Daily Papers

Focusing on simulated dilute polymer solutions, this letter investigates the interactions between flow structures and organized polymer stress sheets for the steady arrowhead coherent structure in a two-dimensional periodic channel flow. Formulating the problem in a frame of reference moving with the arrowhead velocity, streamlines, which are also pathlines in this frame, enables the identification of two distinct topological regions linked to two stagnation points. The streamlines help connecting the spatial distribution of polymer stress within the sheets and the dynamics of polymers transported by the flow. Using stresslines, lines parallel to the eigenvectors of polymer stress, a novel formulation of the viscoelastic stress term in the momentum transport equation proposes a more intuitive interpretation of the relation between the curvature of the stresslines, and the variation of stress along these lines, with the local flow topology. An approximation of this formulation is shown to explain the pressure jump observed in the arrowhead structure as a function of the local curvature of the polymer stress sheet.

Random walks are widely used for mining networks due to the computational efficiency of computing them. For instance, graph representation learning learns a d-dimensional embedding space, so that the nodes that tend to co-occur on random walks (a proxy of being in the same network neighborhood) are close in the embedding space. Specific local network topology (i.e., structure) influences the co-occurrence of nodes on random walks, so random walks of limited length capture only partial topological information, hence diminishing the performance of downstream methods. We explicitly capture all topological neighborhood information and improve performance by introducing orbit adjacencies that quantify the adjacencies of two nodes as co-occurring on a given pair of graphlet orbits, which are symmetric positions on graphlets (small, connected, non-isomorphic, induced subgraphs of a large network). Importantly, we mathematically prove that random walks on up to k nodes capture only a subset of all the possible orbit adjacencies for up to k-node graphlets. Furthermore, we enable orbit adjacency-based analysis of networks by developing an efficient GRaphlet-orbit ADjacency COunter (GRADCO), which exhaustively computes all 28 orbit adjacency matrices for up to four-node graphlets. Note that four-node graphlets suffice, because real networks are usually small-world. In large networks on around 20,000 nodes, GRADCOcomputesthe28matricesinminutes. Onsixrealnetworksfromvarious domains, we compare the performance of node-label predictors obtained by using the network embeddings based on our orbit adjacencies to those based on random walks. We find that orbit adjacencies, which include those unseen by random walks, outperform random walk-based adjacencies, demonstrating the importance of the inclusion of the topological neighborhood information that is unseen by random walks.

The manifold hypothesis, which assumes that data lies on or close to an unknown manifold of low intrinsic dimension, is a staple of modern machine learning research. However, recent work has shown that real-world data exhibits distinct non-manifold structures, i.e. singularities, that can lead to erroneous findings. Detecting such singularities is therefore crucial as a precursor to interpolation and inference tasks. We address this issue by developing a topological framework that (i) quantifies the local intrinsic dimension, and (ii) yields a Euclidicity score for assessing the 'manifoldness' of a point along multiple scales. Our approach identifies singularities of complex spaces, while also capturing singular structures and local geometric complexity in image data.

Detecting intrusions in network traffic is a challenging task, particularly under limited supervision and constantly evolving attack patterns. While recent works have leveraged graph neural networks for network intrusion detection, they often decouple representation learning from anomaly detection, limiting the utility of the embeddings for identifying attacks. We propose GraphIDS, a self-supervised intrusion detection model that unifies these two stages by learning local graph representations of normal communication patterns through a masked autoencoder. An inductive graph neural network embeds each flow with its local topological context to capture typical network behavior, while a Transformer-based encoder-decoder reconstructs these embeddings, implicitly learning global co-occurrence patterns via self-attention without requiring explicit positional information. During inference, flows with unusually high reconstruction errors are flagged as potential intrusions. This end-to-end framework ensures that embeddings are directly optimized for the downstream task, facilitating the recognition of malicious traffic. On diverse NetFlow benchmarks, GraphIDS achieves up to 99.98% PR-AUC and 99.61% macro F1-score, outperforming baselines by 5-25 percentage points.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

Graph Neural Networks (GNNs) had been demonstrated to be inherently susceptible to the problems of over-smoothing and over-squashing. These issues prohibit the ability of GNNs to model complex graph interactions by limiting their effectiveness in taking into account distant information. Our study reveals the key connection between the local graph geometry and the occurrence of both of these issues, thereby providing a unified framework for studying them at a local scale using the Ollivier-Ricci curvature. Specifically, we demonstrate that over-smoothing is linked to positive graph curvature while over-squashing is linked to negative graph curvature. Based on our theory, we propose the Batch Ollivier-Ricci Flow, a novel rewiring algorithm capable of simultaneously addressing both over-smoothing and over-squashing.

Scene flow estimation aims to recover per-point motion from two adjacent LiDAR scans. However, in real-world applications such as autonomous driving, points rarely move independently of others, especially for nearby points belonging to the same object, which often share the same motion. Incorporating this locally rigid motion constraint has been a key challenge in self-supervised scene flow estimation, which is often addressed by post-processing or appending extra regularization. While these approaches are able to improve the rigidity of predicted flows, they lack an architectural inductive bias for local rigidity within the model structure, leading to suboptimal learning efficiency and inferior performance. In contrast, we enforce local rigidity with a lightweight add-on module in neural network design, enabling end-to-end learning. We design a discretized voting space that accommodates all possible translations and then identify the one shared by nearby points by differentiable voting. Additionally, to ensure computational efficiency, we operate on pillars rather than points and learn representative features for voting per pillar. We plug the Voting Module into popular model designs and evaluate its benefit on Argoverse 2 and Waymo datasets. We outperform baseline works with only marginal compute overhead. Code is available at https://github.com/tudelft-iv/VoteFlow.

The study of universal approximation properties (UAP) for neural networks (NN) has a long history. When the network width is unlimited, only a single hidden layer is sufficient for UAP. In contrast, when the depth is unlimited, the width for UAP needs to be not less than the critical width w^*_{min}=max(d_x,d_y), where d_x and d_y are the dimensions of the input and output, respectively. Recently, cai2022achieve shows that a leaky-ReLU NN with this critical width can achieve UAP for L^p functions on a compact domain K, i.e., the UAP for L^p(K,R^{d_y}). This paper examines a uniform UAP for the function class C(K,R^{d_y}) and gives the exact minimum width of the leaky-ReLU NN as w_{min}=max(d_x+1,d_y)+1_{d_y=d_x+1}, which involves the effects of the output dimensions. To obtain this result, we propose a novel lift-flow-discretization approach that shows that the uniform UAP has a deep connection with topological theory.

Recently, data-driven simulators based on graph neural networks have gained attention in modeling physical systems on unstructured meshes. However, they struggle with long-range dependencies in fluid flows, particularly in refined mesh regions. This challenge, known as the 'over-squashing' problem, hinders information propagation. While existing graph rewiring methods address this issue to some extent, they only consider graph topology, overlooking the underlying physical phenomena. We propose Physics-Informed Ollivier-Ricci Flow (PIORF), a novel rewiring method that combines physical correlations with graph topology. PIORF uses Ollivier-Ricci curvature (ORC) to identify bottleneck regions and connects these areas with nodes in high-velocity gradient nodes, enabling long-range interactions and mitigating over-squashing. Our approach is computationally efficient in rewiring edges and can scale to larger simulations. Experimental results on 3 fluid dynamics benchmark datasets show that PIORF consistently outperforms baseline models and existing rewiring methods, achieving up to 26.2 improvement.

Local graph clustering methods aim to detect small clusters in very large graphs without the need to process the whole graph. They are fundamental and scalable tools for a wide range of tasks such as local community detection, node ranking and node embedding. While prior work on local graph clustering mainly focuses on graphs without node attributes, modern real-world graph datasets typically come with node attributes that provide valuable additional information. We present a simple local graph clustering algorithm for graphs with node attributes, based on the idea of diffusing mass locally in the graph while accounting for both structural and attribute proximities. Using high-dimensional concentration results, we provide statistical guarantees on the performance of the algorithm for the recovery of a target cluster with a single seed node. We give conditions under which a target cluster generated from a fairly general contextual random graph model, which includes both the stochastic block model and the planted cluster model as special cases, can be fully recovered with bounded false positives. Empirically, we validate all theoretical claims using synthetic data, and we show that incorporating node attributes leads to superior local clustering performances using real-world graph datasets.

Let (M omega) be a two dimensional symplectic manifold, phi: M to M a symplectomorphism with hyperbolic fixed point x and transversely intersecting stable and unstable manifolds W^s(phi, x) cap W^u(phi, x)=:H(phi, x). The intersection points are called homoclinic points, and the stable and unstable manifold are in this situation Lagrangian submanifolds. For this Lagrangian intersection problem with its infinite number of intersection points and wild oscillation behavior, we first define a Floer homology generated by finite sets of so-called contractible homoclinic points. This generalizes very significantly the Floer homologies generated by (semi)primary points defined by us in earlier works. Nevertheless these Floer homologies only consider quite `local' aspects of W^s(phi, x) cap W^u(phi, x) since their generator sets are finite, but the number of all contractible homoclinic points is infinite. To overcome this issue, we construct a direct limit of these `local' homoclinic Floer homologies over suitable index sets. These direct limits thus accumulate the information gathered by the finitely generated local' homoclinic Floer homologies.

We introduce a classification conjecture for kappa-solutions in 4d Ricci flow. Our conjectured list includes known examples from the literature, but also a new 1-parameter family of Z_2^2times O_3-symmetric bubble-sheet ovals that we construct. We observe that some special cases of the conjecture follow from recent results in the literature. We also introduce a stronger variant of the classification conjecture for ancient asymptotically cylindrical 4d Ricci flows, which does not assume smoothness and nonnegative curvature operator a priori. Assuming this stronger variant holds true, we establish a canonical neighborhood theorem for 4d Ricci flow through cylindrical singularities, which shares some elements in common with Perelman's canonical neighborhood theorem for 3d Ricci flow as well as the mean-convex neighborhood theorem for mean curvature flow through neck-singularities. Finally, we argue that quotient-necks lead to new phenomena, and sketch an example of non-uniqueness for 4d Ricci flow through singularities.

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

We study the realizability of simplicial complexes with a given pair of integer sequences, representing the node degree distribution and the facet size distribution, respectively. While the s-uniform variant of the problem is NP-complete when s geq 3, we identify two populations of input sequences, most of which can be solved in polynomial time using a recursive algorithm that we contribute. Combining with a sampler for the simplicial configuration model [J.-G. Young et al., Phys. Rev. E 96, 032312 (2017)], we facilitate the efficient sampling of simplicial ensembles from arbitrary degree and size distributions. We find that, contrary to expectations based on dyadic networks, increasing the nodes' degrees reduces the number of loops in simplicial complexes. Our work unveils a fundamental constraint on the degree-size sequences and sheds light on further analysis of higher-order phenomena based on local structures.

We introduce Lagrangian Flow Networks (LFlows) for modeling fluid densities and velocities continuously in space and time. By construction, the proposed LFlows satisfy the continuity equation, a PDE describing mass conservation in its differentiable form. Our model is based on the insight that solutions to the continuity equation can be expressed as time-dependent density transformations via differentiable and invertible maps. This follows from classical theory of the existence and uniqueness of Lagrangian flows for smooth vector fields. Hence, we model fluid densities by transforming a base density with parameterized diffeomorphisms conditioned on time. The key benefit compared to methods relying on numerical ODE solvers or PINNs is that the analytic expression of the velocity is always consistent with changes in density. Furthermore, we require neither expensive numerical solvers, nor additional penalties to enforce the PDE. LFlows show higher predictive accuracy in density modeling tasks compared to competing models in 2D and 3D, while being computationally efficient. As a real-world application, we model bird migration based on sparse weather radar measurements.

In the literature, it has been shown that the evolution of the known explicit 3D surface to the target one can be learned from 2D images using the instantaneous flow field, where the known and target 3D surfaces may largely differ in topology. We are interested in capturing 4D shapes whose topology changes largely over time. We encounter that the straightforward extension of the existing 3D-based method to the desired 4D case performs poorly. In this work, we address the challenges in extending 3D neural evolution to 4D under large topological changes by proposing two novel modifications. More precisely, we introduce (i) a new architecture to discretize and encode the deformation and learn the SDF and (ii) a technique to impose the temporal consistency. (iii) Also, we propose a rendering scheme for color prediction based on Gaussian splatting. Furthermore, to facilitate learning directly from 2D images, we propose a learning framework that can disentangle the geometry and appearance from RGB images. This method of disentanglement, while also useful for the 4D evolution problem that we are concentrating on, is also novel and valid for static scenes. Our extensive experiments on various data provide awesome results and, most importantly, open a new approach toward reconstructing challenging scenes with significant topological changes and deformations. Our source code and the dataset are publicly available at https://github.com/insait-institute/N4DE.

We propose Riemannian Flow Matching (RFM), a simple yet powerful framework for training continuous normalizing flows on manifolds. Existing methods for generative modeling on manifolds either require expensive simulation, are inherently unable to scale to high dimensions, or use approximations for limiting quantities that result in biased training objectives. Riemannian Flow Matching bypasses these limitations and offers several advantages over previous approaches: it is simulation-free on simple geometries, does not require divergence computation, and computes its target vector field in closed-form. The key ingredient behind RFM is the construction of a relatively simple premetric for defining target vector fields, which encompasses the existing Euclidean case. To extend to general geometries, we rely on the use of spectral decompositions to efficiently compute premetrics on the fly. Our method achieves state-of-the-art performance on many real-world non-Euclidean datasets, and we demonstrate tractable training on general geometries, including triangular meshes with highly non-trivial curvature and boundaries.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

Normalizing flows are a promising tool for modeling probability distributions in physical systems. While state-of-the-art flows accurately approximate distributions and energies, applications in physics additionally require smooth energies to compute forces and higher-order derivatives. Furthermore, such densities are often defined on non-trivial topologies. A recent example are Boltzmann Generators for generating 3D-structures of peptides and small proteins. These generative models leverage the space of internal coordinates (dihedrals, angles, and bonds), which is a product of hypertori and compact intervals. In this work, we introduce a class of smooth mixture transformations working on both compact intervals and hypertori. Mixture transformations employ root-finding methods to invert them in practice, which has so far prevented bi-directional flow training. To this end, we show that parameter gradients and forces of such inverses can be computed from forward evaluations via the inverse function theorem. We demonstrate two advantages of such smooth flows: they allow training by force matching to simulation data and can be used as potentials in molecular dynamics simulations.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

In this paper, it is shown that if a sequence of resistance metric spaces equipped with measures converges with respect to the local Gromov-Hausdorff-vague topology, and certain non-explosion and metric-entropy conditions are satisfied, then the associated stochastic processes and their local times also converge. The metric-entropy condition can be checked by applying volume estimates of balls. Whilst similar results have been proved previously, the approach of this article is more widely applicable. Indeed, we recover various known conclusions for scaling limits of some deterministic self-similar fractal graphs, critical Galton-Watson trees, the critical Erdos-R\'enyi random graph and the configuration model (in the latter two cases, we prove for the first time the convergence of the models with respect to the resistance metric and also, for the configuration model, we overcome an error in the existing proof of local time convergence). Moreover, we derive new ones for scaling limits of uniform spanning trees and random recursive fractals. The metric-entropy condition also implies convergence of associated Gaussian processes.

Generative Flow Networks (GFlowNets) are amortized sampling methods that learn a distribution over discrete objects proportional to their rewards. GFlowNets exhibit a remarkable ability to generate diverse samples, yet occasionally struggle to consistently produce samples with high rewards due to over-exploration on wide sample space. This paper proposes to train GFlowNets with local search, which focuses on exploiting high-rewarded sample space to resolve this issue. Our main idea is to explore the local neighborhood via backtracking and reconstruction guided by backward and forward policies, respectively. This allows biasing the samples toward high-reward solutions, which is not possible for a typical GFlowNet solution generation scheme, which uses the forward policy to generate the solution from scratch. Extensive experiments demonstrate a remarkable performance improvement in several biochemical tasks. Source code is available: https://github.com/dbsxodud-11/ls_gfn.

