Rozprawy doktorskie na temat „Combination sequences”

Spread spectrum techniques have a number of different applications, including range finding, synchronisation, anti-jamming systems and multiple access communication systems. In each of these applications the properties of the resulting systems depend heavily on the family of spreading sequences employed. As such, the design of spreading sequences is an important area of research. Two areas of spreading sequence design are of particular interest in this work, combination techniques and Interference Free Window (IFW) sequences. Combination techniques allow a new sequence family to be constructed by combining two or more existing families. Such an approach allows some of the desirable properties of the components to be maintained, whilst mitigating the components' disadvantages. In addition, it can facilitate the construction of large families at a greatly reduced computational cost. Combination families are considered through the construction of two new classes of sequences, modified Unified Complex Hadamard Transform (UCHT) sequences, and combination Oppermann sequences, respectively based on UCHT sequences and periodic Oppermann sequences. Numerical optimisation techniques are employed to demonstrate the favourable performance of sequences from these classes compared to conventional families. Second, IFW sequences are considered. In systems where approximate, but not perfect, synchronisation between different users can be maintained, IFW sequences can be employed to greatly reduce both interference between users and interference resulting from multipath spread of each user's signal. Large Area Synchronous (LAS) sequences are a class of sequences which both result from combination techniques and exhibit an IFW. LAS sequences are produced by combining Large Area (LA) sequences and LS sequences. They have been demonstrated to be applicable to multiple access communication systems, particularly through their use in LAS2000, which was proposed for third generation mobile telephony. Work to date has been restricted to only a very small range of examples of these families. In order to examine a wider range of LAS sequences, the construction and resulting properties of LA and LS families are considered. The conditions an LA family must satisfy are codified here, and algorithms which can be used to construct LA families with given parameters are presented. The construction of LS sequences is considered, and relationship between each of the parameters used in this construction and the properties of the final family is examined. Using this expanded understanding of both these sequence families, a far wider range of LAS families, potentially applicable to a wider range of applications, can be considered. Initially, the merits of proposed sequences are considered primarily through their correlation properties. Both maximum and mean squared correlation values are considered, depending on the context. In order to demonstrate their practical applicability, combination Oppermann, modified UCHT and LAS sequences are employed in a simulated communications system, and the resulting bit error rates are examined.

This thesis introduces new techniques for finding genes in genomic sequences. Genes are regions of a genome encoding proteins of an organism. Identification of genes in a genome is an important step in the annotation process after a new genome is sequenced. The prediction accuracy of gene finding can be greatly improved by using experimental evidence. This evidence includes homologies between the genome and databases of known proteins, or evolutionary conservation of genomic sequence in different species.

We propose a flexible framework to incorporate several different sources of such evidence into a gene finder based on a hidden Markov model. Various sources of evidence are expressed as partial probabilistic statements about the annotation of positions in the sequence, and these are combined with the hidden Markov model to obtain the final gene prediction. The opportunity to use partial statements allows us to handle missing information transparently and to cope with the heterogeneous character of individual sources of evidence. On the other hand, this feature makes the combination step more difficult. We present a new method for combining partial probabilistic statements and prove that it is an extension of existing methods for combining complete probability statements. We evaluate the performance of our system and its individual components on data from the human and fruit fly genomes.

The use of sequence evolutionary conservation as a source of evidence in gene finding requires efficient and sensitive tools for finding similar regions in very long sequences. We present a method for improving the sensitivity of existing tools for this task by careful modeling of sequence properties. In particular, we build a hidden Markov model representing a typical homology between two protein coding regions and then use this model to optimize a component of a heuristic algorithm called a spaced seed. The seeds that we discover significantly improve the accuracy and running time of similarity search in protein coding regions, and are directly applicable to our gene finder.

