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Yuzhou Chen

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19 papers

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TMLR Journal 2026 Journal Article

Topology-Guided Graph Pre-training and Prompt Learning on Directed Graphs

Peiyu Liang
Chenguang Yang
Yixuan He
Rong Pan
Yuzhou Chen

In recent years, graph neural networks (GNNs) have been the dominant approach for graph representation learning, leading to new state-of-the-art results on many classification and prediction tasks. However, they are limited by the fact that they cannot effectively learn expressive node representations without the guide of labels, thus suffering from the labeled data scarcity problem. To address the challenges of labeling costs and improve robustness in few-shot scenarios, pre-training on self-supervised tasks has garnered significant attention. Additionally, numerous prompting methods have been proposed as effective ways to bridge the gap between pretext tasks and downstream applications. Although graph pre-training and prompt tuning methods have explored various downstream tasks on undirected graphs, directed graphs have been largely under-explored, and these models suffer limitations in capturing directional and topological information in directed graphs. In this paper, we propose a novel topology-guided directed graph pre-training and prompt tuning model, named TopoDIG, that can effectively capture intrinsic directional structural and local topological features in directed graphs. These features play essential roles in transferring knowledge from a pre-trained model to downstream tasks. TopoDIG consists of an encoder in the form of a magnetic Laplacian matrix, a topological encoder, and a graph prompt learning function. Experimental results on both real-world and synthetic directed graphs demonstrate the superior performance of TopoDIG compared to prominent baseline methods.

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ICRA Conference 2025 Conference Paper

HumanFT: A Human-Like Fingertip Multimodal Visuo-Tactile Sensor

Yifan Wu 0035
Yuzhou Chen
Zhengying Zhu
Xuhao Qin
Chenxi Xiao

Tactile sensors play a crucial role in enabling robots to interact effectively and safely with objects in everyday tasks. In particular, visuotactile sensors have seen increasing usage in two and three-fingered grippers due to their high-quality feedback. However, a significant gap remains in the development of sensors suitable for humanoid robots, especially five-fingered dexterous hands. One reason is because of the challenges in designing and manufacturing sensors that are compact in size. In this paper, we propose HumanFT, a multimodal visuotactile sensor that replicates the shape and functionality of a human fingertip. To bridge the gap between human and robotic tactile sensing, our sensor features real-time force measurements, high-frequency vibration detection, and overtemperature alerts. To achieve this, we developed a suite of fabrication techniques for a new type of elastomer optimized for force propagation and temperature sensing. Besides, our sensor integrates circuits capable of sensing pressure and vibration. These capabilities have been validated through experiments. The proposed design is simple and cost-effective to fabricate. We believe HumanFT can enhance humanoid robots' perception by capturing and interpreting multimodal tactile information.

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TMLR Journal 2025 Journal Article

Stochastic Block Model-Aware Topological Neural Networks for Graph Link Prediction

Yuzhou Chen
Xiao Guo
Shujie Ma

Link prediction is an important learning task for graph-structured data and is indispensable to understanding graphs' properties. Recent works focus on designing complicated graph neural networks (GNNs) architectures to explore and capture various pairwise interactions among graph nodes. Most GNNs are based on combining graph structural and node feature information by iterative message-passing schemes. However, despite GNNs revolutionizing the field of graph representation learning, some thorny questions are raised concerning whether GNNs can efficiently learn the edge probabilities based on topological structures (i.e., higher-order interactions) and node features, and provide statistically rigorous uncertainty estimates. In this paper, we tackle these challenges and propose a novel stochastic block model (SBM)-aware topological neural networks, called SBM-TNN, that uses SBMs to infer the latent community structure of nodes from graph structures and uses persistent homology to encode higher-order information. Furthermore, we theoretically study the entrywise bound and asymptotic normality of the estimated edge probability matrix to quantify the uncertainty in statistical inference of the edge probabilities. Our extensive experiments for link prediction on both graphs and knowledge graphs show that SBM-TNN achieves state-of-the-art performance over a set of popular baseline methods.

