Soledad Villar

Sharut Gupta, Joshua Robinson, Derek Lim et al. · mit

Self-supervised learning converts raw perceptual data such as images to a compact space where simple Euclidean distances measure meaningful variations in data. In this paper, we extend this formulation by adding additional geometric structure to the embedding space by enforcing transformations of input space to correspond to simple (i.e., linear) transformations of embedding space. Specifically, in the contrastive learning setting, we introduce an equivariance objective and theoretically prove that its minima forces augmentations on input space to correspond to rotations on the spherical embedding space. We show that merely combining our equivariant loss with a non-collapse term results in non-trivial representations, without requiring invariance to data augmentations. Optimal performance is achieved by also encouraging approximate invariance, where input augmentations correspond to small rotations. Our method, CARE: Contrastive Augmentation-induced Rotational Equivariance, leads to improved performance on downstream tasks, and ensures sensitivity in embedding space to important variations in data (e.g., color) that standard contrastive methods do not achieve. Code is available at https://github.com/Sharut/CARE.

Soledad Villar, Weichi Yao, David W. Hogg et al.

Units equivariance (or units covariance) is the exact symmetry that follows from the requirement that relationships among measured quantities of physics relevance must obey self-consistent dimensional scalings. Here, we express this symmetry in terms of a (non-compact) group action, and we employ dimensional analysis and ideas from equivariant machine learning to provide a methodology for exactly units-equivariant machine learning: For any given learning task, we first construct a dimensionless version of its inputs using classic results from dimensional analysis, and then perform inference in the dimensionless space. Our approach can be used to impose units equivariance across a broad range of machine learning methods which are equivariant to rotations and other groups. We discuss the in-sample and out-of-sample prediction accuracy gains one can obtain in contexts like symbolic regression and emulation, where symmetry is important. We illustrate our approach with simple numerical examples involving dynamical systems in physics and ecology.

Soledad Villar, David W. Hogg, Weichi Yao et al.

Any representation of data involves arbitrary investigator choices. Because those choices are external to the data-generating process, each choice leads to an exact symmetry, corresponding to the group of transformations that takes one possible representation to another. These are the passive symmetries; they include coordinate freedom, gauge symmetry, and units covariance, all of which have led to important results in physics. In machine learning, the most visible passive symmetry is the relabeling or permutation symmetry of graphs. Our goal is to understand the implications for machine learning of the many passive symmetries in play. We discuss dos and don'ts for machine learning practice if passive symmetries are to be respected. We discuss links to causal modeling, and argue that the implementation of passive symmetries is particularly valuable when the goal of the learning problem is to generalize out of sample. This paper is conceptual: It translates among the languages of physics, mathematics, and machine-learning. We believe that consideration and implementation of passive symmetries might help machine learning in the same ways that it transformed physics in the twentieth century.

Ningyuan Huang, Soledad Villar, Carey E. Priebe et al.

Graph Neural Networks (GNNs) are powerful deep learning methods for Non-Euclidean data. Popular GNNs are message-passing algorithms (MPNNs) that aggregate and combine signals in a local graph neighborhood. However, shallow MPNNs tend to miss long-range signals and perform poorly on some heterophilous graphs, while deep MPNNs can suffer from issues like over-smoothing or over-squashing. To mitigate such issues, existing works typically borrow normalization techniques from training neural networks on Euclidean data or modify the graph structures. Yet these approaches are not well-understood theoretically and could increase the overall computational complexity. In this work, we draw inspirations from spectral graph embedding and propose $\texttt{PowerEmbed}$ -- a simple layer-wise normalization technique to boost MPNNs. We show $\texttt{PowerEmbed}$ can provably express the top-$k$ leading eigenvectors of the graph operator, which prevents over-smoothing and is agnostic to the graph topology; meanwhile, it produces a list of representations ranging from local features to global signals, which avoids over-squashing. We apply $\texttt{PowerEmbed}$ in a wide range of simulated and real graphs and demonstrate its competitive performance, particularly for heterophilous graphs.

Jan Böker, Ron Levie, Ningyuan Huang et al.

