E. Isufi
Please Note
65 records found
1
We present a systematic empirical study of how three label noise protocols—symmetric random flipping, feature-dependent asymmetric flipping, and structure-dependent flipping—affect the learning curve shape of ChebNet across four benchmark graphs spanning homophilic and heterophilic structure, at noise rates η ∈ {0.1, 0.3, 0.5}.
The central finding is that noise does not simply shift the learning curve downward: above a moderate noise rate it reduces the effective slope, so the gap between clean and noisy performance widens as the label budget grows. Feature-dependent asymmetric noise is consistently the most harmful protocol across all datasets and budgets for η ≥ 0.3, while structure-dependent noise is the least harmful on homophilic graphs. On graphs where the model already operates near its performance limit, noise type has little practical effect.
These findings suggest that beyond a moderate noise rate, cleaning existing labels yields greater returns than acquiring more noisy ones, and that the nature of annotation error interacts with graph structure in ways that single-budget evaluations cannot detect. ...
We present a systematic empirical study of how three label noise protocols—symmetric random flipping, feature-dependent asymmetric flipping, and structure-dependent flipping—affect the learning curve shape of ChebNet across four benchmark graphs spanning homophilic and heterophilic structure, at noise rates η ∈ {0.1, 0.3, 0.5}.
The central finding is that noise does not simply shift the learning curve downward: above a moderate noise rate it reduces the effective slope, so the gap between clean and noisy performance widens as the label budget grows. Feature-dependent asymmetric noise is consistently the most harmful protocol across all datasets and budgets for η ≥ 0.3, while structure-dependent noise is the least harmful on homophilic graphs. On graphs where the model already operates near its performance limit, noise type has little practical effect.
These findings suggest that beyond a moderate noise rate, cleaning existing labels yields greater returns than acquiring more noisy ones, and that the nature of annotation error interacts with graph structure in ways that single-budget evaluations cannot detect.
...
Grid Congestion Forecasting
Advanced Graph Neural Networks for Transmission Grid Congestion Forecasting
The proposed approach is a spatio-temporal graph neural network that operates directly on transmission edges rather than nodes. It combines an LSTM encoder for temporal dynamics, a Transformer-based graph message-passing module with updatable edge representations, and a future-aware decoder that ingests day-ahead prices and weather forecasts. The model is trained and evaluated on Italy's seven-zone electricity market over a 2025 test year.
Against baselines ranging from naive persistence to gradient-boosted trees and LSTM, the model achieves the best normalized absolute error, directional accuracy, and congestion detection F1 score, with advantages that persist across all six forecast horizons. Critically, the proposed model achieves the best AUROC, demonstrating its ability to rank truly congested hours above non-congested ones regardless of where the threshold defining congestion is placed.
Through comprehensive experiments and analyses, the model proves to be more accurate than standard industry methods and domain-specific models. Further experiments demonstrate the quality of the forecast per edge and horizon, and break down the contribution of the different choices regarding its design. Moreover, the impact of future features is assessed, showing a significant performance increase in congestion detection.
The central contribution to the renewable energy field is a reproducible, open-data framework that transforms observable market and weather signals into physically grounded flow forecasts, without access to network topology or TSO-proprietary models. ...
The proposed approach is a spatio-temporal graph neural network that operates directly on transmission edges rather than nodes. It combines an LSTM encoder for temporal dynamics, a Transformer-based graph message-passing module with updatable edge representations, and a future-aware decoder that ingests day-ahead prices and weather forecasts. The model is trained and evaluated on Italy's seven-zone electricity market over a 2025 test year.
Against baselines ranging from naive persistence to gradient-boosted trees and LSTM, the model achieves the best normalized absolute error, directional accuracy, and congestion detection F1 score, with advantages that persist across all six forecast horizons. Critically, the proposed model achieves the best AUROC, demonstrating its ability to rank truly congested hours above non-congested ones regardless of where the threshold defining congestion is placed.
