Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved notable success in DTI prediction, many of them have difficulties in effectively integrating the diverse features of drugs, targets and their interactions. To address this limitation, we introduce a novel framework to take advantage of the power of both transductive learning and inductive learning so that features at molecular level and drug-target interaction network level can be exploited. Within this framework is a GNN-based model called Graph-in-Graph (GiG) that represents graphs of drug and target molecular structures as meta-nodes in a drug-target interaction graph, enabling a detailed exploration of their intricate relationships. To evaluate the proposed model, we have compiled a special benchmark comprising drug SMILES, protein sequences, and their interaction data, which is interesting in its own right. Our experimental results demonstrate that the GiG model significantly outperforms existing approaches across all evaluation metrics, highlighting the benefits of integrating different learning paradigms and interaction data.
This paper aims to understand how neural networks learn algorithmic reasoning by addressing two questions: How faithful are learned algorithms when they are effective, and why do neural networks fail to learn effective algorithms otherwise? To answer these questions, we use neural compilation, a technique that directly encodes a source algorithm into neural network parameters, enabling the network to compute the algorithm exactly. This enables comparison between compiled and conventionally learned parameters, intermediate vectors, and behaviors. This investigation is crucial for developing neural networks that robustly learn complexalgorithms from data. Our analysis focuses on graph neural networks (GNNs), which are naturally aligned with algorithmic reasoning tasks, specifically our choices of BFS, DFS, and Bellman-Ford, which cover the spectrum of effective, faithful, and ineffective learned algorithms. Commonly, learning algorithmic reasoning is framed as induction over synthetic data, where a parameterized model is trained on inputs, traces, and outputs produced by an underlying ground truth algorithm. In contrast, we introduce a neural compilation method for GNNs, which sets network parameters analytically, bypassing training. Focusing on GNNs leverages their alignment with algorithmic reasoning, extensive algorithmic induction literature, and the novel application of neural compilation to GNNs. Overall, this paper aims to characterize expressability-trainability gaps - a fundamental shortcoming in learning algorithmic reasoning. We hypothesize that inductive learning is most effective for parallel algorithms contained within the computational class \texttt{NC}.
Graph auto-encoder is considered a framework for unsupervised learning on graph-structured data by representing graphs in a low dimensional space. It has been proved very powerful for graph analytics. In the real world, complex relationships in various entities can be represented by heterogeneous graphs that contain more abundant semantic information than homogeneous graphs. In general, graph auto-encoders based on homogeneous graphs are not applicable to heterogeneous graphs. In addition, little work has been done to evaluate the effect of different semantics on node embedding in heterogeneous graphs for unsupervised graph representation learning. In this work, we propose a novel Heterogeneous Graph Attention Auto-Encoders (HGATE) for unsupervised representation learning on heterogeneous graph-structured data. Based on the consideration of semantic information, our architecture of HGATE reconstructs not only the edges of the heterogeneous graph but also node attributes, through stacked encoder/decoder layers. Hierarchical attention is used to learn the relevance between a node and its meta-path based neighbors, and the relevance among different meta-paths. HGATE is applicable to transductive learning as well as inductive learning. Node classification and link prediction experiments on real-world heterogeneous graph datasets demonstrate the effectiveness of HGATE for both transductive and inductive tasks.
Fraudulent activities have significantly increased across various domains, such as e-commerce, online review platforms, and social networks, making fraud detection a critical task. Spatial Graph Neural Networks (GNNs) have been successfully applied to fraud detection tasks due to their strong inductive learning capabilities. However, existing spatial GNN-based methods often enhance the graph structure by excluding heterophilic neighbors during message passing to align with the homophilic bias of GNNs. Unfortunately, this approach can disrupt the original graph topology and increase uncertainty in predictions. To address these limitations, this paper proposes a novel framework, Dual-channel Heterophilic Message Passing (DHMP), for fraud detection. DHMP leverages a heterophily separation module to divide the graph into homophilic and heterophilic subgraphs, mitigating the low-pass inductive bias of traditional GNNs. It then applies shared weights to capture signals at different frequencies independently and incorporates a customized sampling strategy for training. This allows nodes to adaptively balance the contributions of various signals based on their labels. Extensive experiments on three real-world datasets demonstrate that DHMP outperforms existing methods, highlighting the importance of separating signals with different frequencies for improved fraud detection. The code is available at https://github.com/shaieesss/DHMP.
