Temporal graph classification plays a critical role in applications such as cybersecurity, brain connectivity analysis, social dynamics, and traffic monitoring. Despite its significance, this problem remains underexplored compared to temporal link prediction or node forecasting. Existing methods often rely on snapshot-based or recurrent architectures that either lose fine-grained temporal information or struggle with long-range dependencies. Moreover, local message-passing approaches suffer from oversmoothing and oversquashing, limiting their ability to capture complex temporal structures. We introduce T3FORMER, a novel Topological Temporal Transformer that leverages sliding-window topological and spectral descriptors as first-class tokens, integrated via a specialized Descriptor-Attention mechanism. This design preserves temporal fidelity, enhances robustness, and enables principled cross-modal fusion without rigid discretization. T3former achieves state-of-the-art performance across multiple benchmarks, including dynamic social networks, brain functional connectivity datasets, and traffic networks. It also offers theoretical guarantees of stability under temporal and structural perturbations. Our results highlight the power of combining topological and spectral insights for advancing the frontier of temporal graph learning.

We present CuMPerLay, a novel differentiable vectorization layer that enables the integration of Cubical Multiparameter Persistence (CMP) into deep learning pipelines. While CMP presents a natural and powerful way to topologically work with images, its use is hindered by the complexity of multifiltration structures as well as the vectorization of CMP. In face of these challenges, we introduce a new algorithm for vectorizing MP homologies of cubical complexes. Our CuMPerLay decomposes the CMP into a combination of individual, learnable single-parameter persistence, where the bifiltration functions are jointly learned. Thanks to the differentiability, its robust topological feature vectors can be seamlessly used within state-of-the-art architectures such as Swin Transformers. We establish theoretical guarantees for the stability of our vectorization under generalized Wasserstein metrics. Our experiments on benchmark medical imaging and computer vision datasets show the benefit CuMPerLay on classification and segmentation performance, particularly in limited-data scenarios. Overall, CuMPerLay offers a promising direction for integrating global structural information into deep networks for structured image analysis.

The rise of cryptocurrencies like Bitcoin has not only increased trade volumes but also broadened the use of graph machine learning techniques, such as address embeddings, to analyze transactions and decipher user patterns. Traditional analysis methods rely on simple heuristics and extensive data gathering, while more advanced Graph Neural Networks encounter challenges such as scalability, poor interpretability, and label scarcity in massive blockchain transaction networks. To overcome existing techniques’ computational and interpretability limitations, we introduce a topological approach, Chainlet Orbits, which embeds blockchain addresses by leveraging their topological characteristics in temporal transactions. We employ our innovative address embeddings to investigate financial behavior and e-crime in the Bitcoin and Ethereum networks, focusing on distinctive substructures that arise from user behavior. Our model demonstrates exceptional performance in node classification experiments compared to GNN-based approaches. Furthermore, our approach embeds all daily nodes of the largest blockchain transaction network, Bitcoin, and creates explainable machine learning models in less than 17 minutes which takes days for GNN-based approaches.

Temporal Graph Learning (TGL) aims to discover patterns in evolving networks or temporal graphs and leverage these patterns to predict future interactions. However, most existing research focuses on learning from a single network in isolation, leaving the challenges of within-domain and cross-domain generalization largely unaddressed. In this study, we introduce a new benchmark of 84 real-world temporal transaction networks and propose Temporal Multi-network Transfer (MiNT), a pre-training framework designed to capture transferable temporal dynamics across diverse networks. We train MiNT models on up to 64 transaction networks and evaluate their generalization ability on 20 held-out, unseen networks. Our results show that MiNT consistently outperforms individually trained models, revealing a strong relation between the number of pre-training networks and transfer performance. These findings highlight scaling trends in temporal graph learning and underscore the importance of network diversity in improving generalization. This work establishes the first large-scale benchmark for studying transferability in TGL and lays the groundwork for developing Temporal Graph Foundation Models. Our code is available at \url{https://github.com/benjaminnNgo/ScalingTGNs}

Graph embeddings play a critical role in graph representation learning, allowing machine learning models to explore and interpret graph-structured data. However, existing methods often rely on opaque, high-dimensional embeddings, limiting interpretability and practical visualization. In this work, we introduce Topological Evolution Rate (TopER), a novel, low-dimensional embedding approach grounded in topological data analysis. TopER simplifies a key topological approach, Persistent Homology, by calculating the evolution rate of graph substructures, resulting in intuitive and interpretable visualizations of graph data. This approach not only enhances the exploration of graph datasets but also delivers competitive performance in graph clustering and classification tasks. Our TopER-based models achieve or surpass state-of-the-art results across molecular, biological, and social network datasets in tasks such as classification, clustering, and visualization.

Learning time-evolving objects such as multivariate time series and dynamic networks requires the development of novel knowledge representation mechanisms and neural network architectures, which allow for capturing implicit time-dependent information contained in the data. Such information is typically not directly observed but plays a key role in the learning task performance. In turn, lack of time dimension in knowledge encoding mechanisms for time-dependent data leads to frequent model updates, poor learning performance, and, as a result, subpar decision-making. Here we propose a new approach to a time-aware knowledge representation mechanism that notably focuses on implicit time-dependent topological information along multiple geometric dimensions. In particular, we propose a new approach, named Temporal MultiPersistence (TMP), which produces multidimensional topological fingerprints of the data by using the existing single parameter topological summaries. The main idea behind TMP is to merge the two newest directions in topological representation learning, that is, multi-persistence which simultaneously describes data shape evolution along multiple key parameters, and zigzag persistence to enable us to extract the most salient data shape information over time. We derive theoretical guarantees of TMP vectorizations and show its utility, in application to forecasting on benchmark traffic flow, Ethereum blockchain, and electrocardiogram datasets, demonstrating the competitive performance, especially, in scenarios of limited data records. In addition, our TMP method improves the computational efficiency of the state-of-the-art multipersistence summaries up to 59.5 times.

