Finding Most Compatible Phylogenetic Trees over Multi-State Characters

Peer reviewe

Finding Optimal Tree Decompositions

The task of organizing a given graph into a structure called a tree decomposition is relevant in multiple areas of computer science. In particular, many NP-hard problems can be solved in polynomial time if a suitable tree decomposition of a graph describing the problem instance is given as a part of the input. This motivates the task of finding as good tree decompositions as possible, or ideally, optimal tree decompositions. This thesis is about finding optimal tree decompositions of graphs with respect to several notions of optimality. Each of the considered notions measures the quality of a tree decomposition in the context of an application. In particular, we consider a total of seven problems that are formulated as finding optimal tree decompositions: treewidth, minimum fill-in, generalized and fractional hypertreewidth, total table size, phylogenetic character compatibility, and treelength. For each of these problems we consider the BT algorithm of Bouchitté and Todinca as the method of finding optimal tree decompositions. The BT algorithm is well-known on the theoretical side, but to our knowledge the first time it was implemented was only recently for the 2nd Parameterized Algorithms and Computational Experiments Challenge (PACE 2017). The author’s implementation of the BT algorithm took the second place in the minimum fill-in track of PACE 2017. In this thesis we review and extend the BT algorithm and our implementation. In particular, we improve the eciency of the algorithm in terms of both theory and practice. We also implement the algorithm for each of the seven problems considered, introducing a novel adaptation of the algorithm for the maximum compatibility problem of phylogenetic characters. Our implementation outperforms alternative state-of-the-art approaches in terms of numbers of test instances solved on well-known benchmarks on minimum fill-in, generalized hypertreewidth, fractional hypertreewidth, total table size, and the maximum compatibility problem of phylogenetic characters. Furthermore, to our understanding the implementation is the first exact approach for the treelength problem

BSML: A Binding Schema Markup Language for Data Interchange in Problem Solving Environments (PSEs)

We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with a PSE or application composition system that views model specification and execution as a problem of managing semistructured data. The data interchange problem is addressed by three techniques for processing semistructured data: validation, binding, and conversion. We present BSML and describe its application to a PSE for wireless communications system design

Development and Improvement of Tools and Algorithms for the Problem of Atom Type Perception and for the Assessment of Protein-Ligand-Complex Geometries

In context of the present work, a scoring function for protein-ligand complexes has been developed, not aimed at affinity prediction, but rather a good recognition rate of near native geometries. The developed program DSX makes use of the same formalism as the knowledge-based scoring function DrugScore, hence using the knowledge from crystallographic databases and atom-type specific distance-dependent distribution functions. It is based on newly defined atom-types. Additionally, the program is augmented by two novel potentials which evaluate the torsion angles and (de-)solvation effects. Validation of DSX is based on a literature-known, comprehensive data-set that allows for comparison with other popular scoring functions. DSX is intended for the recognition of near-native binding modes. In this important task, DSX outperforms the competitors, but is also among the best scoring functions regarding the ranking of different compounds. Another essential step in the development of DSX was the automatical assignment of the new atom types. A powerful programming framework was implemented to fulfill this task. Validation was done on a literature-known data-set and showed superior efficiency and quality compared to similar programs where this data was available. The front-end fconv was developed to share this functionality with the scientific community. Multiple features useful in computational drug-design workflows are also included and fconv was made freely available as Open Source Project. Based on the developed potentials for DSX, a number of further applications was created and impemented: The program HotspotsX calculates favorable interaction fields in protein binding pockets that can be used as a starting point for pharmacophoric models and that indicate possible directions for the optimization of lead structures. The program DSFP calculates scores based on fingerprints for given binding geometries. These fingerprints are compared with reference fingerprints that are derived from DSX interactions in known crystal structures of the particular target. Finally, the program DSX_wat was developed to predict stable water networks within a binding pocket. DSX interaction fields are used to calculate the putative water positions

Features and Algorithms for Visual Parsing of Handwritten Mathematical Expressions

Math expressions are an essential part of scientific documents. Handwritten math expressions recognition can benefit human-computer interaction especially in the education domain and is a critical part of document recognition and analysis. Parsing the spatial arrangement of symbols is an essential part of math expression recognition. A variety of parsing techniques have been developed during the past three decades, and fall into two groups. The first group is graph-based parsing. It selects a path or sub-graph which obeys some rule to form a possible interpretation for the given expression. The second group is grammar driven parsing. Grammars and related parameters are defined manually for different tasks. The time complexity of these two groups parsing is high, and they often impose some strict constraints to reduce the computation. The aim of this thesis is working towards building a straightforward and effective parser with as few constraints as possible. First, we propose using a line of sight graph for representing the layout of strokes and symbols in math expressions. It achieves higher F-score than other graph representations and reduces search space for parsing. Second, we modify the shape context feature with Parzen window density estimation. This feature set works well for symbol segmentation, symbol classification and symbol layout analysis. We get a higher symbol segmentation F-score than other systems on CROHME 2014 dataset. Finally, we develop a Maximum Spanning Tree (MST) based parser using Edmonds\u27 algorithm, which extracts an MST from the directed line of sight graph in two passes: first symbols are segmented, and then symbols and spatial relationship are labeled. The time complexity of our MST-based parsing is lower than the time complexity of CYK parsing with context-free grammars. Also, our MST-based parsing obtains higher structure rate and expression rate than CYK parsing when symbol segmentation is accurate. Correct structure means we get the structure of the symbol layout tree correct, even though the label of the edge in the symbol layout tree might be wrong. The performance of our math expression recognition system with MST-based parsing is competitive on CROHME 2012 and 2014 datasets. For future work, how to incorporate symbol classifier result and correct segmentation error in MST-based parsing needs more research

MaxSAT Evaluation 2020 : Solver and Benchmark Descriptions

Non peer reviewe

Investigating good usability consistency within and across the South African super 14 rugby franchise web sites

This study investigates the usability of the South African Super 14 Rugby franchise web sites. Web site usability is a measure of a web site user’s experience when visiting a web site. A web site user’s experience will determine how well a web site’s goals are achieved. The relevant web site goals are, having as many visitors as possible, both unique visitors and repeat visitors, and ensuring that those visitors stay on the web site for as long as possible. This study uses data generation method triangulation to enhance the validity of the findings. The data generation methods are an e-mail questionnaire survey and an expert group consensus method called the Delphi Method. This study shows that within each web site and across all five web sites, there is poor usability consistency. Management guidelines and recommendations for improvements to these web sites are presented, so that the web site goals can be achieved.Computer ScienceM.Sc. (Information Systems