Numerous recent works have analyzed the expressive power of message-passing graph neural networks (MPNNs), primarily utilizing combinatorial techniques such as the $1$-dimensional Weisfeiler-Leman test ($1$-WL) for the graph isomorphism problem. However, the graph isomorphism objective is inherently binary, not giving insights into the degree of similarity between two given graphs. This work resolves this issue by considering continuous extensions of both $1$-WL and MPNNs to graphons. Concretely, we show that the continuous variant of $1$-WL delivers an accurate topological characterization of the expressive power of MPNNs on graphons, revealing which graphs these networks can distinguish and the level of difficulty in separating them. We identify the finest topology where MPNNs separate points and prove a universal approximation theorem. Consequently, we provide a theoretical framework for graph and graphon similarity combining various topological variants of classical characterizations of the $1$-WL. In particular, we characterize the expressive power of MPNNs in terms of the tree distance, which is a graph distance based on the concept of fractional isomorphisms, and substructure counts via tree homomorphisms, showing that these concepts have the same expressive power as the $1$-WL and MPNNs on graphons. Empirically, we validate our theoretical findings by showing that randomly initialized MPNNs, without training, exhibit competitive performance compared to their trained counterparts. Moreover, we evaluate different MPNN architectures based on their ability to preserve graph distances, highlighting the significance of our continuous $1$-WL test in understanding MPNNs' expressivity.

Ningyuan Huang, Ron Levie, Soledad Villar

Graph neural networks (GNNs) are commonly described as being permutation equivariant with respect to node relabeling in the graph. This symmetry of GNNs is often compared to the translation equivariance of Euclidean convolution neural networks (CNNs). However, these two symmetries are fundamentally different: The translation equivariance of CNNs corresponds to symmetries of the fixed domain acting on the image signals (sometimes known as active symmetries), whereas in GNNs any permutation acts on both the graph signals and the graph domain (sometimes described as passive symmetries). In this work, we focus on the active symmetries of GNNs, by considering a learning setting where signals are supported on a fixed graph. In this case, the natural symmetries of GNNs are the automorphisms of the graph. Since real-world graphs tend to be asymmetric, we relax the notion of symmetries by formalizing approximate symmetries via graph coarsening. We present a bias-variance formula that quantifies the tradeoff between the loss in expressivity and the gain in the regularity of the learned estimator, depending on the chosen symmetry group. To illustrate our approach, we conduct extensive experiments on image inpainting, traffic flow prediction, and human pose estimation with different choices of symmetries. We show theoretically and empirically that the best generalization performance can be achieved by choosing a suitably larger group than the graph automorphism, but smaller than the permutation group.

Ben Blum-Smith, Soledad Villar

Inspired by constraints from physical law, equivariant machine learning restricts the learning to a hypothesis class where all the functions are equivariant with respect to some group action. Irreducible representations or invariant theory are typically used to parameterize the space of such functions. In this article, we introduce the topic and explain a couple of methods to explicitly parameterize equivariant functions that are being used in machine learning applications. In particular, we explicate a general procedure, attributed to Malgrange, to express all polynomial maps between linear spaces that are equivariant under the action of a group $G$, given a characterization of the invariant polynomials on a bigger space. The method also parametrizes smooth equivariant maps in the case that $G$ is a compact Lie group.

Charles Clum, Dustin G. Mixon, Soledad Villar et al.

We introduce a sketch-and-solve approach to speed up the Peng-Wei semidefinite relaxation of k-means clustering. When the data is appropriately separated we identify the k-means optimal clustering. Otherwise, our approach provides a high-confidence lower bound on the optimal k-means value. This lower bound is data-driven; it does not make any assumption on the data nor how it is generated. We provide code and an extensive set of numerical experiments where we use this approach to certify approximate optimality of clustering solutions obtained by k-means++.

Luana Ruiz, Ningyuan Huang, Soledad Villar

In this work we propose a random graph model that can produce graphs at different levels of sparsity. We analyze how sparsity affects the graph spectra, and thus the performance of graph neural networks (GNNs) in node classification on dense and sparse graphs. We compare GNNs with spectral methods known to provide consistent estimators for community detection on dense graphs, a closely related task. We show that GNNs can outperform spectral methods on sparse graphs, and illustrate these results with numerical examples on both synthetic and real graphs.

Nabeel Sarwar, Wilson Gregory, George A Kevrekidis et al.

Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and computationally intractable. Here we introduce MarkerMap, a generative model for selecting minimal gene sets which are maximally informative of cell type origin and enable whole transcriptome reconstruction. MarkerMap provides a scalable framework for both supervised marker selection, aimed at identifying specific cell type populations, and unsupervised marker selection, aimed at gene expression imputation and reconstruction. We benchmark MarkerMap's competitive performance against previously published approaches on real single cell gene expression data sets. MarkerMap is available as a pip installable package, as a community resource aimed at developing explainable machine learning techniques for enhancing interpretability in single-cell studies.