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ICML Conference 2025 Conference Paper

TMetaNet: Topological Meta-Learning Framework for Dynamic Link Prediction

Hao Li 0080
Hao Wan
Yuzhou Chen
Dongsheng Ye
Yulia R. Gel
Hao Jiang 0010

Dynamic graphs evolve continuously, presenting challenges for traditional graph learning due to their changing structures and temporal dependencies. Recent advancements have shown potential in addressing these challenges by developing suitable meta-learning-based dynamic graph neural network models. However, most meta-learning approaches for dynamic graphs rely on fixed weight update parameters, neglecting the essential intrinsic complex high-order topological information of dynamically evolving graphs. We have designed Dowker Zigzag Persistence (DZP), an efficient and stable dynamic graph persistent homology representation method based on Dowker complex and zigzag persistence, to capture the high-order features of dynamic graphs. Armed with the DZP ideas, we propose TMetaNet, a new meta-learning parameter update model based on dynamic topological features. By utilizing the distances between high-order topological features, TMetaNet enables more effective adaptation across snapshots. Experiments on real-world datasets demonstrate TMetaNet’s state-of-the-art performance and resilience to graph noise, illustrating its high potential for meta-learning and dynamic graph analysis. Our code is available at https: //github. com/Lihaogx/TMetaNet.

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ICLR Conference 2025 Conference Paper

Topological Zigzag Spaghetti for Diffusion-based Generation and Prediction on Graphs

Yuzhou Chen
Yulia R. Gel

Diffusion models have recently emerged as a new powerful machinery for generative artificial intelligence on graphs, with applications ranging from drug design to knowledge discovery. However, despite their high potential, most, if not all, existing graph diffusion models are limited in their ability to holistically describe the intrinsic higher-order topological graph properties, which obstructs model generalizability and adoption for downstream tasks. We address this fundamental challenge and extract the latent salient topological graph descriptors at different resolutions by leveraging zigzag persistence. We develop a new computationally efficient topological summary, zigzag spaghetti (ZS), which delivers the most inherent topological properties simultaneously over a sequence of graphs at multiple resolutions. We derive theoretical stability guarantees of ZS and present the first attempt to integrate dynamic topological information into graph diffusion models. Our extensive experiments on graph classification and prediction tasks suggest that ZS has a high promise not only to enhance performance of graph diffusion models, with gains up 10\%, but also to substantially booster model robustness.

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IROS Conference 2025 Conference Paper

Touch-Linked Sleeve: A Haptic Interface for Augmented Tactile Perception in Robotic Teleoperation

Yatao Leng
Yuzhou Chen
Ziyuan Tang
Chenxi Xiao

Tactile perception is crucial for robots to interact effectively with their environments, particularly in cluttered settings or when visual sensing is unavailable. However, a major limitation is the insufficient coverage of tactile sensors on current robots, which makes navigating cluttered spaces challenging due to the lack of capability to detect collisions. This limitation also hinders the use of teleoperation systems in such spaces by reducing the human operator’s situational awareness. To address this issue, this paper proposes the Touch-Linked Sleeve (TLS), a haptic mapping system that redirects contact on robot arms to human skin. The system consists of a tactile skin for contact detection and a haptic sleeve that enables human operators to experience telepresented contact. By establishing a transparent mapping between the robot’s tactile skin and the user’s haptic sleeve, operators can intuitively sense contacts from the robot’s perspective. To evaluate the system’s effectiveness, we conducted experiments demonstrating the functionality of both the tactile skin and the haptic sleeve. Moreover, we performed human studies using a virtual reality robot teleoperation interface to simulate navigation and manipulation in a cluttered scenario. The results indicate that the proposed system enhances perceptual transparency during object grasping tasks, leading to improved task completion times, fewer collisions, and improved overall usability.

