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Minimizing a sum of simple submodular functions of limited support is a special case of general submodular function minimization that has seen numerous applications in machine learning. We develop fast techniques for instances where components in the sum are cardinality-based, meaning they depend only on the size of the input set. This variant is one of the most widely applied in practice, encompassing, e.g., common energy functions arising in image segmentation and recent generalized hypergraph cut functions. We develop the first approximation algorithms for this problem, where the approximations can be quickly computed via reduction to a sparse graph cut problem, with graph sparsity controlled by the desired approximation factor. Our method relies on a new connection between sparse graph reduction techniques and piecewise linear approximations to concave functions. Our sparse reduction technique leads to significant improvements in theoretical runtimes, as well as substantial practical gains in problems ranging from benchmark image segmentation tasks to hypergraph clustering problems.

Bridging relationships between individuals situated in different parts of a social network are important conduits for information and resources in social and organizational settings. Dyadic tie strength has often been used as an indicator for whether a relationship is bridging, under the assumption that bridging ties are always weak ties. However, recent empirical evidence suggests that bridging ties are often strong, forcing us to rethink the relationship between social network structure and dyadic tie strength. Here, we provide an analysis based on algebraic topology which clarifies this relationship between network structure and dyadic tie strength. Rather than model the network as a graph, we use a simplicial complex which can explicitly encode group interactions between three or more individuals. First, we show theoretically and empirically that Edge PageRank, an algebraic topological measure originally defined as an extension of the classical PageRank measure, is a valid continuous measure of how well a relationship acts as a bridge. Second, we use the tool of Hodge Decomposition, which allows us to decompose any flow in a simplicial complex into three orthogonal components, to clarify the relationship between dyadic tie strength and network structure. We find that individuals invest less in relationships associated with topological holes in the network, replicating and explaining recent empirical results that bridging relationships spanning short network distances tend to be weak, whereas those spanning longer distances are strong. Our results are validated on 15 large scale datasets and suggest the value of algebraic topological methods in empirical network analysis.

A collection of over 3000 pages of emails sent by Anthony Fauci and his staff were released in an effort to understand the United States government response to the COVID-19 pandemic. We describe how this email data was translated into a resource consisting of json files that make many future studies easy. Findings from our processed data include (i) successful organizational partitions using the simple mincut techniques in Zachary's karate club methodology, (ii) a natural example where the normalized cut and minimum conductance set are extremely different, and (iii) organizational groups identified by optimum modularity clusters that illustrate a working hierarchy. These example uses suggest the data will be useful for future research and pedagogical uses in terms of human and system behavioral interactions. We explain a number of ways to turn email information into a network, a hypergraph, a temporal sequence, and a tensor for subsequent analysis as well as a few examples of such analysis., Comment: Code and data available from https://github.com/nveldt/fauci-email

Graphs are a common model for complex relational data such as social networks and protein interactions, and such data can evolve over time (e.g., new friendships) and be noisy (e.g., unmeasured interactions). Link prediction aims to predict future edges or infer missing edges in the graph, and has diverse applications in recommender systems, experimental design, and complex systems. Even though link prediction algorithms strongly depend on the set of edges in the graph, existing approaches typically do not modify the graph topology to improve performance. Here, we demonstrate how simply adding a set of edges, which we call a \emph{proposal set}, to the graph as a pre-processing step can improve the performance of several link prediction algorithms. The underlying idea is that if the edges in the proposal set generally align with the structure of the graph, link prediction algorithms are further guided towards predicting the right edges; in other words, adding a proposal set of edges is a signal-boosting pre-processing step. We show how to use existing link prediction algorithms to generate effective proposal sets and evaluate this approach on various synthetic and empirical datasets. We find that proposal sets meaningfully improve the accuracy of link prediction algorithms based on both neighborhood heuristics and graph neural networks. Code is available at \url{https://github.com/CUAI/Edge-Proposal-Sets}.

