arXiv subjects

Fragkiskos D. Malliaros

Publications and source records attributed to Fragkiskos D. Malliaros.

At least 19 recordsLinked to original sources

arXiv2026

Atompack: A Storage and Distribution Layer for Read-Heavy Atomistic ML Training Datasets

Atomistic machine learning datasets are increasingly used for training: large immutable snapshots are read repeatedly, shuffled across epochs, staged across clusters' storage systems, and republished as reusable scientific artifacts. This workload differs from interactive scientific curation, where mutable records and ad hoc inspection are often more important than random indexed throughput. We present Atompack, an append-oriented storage format and distribution layer designed around a simple workload: training pipelines usually consume complete molecular records, while the order of records is randomized by the learning algorithm. Atompack appends records efficiently during dataset construction, then commits an immutable index and serves records through a memory-mapped read path optimized for training. We compare Atompack with HDF5, LMDB, and ASE baselines representing array stores, key-value records, serialized records, and object-oriented databases. The benchmarks measure sequential reads, shuffled reads, shared-filesystem behavior, write throughput, and artifact size. On a representative 64-atom workload, Atompack is 96x faster than ASE LMDB on shuffled training-style reads while producing artifacts about 79\% smaller. The results indicate that serving complete molecule records, rather than field chunks or reconstructed objects, improves shuffled training throughput while keeping artifacts compact enough for public distribution.

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arXiv2026

Scaling Higher-Order Graph Learning with Maximal Clique Complexes

Graph neural networks (GNNs) are limited to modeling pairwise interactions, while higher-order models based on cell complexes achieve greater expressivity but often suffer from poor scalability. We introduce simplified and factored cellular Weisfeiler Leman tests (sCWL and fCWL), which preserve the expressivity of the CWL test while improving computational efficiency. We further introduce the maximal clique complex, enabling scalable CWNs with reduced time and memory complexity while retaining strong empirical performance. To avoid explicit clique enumeration, we propose CliqueWalk, a biased random walk that samples maximal cliques and scales linearly with graph size. These contributions yield a scalable topological learning framework for higher-order graph representation.

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arXiv2026

TriForces: Augmenting Atomistic GNNs for Transferable Representations

Machine learning interatomic potentials (MLIPs) achieve excellent accuracy when trained on large Density Functional Theory (DFT) data. To be useful in practice, they must often be adapted to target chemistries using small and expensive task-specific datasets. However, MLIPs transfer inconsistently across domains, with representations that often loose accessible composition and structure information. To address this, we present TriForces, a model-agnostic three-stream framework that separates composition and structure information, combined with self-supervised learning to preserve transferable representations. TriForces improves performance on MatBench and QM9 over baselines without needing DFT labels and enables efficient similar structure retrieval through its learned latent space. On OMat24, in limited-data training regime, TriForces reduces energy MAE by 57% at 20K samples only and improves force MAE across sample sizes. We release pretrained TriForces variants across multiple MLIP architectures with code at https://github.com/Ramlaoui/triforces.

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arXiv2026

Graph Rewiring in GNNs to Mitigate Over-Squashing and Over-Smoothing: A Survey

Graph Neural Networks are powerful models for learning from graph-structured data, yet their effectiveness is often limited by two critical challenges: over-squashing, where information from distant nodes is excessively compressed, and over-smoothing, where repeated propagation makes node representations indistinguishable. Both phenomena stem from the interaction between message passing and the input topology, ultimately degrading information flow and limiting the performance of GNNs. In this survey, we examine graph rewiring techniques, a class of methods designed to modify the graph topology to enhance information propagation in GNNs. We provide a comprehensive review of state-of-the-art rewiring approaches, delving into their theoretical underpinnings, practical implementations, and performance trade-offs.

