Neural networks (NNs), despite their success and wide adoption, still struggle to extrapolate out-of-distribution (OOD), i.e., to inputs that are not well-represented by their training dataset. Addressing the OOD generalization gap is crucial when models are deployed in environments significantly different from the training set, such as applying Graph Neural Networks (GNNs) trained on small graphs to large, real-world graphs. One promising approach for achieving robust OOD generalization is the framework of neural algorithmic alignment, which incorporates ideas from classical algorithms by designing neural architectures that resemble specific algorithmic paradigms (e.g. dynamic programming). The hope is that trained models of this form would have superior OOD capabilities, in much the same way that classical algorithms work for all instances. We employ sparsity regularization as a tool for analyzing the role of algorithmic alignment in achieving OOD generalization, focusing on graph neural networks (GNNs) applied to the canonical shortest path problem. We prove that if a trained GNN minimizes a sparsity-regularized loss over a small set of shortest-path instances, then the GNN implements $K$ steps of the Bellman-Ford algorithm for shortest paths. In fact, if a trained GNN minimizes this loss within an error of $\epsilon$, it computes $K$-step shortest path distances up to error $O(\epsilon)$. Our empirical results support our theory by showing that NNs trained by gradient descent are able to minimize this loss and extrapolate in practice.

The ability to acquire high-resolution, large-scale geospatial data at an unprecedented using LiDAR and other related technologies has intensified the need for scalable algorithms for terrain analysis, including shortest-path-distance (SPD) queries on large-scale terrain digital elevation models (DEMs). In this paper, we present a neural data structure for efficiently answering SPD queries approximately on a large terrain DEM, which is based on the recently proposed neural geodesic field (NeuroGF) framework (Zhang et al., 2023)—the state-of-the-art neural data structure for estimating geodesic distance. In particular, we propose a decoupled-NeuroGF data structure combined with an efficient two-stage mixed-training strategy, which significantly reduces computational bottlenecks and enables efficient training on terrain DEMs at a scale not feasible before. We demonstrate the efficacy of our approach by performing detailed experiments on both synthetic and real data sets. For instance, we can train a small model with around 70000 parameters on a terrain DEM with 16 million nodes in a matter of hours that can answer SPD queries with 1% relative error in at most 10ms per query.

Flow matching (FM) models extend ODE sampler based diffusion models into a general framework, significantly reducing sampling steps through learned vector fields. However, the theoretical understanding of FM models, particularly how their sample trajectories interact with underlying data geometry, remains underexplored. A rigorous theoretical analysis of FM ODE is essential for sample quality, stability, and broader applicability. In this paper, we advance the theory of FM models through a comprehensive analysis of sample trajectories. Central to our theory is the discovery that the denoiser, a key component of FM models, guides ODE dynamics through attracting and absorbing behaviors that adapt to the data geometry. We identify and analyze the three stages of ODE evolution: in the initial and intermediate stages, trajectories move toward the mean and local clusters of the data. At the terminal stage, we rigorously establish the convergence of FM ODE under weak assumptions, addressing scenarios where the data lie on a low-dimensional submanifold—cases that previous results could not handle. Our terminal stage analysis offers insights into the memorization phenomenon and establishes equivariance properties of FM ODEs. These findings bridge critical gaps in understanding flow matching models, with practical implications for optimizing sampling strategies and architectures guided by the intrinsic geometry of data.

In recent years, the remarkable success of graph neural networks (GNNs) on graph-structured data has prompted a surge of methods for explaining GNN predictions. However, the state-of-the-art for GNN explainability remains in flux. Different comparisons find mixed results for different methods, with many explainers struggling on more complex GNN architectures and tasks. This presents an urgent need for a more careful theoretical analysis of competing GNN explanation methods. In this work we take a closer look at GNN explanations in two different settings: input-level explanations, which produce explanatory subgraphs of the input graph, and layerwise explanations, which produce explanatory subgraphs of the computation graph. We establish the first theoretical connections between the popular perturbation-based and classical gradient-based methods, as well as point out connections between other recently proposed methods. At the input level, we demonstrate conditions under which GNNExplainer can be approximated by a simple heuristic based on the sign of the edge gradients. In the layerwise setting, we point out that edge gradients are equivalent to occlusion search for linear GNNs. Finally, we demonstrate how our theoretical results manifest in practice with experiments on both synthetic and real datasets.

Neural networks offer a promising data-driven approach to tackle computationally challenging optimization problems. In this work, we introduce neural approximation frameworks for a family of geometric "extent measure" problems, including shape-fitting descriptors (e.g. minimum enclosing ball or annulus). Central to our approach is the \textit{alignment} of our neural model with a new variant of the classical $\varepsilon$-kernel technique from computational geometry. In particular, we develop a new relaxed-$\varepsilon$-kernel theory that maintains the approximation guarantees of the classical $\varepsilon$-kernels but with the crucial benefit that it can be easily implemented with \textit{bounded model complexity} (i.e, constant number of parameters) by the simple SumFormer neural network. This leads to a simple neural model to approximate objects such as the directional width of any input point set, and empirically shows excellent out-of-distribution generalization. Many geometric extent measures, such as the minimum enclosing spherical shell, cannot be directly captured by $\varepsilon$-kernels. To this end, we show that an encode-process-decode framework with our kernel approximating NN used as the ``process'' module can approximate such extent measures, again, with bounded model complexity where parameters scale only with the approximation error $\varepsilon$ and not the size of the input set. Empirical results on diverse point‐cloud datasets demonstrate the practical performance of our models.

Continuously extending combinatorial optimization objectives is a powerful technique commonly applied to the optimization of set functions. However, few such methods exist for extending functions on permutations, despite the fact that many combinatorial optimization problems, such as the quadratic assignment problem (QAP) and the traveling salesperson problem (TSP), are inherently optimization over permutations. We present Birkhoff Extension (BE), an almost-everywhere-differentiable continuous polytime-computable extension of any real-valued function on permutations to doubly stochastic matrices. Key to this construction is our introduction of a continuous variant of the well-known Birkhoff decomposition. Our extension has several nice properties making it appealing for optimization problems. First, BE provides a rounding guarantee, namely any solution to the extension can be efficiently rounded to a permutation without increasing the function value. Furthermore, an approximate solution in the relaxed case will give rise to an approximate solution in the space of permutations. Second, using BE, any real-valued optimization objective on permutations can be extended to an almost-everywhere-differentiable objective function over the space of doubly stochastic matrices. This makes our BE amenable to not only gradient-descent based optimization, but also unsupervised neural combinatorial optimization where training often requires a differentiable loss. Third, based on the above properties, we present a simple optimization procedure which can be readily combined with existing optimization approaches to offer local improvements (i.e., the quality of the final solution is no worse than the initial solution). Finally, we also adapt our extension to optimization problems over a class of trees, such as Steiner tree and optimization-based hierarchical clustering. We present experimental results to verify our theoretical results on several combinatorial optimization problems related to permutations.

Representation learning on graphs is a fundamental problem that can be crucial in various tasks. Graph neural networks, the dominant approach for graph representation learning, are limited in their representation power. Therefore, it can be beneficial to explicitly extract and incorporate high-order topological and geometric information into these models. In this paper, we propose a principled approach to extract the rich connectivity information of graphs based on the theory of persistent homology. Our method utilizes the topological features to enhance the representation learning of graph neural networks and achieve state-of-the-art performance on various node classification and link prediction benchmarks. We also explore the option of end-to-end learning of the topological features, i.e., treating topological computation as a differentiable operator during learning. Our theoretical analysis and empirical study provide insights and potential guidelines for employing topological features in graph learning tasks.

Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the space. However, measures supported on trees admit a closed-form optimal transport that can be computed in linear time. In this paper, we aim to find an optimal tree structure for a given discrete metric space so that the tree-Wasserstein distance approximates the optimal transport distance in the original space. One of our key ideas is to cast the problem in ultrametric spaces. This helps us optimize over the space of ultrametric trees --- a mixed-discrete and continuous optimization problem --- via projected gradient decent over the space of ultrametric matrices. During optimization, we project the parameters to the ultrametric space via a hierarchical minimum spanning tree algorithm, equivalent to the closest projection to ultrametrics under the supremum norm. Experimental results on real datasets show that our approach outperforms previous approaches (e.g. Flowtree, Quadtree) in approximating optimal transport distances. Finally, experiments on synthetic data generated on ground truth trees show that our algorithm can accurately uncover the underlying trees.

Recent years have witnessed rapid advances in the use of neural networks to solve combinatorial optimization problems. Nevertheless, designing the "right" neural model that can effectively handle a given optimization problem can be challenging, and often there is no theoretical understanding or justification of the resulting neural model. In this paper, we focus on the rectilinear Steiner minimum tree (RSMT) problem, which is of critical importance in IC layout design and as a result has attracted numerous heuristic approaches in the VLSI literature. Our contributions are two-fold. On the methodology front, we propose NN-Steiner which is a novel mixed neural-algorithmic framework for computing RSMTs that leverages the celebrated PTAS algorithmic framework of Arora to solve this problem (and other geometric optimization problems). Our NN-Steiner replaces key algorithmic components within Arora's PTAS by suitable neural components. In particular, NN-Steiner only needs four neural network (NN) components that are called repeatedly within an algorithmic framework. Crucially, each of the four NN components is only of bounded size independent of input size, and thus easy to train. Furthermore, as the NN component is learning a generic algorithmic step, once learned, the resulting mixed neural-algorithmic framework generalizes to much larger instances not seen in training. Our NN-Steiner, to our best knowledge, is the first neural architecture of bounded size that has capacity to approximately solve RSMT (and variants). On the empirical front, we show how NN-Steiner can be implemented and demonstrate the effectiveness of our resulting approach, especially in terms of generalization, by comparing with state-of-the-art methods (both neural and non-neural based).