Through comprehensive experiments and analyses, the model proves to be more accurate than standard industry methods and domain-specific models. Further experiments demonstrate the quality of the forecast per edge and horizon, and break down the contribution of the different choices regarding its design. Moreover, the impact of future features is assessed, showing a significant performance increase in congestion detection.
The central contribution to the renewable energy field is a reproducible, open-data framework that transforms observable market and weather signals into physically grounded flow forecasts, without access to network topology or TSO-proprietary models.
GNN-LLM Hybrids for Node Classification
A Comparative Study of GNN, LLM-based, and Hybrid Models
While Graph Neural Networks (GNNs) have become the dominant solution by leveraging graph topology, they often rely on limited textual representations.
Recent advances, therefore, explore integrating large language models (LLMs) to provide stronger semantic encoding for graph learning. However, existing work often evaluates different LLM integration paradigms under individually designed experimental settings, making it difficult to assess their relative strengths for node classification tasks. In this work, we present a controlled empirical comparison between classical message-passing graph neural networks, parameter-efficient LLM-GNN integration (ENGINE), prompt-based generative reasoning (LLaGA), and a lightweight hybrid model that combines structural message passing with label-aware semantic alignment. We evaluate all models on two widely used textual graph benchmarks, \textsc{Cora} and \textsc{WikiCS}, under a unified transductive evaluation protocol and varying levels of training supervision. Our results show that the performance of ENGINE consistently outperforms strong GNN baselines, whereas LLaGA is more sensitive to inference constraints and evaluation protocols. The additional hybrid model we propose in this thesis further demonstrates complementary benefits, particularly in low-supervision regimes. These findings clarify practical trade-offs between discriminative and generative LLM-based graph models and highlight hybrid designs as a promising direction for efficient and robust node classification on textual graphs. ...
While Graph Neural Networks (GNNs) have become the dominant solution by leveraging graph topology, they often rely on limited textual representations.
Recent advances, therefore, explore integrating large language models (LLMs) to provide stronger semantic encoding for graph learning. However, existing work often evaluates different LLM integration paradigms under individually designed experimental settings, making it difficult to assess their relative strengths for node classification tasks. In this work, we present a controlled empirical comparison between classical message-passing graph neural networks, parameter-efficient LLM-GNN integration (ENGINE), prompt-based generative reasoning (LLaGA), and a lightweight hybrid model that combines structural message passing with label-aware semantic alignment. We evaluate all models on two widely used textual graph benchmarks, \textsc{Cora} and \textsc{WikiCS}, under a unified transductive evaluation protocol and varying levels of training supervision. Our results show that the performance of ENGINE consistently outperforms strong GNN baselines, whereas LLaGA is more sensitive to inference constraints and evaluation protocols. The additional hybrid model we propose in this thesis further demonstrates complementary benefits, particularly in low-supervision regimes. These findings clarify practical trade-offs between discriminative and generative LLM-based graph models and highlight hybrid designs as a promising direction for efficient and robust node classification on textual graphs.
Modelling floods via graph neural networks
With applications to dike-breach floods
To provide a comprehensive perspective on deep learning for flood mapping, we first reviewed the state of the art across different applications, considering a range of flood types, spatial scales, and deep learning architectures. Our analysis shows that deep learning methods generally outperform both traditional numerical approaches and conventional machine learning in terms of speed and accuracy. However, most existing models are tailored to individual case studies, neglect the dynamic evolution of flood waves, and cannot transfer to new topographic settings and boundary conditions not seen during training. Furthermore, current approaches struggle to incorporate physical principles, represent hydraulic structures, and provide physically consistent methods for validating outputs, particularly in the context of uncertainty quantification. Finally, we highlight that dike-breach floods remain largely under-represented in the literature, despite their high uncertainty stemming from flood defence failures.