With the wide-spread availability of complex relational data, semi-supervised node classification in graphs has become a central machine learning problem. Graph neural networks are a recent class of easy-to-train and accurate methods for this problem that map the features in the neighborhood of a node to its label, but they ignore label correlation during inference and their predictions are difficult to interpret. On the other hand, collective classification is a traditional approach based on interpretable graphical models that explicitly model label correlations. Here, we introduce a model that combines the advantages of these two approaches, where we compute the marginal probabilities in a conditional random field, similar to collective classification, and the potentials in the random field are learned through end-to-end training, akin to graph neural networks. In our model, potentials on each node only depend on that node's features, and edge potentials are learned via a coupling matrix. This structure enables simple training with interpretable parameters, scales to large networks, naturally incorporates training labels at inference, and is often more accurate than related approaches. Our approach can be viewed as either an interpretable message-passing graph neural network or a collective classification method with higher capacity and modernized training.

Finding dense subgraphs of a large graph is a standard problem in graph mining that has been studied extensively both for its theoretical richness and its many practical applications. In this paper we introduce a new family of dense subgraph objectives, parameterized by a single parameter $p$, based on computing generalized means of degree sequences of a subgraph. Our objective captures both the standard densest subgraph problem and the maximum $k$-core as special cases, and provides a way to interpolate between and extrapolate beyond these two objectives when searching for other notions of dense subgraphs. In terms of algorithmic contributions, we first show that our objective can be minimized in polynomial time for all $p \geq 1$ using repeated submodular minimization. A major contribution of our work is analyzing the performance of different types of peeling algorithms for dense subgraphs both in theory and practice. We prove that the standard peeling algorithm can perform arbitrarily poorly on our generalized objective, but we then design a more sophisticated peeling method which for $p \geq 1$ has an approximation guarantee that is always at least $1/2$ and converges to 1 as $p \rightarrow \infty$. In practice, we show that this algorithm obtains extremely good approximations to the optimal solution, scales to large graphs, and highlights a range of different meaningful notions of density on graphs coming from numerous domains. Furthermore, it is typically able to approximate the densest subgraph problem better than the standard peeling algorithm, by better accounting for how the removal of one node affects other nodes in its neighborhood.

Standard methods in preference learning involve estimating the parameters of discrete choice models from data of selections (choices) made by individuals from a discrete set of alternatives (the choice set). While there are many models for individual preferences, existing learning methods overlook how choice set assignment affects the data. Often, the choice set itself is influenced by an individual's preferences; for instance, a consumer choosing a product from an online retailer is often presented with options from a recommender system that depend on information about the consumer's preferences. Ignoring these assignment mechanisms can mislead choice models into making biased estimates of preferences, a phenomenon that we call choice set confounding; we demonstrate the presence of such confounding in widely-used choice datasets. To address this issue, we adapt methods from causal inference to the discrete choice setting. We use covariates of the chooser for inverse probability weighting and/or regression controls, accurately recovering individual preferences in the presence of choice set confounding under certain assumptions. When such covariates are unavailable or inadequate, we develop methods that take advantage of structured choice set assignment to improve prediction. We demonstrate the effectiveness of our methods on real-world choice data, showing, for example, that accounting for choice set confounding makes choices observed in hotel booking and commute transportation more consistent with rational utility-maximization., Comment: 12 pages, KDD 2021 version

Hypergraphs are a common model for multiway relationships in data, and hypergraph semi-supervised learning is the problem of assigning labels to all nodes in a hypergraph, given labels on just a few nodes. Diffusions and label spreading are classical techniques for semi-supervised learning in the graph setting, and there are some standard ways to extend them to hypergraphs. However, these methods are linear models, and do not offer an obvious way of incorporating node features for making predictions. Here, we develop a nonlinear diffusion process on hypergraphs that spreads both features and labels following the hypergraph structure, which can be interpreted as a hypergraph equilibrium network. Even though the process is nonlinear, we show global convergence to a unique limiting point for a broad class of nonlinearities, which is the global optimum of a interpretable, regularized semi-supervised learning loss function. The limiting point serves as a node embedding from which we make predictions with a linear model. Our approach is much more accurate than several hypergraph neural networks, and also takes less time to train.

Homophily is the seemingly ubiquitous tendency for people to connect and interact with other individuals who are similar to them. This is a well-documented principle and is fundamental for how society organizes. Although many social interactions occur in groups, homophily has traditionally been measured using a graph model, which only accounts for pairwise interactions involving two individuals. Here, we develop a framework using hypergraphs to quantify homophily from group interactions. This reveals natural patterns of group homophily that appear with gender in scientific collaboration and political affiliation in legislative bill co-sponsorship, and also reveals distinctive gender distributions in group photographs, all of which cannot be fully captured by pairwise measures. At the same time, we show that seemingly natural ways to define group homophily are combinatorially impossible. This reveals important pitfalls to avoid when defining and interpreting notions of group homophily, as higher-order homophily patterns are governed by combinatorial constraints that are independent of human behavior but are easily overlooked.

