Functionality, Robustness and Control of Nonlinear Network Dynamics: Modeling and Understanding the C. elegans Connectome

Thesis (Ph.D.)--University of Washington, 2016-06

Statistical Hurdle Models for Single Cell Gene Expression: Differential Expression and Graphical Modeling

Thesis (Ph.D.)--University of Washington, 2016-06

Modeling the molecular weight distribution of block copolymer formation in a reversible addition-fragmentation chain transfer mediated living radical polymerization

Block copolymers have become an integral part of the preparation of complex architectures through self-assembly. The use of reversible addition-fragmentation chain transfer (RAFT) allows blocks ranging from functional to nonfunctional polymers to be made with predictable molecular weight distributions. This article models block formation by varying many of the kinetic parameters. The simulations provide insight into the overall polydispersities (PDIs) that will be obtained when the chain-transfer constants in the main equilibrium steps are varied from 100 to 0.5. When the first dormant block [polymer-S-C(Z)=S] has a PDI of 1 and the second propagating radical has a low reactivity to the RAFT moiety, the overall PDI will be greater than 1 and dependent on the weight fraction of each block. When the first block has a PDI of 2 and the second propagating radical has a low reactivity to the RAFT moiety, the PDI will decrease to around 1.5 because of random coupling of two broad distributions. It is also shown how we can in principle use only one RAFT agent to obtain block copolymers with any desired molecular weight distribution. We can accomplish this by maintaining the monomer concentration at a constant level in the reactor over the course of the reaction. (c) 2005 Wiley Periodicals, Inc.

Patterns in complex systems modeling

The design, development, and use of complex systems models raises a unique class of challenges and potential pitfalls, many of which are commonly recurring problems. Over time, researchers gain experience in this form of modeling, choosing algorithms, techniques, and frameworks that improve the quality, confidence level, and speed of development of their models. This increasing collective experience of complex systems modellers is a resource that should be captured. Fields such as software engineering and architecture have benefited from the development of generic solutions to recurring problems, called patterns. Using pattern development techniques from these fields, insights from communities such as learning and information processing, data mining, bioinformatics, and agent-based modeling can be identified and captured. Collections of such 'pattern languages' would allow knowledge gained through experience to be readily accessible to less-experienced practitioners and to other domains. This paper proposes a methodology for capturing the wisdom of computational modelers by introducing example visualization patterns, and a pattern classification system for analyzing the relationship between micro and macro behaviour in complex systems models. We anticipate that a new field of complex systems patterns will provide an invaluable resource for both practicing and future generations of modelers.

Towards a Modeling Environment for Earth Systems Simulations

The developments of models in Earth Sciences, e.g. for earthquake prediction and for the simulation of mantel convection, are fare from being finalized. Therefore there is a need for a modelling environment that allows scientist to implement and test new models in an easy but flexible way. After been verified, the models should be easy to apply within its scope, typically by setting input parameters through a GUI or web services. It should be possible to link certain parameters to external data sources, such as databases and other simulation codes. Moreover, as typically large-scale meshes have to be used to achieve appropriate resolutions, the computational efficiency of the underlying numerical methods is important. Conceptional this leads to a software system with three major layers: the application layer, the mathematical layer, and the numerical algorithm layer. The latter is implemented as a C/C++ library to solve a basic, computational intensive linear problem, such as a linear partial differential equation. The mathematical layer allows the model developer to define his model and to implement high level solution algorithms (e.g. Newton-Raphson scheme, Crank-Nicholson scheme) or choose these algorithms form an algorithm library. The kernels of the model are generic, typically linear, solvers provided through the numerical algorithm layer. Finally, to provide an easy-to-use application environment, a web interface is (semi-automatically) built to edit the XML input file for the modelling code. In the talk, we will discuss the advantages and disadvantages of this concept in more details. We will also present the modelling environment escript which is a prototype implementation toward such a software system in Python (see www.python.org). Key components of escript are the Data class and the PDE class. Objects of the Data class allow generating, holding, accessing, and manipulating data, in such a way that the actual, in the particular context best, representation is transparent to the user. They are also the key to establish connections with external data sources. PDE class objects are describing (linear) partial differential equation objects to be solved by a numerical library. The current implementation of escript has been linked to the finite element code Finley to solve general linear partial differential equations. We will give a few simple examples which will illustrate the usage escript. Moreover, we show the usage of escript together with Finley for the modelling of interacting fault systems and for the simulation of mantel convection.

