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Modeling Spatio-Temporal Systems with Graph-based Machine Learning
Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0002-8201-0282
2025 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Most systems in the physical world are spatio-temporal in nature. The clouds move over our heads, vehicles travel on the roads and electricity is transmitted through vast spatial networks. Machine learning offers many opportunities to understand and forecast the evolution of these systems by making use of large amounts of collected data. However, building useful models of such systems requires taking both spatial and temporal correlations into account. We can not accurately forecast the weather in Linköping without knowing if there is hot air blowing in from the south. Similarly, we can not predict if a vehicle is about to make a left turn without knowing its position and velocity relative to other vehicles on the road. This thesis proposes a set of methods for accurately capturing such spatio-temporal dependencies in machine learning models. 

At the core of the thesis is the idea of using graphs as a way to represent the spatial relationships in spatio-temporal systems. Graphs offer a highly flexible framework for this purpose, in particular for situations where observation locations do not lie on a regular spatial grid. Throughout the thesis, spatial graphs are constructed by letting nodes correspond to spatial locations and edges the relationships between them. These graphs are then used to construct different machine learning models, including graph neural networks and probabilistic graphical models. Combining such graph-based components with machine learning methods for time series modeling then allows for capturing the full spatio-temporal structure of the data. 

The main contribution of the thesis lies in exploring a number of methods using graph-based modeling for spatio-temporal data. This includes extending temporal graph neural networks to handle data observed irregularly over time. Temporal graph neural networks are also used to develop a model for vehicle trajectory forecasting, where the edges of the graph correspond to interactions between traffic agents. The thesis additionally includes work on Bayesian modeling, where a connection between Gaussian Markov random fields and graph neural networks allows for building scalable probabilistic models for data defined using graphs. 

A motivation for the methods developed in this thesis is the increasing use of machine learning in earth science. Capturing relevant spatio-temporal relationships is central for building useful models of the earth system. The thesis includes numerous experiments making use of weather and climate data, as well as application-driven work specifically targeting weather forecasting. Recent years have seen rapid progress in using machine learning models for weather forecasting, and the thesis makes multiple contributions in this direction. A probabilistic weather forecasting model is developed by combining graph-based methods with a latent variable formulation. Lastly, machine learning limited area models are also explored, where graph neural networks are used for regional weather forecasting.   

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2025. , p. 97
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 2453
National Category
Computer Sciences Meteorology and Atmospheric Sciences
Identifiers
URN: urn:nbn:se:liu:diva-215665DOI: 10.3384/9789181181173ISBN: 9789181181166 (print)ISBN: 9789181181173 (electronic)OAI: oai:DiVA.org:liu-215665DiVA, id: diva2:1977570
Public defence
2025-08-22, Ada Lovelace, B-huset, Campus Valla, Linköping, 13:15
Opponent
Supervisors
Funder
Swedish Research Council, 2020-04122; 2024-05011Wallenberg AI, Autonomous Systems and Software Program (WASP)ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsAvailable from: 2025-06-26 Created: 2025-06-26 Last updated: 2025-06-26Bibliographically approved
List of papers
1. Temporal Graph Neural Networks for Irregular Data
Open this publication in new window or tab >>Temporal Graph Neural Networks for Irregular Data
2023 (English)In: Proceedings of The 26th International Conference on Artificial Intelligence and Statistics / [ed] Francisco Ruiz, Jennifer Dy, Jan-Willem van de Meent, ML Research Press , 2023, Vol. 206, p. 4515-4531Conference paper, Published paper (Refereed)
Abstract [en]

This paper proposes a temporal graph neural network model for forecasting of graph-structured irregularly observed time series. Our TGNN4I model is designed to handle both irregular time steps and partial observations of the graph. This is achieved by introducing a time-continuous latent state in each node, following a linear Ordinary Differential Equation (ODE) defined by the output of a Gated Recurrent Unit (GRU). The ODE has an explicit solution as a combination of exponential decay and periodic dynamics. Observations in the graph neighborhood are taken into account by integrating graph neural network layers in both the GRU state update and predictive model. The time-continuous dynamics additionally enable the model to make predictions at arbitrary time steps. We propose a loss function that leverages this and allows for training the model for forecasting over different time horizons. Experiments on simulated data and real-world data from traffic and climate modeling validate the usefulness of both the graph structure and time-continuous dynamics in settings with irregular observations. 