Made available in DSpace on 2016-06-02T20:29:23Z (GMT). No. of bitstreams: 1 5471.pdf: 7638931 bytes, checksum: c87748a2f96946166ab14d98ed641bae (MD5) Previous issue date: 2013-08-17
Financiadora de Estudos e Projetos
This present dissertation, structured in the methodology of well-known research as Didactic Engineering, it presents the development of an unpublished class for the teacher on combination analysis in the High School. The objective of this work is to elaborate a didactic material that aids the students in the learning of some concepts of combination analysis in a significant way. The elaborated didactic sequence is inserted in the telephony context and it approaches the current subject on the increment of the 9th digit in the numbers of cellular of the area of the State of São Paulo with code of area 11. The whole sequence was thought so that the student will be the protagonist of its learning, making observations, you conjecture, debating with the colleagues, manipulating materials and solving the problems proposed in the leaves of activities in an autonomous way. The didactic sequence was applied for two groups of 2nd year of the High School in the School Educational Center SESI Bragança Paulista. For they accomplish the activities, the students were divided in groups. All the sheets of activities accomplished by the students and the registrations of observations facts by the teacher during the application of the activities were good as tools to verify the objective plans were reached.
A presente dissertação, estruturada na metodologia de pesquisa conhecida como Engenharia Didática, apresenta o desenvolvimento de uma aula inédita para o professor sobre análise combinatória no Ensino Médio. O objetivo deste trabalho é elaborar um material didático, que auxilie os alunos no aprendizado de alguns conceitos de análise combinatória de forma significativa. A sequência didática elaborada está inserida no contexto de telefonia e aborda o assunto atual sobre o acréscimo do 9º dígito nos números de celulares da região do Estado de São Paulo com código de área 11. Toda a sequência foi pensada de forma que o aluno seja o protagonista de sua aprendizagem, fazendo observações, conjecturas, debatendo com os colegas, manipulando materiais e solucionando os problemas propostos nas folhas de atividades de maneira autônoma. A sequência didática foi aplicada para duas turmas de 2º ano do Ensino Médio na Escola Centro Educacional SESI Bragança Paulista. Para realizarem as atividades, os alunos foram divididos em grupos. Todas as folhas de atividades realizadas pelos alunos e os registros de observações feitos pelo professor durante a aplicação das atividades serviram como ferramentas para verificar se os objetivos traçados foram atingidos.

I study sequent calculus of combined logics in this thesis. Two specific logics are looked at-Logic BI that combines intuitionistic logic and multiplicative intuitionistic linear logic and Logic BBI that combines classical logic and multiplicative linear logic. A proof-theoretical study into logical combinations themsel ves then follows. To consolidate intuition about what this thesis is all about, let us suppose that we know about two different logics, Logic A developed for reasoning about Purpose A and Logic B developed for reasoning about Purpose B. Logic A serves Purpose A very well, but not Purpose B. Logic B serves Purpose B very well but not Purpose A. We wish to fulfill both Purpose A and Purpose B, but presently we can only afford to let one logic guide through our reasoning. What shall we do? One option is to be content with having Logic A with which we handle Purpose A efficiently and Purpose B rather inefficiently. Another option is to choose Logic B instead. But there is yet another option: we combine Logic A and Logic B to derive a new logic Logic C which is still one logic but which serves both Purpose A and Purpose B efficiently. The combined logic is synthetic of the strengths in more basic logics (Logic A and Logic B). As it nicely takes care of our requirements, it may be the best choice among all that have been so far considered. Yet this is not the end of the story. Depending on the manner Logic A and Logic B combine, Logic C may have extensions serving more purposes than just Purpose A and Purpose B. Ensuing is the following problem: we know about Logic A and Logic B, but we may not know about combined logics of the base logics. To understand the combined logics, we need to understand the extensions in which base logics interact each other. Analysis on the interesting parts tends to be non-trivial, however. The mentioned two specific combined logics BI and BBI do not make an exception, for which proof-theoretical development has been particularly slow. It has remained in obscurity how to properly handle base-logic interactions of the combined logics as appearing syntactically. As one objective of this thesis, I provide analysis on the syntactic phenomena of the BI and BBI base-logic interactions within sequent calculus, to augment the knowledge. For BI, I deliver, through appropriate methodologies to reason about the syntactic phenomena of the base-logic interactions, the first BI sequent calculus free of any structural rules. Given its positive consequence to efficient proof searches, this is a significant step forward in further maturity of BI proof theory. Based on the calculus, I prove decidability of a fragment of BI purely syntactically. For BBI which is closely connected to application via separation logic, I develop adequate sequent calculus conventions and consider the implication of the underlying semantics onto syntax. Sound BBI sequent calculi result with a closer syntax-semantics correspondence than previously envisaged. From them, adaptation to separation logic is also considered. To promote the knowledge of combined logics in general within computer science, it is also important that we be able to study logical combinations themselves. Towards this direction of generalisation, I present the concept of phased sequent calculus - sequent calculus which physically separates base logics, and in which a specific manner of logical combination to take place between them can be actually developed and analysed. For a demonstration, the said decidable BI fragment is formulated in phased sequent calculus, and the sense of logical combination in effect is analysed. A decision procedure is presented for the fragment.

