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Baris Coskunuzer

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11 papers

2 author rows

AAAI Conference 2026 Conference Paper

T3former: Temporal Graph Classification with Topological Machine Learning

Md Joshem Uddin
Soham Changani
Baris Coskunuzer

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.

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NeurIPS Conference 2025 Conference Paper

MiNT: Multi-Network Transfer Benchmark for Temporal Graph Learning

Kiarash Shamsi
Tran Gia Bao Ngo
Razieh Shirzadkhani
Shenyang Huang
Farimah Poursafaei
Poupak Azad
Reihaneh Rabbany
Baris Coskunuzer

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}

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TMLR Journal 2025 Journal Article

PROXI: Challenging the GNNs for Link Prediction

Astrit Tola
Jack Myrick
Baris Coskunuzer

Over the past decade, Graph Neural Networks (GNNs) have transformed graph representation learning. In the widely adopted message-passing GNN framework, nodes refine their representations by aggregating information from neighboring nodes iteratively. While GNNs excel in various domains, recent theoretical studies have raised concerns about their capabilities. GNNs aim to address various graph-related tasks by utilizing such node representations, however, this one-size-fits-all approach proves suboptimal for diverse tasks. Motivated by these observations, we conduct empirical tests to compare the performance of current GNN models with more conventional and direct methods in link prediction tasks. Introducing our model, PROXI, which leverages proximity information of node pairs in both graph and attribute spaces, we find that standard machine learning (ML) models perform competitively, even outperforming cutting-edge GNN models when applied to these proximity metrics derived from node neighborhoods and attributes. This holds true across both homophilic and heterophilic networks, as well as small and large benchmark datasets, including those from the Open Graph Benchmark (OGB). Moreover, we show that augmenting traditional GNNs with PROXI significantly boosts their link prediction performance. Our empirical findings corroborate the previously mentioned theoretical observations and imply that there exists ample room for enhancement in current GNN models to reach their potential.

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TMLR Journal 2025 Journal Article

SCNode: Spatial and Contextual Coordinates for Graph Representation Learning

Md Joshem Uddin
Astrit Tola
Varin Singh Sikand
Cuneyt Gurcan Akcora
Baris Coskunuzer

Effective node representation lies at the heart of Graph Neural Networks (GNNs), as it directly impacts their ability to perform downstream tasks such as node classification and link prediction. Most existing GNNs, particularly message passing graph neural networks, rely on neighborhood aggregation to iteratively compute node embeddings. While powerful, this paradigm suffers from well-known limitations of oversquashing, oversmoothing, and underreaching that degrade representation quality. More critically, MPGNNs often assume homophily, where connected nodes share similar features or labels, leading to poor generalization in heterophilic graphs where this assumption breaks down. To address these challenges, we propose *SCNode*, a *Spatial-Contextual Node Embedding* framework designed to perform consistently well in both homophilic and heterophilic settings. SCNode integrates spatial and contextual information, yielding node embeddings that are not only more discriminative but also structurally aware. Our approach introduces new homophily matrices for understanding class interactions and tendencies. Extensive experiments on benchmark datasets show that SCNode achieves superior performance over conventional GNN models, demonstrating its robustness and adaptability in diverse graph structures.

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NeurIPS Conference 2025 Conference Paper

TopER: Topological Embeddings in Graph Representation Learning

Astrit Tola
Funmilola Mary Taiwo
Cuneyt Akcora
Baris Coskunuzer

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.

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ICLR Conference 2024 Conference Paper

GraphPulse: Topological representations for temporal graph property prediction

Kiarash Shamsi
Farimah Poursafaei
Shenyang Huang
Tran Gia Bao Ngo
Baris Coskunuzer
Cuneyt Gurcan Akcora

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.

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AAAI Conference 2024 Conference Paper

Time-Aware Knowledge Representations of Dynamic Objects with Multidimensional Persistence

Baris Coskunuzer
Ignacio Segovia-Dominguez
Yuzhou Chen
Yulia R. Gel

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.

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NeurIPS Conference 2022 Conference Paper

Reduction Algorithms for Persistence Diagrams of Networks: CoralTDA and PrunIT

Cuneyt G Akcora
Murat Kantarcioglu
Yulia Gel
Baris Coskunuzer

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.

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ICLR Conference 2022 Conference Paper

TAMP-S2GCNets: Coupling Time-Aware Multipersistence Knowledge Representation with Spatio-Supra Graph Convolutional Networks for Time-Series Forecasting

Yuzhou Chen
Ignacio Segovia-Dominguez
Baris Coskunuzer
Yulia R. Gel

Graph Neural Networks (GNNs) are proven to be a powerful machinery for learning complex dependencies in multivariate spatio-temporal processes. However, most existing GNNs have inherently static architectures, and as a result, do not explicitly account for time dependencies of the encoded knowledge and are limited in their ability to simultaneously infer latent time-conditioned relations among entities. We postulate that such hidden time-conditioned properties may be captured by the tools of multipersistence, i.e, a emerging machinery in topological data analysis which allows us to quantify dynamics of the data shape along multiple geometric dimensions. We make the first step toward integrating the two rising research directions, that is, time-aware deep learning and multipersistence, and propose a new model, Time-Aware Multipersistence Spatio-Supra Graph Convolutional Network (TAMP-S2GCNets). We summarize inherent time-conditioned topological properties of the data as time-aware multipersistence Euler-Poincar\'e surface and prove its stability. We then construct a supragraph convolution module which simultaneously accounts for the extracted intra- and inter- spatio-temporal dependencies in the data. Our extensive experiments on highway traffic flow, Ethereum token prices, and COVID-19 hospitalizations demonstrate that TAMP-S2GCNets outperforms the state-of-the-art tools in multivariate time series forecasting tasks.

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NeurIPS Conference 2022 Conference Paper

ToDD: Topological Compound Fingerprinting in Computer-Aided Drug Discovery

Andaç Demir
Baris Coskunuzer
Yulia Gel
Ignacio Segovia-Dominguez
Yuzhou Chen
Bulent Kiziltan

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).

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NeurIPS Conference 2021 Conference Paper

Topological Relational Learning on Graphs

Yuzhou Chen
Baris Coskunuzer
Yulia Gel

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.

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