Efe Onaran, Soledad Villar

The shuffled linear regression problem aims to recover linear relationships in datasets where the correspondence between input and output is unknown. This problem arises in a wide range of applications including survey data, in which one needs to decide whether the anonymity of the responses can be preserved while uncovering significant statistical connections. In this work, we propose a novel optimization algorithm for shuffled linear regression based on a posterior-maximizing objective function assuming Gaussian noise prior. We compare and contrast our approach with existing methods on synthetic and real data. We show that our approach performs competitively while achieving empirical running-time improvements. Furthermore, we demonstrate that our algorithm is able to utilize the side information in the form of seeds, which recently came to prominence in related problems.

Carey E. Priebe, Ningyuan Huang, Soledad Villar et al.

Deep neural networks (DNNs) are capable of perfectly fitting the training data, including memorizing noisy data. It is commonly believed that memorization hurts generalization. Therefore, many recent works propose mitigation strategies to avoid noisy data or correct memorization. In this work, we step back and ask the question: Can deep learning be robust against massive label noise without any mitigation? We provide an affirmative answer for the case of symmetric label noise: We find that certain DNNs, including under-parameterized and over-parameterized models, can tolerate massive symmetric label noise up to the information-theoretic threshold. By appealing to classical statistical theory and universal consistency of DNNs, we prove that for multiclass classification, $L_1$-consistent DNN classifiers trained under symmetric label noise can achieve Bayes optimality asymptotically if the label noise probability is less than $\frac{K-1}{K}$, where $K \ge 2$ is the number of classes. Our results show that for symmetric label noise, no mitigation is necessary for $L_1$-consistent estimators. We conjecture that for general label noise, mitigation strategies that make use of the noisy data will outperform those that ignore the noisy data.

George A. Kevrekidis, Zan Ahmad, Mauro Maggioni et al.

Conformal Autoencoders are a neural network architecture that imposes orthogonality conditions between the gradients of latent variables to obtain disentangled representations of data. In this work we show that orthogonality relations within the latent layer of the network can be leveraged to infer the intrinsic dimensionality of nonlinear manifold data sets (locally characterized by the dimension of their tangent space), while simultaneously computing encoding and decoding (embedding) maps. We outline the relevant theory relying on differential geometry, and describe the corresponding gradient-descent optimization algorithm. The method is applied to several data sets and we highlight its applicability, advantages, and shortcomings. In addition, we demonstrate that the same computational technology can be used to build coordinate invariance to local group actions when defined only on a (reduced) submanifold of the embedding space.

Yuxin Ma, Nan Chen, Mateo Díaz et al.

Modern large-scale neural networks are often trained and released in multiple sizes to accommodate diverse inference budgets. To improve efficiency, recent work has explored model upscaling: initializing larger models from trained smaller ones in order to transfer knowledge and accelerate convergence. However, this method can be sensitive to hyperparameters that need to be tuned at the target upscaled model size, which is prohibitively costly to do directly. It remains unclear whether the most common workaround -- tuning on smaller models and extrapolating via hyperparameter scaling laws -- is still sound when using upscaling. We address this with principled approaches to upscaling with respect to model widths and efficiently tuning hyperparameters in this setting. First, motivated by $μ$P and any-dimensional architectures, we introduce a general upscaling method applicable to a broad range of architectures and optimizers, backed by theory guaranteeing that models are equivalent to their widened versions and allowing for rigorous analysis of infinite-width limits. Second, we extend the theory of $μ$Transfer to a hyperparameter transfer technique for models upscaled using our method and empirically demonstrate that this method is effective on realistic datasets and architectures.

Valentino F. Foit, David W. Hogg, Soledad Villar

Many machine learning tasks in the natural sciences are precisely equivariant to particular symmetries. Nonetheless, equivariant methods are often not employed, perhaps because training is perceived to be challenging, or the symmetry is expected to be learned, or equivariant implementations are seen as hard to build. Group averaging is an available technique for these situations. It happens at test time; it can make any trained model precisely equivariant at a (often small) cost proportional to the size of the group; it places no requirements on model structure or training. It is known that, under mild conditions, the group-averaged model will have a provably better prediction accuracy than the original model. Here we show that an inexpensive group averaging can improve accuracy in practice. We take well-established benchmark machine learning models of differential equations in which certain symmetries ought to be obeyed. At evaluation time, we average the models over a small group of symmetries. Our experiments show that this procedure always decreases the average evaluation loss, with improvements of up to 37\% in terms of the VRMSE. The averaging produces visually better predictions for continuous dynamics. This short paper shows that, under certain common circumstances, there are no disadvantages to imposing exact symmetries; the ML4PS community should consider group averaging as a cheap and simple way to improve model accuracy.