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AAAI Conference 2025 Conference Paper

When Witnesses Defend: A Witness Graph Topological Layer for Adversarial Graph Learning

Naheed Anjum Arafat
Debabrota Basu
Yulia Gel
Yuzhou Chen

Capitalizing on the intuitive premise that shape characteristics are more robust to perturbations, we bridge adversarial graph learning with the emerging tools from computational topology, namely, persistent homology representations of graphs. We introduce the concept of witness complex to adversarial analysis on graphs, which allows us to focus only on the salient shape characteristics of graphs, yielded by the subset of the most essential nodes (i.e., landmarks), with minimal loss of topological information on the whole graph. The remaining nodes are then used as witnesses, governing which higher-order graph substructures are incorporated into the learning process. Armed with the witness mechanism, we design Witness Graph Topological Layer (WGTL), which systematically integrates both local and global topological graph feature representations, the impact of which is, in turn, automatically controlled by the robust regularized topological loss. Given the attacker's budget, we derive the important stability guarantees of both local and global topology encodings and the associated robust topological loss. We illustrate the versatility and efficiency of WGTL by its integration with five GNNs and three existing non-topological defense mechanisms. Our extensive experiments demonstrate that WGTL boosts the robustness of GNNs across a range of perturbations and against a range of adversarial attacks.

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AAAI Conference 2024 Conference Paper

SNN-PDE: Learning Dynamic PDEs from Data with Simplicial Neural Networks

Jae Choi
Yuzhou Chen
Huikyo Lee
Hyun Kim
Yulia R. Gel

Dynamics of many complex systems, from weather and climate to spread of infectious diseases, can be described by partial differential equations (PDEs). Such PDEs involve unknown function(s), partial derivatives, and typically multiple independent variables. The traditional numerical methods for solving PDEs assume that the data are observed on a regular grid. However, in many applications, for example, weather and air pollution monitoring delivered by the arbitrary located weather stations of the National Weather Services, data records are irregularly spaced. Furthermore, in problems involving prediction analytics such as forecasting wildfire smoke plumes, the primary focus may be on a set of irregular locations associated with urban development. In recent years, deep learning (DL) methods and, in particular, graph neural networks (GNNs) have emerged as a new promising tool that can complement traditional PDE solvers in scenarios of the irregular spaced data, contributing to the newest research trend of physics informed machine learning (PIML). However, most existing PIML methods tend to be limited in their ability to describe higher dimensional structural properties exhibited by real world phenomena, especially, ones that live on manifolds. To address this fundamental challenge, we bring the elements of the Hodge theory and, in particular, simplicial convolution defined on the Hodge Laplacian to the emerging nexus of DL and PDEs. In contrast to conventional Laplacian and the associated convolution operation, the simplicial convolution allows us to rigorously describe diffusion across higher order structures and to better approximate the complex underlying topology and geometry of the data. The new approach, Simplicial Neural Networks for Partial Differential Equations (SNN PDE) offers a computationally efficient yet effective solution for time dependent PDEs. Our studies of a broad range of synthetic data and wildfire processes demonstrate that SNN PDE improves upon state of the art baselines in handling unstructured grids and irregular time intervals of complex physical systems and offers competitive forecasting capabilities for weather and air quality forecasting.

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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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AAAI Conference 2024 Conference Paper

TopoGCL: Topological Graph Contrastive Learning

Yuzhou Chen
Jose Frias
Yulia R. Gel

Graph contrastive learning (GCL) has recently emerged as a new concept which allows for capitalizing on the strengths of graph neural networks (GNNs) to learn rich representations in a wide variety of applications which involve abundant unlabeled information. However, existing GCL approaches largely tend to overlook the important latent information on higher-order graph substructures. We address this limitation by introducing the concepts of topological invariance and extended persistence on graphs to GCL. In particular, we propose a new contrastive mode which targets topological representations of the two augmented views from the same graph, yielded by extracting latent shape properties of the graph at multiple resolutions. Along with the extended topological layer, we introduce a new extended persistence summary, namely, extended persistence landscapes (EPL) and derive its theoretical stability guarantees. Our extensive numerical results on biological, chemical, and social interaction graphs show that the new Topological Graph Contrastive Learning (TopoGCL) model delivers significant performance gains in unsupervised graph classification for 8 out of 12 considered datasets and also exhibits robustness under noisy scenarios.

