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Villar, Soledad


On the equivalence between graph isomorphism testing and function approximation with GNNs

Neural Information Processing Systems

Graph neural networks (GNNs) have achieved lots of success on graph-structured data. In light of this, there has been increasing interest in studying their representation power. One line of work focuses on the universal approximation of permutation-invariant functions by certain classes of GNNs, and another demonstrates the limitation of GNNs via graph isomorphism tests. Our work connects these two perspectives and proves their equivalence. We further develop a framework of the representation power of GNNs with the language of sigma-algebra, which incorporates both viewpoints.


Can graph neural networks count substructures?

arXiv.org Machine Learning

The ability to detect and count certain substructures in graphs is important for solving many tasks on graph-structured data, especially in the contexts of computational chemistry and biology as well as social network analysis. Inspired by this, we propose to study the expressive power of graph neural networks (GNNs) via their ability to count attributed graph substructures, extending recent works that examine their power in graph isomorphism testing and function approximation. We distinguish between two types of substructure counting: matching-count and containment-count, and establish both positive and negative answers for popular GNN architectures. Specifically, we prove that Message Passing Neural Networks (MPNNs), 2-Weisfeiler-Lehman (2-WL) and 2-Invariant Graph Networks (2-IGNs) cannot perform matching-count of substructures consisting of 3 or more nodes, while they can perform containment-count of star-shaped substructures. We also prove positive results for k-WL and k-IGNs as well as negative results for k-WL with limited number of iterations. We then conduct experiments that support the theoretical results for MPNNs and 2-IGNs, and demonstrate that local relational pooling strategies inspired by Murphy et al. (2019) are more effective for substructure counting. In addition, as an intermediary step, we prove that 2-WL and 2-IGNs are equivalent in distinguishing non-isomorphic graphs, partly answering an open problem raised in Maron et al. (2019).


MREC: a fast and versatile framework for aligning and matching point clouds with applications to single cell molecular data

arXiv.org Machine Learning

Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to partition the data, match the partitions, and then recursively match the points within each pair of identified partitions. The matching itself is done using black box matching procedures that are too expensive to run on the entire data set. Using an absolute measure of the quality of a matching, the framework supports optimization over parameters including partitioning procedures and matching algorithms. By design, MREC can be applied to extremely large data sets. We analyze the procedure to describe when we can expect it to work well and demonstrate its flexibility and power by applying it to a number of alignment problems arising in the analysis of single cell molecular data.


On the equivalence between graph isomorphism testing and function approximation with GNNs

arXiv.org Machine Learning

Graph neural networks (GNNs) have achieved lots of success on graph-structured data. In the light of this, there has been increasing interest in studying their representation power. One line of work focuses on the universal approximation of permutation-invariant functions by certain classes of GNNs, and another demonstrates the limitation of GNNs via graph isomorphism tests. Our work connects these two perspectives and proves their equivalence. We further develop a framework of the representation power of GNNs with the language of sigma-algebra, which incorporates both viewpoints. Using this framework, we compare the expressive power of different classes of GNNs as well as other methods on graphs. In particular, we prove that order-2 Graph G-invariant networks fail to distinguish non-isomorphic regular graphs with the same degree. We then extend them to a new architecture, Ring-GNNs, which succeeds on distinguishing these graphs and provides improvements on real-world social network datasets.


SqueezeFit: Label-aware dimensionality reduction by semidefinite programming

arXiv.org Machine Learning

The last decade of sampling theory has transformed the way we reconstruct signals from measurements. Forexample, the now-established theory of compressed sensing allows one to reconstruct a signal from a number of random linear measurements that is proportional to the complexity of that signal [11, 8, 12], potentially speeding up MRI scans by a factor of five [24]. Today, we witness major technological advancesin machine learning, where neural networks have recently achieved unprecedented performance in image classification and elsewhere [19, 31]. This motivates another fundamental problem for sampling theory: How many samples are necessary to enable signal classification? For instance, why waste time collecting enough samples to completely reconstruct a given signal if you only need to detect whether the signal contains an anomaly?


SUNLayer: Stable denoising with generative networks

arXiv.org Machine Learning

It has been experimentally established that deep neural networks can be used to produce good generative models for real world data. It has also been established that such generative models can be exploited to solve classical inverse problems like compressed sensing and super resolution. In this work we focus on the classical signal processing problem of image denoising. We propose a theoretical setting that uses spherical harmonics to identify what mathematical properties of the activation functions will allow signal denoising with local methods.


Monte Carlo approximation certificates for k-means clustering

arXiv.org Machine Learning

Efficient algorithms for $k$-means clustering frequently converge to suboptimal partitions, and given a partition, it is difficult to detect $k$-means optimality. In this paper, we develop an a posteriori certifier of approximate optimality for $k$-means clustering. The certifier is a sub-linear Monte Carlo algorithm based on Peng and Wei's semidefinite relaxation of $k$-means. In particular, solving the relaxation for small random samples of the dataset produces a high-confidence lower bound on the $k$-means objective, and being sub-linear, our algorithm is faster than $k$-means++ when the number of data points is large. We illustrate the performance of our algorithm with both numerical experiments and a performance guarantee: If the data points are drawn independently from any mixture of two Gaussians over $\mathbb{R}^m$ with identity covariance, then with probability $1-O(1/m)$, our $\operatorname{poly}(m)$-time algorithm produces a 3-approximation certificate with 99% confidence.


A Note on Learning Algorithms for Quadratic Assignment with Graph Neural Networks

arXiv.org Machine Learning

Many inverse problems are formulated as optimization problems over certain appropriate input distributions. Recently, there has been a growing interest in understanding the computational hardness of these optimization problems, not only in the worst case, but in an average-complexity sense under this same input distribution. In this note, we are interested in studying another aspect of hardness, related to the ability to learn how to solve a problem by simply observing a collection of previously solved instances. These are used to supervise the training of an appropriate predictive model that parametrizes a broad class of algorithms, with the hope that the resulting "algorithm" will provide good accuracy-complexity tradeoffs in the average sense. We illustrate this setup on the Quadratic Assignment Problem, a fundamental problem in Network Science. We observe that data-driven models based on Graph Neural Networks offer intriguingly good performance, even in regimes where standard relaxation based techniques appear to suffer.


A polynomial-time relaxation of the Gromov-Hausdorff distance

arXiv.org Machine Learning

The Gromov-Hausdorff distance provides a metric on the set of isometry classes of compact metric spaces. Unfortunately, computing this metric directly is believed to be computationally intractable. Motivated by applications in shape matching and point-cloud comparison, we study a semidefinite programming relaxation of the Gromov-Hausdorff metric. This relaxation can be computed in polynomial time, and somewhat surprisingly is itself a pseudometric. We describe the induced topology on the set of compact metric spaces. Finally, we demonstrate the numerical performance of various algorithms for computing the relaxed distance and apply these algorithms to several relevant data sets. In particular we propose a greedy algorithm for finding the best correspondence between finite metric spaces that can handle hundreds of points.


Clustering subgaussian mixtures by semidefinite programming

arXiv.org Machine Learning

We introduce a model-free relax-and-round algorithm for k-means clustering based on a semidefinite relaxation due to Peng and Wei. The algorithm interprets the SDP output as a denoised version of the original data and then rounds this output to a hard clustering. We provide a generic method for proving performance guarantees for this algorithm, and we analyze the algorithm in the context of subgaussian mixture models. We also study the fundamental limits of estimating Gaussian centers by k-means clustering in order to compare our approximation guarantee to the theoretically optimal k-means clustering solution.