In this thesis, we introduce Graph Neural Networks (GNNs) as hydraulics-inspired Surrogate models for simulating the spatio-temporal evolution of floods. While applicable to different flood types, our focus is on dike-breach floods due to their high uncertainty and particular relevance in the Netherlands and other low-lying areas. We build GNNs that are conceptually analogous to finite-volume methods used to solve the shallow water equations: finite-volume cells are treated as graph nodes, and flux exchanges are learned between adjacent cells by the model. The flood propagation in the proposed SWE-GNN model resembles hydraulics principles and enforces water to propagate only from cells with water. The model works in the same fashion as numerical solvers, auto-regressively predicting the evolution of the hydraulic states over time. By stacking multiple GNN layers, the model captures wider spatial dependencies without requiring small numerical time steps, theoretically needed for stability conditions. We also develop a multi-step ahead loss function combined with curriculum learning that further stabilizes long-term predictions.
We propose a multi-scale GNN formulation that models flood dynamics across different spatial resolutions, enabling the capture of both local and large-scale propagation processes. Time-varying boundary conditions are incorporated through ghost cells, removing the need for separate numerical solvers to initialize simulations. To enhance generalization across unseen unstructured meshes and reduce training data demands, we enforce invariance principles, ensuring the model is independent of coordinate rotations. This multi-scale approach proves both faster and more accurate than its single-scale counterpart. Our methods are validated on a suite of two-dimensional synthetic dike-breach simulations generated with a high-fidelity numerical solver. These datasets progressively increase in complexity by varying initial conditions, location of boundary conditions, size of the domain, computational mesh, and time-varying hydrographs used as boundary condition. Results demonstrate that the GNN generalizes well to unseen topographies, boundary configurations, and mesh configurations, without relying on inputs from numerical simulations. The models achieve a testing critical success index consistently higher than 70% in all datasets. The model also shows generalization to a real case study, dike ring 15 in the Netherlands, with only one fine-tuning simulation.
Finally, we extend the model to explicitly include hydraulic structures and to quantify uncertainty in flood hazard mapping of another real-world case study, dike ring 41 in the Netherlands. The framework is tested for large-scale uncertainty analysis with 10,000 scenarios. All simulations are completed in under 10 hours on a single GPU, corresponding to a speed-up of approximately 10,000 times with respect to the numerical solver, with over half of the scenarios maintaining plausible mass conservation. The combined scenarios are then used to produce probabilistic flood hazard maps, which assume equal likelihood of occurrence for each event. We also analyse the flood uncertainty for a given breach location and return period, showing that the model ensemble can provide better flooding estimates than the deterministic scenario.
This thesis highlights the potential of GNN-based surrogates for time-sensitive flood risk assessments under uncertainty. By demonstrating both accuracy and computational efficiency, it contributes to bridging the gap between complex hydraulic modelling and large-scale flood risk analysis. Despite being applied on dike-breach floods, the framework introduced in this thesis can readily be applied to fluvial and coastal floods without modifications. This open pathways for integrating surrogates into operational decision making and future flood resilience planning.
...
To provide a comprehensive perspective on deep learning for flood mapping, we first reviewed the state of the art across different applications, considering a range of flood types, spatial scales, and deep learning architectures. Our analysis shows that deep learning methods generally outperform both traditional numerical approaches and conventional machine learning in terms of speed and accuracy. However, most existing models are tailored to individual case studies, neglect the dynamic evolution of flood waves, and cannot transfer to new topographic settings and boundary conditions not seen during training. Furthermore, current approaches struggle to incorporate physical principles, represent hydraulic structures, and provide physically consistent methods for validating outputs, particularly in the context of uncertainty quantification. Finally, we highlight that dike-breach floods remain largely under-represented in the literature, despite their high uncertainty stemming from flood defence failures.
