arXiv subjects

Asela Hevapathige

Publications and source records attributed to Asela Hevapathige.

16 recordsLinked to original sources

arXiv2026

Not Just Oversmoothing: Detecting the Echo Chamber Effect in Graph Neural Networks

Oversmoothing is a well-known failure mode of Graph Neural Networks (GNNs). However, most existing diagnostics rely on global aggregation measures that fail to capture the heterogeneous dynamics of message passing. Real-world graphs exhibit pronounced community structure, and message passing operates on two timescales, with representations collapsing rapidly within communities and slowly across them. This creates a critical gap in which intra-community representations can become indistinguishable while inter community separation persists, a failure mode that we refer to as the Echo Chamber Effect. To quantify this effect, we introduce the Echo Chamber Index (ECI), which stratifies pairwise distances by community membership and reveals when global energy diminishes while inter-community separation persists. ECI further shows that feature retention mechanisms can preserve the echo chamber under the conditions of our theoretical analysis. The consequences depend on label structure: when communities align with classes, the echo chamber can sharpen node classification, whereas when they do not, the same collapse makes classification provably harder. Motivated by this analysis, we propose Community-Aware Split Propagation (CASP), a lightweight plugin that decouples intra- and inter-community aggregation and learns their balance from label structure. CASP improves diverse backbone GNNs across most evaluated homophilic and heterophilic settings.

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arXiv2026

Detecting Differences Is Not Understanding Structure: Large Language Models Fail at Graph Isomorphism

Large language models (LLMs) have shown impressive performance on diverse reasoning tasks, yet their capacity for structural reasoning in graphs remains unclear. We investigate whether LLMs can genuinely understand graph isomorphism -a fundamental problem in graph theory. While LLMs achieve near-perfect accuracy on isomorphism detection, we show this performance is illusory. When identical graphs are presented with permuted node labels, LLMs fail to identify their isomorphism. This finding suggests that LLMs exploit patterns rather than reasoning about abstract graph structure. Since permutation invariance is a fundamental requirement for valid structural reasoning, these results indicate that success on graph reasoning benchmarks should not be interpreted as evidence of genuine topological understanding.

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arXiv2026

Knowledge-Inclusive Adaptive Physics-Informed Neural Network for Microbial Interaction Modelling

Physics-Informed Neural Network (PINN) is a way of including knowledge in the form of equations in Machine Learning methods. Beyond equations, knowledge exists in other forms, such as text and network structure. While existing PINN-based approaches discover equation parameters from data, they rely solely on experimental measurements. We propose a new PINN framework that enriches parameter discovery by incorporating auxiliary knowledge sources. We instantiate our framework for microbiology, where generalised Lotka-Volterra (gLV) serves as a biological foundation for modelling microbial communities. We demonstrate that incorporating knowledge improves microbial community modelling. Our framework enriches the gLV parameters using peer-reviewed metagenomics literature, as text provides biological context on external influences that gLV alone cannot capture. We combine this knowledge with experimental measurements of microbial abundance using a data-driven integration approach. We integrate network-based structural knowledge by explicitly modelling microbial interactions. Our knowledge-inclusive framework infers microbial networks, revealing ecological insights. We validate these findings against ecological roles documented in the literature. We evaluate on real and simulated datasets spanning human- and plant-associated microbial communities. Our framework improves over the state-of-the-art by up to 53%, even without knowledge. Knowledge addition yields gains of up to 23% in Bray-Curtis Dissimilarity-based accuracy and 47% in $\mathrm{R}^2$.

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arXiv2026

From Specification to Architecture: A Theory Compiler for Knowledge-Guided Machine Learning

Theory-guided machine learning has demonstrated that including authentic domain knowledge directly into model design improves performance, sample efficiency and out-of-distribution generalisation. Yet the process by which a formal domain theory is translated into architectural constraints remains entirely manual, specific to each domain formalism, and devoid of any formal correctness guarantee. This translation is non-transferable between domains, not verified, and does not scale. We propose the Theory Compiler: a system that accepts a typed, machine-readable domain theory as input and automatically produces an architecture whose function space is provably constrained to be consistent with that theory by construction, not by regularisation. We identify three foundational open problems whose resolution defines our research agenda: (1) designing a universal theory formalisation language with decidable type-checking; (2) constructing a compositionally correct compilation algorithm from theory primitives to architectural modules; and (3) establishing soundness and completeness criteria for formal verification. We further conjecture that compiled architectures match or exceed manually-designed counterparts in generalisation performance while requiring substantially less training data, a claim we ground in classical statistical learning theory. We argue that recent advances in formal machine learning theory, large language models, and the growth of an interdisciplinary research community have made this paradigm achievable for the first time.

