Li, Qiwei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (p. 75-85). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgement --- p.iv / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Repetitive DNA Sequence --- p.3 / Chapter 1.1.1 --- Definition and Categorization of Repeti- tive DNA Sequence --- p.3 / Chapter 1.1.2 --- Definition and Categorization of Tandem Repeats --- p.4 / Chapter 1.1.3 --- Definition and Categorization of Interspersed Repeats --- p.6 / Chapter 1.2 --- Research Significance --- p.7 / Chapter 1.3 --- Contributions --- p.9 / Chapter 1.4 --- Thesis Organization --- p.11 / Chapter 2 --- Literature Review and Overview of Our Method --- p.13 / Chapter 2.1 --- Existing Methods --- p.14 / Chapter 2.2 --- Overview of Our Method --- p.17 / Chapter 3 --- Theoretical Background --- p.22 / Chapter 3.1 --- Multinomial Distributions --- p.23 / Chapter 3.2 --- Dirichlet Distribution --- p.23 / Chapter 3.3 --- Metropolis-Hastings Sampling --- p.25 / Chapter 3.4 --- Gibbs Sampling --- p.26 / Chapter 4 --- Problem Description --- p.28 / Chapter 4.1 --- Generative Model --- p.29 / Chapter 4.1.1 --- Input Data R --- p.31 / Chapter 4.1.2 --- Parameters A (Repeat Segment Starting Positions) --- p.32 / Chapter 4.1.3 --- Parameters S (Repeat Segment Structures) --- p.33 / Chapter 4.1.4 --- Parameters θ(Motif Matrix) --- p.35 / Chapter 4.1.5 --- Parameters Φ (Background Distribution) . --- p.36 / Chapter 4.1.6 --- An Example of the Model Schematic Di- agram --- p.37 / Chapter 4.2 --- Parameter Structure --- p.38 / Chapter 4.3 --- Posterior Distribution --- p.40 / Chapter 4.3.1 --- The Full Posterior Distribution --- p.41 / Chapter 4.3.2 --- The Collapsed Posterior Distribution --- p.42 / Chapter 4.4 --- Conclusion --- p.43 / Chapter 5 --- Methodology --- p.45 / Chapter 5.1 --- Schematic Procedure --- p.46 / Chapter 5.1.1 --- The Basic Schematic Procedure --- p.46 / Chapter 5.1.2 --- The Improved Schematic Procedure --- p.47 / Chapter 5.2 --- Initialization --- p.49 / Chapter 5.3 --- Predictive Update Step for θn and Φn --- p.50 / Chapter 5.4 --- Gibbs Sampling Step for an --- p.50 / Chapter 5.5 --- Metropolis-Hastings Sampling Step for sn --- p.51 / Chapter 5.5.1 --- Rear Indel Move --- p.53 / Chapter 5.5.2 --- Partial Shift Move --- p.56 / Chapter 5.5.3 --- Front Indel Move --- p.56 / Chapter 5.6 --- Phase Shifts --- p.57 / Chapter 5.7 --- Conclusion --- p.58 / Chapter 6 --- Results and Discussion --- p.60 / Chapter 6.1 --- Settings --- p.61 / Chapter 6.2 --- Experiment on Synthetic Data --- p.63 / Chapter 6.3 --- Experiment on Real Data --- p.69 / Chapter 7 --- Conclusion and Future Work --- p.72 / Chapter 7.1 --- Conclusion --- p.72 / Chapter 7.2 --- Future Work --- p.74 / Bibliography --- p.75