Neural networks, as currently designed, fall short of achieving true logical intelligence. Modern AI models rely on standard neural computation-inner-product-based transformations and nonlinear activations-to approximate patterns from data. While effective for inductive learning, this architecture lacks the structural guarantees necessary for deductive inference and logical consistency. As a result, deep networks struggle with rule-based reasoning, structured generalization, and interpretability without extensive post-hoc modifications. This position paper argues that standard neural layers must be fundamentally rethought to integrate logical reasoning. We advocate for Logical Neural Units (LNUs)-modular components that embed differentiable approximations of logical operations (e.g., AND, OR, NOT) directly within neural architectures. We critique existing neurosymbolic approaches, highlight the limitations of standard neural computation for logical inference, and present LNUs as a necessary paradigm shift in AI. Finally, we outline a roadmap for implementation, discussing theoretical foundations, architectural integration, and key challenges for future research.
The increasing level of autonomy of robots poses challenges of trust and social acceptance, especially in human-robot interaction scenarios. This requires an interpretable implementation of robotic cognitive capabilities, possibly based on formal methods as logics for the definition of task specifications. However, prior knowledge is often unavailable in complex realistic scenarios. In this paper, we propose an offline algorithm based on inductive logic programming from noisy examples to extract task specifications (i.e., action preconditions, constraints and effects) directly from raw data of few heterogeneous (i.e., not repetitive) robotic executions. Our algorithm leverages on the output of any unsupervised action identification algorithm from video-kinematic recordings. Combining it with the definition of very basic, almost task-agnostic, commonsense concepts about the environment, which contribute to the interpretability of our methodology, we are able to learn logical axioms encoding preconditions of actions, as well as their effects in the event calculus paradigm. Since the quality of learned specifications depends mainly on the accuracy of the action identification algorithm, we also propose an online framework for incremental refinement of task knowledge from user feedback, guaranteeing safe execution. Results in a standard manipulation task and benchmark for user training in the safety-critical surgical robotic scenario, show the robustness, data- and time-efficiency of our methodology, with promising results towards the scalability in more complex domains.
This paper presents a novel approach combining inductive logic programming with reinforcement learning to improve training performance and explainability. We exploit inductive learning of answer set programs from noisy examples to learn a set of logical rules representing an explainable approximation of the agent policy at each batch of experience. We then perform answer set reasoning on the learned rules to guide the exploration of the learning agent at the next batch, without requiring inefficient reward shaping and preserving optimality with soft bias. The entire procedure is conducted during the online execution of the reinforcement learning algorithm. We preliminarily validate the efficacy of our approach by integrating it into the Q-learning algorithm for the Pac-Man scenario in two maps of increasing complexity. Our methodology produces a significant boost in the discounted return achieved by the agent, even in the first batches of training. Moreover, inductive learning does not compromise the computational time required by Q-learning and learned rules quickly converge to an explanation of the agent policy.
In dynamic decision-making scenarios across business and healthcare, leveraging sample trajectories from diverse populations can significantly enhance reinforcement learning (RL) performance for specific target populations, especially when sample sizes are limited. While existing transfer learning methods primarily focus on linear regression settings, they lack direct applicability to reinforcement learning algorithms. This paper pioneers the study of transfer learning for dynamic decision scenarios modeled by non-stationary finite-horizon Markov decision processes, utilizing neural networks as powerful function approximators and backward inductive learning. We demonstrate that naive sample pooling strategies, effective in regression settings, fail in Markov decision processes.To address this challenge, we introduce a novel ``re-weighted targeting procedure'' to construct ``transferable RL samples'' and propose ``transfer deep $Q^*$-learning'', enabling neural network approximation with theoretical guarantees. We assume that the reward functions are transferable and deal with both situations in which the transition densities are transferable or nontransferable. Our analytical techniques for transfer learning in neural network approximation and transition density transfers have broader implications, extending to supervised transfer learning with neural networks and domain shift scenarios. Empirical experiments on both synthetic and real datasets corroborate the advantages of our method, showcasing its potential for improving decision-making through strategically constructing transferable RL samples in non-stationary reinforcement learning contexts.