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arXiv2026

Invariant-Stratified Propagation for Expressive Graph Neural Networks

Graph Neural Networks (GNNs) face fundamental limitations in expressivity and capturing structural heterogeneity. Standard message-passing architectures are constrained by the 1-dimensional Weisfeiler-Leman (1-WL) test, unable to distinguish graphs beyond degree sequences, and aggregate information uniformly from neighbors, failing to capture how nodes occupy different structural positions within higher-order patterns. While methods exist to achieve higher expressivity, they incur prohibitive computational costs and lack unified frameworks for flexibly encoding diverse structural properties. To address these limitations, we introduce Invariant-Stratified Propagation (ISP), a framework comprising both a novel WL variant (ISP-WL) and its efficient neural network implementation (ISPGNN). ISP stratifies nodes according to graph invariants, processing them in hierarchical strata that reveal structural distinctions invisible to 1-WL. Through hierarchical structural heterogeneity encoding, ISP quantifies differences in nodes' structural positions within higher-order patterns, distinguishing interactions where participants occupy different roles from those with uniform participation. We provide formal theoretical analysis establishing enhanced expressivity beyond 1-WL, convergence guarantees, and inherent resistance to oversmoothing. Extensive experiments across graph classification, node classification, and influence estimation demonstrate consistent improvements over standard architectures and state-of-the-art expressive baselines.

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arXiv2026

Large Language Models for Math Education in Low-Resource Languages: A Study in Sinhala and Tamil

Large language models (LLMs) have achieved strong results in mathematical reasoning, and are increasingly deployed as tutoring and learning support tools in educational settings. However, their reliability for students working in non-English languages, especially low-resource languages, remains poorly understood. We examine this gap by evaluating mathematical reasoning in Sinhala and Tamil -- two languages widely used in South Asian schools but underrepresented in artificial intelligence (AI) research. Using a taxonomy of six math problem types, from basic arithmetic to complex unit conflict and optimization problems, we evaluate four prominent large language models. To avoid translation artifacts that confound language ability with translation quality, we construct a parallel dataset in which each problem is independently authored in Sinhala and Tamil by native speakers, and in English by fluent speakers, all with strong mathematical backgrounds. Our analysis demonstrates that while basic arithmetic reasoning transfers robustly across languages, complex reasoning tasks show significant degradation in Tamil and Sinhala. The pattern of failures varies by model and problem type, suggesting that strong performance in English does not guarantee reliable performance across languages. These findings have direct implications for the deployment of AI tools in multilingual classrooms, and highlight the need for language-specific evaluation before adopting large language models as math tutoring aids in non-English educational contexts.

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arXiv2025

Orthogonal Activation with Implicit Group-Aware Bias Learning for Class Imbalance

Class imbalance is a common challenge in machine learning and data mining, often leading to suboptimal performance in classifiers. While deep learning excels in feature extraction, its performance still deteriorates under imbalanced data. In this work, we propose a novel activation function, named OGAB, designed to alleviate class imbalance in deep learning classifiers. OGAB incorporates orthogonality and group-aware bias learning to enhance feature distinguishability in imbalanced scenarios without explicitly requiring label information. Our key insight is that activation functions can be used to introduce strong inductive biases that can address complex data challenges beyond traditional non-linearity. Our work demonstrates that orthogonal transformations can preserve information about minority classes by maintaining feature independence, thereby preventing the dominance of majority classes in the embedding space. Further, the proposed group-aware bias mechanism automatically identifies data clusters and adjusts embeddings to enhance class separability without the need for explicit supervision. Unlike existing approaches that address class imbalance through preprocessing data modifications or post-processing corrections, our proposed approach tackles class imbalance during the training phase at the embedding learning level, enabling direct integration with the learning process. We demonstrate the effectiveness of our solution on both real-world and synthetic imbalanced datasets, showing consistent performance improvements over both traditional and learnable activation functions.

