Graph Homophily

Graph neural networks are widely used for transductive node classification, with accuracy typically measured on randomly drawn train/validation/test splits. Reported accuracy has been shown to shift substantially across different random splits of the same dataset, making published comparisons between architectures unreliable. The classical remedy in non-graph settings is stratified $k$-fold cross-validation, which ensures each test fold reflects the full class distribution of the dataset. We argue that class stratification alone is insufficient for graphs: nodes are not isolated but connected, and folds that differ in their distribution of local neighbourhood homophily expose the model to systematically different relational conditions that directly affect message-passing behaviour. The resulting cross-fold variation reflects the homophily composition of each split, inflating reported variance beyond what model behaviour alone would produce. To address this, we propose \hp{}, a topology-aware stratification procedure that treats node homophily as the primary stratification axis, aligning folds with respect to local relational consistency alongside the class marginal that standard stratification already controls. Stratifying on homophily alone does not guarantee class balance, so \hp{} incorporates class label as a secondary axis, preserving class representativeness as a natural consequence of the procedure. We evaluate \hp{} on a broad benchmark suite comprising 15 node-classification datasets spanning the full homophily spectrum and 7 GNN architectures. \hp{} achieves a mean stability rank of 1.49 compared to 2.31 for random $k$-fold, achieving the lowest mean stability rank on 13 of 15 datasets while preserving class balance close to class-stratified splits and substantially better than random. We argue that homophily-aware split construction merits broader adoption for GNN evaluation.

SNAP-KG is a framework for assigning newly arriving entities to semantic communities in a growing knowledge graph (KG) using only their raw features, with no graph access and no retraining at inference time. It was evaluated on five multi-view benchmarks and a 2.4M-node OGB-WikiKG2 KG. In each of these datasets, at least one graph view is homophilous, meaning that connected nodes usually belong to the same class, and SNAP-KG performs well on all of them. This paper asks what happens outside that setting. We extend the evaluation to three heterophilous graphs (Texas, Wisconsin, Chameleon) and measure the edge homophily of every view. When no homophilous view is available, clustering quality drops sharply for both SNAP-KG and the transductive baselines used in its original evaluation. What decides this is the homophily of the relation, not the number of relations. Multi-view fusion still helps, but only when at least one homophilous relation provides a reliable foundation. The homophily assumption is therefore shared by the whole method family, not specific to SNAP-KG. We argue that heterophilous multi-view clustering is a separate research problem, outside the scope of this work. As future work, we outline how a heterophily-aware teacher could be distilled into SNAP-KG's projector to serve both homophilous and heterophilous KGs.

Standard open-set node classification methods rely on the homophily assumption, where connected nodes share labels. However, real-world graphs are often heterophilic, exposing the limitations of current methods and posing new challenges to open-set node classification. On the one hand, cross-class connectivity causes representations from different known or unknown classes to become intertwined after aggregation, undermining their discriminative capacity. On the other hand, structural mixture invalidates threshold-based open-set methods and cross-class feature interpolation, leading to unreliable unknown-class rejection. To address these challenges, we propose HOPE, a Heterophily-aware Open-set node classification method with Pseudo-Extrapolation. To adapt open-set graph neural networks (GNNs) to heterophilic scenarios, HOPE uses a structure-augmented feature initialization layer to capture multi-hop structural patterns. Meanwhile, we design a trustworthy neighborhood aggregation mechanism for standard GNNs to dynamically filter noisy cross-class neighbors. To enhance unknown-class rejection, we introduce a heterophily-guided pseudo-extrapolation strategy. It dynamically maintains known-class centers and extrapolates along cross-class neighborhood displacement directions, synthesizing pseudo-unknown proxies near structurally ambiguous regions. Finally, we optimize the network with joint classification and logit margin regularization, routing synthetic proxies into a dedicated rejection slot without imposing geometric margin constraints in the representation space. Extensive experiments on multiple datasets show that HOPE consistently outperforms state-of-the-art models, validating its effectiveness, robustness, and efficiency.

In fair ranked link prediction, demographic parity ($Δ_\mathrm{DP}$) is a common fairness metric. Yet, Mattos et al. (2025) argue that it fails to detect exposure bias because it ignores where links appear in the ranking. In this study, we reproduce this claim by showing that $Δ_\mathrm{DP}$ can indicate aggregate parity even when some subgroup-pair links are systematically ranked lower than others. The proposed rank-aware Normalized Discounted KL-divergence (NDKL), however, does detect such disparities. We also reproduce the effectiveness of MORAL, a post-processing method that improves exposure-based fairness while maintaining competitive utility. Beyond reproduction, we assess robustness using synthetic homophily settings, categorical sensitive attributes, and additional fairness and utility metrics, including subgroup-pair-adapted Attention-Weighted Rank Fairness (AWRF). Overall, our results show that exposure-based metrics uncover biases hidden by $Δ_\mathrm{DP}$ and that MORAL reduces these biases with minimal utility loss across diverse settings and datasets. We release a corrected, reproducible implementation at https://github.com/Floris93100/reproducing-MORAL.