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arXiv2026

Graph Rewiring in GNNs to Mitigate Over-Squashing and Over-Smoothing: A Survey

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arXiv2026

Generalization Bounds for Spectral GNNs via Fourier Domain Analysis

Spectral graph neural networks learn graph filters, but their behavior with increasing depth and polynomial order is not well understood. We analyze these models in the graph Fourier domain, where each layer becomes an element-wise frequency update, separating the fixed spectrum from trainable parameters and making depth and order explicit. In this setting, we show that Gaussian complexity is invariant under the Graph Fourier Transform, which allows us to derive data-dependent, depth, and order-aware generalization bounds together with stability estimates. In the linear case, our bounds are tighter, and on real graphs, the data-dependent term correlates with the generalization gap across polynomial bases, highlighting practical choices that avoid frequency amplification across layers.

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arXiv2026

Training-free Graph-based Imputation of Missing Modalities in Multimodal Recommendation

Multimodal recommender systems (RSs) represent items in the catalog through multimodal data (e.g., product images and descriptions) that, in some cases, might be noisy or (even worse) missing. In those scenarios, the common practice is to drop items with missing modalities and train the multimodal RSs on a subsample of the original dataset. To date, the problem of missing modalities in multimodal recommendation has still received limited attention in the literature, lacking a precise formalisation as done with missing information in traditional machine learning. In this work, we first provide a problem formalisation for missing modalities in multimodal recommendation. Second, by leveraging the user-item graph structure, we re-cast the problem of missing multimodal information as a problem of graph features interpolation on the item-item co-purchase graph. On this basis, we propose four training-free approaches that propagate the available multimodal features throughout the item-item graph to impute the missing features. Extensive experiments on popular multimodal recommendation datasets demonstrate that our solutions can be seamlessly plugged into any existing multimodal RS and benchmarking framework while still preserving (or even widen) the performance gap between multimodal and traditional RSs. Moreover, we show that our graph-based techniques can perform better than traditional imputations in machine learning under different missing modalities settings. Finally, we analyse (for the first time in multimodal RSs) how feature homophily calculated on the item-item graph can influence our graph-based imputations.

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arXiv2025

Continuous Simplicial Neural Networks

Simplicial complexes provide a powerful framework for modeling higher-order interactions in structured data, making them particularly suitable for applications such as trajectory prediction and mesh processing. However, existing simplicial neural networks (SNNs), whether convolutional or attention-based, rely primarily on discrete filtering techniques, which can be restrictive. In contrast, partial differential equations (PDEs) on simplicial complexes offer a principled approach to capture continuous dynamics in such structures. In this work, we introduce continuous simplicial neural network (COSIMO), a novel SNN architecture derived from PDEs on simplicial complexes. We provide theoretical and experimental justifications of COSIMO's stability under simplicial perturbations. Furthermore, we investigate the over-smoothing phenomenon, a common issue in geometric deep learning, demonstrating that COSIMO offers better control over this effect than discrete SNNs. Our experiments on real-world datasets demonstrate that COSIMO achieves competitive performance compared to state-of-the-art SNNs in complex and noisy environments. The implementation codes are available in https://github.com/ArefEinizade2/COSIMO.

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arXiv2025

Retrieval-Constrained Decoding Reveals Underestimated Parametric Knowledge in Language Models

Language models (LMs) encode substantial factual knowledge, but often produce answers judged as incorrect. We hypothesize that many of these answers are actually correct, but are expressed in alternative surface forms that are dismissed due to an overly strict evaluation, leading to an underestimation of models' parametric knowledge. We propose Retrieval-Constrained Decoding (RCD), a decoding strategy that restricts model outputs to unique surface forms. We introduce YAGO-QA, a dataset of 19,137 general knowledge questions. Evaluating open-source LMs from 135M to 70B parameters, we show that standard decoding undervalues their knowledge. For instance, Llama-3.1-70B scores only 32.3% F1 with vanilla decoding but 46.0% with RCD. Similarly, Llama-3.1-8B reaches 33.0% with RCD, outperforming the larger model under vanilla decoding. We publicly share the code and dataset at https://github.com/Rajjaa/disambiguated-LLM.

