Scalable Equilibrium Sampling with Sequential Boltzmann Generators

Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing powerful normalizing flows with importance sampling to obtain statistically independent samples under the target distribution. In this paper, we extend the Boltzmann generator framework and introduce Sequential Boltzmann generators (SBG) with two key improvements. The first is a highly efficient non-equivariant Transformer-based normalizing flow operating directly on all-atom Cartesian coordinates. In contrast to equivariant continuous flows of prior methods, we leverage exactly invertible non-equivariant architectures which are highly efficient both during sample generation and likelihood computation. As a result, this unlocks more sophisticated inference strategies beyond standard importance sampling. More precisely, as a second key improvement we perform inference-time scaling of flow samples using annealed Langevin dynamics which transports samples toward the target distribution leading to lower variance (annealed) importance weights which enable higher fidelity resampling with sequential Monte Carlo. SBG achieves state-of-the-art performance w.r.t. all metrics on molecular systems, demonstrating the first equilibrium sampling in Cartesian coordinates of tri, tetra, and hexapeptides that were so far intractable for prior Boltzmann generators.

Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

How Expressive are Knowledge Graph Foundation Models?

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the motifs that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are binary, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

On the Limitations of Fractal Dimension as a Measure of Generalization

Bounding and predicting the generalization gap of overparameterized neural networks remains a central open problem in theoretical machine learning. Neural network optimization trajectories have been proposed to possess fractal structure, leading to bounds and generalization measures based on notions of fractal dimension on these trajectories. Prominently, both the Hausdorff dimension and the persistent homology dimension have been proposed to correlate with generalization gap, thus serving as a measure of generalization. This work performs an extended evaluation of these topological generalization measures. We demonstrate that fractal dimension fails to predict generalization of models trained from poor initializations. We further identify that the $\ell^2$ norm of the final parameter iterate, one of the simplest complexity measures in learning theory, correlates more strongly with the generalization gap than these notions of fractal dimension. Finally, our study reveals the intriguing manifestation of model-wise double descent in persistent homology-based generalization measures. This work lays the ground for a deeper investigation of the causal relationships between fractal geometry, topological data analysis, and neural network optimization.

Message-Passing Monte Carlo: Generating low-discrepancy point sets via Graph Neural Networks

Discrepancy is a well-known measure for the irregularity of the distribution of a point set. Point sets with small discrepancy are called low-discrepancy and are known to efficiently fill the space in a uniform manner. Low-discrepancy points play a central role in many problems in science and engineering, including numerical integration, computer vision, machine perception, computer graphics, machine learning, and simulation. In this work, we present the first machine learning approach to generate a new class of low-discrepancy point sets named Message-Passing Monte Carlo (MPMC) points. Motivated by the geometric nature of generating low-discrepancy point sets, we leverage tools from Geometric Deep Learning and base our model on Graph Neural Networks. We further provide an extension of our framework to higher dimensions, which flexibly allows the generation of custom-made points that emphasize the uniformity in specific dimensions that are primarily important for the particular problem at hand. Finally, we demonstrate that our proposed model achieves state-of-the-art performance superior to previous methods by a significant margin. In fact, MPMC points are empirically shown to be either optimal or near-optimal with respect to the discrepancy for every dimension and the number of points for which the optimal discrepancy can be determined.

Advancing Graph Convolutional Networks via General Spectral Wavelets

Spectral graph convolution, an important tool of data filtering on graphs, relies on two essential decisions; selecting spectral bases for signal transformation and parameterizing the kernel for frequency analysis. While recent techniques mainly focus on standard Fourier transform and vector-valued spectral functions, they fall short in flexibility to describe specific signal distribution for each node, and expressivity of spectral function. In this paper, we present a novel wavelet-based graph convolution network, namely WaveGC, which integrates multi-resolution spectral bases and a matrix-valued filter kernel. Theoretically, we establish that WaveGC can effectively capture and decouple short-range and long-range information, providing superior filtering flexibility, surpassing existing graph convolutional networks and graph Transformers (GTs). To instantiate WaveGC, we introduce a novel technique for learning general graph wavelets by separately combining odd and even terms of Chebyshev polynomials. This approach strictly satisfies wavelet admissibility criteria. Our numerical experiments showcase the capabilities of the new network. By replacing the Transformer part in existing architectures with WaveGC, we consistently observe improvements in both short-range and long-range tasks. This underscores the effectiveness of the proposed model in handling different scenarios. Our code is available at https://github.com/liun-online/WaveGC.