Place, publisher, year, edition, pages
ML Research Press, 2023
Series
Proceedings of Machine Learning Research, ISSN 2640-3498
Keywords
machine learning, graph, graph neural network, irregular data, time-continuous
National Category
Other Computer and Information Science
Identifiers
urn:nbn:se:liu:diva-193682 (URN)001222727704032 ()2-s2.0-85165169181 (Scopus ID)
Conference
The 26th International Conference on Artificial Intelligence and Statistics (AISTATS), Valencia, Spain, 2023
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsWallenberg AI, Autonomous Systems and Software Program (WASP)Swedish Research Council, 2020-04122
Available from: 2023-05-12 Created: 2023-05-12 Last updated: 2025-06-26Bibliographically approved
2. MTP-GO: Graph-Based Probabilistic Multi-Agent Trajectory Prediction With Neural ODEs
Open this publication in new window or tab >>MTP-GO: Graph-Based Probabilistic Multi-Agent Trajectory Prediction With Neural ODEs
2023 (English)In: IEEE Transactions on Intelligent Vehicles, ISSN 2379-8858, E-ISSN 2379-8904, Vol. 8, no 9, p. 4223-4236Article in journal (Refereed) Published
Abstract [en]

Enabling resilient autonomous motion planning requires robust predictions of surrounding road users’ future behavior. In response to this need and the associated challenges, we introduce our model titled MTP-GO. The model encodes the scene using temporal graph neural networks to produce the inputs to an underlying motion model. The motion model is implemented using neural ordinary differential equations where the state-transition functions are learned with the rest of the model. Multimodal probabilistic predictions are obtained by combining the concept of mixture density networks and Kalman filtering. The results illustrate the predictive capabilities of the proposed model across various data sets, outperforming several state-of-the-art methods on a number of metrics.

Place, publisher, year, edition, pages
IEEE, 2023
Keywords
Predictive models;Trajectory;Computational modeling;Mathematical models;Data models;Roads;Behavioral sciences;Graph neural networks;neural ODEs;trajectory prediction
National Category
Computer graphics and computer vision
Identifiers
urn:nbn:se:liu:diva-203164 (URN)10.1109/TIV.2023.3282308 (DOI)2-s2.0-8516155373 (Scopus ID)
Note

Fundng agencies: the Strategic Research Area at Linköping-Lund in Information Technology (ELLIIT), in part by the Swedish Research Council through the Project Handling Uncertainty in Machine Learning Systems under Grant 2020-04122, and in part by the Knutand Alice Wallenberg Foundation through Wallenberg AI, Autonomous Systemsand Software Program (WASP)

Available from: 2024-04-30 Created: 2024-04-30 Last updated: 2025-06-26
3. Scalable Deep Gaussian Markov Random Fields for General Graphs
Open this publication in new window or tab >>Scalable Deep Gaussian Markov Random Fields for General Graphs
2022 (English)In: Proceedings of the 39th International Conference on Machine Learning / [ed] Kamalika Chaudhuri, Stefanie Jegelka, Le Song, Csaba Szepesvari, Gang Niu, Sivan Sabato, 2022, p. 17117-17137Conference paper, Published paper (Refereed)
Abstract [en]

Machine learning methods on graphs have proven useful in many applications due to their ability to handle generally structured data. The framework of Gaussian Markov Random Fields (GMRFs) provides a principled way to define Gaussian models on graphs by utilizing their sparsity structure. We propose a flexible GMRF model for general graphs built on the multi-layer structure of Deep GMRFs, originally proposed for lattice graphs only. By designing a new type of layer we enable the model to scale to large graphs. The layer is constructed to allow for efficient training using variational inference and existing software frameworks for Graph Neural Networks. For a Gaussian likelihood, close to exact Bayesian inference is available for the latent field. This allows for making predictions with accompanying uncertainty estimates. The usefulness of the proposed model is verified by experiments on a number of synthetic and real world datasets, where it compares favorably to other both Bayesian and deep learning methods.