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arXiv2025

Second-Order Tensorial Partial Differential Equations on Graphs

Processing data on multiple interacting graphs is crucial for many applications, but existing approaches rely mostly on discrete filtering or first-order continuous models, dampening high frequencies and slow information propagation. In this paper, we introduce second-order tensorial partial differential equations on graphs (SoTPDEG) and propose the first theoretically grounded framework for second-order continuous product graph neural networks (GNNs). Our method exploits the separability of cosine kernels in Cartesian product graphs to enable efficient spectral decomposition while preserving high-frequency components. We further provide rigorous over-smoothing and stability analysis under graph perturbations, establishing a solid theoretical foundation. Experimental results on spatiotemporal traffic forecasting illustrate the superiority over the compared methods.

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arXiv2025

ADMP-GNN: Adaptive Depth Message Passing GNN

Graph Neural Networks (GNNs) have proven to be highly effective in various graph learning tasks. A key characteristic of GNNs is their use of a fixed number of message-passing steps for all nodes in the graph, regardless of each node's diverse computational needs and characteristics. Through empirical real-world data analysis, we demonstrate that the optimal number of message-passing layers varies for nodes with different characteristics. This finding is further supported by experiments conducted on synthetic datasets. To address this, we propose Adaptive Depth Message Passing GNN (ADMP-GNN), a novel framework that dynamically adjusts the number of message passing layers for each node, resulting in improved performance. This approach applies to any model that follows the message passing scheme. We evaluate ADMP-GNN on the node classification task and observe performance improvements over baseline GNN models.

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arXiv2025

Dynamic Triangulation-Based Graph Rewiring for Graph Neural Networks

Graph Neural Networks (GNNs) have emerged as the leading paradigm for learning over graph-structured data. However, their performance is limited by issues inherent to graph topology, most notably oversquashing and oversmoothing. Recent advances in graph rewiring aim to mitigate these limitations by modifying the graph topology to promote more effective information propagation. In this work, we introduce TRIGON, a novel framework that constructs enriched, non-planar triangulations by learning to select relevant triangles from multiple graph views. By jointly optimizing triangle selection and downstream classification performance, our method produces a rewired graph with markedly improved structural properties such as reduced diameter, increased spectral gap, and lower effective resistance compared to existing rewiring methods. Empirical results demonstrate that TRIGON outperforms state-of-the-art approaches on node classification tasks across a range of homophilic and heterophilic benchmarks.

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arXiv2025

How Fair is Your Diffusion Recommender Model?

Diffusion-based learning has settled as a rising paradigm in generative recommendation, outperforming traditional approaches built upon variational autoencoders and generative adversarial networks. Despite their effectiveness, concerns have been raised that diffusion models - widely adopted in other machine-learning domains - could potentially lead to unfair outcomes, since they are trained to recover data distributions that often encode inherent biases. Motivated by the related literature, and acknowledging the extensive discussion around bias and fairness aspects in recommendation, we propose, to the best of our knowledge, the first empirical study of fairness for DiffRec, chronologically the pioneer technique in diffusion-based recommendation. Our empirical study involves DiffRec and its variant L-DiffRec, tested against nine recommender systems on two benchmarking datasets to assess recommendation utility and fairness from both consumer and provider perspectives. Specifically, we first evaluate the utility and fairness dimensions separately and, then, within a multi-criteria setting to investigate whether, and to what extent, these approaches can achieve a trade-off between the two. While showing worrying trends in alignment with the more general machine-learning literature on diffusion models, our results also indicate promising directions to address the unfairness issue in future work. The source code is available at https://github.com/danielemalitesta/FairDiffRec.

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arXiv2025

FAROS: Fair Graph Generation via Attribute Switching Mechanisms

Recent advancements in graph diffusion models (GDMs) have enabled the synthesis of realistic network structures, yet ensuring fairness in the generated data remains a critical challenge. Existing solutions attempt to mitigate bias by re-training the GDMs with ad-hoc fairness constraints. Conversely, with this work, we propose FAROS, a novel FAir graph geneRatiOn framework leveraging attribute Switching mechanisms and directly running in the generation process of the pre-trained GDM. Technically, our approach works by altering nodes' sensitive attributes during the generation. To this end, FAROS calculates the optimal fraction of switching nodes, and selects the diffusion step to perform the switch by setting tailored multi-criteria constraints to preserve the node-topology profile from the original distribution (a proxy for accuracy) while ensuring the edge independence on the sensitive attributes for the generated graph (a proxy for fairness). Our experiments on benchmark datasets for link prediction demonstrate that the proposed approach effectively reduces fairness discrepancies while maintaining comparable (or even higher) accuracy performance to other similar baselines. Noteworthy, FAROS is also able to strike a better accuracy-fairness trade-off than other competitors in some of the tested settings under the Pareto optimality concept, demonstrating the effectiveness of the imposed multi-criteria constraints.