Image-based 3D reconstruction has increasingly stunning results over the past few years with the latest improvements in computer vision and graphics. Geometry and topology are two fundamental concepts when dealing with 3D mesh structures. But the latest often remains a side issue in the 3D mesh-based reconstruction literature. Indeed, performing per-vertex elementary displacements over a 3D sphere mesh only impacts its geometry and leaves the topological structure unchanged and fixed. Whereas few attempts propose to update the geometry and the topology, all need to lean on costly 3D ground-truth to determine the faces/edges to prune. We present in this work a method that aims to refine the topology of any 3D mesh through a face-pruning strategy that extensively relies upon 2D alpha masks and camera pose information. Our solution leverages a differentiable renderer that renders each face as a 2D soft map. Its pixel intensity reflects the probability of being covered during the rendering process by such a face. Based on the 2D soft-masks available, our method is thus able to quickly highlight all the incorrectly rendered faces for a given viewpoint. Because our module is agnostic to the network that produces the 3D mesh, it can be easily plugged into any self-supervised image-based (either synthetic or natural) 3D reconstruction pipeline to get complex meshes with a non-spherical topology.

We present a novel learning-based approach to graph representations of road networks employing state-of-the-art graph convolutional neural networks. Our approach is applied to realistic road networks of 17 cities from Open Street Map. While edge features are crucial to generate descriptive graph representations of road networks, graph convolutional networks usually rely on node features only. We show that the highly representative edge features can still be integrated into such networks by applying a line graph transformation. We also propose a method for neighborhood sampling based on a topological neighborhood composed of both local and global neighbors. We compare the performance of learning representations using different types of neighborhood aggregation functions in transductive and inductive tasks and in supervised and unsupervised learning. Furthermore, we propose a novel aggregation approach, Graph Attention Isomorphism Network, GAIN. Our results show that GAIN outperforms state-of-the-art methods on the road type classification problem.

We present a formulation of flow matching as variational inference, which we refer to as variational flow matching (VFM). Based on this formulation we develop CatFlow, a flow matching method for categorical data. CatFlow is easy to implement, computationally efficient, and achieves strong results on graph generation tasks. In VFM, the objective is to approximate the posterior probability path, which is a distribution over possible end points of a trajectory. We show that VFM admits both the CatFlow objective and the original flow matching objective as special cases. We also relate VFM to score-based models, in which the dynamics are stochastic rather than deterministic, and derive a bound on the model likelihood based on a reweighted VFM objective. We evaluate CatFlow on one abstract graph generation task and two molecular generation tasks. In all cases, CatFlow exceeds or matches performance of the current state-of-the-art models.

We propose a novel approach for preserving topological structures of the input space in latent representations of autoencoders. Using persistent homology, a technique from topological data analysis, we calculate topological signatures of both the input and latent space to derive a topological loss term. Under weak theoretical assumptions, we construct this loss in a differentiable manner, such that the encoding learns to retain multi-scale connectivity information. We show that our approach is theoretically well-founded and that it exhibits favourable latent representations on a synthetic manifold as well as on real-world image data sets, while preserving low reconstruction errors.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topological heuristics with the feature-learning ability of neural networks. It summarizes a putative link by random walk probabilities of adjacent paths. Instead of extracting transition probabilities from the original graph, it computes the transition matrix of a "predictive" latent graph by applying attention to learned features; this may be interpreted as feature-sensitive topology fingerprinting. WalkPool can leverage unsupervised node features or be combined with GNNs and trained end-to-end. It outperforms state-of-the-art methods on all common link prediction benchmarks, both homophilic and heterophilic, with and without node attributes. Applying WalkPool to a set of unsupervised GNNs significantly improves prediction accuracy, suggesting that it may be used as a general-purpose graph pooling scheme.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly available tool to manipulate knot diagrams in a real-time, interactive way is yet to be developed. We introduce a method of operating on the geometry of the knot diagram itself without any underlying three-dimensional structure that can underpin such an application. This allows us to directly interact with vector graphics knot diagrams while at the same time computing knot invariants in ways proposed by previous work. An implementation of this method is provided.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Complex networks provide a means to describe cities through their street mesh, expressing characteristics that refer to the structure and organization of an urban zone. Although other studies have used complex networks to model street meshes, we observed a lack of methods to characterize the relationship between cities by using their topological features. Accordingly, this paper aims to describe interactions between cities by using vectors of topological features extracted from their street meshes represented as complex networks. The methodology of this study is based on the use of digital maps. Over the computational representation of such maps, we extract global complex-network features that embody the characteristics of the cities. These vectors allow for the use of multidimensional projection and clustering techniques, enabling a similarity-based comparison of the street meshes. We experiment with 645 cities from the Brazilian state of Sao Paulo. Our results show how the joint of global features describes urban indicators that are deep-rooted in the network's topology and how they reveal characteristics and similarities among sets of cities that are separated from each other.

Topology reasoning aims to comprehensively understand road scenes and present drivable routes in autonomous driving. It requires detecting road centerlines (lane) and traffic elements, further reasoning their topology relationship, i.e., lane-lane topology, and lane-traffic topology. In this work, we first present that the topology score relies heavily on detection performance on lane and traffic elements. Therefore, we introduce a powerful 3D lane detector and an improved 2D traffic element detector to extend the upper limit of topology performance. Further, we propose TopoMLP, a simple yet high-performance pipeline for driving topology reasoning. Based on the impressive detection performance, we develop two simple MLP-based heads for topology generation. TopoMLP achieves state-of-the-art performance on OpenLane-V2 benchmark, i.e., 41.2% OLS with ResNet-50 backbone. It is also the 1st solution for 1st OpenLane Topology in Autonomous Driving Challenge. We hope such simple and strong pipeline can provide some new insights to the community. Code is at https://github.com/wudongming97/TopoMLP.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

The automated extraction of complete and precise road network graphs from remote sensing imagery remains a critical challenge in geospatial computer vision. Segmentation-based approaches, while effective in pixel-level recognition, struggle to maintain topology fidelity after vectorization postprocessing. Graph-growing methods build more topologically faithful graphs but suffer from computationally prohibitive iterative ROI cropping. Graph-generating methods first predict global static candidate road network vertices, and then infer possible edges between vertices. They achieve fast topology-aware inference, but limits the dynamic insertion of vertices. To address these challenges, we propose DeH4R, a novel hybrid model that combines graph-generating efficiency and graph-growing dynamics. This is achieved by decoupling the task into candidate vertex detection, adjacent vertex prediction, initial graph contruction, and graph expansion. This architectural innovation enables dynamic vertex (edge) insertions while retaining fast inference speed and enhancing both topology fidelity and spatial consistency. Comprehensive evaluations on CityScale and SpaceNet benchmarks demonstrate state-of-the-art (SOTA) performance. DeH4R outperforms the prior SOTA graph-growing method RNGDet++ by 4.62 APLS and 10.18 IoU on CityScale, while being approximately 10 times faster. The code will be made publicly available at https://github.com/7777777FAN/DeH4R.

In this paper we demonstrate how sub-Riemannian geometry can be used for manifold learning and surface reconstruction by combining local linear approximations of a point cloud to obtain lower dimensional bundles. Local approximations obtained by local PCAs are collected into a rank k tangent subbundle on R^d, k<d, which we call a principal subbundle. This determines a sub-Riemannian metric on R^d. We show that sub-Riemannian geodesics with respect to this metric can successfully be applied to a number of important problems, such as: explicit construction of an approximating submanifold M, construction of a representation of the point-cloud in R^k, and computation of distances between observations, taking the learned geometry into account. The reconstruction is guaranteed to equal the true submanifold in the limit case where tangent spaces are estimated exactly. Via simulations, we show that the framework is robust when applied to noisy data. Furthermore, the framework generalizes to observations on an a priori known Riemannian manifold.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

We present Topological Point Cloud Clustering (TPCC), a new method to cluster points in an arbitrary point cloud based on their contribution to global topological features. TPCC synthesizes desirable features from spectral clustering and topological data analysis and is based on considering the spectral properties of a simplicial complex associated to the considered point cloud. As it is based on considering sparse eigenvector computations, TPCC is similarly easy to interpret and implement as spectral clustering. However, by focusing not just on a single matrix associated to a graph created from the point cloud data, but on a whole set of Hodge-Laplacians associated to an appropriately constructed simplicial complex, we can leverage a far richer set of topological features to characterize the data points within the point cloud and benefit from the relative robustness of topological techniques against noise. We test the performance of TPCC on both synthetic and real-world data and compare it with classical spectral clustering.

Deep neural representations of 3D shapes as implicit functions have been shown to produce high fidelity models surpassing the resolution-memory trade-off faced by the explicit representations using meshes and point clouds. However, most such approaches focus on representing closed shapes. Unsigned distance function (UDF) based approaches have been proposed recently as a promising alternative to represent both open and closed shapes. However, since the gradients of UDFs vanish on the surface, it is challenging to estimate local (differential) geometric properties like the normals and tangent planes which are needed for many downstream applications in vision and graphics. There are additional challenges in computing these properties efficiently with a low-memory footprint. This paper presents a novel approach that models such surfaces using a new class of implicit representations called the closest surface-point (CSP) representation. We show that CSP allows us to represent complex surfaces of any topology (open or closed) with high fidelity. It also allows for accurate and efficient computation of local geometric properties. We further demonstrate that it leads to efficient implementation of downstream algorithms like sphere-tracing for rendering the 3D surface as well as to create explicit mesh-based representations. Extensive experimental evaluation on the ShapeNet dataset validate the above contributions with results surpassing the state-of-the-art.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

Flow matching casts sample generation as learning a continuous-time velocity field that transports noise to data. Existing flow matching networks typically predict each point's velocity independently, considering only its location and time along its flow trajectory, and ignoring neighboring points. However, this pointwise approach may overlook correlations between points along the generation trajectory that could enhance velocity predictions, thereby improving downstream generation quality. To address this, we propose Graph Flow Matching (GFM), a lightweight enhancement that decomposes the learned velocity into a reaction term -- any standard flow matching network -- and a diffusion term that aggregates neighbor information via a graph neural module. This reaction-diffusion formulation retains the scalability of deep flow models while enriching velocity predictions with local context, all at minimal additional computational cost. Operating in the latent space of a pretrained variational autoencoder, GFM consistently improves Fr\'echet Inception Distance (FID) and recall across five image generation benchmarks (LSUN Church, LSUN Bedroom, FFHQ, AFHQ-Cat, and CelebA-HQ at 256times256), demonstrating its effectiveness as a modular enhancement to existing flow matching architectures.

We present Piecewise Rectified Flow (PeRFlow), a flow-based method for accelerating diffusion models. PeRFlow divides the sampling process of generative flows into several time windows and straightens the trajectories in each interval via the reflow operation, thereby approaching piecewise linear flows. PeRFlow achieves superior performance in a few-step generation. Moreover, through dedicated parameterizations, the obtained PeRFlow models show advantageous transfer ability, serving as universal plug-and-play accelerators that are compatible with various workflows based on the pre-trained diffusion models. The implementations of training and inference are fully open-sourced. https://github.com/magic-research/piecewise-rectified-flow

Recently similarity graphs became the leading paradigm for efficient nearest neighbor search, outperforming traditional tree-based and LSH-based methods. Similarity graphs perform the search via greedy routing: a query traverses the graph and in each vertex moves to the adjacent vertex that is the closest to this query. In practice, similarity graphs are often susceptible to local minima, when queries do not reach its nearest neighbors, getting stuck in suboptimal vertices. In this paper we propose to learn the routing function that overcomes local minima via incorporating information about the graph global structure. In particular, we augment the vertices of a given graph with additional representations that are learned to provide the optimal routing from the start vertex to the query nearest neighbor. By thorough experiments, we demonstrate that the proposed learnable routing successfully diminishes the local minima problem and significantly improves the overall search performance.

We delve into the physics-informed neural reconstruction of smoke and obstacles through sparse-view RGB videos, tackling challenges arising from limited observation of complex dynamics. Existing physics-informed neural networks often emphasize short-term physics constraints, leaving the proper preservation of long-term conservation less explored. We introduce Neural Characteristic Trajectory Fields, a novel representation utilizing Eulerian neural fields to implicitly model Lagrangian fluid trajectories. This topology-free, auto-differentiable representation facilitates efficient flow map calculations between arbitrary frames as well as efficient velocity extraction via auto-differentiation. Consequently, it enables end-to-end supervision covering long-term conservation and short-term physics priors. Building on the representation, we propose physics-informed trajectory learning and integration into NeRF-based scene reconstruction. We enable advanced obstacle handling through self-supervised scene decomposition and seamless integrated boundary constraints. Our results showcase the ability to overcome challenges like occlusion uncertainty, density-color ambiguity, and static-dynamic entanglements. Code and sample tests are at https://github.com/19reborn/PICT_smoke.

We introduce a theoretical framework for differentiable surface evolution that allows discrete topology changes through the use of topological derivatives for variational optimization of image functionals. While prior methods for inverse rendering of geometry rely on silhouette gradients for topology changes, such signals are sparse. In contrast, our theory derives topological derivatives that relate the introduction of vanishing holes and phases to changes in image intensity. As a result, we enable differentiable shape perturbations in the form of hole or phase nucleation. We validate the proposed theory with optimization of closed curves in 2D and surfaces in 3D to lend insights into limitations of current methods and enable improved applications such as image vectorization, vector-graphics generation from text prompts, single-image reconstruction of shape ambigrams and multi-view 3D reconstruction.

Topological Neural Networks (TNNs) incorporate higher-order relational information beyond pairwise interactions, enabling richer representations than Graph Neural Networks (GNNs). Concurrently, topological descriptors based on persistent homology (PH) are being increasingly employed to augment the GNNs. We investigate the benefits of integrating these two paradigms. Specifically, we introduce TopNets as a broad framework that subsumes and unifies various methods in the intersection of GNNs/TNNs and PH such as (generalizations of) RePHINE and TOGL. TopNets can also be readily adapted to handle (symmetries in) geometric complexes, extending the scope of TNNs and PH to spatial settings. Theoretically, we show that PH descriptors can provably enhance the expressivity of simplicial message-passing networks. Empirically, (continuous and E(n)-equivariant extensions of) TopNets achieve strong performance across diverse tasks, including antibody design, molecular dynamics simulation, and drug property prediction.

Generative models such as denoising diffusion models are quickly advancing their ability to approximate highly complex data distributions. They are also increasingly leveraged in scientific machine learning, where samples from the implied data distribution are expected to adhere to specific governing equations. We present a framework that unifies generative modeling and partial differential equation fulfillment by introducing a first-principle-based loss term that enforces generated samples to fulfill the underlying physical constraints. Our approach reduces the residual error by up to two orders of magnitude compared to previous work in a fluid flow case study and outperforms task-specific frameworks in relevant metrics for structural topology optimization. We also present numerical evidence that our extended training objective acts as a natural regularization mechanism against overfitting. Our framework is simple to implement and versatile in its applicability for imposing equality and inequality constraints as well as auxiliary optimization objectives.

The gradients of convex functions are expressive models of non-trivial vector fields. For example, Brenier's theorem yields that the optimal transport map between any two measures on Euclidean space under the squared distance is realized as a convex gradient, which is a key insight used in recent generative flow models. In this paper, we study how to model convex gradients by integrating a Jacobian-vector product parameterized by a neural network, which we call the Input Convex Gradient Network (ICGN). We theoretically study ICGNs and compare them to taking the gradient of an Input-Convex Neural Network (ICNN), empirically demonstrating that a single layer ICGN can fit a toy example better than a single layer ICNN. Lastly, we explore extensions to deeper networks and connections to constructions from Riemannian geometry.