Higher-order network analysis uses the ideas of hypergraphs, simplicial complexes, multilinear and tensor algebra, and more, to study complex systems. These are by now well established mathematical abstractions. What's new is that the ideas can be tested and refined on the type of large-scale data arising in today's digital world. This research area therefore is making an impact across many applications. Here, we provide a brief history, guide, and survey., Comment: Based on the SIAM News online article https://sinews.siam.org/Details-Page/higher-order-network-analysis-takes-off-fueled-by-old-ideas-and-new-data

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

In the analysis of large-scale network data, a fundamental operation is the comparison of observed phenomena to the predictions provided by null models: when we find an interesting structure in a family of real networks, it is important to ask whether this structure is also likely to arise in random networks with similar characteristics to the real ones. A long-standing challenge in network analysis has been the relative scarcity of reasonable null models for networks; arguably the most common such model has been the configuration model, which starts with a graph $G$ and produces a random graph with the same node degrees as $G$. This leads to a very weak form of null model, since fixing the node degrees does not preserve many of the crucial properties of the network, including the structure of its subgraphs. Guided by this challenge, we propose a new family of network null models that operate on the $k$-core decomposition. For a graph $G$, the $k$-core is its maximal subgraph of minimum degree $k$; and the core number of a node $v$ in $G$ is the largest $k$ such that $v$ belongs to the $k$-core of $G$. We provide the first efficient sampling algorithm to solve the following basic combinatorial problem: given a graph $G$, produce a random graph sampled nearly uniformly from among all graphs with the same sequence of core numbers as $G$. This opens the opportunity to compare observed networks $G$ with random graphs that exhibit the same core numbers, a comparison that preserves aspects of the structure of $G$ that are not captured by more local measures like the degree sequence. We illustrate the power of this core-based null model on some fundamental tasks in network analysis, including the enumeration of networks motifs.

Hypergraphs are a natural modeling paradigm for a wide range of complex relational systems. A standard analysis task is to identify clusters of closely related or densely interconnected nodes. Many graph algorithms for this task are based on variants of the stochastic blockmodel, a random graph with flexible cluster structure. However, there are few models and algorithms for hypergraph clustering. Here, we propose a Poisson degree-corrected hypergraph stochastic blockmodel (DCHSBM), a generative model of clustered hypergraphs with heterogeneous node degrees and edge sizes. Approximate maximum-likelihood inference in the DCHSBM naturally leads to a clustering objective that generalizes the popular modularity objective for graphs. We derive a general Louvain-type algorithm for this objective, as well as a a faster, specialized "All-Or-Nothing" (AON) variant in which edges are expected to lie fully within clusters. This special case encompasses a recent proposal for modularity in hypergraphs, while also incorporating flexible resolution and edge-size parameters. We show that AON hypergraph Louvain is highly scalable, including as an example an experiment on a synthetic hypergraph of one million nodes. We also demonstrate through synthetic experiments that the detectability regimes for hypergraph community detection differ from methods based on dyadic graph projections. We use our generative model to analyze different patterns of higher-order structure in school contact networks, U.S. congressional bill cosponsorship, U.S. congressional committees, product categories in co-purchasing behavior, and hotel locations from web browsing sessions, finding interpretable higher-order structure. We then study the behavior of our AON hypergraph Louvain algorithm, finding that it is able to recover ground truth clusters in empirical data sets exhibiting the corresponding higher-order structure., Comment: 23 pages + 7 pages of supplementary information, 3 tables, 4 figures

Semi-supervised learning on graphs is a widely applicable problem in network science and machine learning. Two standard algorithms -- label propagation and graph neural networks -- both operate by repeatedly passing information along edges, the former by passing labels and the latter by passing node features, modulated by neural networks. These two types of algorithms have largely developed separately, and there is little understanding about the structure of network data that would make one of these approaches work particularly well compared to the other or when the approaches can be meaningfully combined. Here, we develop a Markov random field model for the data generation process of node attributes, based on correlations of attributes on and between vertices, that motivates and unifies these algorithmic approaches. We show that label propagation, a linearized graph convolutional network, and their combination can all be derived as conditional expectations under our model, when conditioning on different attributes. In addition, the data model highlights deficiencies in existing graph neural networks (while producing new algorithmic solutions), serves as a rigorous statistical framework for understanding graph learning issues such as over-smoothing, creates a testbed for evaluating inductive learning performance, and provides a way to sample graphs attributes that resemble empirical data. We also find that a new algorithm derived from our data generation model, which we call a Linear Graph Convolution, performs extremely well in practice on empirical data, and provide theoretical justification for why this is the case.

