grained approach to selection by emphasizing skills, e.g., algebra in math or molecular biology in biomedical reasoning. We propose a skill-based recruiting strategy that dynamically selects the most relevant set of expert LLMs for diverse reasoning tasks based on their strengths. Each selected expert then generates its own reasoning, resulting in k outputs from k experts, which are then synthesized into a final high-quality response by an aggregator chosen based on its ability to integrate diverse reasoning outputs. We show that Symbolic-MoE's instance-level expert selection improves performance by a large margin but -- when implemented naively -- can introduce a high computational overhead due to the need for constant model loading and offloading. To address this, we implement a batch strategy that groups instances based on their assigned experts, loading each model only once. This allows us to integrate 16 expert models on 1 GPU with a time cost comparable to or better than prior multi-agent baselines using 4 GPUs. Through extensive evaluations on diverse benchmarks (MMLU-Pro, GPQA, AIME, and MedMCQA), we show that Symbolic-MoE beats strong LLMs like GPT4o-mini, as well as multi-agent approaches, with an absolute avg. gain of 8.15% over the best multi-agent baseline. Moreover, Symbolic-MoE generalizes well to unseen tasks and removes the need for expensive multi-round discussions, outperforming discussion baselines with less computation.

Rana Muhammad Shahroz Khan, Zhen Tan, Sukwon Yun et al.

Most discussions about Large Language Model (LLM) safety have focused on single-agent settings but multi-agent LLM systems now create novel adversarial risks because their behavior depends on communication between agents and decentralized reasoning. In this work, we innovatively focus on attacking pragmatic systems that have constrains such as limited token bandwidth, latency between message delivery, and defense mechanisms. We design a $\textit{permutation-invariant adversarial attack}$ that optimizes prompt distribution across latency and bandwidth-constraint network topologies to bypass distributed safety mechanisms within the system. Formulating the attack path as a problem of $\textit{maximum-flow minimum-cost}$, coupled with the novel $\textit{Permutation-Invariant Evasion Loss (PIEL)}$, we leverage graph-based optimization to maximize attack success rate while minimizing detection risk. Evaluating across models including $\texttt{Llama}$, $\texttt{Mistral}$, $\texttt{Gemma}$, $\texttt{DeepSeek}$ and other variants on various datasets like $\texttt{JailBreakBench}$ and $\texttt{AdversarialBench}$, our method outperforms conventional attacks by up to $7\times$, exposing critical vulnerabilities in multi-agent systems. Moreover, we demonstrate that existing defenses, including variants of $\texttt{Llama-Guard}$ and $\texttt{PromptGuard}$, fail to prohibit our attack, emphasizing the urgent need for multi-agent specific safety mechanisms.

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.

Mufan Qiu, Xinyu Hu, Fengwei Zhan et al.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: $3.6\%$ increase in drug response prediction correlation, $9.6\%$ improvement in single-cell drug classification AUC, and $1.1\%$ average gain in gene perturbation prediction accuracy.

Sukwon Yun, Heming Yao, Burkhard Hoeckendorf et al.

Vision Transformers ($\text{ViTs}$) have become the backbone of vision foundation models, yet their optimization for multi-channel domains - such as cell painting or satellite imagery - remains underexplored. A key challenge in these domains is capturing interactions between channels, as each channel carries different information. While existing works have shown efficacy by treating each channel independently during tokenization, this approach naturally introduces a major computational bottleneck in the attention block - channel-wise comparisons leads to a quadratic growth in attention, resulting in excessive $\text{FLOPs}$ and high training cost. In this work, we shift focus from efficacy to the overlooked efficiency challenge in cross-channel attention and ask: "Is it necessary to model all channel interactions?". Inspired by the philosophy of Sparse Mixture-of-Experts ($\text{MoE}$), we propose MoE-ViT, a Mixture-of-Experts architecture for multi-channel images in $\text{ViTs}$, which treats each channel as an expert and employs a lightweight router to select only the most relevant experts per patch for attention. Proof-of-concept experiments on real-world datasets - JUMP-CP and So2Sat - demonstrate that $\text{MoE-ViT}$ achieves substantial efficiency gains without sacrificing, and in some cases enhancing, performance, making it a practical and attractive backbone for multi-channel imaging.

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.