Clustering is a technique for the analysis of datasets obtained by empirical studies in several disciplines with a major application for biomedical research. Essentially, clustering algorithms are executed by machines aiming at finding groups of related points in a dataset. However, the result of grouping depends on both metrics for point-to-point similarity and rules for point-to-group association. Indeed, non-appropriate metrics and rules can lead to undesirable clustering artifacts. This is especially relevant for datasets, where groups with heterogeneous structures co-exist. In this work, we propose an algorithm that achieves clustering by exploring the paths between points. This allows both, to evaluate the properties of the path (such as gaps, density variations, etc.), and expressing the preference for certain paths. Moreover, our algorithm supports the integration of existing knowledge about admissible and non-admissible clusters by training a path classifier. We demonstrate the accuracy of the proposed method on challenging datasets including points from synthetic shapes in publicly available benchmarks and microscopy data.

Kleinberg [18] stated three axioms that any clustering procedure should satisfy and showed there is no clustering procedure that simultaneously satisfies all three. One of these, called the consistency axiom, requires that when the data is modified in a helpful way, i.e. if points in the same cluster are made more similar and those in different ones made less similar, the algorithm should output the same clustering. To circumvent this impossibility result, research has focused on considering clustering procedures that have a clustering quality measure (or a cost) and showing that a modification of Kleinberg's axioms that takes cost into account lead to feasible clustering procedures. In this work, we take a different approach, based on the observation that the consistency axiom fails to be satisfied when the "correct" number of clusters changes. We modify this axiom by making use of cost functions to determine the correct number of clusters, and require that consistency holds only if the number of clusters remains unchanged. We show that single linkage satisfies the modified axioms, and if the input is well-clusterable, some popular procedures such as k-means also satisfy the axioms, taking a step towards explaining the success of these objective functions for guiding the design of algorithms. 1 Introduction In a highly influential paper, Kleinberg [18] showed that clustering is impossible in the following sense: there exists no clustering function, i.e. a function that takes a point-set and a pairwise dissimilarity function

We provide the first information theoretical tight analysis for inference of latent community structure given a sparse graph along with high dimensional node covariates, correlated with the same latent communities. Our work bridges recent theoretical breakthroughs in detection of latent community structure without nodes covariates and a large body of empirical work using diverse heuristics for combining node covariates with graphs for inference. The tightness of our analysis implies in particular, the information theoretic necessity of combining the different sources of information. Our analysis holds for networks of large degrees as well as for a Gaussian version of the model.

We introduce the Sublevel Set (SS) method, a generic method to obtain sufficient guarantees of near-optimality and uniqueness (up to small perturbations) for a clustering. This method can be instantiated for a variety of clustering loss functions for which convex relaxations exist. Obtaining the guarantees in practice amounts to solving a convex optimization. We demonstrate the applicability of this method by obtaining distribution free guarantees for K-means clustering on realistic data sets.

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark datasets.

We consider the semi-supervised clustering problem where crowdsourcing provides noisy information about the pairwise comparisons on a small subset of data, i.e., whether a sample pair is in the same cluster. We propose a new approach that includes a deep generative model (DGM) to characterize low-level features of the data, and a statistical relational model for noisy pairwise annotations on its subset. The two parts share the latent variables. To make the model automatically trade-off between its complexity and fitting data, we also develop its fully Bayesian variant. The challenge of inference is addressed by fast (natural-gradient) stochastic variational inference algorithms, where we effectively combine variational message passing for the relational part and amortized learning of the DGM under a unified framework. Empirical results on synthetic and real-world datasets show that our model outperforms previous crowdsourced clustering methods.

We study the problem of finding clusters in random bipartite graphs. We present a simple two-step algorithm which provably finds even tiny clusters of size $O(n^\epsilon)$, where $n$ is the number of vertices in the graph and $\epsilon > 0$. Previous algorithms were only able to identify clusters of size $\Omega(\sqrt{n})$. We evaluate the algorithm on synthetic and on real-world data; the experiments show that the algorithm can find extremely small clusters even in presence of high destructive noise.

Completing a data matrix X has become an ubiquitous problem in modern data science, with motivations in recommender systems, computer vision, and networks inference, to name a few. One typical assumption is that X is low-rank. A more general model assumes that each column of X corresponds to one of several low-rank matrices. This paper generalizes these models to what we call mixture matrix completion (MMC): the case where each entry of X corresponds to one of several low-rank matrices. MMC is a more accurate model for recommender systems, and brings more flexibility to other completion and clustering problems. We make four fundamental contributions about this new model. First, we show that MMC is theoretically possible (well-posed). Second, we give its precise information-theoretic identifiability conditions. Third, we derive the sample complexity of MMC. Finally, we give a practical algorithm for MMC with performance comparable to the state-of-the-art for simpler related problems, both on synthetic and real data.

Algorithms for clustering points in metric spaces is a long-studied area of research. Clustering has seen a multitude of work both theoretically, in understanding the approximation guarantees possible for many objective functions such as k-median and k-means clustering, and experimentally, in finding the fastest algorithms and seeding procedures for Lloyd's algorithm. The performance of a given clustering algorithm depends on the specific application at hand, and this may not be known up front. For example, a "typical instance" may vary depending on the application, and different clustering heuristics perform differently depending on the instance. In this paper, we define an infinite family of algorithms generalizing Lloyd's algorithm, with one parameter controlling the the initialization procedure, and another parameter controlling the local search procedure. This family of algorithms includes the celebrated k-means++ algorithm, as well as the classic farthest-first traversal algorithm. We design efficient learning algorithms which receive samples from an application-specific distribution over clustering instances and learn a near-optimal clustering algorithm from the class. We show the best parameters vary significantly across datasets such as MNIST, CIFAR, and mixtures of Gaussians. Our learned algorithms never perform worse than k-means++, and on some datasets we see significant improvements.

We advocate Laplacian K-modes for joint clustering and density mode finding, and propose a concave-convex relaxation of the problem, which yields a parallel algorithm that scales up to large datasets and high dimensions. We optimize a tight bound (auxiliary function) of our relaxation, which, at each iteration, amounts to computing an independent update for each cluster-assignment variable, with guar- anteed convergence. Therefore, our bound optimizer can be trivially distributed for large-scale data sets. Furthermore, we show that the density modes can be obtained as byproducts of the assignment variables via simple maximum-value operations whose additional computational cost is linear in the number of data points. Our formulation does not need storing a full affinity matrix and computing its eigenvalue decomposition, neither does it perform expensive projection steps and Lagrangian-dual inner iterates for the simplex constraints of each point. Fur- thermore, unlike mean-shift, our density-mode estimation does not require inner- loop gradient-ascent iterates. It has a complexity independent of feature-space dimension, yields modes that are valid data points in the input set and is appli- cable to discrete domains as well as arbitrary kernels. We report comprehensive experiments over various data sets, which show that our algorithm yields very competitive performances in term of optimization quality (i.e., the value of the discrete-variable objective at convergence) and clustering accuracy.