Structural topology optimization (TO) is central to engineering design but remains computationally intensive due to complex physics and hard constraints. Existing deep-learning methods are limited to fixed square grids, a few hand-coded boundary conditions, and post-hoc optimization, preventing general deployment. We introduce Optimize Any Topology (OAT), a foundation-model framework that directly predicts minimum-compliance layouts for arbitrary aspect ratios, resolutions, volume fractions, loads, and fixtures. OAT combines a resolution- and shape-agnostic autoencoder with an implicit neural-field decoder and a conditional latent-diffusion model trained on OpenTO, a new corpus of 2.2 million optimized structures covering 2 million unique boundary-condition configurations. On four public benchmarks and two challenging unseen tests, OAT lowers mean compliance up to 90% relative to the best prior models and delivers sub-1 second inference on a single GPU across resolutions from 64 x 64 to 256 x 256 and aspect ratios as high as 10:1. These results establish OAT as a general, fast, and resolution-free framework for physics-aware topology optimization and provide a large-scale dataset to spur further research in generative modeling for inverse design. Code & data can be found at https://github.com/ahnobari/OptimizeAnyTopology.

We present two new classes of algorithms for efficient field integration on graphs encoding point clouds. The first class, SeparatorFactorization(SF), leverages the bounded genus of point cloud mesh graphs, while the second class, RFDiffusion(RFD), uses popular epsilon-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g., shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (particularly for mesh-dynamics modeling), Wasserstein distance computations for point clouds, and the Gromov-Wasserstein variant.

Flow matching is a powerful framework for generating high-quality samples in various applications, especially image synthesis. However, the intensive computational demands of these models, especially during the fine-tuning process and sampling processes, pose significant challenges for low-resource scenarios. This paper introduces Bellman Optimal Step-size Straightening (BOSS) technique for distilling flow-matching generative models: it aims specifically for a few-step efficient image sampling while adhering to a computational budget constraint. First, this technique involves a dynamic programming algorithm that optimizes the step sizes of the pretrained network. Then, it refines the velocity network to match the optimal step sizes, aiming to straighten the generation paths. Extensive experimental evaluations across image generation tasks demonstrate the efficacy of BOSS in terms of both resource utilization and image quality. Our results reveal that BOSS achieves substantial gains in efficiency while maintaining competitive sample quality, effectively bridging the gap between low-resource constraints and the demanding requirements of flow-matching generative models. Our paper also fortifies the responsible development of artificial intelligence, offering a more sustainable generative model that reduces computational costs and environmental footprints. Our code can be found at https://github.com/nguyenngocbaocmt02/BOSS.

A standard Variational Autoencoder, with a Euclidean latent space, is structurally incapable of capturing topological properties of certain datasets. To remove topological obstructions, we introduce Diffusion Variational Autoencoders with arbitrary manifolds as a latent space. A Diffusion Variational Autoencoder uses transition kernels of Brownian motion on the manifold. In particular, it uses properties of the Brownian motion to implement the reparametrization trick and fast approximations to the KL divergence. We show that the Diffusion Variational Autoencoder is capable of capturing topological properties of synthetic datasets. Additionally, we train MNIST on spheres, tori, projective spaces, SO(3), and a torus embedded in R3. Although a natural dataset like MNIST does not have latent variables with a clear-cut topological structure, training it on a manifold can still highlight topological and geometrical properties.

Although the recent rapid evolution of 3D generative neural networks greatly improves 3D shape generation, it is still not convenient for ordinary users to create 3D shapes and control the local geometry of generated shapes. To address these challenges, we propose a diffusion-based 3D generation framework -- locally attentional SDF diffusion, to model plausible 3D shapes, via 2D sketch image input. Our method is built on a two-stage diffusion model. The first stage, named occupancy-diffusion, aims to generate a low-resolution occupancy field to approximate the shape shell. The second stage, named SDF-diffusion, synthesizes a high-resolution signed distance field within the occupied voxels determined by the first stage to extract fine geometry. Our model is empowered by a novel view-aware local attention mechanism for image-conditioned shape generation, which takes advantage of 2D image patch features to guide 3D voxel feature learning, greatly improving local controllability and model generalizability. Through extensive experiments in sketch-conditioned and category-conditioned 3D shape generation tasks, we validate and demonstrate the ability of our method to provide plausible and diverse 3D shapes, as well as its superior controllability and generalizability over existing work. Our code and trained models are available at https://zhengxinyang.github.io/projects/LAS-Diffusion.html

Boundary point detection aims to outline the external contour structure of clusters and enhance the inter-cluster discrimination, thus bolstering the performance of the downstream classification and clustering tasks. However, existing boundary point detectors are sensitive to density heterogeneity or cannot identify boundary points in concave structures and high-dimensional manifolds. In this work, we propose a robust and efficient boundary point detection method based on Local Direction Dispersion (LoDD). The core of boundary point detection lies in measuring the difference between boundary points and internal points. It is a common observation that an internal point is surrounded by its neighbors in all directions, while the neighbors of a boundary point tend to be distributed only in a certain directional range. By considering this observation, we adopt density-independent K-Nearest Neighbors (KNN) method to determine neighboring points and design a centrality metric LoDD using the eigenvalues of the covariance matrix to depict the distribution uniformity of KNN. We also develop a grid-structure assumption of data distribution to determine the parameters adaptively. The effectiveness of LoDD is demonstrated on synthetic datasets, real-world benchmarks, and application of training set split for deep learning model and hole detection on point cloud data. The datasets and toolkit are available at: https://github.com/ZPGuiGroupWhu/lodd.

Modelling interactions is critical in learning complex dynamical systems, namely systems of interacting objects with highly non-linear and time-dependent behaviour. A large class of such systems can be formalized as geometric graphs, i.e., graphs with nodes positioned in the Euclidean space given an arbitrarily chosen global coordinate system, for instance vehicles in a traffic scene. Notwithstanding the arbitrary global coordinate system, the governing dynamics of the respective dynamical systems are invariant to rotations and translations, also known as Galilean invariance. As ignoring these invariances leads to worse generalization, in this work we propose local coordinate frames per node-object to induce roto-translation invariance to the geometric graph of the interacting dynamical system. Further, the local coordinate frames allow for a natural definition of anisotropic filtering in graph neural networks. Experiments in traffic scenes, 3D motion capture, and colliding particles demonstrate that the proposed approach comfortably outperforms the recent state-of-the-art.

Voronoi diagrams are essential geometrical structures with numerous applications, particularly astrophysics-driven finite volume methods. While serial algorithms for constructing these entities are well-established, parallel construction remains challenging. This is especially true in distributed memory systems, where each host manages only a subset of the input points. This process requires redistributing points across hosts and accurately computing the corresponding Voronoi cells. In this paper, we introduce a new distributed construction algorithm, which is implemented in our open-source C++ 3-dimensional Voronoi construction framework. Our approach leverages Delaunay triangulation as an intermediate step, which is then transformed into a Voronoi diagram. We introduce the algorithms we implemented for the precise construction and our load-balancing approach and compare the running time with other state-of-the-art frameworks. MadVoro is a versatile tool that can be applied in various scientific domains, such as mesh decomposition, computational physics, chemistry, and machine learning.

Geometric alignment appears in a variety of applications, ranging from domain adaptation, optimal transport, and normalizing flows in machine learning; optical flow and learned augmentation in computer vision and deformable registration within biomedical imaging. A recurring challenge is the alignment of domains whose topology is not the same; a problem that is routinely ignored, potentially introducing bias in downstream analysis. As a first step towards solving such alignment problems, we propose an unsupervised algorithm for the detection of changes in image topology. The model is based on a conditional variational auto-encoder and detects topological changes between two images during the registration step. We account for both topological changes in the image under spatial variation and unexpected transformations. Our approach is validated on two tasks and datasets: detection of topological changes in microscopy images of cells, and unsupervised anomaly detection brain imaging.

We introduce a new paradigm for generative modeling built on Continuous Normalizing Flows (CNFs), allowing us to train CNFs at unprecedented scale. Specifically, we present the notion of Flow Matching (FM), a simulation-free approach for training CNFs based on regressing vector fields of fixed conditional probability paths. Flow Matching is compatible with a general family of Gaussian probability paths for transforming between noise and data samples -- which subsumes existing diffusion paths as specific instances. Interestingly, we find that employing FM with diffusion paths results in a more robust and stable alternative for training diffusion models. Furthermore, Flow Matching opens the door to training CNFs with other, non-diffusion probability paths. An instance of particular interest is using Optimal Transport (OT) displacement interpolation to define the conditional probability paths. These paths are more efficient than diffusion paths, provide faster training and sampling, and result in better generalization. Training CNFs using Flow Matching on ImageNet leads to consistently better performance than alternative diffusion-based methods in terms of both likelihood and sample quality, and allows fast and reliable sample generation using off-the-shelf numerical ODE solvers.

Simulations of turbulent flows in 3D are one of the most expensive simulations in computational fluid dynamics (CFD). Many works have been written on surrogate models to replace numerical solvers for fluid flows with faster, learned, autoregressive models. However, the intricacies of turbulence in three dimensions necessitate training these models with very small time steps, while generating realistic flow states requires either long roll-outs with many steps and significant error accumulation or starting from a known, realistic flow state - something we aimed to avoid in the first place. Instead, we propose to approach turbulent flow simulation as a generative task directly learning the manifold of all possible turbulent flow states without relying on any initial flow state. For our experiments, we introduce a challenging 3D turbulence dataset of high-resolution flows and detailed vortex structures caused by various objects and derive two novel sample evaluation metrics for turbulent flows. On this dataset, we show that our generative model captures the distribution of turbulent flows caused by unseen objects and generates high-quality, realistic samples amenable for downstream applications without access to any initial state.

We study the problem of visualizing large-scale and high-dimensional data in a low-dimensional (typically 2D or 3D) space. Much success has been reported recently by techniques that first compute a similarity structure of the data points and then project them into a low-dimensional space with the structure preserved. These two steps suffer from considerable computational costs, preventing the state-of-the-art methods such as the t-SNE from scaling to large-scale and high-dimensional data (e.g., millions of data points and hundreds of dimensions). We propose the LargeVis, a technique that first constructs an accurately approximated K-nearest neighbor graph from the data and then layouts the graph in the low-dimensional space. Comparing to t-SNE, LargeVis significantly reduces the computational cost of the graph construction step and employs a principled probabilistic model for the visualization step, the objective of which can be effectively optimized through asynchronous stochastic gradient descent with a linear time complexity. The whole procedure thus easily scales to millions of high-dimensional data points. Experimental results on real-world data sets demonstrate that the LargeVis outperforms the state-of-the-art methods in both efficiency and effectiveness. The hyper-parameters of LargeVis are also much more stable over different data sets.

Due to high utility in many applications, from social networks to blockchain to power grids, deep learning on non-Euclidean objects such as graphs and manifolds, coined Geometric Deep Learning (GDL), continues to gain an ever increasing interest. We propose a new L\'evy Flights Graph Convolutional Networks (LFGCN) method for semi-supervised learning, which casts the L\'evy Flights into random walks on graphs and, as a result, allows both to accurately account for the intrinsic graph topology and to substantially improve classification performance, especially for heterogeneous graphs. Furthermore, we propose a new preferential P-DropEdge method based on the Girvan-Newman argument. That is, in contrast to uniform removing of edges as in DropEdge, following the Girvan-Newman algorithm, we detect network periphery structures using information on edge betweenness and then remove edges according to their betweenness centrality. Our experimental results on semi-supervised node classification tasks demonstrate that the LFGCN coupled with P-DropEdge accelerates the training task, increases stability and further improves predictive accuracy of learned graph topology structure. Finally, in our case studies we bring the machinery of LFGCN and other deep networks tools to analysis of power grid networks - the area where the utility of GDL remains untapped.

Many complicated network problems can be easily understood on small networks. Difficulties arise when small networks are combined into larger ones. Fortunately, the mathematical theory of sheaves was constructed to address just this kind of situation; it extends locally-defined structures to globally valid inferences by way of consistency relations. This paper exhibits examples in network monitoring and filter hardware where sheaves have useful descriptive power.

Diffusion models have made significant contributions to computer vision, sparking a growing interest in the community recently regarding the application of them to graph generation. Existing discrete graph diffusion models exhibit heightened computational complexity and diminished training efficiency. A preferable and natural way is to directly diffuse the graph within the latent space. However, due to the non-Euclidean structure of graphs is not isotropic in the latent space, the existing latent diffusion models effectively make it difficult to capture and preserve the topological information of graphs. To address the above challenges, we propose a novel geometrically latent diffusion framework HypDiff. Specifically, we first establish a geometrically latent space with interpretability measures based on hyperbolic geometry, to define anisotropic latent diffusion processes for graphs. Then, we propose a geometrically latent diffusion process that is constrained by both radial and angular geometric properties, thereby ensuring the preservation of the original topological properties in the generative graphs. Extensive experimental results demonstrate the superior effectiveness of HypDiff for graph generation with various topologies.

Blood vessel networks in the brain play a crucial role in stroke research, where understanding their topology is essential for analyzing blood flow dynamics. However, extracting detailed topological vessel network information from microscopy data remains a significant challenge, mainly due to the scarcity of labeled training data and the need for high topological accuracy. This work combines synthetic data generation with deep learning to automatically extract vessel networks as graphs from volumetric microscopy data. To combat data scarcity, we introduce a comprehensive pipeline for generating large-scale synthetic datasets that mirror the characteristics of real vessel networks. Our three-stage approach progresses from abstract graph generation through vessel mask creation to realistic medical image synthesis, incorporating biological constraints and imaging artifacts at each stage. Using this synthetic data, we develop a two-stage deep learning pipeline of 3D U-Net-based models for node detection and edge prediction. Fine-tuning on real microscopy data shows promising adaptation, improving edge prediction F1 scores from 0.496 to 0.626 by training on merely 5 manually labeled samples. These results suggest that automated vessel network extraction is becoming practically feasible, opening new possibilities for large-scale vascular analysis in stroke research.

Key graph-based problems play a central role in understanding network topology and uncovering patterns of similarity in homogeneous and temporal data. Such patterns can be revealed by analyzing communities formed by nodes, which in turn can be effectively modeled through temporal k-cores. This paper introduces a novel decentralized and incremental algorithm for computing the core decomposition of temporal networks. Decentralized solutions leverage the ability of network nodes to communicate and coordinate locally, addressing complex problems in a scalable, adaptive, and timely manner. By leveraging previously computed coreness values, our approach significantly reduces the activation of nodes and the volume of message exchanges when the network changes over time. This enables scalability with only a minimal trade-off in precision. Experimental evaluations on large real-world networks under varying levels of dynamism demonstrate the efficiency of our solution compared to a state-of-the-art approach, particularly in terms of active nodes, communication overhead, and convergence speed.