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arXiv2025

Graph Neural Network Generalization with Gaussian Mixture Model Based Augmentation

Graph Neural Networks (GNNs) have shown great promise in tasks like node and graph classification, but they often struggle to generalize, particularly to unseen or out-of-distribution (OOD) data. These challenges are exacerbated when training data is limited in size or diversity. To address these issues, we introduce a theoretical framework using Rademacher complexity to compute a regret bound on the generalization error and then characterize the effect of data augmentation. This framework informs the design of GRATIN, an efficient graph data augmentation algorithm leveraging the capability of Gaussian Mixture Models (GMMs) to approximate any distribution. Our approach not only outperforms existing augmentation techniques in terms of generalization but also offers improved time complexity, making it highly suitable for real-world applications.

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arXiv2025

Piecewise Constant Spectral Graph Neural Network

Graph Neural Networks (GNNs) have achieved significant success across various domains by leveraging graph structures in data. Existing spectral GNNs, which use low-degree polynomial filters to capture graph spectral properties, may not fully identify the graph's spectral characteristics because of the polynomial's small degree. However, increasing the polynomial degree is computationally expensive and beyond certain thresholds leads to performance plateaus or degradation. In this paper, we introduce the Piecewise Constant Spectral Graph Neural Network(PieCoN) to address these challenges. PieCoN combines constant spectral filters with polynomial filters to provide a more flexible way to leverage the graph structure. By adaptively partitioning the spectrum into intervals, our approach increases the range of spectral properties that can be effectively learned. Experiments on nine benchmark datasets, including both homophilic and heterophilic graphs, demonstrate that PieCoN is particularly effective on heterophilic datasets, highlighting its potential for a wide range of applications.

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arXiv2025

A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning

Self-supervised learning has become a key method for training deep learning models when labeled data is scarce or unavailable. While graph machine learning holds great promise across various domains, the design of effective pretext tasks for self-supervised graph representation learning remains challenging. Contrastive learning, a popular approach in graph self-supervised learning, leverages positive and negative pairs to compute a contrastive loss function. However, current graph contrastive learning methods often struggle to fully use structural patterns and node similarities. To address these issues, we present a new method called Fused Gromov Wasserstein Subgraph Contrastive Learning (FOSSIL). Our model integrates node-level and subgraph-level contrastive learning, seamlessly combining a standard node-level contrastive loss with the Fused Gromov-Wasserstein distance. This combination helps our method capture both node features and graph structure together. Importantly, our approach works well with both homophilic and heterophilic graphs and can dynamically create views for generating positive and negative pairs. Through extensive experiments on benchmark graph datasets, we show that FOSSIL outperforms or achieves competitive performance compared to current state-of-the-art methods.

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arXiv2024

Post-Hoc Robustness Enhancement in Graph Neural Networks with Conditional Random Fields

Graph Neural Networks (GNNs), which are nowadays the benchmark approach in graph representation learning, have been shown to be vulnerable to adversarial attacks, raising concerns about their real-world applicability. While existing defense techniques primarily concentrate on the training phase of GNNs, involving adjustments to message passing architectures or pre-processing methods, there is a noticeable gap in methods focusing on increasing robustness during inference. In this context, this study introduces RobustCRF, a post-hoc approach aiming to enhance the robustness of GNNs at the inference stage. Our proposed method, founded on statistical relational learning using a Conditional Random Field, is model-agnostic and does not require prior knowledge about the underlying model architecture. We validate the efficacy of this approach across various models, leveraging benchmark node classification datasets.

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