We present a new, stable, mixed finite element (FE) method for linear elastostatics of nearly incompressible solids. The method is the automatic variationally stable FE (AVS-FE) method of Calo, Romkes and Valseth, in which we consider a Petrov-Galerkin weak formulation where the stress and displacement variables are in the space H(div)xH1, respectively. This allows us to employ a fully conforming FE discretization for any elastic solid using classical FE subspaces of H(div) and H1. Hence, the resulting FE approximation yields both continuous stresses and displacements. To ensure stability of the method, we employ the philosophy of the discontinuous Petrov-Galerkin (DPG) method of Demkowicz and Gopalakrishnan and use optimal test spaces. Thus, the resulting FE discretization is stable even as the Poisson ratio approaches 0.5, and the system of linear algebraic equations is symmetric and positive definite. Our method also comes with a built-in a posteriori error estimator as well as well as indicators which are used to drive mesh adaptive refinements. We present several numerical verifications of our method including comparisons to existing FE technologies.

We demonstrate that deep learning techniques can be used to predict motility induced phase separation (MIPS) in suspensions of active Brownian particles (ABPs) by creating a notion of phase at the particle level. Using a fully connected network in conjunction with a graph neural network we use individual particle features to predict to which phase a particle belongs. From this, we are able to compute the fraction of dilute particles to determine if the system is in the homogeneous dilute, dense, or coexistence region. Our predictions are compared against the MIPS binodal computed from simulation. The strong agreement between the two suggests that machine learning provides an effective way to determine the phase behavior of ABPs and could prove useful for determining more complex phase diagrams.

We draw connections between simple neural networks and under-determined linear systems to comprehensively explore several interesting theoretical questions in the study of neural networks. First, we emphatically show that it is unsurprising such networks can achieve zero training loss. More specifically, we provide lower bounds on the width of a single hidden layer neural network such that only training the last linear layer suffices to reach zero training loss. Our lower bounds grow more slowly with data set size than existing work that trains the hidden layer weights. Second, we show that kernels typically associated with the ReLU activation function have fundamental flaws -- there are simple data sets where it is impossible for widely studied bias-free models to achieve zero training loss irrespective of how the parameters are chosen or trained. Lastly, our analysis of gradient descent clearly illustrates how spectral properties of certain matrices impact both the early iteration and long-term training behavior. We propose new activation functions that avoid the pitfalls of ReLU in that they admit zero training loss solutions for any set of distinct data points and experimentally exhibit favorable spectral properties., Comment: 25 pages, 4 figures

Graph Neural Networks (GNNs) are the predominant technique for learning over graphs. However, there is relatively little understanding of why GNNs are successful in practice and whether they are necessary for good performance. Here, we show that for many standard transductive node classification benchmarks, we can exceed or match the performance of state-of-the-art GNNs by combining shallow models that ignore the graph structure with two simple post-processing steps that exploit correlation in the label structure: (i) an "error correlation" that spreads residual errors in training data to correct errors in test data and (ii) a "prediction correlation" that smooths the predictions on the test data. We call this overall procedure Correct and Smooth (C&S), and the post-processing steps are implemented via simple modifications to standard label propagation techniques from early graph-based semi-supervised learning methods. Our approach exceeds or nearly matches the performance of state-of-the-art GNNs on a wide variety of benchmarks, with just a small fraction of the parameters and orders of magnitude faster runtime. For instance, we exceed the best known GNN performance on the OGB-Products dataset with 137 times fewer parameters and greater than 100 times less training time. The performance of our methods highlights how directly incorporating label information into the learning algorithm (as was done in traditional techniques) yields easy and substantial performance gains. We can also incorporate our techniques into big GNN models, providing modest gains. Our code for the OGB results is at https://github.com/Chillee/CorrectAndSmooth.