Multi-scale approaches to Food Sciences: computational QM and MM explorations at the microscopic level

L'obiettivo principale della politica di sicurezza alimentare è quello di garantire la salute dei consumatori attraverso regole e protocolli di sicurezza specifici. Al fine di rispondere ai requisiti di sicurezza alimentare e standardizzazione della qualità, nel 2002 il Parlamento Europeo e il Consiglio dell'UE (Regolamento (CE) 178/2002 (CE, 2002)), hanno cercato di uniformare concetti, principi e procedure in modo da fornire una base comune in materia di disciplina degli alimenti e mangimi provenienti da Stati membri a livello comunitario. La formalizzazione di regole e protocolli di standardizzazione dovrebbe però passare attraverso una più dettagliata e accurata comprensione ed armonizzazione delle proprietà globali (macroscopiche), pseudo-locali (mesoscopiche), ed eventualmente, locali (microscopiche) dei prodotti alimentari. L'obiettivo principale di questa tesi di dottorato è di illustrare come le tecniche computazionali possano rappresentare un valido supporto per l'analisi e ciò tramite (i) l’applicazione di protocolli e (ii) miglioramento delle tecniche ampiamente applicate. Una dimostrazione diretta delle potenzialità già offerte dagli approcci computazionali viene offerta nel primo lavoro in cui un virtual screening basato su docking è stato applicato al fine di valutare la preliminare xeno-androgenicità di alcuni contaminanti alimentari. Il secondo e terzo lavoro riguardano lo sviluppo e la convalida di nuovi descrittori chimico-fisici in un contesto 3D-QSAR. Denominata HyPhar (Hydrophobic Pharmacophore), la nuova metodologia così messa a punto è stata usata per esplorare il tema della selettività tra bersagli molecolari strutturalmente correlati e ha così dimostrato di possedere i necessari requisiti di applicabilità e adattabilità in un contesto alimentare. Nel complesso, i risultati ci permettono di essere fiduciosi nel potenziale impatto che le tecniche in silico potranno avere nella identificazione e chiarificazione di eventi molecolari implicati negli aspetti tossicologici e nutrizionali degli alimenti.

Transaction attributes and buyer-supplier relationships in AMT acquisition and implementation:the case of Malaysia

This paper explores how transaction attributes of technology affect differences in the relationship between technology buyers and suppliers. It also examines the impact on performance of different patterns of relationship between technology buyers and suppliers. Data obtained from 147 manufacturing firms in Malaysia are used to test several hypotheses, which were derived from a review of the literature on technology, transaction cost theory and buyer–supplier relationships (BSR). The research results indicate that the higher the level of technological complexity, specificity and uncertainty, the more firms are likely to engage in a closer relationship with technology suppliers. Even though the majority of firms reported improvements in their performance, results indicate that firms demonstrating a closer relationship with technology suppliers are more likely to achieve higher levels of performance than those that do not. It is also shown that with high levels of transaction attribute, implementation performance suffers more when firms have weak relationships with technology suppliers than with moderate and low levels of transaction attribute.

The precursors and impacts of BSR on AMT acquisition and implementation

This paper reports on the results of research into the connections between transaction attributes and buyer-supplier relationships (BSRs) in advanced manufacturing technology (AMT) acquisition and implementation. The investigation began by examining the impact of the different patterns of BSR on the performance of the AMT acquisition. In understanding the phenomena, the study drew upon and integrated the literature of transaction cost economics theory, BSRs, and AMT, and used this as the basis for a theoretical framework and hypotheses development. This framework was then empirically tested using data that were gathered through a questionnaire survey with 147 companies and analyzed using a structural equation modeling technique. The results of the analysis indicated that the higher the level of technological specificity and uncertainty, the more firms are likely to engage in a stronger relationship with technology suppliers. However, the complexity of the technology being implemented was associated with BSR only indirectly through its association with the level of uncertainty (which has a direct impact upon BSR). The analysis also provided strong support for the premise that developing strong BSR could lead to an improved performance in acquiring and implementing AMT. The implications of the study are offered for both the academic and practitioner audience.