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

Convolutional Neural Networks (CNN) have been successful in processing data signals that are uniformly sampled in the spatial domain (e.g., images). However, most data signals do not natively exist on a grid, and in the process of being sampled onto a uniform physical grid suffer significant aliasing error and information loss. Moreover, signals can exist in different topological structures as, for example, points, lines, surfaces and volumes. It has been challenging to analyze signals with mixed topologies (for example, point cloud with surface mesh). To this end, we develop mathematical formulations for Non-Uniform Fourier Transforms (NUFT) to directly, and optimally, sample nonuniform data signals of different topologies defined on a simplex mesh into the spectral domain with no spatial sampling error. The spectral transform is performed in the Euclidean space, which removes the translation ambiguity from works on the graph spectrum. Our representation has four distinct advantages: (1) the process causes no spatial sampling error during the initial sampling, (2) the generality of this approach provides a unified framework for using CNNs to analyze signals of mixed topologies, (3) it allows us to leverage state-of-the-art backbone CNN architectures for effective learning without having to design a particular architecture for a particular data structure in an ad-hoc fashion, and (4) the representation allows weighted meshes where each element has a different weight (i.e., texture) indicating local properties. We achieve results on par with the state-of-the-art for the 3D shape retrieval task, and a new state-of-the-art for the point cloud to surface reconstruction task.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

We introduce CLR-Wire, a novel framework for 3D curve-based wireframe generation that integrates geometry and topology into a unified Continuous Latent Representation. Unlike conventional methods that decouple vertices, edges, and faces, CLR-Wire encodes curves as Neural Parametric Curves along with their topological connectivity into a continuous and fixed-length latent space using an attention-driven variational autoencoder (VAE). This unified approach facilitates joint learning and generation of both geometry and topology. To generate wireframes, we employ a flow matching model to progressively map Gaussian noise to these latents, which are subsequently decoded into complete 3D wireframes. Our method provides fine-grained modeling of complex shapes and irregular topologies, and supports both unconditional generation and generation conditioned on point cloud or image inputs. Experimental results demonstrate that, compared with state-of-the-art generative approaches, our method achieves substantial improvements in accuracy, novelty, and diversity, offering an efficient and comprehensive solution for CAD design, geometric reconstruction, and 3D content creation.

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

We explore the use of topological data analysis (TDA) combined with machine learning for discriminating standard model backgrounds from the invisible decay of the Z^prime boson associated with monophoton emission at a 3 TeV muon collider. Reconstructed events are mapped into a six-dimensional kinematic space and aggregated into bags of events, from which persistent homology is used to extract Betti number distributions. Within the Multiple Instance Learning paradigm, classifiers trained on these topological descriptors demonstrate significantly improved classification accuracy compared to the conventional ML approaches based on event-wise kinematic inputs. We also draw exclusion contours at 95\% CL in the (m_{Z^prime}, m_chi) parameter space, highlighting the potential of topological features to extend the discovery reach of future collider experiments.

Given an unconditional generative model and a predictor for a target property (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. As a highly efficient technique for steering generative models toward flexible outcomes, training-free guidance has gained increasing attention in diffusion models. However, existing methods only handle data in continuous spaces, while many scientific applications involve both continuous and discrete data (referred to as multimodality). Another emerging trend is the growing use of the simple and general flow matching framework in building generative foundation models, where guided generation remains under-explored. To address this, we introduce TFG-Flow, a novel training-free guidance method for multimodal generative flow. TFG-Flow addresses the curse-of-dimensionality while maintaining the property of unbiased sampling in guiding discrete variables. We validate TFG-Flow on four molecular design tasks and show that TFG-Flow has great potential in drug design by generating molecules with desired properties.

Simulation-free methods for training continuous-time generative models construct probability paths that go between noise distributions and individual data samples. Recent works, such as Flow Matching, derived paths that are optimal for each data sample. However, these algorithms rely on independent data and noise samples, and do not exploit underlying structure in the data distribution for constructing probability paths. We propose Multisample Flow Matching, a more general framework that uses non-trivial couplings between data and noise samples while satisfying the correct marginal constraints. At very small overhead costs, this generalization allows us to (i) reduce gradient variance during training, (ii) obtain straighter flows for the learned vector field, which allows us to generate high-quality samples using fewer function evaluations, and (iii) obtain transport maps with lower cost in high dimensions, which has applications beyond generative modeling. Importantly, we do so in a completely simulation-free manner with a simple minimization objective. We show that our proposed methods improve sample consistency on downsampled ImageNet data sets, and lead to better low-cost sample generation.

Large-scale distributed training in production datacenters constitutes a challenging workload bottlenecked by network communication. In response, both major industry players (e.g., Ultra Ethernet Consortium) and parts of academia have surprisingly, and almost unanimously, agreed that packet spraying is necessary to improve the performance of large-scale distributed training workloads. In this paper, we challenge this prevailing belief and pose the question: How close can a singlepath transport approach an optimal multipath transport? We demonstrate that singlepath transport (from a NIC's perspective) is sufficient and can perform nearly as well as an ideal multipath transport with packet spraying, particularly in the context of distributed training in leaf-spine topologies. Our assertion is based on four key observations about workloads driven by collective communication patterns: (i) flows within a collective start almost simultaneously, (ii) flow sizes are nearly equal, (iii) the completion time of a collective is more crucial than individual flow completion times, and (iv) flows can be split upon arrival. We analytically prove that singlepath transport, using minimal flow splitting (at the application layer), is equivalent to an ideal multipath transport with packet spraying in terms of maximum congestion. Our preliminary evaluations support our claims. This paper suggests an alternative agenda for developing next-generation transport protocols tailored for large-scale distributed training.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

Triangle meshes are fundamental to 3D applications, enabling efficient modification and rasterization while maintaining compatibility with standard rendering pipelines. However, current automatic mesh generation methods typically rely on intermediate representations that lack the continuous surface quality inherent to meshes. Converting these representations into meshes produces dense, suboptimal outputs. Although recent autoregressive approaches demonstrate promise in directly modeling mesh vertices and faces, they are constrained by the limitation in face count, scalability, and structural fidelity. To address these challenges, we propose Nautilus, a locality-aware autoencoder for artist-like mesh generation that leverages the local properties of manifold meshes to achieve structural fidelity and efficient representation. Our approach introduces a novel tokenization algorithm that preserves face proximity relationships and compresses sequence length through locally shared vertices and edges, enabling the generation of meshes with an unprecedented scale of up to 5,000 faces. Furthermore, we develop a Dual-stream Point Conditioner that provides multi-scale geometric guidance, ensuring global consistency and local structural fidelity by capturing fine-grained geometric features. Extensive experiments demonstrate that Nautilus significantly outperforms state-of-the-art methods in both fidelity and scalability. The project page is at https://nautilusmeshgen.github.io.

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks including ModelNet40, ShapeNetPart, and S3DIS.

Autoencoders have been proposed as a powerful tool for model-independent anomaly detection in high-energy physics. The operating principle is that events which do not belong to the space of training data will be reconstructed poorly, thus flagging them as anomalies. We point out that in a variety of examples of interest, the connection between large reconstruction error and anomalies is not so clear. In particular, for data sets with nontrivial topology, there will always be points that erroneously seem anomalous due to global issues. Conversely, neural networks typically have an inductive bias or prior to locally interpolate such that undersampled or rare events may be reconstructed with small error, despite actually being the desired anomalies. Taken together, these facts are in tension with the simple picture of the autoencoder as an anomaly detector. Using a series of illustrative low-dimensional examples, we show explicitly how the intrinsic and extrinsic topology of the dataset affects the behavior of an autoencoder and how this topology is manifested in the latent space representation during training. We ground this analysis in the discussion of a mock "bump hunt" in which the autoencoder fails to identify an anomalous "signal" for reasons tied to the intrinsic topology of n-particle phase space.

In recent years, persistent homology (PH) has been successfully applied to real-world data in many different settings. Despite significant computational advances, PH algorithms do not yet scale to large datasets preventing interesting applications. One approach to address computational issues posed by PH is to select a set of landmarks by subsampling from the data. Currently, these landmark points are chosen either at random or using the maxmin algorithm. Neither is ideal as random selection tends to favour dense areas of the data while the maxmin algorithm is very sensitive to noise. Here, we propose a novel approach to select landmarks specifically for PH that preserves coarse topological information of the original dataset. Our method is motivated by the Mayer-Vietoris sequence and requires only local PH computation thus enabling efficient computation. We test our landmarks on artificial datasets which contain different levels of noise and compare them to standard landmark selection techniques. We demonstrate that our landmark selection outperforms standard methods as well as a subsampling technique based on an outlier-robust version of the k--means algorithm for low sampling densities in noisy data with respect to robustness to outliers.

Accurate segmentation of topological tubular structures, such as blood vessels and roads, is crucial in various fields, ensuring accuracy and efficiency in downstream tasks. However, many factors complicate the task, including thin local structures and variable global morphologies. In this work, we note the specificity of tubular structures and use this knowledge to guide our DSCNet to simultaneously enhance perception in three stages: feature extraction, feature fusion, and loss constraint. First, we propose a dynamic snake convolution to accurately capture the features of tubular structures by adaptively focusing on slender and tortuous local structures. Subsequently, we propose a multi-view feature fusion strategy to complement the attention to features from multiple perspectives during feature fusion, ensuring the retention of important information from different global morphologies. Finally, a continuity constraint loss function, based on persistent homology, is proposed to constrain the topological continuity of the segmentation better. Experiments on 2D and 3D datasets show that our DSCNet provides better accuracy and continuity on the tubular structure segmentation task compared with several methods. Our codes will be publicly available.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

Representing complex objects with basic geometric primitives has long been a topic in computer vision. Primitive-based representations have the merits of compactness and computational efficiency in higher-level tasks such as physics simulation, collision checking, and robotic manipulation. Unlike previous works which extract polygonal meshes from a signed distance function (SDF), in this paper, we present a novel method, named Marching-Primitives, to obtain a primitive-based abstraction directly from an SDF. Our method grows geometric primitives (such as superquadrics) iteratively by analyzing the connectivity of voxels while marching at different levels of signed distance. For each valid connected volume of interest, we march on the scope of voxels from which a primitive is able to be extracted in a probabilistic sense and simultaneously solve for the parameters of the primitive to capture the underlying local geometry. We evaluate the performance of our method on both synthetic and real-world datasets. The results show that the proposed method outperforms the state-of-the-art in terms of accuracy, and is directly generalizable among different categories and scales. The code is open-sourced at https://github.com/ChirikjianLab/Marching-Primitives.git.

Given a complex of groups, we construct a new class of complex of groups that records its local data and offer a functorial perspective on the statement that complexes of groups are locally developable. We also construct a new notion of an immersion of complexes of groups and establish that a locally isometric immersion of a complex of groups into a non-positively curved complex of groups is pi_1-injective. Furthermore, the domain complex of groups is developable and the induced map on geometric realizations of developments is an isometric embedding.

Flow matching (FM) is a general framework for defining probability paths via Ordinary Differential Equations (ODEs) to transform between noise and data samples. Recent approaches attempt to straighten these flow trajectories to generate high-quality samples with fewer function evaluations, typically through iterative rectification methods or optimal transport solutions. In this paper, we introduce Consistency Flow Matching (Consistency-FM), a novel FM method that explicitly enforces self-consistency in the velocity field. Consistency-FM directly defines straight flows starting from different times to the same endpoint, imposing constraints on their velocity values. Additionally, we propose a multi-segment training approach for Consistency-FM to enhance expressiveness, achieving a better trade-off between sampling quality and speed. Preliminary experiments demonstrate that our Consistency-FM significantly improves training efficiency by converging 4.4x faster than consistency models and 1.7x faster than rectified flow models while achieving better generation quality. Our code is available at: https://github.com/YangLing0818/consistency_flow_matching

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

We present TopoMortar, a brick wall dataset that is the first dataset specifically designed to evaluate topology-focused image segmentation methods, such as topology loss functions. TopoMortar enables to investigate in two ways whether methods incorporate prior topological knowledge. First, by eliminating challenges seen in real-world data, such as small training set, noisy labels, and out-of-distribution test-set images, that, as we show, impact the effectiveness of topology losses. Second, by allowing to assess in the same dataset topology accuracy across dataset challenges, isolating dataset-related effects from the effect of incorporating prior topological knowledge. In these two experiments, it is deliberately difficult to improve topology accuracy without actually using topology information, thus, permitting to attribute an improvement in topology accuracy to the incorporation of prior topological knowledge. To this end, TopoMortar includes three types of labels (accurate, noisy, pseudo-labels), two fixed training sets (large and small), and in-distribution and out-of-distribution test-set images. We compared eight loss functions on TopoMortar, and we found that clDice achieved the most topologically accurate segmentations, Skeleton Recall loss performed best particularly with noisy labels, and the relative advantageousness of the other loss functions depended on the experimental setting. Additionally, we show that simple methods, such as data augmentation and self-distillation, can elevate Cross entropy Dice loss to surpass most topology loss functions, and that those simple methods can enhance topology loss functions as well. clDice and Skeleton Recall loss, both skeletonization-based loss functions, were also the fastest to train, making this type of loss function a promising research direction. TopoMortar and our code can be found at https://github.com/jmlipman/TopoMortar

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

This work introduces DADAO: the first decentralized, accelerated, asynchronous, primal, first-order algorithm to minimize a sum of L-smooth and mu-strongly convex functions distributed over a given network of size n. Our key insight is based on modeling the local gradient updates and gossip communication procedures with separate independent Poisson Point Processes. This allows us to decouple the computation and communication steps, which can be run in parallel, while making the whole approach completely asynchronous, leading to communication acceleration compared to synchronous approaches. Our new method employs primal gradients and does not use a multi-consensus inner loop nor other ad-hoc mechanisms such as Error Feedback, Gradient Tracking, or a Proximal operator. By relating the inverse of the smallest positive eigenvalue of the Laplacian matrix chi_1 and the maximal resistance chi_2leq chi_1 of the graph to a sufficient minimal communication rate between the nodes of the network, we show that our algorithm requires O(nfrac{L{mu}}log(1{epsilon})) local gradients and only O(nchi_1chi_2frac{L{mu}}log(1{epsilon})) communications to reach a precision epsilon, up to logarithmic terms. Thus, we simultaneously obtain an accelerated rate for both computations and communications, leading to an improvement over state-of-the-art works, our simulations further validating the strength of our relatively unconstrained method. We also propose a SDP relaxation to find the optimal gossip rate of each edge minimizing the total number of communications for a given graph, resulting in faster convergence compared to standard approaches relying on uniform communication weights. Our source code is released on a public repository.

We study Helly graphs of finite combinatorial dimension, i.e. whose injective hull is finite-dimensional. We describe very simple fine simplicial subdivisions of the injective hull of a Helly graph, following work of Lang. We also give a very explicit simplicial model of the injective hull of a Helly graphs, in terms of cliques which are intersections of balls. We use these subdivisions to prove that any automorphism of a Helly graph with finite combinatorial dimension is either elliptic or hyperbolic. Moreover, every such hyperbolic automorphism has an axis in an appropriate Helly subdivision, and its translation length is rational with uniformly bounded denominator.

A key requirement for graph neural networks is that they must process a graph in a way that does not depend on how the graph is described. Traditionally this has been taken to mean that a graph network must be equivariant to node permutations. Here we show that instead of equivariance, the more general concept of naturality is sufficient for a graph network to be well-defined, opening up a larger class of graph networks. We define global and local natural graph networks, the latter of which are as scalable as conventional message passing graph neural networks while being more flexible. We give one practical instantiation of a natural network on graphs which uses an equivariant message network parameterization, yielding good performance on several benchmarks.

Micro-Aerial Vehicles (MAVs) have the advantage of moving freely in 3D space. However, creating compact and sparse map representations that can be efficiently used for planning for such robots is still an open problem. In this paper, we take maps built from noisy sensor data and construct a sparse graph containing topological information that can be used for 3D planning. We use a Euclidean Signed Distance Field, extract a 3D Generalized Voronoi Diagram (GVD), and obtain a thin skeleton diagram representing the topological structure of the environment. We then convert this skeleton diagram into a sparse graph, which we show is resistant to noise and changes in resolution. We demonstrate global planning over this graph, and the orders of magnitude speed-up it offers over other common planning methods. We validate our planning algorithm in real maps built onboard an MAV, using RGB-D sensing.

