Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

Likelihood-based inference of B-cell clonal families

The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM) framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets

Fast Isogeometric Boundary Element Method based on Independent Field Approximation

An isogeometric boundary element method for problems in elasticity is presented, which is based on an independent approximation for the geometry, traction and displacement field. This enables a flexible choice of refinement strategies, permits an efficient evaluation of geometry related information, a mixed collocation scheme which deals with discontinuous tractions along non-smooth boundaries and a significant reduction of the right hand side of the system of equations for common boundary conditions. All these benefits are achieved without any loss of accuracy compared to conventional isogeometric formulations. The system matrices are approximated by means of hierarchical matrices to reduce the computational complexity for large scale analysis. For the required geometrical bisection of the domain, a strategy for the evaluation of bounding boxes containing the supports of NURBS basis functions is presented. The versatility and accuracy of the proposed methodology is demonstrated by convergence studies showing optimal rates and real world examples in two and three dimensions.Comment: 32 pages, 27 figure

Exploring Outliers in Crowdsourced Ranking for QoE

Outlier detection is a crucial part of robust evaluation for crowdsourceable assessment of Quality of Experience (QoE) and has attracted much attention in recent years. In this paper, we propose some simple and fast algorithms for outlier detection and robust QoE evaluation based on the nonconvex optimization principle. Several iterative procedures are designed with or without knowing the number of outliers in samples. Theoretical analysis is given to show that such procedures can reach statistically good estimates under mild conditions. Finally, experimental results with simulated and real-world crowdsourcing datasets show that the proposed algorithms could produce similar performance to Huber-LASSO approach in robust ranking, yet with nearly 8 or 90 times speed-up, without or with a prior knowledge on the sparsity size of outliers, respectively. Therefore the proposed methodology provides us a set of helpful tools for robust QoE evaluation with crowdsourcing data.Comment: accepted by ACM Multimedia 2017 (Oral presentation). arXiv admin note: text overlap with arXiv:1407.763

Extremal Optimization for Graph Partitioning

Extremal optimization is a new general-purpose method for approximating solutions to hard optimization problems. We study the method in detail by way of the NP-hard graph partitioning problem. We discuss the scaling behavior of extremal optimization, focusing on the convergence of the average run as a function of runtime and system size. The method has a single free parameter, which we determine numerically and justify using a simple argument. Our numerical results demonstrate that on random graphs, extremal optimization maintains consistent accuracy for increasing system sizes, with an approximation error decreasing over runtime roughly as a power law t^(-0.4). On geometrically structured graphs, the scaling of results from the average run suggests that these are far from optimal, with large fluctuations between individual trials. But when only the best runs are considered, results consistent with theoretical arguments are recovered.Comment: 34 pages, RevTex4, 1 table and 20 ps-figures included, related papers available at http://www.physics.emory.edu/faculty/boettcher