arXiv subjects

Amauri H. Souza

Publications and source records attributed to Amauri H. Souza.

11 recordsLinked to original sources

arXiv2026

Learning a Mixture of GFlowNets

Learning an ensemble of GFlowNets to sample from a discrete target distribution has become a common approach for achieving better state space exploration and convergence than that of a monolithic sampler. However, these methods often add a substantial runtime overhead to the base model, and their conceptual connection remains elusive. To address this, we first propose a general-purpose theoretical framework for describing a mixture of GFlowNets, which we specialize into continuously (CI) and discretely indexed (DI) collections. On the one hand, we show CI GFlowNets can be interpreted through the lens of a random features expansion, provably boosting the sampler's expressivity in graph-structured tasks and reducing learning instability via spectral shifting. On the other hand, we demonstrate DI GFlowNets encompass prior approaches for GFlowNet training and provide the foundation for the newly proposed Stratum-Conditioned (SC) GFlowNets. This method, which is inspired by the Doob's h-transform of Markov chains, decomposes the state space according to a prescribed modular function and restricts each component to sample from a distinct subset of it. Importantly, SC GFlowNets support centralized and component-wise embarrassingly parallel training, and we show both of them significantly speed up learning convergence and mode coverage without introducing any non-negligible extra computation.

cs.LG↗

arXiv2026

Cooperative Sheaf Neural Networks

Sheaf diffusion has recently emerged as a promising design pattern for graph representation learning due to its inherent ability to handle heterophilic data and avoid oversmoothing. Meanwhile, cooperative message passing has also been proposed as a way to enhance the flexibility of information diffusion by allowing nodes to independently choose whether to propagate/gather information from/to neighbors. A natural question ensues: is sheaf diffusion capable of exhibiting this cooperative behavior? Here, we provide a negative answer to this question. In particular, we show that existing sheaf diffusion methods fail to achieve cooperative behavior due to the lack of message directionality. To circumvent this limitation, we introduce the notion of cellular sheaves over directed graphs and characterize their in- and out-degree Laplacians. We leverage our construction to propose Cooperative Sheaf Neural Networks (CSNNs). Theoretically, we characterize the receptive field of CSNN and show it allows nodes to selectively attend (listen) to arbitrarily far nodes while ignoring all others in their path, potentially mitigating oversquashing. Our experiments show that CSNN presents overall better performance compared to prior art on sheaf diffusion as well as cooperative graph neural networks.

cs.LG↗

arXiv2026

Mitigating Over-squashing without Rewiring: A Sheaf Effective Resistance Perspective

Graph Neural Networks (GNNs) often struggle to capture long-range dependencies due to over-squashing -- a phenomenon in which the repeated compression of node embeddings into finite-size messages causes representations to collapse. Over-squashing is most often diagnosed as a property of the graph topology, with effective resistance serving as a principled measure of the bottleneck. We provide a complementary view on the matter: building on cellular sheaves, we introduce sheaf effective resistance, a generalization of effective resistance that depends on the sheaf attached to the graph, and we prove that for flat vector bundles, the over-squashing sensitivity in the Jacobian sense is upper bounded by a quantity related to the sheaf effective resistance between the nodes. The bottleneck thus need not lie in the graph itself: it can be relocated, and reduced, by adjusting the sheaf. We instantiate this idea in FlatNSD, a simple message-passing variant of Neural Sheaf Diffusion, and show that it implicitly learns to modulate total sheaf effective resistance, performing well on benchmarks designed to stress over-squashing without altering the original graph topology.

stat.ML↗

arXiv2026

Differentiable Lifting for Topological Neural Networks

Topological neural networks (TNNs) enable leveraging high-order structures on graphs (e.g., cycles and cliques) to boost the expressive power of message-passing neural networks. In turn, however, these structures are typically identified a priori through an unsupervised graph lifting operation. Notwithstanding, this choice is crucial and may have a drastic impact on a TNN's performance on downstream tasks. To circumvent this issue, we propose $\partial$lift (DiffLift), a general framework for learning graph liftings to hypergraphs and cellular- and simplicial complexes in an end-to-end fashion. In particular, our approach leverages learned vertex-level latent representations to identify and parameterize distributions over candidate higher-order cells for inclusion. This results in a scalable model which can be readily integrated into any TNN. Our experiments show that $\partial$lift outperforms existing lifting methods on multiple benchmarks for graph and node classification across different TNN architectures. Notably, our approach leads to gains of up to 45% over static liftings, including both connectivity- and feature-based ones.

cs.LG↗

arXiv2026

The Logical Expressiveness of Topological Neural Networks

Graph neural networks (GNNs) are the standard for learning on graphs, yet they have limited expressive power, often expressed in terms of the Weisfeiler-Leman (WL) hierarchy or within the framework of first-order logic. In this context, topological neural networks (TNNs) have recently emerged as a promising alternative for graph representation learning. By incorporating higher-order relational structures into message-passing schemes, TNNs offer higher representational power than traditional GNNs. However, a fundamental question remains open: what is the logical expressiveness of TNNs? Answering this allows us to characterize precisely which binary classifiers TNNs can represent. In this paper, we address this question by analyzing isomorphism tests derived from the underlying mechanisms of general TNNs. We introduce and investigate the power of higher-order variants of WL-based tests for combinatorial complexes, called $k$-CCWL test. In addition, we introduce the topological counting logic (TC$_k$), an extension of standard counting logic featuring a novel pairwise counting quantifier $ \exists^{N}(x_i,x_j)\, φ(x_i,x_j), $ which explicitly quantifies pairs $(x_i, x_j)$ satisfying property $φ$. We rigorously prove the exact equivalence: $ \text{k-CCWL} \equiv \text{TC}_{k{+}2} \equiv \text{Topological }(k{+}2)\text{-pebble game}.$ These results establish a logical expressiveness theory for TNNs.