In this thesis, we introduce Graph Neural Networks (GNNs) as hydraulics-inspired Surrogate models for simulating the spatio-temporal evolution of floods. While applicable to different flood types, our focus is on dike-breach floods due to their high uncertainty and particular relevance in the Netherlands and other low-lying areas. We build GNNs that are conceptually analogous to finite-volume methods used to solve the shallow water equations: finite-volume cells are treated as graph nodes, and flux exchanges are learned between adjacent cells by the model. The flood propagation in the proposed SWE-GNN model resembles hydraulics principles and enforces water to propagate only from cells with water. The model works in the same fashion as numerical solvers, auto-regressively predicting the evolution of the hydraulic states over time. By stacking multiple GNN layers, the model captures wider spatial dependencies without requiring small numerical time steps, theoretically needed for stability conditions. We also develop a multi-step ahead loss function combined with curriculum learning that further stabilizes long-term predictions.
We propose a multi-scale GNN formulation that models flood dynamics across different spatial resolutions, enabling the capture of both local and large-scale propagation processes. Time-varying boundary conditions are incorporated through ghost cells, removing the need for separate numerical solvers to initialize simulations. To enhance generalization across unseen unstructured meshes and reduce training data demands, we enforce invariance principles, ensuring the model is independent of coordinate rotations. This multi-scale approach proves both faster and more accurate than its single-scale counterpart. Our methods are validated on a suite of two-dimensional synthetic dike-breach simulations generated with a high-fidelity numerical solver. These datasets progressively increase in complexity by varying initial conditions, location of boundary conditions, size of the domain, computational mesh, and time-varying hydrographs used as boundary condition. Results demonstrate that the GNN generalizes well to unseen topographies, boundary configurations, and mesh configurations, without relying on inputs from numerical simulations. The models achieve a testing critical success index consistently higher than 70% in all datasets. The model also shows generalization to a real case study, dike ring 15 in the Netherlands, with only one fine-tuning simulation.
Finally, we extend the model to explicitly include hydraulic structures and to quantify uncertainty in flood hazard mapping of another real-world case study, dike ring 41 in the Netherlands. The framework is tested for large-scale uncertainty analysis with 10,000 scenarios. All simulations are completed in under 10 hours on a single GPU, corresponding to a speed-up of approximately 10,000 times with respect to the numerical solver, with over half of the scenarios maintaining plausible mass conservation. The combined scenarios are then used to produce probabilistic flood hazard maps, which assume equal likelihood of occurrence for each event. We also analyse the flood uncertainty for a given breach location and return period, showing that the model ensemble can provide better flooding estimates than the deterministic scenario.
This thesis highlights the potential of GNN-based surrogates for time-sensitive flood risk assessments under uncertainty. By demonstrating both accuracy and computational efficiency, it contributes to bridging the gap between complex hydraulic modelling and large-scale flood risk analysis. Despite being applied on dike-breach floods, the framework introduced in this thesis can readily be applied to fluvial and coastal floods without modifications. This open pathways for integrating surrogates into operational decision making and future flood resilience planning.
Bidirectional Multi-Scale Graph Learning
Using Hierarchical GNNs for Residential Property Valuation
We introduce a Multi-Scale Bidirectional Spatio-Temporal Graph Neural Network (MBSTGNN) that models transactions and neighbourhoods as dynamic graphs linked through bidirectional message passing. A temporal memory mechanism maintains consistency across time, enabling the model to capture evolving market conditions. Evaluated on Rotterdam housing transactions, MBSTGNN outperforms strong baselines, particularly in sparse-data settings, and produces embeddings that reveal domain-consistent socio-spatial and temporal patterns. These results demonstrate its potential for advancing automated valuation and related spatio-temporal prediction tasks. ...
