arXiv subjects

Guillermo Bernárdez

Publications and source records attributed to Guillermo Bernárdez.

16 recordsLinked to original sources

arXiv2026

Batch Before You Lift: Scalable Topological Deep Learning on Large Graphs

Topological Deep Learning extends graph-based learning to higher-order domains, such as hypergraphs, cellular, and simplicial complexes. These domains are typically constructed from patterns in an input graph through a process of graph lifting. Full-domain training constructs and stores the complete lifted representation before model execution. On large and dense datasets like Reddit (233k nodes and 57.3M edges), this global materialization becomes a severe computational bottleneck, often rendering training infeasible. To address this limitation, we introduce Cluster-TNN, a domain-agnostic framework that avoids this bottleneck by lifting locally instead. After partitioning the input graph during preprocessing, at runtime Cluster-TNN dynamically samples groups of node clusters, reconstructs their induced subgraphs to form mini-batches, and applies the chosen lifting within each mini-batch. Retaining all edges among sampled nodes preserves the connectivity needed to construct higher-order structures across clusters, producing topological mini-batches that existing Topological Neural Networks can process directly. Across 21 matched comparisons with full-graph execution, Cluster-TNN reduces peak GPU memory in every configuration, by 83.2% on average while maintaining competitive predictive performance. Notably, such a reduction enables, to our knowledge, the first training of multiple different higher-order Topological Neural Networks on large datasets such as Reddit and OGBN Products. These results establish Cluster-TNN as a general strategy for scaling Topological Deep Learning beyond the limitations of global domain construction.

cs.LG↗

arXiv2026

Look Before You Lift: Visual and Quantitative Diagnostics for Topological Deep Learning

Topological deep learning (TDL) methods rely on lifting raw data into higher-order discrete domains such as simplicial complexes, cell complexes, and hypergraphs. In practice, this lifting step is often treated as a black box: practitioners select a lifting and then tune architectures, with limited visibility into whether the induced higher-order connectivity is meaningful for the downstream task. To address this missing diagnostic layer, we propose a visualization technique called TopoExplorer that leverages the strictly augmented Hasse graph form of topological datasets for exploratory data analysis. For the first time, practitioners can easily visualize the incidence- and adjacency-based neighborhoods that define the lifted dataset, as well as read off key graph metrics that describe its structural and feature landscape. Via an extensive set of experiments across many datasets and liftings, we show that several of these metrics correlate with downstream model performance, suggesting they can help inform TDL preprocessing design. Our perspective reframes the TDL workflow from lift-train to lift-look-design-train, enabling more principled, interpretable, and efficient model development. TopoExplorer is hosted at https://topoexplorer.pagekite.me, and its source code is available at github.com/geometric-intelligence/topoexplorer.

cs.LG↗

arXiv2026

HOPSE: Scalable Higher-Order Positional and Structural Encoder for Combinatorial Representations

While Graph Neural Networks (GNNs) have proven highly effective at modeling relational data, pairwise connections cannot fully capture multi-way relationships naturally present in complex real-world systems. In response to this, Topological Deep Learning (TDL) leverages more general combinatorial representations--such as simplicial or cellular complexes--to accommodate higher-order interactions. Existing TDL methods often extend GNNs through Higher-Order Message Passing (HOMP), but face critical scalability challenges due to the steep complexity overhead of propagating messages through combinatorial structures. To overcome this limitation, we propose HOPSE (Higher-Order Positional and Structural Encoder), a framework free of message passing layers that uses Hasse graph decompositions to derive efficient and expressive encodings over arbitrary higher-order domains. Notably, HOPSE scales linearly with the size of combinatorial representations while preserving the expressive power and permutation equivariance of the HOMP approaches. Experiments on molecular and topological benchmarks show that it matches or surpasses state-of-the-art performance while consistently achieving speedups over HOMP-based models, opening a new path for scalable TDL. The code is available at https://github.com/geometric-intelligence/topobench.git.