Waves are everywhere. Biological waves, such as gastric slow waves, and electromagnetic waves, such as TV signals and radio waves, are typical examples that we encounter in everyday life. Many waves are emitted from a point source, whose wavefront can be approximated by a line if the point source is far away. When an experimenter records a propagating wave, the data is subject to noise contamination, posing great diffculty in wave analysis. In this thesis, we consider the situation where at most one wave propagates in a two-dimensional space at any particular time and the detector recordings are noisy. We introduce two parametric generative models for wave propagation and one parametric model for noise generation, and develop a multistage procedure which identifies the number of waves in a given data set, followed by an inference on important variables, including the location of the point source, the velocity of the wave and indicator variables of spikes under the Bayesian paradigm. The procedure is illustrated with two real-life examples. The first one is a study on the effect of potassium ion channels using cultured heart cells. The other is on the propagation characteristics of the Tokohu Tsunami in 2011. / 波是無處不在的。生物波如胃慢波，以及電磁波如電視信號和無線電波，都是我們在日常生活中常遇到的波的典型例子。許多波都是點源，而當波從一個遠的點源發射， 其波陣面會近似一條直線。當實驗者記錄波數據時，數據很大機會受到雜訊污染，增加了分析波數據的難度。本文考慮在一個二維空間內，任何特定的時間中，最多只有一個波在傳播，而波數據受到雜訊污染。我們提出了兩個參數模型模擬波的產生和傳播，以及一個參數模型模擬雜訊的產生。我們並建立了一個多階段程序先識別數據中波的數量，然後根據貝葉斯理論，將尖峰訊號分類成波尖峰訊號或雜訊尖峰訊號，以及對波尖峰訊號的重要參數，包括點源的位置和波的速度進行估算。本文提出的方法將應用於兩組真實數據上。第一組是關於細胞鉀離子通道如何影響心肌培養細胞研究，而另一組則分析2011年日本東北海嘯的傳播特性。 / Lau, Yuk Fai. / Thesis M.Phil. Chinese University of Hong Kong 2015. / Includes bibliographical references (leaves 71-74). / Abstracts also in Chinese. / Title from PDF title page (viewed on 18, October, 2016). / Detailed summary in vernacular field only.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

A interação entre agentes inteligentes na disputa por recursos necessários à sobrevivência é um fato onipresente na luta pela vida. Este tipo de interação é estudado e formalizado matematicamente pela teoria dos jogos. Na literatura experimental encontramos vários estudos envolvendo primatas humanos e não humanos em tarefas de jogos estratégicos, mas, até o momento, não foi desenvolvido nenhum modelo deste comportamento com roedores. Estudos do comportamento animal mostram que estes aprendem e aprimoram este tipo de estratégias através de aprendizagem por reforço. O elemento central dos modelos computacionais de aprendizado por reforço é o sinal de violação de expectativa, que sinaliza o quanto um resultado difere, para mais ou para menos, do esperado. Este sinal é utilizado pelo agente para atualização dos valores e, assim, da probabilidade de escolha das opções. A pesquisa neurofisiológica tem consistentemente demonstrado que o sinal fásico emitido pelo sistema dopaminérgico conforma-se muito de perto às características do sinal descrito pela teoria computacional. Dessa maneira, os objetivos do presente estudo são pesquisar (1) se roedores são capazes de jogar um jogo estratégico simples e se a evolução do seu desempenho é consistente com o aprendizado por reforço e (2) se os efeitos de agonistas e antagonistas dopaminérgicos na estratégia de jogo são consistentes com a teoria segundo a qual o sinal dopaminérgico fásico desempenha função central na atualização constante da estratégia de jogo. Nossos resultados demonstram que, neste jogo estratégico, roedores efetivamente são capazes de um desempenho muito próximo do normativo, que seu desempenho é consistente com o aprendizado por reforço e, finalmente, que o sistema dopaminérgico está envolvido no processo de atualização da estratégia. / Intelligent agents competing for the resources necessary for survival is a universal factor in the struggle for life. This type of interaction has been studied and mathematically formalized by game theory. In scientific literature we have come across several studies involving human and non-human primates carrying out strategic game tasks; however, until now, no model for such behavior has been developed for rodents. Animal behavior studies have shown that animals learn and develop strategies through reinforcement learning. A central element of computational models of reinforcement learning is the reward-prediction error signal, which indicates how much a result differs, either positively or negatively, from the expected result. This signal is used by the agent to update the values of its options, and so their probability of being chosen. Neurophysiologic research has consistently shown that the phasic signal emitted by the dopamine system conforms very closely to the characteristics of the signal described by computational theory. The purposes of this study are: (1) to discover whether rodents are capable of playing a simple strategic game and whether the evolution of their performance is consistent with reinforcement learning; and (2) whether the effects of dopamine agonists and antagonists on game strategy are consistent with the theory that phasic dopamine signals have a primary role in the constant update of game strategy. Our results prove that, in this strategic game, rodents are effectively capable of finding a strategy that is very close to the normative one, that their performance is consistent with reinforcement learning and, finally, that the dopamine system is involved in the process of strategic updating.