Many Bangla words are at once personal names and culturally loaded common nouns, "Maya" is both a girl's name and a word for affectionate compassion. Choosing the right reading demands cultural knowledge that is scarce in the pretraining data of modern language models. We introduce Culturally Entangled Homograph (CEH) disambiguation and build a Bangla benchmark of 1,516 expert-verified sentences (3,032 labelled occurrences) in which one word appears twice with two distinct readings, each labelled with a culturally grounded category and an explanation of the reasoning behind it. Across open- and closed-source models, we find a systematic dominant-meaning bias: models default to the common-noun sense and overlook the name. A Bangla-specific model fails under every prompting regime we test, showing that language-specific pretraining alone does not confer cultural grounding. We further show that contrastive chain-of-thought prompting can sharply reduce this bias without training, and that distilling cultural explanations teaches small (1-3B) models to reason toward the correct reading rather than memorise labels, cutting dominant-meaning bias from as high as 100% to under 5% and turning the failed Bangla-specific model into our strongest system. Dataset and code are available at https://github.com/ashuvo25/BanglaCEH.

Breast ultrasound is widely used for screening, yet automated analysis remains challenging due to speckle noise, acquisition variability, and weak separation of benign and malignant cases in standard ultrasound imaging. Graph convolutional networks (GCNs) have recently emerged as a promising approach by leveraging relationships among similar patient samples. However, it remains unclear how the choice of image encoder influences graph construction and downstream classification performance. In this work, we systematically evaluate five image encoders spanning convolutional and transformer-based architectures for GCN-based breast ultrasound classification. Image embeddings are used to construct cosine similarity k-nearest-neighbor graphs, which are classified using a single-layer GCN with a linear classification head. Across three patientwise cross-validation folds, higher-capacity encoders consistently improve graph homophily and downstream classification performance, yielding gains in accuracy, AUC, sensitivity, specificity, and F1-score. Moreover, test-set graph homophily exhibits a strong linear correlation with classification accuracy, with higher-capacity encoders consistently occupying the high-homophily, high-accuracy region suggesting that encoder-driven improvements in graph structure are a key mechanism underlying the observed performance gains. These findings establish encoder selection as a critical factor in graph-based breast ultrasound classification and identify graph homophily as a key indicator linking representation quality to downstream classification performance.

A growing line of work equips large language model (LLM) agents with graph neural networks (GNNs) as callable tools, assuming the agent exercises judgment over when and how much to rely on such a tool. We test this directly. We expose a frozen GNN to a ReAct-style LLM agent as an explicit tool and measure, on node classification over a text-attributed graph (ogbn-arxiv, replicated on WikiCS), whether the agent uses the tool or merely obeys it. We find the agent does not exercise judgment: its predictions agree with the raw GNN's 97.6-99.2% of the time (5 seeds), collapsing into a GNN parrot that adopts the tool's output wholesale and bypasses its own reasoning. Sweeping backbone capability (Qwen2.5 0.5B-7B), the deference is not a weak-model artifact: among models able to invoke the tool, agreement rises with capability (0.60 to 0.98 from 1.5B to 7B). Crucially, the cost of deference does not shrink as capability grows and grows where alternatives emerge: a per-node oracle over the available actions beats the parrot by 0.09-0.18 at 3B and 0.12-0.22 at 7B, roughly doubling at high homophily, because the parrot is pinned to the frozen GNN while the agent's alternatives improve; at 7B a simple neighbour-label tool overtakes the GNN at high homophily (0.81 vs 0.71) yet the agent still defers. A simple selective-invocation gate recovers about half of that high-homophily gap (0.71 to 0.83) but yields no net global gain, and held-out estimates bound the best achievable gate over standard test-time features to at most a third of the oracle headroom: reliable selective invocation looks limited by available information, not merely router design. Our results are a cautionary measurement: evaluations of agent+tool systems cannot assume the agent adds judgment on top of the tool, and selective invocation must be designed in rather than expected to emerge from scale.