Weichi Yao, Kate Storey-Fisher, David W. Hogg et al.

Physical systems obey strict symmetry principles. We expect that machine learning methods that intrinsically respect these symmetries should have higher prediction accuracy and better generalization in prediction of physical dynamics. In this work we implement a principled model based on invariant scalars, and release open-source code. We apply this Scalars method to a simple chaotic dynamical system, the springy double pendulum. We show that the Scalars method outperforms state-of-the-art approaches for learning the properties of physical systems with symmetries, both in terms of accuracy and speed. Because the method incorporates the fundamental symmetries, we expect it to generalize to different settings, such as changes in the force laws in the system.

Nan Chen, Soledad Villar, Soufiane Hayou

Low-Rank Adaptation (LoRA) is a standard tool for parameter-efficient finetuning of large models. While it induces a small memory footprint, its training dynamics can be surprisingly complex as they depend on several hyperparameters such as initialization, adapter rank, and learning rate. In particular, it is unclear how the optimal learning rate scales with adapter rank, which forces practitioners to re-tune the learning rate whenever the rank is changed. In this paper, we introduce Maximal-Update Adaptation ($μ$A), a theoretical framework that characterizes how the "optimal" learning rate should scale with model width and adapter rank to produce stable, non-vanishing feature updates under standard configurations. $μ$A is inspired from the Maximal-Update Parametrization ($μ$P) in pretraining. Our analysis leverages techniques from hyperparameter transfer and reveals that the optimal learning rate exhibits different scaling patterns depending on initialization and LoRA scaling factor. Specifically, we identify two regimes: one where the optimal learning rate remains roughly invariant across ranks, and another where it scales inversely with rank. We further identify a configuration that allows learning rate transfer from LoRA to full finetuning, drastically reducing the cost of learning rate tuning for full finetuning. Experiments across language, vision, vision--language, image generation, and reinforcement learning tasks validate our scaling rules and show that learning rates tuned on LoRA transfer reliably to full finetuning.

Mauricio Velasco, Kaiying O'Hare, Bernardo Rychtenberg et al.

Graph neural networks (GNNs) provide state-of-the-art results in a wide variety of tasks which typically involve predicting features at the vertices of a graph. They are built from layers of graph convolutions which serve as a powerful inductive bias for describing the flow of information among the vertices. Often, more than one data modality is available. This work considers a setting in which several graphs have the same vertex set and a common vertex-level learning task. This generalizes standard GNN models to GNNs with several graph operators that do not commute. We may call this model graph-tuple neural networks (GtNN). In this work, we develop the mathematical theory to address the stability and transferability of GtNNs using properties of non-commuting non-expansive operators. We develop a limit theory of graphon-tuple neural networks and use it to prove a universal transferability theorem that guarantees that all graph-tuple neural networks are transferable on convergent graph-tuple sequences. In particular, there is no non-transferable energy under the convergence we consider here. Our theoretical results extend well-known transferability theorems for GNNs to the case of several simultaneous graphs (GtNNs) and provide a strict improvement on what is currently known even in the GNN case. We illustrate our theoretical results with simple experiments on synthetic and real-world data. To this end, we derive a training procedure that provably enforces the stability of the resulting model.

Ben Blum-Smith, Ningyuan Huang, Marco Cuturi et al.

In this work, we present a mathematical formulation for machine learning of (1) functions on symmetric matrices that are invariant with respect to the action of permutations by conjugation, and (2) functions on point clouds that are invariant with respect to rotations, reflections, and permutations of the points. To achieve this, we provide a general construction of generically separating invariant features using ideas inspired by Galois theory. We construct $O(n^2)$ invariant features derived from generators for the field of rational functions on $n\times n$ symmetric matrices that are invariant under joint permutations of rows and columns. We show that these invariant features can separate all distinct orbits of symmetric matrices except for a measure zero set; such features can be used to universally approximate invariant functions on almost all weighted graphs. For point clouds in a fixed dimension, we prove that the number of invariant features can be reduced, generically without losing expressivity, to $O(n)$, where $n$ is the number of points. We combine these invariant features with DeepSets to learn functions on symmetric matrices and point clouds with varying sizes. We empirically demonstrate the feasibility of our approach on molecule property regression and point cloud distance prediction.

Eitan Levin, Yuxin Ma, Mateo Díaz et al.