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arXiv2026

OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning. Yet most benchmarks focus on the regime $n \gg p$, where the number of graphs $n$ greatly exceeds the number of nodes per graph $p$. This overlooks biological domains such as omics, which operate in the opposite $n \ll p$ regime, characterized by large graphs of genes, transcripts, or proteins across few patient samples. This raises the question: \textit{how do GNNs perform in this low-sample, high-node omics setting?} We introduce \texttt{OgBench} (Omics-Graph Bench), the first benchmarking platform for graph-level prediction in the $n \ll p$ regime characteristic of omics data. We provide a standardized, end-to-end modular infrastructure from raw omics data to families of featured graphs with varied structural properties. We benchmark classical GNNs, as well as GNNs designed for large graphs and omics applications, alongside MLPs and machine learning baselines to establish reference performances. Our results show that widely used GNNs often do not outperform simple MLPs and classical baselines. These findings challenge the prevailing assumption that graph structure inherently adds value in this domain, fostering a critical reassessment of current learning paradigms. Ultimately, by exposing these limitations, OgBench provides the open-source ecosystem necessary for the community to develop and validate novel architectures explicitly tailored for biological graphs. The code is available at https://github.com/geometric-intelligence/ogbench.

cs.LG↗

arXiv2026

When Machine Learning Gets Personal: Evaluating Prediction and Explanation

In high-stakes domains like healthcare, users often expect that sharing personal information with machine learning systems will yield tangible benefits, such as more accurate diagnoses and clearer explanations of contributing factors. However, the validity of this assumption remains largely unexplored. We propose a unified framework to quantify how personalizing a model influences both prediction and explanation. We show that its impacts on prediction and explanation can diverge: a model may become more or less explainable even when prediction is unchanged. For practical settings, we study a standard hypothesis test for detecting personalization effects on demographic groups. We derive a finite-sample lower bound on its probability of error as a function of group sizes, number of personal attributes, and desired benefit from personalization. This provides actionable insights, such as which dataset characteristics are necessary to test an effect, or the maximum effect that can be tested given a dataset. We apply our framework to real-world tabular datasets using feature-attribution methods, uncovering scenarios where effects are fundamentally untestable due to the dataset statistics. Our results highlight the need for joint evaluation of prediction and explanation in personalized models and the importance of designing models and datasets with sufficient information for such evaluation.

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arXiv2026

GraphUniverse: Synthetic Graph Generation for Evaluating Inductive Generalization

A fundamental challenge in graph learning is understanding how models generalize to new, unseen graphs. While synthetic benchmarks offer controlled settings for analysis, existing approaches are confined to single-graph, transductive settings where models train and test on the same graph structure. Addressing this gap, we introduce GraphUniverse, a framework for generating entire families of graphs to enable the first systematic evaluation of inductive generalization at scale. Our core innovation is the generation of graphs with persistent semantic communities, ensuring conceptual consistency while allowing fine-grained control over structural properties like homophily and degree distributions. This enables crucial but underexplored robustness tests, such as performance under controlled distribution shifts. Benchmarking a wide range of architectures -- from GNNs to graph transformers and topological architectures -- reveals that strong transductive performance is a poor predictor of inductive generalization. Furthermore, we find that robustness to distribution shift is highly sensitive not only to model architecture choice but also to the initial graph regime (e.g., high vs. low homophily). Beyond benchmarking, GraphUniverse's flexibility and scalability can facilitate the development of robust and truly generalizable architectures. The framework is open-source at https://github.com/LouisVanLangendonck/GraphUniverse.

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arXiv2025

TopoTune : A Framework for Generalized Combinatorial Complex Neural Networks

Graph Neural Networks (GNNs) effectively learn from relational data by leveraging graph symmetries. However, many real-world systems -- such as biological or social networks -- feature multi-way interactions that GNNs fail to capture. Topological Deep Learning (TDL) addresses this by modeling and leveraging higher-order structures, with Combinatorial Complex Neural Networks (CCNNs) offering a general and expressive approach that has been shown to outperform GNNs. However, TDL lacks the principled and standardized frameworks that underpin GNN development, restricting its accessibility and applicability. To address this issue, we introduce Generalized CCNNs (GCCNs), a simple yet powerful family of TDL models that can be used to systematically transform any (graph) neural network into its TDL counterpart. We prove that GCCNs generalize and subsume CCNNs, while extensive experiments on a diverse class of GCCNs show that these architectures consistently match or outperform CCNNs, often with less model complexity. In an effort to accelerate and democratize TDL, we introduce TopoTune, a lightweight software for defining, building, and training GCCNs with unprecedented flexibility and ease.

