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.

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 $\mathrm{R}^2$.

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.

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.

Beyond Translation: Evaluating Mathematical Reasoning Capabilities of LLMs in Sinhala and Tamil

Large language models (LLMs) demonstrate strong mathematical reasoning in English, but whether these capabilities reflect genuine multilingual reasoning or reliance on translation-based processing in low-resource languages like Sinhala and Tamil remains unclear. We examine this fundamental question by evaluating whether LLMs genuinely reason mathematically in these languages or depend on implicit translation to English-like representations. 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 where each problem is natively authored by fluent speakers with mathematical training in all three languages. 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 apparent multilingual competence may not reflect uniform reasoning capabilities across languages. These findings challenge the common assumption that models exhibiting strong multilingual performance can reason equally effectively across languages, and highlight the need for fine-grained, type-aware evaluation in multilingual settings.

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.

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.

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-\'Emery 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.

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.

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.