Many modern learning tasks require models that can take inputs of varying sizes. Consequently, dimension-independent architectures have been proposed for domains where the inputs are graphs, sets, and point clouds. Recent work on graph neural networks has explored whether a model trained on low-dimensional data can transfer its performance to higher-dimensional inputs. We extend this body of work by introducing a general framework for transferability across dimensions. We show that transferability corresponds precisely to continuity in a limit space formed by identifying small problem instances with equivalent large ones. This identification is driven by the data and the learning task. We instantiate our framework on existing architectures, and implement the necessary changes to ensure their transferability. Finally, we provide design principles for designing new transferable models. Numerical experiments support our findings.

Shiyu Chen, Ningyuan Huang, Soledad Villar

Graph Neural Networks (GNNs) typically scale with the number of graph edges, making them well suited for sparse graphs but less efficient on dense graphs, such as point clouds or molecular interactions. A common remedy is to sparsify the graph via similarity thresholding or distance pruning, but this forces an arbitrary choice of a single interaction scale and discards crucial information from other scales. To overcome this limitation, we introduce a multi-view graph-tuple framework. Instead of a single graph, our graph-tuple framework partitions the graph into disjoint subgraphs, capturing primary local interactions and weaker, long-range connections. We then learn multi-view representations from the graph-tuple via a heterogeneous message-passing architecture inspired by the theory of non-commuting operators, which we formally prove is strictly more expressive and guarantees a lower oracle risk compared to single-graph message-passing models. We instantiate our framework on two scientific domains: molecular property prediction from feature-scarce Coulomb matrices and cosmological parameter inference from geometric point clouds. On both applications, our multi-view graph-tuple models demonstrate better performance than single-graph baselines, highlighting the power and versatility of our multi-view approach.

Andrew Ferguson, Marisa LaFleur, Lars Ruthotto et al. · stanford

This community paper developed out of the NSF Workshop on the Future of Artificial Intelligence (AI) and the Mathematical and Physics Sciences (MPS), which was held in March 2025 with the goal of understanding how the MPS domains (Astronomy, Chemistry, Materials Research, Mathematical Sciences, and Physics) can best capitalize on, and contribute to, the future of AI. We present here a summary and snapshot of the MPS community's perspective, as of Spring/Summer 2025, in a rapidly developing field. The link between AI and MPS is becoming increasingly inextricable; now is a crucial moment to strengthen the link between AI and Science by pursuing a strategy that proactively and thoughtfully leverages the potential of AI for scientific discovery and optimizes opportunities to impact the development of AI by applying concepts from fundamental science. To achieve this, we propose activities and strategic priorities that: (1) enable AI+MPS research in both directions; (2) build up an interdisciplinary community of AI+MPS researchers; and (3) foster education and workforce development in AI for MPS researchers and students. We conclude with a summary of suggested priorities for funding agencies, educational institutions, and individual researchers to help position the MPS community to be a leader in, and take full advantage of, the transformative potential of AI+MPS.

Trung V. Phan, George A. Kevrekidis, Soledad Villar et al.

The machine learning methods for data-driven identification of partial differential equations (PDEs) are typically defined for a given number of spatial dimensions and a choice of coordinates the data have been collected in. This dependence prevents the learned evolution equation from generalizing to other spaces. In this work, we reformulate the problem in terms of coordinate- and dimension-independent representations, paving the way toward what we call ``spatially liberated" PDE learning. To this end, we employ a machine learning approach to predict the evolution of scalar field systems expressed in the formalism of exterior calculus, which is coordinate-free and immediately generalizes to arbitrary dimensions by construction. We demonstrate the performance of this approach in the FitzHugh-Nagumo and Barkley reaction-diffusion models, as well as the Patlak-Keller-Segel model informed by in-situ chemotactic bacteria observations. We provide extensive numerical experiments that demonstrate that our approach allows for seamless transitions across various spatial contexts. We show that the field dynamics learned in one space can be used to make accurate predictions in other spaces with different dimensions, coordinate systems, boundary conditions, and curvatures.

Wilson G. Gregory, Josué Tonelli-Cueto, Nicholas F. Marshall et al.

Tensors are a fundamental data structure for many scientific contexts, such as time series analysis, materials science, and physics, among many others. Improving our ability to produce and handle tensors is essential to efficiently address problems in these domains. In this paper, we show how to exploit the underlying symmetries of functions that map tensors to tensors. More concretely, we develop universally expressive equivariant machine learning architectures on tensors that exploit that, in many cases, these tensor functions are equivariant with respect to the diagonal action of the orthogonal, Lorentz, and/or symplectic groups. We showcase our results on three problems coming from material science, theoretical computer science, and time series analysis. For time series, we combine our method with the increasingly popular path signatures approach, which is also invariant with respect to reparameterizations. Our numerical experiments show that our equivariant models perform better than corresponding non-equivariant baselines.

