Robust Rotation Synchronization via Low-rank and Sparse Matrix Decomposition

This paper deals with the rotation synchronization problem, which arises in global registration of 3D point-sets and in structure from motion. The problem is formulated in an unprecedented way as a "low-rank and sparse" matrix decomposition that handles both outliers and missing data. A minimization strategy, dubbed R-GoDec, is also proposed and evaluated experimentally against state-of-the-art algorithms on simulated and real data. The results show that R-GoDec is the fastest among the robust algorithms.Comment: The material contained in this paper is part of a manuscript submitted to CVI

Bayesian Estimation of Mixed Multinomial Logit Models: Advances and Simulation-Based Evaluations

Variational Bayes (VB) methods have emerged as a fast and computationally-efficient alternative to Markov chain Monte Carlo (MCMC) methods for scalable Bayesian estimation of mixed multinomial logit (MMNL) models. It has been established that VB is substantially faster than MCMC at practically no compromises in predictive accuracy. In this paper, we address two critical gaps concerning the usage and understanding of VB for MMNL. First, extant VB methods are limited to utility specifications involving only individual-specific taste parameters. Second, the finite-sample properties of VB estimators and the relative performance of VB, MCMC and maximum simulated likelihood estimation (MSLE) are not known. To address the former, this study extends several VB methods for MMNL to admit utility specifications including both fixed and random utility parameters. To address the latter, we conduct an extensive simulation-based evaluation to benchmark the extended VB methods against MCMC and MSLE in terms of estimation times, parameter recovery and predictive accuracy. The results suggest that all VB variants with the exception of the ones relying on an alternative variational lower bound constructed with the help of the modified Jensen's inequality perform as well as MCMC and MSLE at prediction and parameter recovery. In particular, VB with nonconjugate variational message passing and the delta-method (VB-NCVMP-Delta) is up to 16 times faster than MCMC and MSLE. Thus, VB-NCVMP-Delta can be an attractive alternative to MCMC and MSLE for fast, scalable and accurate estimation of MMNL models

Recovering complete and draft population genomes from metagenome datasets.

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution

Linear Global Translation Estimation with Feature Tracks

This paper derives a novel linear position constraint for cameras seeing a common scene point, which leads to a direct linear method for global camera translation estimation. Unlike previous solutions, this method deals with collinear camera motion and weak image association at the same time. The final linear formulation does not involve the coordinates of scene points, which makes it efficient even for large scale data. We solve the linear equation based on $L_1$ norm, which makes our system more robust to outliers in essential matrices and feature correspondences. We experiment this method on both sequentially captured images and unordered Internet images. The experiments demonstrate its strength in robustness, accuracy, and efficiency.Comment: Changes: 1. Adopt BMVC2015 style; 2. Combine sections 3 and 5; 3. Move "Evaluation on synthetic data" out to supplementary file; 4. Divide subsection "Evaluation on general data" to subsections "Experiment on sequential data" and "Experiment on unordered Internet data"; 5. Change Fig. 1 and Fig.8; 6. Move Fig. 6 and Fig. 7 to supplementary file; 7 Change some symbols; 8. Correct some typo

Improving Performance of Iterative Methods by Lossy Checkponting

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4)We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%~70% compared with traditional checkpointing and 20%~58% compared with lossless-compressed checkpointing, in the presence of system failures.Comment: 14 pages, 10 figures, HPDC'1

High precision simulations of weak lensing effect on Cosmic Microwave Background polarization

We study accuracy, robustness and self-consistency of pixel-domain simulations of the gravitational lensing effect on the primordial CMB anisotropies due to the large-scale structure of the Universe. In particular, we investigate dependence of the results precision on some crucial parameters of such techniques and propose a semi-analytic framework to determine their values so the required precision is a priori assured and the numerical workload simultaneously optimized. Our focus is on the B-mode signal but we discuss also other CMB observables, such as total intensity, T, and E-mode polarization, emphasizing differences and similarities between all these cases. Our semi-analytic considerations are backed up by extensive numerical results. Those are obtained using a code, nicknamed lenS2HAT -- for Lensing using Scalable Spherical Harmonic Transforms (S2HAT) -- which we have developed in the course of this work. The code implements a version of the pixel-domain approach of Lewis (2005) and permits performing the simulations at very high resolutions and data volumes, thanks to its efficient parallelization provided by the S2HAT library -- a parallel library for a calculation of the spherical harmonic transforms. The code is made publicly available.Comment: 20 pages, 14 figures, submitted to A&A, matches version accepted for publication in A&