Many real-world networks evolve over time, and predicting the evolution of such networks remains a challenging task. Graph Neural Networks (GNNs) have shown empirical success for learning on static graphs, but they lack the ability to effectively learn from nodes and edges with different timestamps. Consequently, the prediction of future properties in temporal graphs remains a relatively under-explored area. In this paper, we aim to bridge this gap by introducing a principled framework, named GraphPulse. The framework combines two important techniques for the analysis of temporal graphs within a Newtonian framework. First, we employ the Mapper method, a key tool in topological data analysis, to extract essential clustering information from graph nodes. Next, we harness the sequential modeling capabilities of Recurrent Neural Networks (RNNs) for temporal reasoning regarding the graph's evolution. Through extensive experimentation, we demonstrate that our model enhances the ROC-AUC metric by 10.2\% in comparison to the top-performing state-of-the-art method across various temporal networks. We provide the implementation of GraphPulse at https://github.com/kiarashamsi/GraphPulse.

We present a transformative approach to histopathological cancer detection and grading by introducing a very powerful feature extraction method based on the latest topological data analysis tools. By analyzing the evolution of topological patterns in different color channels, we discovered that every tumor class leaves its own topological footprint in histopathological images, allowing to extract feature vectors that can be used to reliably identify tumor classes.Our topological signatures, even when combined with traditional machine learning methods, provide very fast and highly accurate results in various settings. While most DL models work well for one type of cancer, our model easily adapts to different scenarios, and consistently gives highly competitive results with the state-of-the-art models on benchmark datasets across multiple cancer types including bone, colon, breast, cervical (cytopathology), and prostate cancer. Unlike most DL models, our proposed Topo-ML model does not need any data augmentation or pre-processing steps and works perfectly on small datasets. The model is computationally very efficient, with end-to-end processing taking only a few hours for datasets consisting of thousands of images.

Topological data analysis (TDA) delivers invaluable and complementary information on the intrinsic properties of data inaccessible to conventional methods. However, high computational costs remain the primary roadblock hindering the successful application of TDA in real-world studies, particularly with machine learning on large complex networks.Indeed, most modern networks such as citation, blockchain, and online social networks often have hundreds of thousands of vertices, making the application of existing TDA methods infeasible. We develop two new, remarkably simple but effective algorithms to compute the exact persistence diagrams of large graphs to address this major TDA limitation. First, we prove that $(k+1)$-core of a graph $G$ suffices to compute its $k^{th}$ persistence diagram, $PD_k(G)$. Second, we introduce a pruning algorithm for graphs to compute their persistence diagrams by removing the dominated vertices. Our experiments on large networks show that our novel approach can achieve computational gains up to 95%. The developed framework provides the first bridge between the graph theory and TDA, with applications in machine learning of large complex networks. Our implementation is available at https://github.com/cakcora/PersistentHomologyWithCoralPrunit.

In computer-aided drug discovery (CADD), virtual screening (VS) is used for comparing a library of compounds against known active ligands to identify the drug candidates that are most likely to bind to a molecular target. Most VS methods to date have focused on using canonical compound representations (e.g., SMILES strings, Morgan fingerprints) or generating alternative fingerprints of the compounds by training progressively more complex variational autoencoders (VAEs) and graph neural networks (GNNs). Although VAEs and GNNs led to significant improvements in VS performance, these methods suffer from reduced performance when scaling to large virtual compound datasets. The performance of these methods has shown only incremental improvements in the past few years. To address this problem, we developed a novel method using multiparameter persistence (MP) homology that produces topological fingerprints of the compounds as multidimensional vectors. Our primary contribution is framing the VS process as a new topology-based graph ranking problem by partitioning a compound into chemical substructures informed by the periodic properties of its atoms and extracting their persistent homology features at multiple resolution levels. We show that the margin loss fine-tuning of pretrained Triplet networks attains highly competitive results in differentiating between compounds in the embedding space and ranking their likelihood of becoming effective drug candidates. We further establish theoretical guarantees for the stability properties of our proposed MP signatures, and demonstrate that our models, enhanced by the MP signatures, outperform state-of-the-art methods on benchmark datasets by a wide and highly statistically significant margin (e.g., 93\% gain for Cleves-Jain and 54\% gain for DUD-E Diverse dataset).

Graph neural networks (GNNs) have emerged as a powerful tool for graph classification and representation learning. However, GNNs tend to suffer from over-smoothing problems and are vulnerable to graph perturbations. To address these challenges, we propose a novel topological neural framework of topological relational inference (TRI) which allows for integrating higher-order graph information to GNNs and for systematically learning a local graph structure. The key idea is to rewire the original graph by using the persistent homology of the small neighborhoods of the nodes and then to incorporate the extracted topological summaries as the side information into the local algorithm. As a result, the new framework enables us to harness both the conventional information on the graph structure and information on higher order topological properties of the graph. We derive theoretical properties on stability of the new local topological representation of the graph and discuss its implications on the graph algebraic connectivity. The experimental results on node classification tasks demonstrate that the new TRI-GNN outperforms all 14 state-of-the-art baselines on 6 out 7 graphs and exhibit higher robustness to perturbations, yielding up to 10\% better performance under noisy scenarios.