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ICRA Conference 2023 Conference Paper

Efficient Planning of Multi-Robot Collective Transport using Graph Reinforcement Learning with Higher Order Topological Abstraction

Steve Paul
Wenyuan Li
Brian Smyth
Yuzhou Chen
Yulia R. Gel
Souma Chowdhury

Efficient multi-robot task allocation (MRTA) is fundamental to various time-sensitive applications such as disaster response, warehouse operations, and construction. This paper tackles a particular class of these problems that we call MRTA-collective transport or MRTA-CT - here tasks present varying workloads and deadlines, and robots are subject to flight range, communication range, and payload constraints. For large instances of these problems involving 100s-1000's of tasks and 10s-100s of robots, traditional non-learning solvers are often time-inefficient, and emerging learning-based policies do not scale well to larger-sized problems without costly retraining. To address this gap, we use a recently proposed encoder-decoder graph neural network involving Capsule networks and multi-head attention mechanism, and innovatively add topological descriptors (TD) as new features to improve transferability to unseen problems of similar and larger size. Persistent homology is used to derive the TD, and proximal policy optimization is used to train our TD-augmented graph neural network. The resulting policy model compares favorably to state-of-the-art non-learning baselines while being much faster. The benefit of using TD is readily evident when scaling to test problems of size larger than those used in training.

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AAAI Conference 2023 Short Paper

Graph of Graphs: A New Knowledge Representation Mechanism for Graph Learning (Student Abstract)

Zhwiei Zhen
Yuzhou Chen
Murat Kantarcioglu
Yulia R. Gel

Supervised graph classification is one of the most actively developing areas in machine learning (ML), with a broad range of domain applications, from social media to bioinformatics. Given a collection of graphs with categorical labels, the goal is to predict correct classes for unlabelled graphs. However, currently available ML tools view each such graph as a standalone entity and, as such, do not account for complex interdependencies among graphs. We propose a novel knowledge representation for graph learning called a {\it Graph of Graphs} (GoG). The key idea is to construct a new abstraction where each graph in the collection is represented by a node, while an edge then reflects similarity among the graphs. Such similarity can be assessed via a suitable graph distance. As a result, the graph classification problem can be then reformulated as a node classification problem. We show that the proposed new knowledge representation approach not only improves classification performance but substantially enhances robustness against label perturbation attacks.

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AAAI Conference 2023 Conference Paper

Topological Pooling on Graphs

Yuzhou Chen
Yulia R. Gel

Graph neural networks (GNNs) have demonstrated a significant success in various graph learning tasks, from graph classification to anomaly detection. There recently has emerged a number of approaches adopting a graph pooling operation within GNNs, with a goal to preserve graph attributive and structural features during the graph representation learning. However, most existing graph pooling operations suffer from the limitations of relying on node-wise neighbor weighting and embedding, which leads to insufficient encoding of rich topological structures and node attributes exhibited by real-world networks. By invoking the machinery of persistent homology and the concept of landmarks, we propose a novel topological pooling layer and witness complex-based topological embedding mechanism that allow us to systematically integrate hidden topological information at both local and global levels. Specifically, we design new learnable local and global topological representations Wit-TopoPool which allow us to simultaneously extract rich discriminative topological information from graphs. Experiments on 11 diverse benchmark datasets against 18 baseline models in conjunction with graph classification tasks indicate that Wit-TopoPool significantly outperforms all competitors across all datasets.