The run-time for optimization tools used in chip design has grown with the complexity of designs to the point where it can take several days to go through one design cycle which has become a bottleneck. Designers want fast tools that can quickly give feedback on a design. Using the input and output data of the tools from past designs, one can attempt to build a machine learning model that predicts the outcome of a design in significantly shorter time than running the tool. The accuracy of such models is affected by the representation of the design data, which is usually a netlist that describes the elements of the digital circuit and how they are connected. Graph representations for the netlist together with graph neural networks have been investigated for such models. However, the characteristics of netlists pose several challenges for existing graph learning frameworks, due to the large number of nodes and the importance of long-range interactions between nodes. To address these challenges, we represent the netlist as a directed hypergraph and propose a Directional Equivariant Hypergraph Neural Network (DE-HNN) for the effective learning of (directed) hypergraphs. Theoretically, we show that our DE-HNN can universally approximate any node or hyperedge based function that satisfies certain permutation equivariant and invariant properties natural for directed hypergraphs. We compare the proposed DE-HNN with several State-of-the-art (SOTA) machine learning models for (hyper)graphs and netlists, and show that the DE-HNN significantly outperforms them in predicting the outcome of optimized place-and-route tools directly from the input netlists.

Graph transformers have recently received significant attention in graph learning, partly due to their ability to capture more global interaction via self-attention. Nevertheless, while higher-order graph neural networks have been reasonably well studied, the exploration of extending graph transformers to higher-order variants is just starting. Both theoretical understanding and empirical results are limited. In this paper, we provide a systematic study of the theoretical expressive power of order-$k$ graph transformers and sparse variants. We first show that, an order-$k$ graph transformer without additional structural information is less expressive than the $k$-Weisfeiler Lehman ($k$-WL) test despite its high computational cost. We then explore strategies to both sparsify and enhance the higher-order graph transformers, aiming to improve both their efficiency and expressiveness. Indeed, sparsification based on neighborhood information can enhance the expressive power, as it provides additional information about input graph structures. In particular, we show that a natural neighborhood-based sparse order-$k$ transformer model is not only computationally efficient, but also expressive – as expressive as $k$-WL test. We further study several other sparse graph attention models that are computationally efficient and provide their expressiveness analysis. Finally, we provide experimental results to show the effectiveness of the different sparsification strategies.

(Directed) graphs with node attributes are a common type of data in various applications and there is a vast literature on developing metrics and efficient algorithms for comparing them. Recently, in the graph learning and optimization communities, a range of new approaches have been developed for comparing graphs with node attributes, leveraging ideas such as the Optimal Transport (OT) and the Weisfeiler-Lehman (WL) graph isomorphism test. Two state-of-the-art representatives are the OTC distance proposed in (O’Connor et al., 2022) and the WL distance in (Chen et al., 2022). Interestingly, while these two distances are developed based on different ideas, we observe that they both view graphs as Markov chains, and are deeply connected. Indeed, in this paper, we propose a unified framework to generate distances for Markov chains (thus including (directed) graphs with node attributes), which we call the Optimal Transport Markov (OTM) distances, that encompass both the OTC and the WL distances. We further introduce a special one-parameter family of distances within our OTM framework, called the discounted WL distance. We show that the discounted WL distance has nice theoretical properties and can address several limitations of the existing OTC and WL distances. Furthermore, contrary to the OTC and the WL distances, our new discounted WL distance can be differentiated after a entropy-regularization similar to the Sinkhorn distance, making it suitable to use in learning frameworks, e.g., as the reconstruction loss in a graph generative model.

A main object of our study is multiset functions — that is, permutation-invariant functions over inputs of varying sizes. Deep Sets, proposed by Zaheer et al. (2017), provides a universal representation for continuous multiset functions on scalars via a sum-decomposable model. Restricting the domain of the functions to finite multisets of $D$-dimensional vectors, Deep Sets also provides a universal approximation that requires a latent space dimension of $O(N^D)$ — where $N$ is an upper bound on the size of input multisets. In this paper, we strengthen this result by proving that universal representation is guaranteed for continuous and discontinuous multiset functions through a latent space dimension of $O(N^D)$ (which we will further improve upon). We then introduce identifiable multisets for which we can uniquely label their elements using an identifier function, namely, finite-precision vectors are identifiable. Based on our analysis of identifiable multisets, we prove that a sum-decomposable model, for general continuous multiset functions requires only a latent dimension of $2DN$, as opposed to $O(N^D)$. We further show that both encoder and decoder functions of the model are continuous — our main contribution to the existing work which lacks such a guarantee. Additionally, this provides a significant improvement over the aforementioned $O(N^D)$ bound, derived for the universal representation of both continuous and discontinuous multiset functions. We then extend our results and provide special sum-decomposition structures to universally represent permutation-invariant tensor functions on identifiable tensors. These families of sum-decomposition models enable us to design deep network architectures and deploy them on a variety of learning tasks on sequences, images, and graphs.

The distinguishing power of graph transformers is tied to the choice of positional encoding: features used to augment the base transformer with information about the graph. There are two primary types of positional encoding: absolute positional encodings (APEs) and relative positional encodings (RPEs). APEs assign features to each node and are given as input to the transformer. RPEs instead assign a feature to each pair of nodes, e.g., shortest-path distance, and are used to augment the attention block. A priori, it is unclear which method is better for maximizing the power of the resulting graph transformer. In this paper, we aim to understand the relationship between these different types of positional encodings. Interestingly, we show that graph transformers using APEs and RPEs are equivalent in their ability to distinguish non-isomorphic graphs. In particular, we demonstrate how to interchange APEs and RPEs while maintaining their distinguishing power in terms of graph transformers. However, in the case of graphs with node features, we show that RPEs may have an advantage over APEs. Based on our theoretical results, we provide a study of different APEs and RPEs—including the shortest-path and resistance distance and the recently introduced stable and expressive positional encoding (SPE)—and compare their distinguishing power in terms of transformers. We believe our work will help navigate the vast number of positional encoding choices and provide guidance on the future design of positional encodings for graph transformers.

Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.

Graphons are general and powerful models for generating graphs of varying size. In this paper, we propose to directly model graphons using neural networks, obtaining Implicit Graphon Neural Representation (IGNR). Existing work in modeling and reconstructing graphons often approximates a target graphon by a fixed resolution piece-wise constant representation. Our IGNR has the benefit that it can represent graphons up to arbitrary resolutions, and enables natural and efficient generation of arbitrary sized graphs with desired structure once the model is learned. Furthermore, we allow the input graph data to be unaligned and have different sizes by leveraging the Gromov-Wasserstein distance. We first demonstrate the effectiveness of our model by showing its superior performance on a graphon learning task. We then propose an extension of IGNR that can be incorporated into an auto-encoder framework, and demonstrate its good performance under a more general setting of graphon learning. We also show that our model is suitable for graph representation learning and graph generation.

The (combinatorial) graph Laplacian is a fundamental object in the analysis of, and optimization on, graphs. Via a topological view, this operator can be extended to a simplicial complex K and therefore offers a way to perform "signal processing" on p-(co)chains of K. Recently, the concept of persistent Laplacian was proposed and studied for a pair of simplicial complexes K ↪ L connected by an inclusion relation, further broadening the use of Laplace-based operators. In this paper, we significantly expand the scope of the persistent Laplacian by generalizing it to a pair of weighted simplicial complexes connected by a weight preserving simplicial map f: K → L. Such a simplicial map setting arises frequently, e.g., when relating a coarsened simplicial representation with an original representation, or the case when the two simplicial complexes are spanned by different point sets, i.e. cases in which it does not hold that K ⊂ L. However, the simplicial map setting is much more challenging than the inclusion setting since the underlying algebraic structure is much more complicated. We present a natural generalization of the persistent Laplacian to the simplicial setting. To shed insight on the structure behind it, as well as to develop an algorithm to compute it, we exploit the relationship between the persistent Laplacian and the Schur complement of a matrix. A critical step is to view the Schur complement as a functorial way of restricting a self-adjoint positive semi-definite operator to a given subspace. As a consequence of this relation, we prove that the qth persistent Betti number of the simplicial map f: K → L equals the nullity of the qth persistent Laplacian Δ_q^{K,L}. We then propose an algorithm for finding the matrix representation of Δ_q^{K,L} which in turn yields a fundamentally different algorithm for computing the qth persistent Betti number of a simplicial map. Finally, we study the persistent Laplacian on simplicial towers under weight-preserving simplicial maps and establish monotonicity results for their eigenvalues.

Message passing graph neural networks (GNNs) are a popular learning architectures for graph-structured data. However, one problem GNNs experience is oversquashing, where a GNN has difficulty sending information between distant nodes. Understanding and mitigating oversquashing has recently received significant attention from the research community. In this paper, we continue this line of work by analyzing oversquashing through the lens of the *effective resistance* between nodes in the input graph. Effective resistance intuitively captures the ``strength'' of connection between two nodes by paths in the graph, and has a rich literature spanning many areas of graph theory. We propose to use *total effective resistance* as a bound of the total amount of oversquashing in a graph and provide theoretical justification for its use. We further develop an algorithm to identify edges to be added to an input graph to minimize the total effective resistance, thereby alleviating oversquashing. We provide empirical evidence of the effectiveness of our total effective resistance based rewiring strategies for improving the performance of GNNs.

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer, then MPNN + VN with only $\mathcal{O}(1)$ depth and $\mathcal{O}(1)$ width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with $\mathcal{O}(n^d)$ width and $\mathcal{O}(1)$ depth can approximate the self-attention layer arbitrarily well, where $d$ is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with $\mathcal{O}(1)$ width and $\mathcal{O}(n)$ depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

The hyperbolic space is widely used for representing hierarchical datasets due to its ability to embed trees with small distortion. However, this property comes at a price of numerical instability such that training hyperbolic learning models will sometimes lead to catastrophic NaN problems, encountering unrepresentable values in floating point arithmetic. In this work, we analyze the limitations of two popular models for the hyperbolic space, namely, the Poincaré ball and the Lorentz model. We find that, under the 64-bit arithmetic system, the Poincaré ball has a relatively larger capacity than the Lorentz model for correctly representing points. However, the Lorentz model is superior to the Poincaré ball from the perspective of optimization, which we theoretically validate. To address these limitations, we identify one Euclidean parametrization of the hyperbolic space which can alleviate these issues. We further extend this Euclidean parametrization to hyperbolic hyperplanes and demonstrate its effectiveness in improving the performance of hyperbolic SVM.