Cette thèse présente une étude sémantico-pragmatique des emplois dialogiques de mais, oui, non et de leurs quatre combinaisons : mais oui, mais non, oui mais et non mais. Les enchaînements dialogiques « X – Mais Y » posent la question de l’unicité du sens du connecteur oppositif, étant donné que la relation entre les énoncés X et Y est très différente de celle qui s’établit entre les énoncés dans les configurations monologiques « X mais Y ». Dans cette thèse, les deux types d’enchaînement avec mais sont analysés dans le cadre de la sémantique dynamique, qui propose de décrire le sens des expressions linguistiques à partir de leur capacité à modifier le contexte. L’opération énonciative de mais est spécifiée à partir des contraintes imposées sur le contexte linguistique environnant, que l’examen de divers usages contextuels de mais en monologue et en dialogue a permis de révéler. Cet examen conduit à conclure que la spécificité des enchaînements dialogiques avec mais n’est pas liée à la sémantique du connecteur, mais à la progression du discours, différente en monologue et en dialogue. Les combinaisons de mais avec oui et avec non sont étudiées après une analyse détaillée du marqueur de validation et du marqueur de rejet. La façon dont ces deux marqueurs interagissent avec le contexte gauche témoigne de leur asymétrie sémantique, confirmée par la possibilité de les utiliser en tant que formes concurrentes pour valider un énoncé négatif. Dans les combinaisons de oui et de non avec mais, le second élément détermine le type de relation signalée : oui mais et non mais marquent l’opposition, tandis que mais oui et mais non traduisent la validation et le rejet. Néanmoins, le premier élément a des incidences sur l’interprétation du second. Ainsi, les réactions mais oui et mais non présentent l’information validée ou rejetée comme déjà admise dans le contexte ou, au contraire, comme exclue et donc impossible à envisager. En revanche, dans les réactions oui mais et non mais, le connecteur oppositif enchaîne sur l’information accessible à la suite de l’emploi du premier marqueur
This dissertation presents a semantic-pragmatic study of dialogic uses of mais, oui, non and their four combinations : mais oui, mais non, oui mais et non mais. The dialogic sequences “X – Mais Y” raise the question of the uniqueness of the oppositive connector, because the relationship between the utterances X and Y is very different from that which is established between both utterances in the “X mais Y” monologic configurations. In this dissertation, the two types of linking with mais are analyzed in the framework of dynamic semantics, which aims to describe the meaning of linguistic expressions from their ability to change the context. The enunciative operation of mais is specified from the constraints on the surrounding linguistic context that the examination of various contextual uses of mais in monologue and dialogue revealed. This examination leads to the conclusion that the specificity of dialogic sequences with mais is not related to the semantics of the connector, but the progress of speech, which is different in monologue and dialogue. Combinations of mais with oui and non are considered after a previous detailed analysis of validation marker and rejection marker. The way these two markers interact with the left context reflects their semantic asymmetry, confirmed by the possibility of using them as competing forms to confirm a negative utterance. In combination of oui and non with mais, the second element determines the type of relationship: oui mais and non mais mark the opposition, while mais oui and mais non reflect validation and rejection. However, the first element has a clear implication on the interpretation of the second one. In that sense mais oui and mais non responses present the validated or rejected information as already accepted in the context or, on the contrary, excluded, and therefore impossible to consider. On the other hand, in reactions with oui mais and non mais the oppositive connector regards the information accessible next to the use of the first marker