cs.LG↗

arXiv2026

On topological descriptors for graph products

Topological descriptors have been increasingly utilized for capturing multiscale structural information in relational data. In this work, we consider various filtrations on the (box) product of graphs and the effect on their outputs on the topological descriptors - the Euler characteristic (EC) and persistent homology (PH). In particular, we establish a complete characterization of the expressive power of EC on general color-based filtrations. We also show that the PH descriptors of (virtual) graph products contain strictly more information than the computation on individual graphs, whereas EC does not. Additionally, we provide algorithms to compute the PH diagrams of the product of vertex- and edge-level filtrations on the graph product. We also substantiate our theoretical analysis with empirical investigations on runtime analysis, expressivity, and graph classification performance. Overall, this work paves way for powerful graph persistent descriptors via product filtrations. Code is available at https://github.com/Aalto-QuML/tda_graph_product.

cs.LG↗

arXiv2026

Graph Persistence goes Spectral

Including intricate topological information (e.g., cycles) provably enhances the expressivity of message-passing graph neural networks (GNNs) beyond the Weisfeiler-Leman (WL) hierarchy. Consequently, Persistent Homology (PH) methods are increasingly employed for graph representation learning. In this context, recent works have proposed decorating classical PH diagrams with vertex and edge features for improved expressivity. However, these methods still fail to capture basic graph structural information. In this paper, we propose SpectRe -- a new topological descriptor for graphs that integrates spectral information into PH diagrams. Notably, SpectRe is strictly more expressive than PH and spectral information on graphs alone. We also introduce notions of global and local stability to analyze existing descriptors and establish that SpectRe is locally stable. Finally, experiments on synthetic and real-world datasets demonstrate the effectiveness of SpectRe and its potential to enhance the capabilities of graph models in relevant learning tasks. Code is available at https://github.com/Aalto-QuML/SpectRe/.

cs.LG↗

arXiv2025

Positional Encoding meets Persistent Homology on Graphs

The local inductive bias of message-passing graph neural networks (GNNs) hampers their ability to exploit key structural information (e.g., connectivity and cycles). Positional encoding (PE) and Persistent Homology (PH) have emerged as two promising approaches to mitigate this issue. PE schemes endow GNNs with location-aware features, while PH methods enhance GNNs with multiresolution topological features. However, a rigorous theoretical characterization of the relative merits and shortcomings of PE and PH has remained elusive. We bridge this gap by establishing that neither paradigm is more expressive than the other, providing novel constructions where one approach fails but the other succeeds. Our insights inform the design of a novel learnable method, PiPE (Persistence-informed Positional Encoding), which is provably more expressive than both PH and PE. PiPE demonstrates strong performance across a variety of tasks (e.g., molecule property prediction, graph classification, and out-of-distribution generalization), thereby advancing the frontiers of graph representation learning. Code is available at https://github.com/Aalto-QuML/PIPE.

cs.LG↗

arXiv2023

Going beyond persistent homology using persistent homology

Representational limits of message-passing graph neural networks (MP-GNNs), e.g., in terms of the Weisfeiler-Leman (WL) test for isomorphism, are well understood. Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem. Specifically, we establish the necessary and sufficient conditions for distinguishing graphs based on the persistence of their connected components, obtained from filter functions on vertex and edge colors. Our constructions expose the limits of vertex- and edge-level PH, proving that neither category subsumes the other. Leveraging these theoretical insights, we propose RePHINE for learning topological features on graphs. RePHINE efficiently combines vertex- and edge-level PH, achieving a scheme that is provably more powerful than both. Integrating RePHINE into MP-GNNs boosts their expressive power, resulting in gains over standard PH on several benchmarks for graph classification.

cs.LG↗

arXiv2022

Provably expressive temporal graph networks

Temporal graph networks (TGNs) have gained prominence as models for embedding dynamic interactions, but little is known about their theoretical underpinnings. We establish fundamental results about the representational power and limits of the two main categories of TGNs: those that aggregate temporal walks (WA-TGNs), and those that augment local message passing with recurrent memory modules (MP-TGNs). Specifically, novel constructions reveal the inadequacy of MP-TGNs and WA-TGNs, proving that neither category subsumes the other. We extend the 1-WL (Weisfeiler-Leman) test to temporal graphs, and show that the most powerful MP-TGNs should use injective updates, as in this case they become as expressive as the temporal WL. Also, we show that sufficiently deep MP-TGNs cannot benefit from memory, and MP/WA-TGNs fail to compute graph properties such as girth. These theoretical insights lead us to PINT -- a novel architecture that leverages injective temporal message passing and relative positional features. Importantly, PINT is provably more expressive than both MP-TGNs and WA-TGNs. PINT significantly outperforms existing TGNs on several real-world benchmarks.

cs.LG↗

arXiv2020

Rethinking pooling in graph neural networks

Graph pooling is a central component of a myriad of graph neural network (GNN) architectures. As an inheritance from traditional CNNs, most approaches formulate graph pooling as a cluster assignment problem, extending the idea of local patches in regular grids to graphs. Despite the wide adherence to this design choice, no work has rigorously evaluated its influence on the success of GNNs. In this paper, we build upon representative GNNs and introduce variants that challenge the need for locality-preserving representations, either using randomization or clustering on the complement graph. Strikingly, our experiments demonstrate that using these variants does not result in any decrease in performance. To understand this phenomenon, we study the interplay between convolutional layers and the subsequent pooling ones. We show that the convolutions play a leading role in the learned representations. In contrast to the common belief, local pooling is not responsible for the success of GNNs on relevant and widely-used benchmarks.

cs.LG↗