Learning distance functions between complex objects, such as the Wasserstein distance to compare point sets, is a common goal in machine learning applications. However, functions on such complex objects (e.g., point sets and graphs) are often required to be invariant to a wide variety of group actions e.g. permutation or rigid transformation. Therefore, continuous and symmetric *product* functions (such as distance functions) on such complex objects must also be invariant to the *product* of such group actions. We call these functions symmetric and factor-wise group invariant functions (or SGFI functions} in short). In this paper, we first present a general neural network architecture for approximating SFGI functions. The main contribution of this paper combines this general NN with a sketching idea in order to develop a specific and efficient neural network which can approximate the $p$-th Wasserstein distance between point sets. Very importantly, the required model complexity is *independent* of the sizes of input point sets. On the theoretical front, to the best of our knowledge, this is the first result showing that there exists a neural network with the capacity to approximate Wasserstein distance with bounded model complexity. Our work provides an interesting integration of sketching ideas for geometric problems with universal approximation of symmetric functions. On the empirical front, we present a range of results showing that our newly proposed neural network architecture performs comparatively or better than other models (including a SOTA Siamese Autoencoder based approach). In particular, our NN generalizes significantly better and trains much faster than the SOTA Siamese AE. Finally, this line of investigation could be useful in exploring effective neural network design for solving a broad range of geometric optimization problems (e.g., $k$-means in a metric space).

Although theoretical properties such as expressive power and over-smoothing of graph neural networks (GNN) have been extensively studied recently, its convergence property is a relatively new direction. In this paper, we investigate the convergence of one powerful GNN, Invariant Graph Network (IGN) over graphs sampled from graphons. We first prove the stability of linear layers for general $k$-IGN (of order $k$) based on a novel interpretation of linear equivariant layers. Building upon this result, we prove the convergence of $k$-IGN under the model of \citet{ruiz2020graphon}, where we access the edge weight but the convergence error is measured for graphon inputs. Under the more natural (and more challenging) setting of \citet{keriven2020convergence} where one can only access 0-1 adjacency matrix sampled according to edge probability, we first show a negative result that the convergence of any IGN is not possible. We then obtain the convergence of a subset of IGNs, denoted as IGN-small, after the edge probability estimation. We show that IGN-small still contains function class rich enough that can approximate spectral GNNs arbitrarily well. Lastly, we perform experiments on various graphon models to verify our statements.

The Weisfeiler-Lehman (WL) test is a classical procedure for graph isomorphism testing. The WL test has also been widely used both for designing graph kernels and for analyzing graph neural networks. In this paper, we propose the Weisfeiler-Lehman (WL) distance, a notion of distance between labeled measure Markov chains (LMMCs), of which labeled graphs are special cases. The WL distance is polynomial time computable and is also compatible with the WL test in the sense that the former is positive if and only if the WL test can distinguish the two involved graphs. The WL distance captures and compares subtle structures of the underlying LMMCs and, as a consequence of this, it is more discriminating than the distance between graphs used for defining the state-of-the-art Wasserstein Weisfeiler-Lehman graph kernel. Inspired by the structure of the WL distance we identify a neural network architecture on LMMCs which turns out to be universal w.r.t. continuous functions defined on the space of all LMMCs (which includes all graphs) endowed with the WL distance. Finally, the WL distance turns out to be stable w.r.t. a natural variant of the Gromov-Wasserstein (GW) distance for comparing metric Markov chains that we identify. Hence, the WL distance can also be construed as a polynomial time lower bound for the GW distance which is in general NP-hard to compute.

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and therefore drastically accelerates simulation. However, such CG procedure induces information losses, which makes accurate backmapping, i.e., restoring fine-grained (FG) coordinates from CG coordinates, a long-standing challenge. Inspired by the recent progress in generative models and equivariant networks, we propose a novel model that rigorously embeds the vital probabilistic nature and geometrical consistency requirements of the backmapping transformation. Our model encodes the FG uncertainties into an invariant latent space and decodes them back to FG geometries via equivariant convolutions. To standardize the evaluation of this domain, we further provide three comprehensive benchmarks based on molecular dynamics trajectories. Extensive experiments show that our approach always recovers more realistic structures and outperforms existing data-driven methods with a significant margin.

Topological features based on persistent homology capture high-order structural information so as to augment graph neural network methods. However, computing extended persistent homology summaries remains slow for large and dense graphs and can be a serious bottleneck for the learning pipeline. Inspired by recent success in neural algorithmic reasoning, we propose a novel graph neural network to estimate extended persistence diagrams (EPDs) on graphs efficiently. Our model is built on algorithmic insights, and benefits from better supervision and closer alignment with the EPD computation algorithm. We validate our method with convincing empirical results on approximating EPDs and downstream graph representation learning tasks. Our method is also efficient; on large and dense graphs, we accelerate the computation by nearly 100 times.

Recent years have witnessed a surge of approaches to use neural networks to help tackle combinatorial optimization problems, including graph optimization problems. However, theoretical understanding of such approaches remains limited. In this paper, we consider the geometric setting, where graphs are induced by points in a fixed dimensional Euclidean space. We show that several graph optimization problems can be approximated by an algorithm that is polynomial in graph size n via a framework we propose, call the Baker-paradigm. More importantly, a key advantage of the Baker-paradigm is that it decomposes the input problem into (at most linear number of) small sub-problems of fixed sizes (independent of the size of the input). For the family of such fixed-size sub-problems, we can now design neural networks with universal approximation guarantees to solve them. This leads to a mixed algorithmic-ML framework, which we call NN-Baker that has the capacity to approximately solve a family of graph optimization problems (e.g, maximum independent set and minimum vertex cover) in time linear to input graph size, and only polynomial to approximation parameter. We instantiate our NN-Baker by a CNN version and GNN version, and demonstrate the effectiveness and efficiency of our approach via a range of experiments.

Recent years have witnessed a tremendous growth using topological summaries, especially the persistence diagrams (encoding the so-called persistent homology) for analyzing complex shapes. Intuitively, persistent homology maps a potentially complex input object (be it a graph, an image, or a point set and so on) to a unified type of feature summary, called the persistence diagrams. One can then carry out downstream data analysis tasks using such persistence diagram representations. A key problem is to compute the distance between two persistence diagrams efficiently. In particular, a persistence diagram is essentially a multiset of points in the plane, and one popular distance is the so-called 1-Wasserstein distance between persistence diagrams. In this paper, we present two algorithms to approximate the 1-Wasserstein distance for persistence diagrams in near-linear time. These algorithms primarily follow the same ideas as two existing algorithms to approximate optimal transport between two finite point-sets in Euclidean spaces via randomly shifted quadtrees. We show how these algorithms can be effectively adapted for the case of persistence diagrams. Our algorithms are much more efficient than previous exact and approximate algorithms, both in theory and in practice, and we demonstrate its efficiency via extensive experiments. They are conceptually simple and easy to implement, and the code is publicly available in github.

Local structural information can increase the adaptability of graph convolutional networks to large graphs with heterogeneous topology. Existing methods only use relatively simplistic topological information, such as node degrees.We present a novel approach leveraging advanced topological information, i.e., persistent homology, which measures the information flow efficiency at different parts of the graph. To fully exploit such structural information in real world graphs, we propose a new network architecture which learns to use persistent homology information to reweight messages passed between graph nodes during convolution. For node classification tasks, our network outperforms existing ones on a broad spectrum of graph benchmarks.

An augmented metric space (X, d_X, f_X) is a metric space (X, d_X) equipped with a function f_X: X → ℝ. It arises commonly in practice, e.g, a point cloud X in ℝ^d where each point x∈ X has a density function value f_X(x) associated to it. Such an augmented metric space naturally gives rise to a 2-parameter filtration. However, the resulting 2-parameter persistence module could still be of wild representation type, and may not have simple indecomposables. In this paper, motivated by the elder-rule for the zeroth homology of a 1-parameter filtration, we propose a barcode-like summary, called the elder-rule-staircode, as a way to encode the zeroth homology of the 2-parameter filtration induced by a finite augmented metric space. Specifically, given a finite (X, d_X, f_X), its elder-rule-staircode consists of n = |X| number of staircase-like blocks in the plane. We show that the fibered barcode, the fibered merge tree, and the graded Betti numbers associated to the zeroth homology of the 2-parameter filtration induced by (X, d_X, f_X) can all be efficiently computed once the elder-rule-staircode is given. Furthermore, for certain special cases, this staircode corresponds exactly to the set of indecomposables of the zeroth homology of the 2-parameter filtration. Finally, we develop and implement an efficient algorithm to compute the elder-rule-staircode in O(n²log n) time, which can be improved to O(n²α(n)) if X is from a fixed dimensional Euclidean space ℝ^d, where α(n) is the inverse Ackermann function.

This paper focuses on developing an efficient algorithm for analyzing a directed network (graph) from a topological viewpoint. A prevalent technique for such topological analysis involves computation of homology groups and their persistence. These concepts are well suited for spaces that are not directed. As a result, one needs a concept of homology that accommodates orientations in input space. Path-homology developed for directed graphs by Grigor'yan, Lin, Muranov and Yau has been effectively adapted for this purpose recently by Chowdhury and Mémoli. They also give an algorithm to compute this path-homology. Our main contribution in this paper is an algorithm that computes this path-homology and its persistence more efficiently for the $1$-dimensional ($H_1$) case. In developing such an algorithm, we discover various structures and their efficient computations that aid computing the $1$-dimensional path-homnology. We implement our algorithm and present some preliminary experimental results.

Physical phenomena in science and engineering are frequently modeled using scalar fields. In scalar field topology, graph-based topological descriptors such as merge trees, contour trees, and Reeb graphs are commonly used to characterize topological changes in the (sub)level sets of scalar fields. One of the biggest challenges and opportunities to advance topology-based visualization is to understand and incorporate uncertainty into such topological descriptors to effectively reason about their underlying data. In this paper, we study a structural average of a set of labeled merge trees and use it to encode uncertainty in data. Specifically, we compute a 1-center tree that minimizes its maximum distance to any other tree in the set under a well-defined metric called the interleaving distance. We provide heuristic strategies that compute structural averages of merge trees whose labels do not fully agree. We further provide an interactive visualization system that resembles a numerical calculator that takes as input a set of merge trees and outputs a tree as their structural average. We also highlight structural similarities between the input and the average and incorporate uncertainty information for visual exploration. We develop a novel measure of uncertainty, referred to as consistency, via a metric-space view of the input trees. Finally, we demonstrate an application of our framework through merge trees that arise from ensembles of scalar fields. Our work is the first to employ interleaving distances and consistency to study a global, mathematically rigorous, structural average of merge trees in the context of uncertainty visualization.