博士
國立中興大學
電機工程學系所
106
In this dissertation, We propose to reduce PAPR in OFDM systems and reduce the computational complexity in conventional Partial Transmission Sequence (C-PTS) techniques. First, we presents a modified PTS algorithm for PAPR reduction of M-QAM OFDM signals by partitioning an OFDM block into non-disjoint OFDM sub-blocks. Since an M-QAM constellation can be written as sum of several QPSK constellations, we can then apply different disjoint partitions on the QPSK OFDM blocks, which result in an equivalent non-disjoint partition on the M-QAM OFDM block. Compared to a disjoint sub-block partition in conventional PTS, simulation results show that the modified PTS with a non-disjoint partition achieves better PAPR reduction in adjacent, interleaved, and random partitioning schemes. Second, we propose the parallel PTS (P-PTS) and serial PTS (S-PTS) methods to reduce the C-PTS complexity, based on the fact that the weighting factors are chosen as codewords of a linear block code. Compared to the C-PTS, the P-PTS and S-PTS methods not only reduce the computational complexity but also provide error correction capability for the weighting factors. Third, we present the PAPR reduction of OFDM signals by executing PTS in tree structure and minimal trellis of block codes. The proposed method uses a linear code with the tree structure and good minimal trellis to select the transmitted OFDM signal with minimum PAPR and to transmit side information with error correction. The goals of combining strategy of tree structure and trellis in PTS are twofold: to provide a low complexity PTS for weighting vector search and to highlight error protection capability for side information. Simulation results show that the proposed scheme achieves good PAPR reduction with lower complexity, compared to other PTS approaches.

碩士
國立中興大學
通訊工程研究所
103
In this thesis, we propose combination of Convolutional Code(CC) with orthogonal frequency division multiplexing (OFDM) system. This method provides the error correction capability for the input data and the phase factor. One of the drawbacksinOFDM system is the high peak- to-average powerratio (PAPR).when the same sub- carrier phases are adding together.Itcauses the high PAPR in OFDM system. We select PartialTransmitSequence(PTS) systemas the main system to reducethe PAPR, and then use thetree structure to control phase factor number to reduce the comput -ational complexity. Finally, this method does not need to transmit additional sideinformation to the receiver.

碩士
國立中興大學
電機工程學系所
107
Orthogonal Frequency Division Multiplexing (OFDM) is a multi-carrier system capable of high-rate data transmission, and has many advantages. One of the important shortcomings is the Peak To Average Power (PAPR). In order to solve this problem, we have many methods such as SLM, PTS, etc. This article is mainly based on PTS. Compared with the traditional partial transmission sequence (PTS), this paper uses tree and trellis structure of error correction (ECC), it can reduce the peak-to-average power ratio and search complexity either, and based on this, it is applied to data of larger length.