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arXiv2025

Proximal Policy Optimization with Graph Neural Networks for Optimal Power Flow

Optimal Power Flow (OPF) is a very traditional research area within the power systems field that seeks for the optimal operation point of electric power plants, and which needs to be solved every few minutes in real-world scenarios. However, due to the nonconvexities that arise in power generation systems, there is not yet a fast, robust solution technique for the full Alternating Current Optimal Power Flow (ACOPF). In the last decades, power grids have evolved into a typical dynamic, non-linear and large-scale control system, known as the power system, so searching for better and faster ACOPF solutions is becoming crucial. Appearance of Graph Neural Networks (GNN) has allowed the natural use of Machine Learning (ML) algorithms on graph data, such as power networks. On the other hand, Deep Reinforcement Learning (DRL) is known for its powerful capability to solve complex decision-making problems. Although solutions that use these two methods separately are beginning to appear in the literature, none has yet combined the advantages of both. We propose a novel architecture based on the Proximal Policy Optimization algorithm with Graph Neural Networks to solve the Optimal Power Flow. The objective is to design an architecture that learns how to solve the optimization problem and that is at the same time able to generalize to unseen scenarios. We compare our solution with the DCOPF in terms of cost after having trained our DRL agent on IEEE 30 bus system and then computing the OPF on that base network with topology changes

cs.AI↗

arXiv2025

Ordered Topological Deep Learning: a Network Modeling Case Study

Computer networks are the foundation of modern digital infrastructure, facilitating global communication and data exchange. As demand for reliable high-bandwidth connectivity grows, advanced network modeling techniques become increasingly essential to optimize performance and predict network behavior. Traditional modeling methods, such as packet-level simulators and queueing theory, have notable limitations --either being computationally expensive or relying on restrictive assumptions that reduce accuracy. In this context, the deep learning-based RouteNet family of models has recently redefined network modeling by showing an unprecedented cost-performance trade-off. In this work, we revisit RouteNet's sophisticated design and uncover its hidden connection to Topological Deep Learning (TDL), an emerging field that models higher-order interactions beyond standard graph-based methods. We demonstrate that, although originally formulated as a heterogeneous Graph Neural Network, RouteNet serves as the first instantiation of a new form of TDL. More specifically, this paper presents OrdGCCN, a novel TDL framework that introduces the notion of ordered neighbors in arbitrary discrete topological spaces, and shows that RouteNet's architecture can be naturally described as an ordered topological neural network. To the best of our knowledge, this marks the first successful real-world application of state-of-the-art TDL principles --which we confirm through extensive testbed experiments--, laying the foundation for the next generation of ordered TDL-driven applications.

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arXiv2024

TopoX: A Suite of Python Packages for Machine Learning on Topological Domains

We introduce TopoX, a Python software suite that provides reliable and user-friendly building blocks for computing and machine learning on topological domains that extend graphs: hypergraphs, simplicial, cellular, path and combinatorial complexes. TopoX consists of three packages: TopoNetX facilitates constructing and computing on these domains, including working with nodes, edges and higher-order cells; TopoEmbedX provides methods to embed topological domains into vector spaces, akin to popular graph-based embedding algorithms such as node2vec; TopoModelX is built on top of PyTorch and offers a comprehensive toolbox of higher-order message passing functions for neural networks on topological domains. The extensively documented and unit-tested source code of TopoX is available under MIT license at https://pyt-team.github.io/}{https://pyt-team.github.io/.

cs.LG↗

arXiv2024

ICML Topological Deep Learning Challenge 2024: Beyond the Graph Domain

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

cs.LG↗

arXiv2023

Topological Graph Signal Compression

Recently emerged Topological Deep Learning (TDL) methods aim to extend current Graph Neural Networks (GNN) by naturally processing higher-order interactions, going beyond the pairwise relations and local neighborhoods defined by graph representations. In this paper we propose a novel TDL-based method for compressing signals over graphs, consisting in two main steps: first, disjoint sets of higher-order structures are inferred based on the original signal --by clustering $N$ datapoints into $K\ll N$ collections; then, a topological-inspired message passing gets a compressed representation of the signal within those multi-element sets. Our results show that our framework improves both standard GNN and feed-forward architectures in compressing temporal link-based signals from two real-word Internet Service Provider Networks' datasets --from $30\%$ up to $90\%$ better reconstruction errors across all evaluation scenarios--, suggesting that it better captures and exploits spatial and temporal correlations over the whole graph-based network structure.

cs.LG↗

arXiv2023

GraphCC: A Practical Graph Learning-based Approach to Congestion Control in Datacenters