In 1983, Gromov introduced the notion of distortion of a knot, and asked if there are knots with arbitrarily large distortion. In 2011, Pardon proved that the distortion of T_{p,q} is at least min{p,q} up to a constant factor. We prove that the distortion of T_{p, p+1}# K is at least p up to a constant, independent of K. We also prove that any embedding of a minimal genus Seifert surface for T_{p,p+1}# K in R^3 has small extrinsic systole, in the sense that it contains a non-contractible loop with small R^3-diameter relative to the length of the knot. These results are related to combinatorial properties of the monodromy map associated to torus knots.

Local stochastic gradient descent (Local-SGD), also referred to as federated averaging, is an approach to distributed optimization where each device performs more than one SGD update per communication. This work presents an empirical study of {\it asynchronous} Local-SGD for training language models; that is, each worker updates the global parameters as soon as it has finished its SGD steps. We conduct a comprehensive investigation by examining how worker hardware heterogeneity, model size, number of workers, and optimizer could impact the learning performance. We find that with naive implementations, asynchronous Local-SGD takes more iterations to converge than its synchronous counterpart despite updating the (global) model parameters more frequently. We identify momentum acceleration on the global parameters when worker gradients are stale as a key challenge. We propose a novel method that utilizes a delayed Nesterov momentum update and adjusts the workers' local training steps based on their computation speed. This approach, evaluated with models up to 150M parameters on the C4 dataset, matches the performance of synchronous Local-SGD in terms of perplexity per update step, and significantly surpasses it in terms of wall clock time.

Time series reasoning treats time as a first-class axis and incorporates intermediate evidence directly into the answer. This survey defines the problem and organizes the literature by reasoning topology with three families: direct reasoning in one step, linear chain reasoning with explicit intermediates, and branch-structured reasoning that explores, revises, and aggregates. The topology is crossed with the main objectives of the field, including traditional time series analysis, explanation and understanding, causal inference and decision making, and time series generation, while a compact tag set spans these axes and captures decomposition and verification, ensembling, tool use, knowledge access, multimodality, agent loops, and LLM alignment regimes. Methods and systems are reviewed across domains, showing what each topology enables and where it breaks down in faithfulness or robustness, along with curated datasets, benchmarks, and resources that support study and deployment (https://github.com/blacksnail789521/Time-Series-Reasoning-Survey). Evaluation practices that keep evidence visible and temporally aligned are highlighted, and guidance is distilled on matching topology to uncertainty, grounding with observable artifacts, planning for shift and streaming, and treating cost and latency as design budgets. We emphasize that reasoning structures must balance capacity for grounding and self-correction against computational cost and reproducibility, while future progress will likely depend on benchmarks that tie reasoning quality to utility and on closed-loop testbeds that trade off cost and risk under shift-aware, streaming, and long-horizon settings. Taken together, these directions mark a shift from narrow accuracy toward reliability at scale, enabling systems that not only analyze but also understand, explain, and act on dynamic worlds with traceable evidence and credible outcomes.

The learnability of different neural architectures can be characterized directly by computable measures of data complexity. In this paper, we reframe the problem of architecture selection as understanding how data determines the most expressive and generalizable architectures suited to that data, beyond inductive bias. After suggesting algebraic topology as a measure for data complexity, we show that the power of a network to express the topological complexity of a dataset in its decision region is a strictly limiting factor in its ability to generalize. We then provide the first empirical characterization of the topological capacity of neural networks. Our empirical analysis shows that at every level of dataset complexity, neural networks exhibit topological phase transitions. This observation allowed us to connect existing theory to empirically driven conjectures on the choice of architectures for fully-connected neural networks.

Scene flow estimation predicts the 3D motion at each point in successive LiDAR scans. This detailed, point-level, information can help autonomous vehicles to accurately predict and understand dynamic changes in their surroundings. Current state-of-the-art methods require annotated data to train scene flow networks and the expense of labeling inherently limits their scalability. Self-supervised approaches can overcome the above limitations, yet face two principal challenges that hinder optimal performance: point distribution imbalance and disregard for object-level motion constraints. In this paper, we propose SeFlow, a self-supervised method that integrates efficient dynamic classification into a learning-based scene flow pipeline. We demonstrate that classifying static and dynamic points helps design targeted objective functions for different motion patterns. We also emphasize the importance of internal cluster consistency and correct object point association to refine the scene flow estimation, in particular on object details. Our real-time capable method achieves state-of-the-art performance on the self-supervised scene flow task on Argoverse 2 and Waymo datasets. The code is open-sourced at https://github.com/KTH-RPL/SeFlow along with trained model weights.

Over recent decades, significant advancements in cross-modal retrieval are mainly driven by breakthroughs in visual and linguistic modeling. However, a recent study shows that multi-modal data representations tend to cluster within a limited convex cone (as representation degeneration problem), which hinders retrieval performance due to the inseparability of these representations. In our study, we first empirically validate the presence of the representation degeneration problem across multiple cross-modal benchmarks and methods. Next, to address it, we introduce a novel method, called InvGC, a post-processing technique inspired by graph convolution and average pooling. Specifically, InvGC defines the graph topology within the datasets and then applies graph convolution in a subtractive manner. This method effectively separates representations by increasing the distances between data points. To improve the efficiency and effectiveness of InvGC, we propose an advanced graph topology, LocalAdj, which only aims to increase the distances between each data point and its nearest neighbors. To understand why InvGC works, we present a detailed theoretical analysis, proving that the lower bound of recall will be improved after deploying InvGC. Extensive empirical results show that InvGC and InvGC w/LocalAdj significantly mitigate the representation degeneration problem, thereby enhancing retrieval performance. Our code is available at https://github.com/yimuwangcs/Better_Cross_Modal_Retrieval

Geometric Deep Learning has recently made striking progress with the advent of continuous Deep Implicit Fields. They allow for detailed modeling of watertight surfaces of arbitrary topology while not relying on a 3D Euclidean grid, resulting in a learnable parameterization that is not limited in resolution. Unfortunately, these methods are often not suitable for applications that require an explicit mesh-based surface representation because converting an implicit field to such a representation relies on the Marching Cubes algorithm, which cannot be differentiated with respect to the underlying implicit field. In this work, we remove this limitation and introduce a differentiable way to produce explicit surface mesh representations from Deep Signed Distance Functions. Our key insight is that by reasoning on how implicit field perturbations impact local surface geometry, one can ultimately differentiate the 3D location of surface samples with respect to the underlying deep implicit field. We exploit this to define MeshSDF, an end-to-end differentiable mesh representation which can vary its topology. We use two different applications to validate our theoretical insight: Single-View Reconstruction via Differentiable Rendering and Physically-Driven Shape Optimization. In both cases our differentiable parameterization gives us an edge over state-of-the-art algorithms.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

Masked graph autoencoders have emerged as a powerful graph self-supervised learning method that has yet to be fully explored. In this paper, we unveil that the existing discrete edge masking and binary link reconstruction strategies are insufficient to learn topologically informative representations, from the perspective of message propagation on graph neural networks. These limitations include blocking message flows, vulnerability to over-smoothness, and suboptimal neighborhood discriminability. Inspired by these understandings, we explore non-discrete edge masks, which are sampled from a continuous and dispersive probability distribution instead of the discrete Bernoulli distribution. These masks restrict the amount of output messages for each edge, referred to as "bandwidths". We propose a novel, informative, and effective topological masked graph autoencoder using bandwidth masking and a layer-wise bandwidth prediction objective. We demonstrate its powerful graph topological learning ability both theoretically and empirically. Our proposed framework outperforms representative baselines in both self-supervised link prediction (improving the discrete edge reconstructors by at most 20%) and node classification on numerous datasets, solely with a structure-learning pretext. Our implementation is available at https://github.com/Newiz430/Bandana.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

MeanFlow has recently emerged as a powerful framework for few-step generative modeling trained from scratch, but its success is not yet fully understood. In this work, we show that the MeanFlow objective naturally decomposes into two parts: trajectory flow matching and trajectory consistency. Through gradient analysis, we find that these terms are strongly negatively correlated, causing optimization conflict and slow convergence. Motivated by these insights, we introduce alpha-Flow, a broad family of objectives that unifies trajectory flow matching, Shortcut Model, and MeanFlow under one formulation. By adopting a curriculum strategy that smoothly anneals from trajectory flow matching to MeanFlow, alpha-Flow disentangles the conflicting objectives, and achieves better convergence. When trained from scratch on class-conditional ImageNet-1K 256x256 with vanilla DiT backbones, alpha-Flow consistently outperforms MeanFlow across scales and settings. Our largest alpha-Flow-XL/2+ model achieves new state-of-the-art results using vanilla DiT backbones, with FID scores of 2.58 (1-NFE) and 2.15 (2-NFE).

Generalized Tur\'an problems ask for the maximum number of copies of a graph H in an n-vertex, F-free graph, denoted by ex(n,H,F). We show how to extend the new, localized approach of Bradac, Malec, and Tompkins to generalized Tur\'{a}n problems. We weight the copies of H (typically taking H=K_t), instead of the edges, based on the size of the largest clique, path, or star containing the vertices of the copy of H, and in each case prove a tight upper bound on the sum of the weights. A consequence of our new localized theorems is an asymptotic determination of ex(n,H,K_{1,r}) for every H having at least one dominating vertex and mex(m,H,K_{1,r}) for every H having at least two dominating vertices.

Topology reasoning aims to provide a precise understanding of road scenes, enabling autonomous systems to identify safe and efficient routes. In this paper, we present RoadPainter, an innovative approach for detecting and reasoning the topology of lane centerlines using multi-view images. The core concept behind RoadPainter is to extract a set of points from each centerline mask to improve the accuracy of centerline prediction. We start by implementing a transformer decoder that integrates a hybrid attention mechanism and a real-virtual separation strategy to predict coarse lane centerlines and establish topological associations. Then, we generate centerline instance masks guided by the centerline points from the transformer decoder. Moreover, we derive an additional set of points from each mask and combine them with previously detected centerline points for further refinement. Additionally, we introduce an optional module that incorporates a Standard Definition (SD) map to further optimize centerline detection and enhance topological reasoning performance. Experimental evaluations on the OpenLane-V2 dataset demonstrate the state-of-the-art performance of RoadPainter.

Data-driven modeling of fluid dynamics has advanced rapidly with neural PDE solvers, yet a fair and strong benchmark remains fragmented due to the absence of unified PDE datasets and standardized evaluation protocols. Although architectural innovations are abundant, fair assessment is further impeded by the lack of clear disentanglement between spatial, temporal and loss modules. In this paper, we introduce FD-Bench, the first fair, modular, comprehensive and reproducible benchmark for data-driven fluid simulation. FD-Bench systematically evaluates 85 baseline models across 10 representative flow scenarios under a unified experimental setup. It provides four key contributions: (1) a modular design enabling fair comparisons across spatial, temporal, and loss function modules; (2) the first systematic framework for direct comparison with traditional numerical solvers; (3) fine-grained generalization analysis across resolutions, initial conditions, and temporal windows; and (4) a user-friendly, extensible codebase to support future research. Through rigorous empirical studies, FD-Bench establishes the most comprehensive leaderboard to date, resolving long-standing issues in reproducibility and comparability, and laying a foundation for robust evaluation of future data-driven fluid models. The code is open-sourced at https://anonymous.4open.science/r/FD-Bench-15BC.

We present FrameFlow, a method for fast protein backbone generation using SE(3) flow matching. Specifically, we adapt FrameDiff, a state-of-the-art diffusion model, to the flow-matching generative modeling paradigm. We show how flow matching can be applied on SE(3) and propose modifications during training to effectively learn the vector field. Compared to FrameDiff, FrameFlow requires five times fewer sampling timesteps while achieving two fold better designability. The ability to generate high quality protein samples at a fraction of the cost of previous methods paves the way towards more efficient generative models in de novo protein design.

Despite Flow Matching and diffusion models having emerged as powerful generative paradigms for continuous variables such as images and videos, their application to high-dimensional discrete data, such as language, is still limited. In this work, we present Discrete Flow Matching, a novel discrete flow paradigm designed specifically for generating discrete data. Discrete Flow Matching offers several key contributions: (i) it works with a general family of probability paths interpolating between source and target distributions; (ii) it allows for a generic formula for sampling from these probability paths using learned posteriors such as the probability denoiser (x-prediction) and noise-prediction (epsilon-prediction); (iii) practically, focusing on specific probability paths defined with different schedulers considerably improves generative perplexity compared to previous discrete diffusion and flow models; and (iv) by scaling Discrete Flow Matching models up to 1.7B parameters, we reach 6.7% Pass@1 and 13.4% Pass@10 on HumanEval and 6.7% Pass@1 and 20.6% Pass@10 on 1-shot MBPP coding benchmarks. Our approach is capable of generating high-quality discrete data in a non-autoregressive fashion, significantly closing the gap between autoregressive models and discrete flow models.

Safety-critical applications such as autonomous vehicles and social robots require fast computation and accurate probability density estimation on trajectory prediction. To address both requirements, this paper presents a new normalizing flow-based trajectory prediction model named FlowChain. FlowChain is a stack of conditional continuously-indexed flows (CIFs) that are expressive and allow analytical probability density computation. This analytical computation is faster than the generative models that need additional approximations such as kernel density estimation. Moreover, FlowChain is more accurate than the Gaussian mixture-based models due to fewer assumptions on the estimated density. FlowChain also allows a rapid update of estimated probability densities. This update is achieved by adopting the newest observed position and reusing the flow transformations and its log-det-jacobians that represent the motion trend. This update is completed in less than one millisecond because this reuse greatly omits the computational cost. Experimental results showed our FlowChain achieved state-of-the-art trajectory prediction accuracy compared to previous methods. Furthermore, our FlowChain demonstrated superiority in the accuracy and speed of density estimation. Our code is available at https://github.com/meaten/FlowChain-ICCV2023

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

Generative flow networks (GFlowNets) are a family of algorithms that learn a generative policy to sample discrete objects x with non-negative reward R(x). Learning objectives guarantee the GFlowNet samples x from the target distribution p^*(x) propto R(x) when loss is globally minimized over all states or trajectories, but it is unclear how well they perform with practical limits on training resources. We introduce an efficient evaluation strategy to compare the learned sampling distribution to the target reward distribution. As flows can be underdetermined given training data, we clarify the importance of learned flows to generalization and matching p^*(x) in practice. We investigate how to learn better flows, and propose (i) prioritized replay training of high-reward x, (ii) relative edge flow policy parametrization, and (iii) a novel guided trajectory balance objective, and show how it can solve a substructure credit assignment problem. We substantially improve sample efficiency on biochemical design tasks.

Although polygon meshes have been a standard representation in geometry processing, their irregular and combinatorial nature hinders their suitability for learning-based applications. In this work, we introduce a novel learnable mesh representation through a set of local 3D sample Points and their associated Normals and Quadric error metrics (QEM) w.r.t. the underlying shape, which we denote PoNQ. A global mesh is directly derived from PoNQ by efficiently leveraging the knowledge of the local quadric errors. Besides marking the first use of QEM within a neural shape representation, our contribution guarantees both topological and geometrical properties by ensuring that a PoNQ mesh does not self-intersect and is always the boundary of a volume. Notably, our representation does not rely on a regular grid, is supervised directly by the target surface alone, and also handles open surfaces with boundaries and/or sharp features. We demonstrate the efficacy of PoNQ through a learning-based mesh prediction from SDF grids and show that our method surpasses recent state-of-the-art techniques in terms of both surface and edge-based metrics.