Despite impressive capability in learning over graph-structured data, graph neural networks (GNN) suffer from adversarial topology perturbation in both training and inference phases. While adversarial training has demonstrated remarkable effectiveness in image classification tasks, its suitability for GNN models has been doubted until a recent advance that shifts the focus from transductive to inductive learning. Still, GNN robustness in the inductive setting is under-explored, and it calls for deeper understanding of GNN adversarial training. To this end, we propose a new concept of graph subspace energy (GSE) -- a generalization of graph energy that measures graph stability -- of the adjacency matrix, as an indicator of GNN robustness against topology perturbations. To further demonstrate the effectiveness of such concept, we propose an adversarial training method with the perturbed graphs generated by maximizing the GSE regularization term, referred to as AT-GSE. To deal with the local and global topology perturbations raised respectively by LRBCD and PRBCD, we employ randomized SVD (RndSVD) and Nystrom low-rank approximation to favor the different aspects of the GSE terms. An extensive set of experiments shows that AT-GSE outperforms consistently the state-of-the-art GNN adversarial training methods over different homophily and heterophily datasets in terms of adversarial accuracy, whilst more surprisingly achieving a superior clean accuracy on non-perturbed graphs.
Breast compression simulation is essential for accurate image registration from 3D modalities to X-ray procedures like mammography. It accounts for tissue shape and position changes due to compression, ensuring precise alignment and improved analysis. Although Finite Element Analysis (FEA) is reliable for approximating soft tissue deformation, it struggles with balancing accuracy and computational efficiency. Recent studies have used data-driven models trained on FEA results to speed up tissue deformation predictions. We propose to explore Physics-based Graph Neural Networks (PhysGNN) for breast compression simulation. PhysGNN has been used for data-driven modelling in other domains, and this work presents the first investigation of their potential in predicting breast deformation during mammographic compression. Unlike conventional data-driven models, PhysGNN, which incorporates mesh structural information and enables inductive learning on unstructured grids, is well-suited for capturing complex breast tissue geometries. Trained on deformations from incremental FEA simulations, PhysGNN's performance is evaluated by comparing predicted nodal displacements with those from finite element (FE) simulations. This deep learning (DL) framework shows promise for accurate, rapid breast deformation approximations, offering enhanced computational efficiency for real-world scenarios.
The expanding complexity and dimensionality in the search space can adversely affect inductive learning in fuzzy rule classifiers, thus impacting the scalability and accuracy of fuzzy systems. This research specifically addresses the challenge of diabetic classification by employing the Brain Storm Optimization (BSO) algorithm to propose a novel fuzzy system that redefines rule generation for this context. An exponential model is integrated into the standard BSO algorithm to enhance rule derivation, tailored specifically for diabetes-related data. The innovative fuzzy system is then applied to classification tasks involving diabetic datasets, demonstrating a substantial improvement in classification accuracy, as evidenced by our experiments.