Series
Proceedings of Machine Learning Research, ISSN 2640-3498 ; 162
Keywords
machine learning, graphs, gmrf, deep gmrf, variational inference, gaussian, markov random field
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:liu:diva-187178 (URN)000900064907012 ()
Conference
The 39th International Conference on Machine Learning, ICML, 17-23 July 2022, Baltimore, Maryland, USA
Funder
Wallenberg AI, Autonomous Systems and Software Program (WASP)ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish Research Council, 2020-04122
Available from: 2022-08-10 Created: 2022-08-10 Last updated: 2025-06-26
4. Probabilistic Weather Forecasting with Hierarchical Graph Neural Networks
Open this publication in new window or tab >>Probabilistic Weather Forecasting with Hierarchical Graph Neural Networks
2024 (English)In: Advances in Neural Information Processing Systems: 38th Conference on Neural Information Processing Systems (NeurIPS 2024) / [ed] A. Globerson and L. Mackey and D. Belgrave and A. Fan and U. Paquet and J. Tomczak and C. Zhang, Neural Information Processing Systems, 2024, Vol. 37, p. 41577-41648Conference paper, Published paper (Refereed)
Abstract [en]

In recent years, machine learning has established itself as a powerful tool forhigh-resolution weather forecasting. While most current machine learning modelsfocus on deterministic forecasts, accurately capturing the uncertainty in thechaotic weather system calls for probabilistic modeling. We propose a probabilisticweather forecasting model called Graph-EFM, combining a flexible latent-variableformulation with the successful graph-based forecasting framework. The use of ahierarchical graph construction allows for efficient sampling of spatially coherentforecasts. Requiring only a single forward pass per time step, Graph-EFM allowsfor fast generation of arbitrarily large ensembles. We experiment with the modelon both global and limited area forecasting. Ensemble forecasts from Graph-EFMachieve equivalent or lower errors than comparable deterministic models, with theadded benefit of accurately capturing forecast uncertainty.

Place, publisher, year, edition, pages
Neural Information Processing Systems, 2024
Keywords
weather forecasting, graph neural network, probabilistic, ensemble forecasting, latent variable model, earth system modeling
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-212805 (URN)9798331314385 (ISBN)
Conference
38th Conference on Neural Information Processing Systems (NeurIPS 2024), 10-15 December 2024, Vancouver, Canada.
Available from: 2025-04-03 Created: 2025-04-03 Last updated: 2025-06-26Bibliographically approved
5. Building Machine Learning Limited Area Models: Kilometer-Scale Weather Forecasting in Realistic Settings
Open this publication in new window or tab >>Building Machine Learning Limited Area Models: Kilometer-Scale Weather Forecasting in Realistic Settings
Show others...
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Machine learning is revolutionizing global weather forecasting, with models that efficiently produce highly accurate forecasts. Apart from global forecasting there is also a large value in high-resolution regional weather forecasts, focusing on accurate simulations of the atmosphere for a limited area. Initial attempts have been made to use machine learning for such limited area scenarios, but these experiments do not consider realistic forecasting settings and do not investigate the many design choices involved. We present a framework for building kilometer-scale machine learning limited area models with boundary conditions imposed through a flexible boundary forcing method. This enables boundary conditions defined either from reanalysis or operational forecast data. Our approach employs specialized graph constructions with rectangular and triangular meshes, along with multi-step rollout training strategies to improve temporal consistency. We perform systematic evaluation of different design choices, including the boundary width, graph construction and boundary forcing integration. Models are evaluated across both a Danish and a Swiss domain, two regions that exhibit different orographical characteristics. Verification is performed against both gridded analysis data and in-situ observations, including a case study for the storm Ciara in February 2020. Both models achieve skillful predictions across a wide range of variables, with our Swiss model outperforming the numerical weather prediction baseline for key surface variables. With their substantially lower computational cost, our findings demonstrate great potential for machine learning limited area models in the future of regional weather forecasting.

National Category
Meteorology and Atmospheric Sciences Computer Sciences
Identifiers
urn:nbn:se:liu:diva-215667 (URN)10.48550/arXiv.2504.09340 (DOI)
Available from: 2025-06-26 Created: 2025-06-26 Last updated: 2025-06-26

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1234562 of 6
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Output format
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