We introduce a Multi-Scale Bidirectional Spatio-Temporal Graph Neural Network (MBSTGNN) that models transactions and neighbourhoods as dynamic graphs linked through bidirectional message passing. A temporal memory mechanism maintains consistency across time, enabling the model to capture evolving market conditions. Evaluated on Rotterdam housing transactions, MBSTGNN outperforms strong baselines, particularly in sparse-data settings, and produces embeddings that reveal domain-consistent socio-spatial and temporal patterns. These results demonstrate its potential for advancing automated valuation and related spatio-temporal prediction tasks.
We use the user–user covariance (or its inverse, the precision matrix) as a graph shift operator (GSO) and train SelectionGNN-based VNNs on the MovieLens-100K dataset.
Two training regimes are evaluated: (i) RMSE-only (No-BAM-SVNN) and (ii) a compound loss that also includes novelty and diversity terms (BAM-SVNN).
For each regime we sweep six graph configurations: covariance/precision crossed with {dense, hard-threshold, soft-threshold} sparsification, under five random seeds, yielding 30 runs per regime.
Baseline comparisons include PCA, a naive mean–std model, and a random predictor.
The best SVNN configuration increases recommendation Novelty by 2.8 percentage points and matches PCA’s Diversity while incurring only a 0.03 RMSE penalty.
Hard-thresholded precision graphs provide the lowest SVNN RMSE (0.952), whereas dense covariance graphs maximise diversity (0.868).
Integrating novelty/diversity directly into the loss offers no additional benefit yet multiplies runtime by x33.
One-way ANOVA indicates that model family explains 97.6% of RMSE variance (\(\eta^2=0.976\)) and 77.8% of novelty variance.
This work is the first to benchmark (sparsified) VNNs on beyond-accuracy metrics, demonstrating a favourable accuracy–novelty trade-off and clarifying when sparsification and BAM-weighted training pay off.
All code, data splits and statistical notebooks are released for full reproducibility. ...
We use the user–user covariance (or its inverse, the precision matrix) as a graph shift operator (GSO) and train SelectionGNN-based VNNs on the MovieLens-100K dataset.
Two training regimes are evaluated: (i) RMSE-only (No-BAM-SVNN) and (ii) a compound loss that also includes novelty and diversity terms (BAM-SVNN).
For each regime we sweep six graph configurations: covariance/precision crossed with {dense, hard-threshold, soft-threshold} sparsification, under five random seeds, yielding 30 runs per regime.
Baseline comparisons include PCA, a naive mean–std model, and a random predictor.
The best SVNN configuration increases recommendation Novelty by 2.8 percentage points and matches PCA’s Diversity while incurring only a 0.03 RMSE penalty.
Hard-thresholded precision graphs provide the lowest SVNN RMSE (0.952), whereas dense covariance graphs maximise diversity (0.868).
Integrating novelty/diversity directly into the loss offers no additional benefit yet multiplies runtime by x33.
One-way ANOVA indicates that model family explains 97.6% of RMSE variance (\(\eta^2=0.976\)) and 77.8% of novelty variance.
This work is the first to benchmark (sparsified) VNNs on beyond-accuracy metrics, demonstrating a favourable accuracy–novelty trade-off and clarifying when sparsification and BAM-weighted training pay off.
All code, data splits and statistical notebooks are released for full reproducibility.
Data augmentation for Sparse Graph Traversals
Exploring data augmentation options to enhance deep learning model performance
Despite limited improvements, this study establishes a foundation for future research in graph-based trajectory augmentation. Integrating richer trip-level features, such as dynamic environmental conditions or behavioral data, with structural augmentation could lead to more effective training data and improved model generalization. ...
Despite limited improvements, this study establishes a foundation for future research in graph-based trajectory augmentation. Integrating richer trip-level features, such as dynamic environmental conditions or behavioral data, with structural augmentation could lead to more effective training data and improved model generalization.