Graph neural networks (GNNs) are widely deployed on relational data, yet they can leak sensitive or proprietary information about the training graph adjacency, e.g., social ties, transactions, and interactions. This work studies graph reconstruction attacks (GRA), a form of model inversion that reconstructs the training adjacency from a trained GNN, given different levels of attacker-side information. We first provide a systematic characterization of when and why adjacency becomes recoverable through features, labels, embeddings, and predictions, with leakage modulated by graph homophily, heterophily, and the model's inductive bias. Motivated by these findings, we view GNN inference through a Markov chain approximation lens, treating the layered forward computation as a chain of topology-dependent representations. Building on this view, we develop complementary attack and defense methods. On the attack side, we propose MC-GRA (+), which reconstructs the adjacency by optimizing a surrogate adjacency whose GNN-induced representations align with those of the target model at each layer. On the defense side, we propose MC-GPB (+), which suppresses adjacency-dependent information throughout the representation chain while aiming to preserve classification accuracy under a privacy-utility trade-off. Experiments across homophilic/heterophilic graph benchmarks and GNNs show that our attacks improve reconstruction fidelity over prior methods, while our defenses reduce reconstruction success with only minor accuracy loss.

Contextual Automatic Speech Recognition (ASR) faces challenges with large-scale keyword dictionaries, as excessive irrelevant candidates introduce noise that degrades accuracy. To address this, dynamic filtering typically uses a base ASR model to generate preliminary hypotheses, followed by semantic text retrievers to fetch a concise subset of relevant keywords. However, this approach frequently fails in Chinese ASR. Base models often produce homophonic or near-homophonic errors that preserve the phonetic cues of the target keywords but severely distort their semantic meaning, rendering standard semantic retrievers ineffective. To resolve this, we propose a filtering framework that jointly integrates Semantic, Pinyin, and Glyph features (JSPG). Pinyin effectively retrieves targets based on phonetic similarity, while glyph provides complementary structural cues to filter out numerous irrelevant homophones inherent in Chinese. To bridge the gap between character-level pinyin/glyph metrics and sequence-level filtering, we introduce an extended Smith-Waterman algorithm that computes similarity scores between the N-best hypothesis sequences and keywords. Experiments on the Aishell-1 and RWCS-NER datasets demonstrate that JSPG significantly outperforms single-feature baselines. Furthermore, downstream contextual ASR models guided by JSPG achieve substantial improvements in keyword recognition accuracy.

Graph neural networks (GNNs) have achieved remarkable success in relational learning. However, their vulnerability to graph backdoor attacks (GBAs) poses a significant barrier to broader adoption in high-stakes applications. Despite recent advances in graph backdoor defense (GBD), existing methods primarily focus on subgraph-based GBAs, relying on the assumption that poisoned target nodes are explicitly connected to subgraph triggers. Our empirical results reveal that such structure-centric approaches fail to defend against emerging feature-based GBAs that preserve graph topology. Therefore, in this paper, we study a novel problem of universal graph backdoor defense. First, we investigate the shared effects of both attack types from a feature-based homophily perspective, which characterizes local feature consistency between nodes and their neighborhoods. Thorough theoretical and empirical analyses demonstrate that, regardless of trigger mechanisms, backdoors induced by GBAs exhibit lower feature-based homophily than clean nodes, indicating a discrepancy in local feature similarity. Motivated by this insight, we propose to leverage node-level local feature consistency, modeled by a neighbor-aware reconstruction loss, to distinguish backdoors from clean nodes. Then, a robust training strategy is developed to eliminate trigger effects while reducing noise induced by detection uncertainty. Extensive experiments demonstrate that our framework significantly degrades the attack success rate and maintains competitive clean accuracy under both subgraph-based and feature-based attacks.

Large language models (LLMs) are increasingly used as substitutes for human subjects in behavioral simulations, including synthetic social network generation. Yet it remains unclear how their relational outputs depend on prompt design, cultural framing, prompt language, and model scale. Building on homophily theory and structural balance theory, we formalize four LLM-based tie-formation mechanisms: sequential, global, local, and iterative, and treat them as distinct conditional distributions over edge sets. Using a fixed roster of 50 demographically grounded personas, we generate 192 verified directed networks across four cultural contexts, four prompt languages, three GPT-4.1 variants, and four prompting architectures, with two seeds per condition. We find that cultural framing shifts inbreeding homophily and largest-component connectivity. Political affiliation dominates tie formation under three methods, while the global method substitutes age, showing that prompt architecture functions as a substantive sociological variable. Model scale produces a stable divergence ranking, with the smallest variant behaving qualitatively differently rather than merely noisily. Prompt language alone sharply shifts religion homophily, especially under Hindi prompting, while leaving political homophily nearly invariant. LLM-generated networks match real social graphs on clustering and modularity better than standard graph baselines, yet encode demographic biases above empirical levels. These results show that prompt choices often treated as implementation details encode substantive sociological assumptions.

