Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

However, such an approach is highly empirical and provides an indirect evaluation affected by external factors.

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern protein function, such as global domains and long-range allosteric regulation. In this work, we argue that the network architecture itself should mirror this biological hierarchy. We introduce Geometric Graph U-Nets, a new class of models that learn multi-scale representations by recursively coarsening and refining the protein graph. We prove that this hierarchical design can theoretically more expressive than standard Geometric GNNs. Empirically, on the task of protein fold classification, Geometric U-Nets substantially outperform invariant and equivariant baselines, demonstrating their ability to learn the global structural patterns that define protein folds. Our work provides a principled foundation for designing geometric deep learning architectures that can learn the multi-scale structure of biomolecules.

Traveling Salesman Problem (TSP) is a classic NP-hard problem that has garnered significant attention from both academia and industry. While neural-based methods have shown promise for solving TSPs, they still face challenges in scaling to larger instances, particularly in memory constraints associated with global heatmaps, edge weights, or access matrices, as well as in generating high-quality initial solutions and insufficient global guidance for efficiently navigating vast search spaces. To address these challenges, we propose a Hyper Tour Guided Neighborhood Search (HyperNS) method for large-scale TSP instances. Inspired by the ``clustering first, route second" strategy, our approach initially divides the TSP instance into clusters using a sparse heatmap graph and abstracts them as supernodes, followed by the generation of a hyper tour to guide both the initialization and optimization processes. This method reduces the search space by focusing on edges relevant to the hyper tour, leading to more efficient and effective optimization. Experimental results on both synthetic and real-world datasets demonstrate that our approach outperforms existing neural-based methods, particularly in handling larger-scale instances, offering a significant reduction in the gap to the optimal solution.

A signature of human cognitive control is conflict adaptation: improved performance on a high-conflict trial following another high-conflict trial. This phenomenon offers an account for how cognitive control, a scarce resource, is recruited. Using a sequential Stroop task, we find that 12 of 13 vision-language models (VLMs) tested exhibit behavior consistent with conflict adaptation, with the lone exception likely reflecting a ceiling effect. To understand the representational basis of this behavior, we use sparse autoencoders (SAEs) to identify task-relevant supernodes in InternVL 3.5 4B. Partially overlapping supernodes emerge for text and color in both early and late layers, and their relative sizes mirror the automaticity asymmetry between reading and color naming in humans. We further isolate a conflict-modulated supernode in layers 24-25 whose ablation significantly increases Stroop errors while minimally affecting congruent trials.

We study the problem of graph coarsening within the Gromov-Wasserstein geometry. Specifically, we propose two algorithms that leverage a novel representation of the distortion induced by merging pairs of nodes. The first method, termed Greedy Pair Coarsening (GPC), iteratively merges pairs of nodes that locally minimize a measure of distortion until the desired size is achieved. The second method, termed $k$-means Greedy Pair Coarsening (KGPC), leverages clustering based on pairwise distortion metrics to directly merge clusters of nodes. We provide conditions guaranteeing optimal coarsening for our methods and validate their performance on six large-scale datasets and a downstream clustering task. Results show that the proposed methods outperform existing approaches on a wide range of parameters and scenarios.

We sincerely thank all reviewers for their time and helpful comments. Below please see our response to the comments. "successful if the target data distribution is a convex combination of source distributions?" Y es, this is a This situation is like extrapolation, and additional assumptions may be needed. (by Eberhardt and Scheines, 2007). "synthetic tailored to the assumptions" & "image example with two variables."