Regularization plays a crucial role in supervised learning. Most existing methods enforce a global regularization in a structure agnostic manner. In this paper, we initiate a new direction and propose to enforce the structural simplicity of the classification boundary by regularizing over its topological complexity. In particular, our measurement of topological complexity incorporates the importance of topological features (e.g., connected components, handles, and so on) in a meaningful manner, and provides a direct control over spurious topological structures. We incorporate the new measurement as a topological penalty in training classifiers. We also propose an efficient algorithm to compute the gradient of such penalty. Our method provides a novel way to topologically simplify the global structure of the model, without having to sacrifice too much of the flexibility of the model. We demonstrate the effectiveness of our new topological regularizer on a range of synthetic and real-world datasets.

The Gromov-Hausdorff distance is a natural way to measure the distortion between two metric spaces. However, there has been only limited algorithmic development to compute or approximate this distance. We focus on computing the Gromov-Hausdorff distance between two metric trees. Roughly speaking, a metric tree is a metric space that can be realized by the shortest path metric on a tree. Any finite tree with positive edge weight can be viewed as a metric tree where the weight is treated as edge length and the metric is the induced shortest path metric in the tree. Previously, Agarwal et al. showed that even for trees with unit edge length, it is NP-hard to approximate the Gromov-Hausdorff distance between them within a factor of 3. In this paper, we present a fixed-parameter tractable (FPT) algorithm that can approximate the Gromov-Hausdorff distance between two general metric trees within a multiplicative factor of 14. Interestingly, the development of our algorithm is made possible by a connection between the Gromov-Hausdorff distance for metric trees and the interleaving distance for the so-called merge trees. The merge trees arise in practice naturally as a simple yet meaningful topological summary (it is a variant of the Reeb graphs and contour trees), and are of independent interest. It turns out that an exact or approximation algorithm for the interleaving distance leads to an approximation algorithm for the Gromov-Hausdorff distance. One of the key contributions of our work is that we re-define the interleaving distance in a way that makes it easier to develop dynamic programming approaches to compute it. We then present a fixed-parameter tractable algorithm to compute the interleaving distance between two merge trees exactly, which ultimately leads to an FPT-algorithm to approximate the Gromov-Hausdorff distance between two metric trees. This exact FPT-algorithm to compute the interleaving distance between merge trees is of interest itself, as it is known that it is NP-hard to approximate it within a factor of 3, and previously the best known algorithm has an approximation factor of O(sqrt{n}) even for trees with unit edge length.

Automatic Extraction of road network from satellite images is a goal that can benefit and even enable new technologies. Methods that combine machine learning (ML) and computer vision have been proposed in recent years which make the task semi-automatic by requiring the user to provide curated training samples. The process can be fully automatized if training samples can be produced algorithmically. In this work, we develop such a technique by infusing a persistence-guided discrete Morse based graph reconstruction algorithm into ML framework. We elucidate our contributions in two phases. First, in a semi-automatic framework, we combine a discrete-Morse based graph reconstruction algorithm with an existing CNN framework to segment input satellite images. We show that this leads to reconstructions with better connectivity and less noise. Next, in a fully automatic framework, we leverage the power of the discrete-Morse based graph reconstruction algorithm to train a CNN from a collection of images without labelled data and use the same algorithm to produce the final output from the segmented images created by the trained CNN. We apply the discrete-Morse based graph reconstruction algorithm iteratively to improve the accuracy of the CNN. We show experimental results on datasets from SpaceNet Challenge. Full version of the paper appears in [8].

Cardiac trabeculae are fine rod-like muscles whose ends are attached to the inner walls of ventricles. Accurate extraction of trabeculae is important yet challenging, due to the background noise and limited resolution of cardiac images. Existing works proposed to handle this task by modeling the trabeculae as topological handles for better extraction. Computing optimal representation of these handles is essential yet very expensive. In this work, we formulate the problem as a heuristic search problem, and propose novel heuristic functions based on advanced topological techniques. We show in experiments that the proposed heuristic functions improve the computation in both time and memory.

Random graphs are mathematical models that have applications in a wide range of domains. We study the following model where one adds Erdős--Rényi (ER) type perturbation to a random geometric graph. More precisely, assume $G_\mathcal{X}^{*}$ is a random geometric graph sampled from a nice measure on a metric space $\mathcal{X} = (X,d)$. The input observed graph $\widehat{G}(p,q)$ is generated by removing each existing edge from $G_\mathcal{X}^*$ with probability $p$, while inserting each non-existent edge to $G_\mathcal{X}^{*}$ with probability $q$. We refer to such random $p$-deletion and $q$-insertion as ER-perturbation. Although these graphs are related to the objects in the continuum percolation theory, our understanding of them is still rather limited. In this paper we consider a localized version of the classical notion of clique number for the aforementioned ER-perturbed random geometric graphs: Specifically, we study the edge clique number for each edge in a graph, defined as the size of the largest clique(s) in the graph containing that edge. The clique number of the graph is simply the largest edge clique number. Interestingly, given a ER-perturbed random geometric graph, we show that the edge clique number presents two fundamentally different types of behaviors, depending on which "type" of randomness it is generated from. As an application of the above results, we show that by using a filtering process based on the edge clique number, we can recover the shortest-path metric of the random geometric graph $G_\mathcal{X}^*$ within a multiplicative factor of $3$, from an ER-perturbed observed graph $\widehat{G}(p,q)$, for a significantly wider range of insertion probability $q$ than in previous work.

Recently a new feature representation and data analysis methodology based on a topological tool called persistent homology (and its persistence diagram summary) has gained much momentum. A series of methods have been developed to map a persistence diagram to a vector representation so as to facilitate the downstream use of machine learning tools. In these approaches, the importance (weight) of different persistence features are usually pre-set. However often in practice, the choice of the weight-function should depend on the nature of the specific data at hand. It is thus highly desirable to learn a best weight-function (and thus metric for persistence diagrams) from labelled data. We study this problem and develop a new weighted kernel, called WKPI, for persistence summaries, as well as an optimization framework to learn the weight (and thus kernel). We apply the learned kernel to the challenging task of graph classification, and show that our WKPI-based classification framework obtains similar or (sometimes significantly) better results than the best results from a range of previous graph classification frameworks on a collection of benchmark datasets.

Classical matrix perturbation results, such as Weyl’s theorem for eigenvalues and the Davis-Kahan theorem for eigenvectors, are general purpose. These classical bounds are tight in the worst case, but in many settings sub-optimal in the typical case. In this paper, we present perturbation bounds which consider the nature of the perturbation and its interaction with the unperturbed structure in order to obtain significant improvements over the classical theory in many scenarios, such as when the perturbation is random. We demonstrate the utility of these new results by analyzing perturbations in the stochastic blockmodel where we derive much tighter bounds than provided by the classical theory.

We study Vietoris-Rips and Cech complexes of metric wedge sums and metric gluings. We show that the Vietoris-Rips (resp. Cech) complex of a wedge sum, equipped with a natural metric, is homotopy equivalent to the wedge sum of the Vietoris-Rips (resp. Cech) complexes. We also provide generalizations for certain metric gluings, i.e. when two metric spaces are glued together along a common isometric subset. As our main example, we deduce the homotopy type of the Vietoris-Rips complex of two metric graphs glued together along a sufficiently short path. As a result, we can describe the persistent homology, in all homological dimensions, of the Vietoris-Rips complexes of a wide class of metric graphs.

Recovering hidden graph-like structures from potentially noisy data is a fundamental task in modern data analysis. Recently, a persistence-guided discrete Morse-based framework to extract a geometric graph from low-dimensional data has become popular. However, to date, there is very limited theoretical understanding of this framework in terms of graph reconstruction. This paper makes a first step towards closing this gap. Specifically, first, leveraging existing theoretical understanding of persistence-guided discrete Morse cancellation, we provide a simplified version of the existing discrete Morse-based graph reconstruction algorithm. We then introduce a simple and natural noise model and show that the aforementioned framework can correctly reconstruct a graph under this noise model, in the sense that it has the same loop structure as the hidden ground-truth graph, and is also geometrically close. We also provide some experimental results for our simplified graph-reconstruction algorithm.

Abstract Point cloud data is one of the most common types of input for geometric processing applications. In this paper, we study the point cloud density adaptation problem that underlies many pre‐processing tasks of points data. Specifically, given a (sparse) set of points Q sampling an unknown surface and a target density function, the goal is to adapt Q to match the target distribution. We propose a simple and robust framework that is effective at achieving both local uniformity and precise global density distribution control. Our approach relies on the Gaussian‐weighted graph Laplacian and works purely in the points setting. While it is well known that graph Laplacian is related to mean‐curvature flow and thus has denoising ability, our algorithm uses certain information encoded in the graph Laplacian that is orthogonal to the mean‐curvature flow. Furthermore, by leveraging the natural scale parameter contained in the Gaussian kernel and combining it with a simulated annealing idea, our algorithm moves points in a multi‐scale manner. The resulting algorithm relies much less on the input points to have a good initial distribution (neither uniform nor close to the target density distribution) than many previous refinement‐based methods. We demonstrate the simplicity and effectiveness of our algorithm with point clouds sampled from different underlying surfaces with various geometric and topological properties.

The Gromov-Hausdorff (GH) distance is a natural way to measure distance between two metric spaces. We prove that it is NP-hard to approximate the GH distance better than a factor of 3 for geodesic metrics on a pair of trees. We complement this result by providing a polynomial time O (min n , √ rn )-approximation algorithm for computing the GH distance between a pair of metric trees, where r is the ratio of the longest edge length in both trees to the shortest edge length. For metric trees with unit length edges, this yields an O (√ n )-approximation algorithm 1 .