Revealing Decurve Flows for Generalized Graph Propagation

This study addresses the limitations of the traditional analysis of message-passing, central to graph learning, by defining {\em \textbf{generalized propagation}} with directed and weighted graphs. The significance manifest in two ways. \textbf{Firstly}, we propose {\em Generalized Propagation Neural Networks} (\textbf{GPNNs}), a framework that unifies most propagation-based graph neural networks. By generating directed-weighted propagation graphs with adjacency function and connectivity function, GPNNs offer enhanced insights into attention mechanisms across various graph models. We delve into the trade-offs within the design space with empirical experiments and emphasize the crucial role of the adjacency function for model expressivity via theoretical analysis. \textbf{Secondly}, we propose the {\em Continuous Unified Ricci Curvature} (\textbf{CURC}), an extension of celebrated {\em Ollivier-Ricci Curvature} for directed and weighted graphs. Theoretically, we demonstrate that CURC possesses continuity, scale invariance, and a lower bound connection with the Dirichlet isoperimetric constant validating bottleneck analysis for GPNNs. We include a preliminary exploration of learned propagation patterns in datasets, a first in the field. We observe an intriguing ``{\em \textbf{decurve flow}}'' - a curvature reduction during training for models with learnable propagation, revealing the evolution of propagation over time and a deeper connection to over-smoothing and bottleneck trade-off.

Link Prediction with Relational Hypergraphs

Link prediction with knowledge graphs has been thoroughly studied in graph machine learning, leading to a rich landscape of graph neural network architectures with successful applications. Nonetheless, it remains challenging to transfer the success of these architectures to link prediction with relational hypergraphs. The presence of relational hyperedges makes link prediction a task between $k$ nodes for varying choices of $k$, which is substantially harder than link prediction with knowledge graphs, where every relation is binary ($k=2$). In this paper, we propose two frameworks for link prediction with relational hypergraphs and conduct a thorough analysis of the expressive power of the resulting model architectures via corresponding relational Weisfeiler-Leman algorithms, and also via some natural logical formalisms. Through extensive empirical analysis, we validate the power of the proposed model architectures on various relational hypergraph benchmarks. The resulting model architectures substantially outperform every baseline for inductive link prediction, and lead to state-of-the-art results for transductive link prediction. Our study therefore unlocks applications of graph neural networks to fully relational structures.

Setting the Record Straight on Transformer Oversmoothing

Transformer-based models have recently become wildly successful across a diverse set of domains. At the same time, recent work has shown that Transformers are inherently low-pass filters that gradually oversmooth the inputs, reducing the expressivity of their representations. A natural question is: How can Transformers achieve these successes given this shortcoming? In this work we show that in fact Transformers are not inherently low-pass filters. Instead, whether Transformers oversmooth or not depends on the eigenspectrum of their update equations. Our analysis extends prior work in oversmoothing and in the closely-related phenomenon of rank collapse. We show that many successful Transformer models have attention and weights which satisfy conditions that avoid oversmoothing. Based on this analysis, we derive a simple way to parameterize the weights of the Transformer update equations that allows for control over its spectrum, ensuring that oversmoothing does not occur. Compared to a recent solution for oversmoothing, our approach improves generalization, even when training with more layers, fewer datapoints, and data that is corrupted.

How does over-squashing affect the power of GNNs?

Graph Neural Networks (GNNs) are the state-of-the-art model for machine learning on graph-structured data. The most popular class of GNNs operate by exchanging information between adjacent nodes, and are known as Message Passing Neural Networks (MPNNs). Given their widespread use, understanding the expressive power of MPNNs is a key question. However, existing results typically consider settings with uninformative node features. In this paper, we provide a rigorous analysis to determine which function classes of node features can be learned by an MPNN of a given capacity. We do so by measuring the level of pairwise interactions between nodes that MPNNs allow for. This measure provides a novel quantitative characterization of the so-called over-squashing effect, which is observed to occur when a large volume of messages is aggregated into fixed-size vectors. Using our measure, we prove that, to guarantee sufficient communication between pairs of nodes, the capacity of the MPNN must be large enough, depending on properties of the input graph structure, such as commute times. For many relevant scenarios, our analysis results in impossibility statements in practice, showing that over-squashing hinders the expressive power of MPNNs. We validate our theoretical findings through extensive controlled experiments and ablation studies.