We propose SAM-Road, an adaptation of the Segment Anything Model (SAM) for extracting large-scale, vectorized road network graphs from satellite imagery. To predict graph geometry, we formulate it as a dense semantic segmentation task, leveraging the inherent strengths of SAM. The image encoder of SAM is fine-tuned to produce probability masks for roads and intersections, from which the graph vertices are extracted via simple non-maximum suppression. To predict graph topology, we designed a lightweight transformer-based graph neural network, which leverages the SAM image embeddings to estimate the edge existence probabilities between vertices. Our approach directly predicts the graph vertices and edges for large regions without expensive and complex post-processing heuristics, and is capable of building complete road network graphs spanning multiple square kilometers in a matter of seconds. With its simple, straightforward, and minimalist design, SAM-Road achieves comparable accuracy with the state-of-the-art method RNGDet++, while being 40 times faster on the City-scale dataset. We thus demonstrate the power of a foundational vision model when applied to a graph learning task. The code is available at https://github.com/htcr/sam_road.

Normalizing Flows explicitly maximize a full-dimensional likelihood on the training data. However, real data is typically only supported on a lower-dimensional manifold leading the model to expend significant compute on modeling noise. Injective Flows fix this by jointly learning a manifold and the distribution on it. So far, they have been limited by restrictive architectures and/or high computational cost. We lift both constraints by a new efficient estimator for the maximum likelihood loss, compatible with free-form bottleneck architectures. We further show that naively learning both the data manifold and the distribution on it can lead to divergent solutions, and use this insight to motivate a stable maximum likelihood training objective. We perform extensive experiments on toy, tabular and image data, demonstrating the competitive performance of the resulting model.

This work introduces TopoBenchmarkX, a modular open-source library designed to standardize benchmarking and accelerate research in Topological Deep Learning (TDL). TopoBenchmarkX maps the TDL pipeline into a sequence of independent and modular components for data loading and processing, as well as model training, optimization, and evaluation. This modular organization provides flexibility for modifications and facilitates the adaptation and optimization of various TDL pipelines. A key feature of TopoBenchmarkX is that it allows for the transformation and lifting between topological domains. This enables, for example, to obtain richer data representations and more fine-grained analyses by mapping the topology and features of a graph to higher-order topological domains such as simplicial and cell complexes. The range of applicability of TopoBenchmarkX is demonstrated by benchmarking several TDL architectures for various tasks and datasets.

Triggered by limitations of graph-based deep learning methods in terms of computational expressivity and model flexibility, recent years have seen a surge of interest in computational models that operate on higher-order topological domains such as hypergraphs and simplicial complexes. While the increased expressivity of these models can indeed lead to a better classification performance and a more faithful representation of the underlying system, the computational cost of these higher-order models can increase dramatically. To this end, we here explore a simplicial complex neural network learning architecture based on random walks and fast 1D convolutions (SCRaWl), in which we can adjust the increase in computational cost by varying the length and number of random walks considered while accounting for higher-order relationships. Importantly, due to the random walk-based design, the expressivity of the proposed architecture is provably incomparable to that of existing message-passing simplicial neural networks. We empirically evaluate SCRaWl on real-world datasets and show that it outperforms other simplicial neural networks.

Transport maps can ease the sampling of distributions with non-trivial geometries by transforming them into distributions that are easier to handle. The potential of this approach has risen with the development of Normalizing Flows (NF) which are maps parameterized with deep neural networks trained to push a reference distribution towards a target. NF-enhanced samplers recently proposed blend (Markov chain) Monte Carlo methods with either (i) proposal draws from the flow or (ii) a flow-based reparametrization. In both cases, the quality of the learned transport conditions performance. The present work clarifies for the first time the relative strengths and weaknesses of these two approaches. Our study concludes that multimodal targets can be reliably handled with flow-based proposals up to moderately high dimensions. In contrast, methods relying on reparametrization struggle with multimodality but are more robust otherwise in high-dimensional settings and under poor training. To further illustrate the influence of target-proposal adequacy, we also derive a new quantitative bound for the mixing time of the Independent Metropolis-Hastings sampler.

We present a flow-based approach to the optimal transport (OT) problem between two continuous distributions pi_0,pi_1 on R^d, of minimizing a transport cost E[c(X_1-X_0)] in the set of couplings (X_0,X_1) whose marginal distributions on X_0,X_1 equals pi_0,pi_1, respectively, where c is a cost function. Our method iteratively constructs a sequence of neural ordinary differentiable equations (ODE), each learned by solving a simple unconstrained regression problem, which monotonically reduce the transport cost while automatically preserving the marginal constraints. This yields a monotonic interior approach that traverses inside the set of valid couplings to decrease the transport cost, which distinguishes itself from most existing approaches that enforce the coupling constraints from the outside. The main idea of the method draws from rectified flow, a recent approach that simultaneously decreases the whole family of transport costs induced by convex functions c (and is hence multi-objective in nature), but is not tailored to minimize a specific transport cost. Our method is a single-object variant of rectified flow that guarantees to solve the OT problem for a fixed, user-specified convex cost function c.

In the domain of 3D content creation, achieving optimal mesh topology through AI models has long been a pursuit for 3D artists. Previous methods, such as MeshGPT, have explored the generation of ready-to-use 3D objects via mesh auto-regressive techniques. While these methods produce visually impressive results, their reliance on token-by-token predictions in the auto-regressive process leads to several significant limitations. These include extremely slow generation speeds and an uncontrollable number of mesh faces. In this paper, we introduce MeshCraft, a novel framework for efficient and controllable mesh generation, which leverages continuous spatial diffusion to generate discrete triangle faces. Specifically, MeshCraft consists of two core components: 1) a transformer-based VAE that encodes raw meshes into continuous face-level tokens and decodes them back to the original meshes, and 2) a flow-based diffusion transformer conditioned on the number of faces, enabling the generation of high-quality 3D meshes with a predefined number of faces. By utilizing the diffusion model for the simultaneous generation of the entire mesh topology, MeshCraft achieves high-fidelity mesh generation at significantly faster speeds compared to auto-regressive methods. Specifically, MeshCraft can generate an 800-face mesh in just 3.2 seconds (35times faster than existing baselines). Extensive experiments demonstrate that MeshCraft outperforms state-of-the-art techniques in both qualitative and quantitative evaluations on ShapeNet dataset and demonstrates superior performance on Objaverse dataset. Moreover, it integrates seamlessly with existing conditional guidance strategies, showcasing its potential to relieve artists from the time-consuming manual work involved in mesh creation.

A graph homomorphism is a map between two graphs that preserves adjacency relations. We consider the problem of sampling a random graph homomorphism from a graph into a large network. We propose two complementary MCMC algorithms for sampling random graph homomorphisms and establish bounds on their mixing times and the concentration of their time averages. Based on our sampling algorithms, we propose a novel framework for network data analysis that circumvents some of the drawbacks in methods based on independent and neighborhood sampling. Various time averages of the MCMC trajectory give us various computable observables, including well-known ones such as homomorphism density and average clustering coefficient and their generalizations. Furthermore, we show that these network observables are stable with respect to a suitably renormalized cut distance between networks. We provide various examples and simulations demonstrating our framework through synthetic networks. We also demonstrate the performance of our framework on the tasks of network clustering and subgraph classification on the Facebook100 dataset and on Word Adjacency Networks of a set of classic novels.

We introduce ReMatching, a novel shape correspondence solution based on the functional maps framework. Our method, by exploiting a new and appropriate re-meshing paradigm, can target shape-matching tasks even on meshes counting millions of vertices, where the original functional maps does not apply or requires a massive computational cost. The core of our procedure is a time-efficient remeshing algorithm which constructs a low-resolution geometry while acting conservatively on the original topology and metric. These properties allow translating the functional maps optimization problem on the resulting low-resolution representation, thus enabling efficient computation of correspondences with functional map approaches. Finally, we propose an efficient technique for extending the estimated correspondence to the original meshes. We show that our method is more efficient and effective through quantitative and qualitative comparisons, outperforming state-of-the-art pipelines in quality and computational cost.

Text-to-image (T2I) diffusion/flow models have drawn considerable attention recently due to their remarkable ability to deliver flexible visual creations. Still, high-resolution image synthesis presents formidable challenges due to the scarcity and complexity of high-resolution content. To this end, we present HiFlow, a training-free and model-agnostic framework to unlock the resolution potential of pre-trained flow models. Specifically, HiFlow establishes a virtual reference flow within the high-resolution space that effectively captures the characteristics of low-resolution flow information, offering guidance for high-resolution generation through three key aspects: initialization alignment for low-frequency consistency, direction alignment for structure preservation, and acceleration alignment for detail fidelity. By leveraging this flow-aligned guidance, HiFlow substantially elevates the quality of high-resolution image synthesis of T2I models and demonstrates versatility across their personalized variants. Extensive experiments validate HiFlow's superiority in achieving superior high-resolution image quality over current state-of-the-art methods.

Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over 10^5 nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.

Current diffusion or flow-based generative models for 3D shapes divide to two: distilling pre-trained 2D image diffusion models, and training directly on 3D shapes. When training a diffusion or flow models on 3D shapes a crucial design choice is the shape representation. An effective shape representation needs to adhere three design principles: it should allow an efficient conversion of large 3D datasets to the representation form; it should provide a good tradeoff of approximation power versus number of parameters; and it should have a simple tensorial form that is compatible with existing powerful neural architectures. While standard 3D shape representations such as volumetric grids and point clouds do not adhere to all these principles simultaneously, we advocate in this paper a new representation that does. We introduce Mosaic-SDF (M-SDF): a simple 3D shape representation that approximates the Signed Distance Function (SDF) of a given shape by using a set of local grids spread near the shape's boundary. The M-SDF representation is fast to compute for each shape individually making it readily parallelizable; it is parameter efficient as it only covers the space around the shape's boundary; and it has a simple matrix form, compatible with Transformer-based architectures. We demonstrate the efficacy of the M-SDF representation by using it to train a 3D generative flow model including class-conditioned generation with the 3D Warehouse dataset, and text-to-3D generation using a dataset of about 600k caption-shape pairs.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

Mapping is crucial for spatial reasoning, planning and robot navigation. Existing approaches range from metric, which require precise geometry-based optimization, to purely topological, where image-as-node based graphs lack explicit object-level reasoning and interconnectivity. In this paper, we propose a novel topological representation of an environment based on "image segments", which are semantically meaningful and open-vocabulary queryable, conferring several advantages over previous works based on pixel-level features. Unlike 3D scene graphs, we create a purely topological graph with segments as nodes, where edges are formed by a) associating segment-level descriptors between pairs of consecutive images and b) connecting neighboring segments within an image using their pixel centroids. This unveils a "continuous sense of a place", defined by inter-image persistence of segments along with their intra-image neighbours. It further enables us to represent and update segment-level descriptors through neighborhood aggregation using graph convolution layers, which improves robot localization based on segment-level retrieval. Using real-world data, we show how our proposed map representation can be used to i) generate navigation plans in the form of "hops over segments" and ii) search for target objects using natural language queries describing spatial relations of objects. Furthermore, we quantitatively analyze data association at the segment level, which underpins inter-image connectivity during mapping and segment-level localization when revisiting the same place. Finally, we show preliminary trials on segment-level `hopping' based zero-shot real-world navigation. Project page with supplementary details: oravus.github.io/RoboHop/

Normalizing flows (NFs) have become a prominent method for deep generative models that allow for an analytic probability density estimation and efficient synthesis. However, a flow-based network is considered to be inefficient in parameter complexity because of reduced expressiveness of bijective mapping, which renders the models unfeasibly expensive in terms of parameters. We present an alternative parameterization scheme called NanoFlow, which uses a single neural density estimator to model multiple transformation stages. Hence, we propose an efficient parameter decomposition method and the concept of flow indication embedding, which are key missing components that enable density estimation from a single neural network. Experiments performed on audio and image models confirm that our method provides a new parameter-efficient solution for scalable NFs with significant sublinear parameter complexity.

Guidance of generative models is typically achieved by modifying the probability flow vector field through the addition of a guidance field. In this paper, we instead propose the Source-Guided Flow Matching (SGFM) framework, which modifies the source distribution directly while keeping the pre-trained vector field intact. This reduces the guidance problem to a well-defined problem of sampling from the source distribution. We theoretically show that SGFM recovers the desired target distribution exactly. Furthermore, we provide bounds on the Wasserstein error for the generated distribution when using an approximate sampler of the source distribution and an approximate vector field. The key benefit of our approach is that it allows the user to flexibly choose the sampling method depending on their specific problem. To illustrate this, we systematically compare different sampling methods and discuss conditions for asymptotically exact guidance. Moreover, our framework integrates well with optimal flow matching models since the straight transport map generated by the vector field is preserved. Experimental results on synthetic 2D benchmarks, physics-informed generative tasks, and imaging inverse problems demonstrate the effectiveness and flexibility of the proposed framework.

For any closed hyperbolic Riemann surface X, we show that the extremal length of the Liouville current is determined solely by the topology of \(X\). This confirms a conjecture of Mart\'inez-Granado and Thurston. We also obtain an upper bound, depending only on X, for the diameter of extremal metrics on X with area one.

A suitable feature representation that can both preserve the data intrinsic information and reduce data complexity and dimensionality is key to the performance of machine learning models. Deeply rooted in algebraic topology, persistent homology (PH) provides a delicate balance between data simplification and intrinsic structure characterization, and has been applied to various areas successfully. However, the combination of PH and machine learning has been hindered greatly by three challenges, namely topological representation of data, PH-based distance measurements or metrics, and PH-based feature representation. With the development of topological data analysis, progresses have been made on all these three problems, but widely scattered in different literatures. In this paper, we provide a systematical review of PH and PH-based supervised and unsupervised models from a computational perspective. Our emphasizes are the recent development of mathematical models and tools, including PH softwares and PH-based functions, feature representations, kernels, and similarity models. Essentially, this paper can work as a roadmap for the practical application of PH-based machine learning tools. Further, we consider different topological feature representations in different machine learning models, and investigate their impacts on the protein secondary structure classification.

A Sheaf Neural Network (SNN) is a type of Graph Neural Network (GNN) that operates on a sheaf, an object that equips a graph with vector spaces over its nodes and edges and linear maps between these spaces. SNNs have been shown to have useful theoretical properties that help tackle issues arising from heterophily and over-smoothing. One complication intrinsic to these models is finding a good sheaf for the task to be solved. Previous works proposed two diametrically opposed approaches: manually constructing the sheaf based on domain knowledge and learning the sheaf end-to-end using gradient-based methods. However, domain knowledge is often insufficient, while learning a sheaf could lead to overfitting and significant computational overhead. In this work, we propose a novel way of computing sheaves drawing inspiration from Riemannian geometry: we leverage the manifold assumption to compute manifold-and-graph-aware orthogonal maps, which optimally align the tangent spaces of neighbouring data points. We show that this approach achieves promising results with less computational overhead when compared to previous SNN models. Overall, this work provides an interesting connection between algebraic topology and differential geometry, and we hope that it will spark future research in this direction.