Shared decision making (SDM) is rarely used in pediatric clinical practice. The purpose of this dissertation was to explore factors influencing SDM implementation in pediatric clinical practice. We conducted three studies that were guided by the Ottawa Model of Research Use (OMRU): Study 1 was a systematic review using Cochrane methods and the Mixed Methods Appraisal Tool to determine pediatric SDM barriers and facilitators from multiple perspectives. Eighty studies, of low to high quality, were included. At each OMRU level, frequently cited barriers were: option features (decision), poor quality information (innovation), emotional state (adopter), power relations (relational), and insufficient time (environment). Frequently cited facilitators were: lower stake decisions (decision), agreement with SDM (adopter), high quality information (innovation), trust and respect (relational), and SDM tools/resources (environment). Across participant types, frequently cited barriers were: insufficient time (healthcare providers (HCP)), option features (parents), power imbalances (children), and HCPs’ SDM skills (observers). Frequently cited facilitators were: good quality information (HCPs) and agreement with SDM (parents/children). Study 2 was a post-test design that evaluated SDM knowledge and acceptability of learners who completed the Ottawa Decision Support Tutorial (ODST). Most learners were HCPs (62%). Overall, ODST learners had a median knowledge test score of 8/10 (IQR = 7-9; n=6604) and 90% reported good or excellent impressions (n=4276) after completing the tutorial. Few learners suggested improvements. Study 3 used mixed methods to evaluate pediatric HCPs’ perceived SDM barriers and facilitators after training (ODST plus workshop). Participants completed a SDM barrier survey (n=60; 88% response rate) and semi-structured interview (n=11). Their intention to use SDM was high (mean score = 5.6/7, SD=0.8). However, 90% of respondents reported minimal SDM use after training. Main barriers were lack of buy-in (adopter level) and time constraints (environmental level). Healthcare providers wanted a team-based approach to SDM training (training level). Adopters face numerous and diverse barriers to SDM use, before and after SDM training. Pediatric HCPs who completed the ODST were knowledgeable about SDM. Despite positive intentions, training alone was insufficient to achieve routine SDM use. These findings can inform intervention development to promote SDM implementation in pediatric clinical practice.

We sought increased understanding of men's decision-making process for prostate-specific antigen (PSA) screening, especially among elderly men, and a more knowledgeable basis for interventions to modify screening rates. A cross-sectional postal questionnaire assessed measures consistent with the Theory of Planned Behavior among a population-based age-stratified random sample of 452 Iowa men who were free of prostate cancer and aware of PSA. Our primary outcome was intention to receive PSA screening within a year; this encompassed the degree men wanted and planned to be screened. We examined three explanatory variables via structural equation modeling: attitude, social influence, and perceived control. Attitude included the degree screening is important-unnecessary, reassuring-worrisome, and useful-useless. Social influence encompassed the extent a man believed people expect him to, and think he should be screened. Perceived control covered the degree a man can be screened, if desired, and how much control he has over screening. We then examined attitude, social influence, and perceived control as dependent variables. We examined how potential outcomes of screening influenced attitude, how specific people affected overall social influence, and how specific factors influenced perceived control. Roughly 75% expressed intent to receive PSA screening within a year. Attitude, social influence, and perceived control each contributed significantly to the explanation of intentions (p<0.001); the model accounted for 72% of the variability in intention. Detecting cancer early, obtaining peace of mind, knowing their PSA value, and false test results were potential outcomes and each convincingly influenced attitude. A man's wife, primary care physician, urologist, family, friends, and people with cancer each visibly swayed overall perceived social influence. The impacts of health insurance, transportation, information, health problems, including PSA in routine exams, and primary care physicians on perceived control was less clear. Elderly men were unaware of the PSA controversy and believed physicians recommend screening men their age. Our results suggest potential strategies to modify screening rates that include messages to modify men's attitudes about PSA screening and messages that target socially influential people. Being uninformed appears to be an important problem among elderly men who receive PSA screening.

Previous research has demonstrated that intuitive judgments of timeloss are often biased: overestimated when a high speed is slowed down and underestimated when a low speed is decreased further. Yet, no findings provide cognitive explanations of the bias. The present study (a) collected numerical judgments of time-loss by assigning participants to seven speed matching problems, and (b) collected verbal protocols of participants judgment processes. To identify different decision rules on the individual level, a spectral analysis of judgments was used. The findings show that the ratio rule was most frequently used and similar to the well researched time-saving bias, a ratio heuristic and a difference heuristic could model a majority of the timeloss bias. The validity of the method is supported by a significant correspondence between the spectral analysis measure and the qualitative analysis for consistent participants. By including affect as a third variable, future research could get a closer understanding of the bias effect in real life and consequently develop strategies that can improve road safety.