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arXiv2025

Beyond Fixed Depth: Adaptive Graph Neural Networks for Node Classification Under Varying Homophily

Graph Neural Networks (GNNs) have achieved significant success in addressing node classification tasks. However, the effectiveness of traditional GNNs degrades on heterophilic graphs, where connected nodes often belong to different labels or properties. While recent work has introduced mechanisms to improve GNN performance under heterophily, certain key limitations still exist. Most existing models apply a fixed aggregation depth across all nodes, overlooking the fact that nodes may require different propagation depths based on their local homophily levels and neighborhood structures. Moreover, many methods are tailored to either homophilic or heterophilic settings, lacking the flexibility to generalize across both regimes. To address these challenges, we develop a theoretical framework that links local structural and label characteristics to information propagation dynamics at the node level. Our analysis shows that optimal aggregation depth varies across nodes and is critical for preserving class-discriminative information. Guided by this insight, we propose a novel adaptive-depth GNN architecture that dynamically selects node-specific aggregation depths using theoretically grounded metrics. Our method seamlessly adapts to both homophilic and heterophilic patterns within a unified model. Extensive experiments demonstrate that our approach consistently enhances the performance of standard GNN backbones across diverse benchmarks.

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arXiv2025

Bridging Computational Social Science and Deep Learning: Cultural Dissemination-Inspired Graph Neural Networks

Graph Neural Networks (GNNs) have become vital in applications like document classification in citation networks, epidemic forecasting, viral marketing, user recommendation in social networks, and network monitoring. However, their deployment faces three key challenges: feature oversmoothing in deep architectures, poor handling of heterogeneous relationships, and monolithic feature aggregation. To address these, we introduce AxelGNN, a novel architecture based on Axelrod's cultural dissemination model that incorporates three key innovations: (1) similarity-gated interactions that adaptively promote convergence or divergence based on feature similarity, (2) segment-wise feature copying that enables fine-grained aggregation of semantic feature groups rather than monolithic vectors, and (3) global polarization that maintains multiple distinct representation clusters to prevent oversmoothing. This model demonstrates empirically the capability to handle both homophilic and heterophilic graphs within a single architecture, without requiring specialized model selection based on graph characteristics. Our experiments demonstrate that AxelGNN achieves competitive or superior performance compared to existing methods in node classification and influence estimation while maintaining computational efficiency.

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arXiv2025

AxelSMOTE: An Agent-Based Oversampling Algorithm for Imbalanced Classification

Class imbalance in machine learning poses a significant challenge, as skewed datasets often hinder performance on minority classes. Traditional oversampling techniques, which are commonly used to alleviate class imbalance, have several drawbacks: they treat features independently, lack similarity-based controls, limit sample diversity, and fail to manage synthetic variety effectively. To overcome these issues, we introduce AxelSMOTE, an innovative agent-based approach that views data instances as autonomous agents engaging in complex interactions. Based on Axelrod's cultural dissemination model, AxelSMOTE implements four key innovations: (1) trait-based feature grouping to preserve correlations; (2) a similarity-based probabilistic exchange mechanism for meaningful interactions; (3) Beta distribution blending for realistic interpolation; and (4) controlled diversity injection to avoid overfitting. Experiments on eight imbalanced datasets demonstrate that AxelSMOTE outperforms state-of-the-art sampling methods while maintaining computational efficiency.

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arXiv2025

Graph Neural Diffusion via Generalized Opinion Dynamics

There has been a growing interest in developing diffusion-based Graph Neural Networks (GNNs), building on the connections between message passing mechanisms in GNNs and physical diffusion processes. However, existing methods suffer from three critical limitations: (1) they rely on homogeneous diffusion with static dynamics, limiting adaptability to diverse graph structures; (2) their depth is constrained by computational overhead and diminishing interpretability; and (3) theoretical understanding of their convergence behavior remains limited. To address these challenges, we propose GODNF, a Generalized Opinion Dynamics Neural Framework, which unifies multiple opinion dynamics models into a principled, trainable diffusion mechanism. Our framework captures heterogeneous diffusion patterns and temporal dynamics via node-specific behavior modeling and dynamic neighborhood influence, while ensuring efficient and interpretable message propagation even at deep layers. We provide a rigorous theoretical analysis demonstrating GODNF's ability to model diverse convergence configurations. Extensive empirical evaluations of node classification and influence estimation tasks confirm GODNF's superiority over state-of-the-art GNNs.