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AAAI Conference 2022 Conference Paper

BScNets: Block Simplicial Complex Neural Networks

Yuzhou Chen
Yulia R. Gel
H. Vincent Poor

Simplicial neural networks (SNN) have recently emerged as the newest direction in graph learning which expands the idea of convolutional architectures from node space to simplicial complexes on graphs. Instead of pre-dominantly assessing pairwise relations among nodes as in the current practice, simplicial complexes allow us to describe higher-order interactions and multi-node graph structures. By building upon connection between the convolution operation and the new block Hodge-Laplacian, we propose the first SNN for link prediction. Our new Block Simplicial Complex Neural Networks (BScNets) model generalizes the existing graph convolutional network (GCN) frameworks by systematically incorporating salient interactions among multiple higher-order graph structures of different dimensions. We discuss theoretical foundations behind BScNets and illustrate its utility for link prediction on eight real-world and synthetic datasets. Our experiments indicate that BScNets outperforms the state-ofthe-art models by a significant margin while maintaining low computation costs. Finally, we show utility of BScNets as the new promising alternative for tracking spread of infectious diseases such as COVID-19 and measuring the effectiveness of the healthcare risk mitigation strategies.

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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

Time-Conditioned Dances with Simplicial Complexes: Zigzag Filtration Curve based Supra-Hodge Convolution Networks for Time-series Forecasting

Yuzhou Chen
Yulia Gel
H. Vincent Poor

Graph neural networks (GNNs) offer a new powerful alternative for multivariate time series forecasting, demonstrating remarkable success in a variety of spatio-temporal applications, from urban flow monitoring systems to health care informatics to financial analytics. Yet, such GNN models pre-dominantly capture only lower order interactions, that is, pairwise relations among nodes, and also largely ignore intrinsic time-conditioned information on the underlying topology of multivariate time series. To address these limitations, we propose a new time-aware GNN architecture which amplifies the power of the recently emerged simplicial neural networks with a time-conditioned topological knowledge representation in a form of zigzag persistence. That is, our new approach, Zigzag Filtration Curve based Supra-Hodge Convolution Networks (ZFC-SHCN) is built upon the two main components: (i) a new highly computationally efficientzigzag persistence curve which allows us to systematically encode time-conditioned topological information, and (ii) a new temporal multiplex graph representation module for learning higher-order network interactions. We discuss theoretical properties of the proposed time-conditioned topological knowledge representation and extensively validate the new time-aware ZFC-SHCN model in conjunction with time series forecasting on a broad range of synthetic and real-world datasets: traffic flows, COVID-19 biosurveillance, Ethereum blockchain, surface air temperature, wind energy, and vector autoregressions. Our experiments demonstrate that the ZFC-SHCN achieves the state-of-the-art performance with lower requirements on computational costs.

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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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ICML Conference 2021 Conference Paper

Z-GCNETs: Time Zigzags at Graph Convolutional Networks for Time Series Forecasting

Yuzhou Chen
Ignacio Segovia-Dominguez
Yulia R. Gel

There recently has been a surge of interest in developing a new class of deep learning (DL) architectures that integrate an explicit time dimension as a fundamental building block of learning and representation mechanisms. In turn, many recent results show that topological descriptors of the observed data, encoding information on the shape of the dataset in a topological space at different scales, that is, persistent homology of the data, may contain important complementary information, improving both performance and robustness of DL. As convergence of these two emerging ideas, we propose to enhance DL architectures with the most salient time-conditioned topological information of the data and introduce the concept of zigzag persistence into time-aware graph convolutional networks (GCNs). Zigzag persistence provides a systematic and mathematically rigorous framework to track the most important topological features of the observed data that tend to manifest themselves over time. To integrate the extracted time-conditioned topological descriptors into DL, we develop a new topological summary, zigzag persistence image, and derive its theoretical stability guarantees. We validate the new GCNs with a time-aware zigzag topological layer (Z-GCNETs), in application to traffic forecasting and Ethereum blockchain price prediction. Our results indicate that Z-GCNET outperforms 13 state-of-the-art methods on 4 time series datasets.

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