In many data analysis applications the following scenario is commonplace: we are given a point set that is supposed to sample a hidden ground truth K in a metric space, but it got corrupted with noise so that some of the data points lie far away from K creating outliers also termed as ambient noise. One of the main goals of denoising algorithms is to eliminate such noise so that the curated data lie within a bounded Hausdorff distance of K. Popular denoising approaches such as deconvolution and thresholding often require the user to set several parameters and/or to choose an appropriate noise model while guaranteeing only asymptotic convergence. Our goal is to lighten this burden as much as possible while ensuring theoretical guarantees in all cases. Specifically, first, we propose a simple denoising algorithm that requires only a single parameter but provides a theoretical guarantee on the quality of the output on general input points. We argue that this single parameter cannot be avoided. We next present a simple algorithm that avoids even this parameter by paying for it with a slight strengthening of the sampling condition on the input points which is not unrealistic. We also provide some preliminary empirical evidence that our algorithms are effective in practice.

In this video, we present a research project on cardiac trabeculae segmentation. Trabeculae are fine muscle columns within human ventricles whose both ends are attached to the wall. Extracting these structures are very challenging even with state-of-the-art image segmentation techniques. We observed that these structures form natural topological handles. Based on such observation, we developed a topological approach, which employs advanced computational topology methods and achieve high quality segmentation results.

Data analysis often concerns not only the space where data come from, but also various types of maps attached to data. In recent years, several related structures have been used to study maps on data, including Reeb spaces, mappers and multiscale mappers. The construction of these structures also relies on the so-called nerve of a cover of the domain. In this paper, we aim to analyze the topological information encoded in these structures in order to provide better understanding of these structures and facilitate their practical usage. More specifically, we show that the one-dimensional homology of the nerve complex N(U) of a path-connected cover U of a domain X cannot be richer than that of the domain X itself. Intuitively, this result means that no new H_1-homology class can be "created" under a natural map from X to the nerve complex N(U). Equipping X with a pseudometric d, we further refine this result and characterize the classes of H_1(X) that may survive in the nerve complex using the notion of size of the covering elements in U. These fundamental results about nerve complexes then lead to an analysis of the H_1-homology of Reeb spaces, mappers and multiscale mappers. The analysis of H_1-homology groups unfortunately does not extend to higher dimensions. Nevertheless, by using a map-induced metric, establishing a Gromov-Hausdorff convergence result between mappers and the domain, and interleaving relevant modules, we can still analyze the persistent homology groups of (multiscale) mappers to establish a connection to Reeb spaces.

Graphs and network data are ubiquitous across a wide spectrum of scientific and application domains. Often in practice, an input graph can be considered as an observed snapshot of a (potentially continuous) hidden domain or process. Subsequent analysis, processing, and inferences are then performed on this observed graph. In this paper we advocate the perspective that an observed graph is often a noisy version of some discretized 1-skeleton of a hidden domain, and specifically we will consider the following natural network model: We assume that there is a true graph G^* which is a certain proximity graph for points sampled from a hidden domain X; while the observed graph G is an Erdos-Renyi type perturbed version of G^*. Our network model is related to, and slightly generalizes, the much-celebrated small-world network model originally proposed by Watts and Strogatz. However, the main question we aim to answer is orthogonal to the usual studies of network models (which often focuses on characterizing / predicting behaviors and properties of real-world networks). Specifically, we aim to recover the metric structure of G^* (which reflects that of the hidden space X as we will show) from the observed graph G. Our main result is that a simple filtering process based on the Jaccard index can recover this metric within a multiplicative factor of 2 under our network model. Our work makes one step towards the general question of inferring structure of a hidden space from its observed noisy graph representation. In addition, our results also provide a theoretical understanding for Jaccard-Index-based denoising approaches.

With the rapid growth of publicly available GPS traces, robust and efficient automatic road network reconstruction has become a crucial task in GIS data analysis and applications. In [20], an effective and robust road network reconstruction algorithm was developed based on the discrete Morse theory, which has the state-of-the-art performance in automatic road-network reconstruction. Based on a discrete Morse-based graph reconstruction framework, we provide two improvements of the previous algorithm [20]: (1) we further simplify it and obtain a better empirical time performance; and (2) we develop a simple but effective editing strategy that helps adding missing road segments in the output reconstruction.

In this article we propose a novel visualization method to explore graphs with numerical attributes associated with nodes - referred to as scalar graphs. The proposed visualization strategy seeks to simultaneously uncover the relationship between attribute values and graph topology, and relies on transforming the network to generate a terrain map. A key objective here is to ensure that the terrain map reveals the overall distribution of components-of-interest (e.g. dense subgraphs, kcores) and the relationships among them while being sensitive to the attribute values over the graph.

Clustering data with both continuous and discrete attributes is a challenging task. Existing methods lack a principled probabilistic formulation. In this paper, we propose a clustering method based on a tree-structured graphical model to describe the generation process of mixed-type data. Our tree-structured model factorized into a product of pairwise interactions, and thus localizes the interaction between feature variables of different types. To provide a robust clustering method based on the tree-model, we adopt a topographical view and compute peaks of the density function and their attractive basins for clustering. Furthermore, we leverage the theory from topology data analysis to adaptively merge trivial peaks into large ones in order to achieve meaningful clusterings. Our method outperforms state-of-the-art methods on mixed-type data.

The value proposition of a dataset often resides in the implicit interconnections or explicit relationships (patterns) among individual entities, and is often modeled as a graph. Effective visualization of such graphs can lead to key insights uncovering such value. In this article we propose a visualization method to explore attributed graphs with numerical attributes associated with nodes (or edges). Such numerical attributes can represent raw content information, similarities, or derived information reflecting important network measures such as triangle density and centrality. The proposed visualization strategy seeks to simultaneously uncover the relationship between attribute values and graph topology, and relies on transforming the network to generate a terrain map. A key objective here is to ensure that the terrain map reveals the overall distribution of components-of-interest (e.g. dense subgraphs, k-cores) and the relationships among them while being sensitive to the attribute values over the graph. We also design extensions that can capture the relationship across multiple numerical attributes. We demonstrate the efficacy of our method on several real-world data science tasks while scaling to large graphs with millions of nodes.

In topology inference from data, current approaches face two major problems. One concerns the selection of a correct parameter to build an appropriate complex on top of the data points; the other involves with the typical ‘large’ size of this complex. We address these two issues in the context of inferring homology from sample points of a smooth manifold of known dimension sitting in an Euclidean space ℝk. We show that, for a sample size of n points, we can identify a set of O(n2) points (as opposed to Voronoi vertices) approximating a subset of the medial axis that suffices to compute a distance sandwiched between the well known local feature size and the local weak feature size (in fact, the approximating set can be further reduced in size to O(n)). This distance, called the lean feature size, helps pruning the input set at least to the level of local feature size while making the data locally uniform. The local uniformity in turn helps in building a complex for homology inference on top of the sparsified data without requiring any user-supplied distance threshold. Unlike most topology inference results, ours does not require that the input is dense relative to a global feature such as reach or weak feature size; instead it can be adaptive with respect to the local feature size. We present some empirical evidence in support of our theoretical claims.

We initiate the study of metric embeddings with outliers. Given some finite metric space we wish to remove a small set of points and to find either an isometric or a low-distortion embedding of the remaining points into some host metric space. This is a natural problem that captures scenarios where a small fraction of points in the input corresponds to noise. We present polynomial-time approximation algorithms for computing outlier embeddings into Euclidean space, trees, and ultrametrics. In the case of isometric embeddings the objective is to minimize the number of outliers, while in the case of non-isometries we have a bi-criteria optimization problem where the goal is to minimize both the number of outliers and the distortion. We complement our approximation algorithms with NP-hardness results for these problems. We conclude with a brief experimental evaluation of our non-isometric outlier embedding on synthetic and real-world data sets.

In topological data analysis, a point cloud data P extracted from a metric space is often analyzed by computing the persistence diagram or barcodes of a sequence of Rips complexes built on P indexed by a scale parameter. Unfortunately, even for input of moderate size, the size of the Rips complex may become prohibitively large as the scale parameter increases. Starting with the Sparse Rips filtration introduced by Sheehy, some existing methods aim to reduce the size of the complex so as to improve the time efficiency as well. However, as we demonstrate, existing approaches still fall short of scaling well, especially for high dimensional data. In this paper, we investigate the advantages and limitations of existing approaches. Based on insights gained from the experiments, we propose an efficient new algorithm, called SimBa, for approximating the persistent homology of Rips filtrations with quality guarantees. Our new algorithm leverages a batch collapse strategy as well as a new sparse Rips-like filtration. We experiment on a variety of low and high dimensional data sets. We show that our strategy presents a significant size reduction, and our algorithm for approximating Rips filtration persistence is order of magnitude faster than existing methods in practice.

In this work we develop a theory of hierarchical clustering for graphs. Our modelling assumption is that graphs are sampled from a graphon, which is a powerful and general model for generating graphs and analyzing large networks. Graphons are a far richer class of graph models than stochastic blockmodels, the primary setting for recent progress in the statistical theory of graph clustering. We define what it means for an algorithm to produce the ``correct" clustering, give sufficient conditions in which a method is statistically consistent, and provide an explicit algorithm satisfying these properties.

Summarizing topological information from datasets and maps defined on them is a central theme in topological data analysis. Mapper, a tool for such summarization, takes as input both a possibly high dimensional dataset and a map defined on the data, and produces a summary of the data by using a cover of the codomain of the map. This cover, via a pullback operation to the domain, produces a simplicial complex connecting the data points. The resulting view of the data through a cover of the codomain offers flexibility in analyzing the data. However, it offers only a view at a fixed scale at which the cover is constructed. Inspired by the concept, we explore a notion of a tower of covers which induces a tower of simplicial complexes connected by simplicial maps, which we call multiscale mapper. We study the resulting structure, and design practical algorithms to compute its persistence diagrams efficiently. Specifically, when the domain is a simplicial complex and the map is a real-valued piecewise-linear function, the algorithm can compute the exact persistence diagram only from the 1-skeleton of the input complex. For general maps, we present a combinatorial version of the algorithm that acts only on vertex sets connected by the 1-skeleton graph, and this algorithm approximates the exact persistence diagram thanks to a stability result that we show to hold.

