Bioconsensus


Book Description

This volume is based on two DIMACS working group meetings on ''Bioconsensus''. It provides a valuable introduction and reference to the various aspects of this rapidly developing field. The meetings brought together mathematical and biological scientists to discuss the uses in the biological sciences of methods of consensus and social choice. These two lively meetings contributed much toward establishing the new field of ''bioconsensus''. Yet this book is much more than just a report of two meetings. It includes some historical background, as well as a substantial introduction to the axiomatic foundations of the field of bioconsensus and some practical applications of consensus methods to real data. Also included are contributed papers from experts who were not at the meetings. The book is intended for mathematical biologists, evolutionary biologists, and computer scientists.




Random Explorations


Book Description

The title “Random Explorations” has two meanings. First, a few topics of advanced probability are deeply explored. Second, there is a recurring theme of analyzing a random object by exploring a random path. This book is an outgrowth of lectures by the author in the University of Chicago Research Experiences for Undergraduate (REU) program in 2020. The idea of the course was to expose advanced undergraduates to ideas in probability research. The book begins with Markov chains with an emphasis on transient or killed chains that have finite Green's function. This function, and its inverse called the Laplacian, is discussed next to relate two objects that arise in statistical physics, the loop-erased random walk (LERW) and the uniform spanning tree (UST). A modern approach is used including loop measures and soups. Understanding these approaches as the system size goes to infinity requires a deep understanding of the simple random walk so that is studied next, followed by a look at the infinite LERW and UST. Another model, the Gaussian free field (GFF), is introduced and related to loop measure. The emphasis in the book is on discrete models, but the final chapter gives an introduction to the continuous objects: Brownian motion, Brownian loop measures and soups, Schramm-Loewner evolution (SLE), and the continuous Gaussian free field. A number of exercises scattered throughout the text will help a serious reader gain better understanding of the material.




Algorithms and Computation


Book Description

Annotation This book constitutes the refereed proceedings of the 21st International Symposium on Algorithms and Computation, ISAAC 2010, held in Jeju, South Korea in December 2010.The 77 revised full papers presented were carefully reviewed and selected from 182 submissions for inclusion in the book. This volume contains topics such as approximation algorithm; complexity; data structure and algorithm; combinatorial optimization; graph algorithm; computational geometry; graph coloring; fixed parameter tractability; optimization; online algorithm; and scheduling.




Scientific Computation


Book Description

Using real-life applications, this graduate-level textbook introduces different mathematical methods of scientific computation to solve minimization problems using examples ranging from locating an aircraft, finding the best time to replace a computer, analyzing developments on the stock market, and constructing phylogenetic trees. The textbook focuses on several methods, including nonlinear least squares with confidence analysis, singular value decomposition, best basis, dynamic programming, linear programming, and various optimization procedures. Each chapter solves several realistic problems, introducing the modeling optimization techniques and simulation as required. This allows readers to see how the methods are put to use, making it easier to grasp the basic ideas. There are also worked examples, practical notes, and background materials to help the reader understand the topics covered. Interactive exercises are available at www.cambridge.org/9780521849890.




ReCombinatorics


Book Description

Combinatorial structure and algorithms for deducing genetic recombination history, represented by ancestral recombination graphs and other networks, and their role in the emerging field of phylogenetic networks. In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems. Phylogenetic trees have been the traditional means to represent evolutionary history, but there is a growing realization that networks rather than trees are often needed, most notably for recent human history. This has led to the development of ARGs in population genetics and, more broadly, to phylogenetic networks. ReCombinatorics offers an in-depth, rigorous examination of current research on the combinatorial, graph-theoretic structure of ARGs and explicit phylogenetic networks, and algorithms to reconstruct or deduce information about those networks. ReCombinatorics, a groundbreaking contribution to the emerging field of phylogenetic networks, connects and unifies topics in population genetics and phylogenetics that have traditionally been discussed separately and considered to be unrelated. It covers the necessary combinatorial and algorithmic background material; the various biological phenomena; the mathematical, population genetic, and phylogenetic models that capture the essential elements of these phenomena; the combinatorial and algorithmic problems that derive from these models; the theoretical results that have been obtained; related software that has been developed; and some empirical testing of the software on simulated and real biological data.




Plant Systematics


Book Description

Plant Systematics, Third Edition, has made substantial contributions to plant systematics courses at the upper-undergraduate and first year graduate level, with the first edition winning The New York Botanical Garden's Henry Allan Gleason Award for outstanding recent publication in plant taxonomy, plant ecology or plant geography. This third edition continues to provide the basis for teaching an introduction to the morphology, evolution and classification of land plants. A foundation of the approach, methods, research goals, evidence and terminology of plant systematics are presented, along with the most recent knowledge of evolutionary relationships of plants and practical information vital to the field. In this new edition, the author includes greatly expanded treatments on families of flowering plants, as well as tropical trees (all with full-color plates), and an updated explanation of maximum likelihood and Bayesian inference algorithms. Chapters on morphology and plant nomenclature have also been enhanced with new material. - Covers research developments in plant molecular biology - Features clear, detailed cladograms, drawings and photos - Includes major revisions to chapters on phylogenetic systematics and plant morphology




Theory and Applications of Models of Computation


Book Description

This book constitutes the refereed proceedings of the 4th International Conference on Theory and Applications of Models of Computation, TAMC 2007, held in Shanghai, China in May 2007. It addresses all major areas in computer science; mathematics, especially logic; and the physical sciences, particularly with regard to computation and computability theory. The papers particularly focus on algorithms, complexity and computability theory.




Variable Neighborhood Search


Book Description

This book constitutes the refereed post-conference proceedings of the 6th International Conference on Variable Neighborhood Search, ICVNS 2018, held in Sithonia, Greece, in October 2018. ICVNS 2018 received 49 submissions of which 23 full papers were carefully reviewed and selected. VNS is a metaheuristic based on systematic changes in the neighborhood structure within a search for solving optimization problems and related tasks. The main goal of ICVNS 2018 was to provide a stimulating environment in which researchers coming from various scientific fields could share and discuss their knowledge, expertise, and ideas related to the VNS metaheuristic and its applications.




Phylogenetics


Book Description

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.




Tree Planters' Notes


Book Description

Some no. include reports compiled from information furnished by State Foresters (and others).