Federated learning is an active research topic since it enables several participants to jointly train a model without sharing local data. Currently, cross-silo federated learning is a popular training setting that utilizes a few hundred reliable data silos with high-speed access links to training a model. While this approach has been widely applied in real-world scenarios, designing a robust topology to reduce the training time remains an open problem. In this paper, we present a new multigraph topology for cross-silo federated learning. We first construct the multigraph using the overlay graph. We then parse this multigraph into different simple graphs with isolated nodes. The existence of isolated nodes allows us to perform model aggregation without waiting for other nodes, hence effectively reducing the training time. Intensive experiments on three public datasets show that our proposed method significantly reduces the training time compared with recent state-of-the-art topologies while maintaining the accuracy of the learned model. Our code can be found at https://github.com/aioz-ai/MultigraphFL

We present a novel generative 3D modeling system, coined CraftsMan, which can generate high-fidelity 3D geometries with highly varied shapes, regular mesh topologies, and detailed surfaces, and, notably, allows for refining the geometry in an interactive manner. Despite the significant advancements in 3D generation, existing methods still struggle with lengthy optimization processes, irregular mesh topologies, noisy surfaces, and difficulties in accommodating user edits, consequently impeding their widespread adoption and implementation in 3D modeling software. Our work is inspired by the craftsman, who usually roughs out the holistic figure of the work first and elaborates the surface details subsequently. Specifically, we employ a 3D native diffusion model, which operates on latent space learned from latent set-based 3D representations, to generate coarse geometries with regular mesh topology in seconds. In particular, this process takes as input a text prompt or a reference image and leverages a powerful multi-view (MV) diffusion model to generate multiple views of the coarse geometry, which are fed into our MV-conditioned 3D diffusion model for generating the 3D geometry, significantly improving robustness and generalizability. Following that, a normal-based geometry refiner is used to significantly enhance the surface details. This refinement can be performed automatically, or interactively with user-supplied edits. Extensive experiments demonstrate that our method achieves high efficacy in producing superior-quality 3D assets compared to existing methods. HomePage: https://craftsman3d.github.io/, Code: https://github.com/wyysf-98/CraftsMan

We study the scaling properties of avalanche activity in the two-dimensional Abelian sandpile model. Instead of the conventional avalanche size distribution, we analyze the site activity distribution, which measures how often a site participates in avalanches when grains are added across the lattice. Using numerical simulations for system sizes up to \(L = 160\), averaged over \(10^4\) configurations, we determine the probability distribution \(P(A, L)\) of site activities. The results show that \(P(A, L)\) follows a finite-size scaling form \[ P(A, L) \sim L^{-2} F\Big(A{L^2}\Big). \] For small values \(A \ll L^2\) the scaling function behaves as \[ F(u) \sim u^{-1/2}, \quad corresponding to \quad P(A) \sim 1{L}, \] while for large activities \(A \sim O(L^2)\) the distribution decays as \[ F(u) \sim \exp\big(-c_3 u - c_4 u^2\big). \] The crossover between these two regimes occurs at \[ A^* \sim 0.1 \, L^2, \] marking the threshold between typical and highly excitable sites. This characterization of local avalanche activity provides complementary information to the usual avalanche size statistics, highlighting how local regions serve as frequent conduits for critical dynamics. These results may help connect sandpile models to real-world self-organized critical systems where only partial local activity can be observed.

Flow matching has recently emerged as a powerful alternative to diffusion models, providing a continuous-time formulation for generative modeling and representation learning. Yet, we show that this framework suffers from a fundamental instability in the low-noise regime. As noise levels approach zero, arbitrarily small perturbations in the input can induce large variations in the velocity target, causing the condition number of the learning problem to diverge. This ill-conditioning not only slows optimization but also forces the encoder to reallocate its limited Jacobian capacity toward noise directions, thereby degrading semantic representations. We provide the first theoretical analysis of this phenomenon, which we term the low-noise pathology, establishing its intrinsic link to the structure of the flow matching objective. Building on these insights, we propose Local Contrastive Flow (LCF), a hybrid training protocol that replaces direct velocity regression with contrastive feature alignment at small noise levels, while retaining standard flow matching at moderate and high noise. Empirically, LCF not only improves convergence speed but also stabilizes representation quality. Our findings highlight the critical importance of addressing low-noise pathologies to unlock the full potential of flow matching for both generation and representation learning.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

We propose a principled and effective framework for one-step generative modeling. We introduce the notion of average velocity to characterize flow fields, in contrast to instantaneous velocity modeled by Flow Matching methods. A well-defined identity between average and instantaneous velocities is derived and used to guide neural network training. Our method, termed the MeanFlow model, is self-contained and requires no pre-training, distillation, or curriculum learning. MeanFlow demonstrates strong empirical performance: it achieves an FID of 3.43 with a single function evaluation (1-NFE) on ImageNet 256x256 trained from scratch, significantly outperforming previous state-of-the-art one-step diffusion/flow models. Our study substantially narrows the gap between one-step diffusion/flow models and their multi-step predecessors, and we hope it will motivate future research to revisit the foundations of these powerful models.

This paper studies generative flow networks (GFlowNets) to sample objects from the Boltzmann energy distribution via a sequence of actions. In particular, we focus on improving GFlowNet with partial inference: training flow functions with the evaluation of the intermediate states or transitions. To this end, the recently developed forward-looking GFlowNet reparameterizes the flow functions based on evaluating the energy of intermediate states. However, such an evaluation of intermediate energies may (i) be too expensive or impossible to evaluate and (ii) even provide misleading training signals under large energy fluctuations along the sequence of actions. To resolve this issue, we propose learning energy decompositions for GFlowNets (LED-GFN). Our main idea is to (i) decompose the energy of an object into learnable potential functions defined on state transitions and (ii) reparameterize the flow functions using the potential functions. In particular, to produce informative local credits, we propose to regularize the potential to change smoothly over the sequence of actions. It is also noteworthy that training GFlowNet with our learned potential can preserve the optimal policy. We empirically verify the superiority of LED-GFN in five problems including the generation of unstructured and maximum independent sets, molecular graphs, and RNA sequences.

Grid-based structures are commonly used to encode explicit features for graphics primitives such as images, signed distance functions (SDF), and neural radiance fields (NeRF) due to their simple implementation. However, in n-dimensional space, calculating the value of a sampled point requires interpolating the values of its 2^n neighboring vertices. The exponential scaling with dimension leads to significant computational overheads. To address this issue, we propose a simplex-based approach for encoding graphics primitives. The number of vertices in a simplex-based structure increases linearly with dimension, making it a more efficient and generalizable alternative to grid-based representations. Using the non-axis-aligned simplicial structure property, we derive and prove a coordinate transformation, simplicial subdivision, and barycentric interpolation scheme for efficient sampling, which resembles transformation procedures in the simplex noise algorithm. Finally, we use hash tables to store multiresolution features of all interest points in the simplicial grid, which are passed into a tiny fully connected neural network to parameterize graphics primitives. We implemented a detailed simplex-based structure encoding algorithm in C++ and CUDA using the methods outlined in our approach. In the 2D image fitting task, the proposed method is capable of fitting a giga-pixel image with 9.4% less time compared to the baseline method proposed by instant-ngp, while maintaining the same quality and compression rate. In the volumetric rendering setup, we observe a maximum 41.2% speedup when the samples are dense enough.

Mechanically interlocked polymers (MIPs) are a novel class of polymer structures in which the components are connected by mechanical bonds instead of covalent bonds. We measure the single-molecule rheological properties of polyrotaxanes, daisy chains, and polycatenanes under steady shear and steady uniaxial extension using coarse-grained Brownian dynamics simulations with hydrodynamic interactions. We obtain key rheological features, including tumbling dynamics, molecular extension, stress, and viscosity. By systematically varying structural features, we demonstrate how MIP topology governs flow response. Compared to linear polymers, all three MIP architectures exhibit enhanced tumbling in shear flow and lower normal stress differences in extensional flow. While polyrotaxanes show higher shear and extensional viscosities, polycatenanes and daisy chains have lower viscosities. In extensional flow, polyrotaxanes and polycatenanes extend earlier than linear polymers. We find that mechanical bonds suppress shear thinning and alter the coil-stretch transition observed in linear polymers. These effects arise from the mechanically bonded rings in MIPs, which expand the polymer profile in gradient direction and increase backbone stiffness due to ring-backbone repulsions. This study provides key insights into MIP flow properties, providing the foundation for their systematic development in engineering applications.

Geometric Deep Learning has recently made striking progress with the advent of continuous deep implicit fields. They allow for detailed modeling of watertight surfaces of arbitrary topology while not relying on a 3D Euclidean grid, resulting in a learnable parameterization that is unlimited in resolution. Unfortunately, these methods are often unsuitable for applications that require an explicit mesh-based surface representation because converting an implicit field to such a representation relies on the Marching Cubes algorithm, which cannot be differentiated with respect to the underlying implicit field. In this work, we remove this limitation and introduce a differentiable way to produce explicit surface mesh representations from Deep Implicit Fields. Our key insight is that by reasoning on how implicit field perturbations impact local surface geometry, one can ultimately differentiate the 3D location of surface samples with respect to the underlying deep implicit field. We exploit this to define DeepMesh - an end-to-end differentiable mesh representation that can vary its topology. We validate our theoretical insight through several applications: Single view 3D Reconstruction via Differentiable Rendering, Physically-Driven Shape Optimization, Full Scene 3D Reconstruction from Scans and End-to-End Training. In all cases our end-to-end differentiable parameterization gives us an edge over state-of-the-art algorithms.

The conjugate gradient method is a crucial first-order optimization method that generally converges faster than the steepest descent method, and its computational cost is much lower than that of second-order methods. However, while various types of conjugate gradient methods have been studied in Euclidean spaces and on Riemannian manifolds, there is little study for those in distributed scenarios. This paper proposes a decentralized Riemannian conjugate gradient descent (DRCGD) method that aims at minimizing a global function over the Stiefel manifold. The optimization problem is distributed among a network of agents, where each agent is associated with a local function, and the communication between agents occurs over an undirected connected graph. Since the Stiefel manifold is a non-convex set, a global function is represented as a finite sum of possibly non-convex (but smooth) local functions. The proposed method is free from expensive Riemannian geometric operations such as retractions, exponential maps, and vector transports, thereby reducing the computational complexity required by each agent. To the best of our knowledge, DRCGD is the first decentralized Riemannian conjugate gradient algorithm to achieve global convergence over the Stiefel manifold.

In centralized settings, it is well known that stochastic gradient descent (SGD) avoids saddle points and converges to local minima in nonconvex problems. However, similar guarantees are lacking for distributed first-order algorithms. The paper studies distributed stochastic gradient descent (D-SGD)--a simple network-based implementation of SGD. Conditions under which D-SGD avoids saddle points and converges to local minima are studied. First, we consider the problem of computing critical points. Assuming loss functions are nonconvex and possibly nonsmooth, it is shown that, for each fixed initialization, D-SGD converges to critical points of the loss with probability one. Next, we consider the problem of avoiding saddle points. In this case, we again assume that loss functions may be nonconvex and nonsmooth, but are smooth in a neighborhood of a saddle point. It is shown that, for any fixed initialization, D-SGD avoids such saddle points with probability one. Results are proved by studying the underlying (distributed) gradient flow, using the ordinary differential equation (ODE) method of stochastic approximation, and extending classical techniques from dynamical systems theory such as stable manifolds. Results are proved in the general context of subspace-constrained optimization, of which D-SGD is a special case.

We consider the incompressible Euler and Navier-Stokes equations on the three dimensional torus, in velocity form, perturbed by a transport or transport-stretching Stratonovich noise. Closed control of the noise contributions in energy estimates are demonstrated, for any positive integer ordered Sobolev Space and the equivalent Stokes Space; difficulty arises due to the presence of the Leray Projector disrupting cancellation of the top order derivative. This is particularly pertinent in the case of a transport noise without stretching, where the vorticity form cannot be used. As a consequence we obtain, for the first time, the existence of a local strong solution to the corresponding stochastic Euler equation. Furthermore, smooth solutions are shown to exist until blow-up in L^1left([0,T];W^{1,infty}right).

We present a new approach for the approximate K-nearest neighbor search based on navigable small world graphs with controllable hierarchy (Hierarchical NSW, HNSW). The proposed solution is fully graph-based, without any need for additional search structures, which are typically used at the coarse search stage of the most proximity graph techniques. Hierarchical NSW incrementally builds a multi-layer structure consisting from hierarchical set of proximity graphs (layers) for nested subsets of the stored elements. The maximum layer in which an element is present is selected randomly with an exponentially decaying probability distribution. This allows producing graphs similar to the previously studied Navigable Small World (NSW) structures while additionally having the links separated by their characteristic distance scales. Starting search from the upper layer together with utilizing the scale separation boosts the performance compared to NSW and allows a logarithmic complexity scaling. Additional employment of a heuristic for selecting proximity graph neighbors significantly increases performance at high recall and in case of highly clustered data. Performance evaluation has demonstrated that the proposed general metric space search index is able to strongly outperform previous opensource state-of-the-art vector-only approaches. Similarity of the algorithm to the skip list structure allows straightforward balanced distributed implementation.

Toward infinite-scale 3D city synthesis, we propose a novel framework, InfiniCity, which constructs and renders an unconstrainedly large and 3D-grounded environment from random noises. InfiniCity decomposes the seemingly impractical task into three feasible modules, taking advantage of both 2D and 3D data. First, an infinite-pixel image synthesis module generates arbitrary-scale 2D maps from the bird's-eye view. Next, an octree-based voxel completion module lifts the generated 2D map to 3D octrees. Finally, a voxel-based neural rendering module texturizes the voxels and renders 2D images. InfiniCity can thus synthesize arbitrary-scale and traversable 3D city environments, and allow flexible and interactive editing from users. We quantitatively and qualitatively demonstrate the efficacy of the proposed framework. Project page: https://hubert0527.github.io/infinicity/

Recently, an intriguing class of non-convex optimization problems has emerged in the context of learning directed acyclic graphs (DAGs). These problems involve minimizing a given loss or score function, subject to a non-convex continuous constraint that penalizes the presence of cycles in a graph. In this work, we delve into the optimization challenges associated with this class of non-convex programs. To address these challenges, we propose a bi-level algorithm that leverages the non-convex constraint in a novel way. The outer level of the algorithm optimizes over topological orders by iteratively swapping pairs of nodes within the topological order of a DAG. A key innovation of our approach is the development of an effective method for generating a set of candidate swapping pairs for each iteration. At the inner level, given a topological order, we utilize off-the-shelf solvers that can handle linear constraints. The key advantage of our proposed algorithm is that it is guaranteed to find a local minimum or a KKT point under weaker conditions compared to previous work and finds solutions with lower scores. Extensive experiments demonstrate that our method outperforms state-of-the-art approaches in terms of achieving a better score. Additionally, our method can also be used as a post-processing algorithm to significantly improve the score of other algorithms. Code implementing the proposed method is available at https://github.com/duntrain/topo.

Tangles were originally introduced as a concept to formalize regions of high connectivity in graphs. In recent years, they have also been discovered as a link between structural graph theory and data science: when interpreting similarity in data sets as connectivity between points, finding clusters in the data essentially amounts to finding tangles in the underlying graphs. This paper further explores the potential of tangles in data sets as a means for a formal study of clusters. Real-world data often follow a normal distribution. Accounting for this, we develop a quantitative theory of tangles in data sets drawn from Gaussian mixtures. To this end, we equip the data with a graph structure that models similarity between the points and allows us to apply tangle theory to the data. We provide explicit conditions under which tangles associated with the marginal Gaussian distributions exist asymptotically almost surely. This can be considered as a sufficient formal criterion for the separabability of clusters in the data.

We present rectified flow, a surprisingly simple approach to learning (neural) ordinary differential equation (ODE) models to transport between two empirically observed distributions \pi_0 and \pi_1, hence providing a unified solution to generative modeling and domain transfer, among various other tasks involving distribution transport. The idea of rectified flow is to learn the ODE to follow the straight paths connecting the points drawn from \pi_0 and \pi_1 as much as possible. This is achieved by solving a straightforward nonlinear least squares optimization problem, which can be easily scaled to large models without introducing extra parameters beyond standard supervised learning. The straight paths are special and preferred because they are the shortest paths between two points, and can be simulated exactly without time discretization and hence yield computationally efficient models. We show that the procedure of learning a rectified flow from data, called rectification, turns an arbitrary coupling of \pi_0 and \pi_1 to a new deterministic coupling with provably non-increasing convex transport costs. In addition, recursively applying rectification allows us to obtain a sequence of flows with increasingly straight paths, which can be simulated accurately with coarse time discretization in the inference phase. In empirical studies, we show that rectified flow performs superbly on image generation, image-to-image translation, and domain adaptation. In particular, on image generation and translation, our method yields nearly straight flows that give high quality results even with a single Euler discretization step.

