The power of human computation is founded on the capabilities of humans to process qualitative information in a manner that is hard to reproduce with a computer. However, all machine learning algorithms rely on mathematical operations, such as sums, averages, least squares etc. that are less suitable for human computation. This paper is an effort to combine these two aspects of data processing. We consider the problem of computing a centroid of a data set, a key component in many data-analysis applications such as clustering, using a very simple human intelligence task (HIT). In this task the workers must choose the outlier from a set of three items. After presenting a number of such triplets to the workers, the item chosen the least number of times as the outlier is selected as the centroid. We provide a proof that the centroid determined by this procedure is equal the mean of a univariate normal distribution. Furthermore, as a demonstration of the viability of our method, we implement a human computation based variant of the k-means clustering algorithm. We present experiments where the proposed method is used to find an "average" image in a collection, and cluster images to semantic categories.

Many algorithms have been proposed for fitting network models with communities, but most of them do not scale well to large networks, and often fail on sparse networks. Here we propose a new fast pseudo-likelihood method for fitting the stochastic block model for networks, as well as a variant that allows for an arbitrary degree distribution by conditioning on degrees. We show that the algorithms perform well under a range of settings, including on very sparse networks, and illustrate on the example of a network of political blogs. We also propose spectral clustering with perturbations, a method of independent interest, which works well on sparse networks where regular spectral clustering fails, and use it to provide an initial value for pseudo-likelihood. We prove that pseudo-likelihood provides consistent estimates of the communities under a mild condition on the starting value, for the case of a block model with two communities.

High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the subclonal lineages of tumor cells present in the sample can be reconstructed from these SNV frequency measurements. However, automated methods to do this reconstruction are not available and the conditions under which reconstruction is possible have not been described. We describe the conditions under which the evolutionary history can be uniquely reconstructed from SNV frequencies from single or multiple samples from the tumor population and we introduce a new statistical model, PhyloSub, that infers the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells. It uses a Bayesian nonparametric prior over trees that groups SNVs into major subclonal lineages and automatically estimates the number of lineages and their ancestry. We sample from the joint posterior distribution over trees to identify evolutionary histories and cell population frequencies that have the highest probability of generating the observed SNV frequency data. When multiple phylogenies are consistent with a given set of SNV frequencies, PhyloSub represents the uncertainty in the tumor phylogeny using a partial order plot. Experiments on a simulated dataset and two real datasets comprising tumor samples from acute myeloid leukemia and chronic lymphocytic leukemia patients demonstrate that PhyloSub can infer both linear (or chain) and branching lineages and its inferences are in good agreement with ground truth, where it is available.

This paper presents a novel algorithm, based upon the dependent Dirichlet process mixture model (DDPMM), for clustering batch-sequential data containing an unknown number of evolving clusters. The algorithm is derived via a low-variance asymptotic analysis of the Gibbs sampling algorithm for the DDPMM, and provides a hard clustering with convergence guarantees similar to those of the k-means algorithm. Empirical results from a synthetic test with moving Gaussian clusters and a test with real ADS-B aircraft trajectory data demonstrate that the algorithm requires orders of magnitude less computational time than contemporary probabilistic and hard clustering algorithms, while providing higher accuracy on the examined datasets.

This paper provides new algorithms for distributed clustering for two popular center-based objectives, k-median and k-means. These algorithms have provable guarantees and improve communication complexity over existing approaches. Following a classic approach in clustering by \cite{har2004coresets}, we reduce the problem of finding a clustering with low cost to the problem of finding a coreset of small size. We provide a distributed method for constructing a global coreset which improves over the previous methods by reducing the communication complexity, and which works over general communication topologies. Experimental results on large scale data sets show that this approach outperforms other coreset-based distributed clustering algorithms.