Hierarchical clustering is a popular method for analyzing data which associates a tree to a dataset. Hartigan consistency has been used extensively as a framework to analyze such clustering algorithms from a statistical point of view. Still, as we show in the paper, a tree which is Hartigan consistent with a given density can look very different than the correct limit tree. Specifically, Hartigan consistency permits two types of undesirable configurations which we term \emphover-segmentation and \emphimproper nesting. Moreover, Hartigan consistency is a limit property and does not directly quantify difference between trees. In this paper we identify two limit properties, \emphseparation and \emphminimality, which address both over-segmentation and improper nesting and together imply (but are not implied by) Hartigan consistency. We proceed to introduce a \emphmerge distortion metric between hierarchical clusterings and show that convergence in our distance implies both separation and minimality. We also prove that uniform separation and minimality imply convergence in the merge distortion metric. Furthermore, we show that our merge distortion metric is stable under perturbations of the density. Finally, we demonstrate applicability of these concepts by proving convergence results for two clustering algorithms. First, we show convergence (and hence separation and minimality) of the recent robust single linkage algorithm of Chaudhuri and Dasgupta (2010). Second, we provide convergence results on manifolds for topological split tree clustering.

We study the problem of maintaining the contour tree T of a terrain Sigma, represented as a triangulated xy-monotone surface, as the heights of its vertices vary continuously with time. We characterize the combinatorial changes in T and how they relate to topological changes in Sigma. We present a kinetic data structure (KDS) for maintaining T efficiently. It maintains certificates that fail, i.e., an event occurs, only when the heights of two adjacent vertices become equal or two saddle vertices appear on the same contour. Assuming that the heights of two vertices of Sigma become equal only O(1) times and these instances can be computed in O(1) time, the KDS processes O(kappa + n) events, where n is the number of vertices in Sigma and kappa is the number of events at which the combinatorial structure of T changes, and processes each event in O(log n) time. The KDS can be extended to maintain an augmented contour tree and a join/split tree.

The Reeb graph is a construction that studies a topological space through the lens of a real valued function. It has been commonly used in applications, however its use on real data means that it is desirable and increasingly necessary to have methods for comparison of Reeb graphs. Recently, several metrics on the set of Reeb graphs have been proposed. In this paper, we focus on two: the functional distortion distance and the interleaving distance. The former is based on the Gromov-Hausdorff distance, while the latter utilizes the equivalence between Reeb graphs and a particular class of cosheaves. However, both are defined by constructing a near-isomorphism between the two graphs of study. In this paper, we show that the two metrics are strongly equivalent on the space of Reeb graphs. Our result also implies the bottleneck stability for persistence diagrams in terms of the Reeb graph interleaving distance.

Given a real-valued function f defined over a manifold M embedded in R^d, we are interested in recovering structural information about f from the sole information of its values on a finite sample P. Existing methods provide approximation to the persistence diagram of f when geometric noise and functional noise are bounded. However, they fail in the presence of aberrant values, also called outliers, both in theory and practice. We propose a new algorithm that deals with outliers. We handle aberrant functional values with a method inspired from the k-nearest neighbors regression and the local median filtering, while the geometric outliers are handled using the distance to a measure. Combined with topological results on nested filtrations, our algorithm performs robust topological analysis of scalar fields in a wider range of noise models than handled by current methods. We provide theoretical guarantees and experimental results on the quality of our approximation of the sampled scalar field.

Metric graphs are ubiquitous in science and engineering. For example, many data are drawn from hidden spaces that are graph-like, such as the cosmic web. A metric graph offers one of the simplest yet still meaningful ways to represent the non-linear structure hidden behind the data. In this paper, we propose a new distance between two finite metric graphs, called the persistence-distortion distance, which draws upon a topological idea. This topological perspective along with the metric space viewpoint provide a new angle to the graph matching problem. Our persistence-distortion distance has two properties not shared by previous methods: First, it is stable against the perturbations of the input graph metrics. Second, it is a continuous distance measure, in the sense that it is defined on an alignment of the underlying spaces of input graphs, instead of merely their nodes. This makes our persistence-distortion distance robust against, for example, different discretizations of the same underlying graph. Despite considering the input graphs as continuous spaces, that is, taking all points into account, we show that we can compute the persistence-distortion distance in polynomial time. The time complexity for the discrete case where only graph nodes are considered is much faster.

In recent years, with the rapid growth in the amount of publicly available Volunteered Geographic Information (VGI) data, automatic map generation from GPS trajectories has attracted great attention. Maps generated from these data can for example complement commercial maps in less developed areas. Two main challenges in the automatic generation of maps from volunteered GPS data are the handling of noise and of non-homogeneous sampling of road segments (for example, roads in downtown area can receive significantly more GPS traces than roads in residential areas). In this paper, we present a novel framework for map reconstruction based on a topological idea: the Morse theory. In particular, the use of Morse theory and topological simplification allows us to handle the issues of both noise and non-homogeneous sampling in an elegant unified framework. Our algorithm is significantly simpler than previous approaches, both conceptually and implementation speaking. Little pre- and post-processing is required, and yet the algorithm can reconstruct robust road-networks from challenging data sets (such as GPS traces for Berlin or Beijing cities) that are comparable or better than the output of previous state-of-the-art approaches. The new algorithm is also orders of magnitude faster than previous approaches on large data sets (for example, the entire processing of the Berlin city data with about 27189 trajectories takes less than one minute).

We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions.

Algorithms for persistent homology are well-studied where homomorphisms are induced by inclusion maps. In this paper, we propose a practical algorithm for computing persistence under Z2 coefficients for a (monotone) sequence of general simplicial maps and show how these maps arise naturally in some applications of topological data analysis.

Let f be a continuous function defined on a topological space. As we increase the function value, connected components in the level set of f appear, disappear, merge, or split, and the Reeb graph tracks these changes. The join and split trees of f track the changes of connected components in the sublevel and superlevel set respectively. If the Reeb graph is loop-free, then it is a tree called the contour tree. Given a piecewise linear function f defined on a simplicial complex K, Carr, Snoeyink and Axen proposed a simple and elegant algorithm to compute the contour tree of f by "merging" its join and split trees in near-linear time.

Measuring the similarity of curves is a fundamental problem arising in many application fields. There has been considerable interest in several such measures, both in Euclidean space and in more general setting such as curves on Riemannian surfaces or curves in the plane minus a set of obstacles. However, so far, efficiently computable similarity measures for curves on general surfaces remain elusive. This paper aims at developing a natural curve similarity measure that can be easily extended and computed for curves on general orientable 2-manifolds. Specifically, we measure similarity between homotopic curves based on how hard it is to deform one curve into the other one continuously, and define this "hardness" as the minimum possible surface area swept by a homotopy between the curves. We consider cases where curves are embedded in the plane or on a triangulated orientable surface with genus $g$, and we present efficient algorithms (which are either quadratic or near linear time, depending on the setting) for both cases.

The efficiency of extracting topological information from point data depends largely on the complex that is built on top of the data points. From a computational viewpoint, the most favored complexes for this purpose have so far been Vietoris-Rips and witness complexes. While the ietoris-Rips complex is simple to compute and is a good vehicle for extracting topology of sampled spaces, its size is huge--particularly in high dimensions. The witness complex on the other hand enjoys a smaller size because of a subsampling, but fails to capture the topology in high dimensions unless imposed with extra structures. We investigate a complex called the graph induced complex that, to some extent, enjoys the advantages of both. It works on a subsample but still retains the power of capturing the topology as the Vietoris-Rips complex. It only needs a graph connecting the original sample points from which it builds a complex on the subsample thus taming the size considerably. We show that, using the graph induced complex one can (i) infer the one-dimensional homology of a manifold from a very lean subsample, (ii) reconstruct a surface in three dimension from a sparse subsample without computing Delaunay triangulations, (iii) infer the persistent homology groups of compact sets from a sufficiently dense sample. We provide experimental evidences in support of our theory.

Recently, various applications have motivated the study of spectral structures (eigenvalues and eigenfunctions) of the so-called Laplace-Beltrami operator of a manifold and their discrete versions. A popular choice for the discrete version is the so-called Gaussian weighted graph Laplacian which can be applied to point cloud data that samples a manifold. Naturally, the question of stability of the spectrum of this discrete Laplacian under the perturbation of the sampled manifold becomes important for its practical usage. Previous results showed that the spectra of both the manifold Laplacian and discrete Laplacian are stable when the perturbation is “nice” in the sense that it is restricted to a diffeomorphism with minor area distortion. However, this forbids, for example, small topological changes.

Blue noise sampling is an important component in many graphics applications, but existing techniques consider mainly the spatial positions of samples, making them less effective when handling problems with non-spatial features. Examples include biological distribution in which plant spacing is influenced by non-positional factors such as tree type and size, photon mapping in which photon flux and direction are not a direct function of the attached surface, and point cloud sampling in which the underlying surface is unknown a priori. These scenarios can benefit from blue noise sample distributions, but cannot be adequately handled by prior art. Inspired by bilateral filtering, we propose a bilateral blue noise sampling strategy. Our key idea is a general formulation to modulate the traditional sample distance measures, which are determined by sample position in spatial domain, with a similarity measure that considers arbitrary per sample attributes. This modulation leads to the notion of bilateral blue noise whose properties are influenced by not only the uniformity of the sample positions but also the similarity of the sample attributes. We describe how to incorporate our modulation into various sample analysis and synthesis methods, and demonstrate applications in object distribution, photon density estimation, and point cloud sub-sampling.