This monograph presents the core principles that have guided the development of diffusion models, tracing their origins and showing how diverse formulations arise from shared mathematical ideas. Diffusion modeling starts by defining a forward process that gradually corrupts data into noise, linking the data distribution to a simple prior through a continuum of intermediate distributions. The goal is to learn a reverse process that transforms noise back into data while recovering the same intermediates. We describe three complementary views. The variational view, inspired by variational autoencoders, sees diffusion as learning to remove noise step by step. The score-based view, rooted in energy-based modeling, learns the gradient of the evolving data distribution, indicating how to nudge samples toward more likely regions. The flow-based view, related to normalizing flows, treats generation as following a smooth path that moves samples from noise to data under a learned velocity field. These perspectives share a common backbone: a time-dependent velocity field whose flow transports a simple prior to the data. Sampling then amounts to solving a differential equation that evolves noise into data along a continuous trajectory. On this foundation, the monograph discusses guidance for controllable generation, efficient numerical solvers, and diffusion-motivated flow-map models that learn direct mappings between arbitrary times. It provides a conceptual and mathematically grounded understanding of diffusion models for readers with basic deep-learning knowledge.

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the topological properties of graphs since learning to denoise the noisy samples does not explicitly learn the graph structures to be generated. To tackle this limitation, we propose a generative framework that models the topology of graphs by explicitly learning the final graph structures of the diffusion process. Specifically, we design the generative process as a mixture of endpoint-conditioned diffusion processes which is driven toward the predicted graph that results in rapid convergence. We further introduce a simple parameterization of the mixture process and develop an objective for learning the final graph structure, which enables maximum likelihood training. Through extensive experimental validation on general graph and 2D/3D molecule generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous (e.g. 3D coordinates) and discrete (e.g. atom types) features. Our code is available at https://github.com/harryjo97/GruM.

Complex networks can be used for modeling street meshes and urban agglomerates. With such a model, many aspects of a city can be investigated to promote a better quality of life to its citizens. Along these lines, this paper proposes a set of distance-based pattern-discovery algorithmic instruments to improve urban structures modeled as complex networks, detecting nodes that lack access from/to points of interest in a given city. Furthermore, we introduce a greedy algorithm that is able to recommend improvements to the structure of a city by suggesting where points of interest are to be placed. We contribute to a thorough process to deal with complex networks, including mathematical modeling and algorithmic innovation. The set of our contributions introduces a systematic manner to treat a recurrent problem of broad interest in cities.

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first multi-modal deep generative model grounded in the flow-matching framework for the design of full-atom peptides that target specific protein receptors. Drawing inspiration from the crucial roles of residue backbone orientations and side-chain dynamics in protein-peptide interactions, we characterize the peptide structure using rigid backbone frames within the SE(3) manifold and side-chain angles on high-dimensional tori. Furthermore, we represent discrete residue types in the peptide sequence as categorical distributions on the probability simplex. By learning the joint distributions of each modality using derived flows and vector fields on corresponding manifolds, our method excels in the fine-grained design of full-atom peptides. Harnessing the multi-modal paradigm, our approach adeptly tackles various tasks such as fix-backbone sequence design and side-chain packing through partial sampling. Through meticulously crafted experiments, we demonstrate that PepFlow exhibits superior performance in comprehensive benchmarks, highlighting its significant potential in computational peptide design and analysis.

Crystalline materials are a fundamental component in next-generation technologies, yet modeling their distribution presents unique computational challenges. Of the plausible arrangements of atoms in a periodic lattice only a vanishingly small percentage are thermodynamically stable, which is a key indicator of the materials that can be experimentally realized. Two fundamental tasks in this area are to (a) predict the stable crystal structure of a known composition of elements and (b) propose novel compositions along with their stable structures. We present FlowMM, a pair of generative models that achieve state-of-the-art performance on both tasks while being more efficient and more flexible than competing methods. We generalize Riemannian Flow Matching to suit the symmetries inherent to crystals: translation, rotation, permutation, and periodic boundary conditions. Our framework enables the freedom to choose the flow base distributions, drastically simplifying the problem of learning crystal structures compared with diffusion models. In addition to standard benchmarks, we validate FlowMM's generated structures with quantum chemistry calculations, demonstrating that it is about 3x more efficient, in terms of integration steps, at finding stable materials compared to previous open methods.

Consider a random uniform sample of n points in a compact region A of Euclidean d-space, d geq 2, with a smooth or (when d=2) polygonal boundary. Fix k bf N. Let T_{n,k} be the threshold r at which the geometric graph on these n vertices with distance parameter r becomes k-connected. We show that if d=2 then n (pi/|A|) T_{n,1}^2 - log n is asymptotically standard Gumbel. For (d,k) neq (2,1), it is n (theta_d/|A|) T_{n,k}^d - (2-2/d) log n - (4-2k-2/d) log log n that converges in distribution to a nondegenerate limit, where theta_d is the volume of the unit ball. The limit is Gumbel with scale parameter 2 except when (d,k)=(2,2) where the limit is two component extreme value distributed. The different cases reflect the fact that boundary effects are more more important in some cases than others. We also give similar results for the largest k-nearest neighbour link U_{n,k} in the sample, and show T_{n,k}=U_{n,k} with high probability. We provide estimates on rates of convergence and give similar results for Poisson samples in A. Finally, we give similar results even for non-uniform samples, with a less explicit sequence of centring constants.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

We introduce Clifford Group Equivariant Simplicial Message Passing Networks, a method for steerable E(n)-equivariant message passing on simplicial complexes. Our method integrates the expressivity of Clifford group-equivariant layers with simplicial message passing, which is topologically more intricate than regular graph message passing. Clifford algebras include higher-order objects such as bivectors and trivectors, which express geometric features (e.g., areas, volumes) derived from vectors. Using this knowledge, we represent simplex features through geometric products of their vertices. To achieve efficient simplicial message passing, we share the parameters of the message network across different dimensions. Additionally, we restrict the final message to an aggregation of the incoming messages from different dimensions, leading to what we term shared simplicial message passing. Experimental results show that our method is able to outperform both equivariant and simplicial graph neural networks on a variety of geometric tasks.

Image segmentation is a largely researched field where neural networks find vast applications in many facets of technology. Some of the most popular approaches to train segmentation networks employ loss functions optimizing pixel-overlap, an objective that is insufficient for many segmentation tasks. In recent years, their limitations fueled a growing interest in topology-aware methods, which aim to recover the correct topology of the segmented structures. However, so far, none of the existing approaches achieve a spatially correct matching between the topological features of ground truth and prediction. In this work, we propose the first topologically and feature-wise accurate metric and loss function for supervised image segmentation, which we term Betti matching. We show how induced matchings guarantee the spatially correct matching between barcodes in a segmentation setting. Furthermore, we propose an efficient algorithm to compute the Betti matching of images. We show that the Betti matching error is an interpretable metric to evaluate the topological correctness of segmentations, which is more sensitive than the well-established Betti number error. Moreover, the differentiability of the Betti matching loss enables its use as a loss function. It improves the topological performance of segmentation networks across six diverse datasets while preserving the volumetric performance. Our code is available in https://github.com/nstucki/Betti-matching.

As the most common representation for 3D shapes, mesh is often stored discretely with arrays of vertices and faces. However, 3D shapes in the real world are presented continuously. In this paper, we propose to learn a continuous representation for meshes with fixed topology, a common and practical setting in many faces-, hand-, and body-related applications. First, we split the template into multiple closed manifold genus-0 meshes so that each genus-0 mesh can be parameterized onto the unit sphere. Then we learn spherical implicit surface (SIS), which takes a spherical coordinate and a global feature or a set of local features around the coordinate as inputs, predicting the vertex corresponding to the coordinate as an output. Since the spherical coordinates are continuous, SIS can depict a mesh in an arbitrary resolution. SIS representation builds a bridge between discrete and continuous representation in 3D shapes. Specifically, we train SIS networks in a self-supervised manner for two tasks: a reconstruction task and a super-resolution task. Experiments show that our SIS representation is comparable with state-of-the-art methods that are specifically designed for meshes with a fixed resolution and significantly outperforms methods that work in arbitrary resolutions.

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these approaches encode, as well as performance trade-offs between them. However, the question of which structural properties yield the most effective encoding remains open. In this paper, we investigate this question from a geometric perspective. We propose a novel structural encoding based on discrete Ricci curvature (Local Curvature Profiles, short LCP) and show that it significantly outperforms existing encoding approaches. We further show that combining local structural encodings, such as LCP, with global positional encodings improves downstream performance, suggesting that they capture complementary geometric information. Finally, we compare different encoding types with (curvature-based) rewiring techniques. Rewiring has recently received a surge of interest due to its ability to improve the performance of Graph Neural Networks by mitigating over-smoothing and over-squashing effects. Our results suggest that utilizing curvature information for structural encodings delivers significantly larger performance increases than rewiring.

Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using rotation-equivariant operations. However, contrary to images, graphs generally have irregular topology. This makes it challenging to define a rotation-equivariant convolution operation on these structures. In this work, we propose Spherical Graph Convolutional Network (S-GCN) that processes 3D models of proteins represented as molecular graphs. In a protein molecule, individual amino acids have common topological elements. This allows us to unambiguously associate each amino acid with a local coordinate system and construct rotation-equivariant spherical filters that operate on angular information between graph nodes. Within the framework of the protein model quality assessment problem, we demonstrate that the proposed spherical convolution method significantly improves the quality of model assessment compared to the standard message-passing approach. It is also comparable to state-of-the-art methods, as we demonstrate on Critical Assessment of Structure Prediction (CASP) benchmarks. The proposed technique operates only on geometric features of protein 3D models. This makes it universal and applicable to any other geometric-learning task where the graph structure allows constructing local coordinate systems.

This paper investigates the generalization of Principal Component Analysis (PCA) to Riemannian manifolds. We first propose a new and general type of family of subspaces in manifolds that we call barycentric subspaces. They are implicitly defined as the locus of points which are weighted means of k+1 reference points. As this definition relies on points and not on tangent vectors, it can also be extended to geodesic spaces which are not Riemannian. For instance, in stratified spaces, it naturally allows principal subspaces that span several strata, which is impossible in previous generalizations of PCA. We show that barycentric subspaces locally define a submanifold of dimension k which generalizes geodesic subspaces.Second, we rephrase PCA in Euclidean spaces as an optimization on flags of linear subspaces (a hierarchy of properly embedded linear subspaces of increasing dimension). We show that the Euclidean PCA minimizes the Accumulated Unexplained Variances by all the subspaces of the flag (AUV). Barycentric subspaces are naturally nested, allowing the construction of hierarchically nested subspaces. Optimizing the AUV criterion to optimally approximate data points with flags of affine spans in Riemannian manifolds lead to a particularly appealing generalization of PCA on manifolds called Barycentric Subspaces Analysis (BSA).

Traffic signal control is an emerging application scenario for reinforcement learning. Besides being as an important problem that affects people's daily life in commuting, traffic signal control poses its unique challenges for reinforcement learning in terms of adapting to dynamic traffic environment and coordinating thousands of agents including vehicles and pedestrians. A key factor in the success of modern reinforcement learning relies on a good simulator to generate a large number of data samples for learning. The most commonly used open-source traffic simulator SUMO is, however, not scalable to large road network and large traffic flow, which hinders the study of reinforcement learning on traffic scenarios. This motivates us to create a new traffic simulator CityFlow with fundamentally optimized data structures and efficient algorithms. CityFlow can support flexible definitions for road network and traffic flow based on synthetic and real-world data. It also provides user-friendly interface for reinforcement learning. Most importantly, CityFlow is more than twenty times faster than SUMO and is capable of supporting city-wide traffic simulation with an interactive render for monitoring. Besides traffic signal control, CityFlow could serve as the base for other transportation studies and can create new possibilities to test machine learning methods in the intelligent transportation domain.

The topology of the hyperlink graph among pages expressing different opinions may influence the exposure of readers to diverse content. Structural bias may trap a reader in a polarized bubble with no access to other opinions. We model readers' behavior as random walks. A node is in a polarized bubble if the expected length of a random walk from it to a page of different opinion is large. The structural bias of a graph is the sum of the radii of highly-polarized bubbles. We study the problem of decreasing the structural bias through edge insertions. Healing all nodes with high polarized bubble radius is hard to approximate within a logarithmic factor, so we focus on finding the best k edges to insert to maximally reduce the structural bias. We present RePBubLik, an algorithm that leverages a variant of the random walk closeness centrality to select the edges to insert. RePBubLik obtains, under mild conditions, a constant-factor approximation. It reduces the structural bias faster than existing edge-recommendation methods, including some designed to reduce the polarization of a graph.

Flow-based generative models are powerful exact likelihood models with efficient sampling and inference. Despite their computational efficiency, flow-based models generally have much worse density modeling performance compared to state-of-the-art autoregressive models. In this paper, we investigate and improve upon three limiting design choices employed by flow-based models in prior work: the use of uniform noise for dequantization, the use of inexpressive affine flows, and the use of purely convolutional conditioning networks in coupling layers. Based on our findings, we propose Flow++, a new flow-based model that is now the state-of-the-art non-autoregressive model for unconditional density estimation on standard image benchmarks. Our work has begun to close the significant performance gap that has so far existed between autoregressive models and flow-based models. Our implementation is available at https://github.com/aravindsrinivas/flowpp

Scene flow estimation is a long-standing problem in computer vision, where the goal is to find the 3D motion of a scene from its consecutive observations. Recently, there have been efforts to compute the scene flow from 3D point clouds. A common approach is to train a regression model that consumes source and target point clouds and outputs the per-point translation vector. An alternative is to learn point matches between the point clouds concurrently with regressing a refinement of the initial correspondence flow. In both cases, the learning task is very challenging since the flow regression is done in the free 3D space, and a typical solution is to resort to a large annotated synthetic dataset. We introduce SCOOP, a new method for scene flow estimation that can be learned on a small amount of data without employing ground-truth flow supervision. In contrast to previous work, we train a pure correspondence model focused on learning point feature representation and initialize the flow as the difference between a source point and its softly corresponding target point. Then, in the run-time phase, we directly optimize a flow refinement component with a self-supervised objective, which leads to a coherent and accurate flow field between the point clouds. Experiments on widespread datasets demonstrate the performance gains achieved by our method compared to existing leading techniques while using a fraction of the training data. Our code is publicly available at https://github.com/itailang/SCOOP.

Latent heat thermal energy storage (LHTES) systems are compelling candidates for energy storage, primarily owing to their high storage density. Improving their performance is crucial for developing the next-generation efficient and cost effective devices. Topology optimization (TO) has emerged as a powerful computational tool to design LHTES systems by optimally distributing a high-conductivity material (HCM) and a phase change material (PCM). However, conventional TO typically limits to optimizing the geometry for a fixed, pre-selected materials. This approach does not leverage the large and expanding databases of novel materials. Consequently, the co-design of material and geometry for LHTES remains a challenge and unexplored. To address this limitation, we present an automated design framework for the concurrent optimization of material choice and topology. A key challenge is the discrete nature of material selection, which is incompatible with the gradient-based methods used for TO. We overcome this by using a data-driven variational autoencoder (VAE) to project discrete material databases for both the HCM and PCM onto continuous and differentiable latent spaces. These continuous material representations are integrated into an end-to-end differentiable, transient nonlinear finite-element solver that accounts for phase change. We demonstrate this framework on a problem aimed at maximizing the discharged energy within a specified time, subject to cost constraints. The effectiveness of the proposed method is validated through several illustrative examples.