碩士
國立中山大學
機械與機電工程學系研究所
98
An epicyclic-type automatic transmission is a device which is connected from engine to driving wheels, and the main purpose is to maintain the revolution speed of engine to be in a desired working range while accelerating or decelerating the automobile. The epicyclic -type automatic transmissions in production are mostly Ravigneaux-type epicyclic mechanisms, and in recent year, the development of automatic transmissions for automobile is oriented to the orientation of setting an single epicyclic gear mechanism instead of the input to bring various inputs of revolution speed to increase the total number of speed ratios of an automatic transmission, and such type of epicyclic is called combinational epicyclic-type automatic transmissions for automobiles. For the incompletion in the relative design methodology, a systematic methodology of designing mechanism and clutching-sequence of combinational epicyclic-type automobile transmission is described. First, fundamental principle of the combination and operations of automatic transmissions are analyzed to establish the design requirements. Second, a procedure of structure synthesis of combinational epicyclic-type automobile transmission is brought up which the planar graphic method is applied for. Third, based on Speed Ratio Relationship of each clutching sequence, a procedure of gearing-sequence is introduced. Finally, on the basis of the analytic method, the teeth of gears is to be clarified. The result of this work obtains five types of the combinational epicyclic-type automatic transmissions which could reach six speeds.

碩士
國立中興大學
通訊工程研究所
104
In this paper, we proposed three methods of orthogonal frequency division multiplexing (OFDM) system combined partial transmit sequence (PTS) with low complexity. In the PTS, as sub-blocks increase, the performance of reducing peak-to-average power ratio (PAPR) is getting better, but complexity grow exponentially. The first method is to reduce the complexity of PTS by iteration, and uses the information obtained from last time to get better performance, so it can use less sub-blocks to get the same performance as PTS .The second method is to reduce much complexity by modified tree structure than RC-PTS. The last is to reduce complexity of tree structure by Fano algorithm, and changes the parallel form of tree structure into series form. In this method, we also add the threshold to let complexity lower.

No
Cytochrome P450 (CYP) is one of the most important drug-metabolizing enzyme families, which participates in the biotransformation of many endogenous and exogenous compounds. Quantitative analysis of CYP expression levels is important when studying the efficacy of new drug molecules and assessing drug-drug interactions in drug development. At present, chemical probe-based assay is the most widely used approach for the evaluation of CYP activity although there are cross-reactions between the isoforms with high sequence homologies. Therefore, quantification of each isozyme is highly desired in regard to meeting the ever-increasing requirements for carrying out pharmacokinetics and personalized medicine in the academic, pharmaceutical, and clinical setting. Herein, an absolute quantification method was employed for the analysis of the seven isoforms CYP1A2, 2B6, 3A4, 3A5, 2C9, 2C19, and 2E1 using a proteome-derived approach in combination with stable isotope dilution assay. The average absolute amount measured from twelve human liver microsomes samples were 39.3, 4.3, 54.0, 4.6, 10.3, 3.0, and 9.3 (pmol/mg protein) for 1A2, 2B6, 3A4, 3A5, 2C9, 2C19, and 2E1, respectively. Importantly, the expression level of CYP3A4 showed high correlation (r = 0.943, p < 0.0001) with the functional activity, which was measured using bufalin-a highly selective chemical probe we have developed. The combination of MRM identification and analysis of the functional activity, as in the case of CYP3A4, provides a protocol which can be extended to other functional enzyme studies with wide application in pharmaceutical research.

No-till acreage is increasing in the United States as producers begin to recognize the environmental and economic benefits of this management system. Although the potential to receive carbon credits or payments for maintaining or initiating no-till may encourage producers to employ these practices, crop yields will be a factor in management decisions. Our objective was to examine the effects of combinations of cropping sequences and winter biocovers upon glyphosate-tolerant corn, cotton, and soybean yields under long-term no-tillage at two locations in Tennessee. Research was conducted during the first four-year phase (2002-2005) of a two-phase agronomic systems study (2002-2009) at the Research and Education Center at Milan (RECM) in Milan, Tennessee, and the Middle Tennessee Research and Education Center (MTREC) in Spring Hill, Tennessee. The experiment was a randomized complete block design with split block treatments, with the main plots consisting of 13 different cropping sequences of corn, cotton, and soybean at RECM and eight different cropping sequences of corn and soybean at MTREC. The subplots consisted of hairy vetch, wheat, poultry litter and fallow biocovers applied perpendicular to the sequences. Rotated corn and soybean yields were comparable to or higher than their respective monoculture sequences at both locations. At RECM, cotton yields took longer to respond to rotation as rotated cotton yields only outperformed continuous cotton in the final year. At both sites, corn and soybean yields were highest under fallow and poultry litter biocovers, respectively. Cotton yields were highest under poultry litter at RECM. Interaction effects of cropping sequence x biocovers were inconsistent as interaction effects were only observed on corn yields at MTREC in 2004 and 2005. Hairy vetch, wheat, and poultry increased yields when changing from continuous corn to rotated corn. The presence of some cropping sequence x biocover interaction effects is encouraging and perhaps suggests a longer time period may be needed for the combined effects of crop sequence and biocovers upon crop yields to become apparent. Results from the next four years of the experiment will provide more information on the long-term effects of crop sequence and biocovers on corn, soybean, and cotton yields.