A special family of non-trivial loops on a surface called handle and tunnel loops associates closely to geometric features of "handles" and "tunnels" respectively in a 3D model. The identification of these handle and tunnel loops can benefit a broad range of applications from topology simplification/repair, and surface parameterization, to feature and shape recognition. Many of the existing efficient algorithms for computing non-trivial loops cannot be used to compute these special type of loops. The two algorithms known for computing handle and tunnel loops provably have a serious drawback that they both require a tessellation of the interior and exterior spaces bounded by the surface. Computing such a tessellation of three dimensional space around the surface is a non-trivial task and can be quite expensive. Furthermore, such a tessellation may need to refine the surface mesh, thus causing the undesirable side-effect of outputting the loops on an altered surface mesh. In this paper, we present an efficient algorithm to compute a basis for handle and tunnel loops without requiring any 3D tessellation. This saves time considerably for large meshes making the algorithm scalable while computing the loops on the original input mesh and not on some refined version of it. We use the concept of the Reeb graph which together with several key theoretical insights on linking number provide an initial set of loops that provably constitute a handle and a tunnel basis. We further develop a novel strategy to tighten these handle and tunnel basis loops to make them geometrically relevant. We demonstrate the efficiency and effectiveness of our algorithm as well as show its robustness against noise, and other anomalies in the input.

Abstract Reconstructing a surface mesh from a set of discrete point samples is a fundamental problem in geometric modeling. It becomes challenging in presence of ‘singularities’ such as boundaries, sharp features, and non‐manifolds. A few of the current research in reconstruction have addressed handling some of these singularities, but a unified approach to handle them all is missing. In this paper we allow the presence of various singularities by requiring that the sampled object is a collection of smooth surface patches with boundaries that can meet or intersect. Our algorithm first identifies and reconstructs the features where singularities occur. Next, it reconstructs the surface patches containing these feature curves. The identification and reconstruction of feature curves are achieved by a novel combination of the Gaussian weighted graph Laplacian and the Reeb graphs. The global reconstruction is achieved by a method akin to the well known Cocone reconstruction, but with weighted Delaunay triangulation that allows protecting the feature samples with balls. We provide various experimental results to demonstrate the effectiveness of our feature‐preserving singular surface reconstruction algorithm.

Availability of an effective tool for protein multiple structural alignment (MSTA) is essential for discovery and analysis of biologically significant structural motifs that can help solve functional annotation and drug design problems. Existing MSTA methods collect residue correspondences mostly through pairwise comparison of consecutive fragments, which can lead to suboptimal alignments, especially when the similarity among the proteins is low. We introduce a novel strategy based on: building a contact-window based motif library from the protein structural data, discovery and extension of common alignment seeds from this library, and optimal superimposition of multiple structures according to these alignment seeds by an enhanced partial order curve comparison method. The ability of our strategy to detect multiple correspondences simultaneously, to catch alignments globally, and to support flexible alignments, endorse a sensitive and robust automated algorithm that can expose similarities among protein structures even under low similarity conditions. Our method yields better alignment results compared to other popular MSTA methods, on several protein structure data sets that span various structural folds and represent different protein similarity levels. A web-based alignment tool, a downloadable executable, and detailed alignment results for the data sets used here are available at http://sacan.biomed. drexel.edu/Smolign and http://bio.cse.ohio-state.edu/Smolign.

Given a continuous function f:X -> S on a topological space X, its level set f-1(a) changes continuously as the real value a changes. Consequently, the connected components in the level sets appear, disappear, split and merge. The Reeb graph of f summarizes this information into a graph structure. Previous work on Reeb graph mainly focused on its efficient computation. In this paper, we initiate the study of two important aspects of the Reeb graph which can facilitate its broader applications in shape and data analysis. The first one is the approximation of the Reeb graph of a function on a smooth compact manifold M without boundary. The approximation is computed from a set of points P sampled from M. By leveraging a relation between the Reeb graph and the so-called vertical homology group, as well as between cycles in M and in a Rips complex constructed from P, we compute the H1-homology of the Reeb graph from P. It takes O(n log n) expected time, where n is the size of the 2-skeleton of the Rips complex. As a by-product, when M is an orientable 2-manifold, we also obtain an efficient near-linear time (expected) algorithm to compute the rank of H1(MM) from point data. The best known previous algorithm for this problem takes O(n3) time for point data.

Recovering hidden structure from complex and noisy non-linear data is one of the most fundamental problems in machine learning and statistical inference. While such data is often high-dimensional, it is of interest to approximate it with a low-dimensional or even one-dimensional space, since many important aspects of data are often intrinsically low-dimensional. Furthermore, there are many scenarios where the underlying structure is graph-like, e.g, river/road networks or various trajectories. In this paper, we develop a framework to extract, as well as to simplify, a one-dimensional "skeleton" from unorganized data using the Reeb graph. Our algorithm is very simple, does not require complex optimizations and can be easily applied to unorganized high-dimensional data such as point clouds or proximity graphs. It can also represent arbitrary graph structures in the data. We also give theoretical results to justify our method. We provide a number of experiments to demonstrate the effectiveness and generality of our algorithm, including comparisons to existing methods, such as principal curves. We believe that the simplicity and practicality of our algorithm will help to promote skeleton graphs as a data analysis tool for a broad range of applications.

Inference of topological and geometric attributes of a hidden manifold from its point data is a fundamental problem arising in many scientific studies and engineering applications. In this paper we present an algorithm to compute a set of loops from a point data that presumably sample a smooth manifold M ⊂ Rd. These loops approximate a shortest basis of the one dimensional homology group H1(M) over coefficients in finite field Z2. Previous results addressed the issue of computing the rank of the homology groups from point data, but there is no result on approximating the shortest basis of a manifold from its point sample. In arriving our result, we also present a polynomial time algorithm for computing a shortest basis of H1 (Κ) for any finite simplicial complex Κ whose edges have non-negative weights.

Given a continuous scalar field ƒ: X → where X is a topological space, a level set of ƒ is a set {x ∈ X : ƒ (x) = α} for some value α ∈ IR. The level sets of ƒ can be subdivided into connected components. As α changes continuously, the connected components in the level sets appear, disappear, split and merge. The Reeb graph of ƒ encodes these changes in connected components of level sets. It provides a simple yet meaningful abstraction of the input domain. As such, it has been used in a range of applications in fields such as graphics and scientific visualization.

Spectral methods have been widely used in a broad range of applications fields. One important object involved in such methods is the Laplace-Beltrami operator of a manifold. Indeed, a variety of work in graphics and geometric optimization uses the eigen-structures (i.e, the eigenvalues and eigenfunctions) of the Laplace operator. Applications include mesh smoothing, compression, editing, shape segmentation, matching, parameterization, and so on. While the Laplace operator is defined (mathematically) for a smooth domain, these applications often approximate a smooth manifold by a discrete mesh. The spectral structure of the manifold Laplacian is estimated from some discrete Laplace operator constructed from this mesh. In this paper, we study the important question of how well the spectrum computed from the discrete mesh approximates the true spectrum of the manifold Laplacian. We exploit a recent result on mesh Laplacian and provide the first convergence result to relate the spectrum constructed from a general mesh (approximating an m-manifold embedded in ℝd) with the true spectrum. We also study how stable these eigenvalues and their discrete approximations are when the underlying manifold is perturbed, and provide explicit bounds for the Laplacian spectra of two “close” manifolds, as well as a convergence result for their discrete approximations. Finally, we present various experimental results to demonstrate that these discrete spectra are both accurate and robust in practice.

Abstract Although understanding of shape features in the context of shape matching and retrieval has made considerable progress in recent years, the case for partial and incomplete models in presence of pose variations still begs a robust and efficient solution. A signature that encodes features at multi‐scales in a pose invariant manner is more appropriate for this case. The Heat Kernel Signature function from spectral theory exhibits this multi‐scale property. We show how this concept can be merged with the persistent homology to design a novel efficient pose‐oblivious matching algorithm for all models, be they partial, incomplete, or complete. We make the algorithm scalable so that it can handle large data sets. Several test results show the robustness of our approach.

Abstract Visual representation techniques enable perception and exploration of scientific data. Following the topological landscapes metaphor of Weber et al., we provide a new algorithm for visualizing scalar functions defined on simply connected domains of arbitrary dimension. For a potentially high dimensional scalar field, our algorithm produces a collection of, in some sense complete, two‐dimensional terrain models whose contour trees and corresponding topological persistences are identical to those of the input scalar field. The algorithm exactly preserves the volume of each region corresponding to an arc in the contour tree. We also introduce an efficiently computable metric on terrain models we generate. Based on this metric, we develop a tool that can help the users to explore the space of possible terrain models.

We study the shape matching problem under the Hausdorff distance and its variants. In the first part of the article, we consider two sets A,B of balls in R d , d =2,3, and wish to find a translation t that minimizes the Hausdorff distance between A+t , the set of all balls in A shifted by t , and B . We consider several variants of this problem. First, we extend the notion of Hausdorff distance from sets of points to sets of balls, so that each ball has to be matched with the nearest ball in the other set. We also consider the problem in the standard setting, by computing the Hausdorff distance between the unions of the two sets (as point sets). Second, we consider either all possible translations t (as is the standard approach), or consider only translations that keep the balls of A+t disjoint from those of B . We propose several exact and approximation algorithms for these problems. In the second part of the article, we note that the Hausdorff distance is sensitive to outliers, and thus consider two variants that are more robust: the root-mean-square (rms) and the summed Hausdorff distance. We propose efficient approximation algorithms for computing the minimum rms and the minimum summed Hausdorff distances under translation, between two point sets in R d . In order to obtain a fast algorithm for the summed Hausdorff distance, we propose a deterministic efficient dynamic data structure for maintaining an ϵ-approximation of the 1-median of a set of points in R d , under insertions and deletions.

Integration over a domain, such as a Euclidean space or a Riemannian manifold, is a fundamental problem across scientific fields. Many times, the underlying domain is only accessible through a discrete approximation, such as a set of points sampled from it, and it is crucial to be able to estimate integral in such discrete settings. In this paper, we study the problem of estimating the integral of a function defined over a k-submanifold embedded in $d$-dimensional space, from its function values at a set of sample points. Previously, such estimation is usually obtained in a statistical setting, where input data is typically assumed to be drawn from certain probabilistic distribution. Our paper is the first to consider this important problem of estimating integral from point clouds data (PCD) under the more general non-statistical setting, and provide certain theoretical guarantees. Our approaches consider the problem from a geometric point of view. Specifically, we estimate the integral by computing a weighted sum, and propose two weighting schemes: the Voronoi and the Principle Eigenvector schemes. The running time of both methods depends mostly on the intrinsic dimension of the underlying manifold, instead of on the ambient dimensions. We show that the estimation based on the Voronoi scheme converges to the true integral under the so-called (ε, δ)-sampling condition with explicit error bound presented. This is the first result of this sort for estimating integral from general PCD. For the Principle Eigenvector scheme, although no theoretical guarantee is established, we present its connection to the Heat diffusion operator, and illustrate justifications behind its construction. Experimental results show that both new methods consistently produce more accurate integral estimations than common statistical methods under various sampling conditions.

