Unsupervised cryo-EM data clustering through adaptively constrained K-means algorithm

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.Comment: 35 pages, 14 figure

Space Exploration via Proximity Search

We investigate what computational tasks can be performed on a point set in $\Re^d$, if we are only given black-box access to it via nearest-neighbor search. This is a reasonable assumption if the underlying point set is either provided implicitly, or it is stored in a data structure that can answer such queries. In particular, we show the following: (A) One can compute an approximate bi-criteria $k$-center clustering of the point set, and more generally compute a greedy permutation of the point set. (B) One can decide if a query point is (approximately) inside the convex-hull of the point set. We also investigate the problem of clustering the given point set, such that meaningful proximity queries can be carried out on the centers of the clusters, instead of the whole point set

The Evolution of Beliefs over Signed Social Networks

We study the evolution of opinions (or beliefs) over a social network modeled as a signed graph. The sign attached to an edge in this graph characterizes whether the corresponding individuals or end nodes are friends (positive links) or enemies (negative links). Pairs of nodes are randomly selected to interact over time, and when two nodes interact, each of them updates its opinion based on the opinion of the other node and the sign of the corresponding link. This model generalizes DeGroot model to account for negative links: when two enemies interact, their opinions go in opposite directions. We provide conditions for convergence and divergence in expectation, in mean-square, and in almost sure sense, and exhibit phase transition phenomena for these notions of convergence depending on the parameters of the opinion update model and on the structure of the underlying graph. We establish a {\it no-survivor} theorem, stating that the difference in opinions of any two nodes diverges whenever opinions in the network diverge as a whole. We also prove a {\it live-or-die} lemma, indicating that almost surely, the opinions either converge to an agreement or diverge. Finally, we extend our analysis to cases where opinions have hard lower and upper limits. In these cases, we study when and how opinions may become asymptotically clustered to the belief boundaries, and highlight the crucial influence of (strong or weak) structural balance of the underlying network on this clustering phenomenon

The Bane of Low-Dimensionality Clustering

In this paper, we give a conditional lower bound of $n^{\Omega(k)}$ on running time for the classic k-median and k-means clustering objectives (where n is the size of the input), even in low-dimensional Euclidean space of dimension four, assuming the Exponential Time Hypothesis (ETH). We also consider k-median (and k-means) with penalties where each point need not be assigned to a center, in which case it must pay a penalty, and extend our lower bound to at least three-dimensional Euclidean space. This stands in stark contrast to many other geometric problems such as the traveling salesman problem, or computing an independent set of unit spheres. While these problems benefit from the so-called (limited) blessing of dimensionality, as they can be solved in time $n^{O(k^{1-1/d})}$ or $2^{n^{1-1/d}}$ in d dimensions, our work shows that widely-used clustering objectives have a lower bound of $n^{\Omega(k)}$, even in dimension four. We complete the picture by considering the two-dimensional case: we show that there is no algorithm that solves the penalized version in time less than $n^{o(\sqrt{k})}$, and provide a matching upper bound of $n^{O(\sqrt{k})}$. The main tool we use to establish these lower bounds is the placement of points on the moment curve, which takes its inspiration from constructions of point sets yielding Delaunay complexes of high complexity

Information-theoretic bounds and phase transitions in clustering, sparse PCA, and submatrix localization

We study the problem of detecting a structured, low-rank signal matrix corrupted with additive Gaussian noise. This includes clustering in a Gaussian mixture model, sparse PCA, and submatrix localization. Each of these problems is conjectured to exhibit a sharp information-theoretic threshold, below which the signal is too weak for any algorithm to detect. We derive upper and lower bounds on these thresholds by applying the first and second moment methods to the likelihood ratio between these "planted models" and null models where the signal matrix is zero. Our bounds differ by at most a factor of root two when the rank is large (in the clustering and submatrix localization problems, when the number of clusters or blocks is large) or the signal matrix is very sparse. Moreover, our upper bounds show that for each of these problems there is a significant regime where reliable detection is information- theoretically possible but where known algorithms such as PCA fail completely, since the spectrum of the observed matrix is uninformative. This regime is analogous to the conjectured 'hard but detectable' regime for community detection in sparse graphs.Comment: For sparse PCA and submatrix localization, we determine the information-theoretic threshold exactly in the limit where the number of blocks is large or the signal matrix is very sparse based on a conditional second moment method, closing the factor of root two gap in the first versio