Congestion Control (CC) plays a fundamental role in optimizing traffic in Data Center Networks (DCN). Currently, DCNs mainly implement two main CC protocols: DCTCP and DCQCN. Both protocols -- and their main variants -- are based on Explicit Congestion Notification (ECN), where intermediate switches mark packets when they detect congestion. The ECN configuration is thus a crucial aspect on the performance of CC protocols. Nowadays, network experts set static ECN parameters carefully selected to optimize the average network performance. However, today's high-speed DCNs experience quick and abrupt changes that severely change the network state (e.g., dynamic traffic workloads, incast events, failures). This leads to under-utilization and sub-optimal performance. This paper presents GraphCC, a novel Machine Learning-based framework for in-network CC optimization. Our distributed solution relies on a novel combination of Multi-agent Reinforcement Learning (MARL) and Graph Neural Networks (GNN), and it is compatible with widely deployed ECN-based CC protocols. GraphCC deploys distributed agents on switches that communicate with their neighbors to cooperate and optimize the global ECN configuration. In our evaluation, we test the performance of GraphCC under a wide variety of scenarios, focusing on the capability of this solution to adapt to new scenarios unseen during training (e.g., new traffic workloads, failures, upgrades). We compare GraphCC with a state-of-the-art MARL-based solution for ECN tuning -- ACC -- and observe that our proposed solution outperforms the state-of-the-art baseline in all of the evaluation scenarios, showing improvements up to $20\%$ in Flow Completion Time as well as significant reductions in buffer occupancy ($38.0-85.7\%$).

cs.NI↗

arXiv2023

MAGNNETO: A Graph Neural Network-based Multi-Agent system for Traffic Engineering

Current trends in networking propose the use of Machine Learning (ML) for a wide variety of network optimization tasks. As such, many efforts have been made to produce ML-based solutions for Traffic Engineering (TE), which is a fundamental problem in ISP networks. Nowadays, state-of-the-art TE optimizers rely on traditional optimization techniques, such as Local search, Constraint Programming, or Linear programming. In this paper, we present MAGNNETO, a distributed ML-based framework that leverages Multi-Agent Reinforcement Learning and Graph Neural Networks for distributed TE optimization. MAGNNETO deploys a set of agents across the network that learn and communicate in a distributed fashion via message exchanges between neighboring agents. Particularly, we apply this framework to optimize link weights in OSPF, with the goal of minimizing network congestion. In our evaluation, we compare MAGNNETO against several state-of-the-art TE optimizers in more than 75 topologies (up to 153 nodes and 354 links), including realistic traffic loads. Our experimental results show that, thanks to its distributed nature, MAGNNETO achieves comparable performance to state-of-the-art TE optimizers with significantly lower execution times. Moreover, our ML-based solution demonstrates a strong generalization capability to successfully operate in new networks unseen during training.

cs.NI↗

arXiv2021

Is Machine Learning Ready for Traffic Engineering Optimization?

Traffic Engineering (TE) is a basic building block of the Internet. In this paper, we analyze whether modern Machine Learning (ML) methods are ready to be used for TE optimization. We address this open question through a comparative analysis between the state of the art in ML and the state of the art in TE. To this end, we first present a novel distributed system for TE that leverages the latest advancements in ML. Our system implements a novel architecture that combines Multi-Agent Reinforcement Learning (MARL) and Graph Neural Networks (GNN) to minimize network congestion. In our evaluation, we compare our MARL+GNN system with DEFO, a network optimizer based on Constraint Programming that represents the state of the art in TE. Our experimental results show that the proposed MARL+GNN solution achieves equivalent performance to DEFO in a wide variety of network scenarios including three real-world network topologies. At the same time, we show that MARL+GNN can achieve significant reductions in execution time (from the scale of minutes with DEFO to a few seconds with our solution).

cs.NI↗

arXiv2021

The Graph Neural Networking Challenge: A Worldwide Competition for Education in AI/ML for Networks

During the last decade, Machine Learning (ML) has increasingly become a hot topic in the field of Computer Networks and is expected to be gradually adopted for a plethora of control, monitoring and management tasks in real-world deployments. This poses the need to count on new generations of students, researchers and practitioners with a solid background in ML applied to networks. During 2020, the International Telecommunication Union (ITU) has organized the "ITU AI/ML in 5G challenge'', an open global competition that has introduced to a broad audience some of the current main challenges in ML for networks. This large-scale initiative has gathered 23 different challenges proposed by network operators, equipment manufacturers and academia, and has attracted a total of 1300+ participants from 60+ countries. This paper narrates our experience organizing one of the proposed challenges: the "Graph Neural Networking Challenge 2020''. We describe the problem presented to participants, the tools and resources provided, some organization aspects and participation statistics, an outline of the top-3 awarded solutions, and a summary with some lessons learned during all this journey. As a result, this challenge leaves a curated set of educational resources openly available to anyone interested in the topic.

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