The Wavelet Trie: Maintaining an Indexed Sequence of Strings in Compressed Space

An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of column-oriented databases, log processing, and other storage and query tasks. In these applications each string can appear several times and the order of the strings in the sequence is relevant. The prefix structure of the strings is relevant as well: common prefixes are sought in strings to extract interesting features from the sequence. Moreover, space-efficiency is highly desirable as it translates directly into higher performance, since more data can fit in fast memory. We introduce and study the problem of compressed indexed sequence of strings, representing indexed sequences of strings in nearly-optimal compressed space, both in the static and dynamic settings, while preserving provably good performance for the supported operations. We present a new data structure for this problem, the Wavelet Trie, which combines the classical Patricia Trie with the Wavelet Tree, a succinct data structure for storing a compressed sequence. The resulting Wavelet Trie smoothly adapts to a sequence of strings that changes over time. It improves on the state-of-the-art compressed data structures by supporting a dynamic alphabet (i.e. the set of distinct strings) and prefix queries, both crucial requirements in the aforementioned applications, and on traditional indexes by reducing space occupancy to close to the entropy of the sequence

A summary of NASTRAN fluid/structure interaction capabilities

A summary of fluid/structure interaction capabilities for the NASTRAN computer program is presented. Indirect applications of the program towards solving this class of problem were concentrated on. For completeness and comparitive purposes, direct usage of NASTRAN is briefly discussed. The solution technology addresses both steady state and transient dynamic response problems

Developmental biology of wood formation

The wood-forming vascular cambium is responsible for the production of a large part of the biomass on this planet. Yet, there is only limited knowledge on how cell proliferation and differentiation in the cambial meristem are regulated. In this thesis the wood-forming tissues of aspen were used as a model system to identify and characterize molecular factors related to cambial meristem activity. An important regulator of cambial meristem activity is the plant hormone auxin. As polar transport is crucial for the delivery of auxin to the cambial zone, we identified homologues of known regulators of polar auxin transport and described their regulation by environmental and developmental factors. Translating changes in auxin concentration into changes in gene expression involves members of the Aux/IAA gene family. Aspen homologues of Aux/IAA genes were cloned and found to be expressed in a highly tissue-specific fashion, which is further influenced by developmental events and changes in the environment. A major response of trees to environmental changes is the suspension of meristematic growth during winter dormancy. A comparison of gene expression in active and dormant cambia revealed dramatic changes in the transcriptome including the expression of many cold and stress related genes during winter. During the process of wood formation, cells originating in the vascular cambium go through an elaborate process of cell division, cell expansion, secondary wall formation and programmed cell death. Large-scale analysis of gene expression was used to create transcriptional maps of the differentiation process. This extensive dataset allowed us to confirm the proposed functions of various genes involved in wood formation, assign other known genes to specific stages along the developmental gradient and identify a large number of novel potential regulators of wood formation. The data further suggest that the cambial meristem shares regulatory mechanisms with other meristems in addition to its own, specific factors

The JCMT Gould Belt Survey: properties of star-forming filaments in Orion A North

We develop and apply a Hessian-based filament detection algorithm to submillimetre continuum observations of Orion A North. The resultant filament radial density profiles are fitted with beam-convolved line-of-sight Plummer-profiles using Markov chain Monte Carlo techniques. The posterior distribution of the radial decay parameter demonstrates that the majority of filaments exhibit p = 1.5–3, with a mode at p = 2.2, suggesting deviation from the Ostriker p = 4 isothermal, equilibrium, self-gravitating cylinder. The spatial distribution of young stellar objects relative to the high column density filaments is investigated, yielding a lower limit on the star-forming age of the integral-shaped filament ∼1.4 Myr. Additionally, inferred lifetimes of filaments are examined which suggest long-term filament accretion, varying rates of star formation, or both. Theoretical filament stability measures are determined with the aid of HARP C18O J = 3–2 observations and indicate that the majority of filaments are gravitationally subcritical, despite the presence of young protostars. The results from this investigation are consistent with the one-dimensional accretion flow filament model recently observed in numerical simulations