Wilson G. Gregory, David W. Hogg, Ben Blum-Smith et al.

Machine learning methods are increasingly being employed as surrogate models in place of computationally expensive and slow numerical integrators for a bevy of applications in the natural sciences. However, while the laws of physics are relationships between scalars, vectors, and tensors that hold regardless of the frame of reference or chosen coordinate system, surrogate machine learning models are not coordinate-free by default. We enforce coordinate freedom by using geometric convolutions in three model architectures: a ResNet, a Dilated ResNet, and a UNet. In numerical experiments emulating 2D compressible Navier-Stokes, we see better accuracy and improved stability compared to baseline surrogate models in almost all cases. The ease of enforcing coordinate freedom without making major changes to the model architecture provides an exciting recipe for any CNN-based method applied to an appropriate class of problems

Ashwin De Silva, Rahul Ramesh, Lyle Ungar et al.

Learning is a process which can update decision rules, based on past experience, such that future performance improves. Traditionally, machine learning is often evaluated under the assumption that the future will be identical to the past in distribution or change adversarially. But these assumptions can be either too optimistic or pessimistic for many problems in the real world. Real world scenarios evolve over multiple spatiotemporal scales with partially predictable dynamics. Here we reformulate the learning problem to one that centers around this idea of dynamic futures that are partially learnable. We conjecture that certain sequences of tasks are not retrospectively learnable (in which the data distribution is fixed), but are prospectively learnable (in which distributions may be dynamic), suggesting that prospective learning is more difficult in kind than retrospective learning. We argue that prospective learning more accurately characterizes many real world problems that (1) currently stymie existing artificial intelligence solutions and/or (2) lack adequate explanations for how natural intelligences solve them. Thus, studying prospective learning will lead to deeper insights and solutions to currently vexing challenges in both natural and artificial intelligences.

Ningyuan Huang, Soledad Villar

Graph neural networks are designed to learn functions on graphs. Typically, the relevant target functions are invariant with respect to actions by permutations. Therefore the design of some graph neural network architectures has been inspired by graph-isomorphism algorithms. The classical Weisfeiler-Lehman algorithm (WL) -- a graph-isomorphism test based on color refinement -- became relevant to the study of graph neural networks. The WL test can be generalized to a hierarchy of higher-order tests, known as $k$-WL. This hierarchy has been used to characterize the expressive power of graph neural networks, and to inspire the design of graph neural network architectures. A few variants of the WL hierarchy appear in the literature. The goal of this short note is pedagogical and practical: We explain the differences between the WL and folklore-WL formulations, with pointers to existing discussions in the literature. We illuminate the differences between the formulations by visualizing an example.

Soledad Villar, David W. Hogg, Kate Storey-Fisher et al.

There has been enormous progress in the last few years in designing neural networks that respect the fundamental symmetries and coordinate freedoms of physical law. Some of these frameworks make use of irreducible representations, some make use of high-order tensor objects, and some apply symmetry-enforcing constraints. Different physical laws obey different combinations of fundamental symmetries, but a large fraction (possibly all) of classical physics is equivariant to translation, rotation, reflection (parity), boost (relativity), and permutations. Here we show that it is simple to parameterize universally approximating polynomial functions that are equivariant under these symmetries, or under the Euclidean, Lorentz, and Poincaré groups, at any dimensionality $d$. The key observation is that nonlinear O($d$)-equivariant (and related-group-equivariant) functions can be universally expressed in terms of a lightweight collection of scalars -- scalar products and scalar contractions of the scalar, vector, and tensor inputs. We complement our theory with numerical examples that show that the scalar-based method is simple, efficient, and scalable.

David W. Hogg, Soledad Villar

There are many uses for linear fitting; the context here is interpolation and denoising of data, as when you have calibration data and you want to fit a smooth, flexible function to those data. Or you want to fit a flexible function to de-trend a time series or normalize a spectrum. In these contexts, investigators often choose a polynomial basis, or a Fourier basis, or wavelets, or something equally general. They also choose an order, or number of basis functions to fit, and (often) some kind of regularization. We discuss how this basis-function fitting is done, with ordinary least squares and extensions thereof. We emphasize that it is often valuable to choose far more parameters than data points, despite folk rules to the contrary: Suitably regularized models with enormous numbers of parameters generalize well and make good predictions for held-out data; over-fitting is not (mainly) a problem of having too many parameters. It is even possible to take the limit of infinite parameters, at which, if the basis and regularization are chosen correctly, the least-squares fit becomes the mean of a Gaussian process. We recommend cross-validation as a good empirical method for model selection (for example, setting the number of parameters and the form of the regularization), and jackknife resampling as a good empirical method for estimating the uncertainties of the predictions made by the model. We also give advice for building stable computational implementations.