We present an algorithm for approximating the Laplace-Beltrami operator from an arbitrary point cloud obtained from a k-dimensional manifold embedded in the d-dimensional space. We show that this PCD Laplace (Point-Cloud Data Laplace) operator converges to the Laplace-Beltrami operator on the underlying manifold as the point cloud becomes denser. Unlike the previous work, we do not assume that the data samples are independent identically distributed from a probability distribution and do not require a global mesh. The resulting algorithm is easy to implement. We present experimental results indicating that even for point sets sampled from a uniform distribution, PCD Laplace converges faster than the weighted graph Laplacian. We also show that using our PCD Laplacian we can directly estimate certain geometric invariants, such as manifold area.

Curve matching is a fundamental problem that occurs in many applications. In this paper, we study the problem of measuring partial similarity between curves. Specifically, given two curves, we wish to maximize the total length of subcurves that are close to each other, where closeness is measured by the Fréchet distance, a common distance measure for curves. The resulting maximal length is called the partial Fréchet similarity between the two input curves. Given two polygonal curves P and Q in IRd of size m and n, respectively, we present the first exact algorithm that runs in polynomial time to compute ℱδ(P, Q), the partial Fréchet similarity between P and Q, under the L1 and L∞ norms. Specifically, we formulate the problem of computing ℱδ(P, Q) as a longest path problem, and solve it in O(mn(m + n) log(mn)) time, under the L1 or L∞ norm, using a “shortest-path map” type decomposition. To the best of our knowledge, this is the first paper to study this natural definition of partial curve similarity in the continuous setting (with all points in the curve considered), and present a polynomial-time exact algorithm for it.

Abstract The gradient of a function defined on a manifold is perhaps one of the most important differential objects in data analysis. Most often in practice, the input function is available only at discrete points sampled from the underlying manifold, and the manifold is approximated by either a mesh or simply a point cloud. While many methods exist for computing gradients of a function defined over a mesh, computing and simplifying gradients and related quantities such as critical points, of a function from a point cloud is non‐trivial. In this paper, we initiate the investigation of computing gradients under a different metric on the manifold from the original natural metric induced from the ambient space. Specifically, we map the input manifold to the eigenspace spanned by its Laplacian eigenfunctions, and consider the so‐called diffusion distance metric associated with it. We show the relation of gradient under this metric with that under the original metric. It turns out that once the Laplace operator is constructed, it is easier to approximate gradients in the eigenspace for discrete inputs (especially point clouds) and it is robust to noises in the input function and in the underlying manifold. More importantly, we can easily smooth the gradient field at different scales within this eigenspace framework. We demonstrate the use of our new eigen‐gradients with two applications: approximating / simplifying the critical points of a function, and the Jacobi sets of two input functions (which describe the correlation between these two functions), from point clouds data.

In recent years a considerable amount of work in graphics and geometric optimization used tools based on the Laplace-Beltrami operator on a surface. The applications of the Laplacian include mesh editing, surface smoothing, and shape interpolations among others. However, it has been shown [13, 24, 26] that the popular cotangent approximation schemes do not provide convergent point-wise (or even L2) estimates, while many applications rely on point-wise estimation. Existence of such schemes has been an open question [13].

Communication between arbitrary pairs of nodes has become critical to support in emerging sensor networking applications. Traditional routing techniques for multi-hop wireless networks either require high control overhead in computing and maintaining routes, or may lead to unbounded route-stretch. In order to bound the route-stretch, we propose a distributed shortest-path roadmap based routing paradigm that embodies two ideas: routing hole approximation that summaries the critical information about hole boundaries and controlled advertisement that advertises the boundary information of each hole within limited neighborhoods. We show that our approach makes a desired tradeoff between the worst case route-stretch and the message overhead through both analysis and simulations.

BACKGROUND: Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data. Hence there is a pressing need to be able to interpret and identify novel folding features from them. RESULTS: In this paper, we model each folding trajectory as a multi-dimensional curve. We then develop an effective multiple curve comparison (MCC) algorithm, called the enhanced partial order (EPO) algorithm, to extract features from a set of diverse folding trajectories, including both successful and unsuccessful simulation runs. The EPO algorithm addresses several new challenges presented by comparing high dimensional curves coming from folding trajectories. A detailed case study on miniprotein Trp-cage 1 demonstrates that our algorithm can detect similarities at rather low level, and extract biologically meaningful folding events. CONCLUSION: The EPO algorithm is general and applicable to a wide range of applications. We demonstrate its generality and effectiveness by applying it to aligning multiple protein structures with low similarities. For user's convenience, we provide a web server for the algorithm at http://db.cse.ohio-state.edu/EPO.

MOTIVATION: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features. RESULTS: We propose Local Feature Mining in Proteins (LFM-Pro) as a framework for automatically discovering family-specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and biochemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on trypsin-like serine proteases family of proteins and on a challenging classification dataset via comparison with DALI. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features. AVAILABILITY: The software and the datasets are freely available for academic research use at http://bioinfo.ceng.metu.edu.tr/Pub/LFMPro.

High power consumption not only leads to short battery life for hand-held devices but also causes on-chip thermal and reliability problems in general. As power consumption is proportional to the square of supply voltage, reducing supply voltage can significantly reduce power consumption. Multi-supply voltage (MSV) has previously been introduced to provide finer grain power and performance tradeoff. In this paper, we propose a methodology on top of a set of algorithms to exploit nontrivial voltage island boundaries for optimal power versus design-cost tradeoff under performance requirement. Our algorithms are efficient, robust, and error-bounded and can be flexibly tuned to optimize for various design objectives (e.g., minimal power within a given number of voltage islands, or minimal fragmentation in voltage islands within a given power bound) depending on the design requirement. Our experiment on real industry designs shows a tenfold improvement of our method over current logical-boundary-based industry approach.

High power consumption not only leads to short battery life for handheld devices, but also causes on-chip thermal and reliability problems in general. As power consumption is proportional to the square of supply voltage, reducing supply voltage can significantly reduce power consumption. Multi-supply voltage (MSV) has previously been introduced to provide finer-grain power and performance trade-off. In this work we propose a methodology on top of a set of algorithms to exploit non-trivial voltage island boundaries for optimal power versus design cost trade-off under performance requirement. Our algorithms are efficient, robust and error-bounded, and can be flexibly tuned to optimize for various design objectives (e.g., minimal power within a given number of voltage islands, or minimal fragmentation in voltage islands within a given power bound) depending on the design requirement. Our experiment on real industry designs shows a ten-fold improvement of our method over current logical-boundary based industry approach.

Given a smoothly embedded 2-manifold in ℝ3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking.

A triangulation of a set S of points in the plane is a subdivision of the convex hull of S into triangles whose vertices are points of S. Given a set S of n points in ℝ3, each moving independently, we wish to maintain a triangulation of S. The triangulation needs to be updated periodically as the points in S move, so the goal is to maintain a triangulation with small number of topological events, each being the insertion or deletion of an edge. We propose a kinetic data structure (KDS) that processes n2 2O(√log n•log log n ) topological events, with high probability, if the trajectories of input points are algebraic curves of fixed degree. Each topological event can be processed in O(log n) time. This is the first known KDS for maintaining a triangulation that processes near-quadratic number of topological events, and almost matches the Ω(n2) lower bound, [1]. The number of topological events can be reduced to nk • 2O(√log k•log log n ) if only K of the points are moving.

Given a set $\mathcal{H}$ of n hyperplanes in ${\Bbb R}^d$, we present an algorithm that $\eps$-approximates the extent between the top and bottom k levels of the arrangement of $\mathcal{H}$ in time $O(n + (k/\eps)^c)$, where c is a constant depending on d. The algorithm relies on computing a subset of $\mathcal{H}$ of size $O(k/\eps^{d-1})$, in near linear time, such that the k-level of the arrangement of the subset approximates that of the original arrangement. Using this algorithm, we propose efficient approximation algorithms for shape fitting with outliers for various shapes. These are the first algorithms to handle outliers efficiently for the shape fitting problems considered.

We study the shape matching problem under the Hausdorff distance and its variants. Specifically, we consider two sets A,B of balls in Rd, d=2,3, and wish to find a translation t that minimizes the Hausdorff distance between A+t, the set of all balls in A shifted by t, and B. We consider several variants of this problem. First, we extend the notion of Hausdorff distance from sets of points to sets of balls, so that each ball has to be matched with the nearest ball in the other set. We also consider the problem in the standard setting, by computing the Hausdorff distance between the unions of the two sets (as point sets). Second, we consider either all possible translates t (as is the standard approach), or consider only translations that keep the balls of A+t disjoint from those of B. We propose several exact and approximation algorithms for these problems. Since the Hausdorff distance is sensitive to outliers, we also propose efficient approximation algorithms for computing the minimum root mean-square (rms) and the minimum summed Hausdorff distance, under translation, between two point sets in Rd. In order to obtain a fast algorithm for the summed Hausdorff distance, we propose a deterministic efficient dynamic data structure for maintaining an e-approximation of the 1-median of a set of points, under insertion and deletion.

Given a set H of n hyperplanes in IR d, we present an algorithm that ε-approximates the extent between the top and bottom k levels of the arrangement of H in time O(n+(k/ε) c), where c is a constant depending on d. The algorithm relies on computing a subset of H of size O(k/ε d−1), in near linear time, such that the k-level of the arrangement of the subset approximates that of the original arrangement. Using this algorithm, we propose efficient approximation algorithms for shape fitting with outliers for various shapes. This is the first algorithms to handle outliers efficiently for the shape fitting problems considered. 1