Neil Robertson

Bio: Neil Robertson is an academic researcher from Ohio State University. The author has contributed to research in topics: Planar graph & Graph minor. The author has an hindex of 41, co-authored 78 publications receiving 12524 citations. Previous affiliations of Neil Robertson include Telcordia Technologies & Georgia Institute of Technology.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Abstract: MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

Dynamic bayesian networks: representation, inference and learning

Abstract: Dynamic Bayesian Networks: Representation, Inference and Learning by Kevin Patrick Murphy Doctor of Philosophy in Computer Science University of California, Berkeley Professor Stuart Russell, Chair Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and bio-sequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linear-Gaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data. In particular, the main novel technical contributions of this thesis are as follows: a way of representing Hierarchical HMMs as DBNs, which enables inference to be done in O(T ) time instead of O(T ), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T ) space instead of O(T ); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of applying Rao-Blackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.

Spectra of graphs

Abstract: This book gives an elementary treatment of the basic material about graph spectra, both for ordinary, and Laplace and Seidel spectra. The text progresses systematically, by covering standard topics before presenting some new material on trees, strongly regular graphs, two-graphs, association schemes, p-ranks of configurations and similar topics. Exercises at the end of each chapter provide practice and vary from easy yet interesting applications of the treated theory, to little excursions into related topics. Tables, references at the end of the book, an author and subject index enrich the text. Spectra of Graphs is written for researchers, teachers and graduate students interested in graph spectra. The reader is assumed to be familiar with basic linear algebra and eigenvalues, although some more advanced topics in linear algebra, like the Perron-Frobenius theorem and eigenvalue interlacing are included.

Digraphs Theory Algorithms And Applications

Abstract: The theory of directed graphs has developed enormously over recent decades, yet this book (first published in 2000) remains the only book to cover more than a small fraction of the results. New research in the field has made a second edition a necessity. Substantially revised, reorganised and updated, the book now comprises eighteen chapters, carefully arranged in a straightforward and logical manner, with many new results and open problems. As well as covering the theoretical aspects of the subject, with detailed proofs of many important results, the authors present a number of algorithms, and whole chapters are devoted to topics such as branchings, feedback arc and vertex sets, connectivity augmentations, sparse subdigraphs with prescribed connectivity, and also packing, covering and decompositions of digraphs. Throughout the book, there is a strong focus on applications which include quantum mechanics, bioinformatics, embedded computing, and the travelling salesman problem. Detailed indices and topic-oriented chapters ease navigation, and more than 650 exercises, 170 figures and 150 open problems are included to help immerse the reader in all aspects of the subject. Digraphs is an essential, comprehensive reference for undergraduate and graduate students, and researchers in mathematics, operations research and computer science. It will also prove invaluable to specialists in related areas, such as meteorology, physics and computational biology.

Invitation to fixed-parameter algorithms

Abstract: PART I: FOUNDATIONS 1. Introduction to Fixed-Parameter Algorithms 2. Preliminaries and Agreements 3. Parameterized Complexity Theory - A Primer 4. Vertex Cover - An Illustrative Example 5. The Art of Problem Parameterization 6. Summary and Concluding Remarks PART II: ALGORITHMIC METHODS 7. Data Reduction and Problem Kernels 8. Depth-Bounded Search Trees 9. Dynamic Programming 10. Tree Decompositions of Graphs 11. Further Advanced Techniques 12. Summary and Concluding Remarks PART III: SOME THEORY, SOME CASE STUDIES 13. Parameterized Complexity Theory 14. Connections to Approximation Algorithms 15. Selected Case Studies 16. Zukunftsmusik References Index