Ningyuan Huang, David W. Hogg, Soledad Villar

Overparameterization in deep learning is powerful: Very large models fit the training data perfectly and yet often generalize well. This realization brought back the study of linear models for regression, including ordinary least squares (OLS), which, like deep learning, shows a "double-descent" behavior: (1) The risk (expected out-of-sample prediction error) can grow arbitrarily when the number of parameters $p$ approaches the number of samples $n$, and (2) the risk decreases with $p$ for $p>n$, sometimes achieving a lower value than the lowest risk for $p<n$. The divergence of the risk for OLS can be avoided with regularization. In this work, we show that for some data models it can also be avoided with a PCA-based dimensionality reduction (PCA-OLS, also known as principal component regression). We provide non-asymptotic bounds for the risk of PCA-OLS by considering the alignments of the population and empirical principal components. We show that dimensionality reduction improves robustness while OLS is arbitrarily susceptible to adversarial attacks, particularly in the overparameterized regime. We compare PCA-OLS theoretically and empirically with a wide range of projection-based methods, including random projections, partial least squares (PLS), and certain classes of linear two-layer neural networks. These comparisons are made for different data generation models to assess the sensitivity to signal-to-noise and the alignment of regression coefficients with the features. We find that methods in which the projection depends on the training data can outperform methods where the projections are chosen independently of the training data, even those with oracle knowledge of population quantities, another seemingly paradoxical phenomenon that has been identified previously. This suggests that overparameterization may not be necessary for good generalization.

Zhengdao Chen, Lei Chen, Soledad Villar et al.

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: induced-subgraph-count and subgraph-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 induced-subgraph-count of substructures consisting of 3 or more nodes, while they can perform subgraph-count of star-shaped substructures. 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). We also prove positive results for k-WL and k-IGNs as well as negative results for k-WL with a finite number of iterations. We then conduct experiments that support the theoretical results for MPNNs and 2-IGNs. Moreover, motivated by substructure counting and inspired by Murphy et al. (2019), we propose the Local Relational Pooling model and demonstrate that it is not only effective for substructure counting but also able to achieve competitive performance on molecular prediction tasks.

Andrew J. Blumberg, Mathieu Carriere, Michael A. Mandell et al.

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.

Weichi Yao, Afonso S. Bandeira, Soledad Villar

This note explores the applicability of unsupervised machine learning techniques towards hard optimization problems on random inputs. In particular we consider Graph Neural Networks (GNNs) -- a class of neural networks designed to learn functions on graphs -- and we apply them to the max-cut problem on random regular graphs. We focus on the max-cut problem on random regular graphs because it is a fundamental problem that has been widely studied. In particular, even though there is no known explicit solution to compare the output of our algorithm to, we can leverage the known asymptotics of the optimal max-cut value in order to evaluate the performance of the GNNs. In order to put the performance of the GNNs in context, we compare it with the classical semidefinite relaxation approach by Goemans and Williamson~(SDP), and with extremal optimization, which is a local optimization heuristic from the statistical physics literature. The numerical results we obtain indicate that, surprisingly, Graph Neural Networks attain comparable performance to the Goemans and Williamson SDP. We also observe that extremal optimization consistently outperforms the other two methods. Furthermore, the performances of the three methods present similar patterns, that is, for sparser, and for larger graphs, the size of the found cuts are closer to the asymptotic optimal max-cut value.

Zhengdao Chen, Soledad Villar, Lei Chen et al.

Graph Neural Networks (GNNs) have achieved much success on graph-structured data. In light of this, there have been increasing interests in studying their expressive power. One line of work studies the capability of GNNs to approximate permutation-invariant functions on graphs, and another focuses on the their power as tests for graph isomorphism. Our work connects these two perspectives and proves their equivalence. We further develop a framework of the expressive power of GNNs that incorporates both of these viewpoints using the language of sigma-algebra, through which we compare the expressive power of different types of GNNs together with other graph isomorphism tests. In particular, we prove that the second-order Invariant Graph Network fails to distinguish non-isomorphic regular graphs with the same degree. Then, we extend it to a new architecture, Ring-GNN, which succeeds in distinguishing these graphs and achieves good performances on real-world datasets.