We present an innovative framework for traffic dynamics analysis using High-Order Evolving Graphs, designed to improve spatio-temporal representations in autonomous driving contexts. Our approach constructs temporal bidirectional bipartite graphs that effectively model the complex interactions within traffic scenes in real-time. By integrating Graph Neural Networks (GNNs) with high-order multi-aggregation strategies, we significantly enhance the modeling of traffic scene dynamics, providing a more accurate and detailed analysis of these interactions. Additionally, we incorporate inductive learning techniques inspired by the GraphSAGE framework, enabling our model to adapt to new and unseen traffic scenarios without the need for retraining, thus ensuring robust generalization. Through extensive experiments on the ROAD and ROAD Waymo datasets, we establish a comprehensive baseline for further developments, demonstrating the potential of our method in accurately capturing traffic behavior. Our results emphasize the value of high-order statistical moments and feature-gated attention mechanisms in improving traffic behavior analysis, laying the groundwork for advancing autonomous driving technologies. Our source code is available at: https://github.com/Addy-1998/High_Order_Graphs
Denoising Diffusion Probabilistic Models (DDPMs) represent a contemporary class of generative models with exceptional qualities in both synthesis and maximizing the data likelihood. These models work by traversing a forward Markov Chain where data is perturbed, followed by a reverse process where a neural network learns to undo the perturbations and recover the original data. There have been increasing efforts exploring the applications of DDPMs in the graph domain. However, most of them have focused on the generative perspective. In this paper, we aim to build a novel generative model for link prediction. In particular, we treat link prediction between a pair of nodes as a conditional likelihood estimation of its enclosing sub-graph. With a dedicated design to decompose the likelihood estimation process via the Bayesian formula, we are able to separate the estimation of sub-graph structure and its node features. Such designs allow our model to simultaneously enjoy the advantages of inductive learning and the strong generalization capability. Remarkably, comprehensive experiments across various datasets validate that our proposed method presents numerous advantages: (1) transferability across datasets without retraining, (2) promising generalization on limited training data, and (3) robustness against graph adversarial attacks.
This work presents a novel systematic methodology to analyse the capabilities and limitations of Large Language Models (LLMs) with feedback from a formal inference engine, on logic theory induction. The analysis is complexity-graded w.r.t. rule dependency structure, allowing quantification of specific inference challenges on LLM performance. Integrating LLMs with formal methods is a promising frontier in the Natural Language Processing field, as an important avenue for improving model inference control and explainability. In particular, inductive learning over complex sets of facts and rules, poses unique challenges for current autoregressive models, as they lack explicit symbolic grounding. While they can be complemented by formal systems, the properties delivered by LLMs regarding inductive learning, are not well understood and quantified. Empirical results indicate that the largest LLMs can achieve competitive results against a SOTA Inductive Logic Programming (ILP) system baseline, but also that tracking long predicate relationship chains is a more difficult obstacle than theory complexity for LLMs.
We propose Fast-and-Frugal Text-Graph (FnF-TG) Transformers, a Transformer-based framework that unifies textual and structural information for inductive link prediction in text-attributed knowledge graphs. We demonstrate that, by effectively encoding ego-graphs (1-hop neighbourhoods), we can reduce the reliance on resource-intensive textual encoders. This makes the model both fast at training and inference time, as well as frugal in terms of cost. We perform a comprehensive evaluation on three popular datasets and show that FnF-TG can achieve superior performance compared to previous state-of-the-art methods. We also extend inductive learning to a fully inductive setting, where relations don't rely on transductive (fixed) representations, as in previous work, but are a function of their textual description. Additionally, we introduce new variants of existing datasets, specifically designed to test the performance of models on unseen relations at inference time, thus offering a new test-bench for fully inductive link prediction.
Graph neural networks (GNNs) have become instrumental in diverse real-world applications, offering powerful graph learning capabilities for tasks such as social networks and medical data analysis. Despite their successes, GNNs are vulnerable to adversarial attacks, including membership inference attacks (MIA), which threaten privacy by identifying whether a record was part of the model's training data. While existing research has explored MIA in GNNs under graph inductive learning settings, the more common and challenging graph transductive learning setting remains understudied in this context. This paper addresses this gap and proposes an effective two-stage defense, Graph Transductive Defense (GTD), tailored to graph transductive learning characteristics. The gist of our approach is a combination of a train-test alternate training schedule and flattening strategy, which successfully reduces the difference between the training and testing loss distributions. Extensive empirical results demonstrate the superior performance of our method (a decrease in attack AUROC by $9.42\%$ and an increase in utility performance by $18.08\%$ on average compared to LBP), highlighting its potential for seamless integration into various classification models with minimal overhead.
