抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

From the Publisher:
This book explores the meta-heuristics approach called tabu search, which is dramatically changing our ability to solve a hostof problems that stretch over the realms of resource planning,telecommunications, VLSI design, financial analysis, scheduling, spaceplanning, energy distribution, molecular engineering, logistics,pattern classification, flexible manufacturing, waste management,mineral exploration, biomedical analysis, environmental conservationand scores of other problems. The major ideas of tabu search arepresented with examples that show their relevance to multipleapplications. Numerous illustrations and diagrams are used to clarifyprinciples that deserve emphasis, and that have not always been wellunderstood or applied. The book's goal is to provide ''hands-on' knowledge and insight alike, rather than to focus exclusively eitheron computational recipes or on abstract themes. This book is designedto be useful and accessible to researchers and practitioners inmanagement science, industrial engineering, economics, and computerscience. It can appropriately be used as a textbook in a masterscourse or in a doctoral seminar. Because of its emphasis on presentingideas through illustrations and diagrams, and on identifyingassociated practical applications, it can also be used as asupplementary text in upper division undergraduate courses. 

Finally, there are many more applications of tabu search than canpossibly be covered in a single book, and new ones are emerging everyday. The book's goal is to provide a grounding in the essential ideasof tabu search that will allow readers to create successfulapplications of their own. Along with the essentialideas,understanding of advanced issues is provided, enabling researchers togo beyond today's developments and create the methods of tomorrow.

Tabu Search

物件導向軟體之架構(Object-Oriented Software Construction)探討

Most existing model-based approaches to anomaly detection construct a profile of normal instances, then identify instances that do not conform to the normal profile as anomalies. This paper proposes a fundamentally different model-based method that explicitly isolates anomalies instead of profiles normal points. To our best knowledge, the concept of isolation has not been explored in current literature. The use of isolation enables the proposed method, iForest, to exploit sub-sampling to an extent that is not feasible in existing methods, creating an algorithm which has a linear time complexity with a low constant and a low memory requirement. Our empirical evaluation shows that iForest performs favourably to ORCA, a near-linear time complexity distance-based method, LOF and random forests in terms of AUC and processing time, and especially in large data sets. iForest also works well in high dimensional problems which have a large number of irrelevant attributes, and in situations where training set does not contain any anomalies.

Isolation Forest

The field of metaheuristics for the application to combinatorial optimization problems is a rapidly growing field of research. This is due to the importance of combinatorial optimization problems for the scientific as well as the industrial world. We give a survey of the nowadays most important metaheuristics from a conceptual point of view. We outline the different components and concepts that are used in the different metaheuristics in order to analyze their similarities and differences. Two very important concepts in metaheuristics are intensification and diversification. These are the two forces that largely determine the behavior of a metaheuristic. They are in some way contrary but also complementary to each other. We introduce a framework, that we call the I&D frame, in order to put different intensification and diversification components into relation with each other. Outlining the advantages and disadvantages of different metaheuristic approaches we conclude by pointing out the importance of hybridization of metaheuristics as well as the integration of metaheuristics and other methods for optimization.

/pdf/metaheuristics-in-combinatorial-optimization-overview-and-menr0q3bxw.pdf

Metaheuristics in combinatorial optimization: Overview and conceptual comparison

SUMMARY This paper describes a new pull-based production system called CONWIP. Practical advantages of CONWIP over push and other pull systems are given. Theoretical arguments in favour of the system are outlined and simulation studies are included to give insight into the system's performance.

CONWIP: a pull alternative to kanban

We describe Pyomo, an open source software package for modeling and solving mathematical programs in Python. Pyomo can be used to define abstract and concrete problems, create problem instances, and solve these instances with standard open-source and commercial solvers. Pyomo provides a capability that is commonly associated with algebraic modeling languages such as AMPL, AIMMS, and GAMS. In contrast, Pyomo's modeling objects are embedded within a full-featured high- level programming language with a rich set of supporting libraries. Pyomo leverages the capabilities of the Coopr software library, which together with Pyomo is part of IBM's COIN-OR open-source initiative for operations research software. Coopr inte- grates Python packages for defining optimizers, modeling optimization applications, and managing computational experiments. Numerous examples illustrating advanced scripting applications are provided.

Pyomo: modeling and solving mathematical programs in Python

This book provides a complete and comprehensive reference/guide to Pyomo (Python Optimization Modeling Objects) for both beginning and advanced modelers, including students at the undergraduate and graduate levels, academic researchers, and practitioners. The text illustrates the breadth of the modeling and analysis capabilities that are supported by the software and support of complex real-world applications. Pyomo is an open source software package for formulating and solving large-scale optimization and operations research problems. The text begins with a tutorial on simple linear and integer programming models. A detailed reference of Pyomo's modeling components is illustrated with extensive examples, including a discussion of how to load data from data sources like spreadsheets and databases. Chapters describing advanced modeling capabilities for nonlinear and stochastic optimization are also included. The Pyomo software provides familiar modeling features within Python, a powerful dynamic programming language that has a very clear, readable syntax and intuitive object orientation. Pyomo includes Python classes for defining sparse sets, parameters, and variables, which can be used to formulate algebraic expressions that define objectives and constraints. Moreover, Pyomo can be used from a command-line interface and within Python's interactive command environment, which makes it easy to create Pyomo models, apply a variety of optimizers, and examine solutions. The software supports a different modeling approach than commercial AML (Algebraic Modeling Languages) tools, and is designed for flexibility, extensibility, portability, and maintainability but also maintains the central ideas in modern AMLs.

https://calhoun.nps.edu/bitstream/10945/37919/1/Dimitrov-PyomoReview.pdf

Pyomo - Optimization Modeling in Python

New insights are given into why the problem of detecting multivariate outliers can be difficult and why the difficulty increases with the dimension of the data. Significant improvements in methods for detecting outliers are described, and extensive simulation experiments demonstrate that a hybrid method extends the practical boundaries of outlier detection capabilities. Based on simulation results and examples from the literature, the question of what levels of contamination can be detected by this algorithm as a function of dimension, computation time, sample size, contamination fraction, and distance of the contamination from the main body of data is investigated. Software to implement the methods is available from the authors and STATLIB.

/pdf/identification-of-outliers-in-multivariate-data-57r3zyuj8g.pdf

Identification of Outliers in Multivariate Data

Numerous planning problems can be formulated as multi-stage stochastic programs and many possess key discrete (integer) decision variables in one or more of the stages. Progressive hedging (PH) is a scenario-based decomposition technique that can be leveraged to solve such problems. Originally devised for problems possessing only continuous variables, PH has been successfully applied as a heuristic to solve multi-stage stochastic programs with integer variables. However, a variety of critical issues arise in practice when implementing PH for the discrete case, especially in the context of very difficult or large-scale mixed-integer problems. Failure to address these issues properly results in either non-convergence of the heuristic or unacceptably long run-times. We investigate these issues and describe algorithmic innovations in the context of a broad class of scenario-based resource allocation problem in which decision variables represent resources available at a cost and constraints enforce the need for sufficient combinations of resources. The necessity and efficacy of our techniques is empirically assessed on a two-stage stochastic network flow problem with integer variables in both stages.

https://link.springer.com/content/pdf/10.1007%2Fs10287-010-0125-4.pdf

David L. Woodruff

Papers

CONWIP: a pull alternative to kanban

Pyomo: modeling and solving mathematical programs in Python

Pyomo - Optimization Modeling in Python

Identification of Outliers in Multivariate Data

Progressive hedging innovations for a class of stochastic mixed-integer resource allocation problems