Culver McWhirter, Dustin G. Mixon, Soledad Villar

Given labeled points in a high-dimensional vector space, we seek a low-dimensional subspace such that projecting onto this subspace maintains some prescribed distance between points of differing labels. Intended applications include compressive classification. Taking inspiration from large margin nearest neighbor classification, this paper introduces a semidefinite relaxation of this problem. Unlike its predecessors, this relaxation is amenable to theoretical analysis, allowing us to provably recover a planted projection operator from the data.

Ruhui Jin, Dustin G. Mixon, Soledad Villar

Deep neural networks are often used to implement powerful generative models for real-world data. Notable applications include image denoising, as well as other classical inverse problems like compressed sensing and super-resolution. To provide a rigorous but simplified analysis of generative models, in this work, we introduce an elegant theoretical framework based on spherical harmonics, namely \textbf{SUNLayer}. Our theoretical framework identifies explicit conditions on activation functions that guarantee denoising under local optimization. Numerical experiments examine the theoretical properties on commonly used activation functions and demonstrate their stable denoising performance.

Dustin G. Mixon, Soledad Villar

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.

Alex Nowak, Soledad Villar, Afonso S. Bandeira et al.

Inverse problems correspond to a certain type of optimization problems formulated over 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 revised 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 'planted solutions' are used to supervise the training of an appropriate predictive model that parametrizes a broad class of algorithms, with the hope that the resulting model 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.

Soledad Villar, Afonso S. Bandeira, Andrew J. Blumberg et al.

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.

Dustin G. Mixon, Soledad Villar, Rachel Ward

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.

Takayuki Iguchi, Dustin G. Mixon, Jesse Peterson et al.

Recently, Bandeira [arXiv:1509.00824] introduced a new type of algorithm (the so-called probably certifiably correct algorithm) that combines fast solvers with the optimality certificates provided by convex relaxations. In this paper, we devise such an algorithm for the problem of k-means clustering. First, we prove that Peng and Wei's semidefinite relaxation of k-means is tight with high probability under a distribution of planted clusters called the stochastic ball model. Our proof follows from a new dual certificate for integral solutions of this semidefinite program. Next, we show how to test the optimality of a proposed k-means solution using this dual certificate in quasilinear time. Finally, we analyze a version of spectral clustering from Peng and Wei that is designed to solve k-means in the case of two clusters. In particular, we show that this quasilinear-time method typically recovers planted clusters under the stochastic ball model.

Takayuki Iguchi, Dustin G. Mixon, Jesse Peterson et al.

Recently, Awasthi et al. introduced an SDP relaxation of the $k$-means problem in $\mathbb R^m$. In this work, we consider a random model for the data points in which $k$ balls of unit radius are deterministically distributed throughout $\mathbb R^m$, and then in each ball, $n$ points are drawn according to a common rotationally invariant probability distribution. For any fixed ball configuration and probability distribution, we prove that the SDP relaxation of the $k$-means problem exactly recovers these planted clusters with probability $1-e^{-Ω(n)}$ provided the distance between any two of the ball centers is $>2+ε$, where $ε$ is an explicit function of the configuration of the ball centers, and can be arbitrarily small when $m$ is large.

Pranjal Awasthi, Afonso S. Bandeira, Moses Charikar et al.

We study exact recovery conditions for convex relaxations of point cloud clustering problems, focusing on two of the most common optimization problems for unsupervised clustering: $k$-means and $k$-median clustering. Motivations for focusing on convex relaxations are: (a) they come with a certificate of optimality, and (b) they are generic tools which are relatively parameter-free, not tailored to specific assumptions over the input. More precisely, we consider the distributional setting where there are $k$ clusters in $\mathbb{R}^m$ and data from each cluster consists of $n$ points sampled from a symmetric distribution within a ball of unit radius. We ask: what is the minimal separation distance between cluster centers needed for convex relaxations to exactly recover these $k$ clusters as the optimal integral solution? For the $k$-median linear programming relaxation we show a tight bound: exact recovery is obtained given arbitrarily small pairwise separation $ε> 0$ between the balls. In other words, the pairwise center separation is $Δ> 2+ε$. Under the same distributional model, the $k$-means LP relaxation fails to recover such clusters at separation as large as $Δ= 4$. Yet, if we enforce PSD constraints on the $k$-means LP, we get exact cluster recovery at center separation $Δ> 2\sqrt2(1+\sqrt{1/m})$. In contrast, common heuristics such as Lloyd's algorithm (a.k.a. the $k$-means algorithm) can fail to recover clusters in this setting; even with arbitrarily large cluster separation, k-means++ with overseeding by any constant factor fails with high probability at exact cluster recovery. To complement the theoretical analysis, we provide an experimental study of the recovery guarantees for these various methods, and discuss several open problems which these experiments suggest.