Graph Neural Networks (GNNs) have demonstrated impressive performance in learning representations from graph-structured data. However, their message-passing mechanism inherently relies on the assumption of label consistency among connected nodes, limiting their applicability to low-homophily settings. Moreover, since message passing operates as a hierarchical diffusion process, GNNs face challenges in capturing long-range dependencies. As network depth increases, the structural noise along heterophilic edges tends to be amplified, resulting in over-smoothing. This issue becomes especially prominent in highly heterophilic graphs, where the propagation of inconsistent semantics across the topology continually exacerbates misaggregation. To address this issue, we propose a novel framework named Layer Embedding Deep Fusion Graph Neural Network (LEDF-GNN). Specifically, we design a Layer Embedding Deep Fusion (LEDF) operator that nonlinearly fuses multi-layer embeddings to capture inter-layer dependencies and effectively alleviate deep propagation degradation. Meanwhile, to mitigate structural heterophily, LEDF-GNN employs a Dual-Topology Parallel Strategy (DTPS) that simultaneously leverages the original and reconstructed topologies, allowing for adaptive structure-semantics co-optimization under diverse homophily conditions. Extensive semi-supervised classification experiments on the citation and image benchmarks demonstrate that, under both homophilic and heterophilic settings, LEDF-GNN consistently outperforms state-of-the-art baselines, validating its effectiveness and generalization capability across diverse graph types.

Conventional audio equalization is a static process that requires manual and cumbersome adjustments to adapt to changing listening contexts (e.g., mood, location, or social setting). In this paper, we introduce a Large Language Model (LLM)-based alternative that maps natural language text prompts to equalization settings. This enables a conversational approach to sound system control. By utilizing data collected from a controlled listening experiment, our models exploit in-context learning and parameter-efficient fine-tuning techniques to reliably align with population-preferred equalization settings. Our evaluation methods, which leverage distributional metrics that capture users' varied preferences, show statistically significant improvements in distributional alignment over random sampling and static preset baselines. These results indicate that LLMs could function as ``artificial equalizers," contributing to the development of more accessible, context-aware, and expert-level audio tuning methods.

Large language models (LLMs) have demonstrated promising capabilities in Text-Attributed Graph (TAG) understanding. Recent studies typically focus on verbalizing the graph structures via handcrafted prompts, feeding the target node and its neighborhood context into LLMs. However, constrained by the context window, existing methods mainly resort to random sampling, often implemented via dropping node/edge randomly, which inevitably introduces noise and cause reasoning instability. We argue that graphs inherently contain rich structural and semantic information, and that their effective exploitation can unlock potential gains in LLMs reasoning performance. To this end, we propose Homophily-aware Structural and Semantic Compression for LLMs (HS2C), a framework centered on exploiting graph homophily. Structurally, guided by the principle of Structural Entropy minimization, we perform a global hierarchical partition that decodes the graph's essential topology. This partition identifies naturally cohesive, homophilic communities, while discarding stochastic connectivity noise. Semantically, we deliver the detected structural homophily to the LLM, empowering it to perform differentiated semantic aggregation based on predefined community type. This process compresses redundant background contexts into concise community-level consensus, selectively preserving semantically homophilic information aligned with the target nodes. Extensive experiments on 10 node-level benchmarks across LLMs of varying sizes and families demonstrate that, by feeding LLMs with structurally and semantically compressed inputs, HS2C simultaneously enhances the compression rate and downstream inference accuracy, validating its superiority and scalability. Extensions to 7 diverse graph-level benchmarks further consolidate HS2C's task generalizability.

Over the past decade, Graph Neural Networks (GNNs) have achieved great success on machine learning tasks with relational data. However, recent studies have found that heterophily can cause significant performance degradation of GNNs, especially on node-level tasks. Numerous heterophilic benchmark datasets have been put forward to validate the efficacy of heterophily-specific GNNs, and various homophily metrics have been designed to help recognize these challenging datasets. Nevertheless, there still exist multiple pitfalls that severely hinder the proper evaluation of new models and metrics: 1) lack of hyperparameter tuning; 2) insufficient evaluation on the truly challenging heterophilic datasets; 3) missing quantitative evaluation for homophily metrics on synthetic graphs. To overcome these challenges, we first train and fine-tune baseline models on $27$ most widely used benchmark datasets, and categorize them into three distinct groups: malignant, benign and ambiguous heterophilic datasets. We identify malignant and ambiguous heterophily as the truly challenging subsets of tasks, and to our best knowledge, we are the first to propose such taxonomy. Then, we re-evaluate $11$ state-of-the-arts (SOTA) GNNs, covering six popular methods, with fine-tuned hyperparameters on different groups of heterophilic datasets. Based on the model performance, we comprehensively reassess the effectiveness of different methods on heterophily. At last, we evaluate $11$ popular homophily metrics on synthetic graphs with three different graph generation approaches. To overcome the unreliability of observation-based comparison and evaluation, we conduct the first quantitative evaluation and provide detailed analysis.