The objective of this research was to compare the effects of combinations of a wide range of cropping sequences and soil bio-covers on soil organic carbon (SOC) and Heterodera glycines under no-tillage. The experiment used a split-block design with four replications at the Milan (RECM) and Middle TN (MTREC) Research & Education Centers. The whole-block treatment was cropping sequences of corn (Zea mays), soybean (Glycine max), and cotton (Gossypium hirsutum). The split-block was bio-covers of winter wheat (Triticum aestivum), hairy vetch (Vicia villosa), poultry litter, and fallow. Soil samples were taken over four years of experimentation. A novel technique was developed to measure SOC called near infrared reflectance spectroscopy (NIR). Partial least squares regression was used to predict SOC as measured by NIR. Results were compared to assess the reliability of NIR determination of organic carbon. NIR analysis correlated well (r greater than 0.9) with SOC as determined by combustion. NIR was therefore considered sufficiently accurate for quantifying soil organic carbon. Overall, both sites showed a small but consistent loss in carbon over all treatments. The average losses of SOC at the 0-5 cm depth were 1.06 and 1.40 Mg ha-1 at RECM and MTREC, respectively. In the subsurface, mean SOC loss at RECM was 1.43 Mg ha-1. Conversely, the subsurface SOC at MTREC was 3.14 Mg ha-1 higher than preexperiment levels. Crop sequence had a significant effect on change in SOC (P ≤ 0.05) in both surface and subsurface regions at RECM. Sequences with two or more years of cotton tended to lose significantly more (P ≤ 0.05) SOC than those with two or more years of soybean. The poultry litter bio-cover lost less surface SOC (0.58 Mg ha-1) than those under vetch (1.33 Mg ha-1) or fallow (1.8 Mg ha-1). Soybean cyst nematode (SCN) eggs were found in sequences containing no soybean throughout the experiment, indicating survival of over seven years without soybean. Sequences with two or more years of soybean had significantly higher (P ≤ 0.01) SCN egg density than others, with continuous soybean having the greatest egg population density. One year of rotation with a non-host crop typically reduced SCN egg population density by more than 50%.

碩士
國立臺北科技大學
商業自動化與管理研究所
99
The main study is to find out better combination sequence of online consumer experience, which includes indirect experience (IE), virtual experience (VE) and virtual avatar experience (VAE), and to discuss the impact of consumer experience value and persuasive effect under different delay reason. The study results reveal that (a) the combinations sequence of (VE->IE->VAE), (VE->VAE->IE) and (VAE->VE->IE) have better effects on experience value and persuasive effect; (b) Under shopping delay situation, consumers with low product knowledge or consumer who has uncertain need be given the combination sequence of VAE->VE->IE has better effect on experience value and persuasive effect; (c) Under shopping delay situation, consumers with high product knowledge consumer who has time pressure be given the combination sequence of VE->IE->VAE has better effect on experience value and persuasive effect;(d) There were positive relationships between the consumer experience and advertising effect.

