Fiedler Vector Approximation via Interacting Random Walks

The Fiedler vector of a graph, namely the eigenvector corresponding to the second smallest eigenvalue of a graph Laplacian matrix, plays an important role in spectral graph theory with applications in problems such as graph bi-partitioning and envelope reduction. Algorithms designed to estimate this quantity usually rely on a priori knowledge of the entire graph, and employ techniques such as graph sparsification and power iterations, which have obvious shortcomings in cases where the graph is unknown, or changing dynamically. In this paper, we develop a framework in which we construct a stochastic process based on a set of interacting random walks on a graph and show that a suitably scaled version of our stochastic process converges to the Fiedler vector for a sufficiently large number of walks. Like other techniques based on exploratory random walks and on-the-fly computations, such as Markov Chain Monte Carlo (MCMC), our algorithm overcomes challenges typically faced by power iteration based approaches. But, unlike any existing random walk based method such as MCMCs where the focus is on the leading eigenvector, our framework with interacting random walks converges to the Fiedler vector (second eigenvector). We also provide numerical results to confirm our theoretical findings on different graphs, and show that our algorithm performs well over a wide range of parameters and the number of random walks. Simulations results over time varying dynamic graphs are also provided to show the efficacy of our random walk based technique in such settings. As an important contribution, we extend our results and show that our framework is applicable for approximating not just the Fiedler vector of graph Laplacians, but also the second eigenvector of any time reversible Markov Chain kernel via interacting random walks.Comment: in ACM SIGMETRICS, Boston, MA, June 2020, to appear. (Also will be in Proc. ACM Meas. Anal. Comput. Syst (POMACS), March 2020

Estimation of Scribble Placement for Painting Colorization

Image colorization has been a topic of interest since the mid 70’s and several algorithms have been proposed that given a grayscale image and color scribbles (hints) produce a colorized image. Recently, this approach has been introduced in the field of art conservation and cultural heritage, where B&W photographs of paintings at previous stages have been colorized. However, the questions of what is the minimum number of scribbles necessary and where they should be placed in an image remain unexplored. Here we address this limitation using an iterative algorithm that provides insights as to the relationship between locally vs. globally important scribbles. Given a color image we randomly select scribbles and we attempt to color the grayscale version of the original.We define a scribble contribution measure based on the reconstruction error. We demonstrate our approach using a widely used colorization algorithm and images from a Picasso painting and the peppers test image. We show that areas isolated by thick brushstrokes or areas with high textural variation are locally important but contribute very little to the overall representation accuracy. We also find that for the case of Picasso on average 10% of scribble coverage is enough and that flat areas can be presented by few scribbles. The proposed method can be used verbatim to test any colorization algorithm

Computational structure‐based drug design: Predicting target flexibility

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft

Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or are expensive to acquire. On the other hand, observational data of the organism in steady state (e.g. wild-type) are more readily available, but their informational content is inadequate for the task at hand. We develop a computational approach to appropriately utilize both data sources for estimating a regulatory network. The proposed approach is based on a three-step algorithm to estimate the underlying directed but cyclic network, that uses as input both perturbation screens and steady state gene expression data. In the first step, the algorithm determines causal orderings of the genes that are consistent with the perturbation data, by combining an exhaustive search method with a fast heuristic that in turn couples a Monte Carlo technique with a fast search algorithm. In the second step, for each obtained causal ordering, a regulatory network is estimated using a penalized likelihood based method, while in the third step a consensus network is constructed from the highest scored ones. Extensive computational experiments show that the algorithm performs well in reconstructing the underlying network and clearly outperforms competing approaches that rely only on a single data source. Further, it is established that the algorithm produces a consistent estimate of the regulatory network.Comment: 24 pages, 4 figures, 6 table

Analysis of stochastic probing methods for estimating the trace of functions of sparse symmetric matrices

We consider the problem of estimating the trace of a matrix function $f(A)$. In certain situations, in particular if $f(A)$ cannot be well approximated by a low-rank matrix, combining probing methods based on graph colorings with stochastic trace estimation techniques can yield accurate approximations at moderate cost. So far, such methods have not been thoroughly analyzed, though, but were rather used as efficient heuristics by practitioners. In this manuscript, we perform a detailed analysis of stochastic probing methods and, in particular, expose conditions under which the expected approximation error in the stochastic probing method scales more favorably with the dimension of the matrix than the error in non-stochastic probing. Extending results from [E. Aune, D. P. Simpson, J. Eidsvik, Parameter estimation in high dimensional Gaussian distributions, Stat. Comput., 24, pp. 247--263, 2014], we also characterize situations in which using just one stochastic vector is always -- not only in expectation -- better than the deterministic probing method. Several numerical experiments illustrate our theory and compare with existing methods