Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons

De-aliasing Undersampled Volume Images for Visualization

We present and illustrate a new technique, Image Correlation Supersampling (ICS), for resampling volume data that are undersampled in one dimension. The resulting data satisfies the sampling theorem, and, therefore, many visualization algorithms that assume the theorem is satisfied can be applied to the data. Without the supersampling the visualization algorithms create artifacts due to aliasing. The assumptions made in developing the algorithm are often satisfied by data that is undersampled temporally. Through this supersampling we can completely characterize phenomena with measurements at a coarser temporal sampling rate than would otherwise be necessary. This can save acquisition time and storage space, permit the study of faster phenomena, and allow their study without introducing aliasing artifacts. The resampling technique relies on a priori knowledge of the measured phenomenon, and applies, in particular, to scalar concentration measurements of fluid flow. Because of the characteristics of fluid flow, an image deformation that takes each slice image to the next can be used to calculate intermediate slice images at arbitrarily fine spacing. We determine the deformation with an automatic, multi-resolution algorithm

RLFC: Random Access Light Field Compression using Key Views and Bounded Integer Encoding

We present a new hierarchical compression scheme for encoding light field images (LFI) that is suitable for interactive rendering. Our method (RLFC) exploits redundancies in the light field images by constructing a tree structure. The top level (root) of the tree captures the common high-level details across the LFI, and other levels (children) of the tree capture specific low-level details of the LFI. Our decompressing algorithm corresponds to tree traversal operations and gathers the values stored at different levels of the tree. Furthermore, we use bounded integer sequence encoding which provides random access and fast hardware decoding for compressing the blocks of children of the tree. We have evaluated our method for 4D two-plane parameterized light fields. The compression rates vary from 0.08 - 2.5 bits per pixel (bpp), resulting in compression ratios of around 200:1 to 20:1 for a PSNR quality of 40 to 50 dB. The decompression times for decoding the blocks of LFI are 1 - 3 microseconds per channel on an NVIDIA GTX-960 and we can render new views with a resolution of 512X512 at 200 fps. Our overall scheme is simple to implement and involves only bit manipulations and integer arithmetic operations.Comment: Accepted for publication at Symposium on Interactive 3D Graphics and Games (I3D '19

An Evaluation of Popular Copy-Move Forgery Detection Approaches

A copy-move forgery is created by copying and pasting content within the same image, and potentially post-processing it. In recent years, the detection of copy-move forgeries has become one of the most actively researched topics in blind image forensics. A considerable number of different algorithms have been proposed focusing on different types of postprocessed copies. In this paper, we aim to answer which copy-move forgery detection algorithms and processing steps (e.g., matching, filtering, outlier detection, affine transformation estimation) perform best in various postprocessing scenarios. The focus of our analysis is to evaluate the performance of previously proposed feature sets. We achieve this by casting existing algorithms in a common pipeline. In this paper, we examined the 15 most prominent feature sets. We analyzed the detection performance on a per-image basis and on a per-pixel basis. We created a challenging real-world copy-move dataset, and a software framework for systematic image manipulation. Experiments show, that the keypoint-based features SIFT and SURF, as well as the block-based DCT, DWT, KPCA, PCA and Zernike features perform very well. These feature sets exhibit the best robustness against various noise sources and downsampling, while reliably identifying the copied regions.Comment: Main paper: 14 pages, supplemental material: 12 pages, main paper appeared in IEEE Transaction on Information Forensics and Securit

Uncertainty in phylogenetic tree estimates

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly model the multivariate uncertainty of tree estimates. We consider both the cases where uncertainty information arises extrinsically (through covariate information) and intrinsically (through the tree estimates themselves). The importance of accounting for tree uncertainty in tree space is demonstrated in two case studies. In the first instance, differences between gene trees are small relative to their uncertainties, while in the second, the differences are relatively large. Our main goal is visualization of tree uncertainty, and we demonstrate advantages of our method with respect to reproducibility, speed and preservation of topological differences compared to visualization based on multidimensional scaling. The proposal highlights that phylogenetic trees are estimated in an extremely high-dimensional space, resulting in uncertainty information that cannot be discarded. Most importantly, it is a method that allows biologists to diagnose whether differences between gene trees are biologically meaningful, or due to uncertainty in estimation.Comment: Final version accepted to Journal of Computational and Graphical Statistic