South Africa’s electricity supply is under pressure. Mining is one of South Africa’s largest electricity consumers with electricity-intensive services such as compressed air, cooling, ventilation, etc. More than 40% of mine electricity consumption is used for cooling and ventilation. There is a need to reduce the operational cost on a mine as electricity prices are set to increase at least 2% above South Africa’s inflation target. The mine-cooling and ventilation system was investigated for energy cost-saving. No clear energy and cost-saving strategy for the entire mine-cooling and ventilation system was found. Projects are implemented ad hoc and scattered throughout the system. A strategy is needed to help realise the total saving available on the entire mine-cooling and ventilation system. An implementation strategy for load-management and energy-saving projects on a mine-cooling and ventilation system was developed. A peak clip project on the surface BAC was developed and added to the strategy. The resultant strategy attains all savings throughout the entire mine-cooling and ventilation system. A peak clip project on the surface BAC of a typical mine results in an annual saving of R1.4 million. Implementing this new project on other mines could save R11 million annually. Implementing the sequenced combination of cooperative projects on a typical mine results in a saving of R30 million. That is a saving of 38% on the ventilation and cooling cost and 16% on the total mine electricity bill.
PhD (Mechanical Engineering), North-West University, Potchefstroom Campus, 2014

Tse, Sui Man.
Thesis (M.Phil.)--Chinese University of Hong Kong, 2007.
Includes bibliographical references (leaves 95-104).
Abstracts in English and Chinese.
Abstract --- p.i
Acknowledgement --- p.v
Chapter 1 --- Introduction --- p.1
Chapter 1.1 --- Motivation --- p.1
Chapter 1.1.1 --- Basic Concepts and Definitions --- p.2
Chapter 1.2 --- Evolutionary Algorithms --- p.5
Chapter 1.2.1 --- Chromosome Encoding --- p.6
Chapter 1.2.2 --- Selection --- p.7
Chapter 1.2.3 --- Crossover --- p.9
Chapter 1.2.4 --- Mutation --- p.10
Chapter 1.2.5 --- Elitism --- p.11
Chapter 1.2.6 --- Niching --- p.11
Chapter 1.2.7 --- Population Manipulation --- p.13
Chapter 1.2.8 --- Building Blocks --- p.13
Chapter 1.2.9 --- Termination Conditions --- p.14
Chapter 1.2.10 --- Co-evolution --- p.14
Chapter 1.3 --- Local Search --- p.15
Chapter 1.4 --- Memetic Algorithms --- p.16
Chapter 1.5 --- Objective --- p.17
Chapter 1.6 --- Summary --- p.17
Chapter 2 --- Background --- p.18
Chapter 2.1 --- Multiple Drugs Tumor Chemotherapy --- p.18
Chapter 2.2 --- Bioinformatics --- p.22
Chapter 2.2.1 --- Basics of Bioinformatics --- p.24
Chapter 2.2.2 --- Applications on Biomedical Systems --- p.26
Chapter 3 --- A New Drug Administration Dynamic Model --- p.29
Chapter 3.1 --- Three Drugs Mathematical Model --- p.31
Chapter 3.1.1 --- Rate of Change of Different Subpopulations --- p.32
Chapter 3.1.2 --- Rate of Change of Different Drug Concen- trations --- p.35
Chapter 3.1.3 --- Toxicity Effects --- p.35
Chapter 3.1.4 --- Summary --- p.36
Chapter 4 --- Memetic Algorithm - Iterative Dynamic Program- ming (MA-IDP) --- p.38
Chapter 4.1 --- Problem Formulation: Optimal Control Problem (OCP) for Mutlidrug Optimization --- p.38
Chapter 4.2 --- Proposed Memetic Optimization Algorithm --- p.40
Chapter 4.2.1 --- Iterative Dynamic Programming (IDP) . . --- p.40
Chapter 4.2.2 --- Adaptive Elitist-population-based Genetic Algorithm (AEGA) --- p.44
Chapter 4.2.3 --- Memetic Algorithm 一 Iterative Dynamic Programming (MA-IDP) --- p.50
Chapter 4.3 --- Summary --- p.56
Chapter 5 --- MA-IDP: Experiments and Results --- p.57
Chapter 5.1 --- Experiment Settings --- p.57
Chapter 5.2 --- Optimization Results --- p.61
Chapter 5.3 --- Extension to Other Mutlidrug Scheduling Model . --- p.62
Chapter 5.4 --- Summary --- p.65
Chapter 6 --- DNA Sequencing by Hybridization (SBH) --- p.66
Chapter 6.1 --- Problem Formulation: Reconstructing a DNA Sequence from Hybridization Data --- p.70
Chapter 6.2 --- Proposed Memetic Optimization Algorithm --- p.71
Chapter 6.2.1 --- Chromosome Encoding --- p.71
Chapter 6.2.2 --- Fitness Function --- p.73
Chapter 6.2.3 --- Crossover --- p.74
Chapter 6.2.4 --- Hill Climbing Local Search for Sequencing by Hybridization --- p.76
Chapter 6.2.5 --- Elitism and Diversity --- p.79
Chapter 6.2.6 --- Outline of Algorithm: MA-HC-SBH --- p.81
Chapter 6.3 --- Summary --- p.82
Chapter 7 --- DNA Sequencing by Hybridization (SBH): Experiments and Results --- p.83
Chapter 7.1 --- Experiment Settings --- p.83
Chapter 7.2 --- Experiment Results --- p.85
Chapter 7.3 --- Summary --- p.89
Chapter 8 --- Conclusion --- p.90
Chapter 8.1 --- Multiple Drugs Cancer Chemotherapy Schedule Optimization --- p.90
Chapter 8.2 --- Use of the MA-IDP --- p.91
Chapter 8.3 --- DNA Sequencing by Hybridization (SBH) --- p.92
Chapter 8.4 --- Use of the MA-HC-SBH --- p.92
Chapter 8.5 --- Future Work --- p.93
Chapter 8.6 --- Item Learned --- p.93
Chapter 8.7 --- Papers Published --- p.94
Bibliography --- p.95