The difficulty of decision - making by women who are widows compared to when they were wives was studied. The areas of decision-making that were rated as to difficult concerned family finance, child care, homemaking (family foods, clothing, home furnishings, and housing), social activities, and yard and car care. The sample consisted of 33 widows living in Logan, Utah during Spring Quarter, 1971. The subjects had at least one child living at home and had been widowed at least one year. The instruments used were: ( l) a background questionnaire, and (2) a decision-making questionnaire. The statistical test used for analysis was the sign (binomial) test. Decisions concerning family finance, child care, cleaning and upkeep of the home, and yard care were more difficult for the women as widows than such decisions had been for them as wives. Decisions concerning food, clothing, and home furnishings were not more difficult for the women as widows. Decisions concerning washing the car were not more difficult, while decisions about maintenance, servicing, and repairs for the car were more difficult for the women as widows. Decisions concerning social activities that are often done as individuals, not couples, were not more difficult for the women as widows. Decisions concerning those social activities that couples often participate in were more difficult for the women as widows than such decisions had been for them as wives.

The usage of automated decision making-systems by public institutions letting the system decide on the approval, determination or denial of individuals benefits as an example, is an effective measure in making more amount of work done in a shorter time period and to a lower cost than if it would have been done by humans. But still, although the technology has developed into being able to help us in this way, so has also the potential problems that these systems can cause while they are operating. The ones primarily affected here will be the individuals that are denied their benefits, health care, or pensions. The systems can maintain hidden, historical stigmatizations and prejudices, disproportionally affecting members of a certain historically marginalized group in a negative way through its decisions, simply because the systems have learned to do so. There is also a risk that the actual programmer includes her or his own bias, as well as incorrect translation of applicable legislations or policies causing the finalized system to make decisions on unknown bases, demanding more, less or completely other things than those requirements that are set up by the public and written laws. The language in which these systems works are in mathematical algorithms, which most ordinary individuals, public employees or courts will not understand. If suspecting that you could have been discriminated against by an automated decision, the requirements for successfully claim a violation of discrimination in US-, Canadian- and Swedish courts, ECtHR and ECJ demands you to show on which of your characteristics you were discriminated, and in comparison to which other group, a group that instead has been advantaged. Still, without any reasons or explanations to why the decision has been taken available for you as an applicant or for the court responsible, the inability to identify such comparator can lead to several cases of actual indirect discriminations being denied. A solution to this could be to follow the advice of Sophia Moreau’s theory, focusing on the actual harm that the individual claim to have suffered instead of on categorizing her or him due to certain traits, or on finding a suitable comparator. This is similar to a ruling of the Swedish Court of Appeal, where a comparator was not necessary in order to establish that the applicant had been indirectly discriminated by a public institution. Instead, the biggest focus in this case was on the harm that the applicant claimed to have suffered, and then on investigating whether this difference in treatment could be objectively justified. In order for Swedish and European legislation to be able to meet the challenges that can arise through the usage of automated decision making-systems, this model of the Swedish Court of Appeal could be a better suited model to help individuals being affected by an automated decision of a public institution, being potentially indirectly discriminative.

Words need a context to be understood. Visual patterns also need a context to convey their meaning. When patterns represent quantities in business graphics, decision makers (DMs) depend on contrasting visual contexts to discern patterns and discover relationships. Depending on the context in which DMs see trends, differences between two trends may point to a problem, to continuity, or to an opportunity. Can enhancing the context in computer graphics help DMs visualize problems? To answer this research question, three experiments were done in the field on computer graphics. One hundred five DMs tried 17 different contexts for time-series trends displayed on a microcomputer monitor. The research objective was to find out whether changing the context in graphics affected the decision efficiency (accuracy/response time) of DMs in determining relationships among trends. Essential for measuring the effect were interactive computer programs that displayed random trends in graphics of differing contexts, collected the DMs' answers to questions about the trends, and graded 1133 graphics based on the answers, response times, and trend data. The experimental results supported the hypothesis that computers can enhance the visual context surrounding time-series trends so that DMs can better visualize problems. Results were based on comparisons of DMs' decision efficiencies between trial graphics with differing contextual enhancements and based on answers to questions about the trial graphics. The results were tested with nonparametric statistics at the 0.05 significance level. Specific findings were: (1) Computer-supplied forecasts, as an enhancement, significantly helped DMs discover differences among trends. (2) Although not statistically significant, stratified presentation of trends and fading chartjunk tended to increase DMs' efficiencies. (3) Adding two colors, as an enhancement, made no difference in efficiency over black and white. (4) Paired trends in windows did not affect efficiency significantly. (5) Sequentially traced trends and composites of enhancements did not affect efficiency significantly. (6) DMs preferred stratified trends most and had the most confidence in graphics with fading context. They least liked and had the least confidence in black-and-white graphics.