Recommender systems via Covariance Neural Networks
Using precision matrices as Graph Collaborative Filter
The key contribution of this dissertation is proposing methodologies for signal processing over dynamic networks which are aimed at the two aforementioned tasks. For dynamic networks with incoming nodes, we process signals by introducing a parametric stochastic attachment model. In this model, the incoming nodes connect with probability to existing nodes with certain weights. This uncertainty allows us to model input output relations and allows us to cast them in the context of different graph signal processing tasks. We learn the model attachment parameters in a task-aware setting, allowing us to interpret topology identification in task-aware settings. Separately, we also propose filter design strategies for processing signals both at the incoming and existing nodes using stochastic attachment models.
Another contribution of this dissertation is to extend graph signal processing with graph filters to the scenario where the graph keeps growing in size with streaming data. We propose online graph filter design which updates the filter online, based on incoming nodes. We design this both for scenarios where the incoming node connectivity is known and unknown. In the unknown connectivity case, we study the performance difference between knowing and not knowing the topology and how the stochastic attachment influences it. We also show that by adapting the stochastic attachment, we can learn faster from the data stream.
Finally,we consider the task of topology decomposition and identification for dynamic networks with fixed nodes but changing edge support. We build a tensor of partially observed adjacency matrices corresponding to such a dynamic topology and express this in terms of underlying latent graphs and their temporal signatures. Furthermore, we account for the time-varying graph signals as a prior to aid identifying these latent graphs and missing components of the topology. These latent graphs are individually and collectively expressive and provide interpretable decompositions along with outperforming traditional structure agnostic low-rank decompositions. ...
The key contribution of this dissertation is proposing methodologies for signal processing over dynamic networks which are aimed at the two aforementioned tasks. For dynamic networks with incoming nodes, we process signals by introducing a parametric stochastic attachment model. In this model, the incoming nodes connect with probability to existing nodes with certain weights. This uncertainty allows us to model input output relations and allows us to cast them in the context of different graph signal processing tasks. We learn the model attachment parameters in a task-aware setting, allowing us to interpret topology identification in task-aware settings. Separately, we also propose filter design strategies for processing signals both at the incoming and existing nodes using stochastic attachment models.
Another contribution of this dissertation is to extend graph signal processing with graph filters to the scenario where the graph keeps growing in size with streaming data. We propose online graph filter design which updates the filter online, based on incoming nodes. We design this both for scenarios where the incoming node connectivity is known and unknown. In the unknown connectivity case, we study the performance difference between knowing and not knowing the topology and how the stochastic attachment influences it. We also show that by adapting the stochastic attachment, we can learn faster from the data stream.
Finally,we consider the task of topology decomposition and identification for dynamic networks with fixed nodes but changing edge support. We build a tensor of partially observed adjacency matrices corresponding to such a dynamic topology and express this in terms of underlying latent graphs and their temporal signatures. Furthermore, we account for the time-varying graph signals as a prior to aid identifying these latent graphs and missing components of the topology. These latent graphs are individually and collectively expressive and provide interpretable decompositions along with outperforming traditional structure agnostic low-rank decompositions.
Learning on Simplicial Complexes
From Convolutions to Generative Models
The main theme of the thesis is to develop principled machine learning models for signals on simplicial complexes. By principled, we mean that the models leverage the intrinsic priors of the domain and the signals, namely, the topological structure of simplicial compelxes and the Hodge decomposition of simplicial signals. The latter states that, for example, edge flows can be decomposed into a divergence-free part and a curl-free part, each modeling the distinct properties of real-world flows — the conservation of flows (e.g., water flows) and the rotational properties of flows (e.g., electric currents).... ...
The main theme of the thesis is to develop principled machine learning models for signals on simplicial complexes. By principled, we mean that the models leverage the intrinsic priors of the domain and the signals, namely, the topological structure of simplicial compelxes and the Hodge decomposition of simplicial signals. The latter states that, for example, edge flows can be decomposed into a divergence-free part and a curl-free part, each modeling the distinct properties of real-world flows — the conservation of flows (e.g., water flows) and the rotational properties of flows (e.g., electric currents)....