Combinatorial objects can be represented by strings, such as 21534 for the permutation (1 2) (3 5 4), or 110100 for the binary tree corresponding to the balanced parentheses (()()). Given a string s = s1 s2 sn, the right-shift operation shift(s, i, j) replaces the substring si si+1..sj by si+1..sj si. In other words, si is right-shifted into position j by applying the permutation (j j−1 .. i) to the indices of s. Right-shifts include prefix-shifts (i = 1) and adjacent-transpositions (j = i+1). A fixed-content language is a set of strings that contain the same multiset of symbols. Given a fixed-content language, a shift Gray code is a list of its strings where consecutive strings differ by a shift. This thesis asks if shift Gray codes exist for a variety of combinatorial objects. This abstract question leads to a number of practical answers. The first prefix-shift Gray code for multiset permutations is discovered, and it provides the first algorithm for generating multiset permutations in O(1)-time while using O(1) additional variables. Applications of these results include more efficient exhaustive solutions to stacker-crane problems, which are natural NP-complete traveling salesman variants. This thesis also produces the fastest algorithm for generating balanced parentheses in an array, and the first minimal-change order for fixed-content necklaces and Lyndon words. These results are consequences of the following theorem: Every bubble language has a right-shift Gray code. Bubble languages are fixed-content languages that are closed under certain adjacent-transpositions. These languages generalize classic combinatorial objects: k-ary trees, ordered trees with fixed branching sequences, unit interval graphs, restricted Schr oder and Motzkin paths, linear-extensions of B-posets, and their unions, intersections, and quotients. Each Gray code is circular and is obtained from a new variation of lexicographic order known as cool-lex order. Gray codes using only shift(s, 1, n) and shift(s, 1, n−1) are also found for multiset permutations. A universal cycle that omits the last (redundant) symbol from each permutation is obtained by recording the first symbol of each permutation in this Gray code. As a special case, these shorthand universal cycles provide a new fixed-density analogue to de Bruijn cycles, and the first universal cycle for the "middle levels" (binary strings of length 2k + 1 with sum k or k + 1).