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arXiv2025

Arch-VQ: Discrete Architecture Representation Learning with Autoregressive Priors

Existing neural architecture representation learning methods focus on continuous representation learning, typically using Variational Autoencoders (VAEs) to map discrete architectures onto a continuous Gaussian distribution. However, sampling from these spaces often leads to a high percentage of invalid or duplicate neural architectures, likely due to the unnatural mapping of inherently discrete architectural space onto a continuous space. In this work, we revisit architecture representation learning from a fundamentally discrete perspective. We propose Arch-VQ, a framework that learns a discrete latent space of neural architectures using a Vector-Quantized Variational Autoencoder (VQ-VAE), and models the latent prior with an autoregressive transformer. This formulation yields discrete architecture representations that are better aligned with the underlying search space while decoupling representation learning from prior modeling. Across NASBench-101, NASBench-201, and DARTS search spaces, Arch-VQ improves the quality of generated architectures, increasing the rate of valid and unique generations by 22%, 26%, and 135%, respectively, over state-of-the-art baselines. We further show that modeling discrete embeddings autoregressively enhances downstream neural predictor performance, establishing the practical utility of this discrete formulation.

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arXiv2025

Depth-Adaptive Graph Neural Networks via Learnable Bakry-'Emery Curvature

Graph Neural Networks (GNNs) have demonstrated strong representation learning capabilities for graph-based tasks. Recent advances on GNNs leverage geometric properties, such as curvature, to enhance its representation capabilities by modeling complex connectivity patterns and information flow within graphs. However, most existing approaches focus solely on discrete graph topology, overlooking diffusion dynamics and task-specific dependencies essential for effective learning. To address this, we propose integrating Bakry-Émery curvature, which captures both structural and task-driven aspects of information propagation. We develop an efficient, learnable approximation strategy, making curvature computation scalable for large graphs. Furthermore, we introduce an adaptive depth mechanism that dynamically adjusts message-passing layers per vertex based on its curvature, ensuring efficient propagation. Our theoretical analysis establishes a link between curvature and feature distinctiveness, showing that high-curvature vertices require fewer layers, while low-curvature ones benefit from deeper propagation. Extensive experiments on benchmark datasets validate the effectiveness of our approach, showing consistent performance improvements across diverse graph learning tasks.

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arXiv2025

Permutation-Invariant Graph Partitioning:How Graph Neural Networks Capture Structural Interactions?

Graph Neural Networks (GNNs) have paved the way for being a cornerstone in graph-related learning tasks. Yet, the ability of GNNs to capture structural interactions within graphs remains under-explored. In this work, we address this gap by drawing on the insight that permutation invariant graph partitioning enables a powerful way of exploring structural interactions. We establish theoretical connections between permutation invariant graph partitioning and graph isomorphism, and then propose Graph Partitioning Neural Networks (GPNNs), a novel architecture that efficiently enhances the expressive power of GNNs in learning structural interactions. We analyze how partitioning schemes and structural interactions contribute to GNN expressivity and their trade-offs with complexity. Empirically, we demonstrate that GPNNs outperform existing GNN models in capturing structural interactions across diverse graph benchmark tasks.

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arXiv2025

Deep Learning Meets Oversampling: A Learning Framework to Handle Imbalanced Classification

Despite extensive research spanning several decades, class imbalance is still considered a profound difficulty for both machine learning and deep learning models. While data oversampling is the foremost technique to address this issue, traditional sampling techniques are often decoupled from the training phase of the predictive model, resulting in suboptimal representations. To address this, we propose a novel learning framework that can generate synthetic data instances in a data-driven manner. The proposed framework formulates the oversampling process as a composition of discrete decision criteria, thereby enhancing the representation power of the model's learning process. Extensive experiments on the imbalanced classification task demonstrate the superiority of our framework over state-of-the-art algorithms.

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arXiv2024

DeepSN: A Sheaf Neural Framework for Influence Maximization

Influence maximization is key topic in data mining, with broad applications in social network analysis and viral marketing. In recent years, researchers have increasingly turned to machine learning techniques to address this problem. They have developed methods to learn the underlying diffusion processes in a data-driven manner, which enhances the generalizability of the solution, and have designed optimization objectives to identify the optimal seed set. Nonetheless, two fundamental gaps remain unsolved: (1) Graph Neural Networks (GNNs) are increasingly used to learn diffusion models, but in their traditional form, they often fail to capture the complex dynamics of influence diffusion, (2) Designing optimization objectives is challenging due to combinatorial explosion when solving this problem. To address these challenges, we propose a novel framework, DeepSN. Our framework employs sheaf neural diffusion to learn diverse influence patterns in a data-driven, end-to-end manner, providing enhanced separability in capturing diffusion characteristics. We also propose an optimization technique that accounts for overlapping influence between vertices, which helps to reduce the search space and identify the optimal seed set effectively and efficiently. Finally, we conduct extensive experiments on both synthetic and real-world datasets to demonstrate the effectiveness of our framework.

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