Extensions to the ant-miner classification rule discovery algorithm

Ant-Miner is an application of ACO in data mining. It has been introduced by Parpinelli et al. in 2002 as an ant-based algorithm for the discovery of classification rules. Ant-Miner has proved to be a very promising technique for classification rules discovery. Ant-Miner generates a fewer number of rules, fewer terms per each rule and performs competitively in terms of efficiency compared to the C4.5 algorithm (see experimental results in [20]). Hence, it has been a focus area of research and a lot of modification has been done to it in order to increase its quality in terms of classification accuracy and output rules comprehensibility (reducing the size of the rule set). The thesis proposes five extensions to Ant-Miner. 1) The thesis proposes the use of a logical negation operator in the antecedents of constructed rules, so the terms in the rule antecedents could be in the form of . This tends to generate rules with higher coverage and reduce the size of the generated rule set. 2) The thesis proposes the use stubborn ants, an ACO-variation in which an ant is allowed to take into consideration its own personal past history. Stubborn ants tend to generate rules with higher classification accuracy in fewer trials per iteration. 3) The thesis proposes the use multiple types of pheromone; one for each permitted rule class, i.e. an ant would first select the rule class and then deposit the corresponding type of pheromone. The multi-pheromone system improves the quality of the output in terms of classification accuracy as well as it comprehensibility. 4) Along with the multi-pheromone system, the thesis proposes a new pheromone update strategy, called quality contrast intensifier. Such a strategy rewards rules with high confidence by depositing more pheromone and penalizes rules with low confidence by removing pheromone. 5) The thesis proposes that each ant to have its own value of α and β parameters, which in a sense means that each ant has its own individual personality. In order to verify the efficiency of these modifications, several cross-validation experiments have been applied on each of eight datasets used in the experiment. Average output results have been recorded, and a test of statistical significance has been applied to indicate improvement significance. Empirical results show improvements in the algorithm\u27s performance in terms of the simplicity of the generated rule set, the number of trials, and the predictive accuracy

Orbital Optimization in the Density Matrix Renormalization Group, with applications to polyenes and \beta-carotene

In previous work we have shown that the Density Matrix Renormalization Group (DMRG) enables near-exact calculations in active spaces much larger than are possible with traditional Complete Active Space algorithms. Here, we implement orbital optimisation with the Density Matrix Renormalization Group to further allow the self-consistent improvement of the active orbitals, as is done in the Complete Active Space Self-Consistent Field (CASSCF) method. We use our resulting DMRGCASSCF method to study the low-lying excited states of the all-trans polyenes up to C24H26 as well as \beta-carotene, correlating with near-exact accuracy the optimised complete \pi-valence space with up to 24 active electrons and orbitals, and analyse our results in the light of the recent discovery from Resonance Raman experiments of new optically dark states in the spectrum.Comment: 16 pages, 8 figure

A framework for developing finite element codes for multi- disciplinary applications

The world of computing simulation has experienced great progresses in recent years and requires more exigent multidisciplinary challenges to satisfy the new upcoming demands. Increasing the importance of solving multi-disciplinary problems makes developers put more attention to these problems and deal with difficulties involved in developing software in this area. Conventional finite element codes have several difficulties in dealing with multi-disciplinary problems. Many of these codes are designed and implemented for solving a certain type of problems, generally involving a single field. Extending these codes to deal with another field of analysis usually consists of several problems and large amounts of modifications and implementations. Some typical difficulties are: predefined set of degrees of freedom per node, data structure with fixed set of defined variables, global list of variables for all entities, domain based interfaces, IO restriction in reading new data and writing new results and algorithm definition inside the code. A common approach is to connect different solvers via a master program which implements the interaction algorithms and also transfers data from one solver to another. This approach has been used successfully in practice but results duplicated implementation and redundant overhead of data storing and transferring which may be significant depending to the solvers data structure. The objective of this work is to design and implement a framework for building multi-disciplinary finite element programs. Generality, reusability, extendibility, good performance and memory efficiency are considered to be the main points in design and implementation of this framework. Preparing the structure for team development is another objective because usually a team of experts in different fields are involved in the development of multi-disciplinary code. Kratos, the framework created in this work, provides several tools for easy implementation of finite element applications and also provides a common platform for natural interaction of its applications in different ways. This is done not only by a number of innovations but also by collecting and reusing several existing works. In this work an innovative variable base interface is designed and implemented which is used at different levels of abstraction and showed to be very clear and extendible. Another innovation is a very efficient and flexible data structure which can be used to store any type of data in a type-safe manner. An extendible IO is also created to overcome another bottleneck in dealing with multi-disciplinary problems. Collecting different concepts of existing works and adapting them to coupled problems is considered to be another innovation in this work. Examples are using an interpreter, different data organizations and variable number of dofs per node. The kernel and application approach is used to reduce the possible conflicts arising between developers of different fields and layers are designed to reflect the working space of different developers also considering their programming knowledge. Finally several technical details are applied in order to increase the performance and efficiency of Kratos which makes it practically usable. This work is completed by demonstrating the framework’s functionality in practice. First some classical single field applications like thermal, fluid and structural applications are implemented and used as benchmark to prove its performance. These applications are used to solve coupled problems in order to demonstrate the natural interaction facility provided by the framework. Finally some less classical coupled finite element algorithms are implemented to show its high flexibility and extendibility