This study aims to overcome the limitations of conventional deep-learning approaches based on convolutional neural networks in complex geometries and unstructured meshes by exploring the potential of Graph U-Nets for unsteady flow-field prediction. We present a comprehensive investigation of Graph U-Nets, originally developed for classification tasks, now tailored for mesh-agnostic spatio-temporal forecasting of fluid dynamics. Our focus is on enhancing their performance through systematic hyperparameter tuning and architectural modifications. We propose novel approaches to improve mesh-agnostic spatio-temporal prediction of transient flow fields using Graph U-Nets, enabling accurate prediction on diverse mesh configurations. Key enhancements to the Graph U-Net architecture, including the Gaussian-mixture-model convolutional operator and noise injection approaches, provide increased flexibility in modeling node dynamics: the former reduces prediction error by 95\% compared to conventional convolutional operators, while the latter improves long-term prediction robustness, resulting in an error reduction of 86\%. We demonstrate the effectiveness of these enhancements in both transductive and inductive learning settings, showcasing the adaptability of Graph U-Nets to various flow conditions and mesh structures. This work contributes to the field of reduced-order modeling for computational fluid dynamics by establishing Graph U-Nets as a viable and flexible alternative to convolutional neural networks, capable of accurately and efficiently predicting complex fluid flow phenomena across diverse scenarios.
In the algorithm selection research, the discussion surrounding algorithm features has been significantly overshadowed by the emphasis on problem features. Although a few empirical studies have yielded evidence regarding the effectiveness of algorithm features, the potential benefits of incorporating algorithm features into algorithm selection models and their suitability for different scenarios remain unclear. In this paper, we address this gap by proposing the first provable guarantee for algorithm selection based on algorithm features, taking a generalization perspective. We analyze the benefits and costs associated with algorithm features and investigate how the generalization error is affected by different factors. Specifically, we examine adaptive and predefined algorithm features under transductive and inductive learning paradigms, respectively, and derive upper bounds for the generalization error based on their model's Rademacher complexity. Our theoretical findings not only provide tight upper bounds, but also offer analytical insights into the impact of various factors, such as the training scale of problem instances and candidate algorithms, model parameters, feature values, and distributional differences between the training and test data. Notably, we demonstrate how models will benefit from algorithm features in complex scenarios involving many algorithms, and proves the positive correlation between generalization error bound and $\chi^2$-divergence of distributions.
From a telecommunication standpoint, the surge in users and services challenges next-generation networks with escalating traffic demands and limited resources. Accurate traffic prediction can offer network operators valuable insights into network conditions and suggest optimal allocation policies. Recently, spatio-temporal forecasting, employing Graph Neural Networks (GNNs), has emerged as a promising method for cellular traffic prediction. However, existing studies, inspired by road traffic forecasting formulations, overlook the dynamic deployment and removal of base stations, requiring the GNN-based forecaster to handle an evolving graph. This work introduces a novel inductive learning scheme and a generalizable GNN-based forecasting model that can process diverse graphs of cellular traffic with one-time training. We also demonstrate that this model can be easily leveraged by transfer learning with minimal effort, making it applicable to different areas. Experimental results show up to 9.8% performance improvement compared to the state-of-the-art, especially in rare-data settings with training data reduced to below 20%.
Graph neural networks (GNNs) have emerged as a powerful tool for effectively mining and learning from graph-structured data, with applications spanning numerous domains. However, most research focuses on static graphs, neglecting the dynamic nature of real-world networks where topologies and attributes evolve over time. By integrating sequence modeling modules into traditional GNN architectures, dynamic GNNs aim to bridge this gap, capturing the inherent temporal dependencies of dynamic graphs for a more authentic depiction of complex networks. This paper provides a comprehensive review of the fundamental concepts, key techniques, and state-of-the-art dynamic GNN models. We present the mainstream dynamic GNN models in detail and categorize models based on how temporal information is incorporated. We also discuss large-scale dynamic GNNs and pre-training techniques. Although dynamic GNNs have shown superior performance, challenges remain in scalability, handling heterogeneous information, and lack of diverse graph datasets. The paper also discusses possible future directions, such as adaptive and memory-enhanced models, inductive learning, and theoretical analysis.