Given a subset S of vertices of an undirected graph G, the cut-improvement problem asks us to find a subset S that is similar to A but has smaller conductance. A very elegant algorithm for this problem has been given by Andersen and Lang [AL08] and requires solving a small number of single-commodity maximum flow computations over the whole graph G. In this paper, we introduce LocalImprove, the first cut-improvement algorithm that is local, i.e. that runs in time dependent on the size of the input set A rather than on the size of the entire graph. Moreover, LocalImprove achieves this local behaviour while essentially matching the same theoretical guarantee as the global algorithm of Andersen and Lang. The main application of LocalImprove is to the design of better local-graph-partitioning algorithms. All previously known local algorithms for graph partitioning are random-walk based and can only guarantee an output conductance of O(\sqrt{OPT}) when the target set has conductance OPT \in [0,1]. Very recently, Zhu, Lattanzi and Mirrokni [ZLM13] improved this to O(OPT / \sqrt{CONN}) where the internal connectivity parameter CONN \in [0,1] is defined as the reciprocal of the mixing time of the random walk over the graph induced by the target set. In this work, we show how to use LocalImprove to obtain a constant approximation O(OPT) as long as CONN/OPT = Omega(1). This yields the first flow-based algorithm. Moreover, its performance strictly outperforms the ones based on random walks and surprisingly matches that of the best known global algorithm, which is SDP-based, in this parameter regime [MMV12]. Finally, our results show that spectral methods are not the only viable approach to the construction of local graph partitioning algorithm and open door to the study of algorithms with even better approximation and locality guarantees.

The paper introduces the concept of a cluster structure to define a joint distribution of the sample size and its exchangeable random partitions. The cluster structure allows the probability distribution of the random partitions of a subset of the sample to be dependent on the sample size, a feature not presented in a partition structure. A generalized negative binomial process count-mixture model is proposed to generate a cluster structure, where in the prior the number of clusters is finite and Poisson distributed and the cluster sizes follow a truncated negative binomial distribution. The number and sizes of clusters can be controlled to exhibit distinct asymptotic behaviors. Unique model properties are illustrated with example clustering results using a generalized Polya urn sampling scheme. The paper provides new methods to generate exchangeable random partitions and to control both the cluster-number and cluster-size distributions.

Spectral clustering is widely used to partition graphs into distinct modules or communities. Existing methods for spectral clustering use the eigenvalues and eigenvectors of the graph Laplacian, an operator that is closely associated with random walks on graphs. We propose a new spectral partitioning method that exploits the properties of epidemic diffusion. An epidemic is a dynamic process that, unlike the random walk, simultaneously transitions to all the neighbors of a given node. We show that the replicator, an operator describing epidemic diffusion, is equivalent to the symmetric normalized Laplacian of a reweighted graph with edges reweighted by the eigenvector centralities of their incident nodes. Thus, more weight is given to edges connecting more central nodes. We describe a method that partitions the nodes based on the componentwise ratio of the replicator's second eigenvector to the first, and compare its performance to traditional spectral clustering techniques on synthetic graphs with known community structure. We demonstrate that the replicator gives preference to dense, clique-like structures, enabling it to more effectively discover communities that may be obscured by dense intercommunity linking.

There have lately been several suggestions for parametrized distances on a graph that generalize the shortest path distance and the commute time or resistance distance. The need for developing such distances has risen from the observation that the above-mentioned common distances in many situations fail to take into account the global structure of the graph. In this article, we develop the theory of one family of graph node distances, known as the randomized shortest path dissimilarity, which has its foundation in statistical physics. We show that the randomized shortest path dissimilarity can be easily computed in closed form for all pairs of nodes of a graph. Moreover, we come up with a new definition of a distance measure that we call the free energy distance. The free energy distance can be seen as an upgrade of the randomized shortest path dissimilarity as it defines a metric, in addition to which it satisfies the graph-geodetic property. The derivation and computation of the free energy distance are also straightforward. We then make a comparison between a set of generalized distances that interpolate between the shortest path distance and the commute time, or resistance distance. This comparison focuses on the applicability of the distances in graph node clustering and classification. The comparison, in general, shows that the parametrized distances perform well in the tasks. In particular, we see that the results obtained with the free energy distance are among the best in all the experiments.

Functional magnetic resonance imaging (fMRI) produces data about activity inside the brain, from which spatial maps can be extracted by independent component analysis (ICA). In datasets, there are n spatial maps that contain p voxels. The number of voxels is very high compared to the number of analyzed spatial maps. Clustering of the spatial maps is usually based on correlation matrices. This usually works well, although such a similarity matrix inherently can explain only a certain amount of the total variance contained in the high-dimensional data where n is relatively small but p is large. For high-dimensional space, it is reasonable to perform dimensionality reduction before clustering. In this research, we used the recently developed diffusion map for dimensionality reduction in conjunction with spectral clustering. This research revealed that the diffusion map based clustering worked as well as the more traditional methods, and produced more compact clusters when needed.