Whole-proteome tree of life suggests a deep burst of organism diversity.

An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an "alignment-free" method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 "Supergroups," 6 "Major Groups," or 35+ "Groups"; 2) the order of emergence of the "founders" of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a "deep burst" at the very beginning period near the root of the ToL-an explosive birth of life's diversity

From Theory to Practice: Plug and Play with Succinct Data Structures

Engineering efficient implementations of compact and succinct structures is a time-consuming and challenging task, since there is no standard library of easy-to- use, highly optimized, and composable components. One consequence is that measuring the practical impact of new theoretical proposals is a difficult task, since older base- line implementations may not rely on the same basic components, and reimplementing from scratch can be very time-consuming. In this paper we present a framework for experimentation with succinct data structures, providing a large set of configurable components, together with tests, benchmarks, and tools to analyze resource requirements. We demonstrate the functionality of the framework by recomposing succinct solutions for document retrieval.Comment: 10 pages, 4 figures, 3 table

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

No-reference bitstream-based visual quality impairment detection for high definition H.264/AVC encoded video sequences

Ensuring and maintaining adequate Quality of Experience towards end-users are key objectives for video service providers, not only for increasing customer satisfaction but also as service differentiator. However, in the case of High Definition video streaming over IP-based networks, network impairments such as packet loss can severely degrade the perceived visual quality. Several standard organizations have established a minimum set of performance objectives which should be achieved for obtaining satisfactory quality. Therefore, video service providers should continuously monitor the network and the quality of the received video streams in order to detect visual degradations. Objective video quality metrics enable automatic measurement of perceived quality. Unfortunately, the most reliable metrics require access to both the original and the received video streams which makes them inappropriate for real-time monitoring. In this article, we present a novel no-reference bitstream-based visual quality impairment detector which enables real-time detection of visual degradations caused by network impairments. By only incorporating information extracted from the encoded bitstream, network impairments are classified as visible or invisible to the end-user. Our results show that impairment visibility can be classified with a high accuracy which enables real-time validation of the existing performance objectives

Succinct progress measures for solving parity games

The recent breakthrough paper by Calude et al. has given the first algorithm for solving parity games in quasi-polynomial time, where previously the best algorithms were mildly subexponential. We devise an alternative quasi-polynomial time algorithm based on progress measures, which allows us to reduce the space required from quasi-polynomial to nearly linear. Our key technical tools are a novel concept of ordered tree coding, and a succinct tree coding result that we prove using bounded adaptive multi-counters, both of which are interesting in their own right

Constructing Merger Trees that Mimic N-Body Simulations

We present a simple and efficient empirical algorithm for constructing dark-matter halo merger trees that reproduce the distribution of trees in the Millennium cosmological $N$-body simulation. The generated trees are significantly better than EPS trees. The algorithm is Markovian, and it therefore fails to reproduce the non-Markov features of trees across short time steps, except for an accurate fit to the evolution of the average main progenitor. However, it properly recovers the full main progenitor distribution and the joint distributions of all the progenitors over long-enough time steps, $\Delta \omega \simeq \Delta z>0.5$, where $\omega \simeq 1.69/D(t)$ is the self-similar time variable and $D(t)$ refers to the linear growth of density fluctuations. We find that the main progenitor distribution is log-normal in the variable $\sigma^2(M)$, the variance of linear density fluctuations in a sphere encompassing mass $M$. The secondary progenitors are successfully drawn one by one from the remaining mass using a similar distribution function. These empirical findings may be clues to the underlying physics of merger-tree statistics. As a byproduct, we provide useful, accurate analytic time-invariant approximations for the main progenitor accretion history and for halo merger rates.Comment: 13 pages, 9 figures. Accepted for MNRAS. Minor changes from version

Multiple Context-Free Tree Grammars: Lexicalization and Characterization

Multiple (simple) context-free tree grammars are investigated, where "simple" means "linear and nondeleting". Every multiple context-free tree grammar that is finitely ambiguous can be lexicalized; i.e., it can be transformed into an equivalent one (generating the same tree language) in which each rule of the grammar contains a lexical symbol. Due to this transformation, the rank of the nonterminals increases at most by 1, and the multiplicity (or fan-out) of the grammar increases at most by the maximal rank of the lexical symbols; in particular, the multiplicity does not increase when all lexical symbols have rank 0. Multiple context-free tree grammars have the same tree generating power as multi-component tree adjoining grammars (provided the latter can use a root-marker). Moreover, every multi-component tree adjoining grammar that is finitely ambiguous can be lexicalized. Multiple context-free tree grammars have the same string generating power as multiple context-free (string) grammars and polynomial time parsing algorithms. A tree language can be generated by a multiple context-free tree grammar if and only if it is the image of a regular tree language under a deterministic finite-copying macro tree transducer. Multiple context-free tree grammars can be used as a synchronous translation device.Comment: 78 pages, 13 figure