Attentional shifts towards an expected visual target alter the level of alpha-band oscillatory activity in the human calcarine cortex

Neuronal operations associated with the top-down control process of shifting attention from one locus to another involve a network of cortical regions, and their influence is deemed fundamental to visual perception. However, the extent and nature of these operations within primary visual areas are unknown. In this paper, we used magnetoencephalography (MEG) in combination with magnetic resonance imaging (MRI) to determine whether, prior to the onset of a visual stimulus, neuronal activity within early visual cortex is affected by covert attentional shifts. Time/frequency analyses were used to identify the nature of this activity. Our results show that shifting attention towards an expected visual target results in a late-onset (600 ms postcue onset) depression of alpha activity which persists until the appearance of the target. Independent component analysis (ICA) and dipolar source modeling confirmed that the neuronal changes we observed originated from within the calcarine cortex. Our results further show that the amplitude changes in alpha activity were induced not evoked (i.e., not phase-locked to the cued attentional task). We argue that the decrease in alpha prior to the onset of the target may serve to prime the early visual cortex for incoming sensory information. We conclude that attentional shifts affect activity within the human calcarine cortex by altering the amplitude of spontaneous alpha rhythms and that subsequent modulation of visual input with attentional engagement follows as a consequence of these localized changes in oscillatory activity. © 2005 Elsevier B.V. All rights reserved.

A co-ordinated business object approach for supporting tactical level management decisions

The proliferation of data throughout the strategic, tactical and operational areas within many organisations, has provided a need for the decision maker to be presented with structured information that is appropriate for achieving allocated tasks. However, despite this abundance of data, managers at all levels in the organisation commonly encounter a condition of ‘information overload’, that results in a paucity of the correct information. Specifically, this thesis will focus upon the tactical domain within the organisation and the information needs of management who reside at this level. In doing so, it will argue that the link between decision making at the tactical level in the organisation, and low-level transaction processing data, should be through a common object model that used a framework based upon knowledge leveraged from co-ordination theory. In order to achieve this, the Co-ordinated Business Object Model (CBOM) was created. Detailing a two-tier framework, the first tier models data based upon four interactive object models, namely, processes, activities, resources and actors. The second tier analyses the data captured by the four object models, and returns information that can be used to support tactical decision making. In addition, the Co-ordinated Business Object Support System (CBOSS), is a prototype tool that has been developed in order to both support the CBOM implementation, and to also demonstrate the functionality of the CBOM as a modelling approach for supporting tactical management decision making. Containing a graphical user interface, the system’s functionality allows the user to create and explore alternative implementations of an identified tactical level process. In order to validate the CBOM, three verification tests have been completed. The results provide evidence that the CBOM framework helps bridge the gap between low level transaction data, and the information that is used to support tactical level decision making.

Buyer-supplier relationships in advanced manufacturing technology acquisition and implementation : a study in Malaysia

This thesis reports the results of research into the connections between transaction attributes and buyer-supplier relationships (BSR) in advanced manufacturing technology (AMT) acquisitions and implementation. It also examines the impact of the different patterns of BSR on performance. Specifically, it addresses the issues of how the three transaction attributes; namely level of complexity, level of asset specificity, and level of uncertainty, can affect the relationships between the technology buyer and suppler in AMT acquisition and implementation, and then to see the impact of different patterns of BSR on the two aspect of performance; namely technology and implementation performance. In understanding the pohenomena, the study mainly draws on and integrates the literature of transaction cost economics theory,buyer-supplier relationships and advanced manufacturing technology as a basis of theoretical framework and hypotheses development.data were gathered through a questionnaire survey with 147 responses and seven semi-structured interviews of manufacturing firms in Malaysia. Quantitative data were analysed mainly using the AMOS (Analysis of Moment Structure) package for structural equation modeling and SPSS (Statistical Package for Social Science) for analysis of variance (ANOVA). Data from interview sessions were used to develop a case study with the intention of providing a richer and deeper understanding on the subject under investigation and to offer triangulation in the research process. he results of the questionnaire survey indicate that the higher the level of technological specificity and uncertainty, the more firms are likely to engage in a closer relationship with technology suppliers.However, the complexity of the technology being implemented is associated with BSR only because it is associated with the level of uncertainty that has direct impact upon BSR.The analysis also provides strong support for the premise that developing strong BSR could lead to an improved performance. However, with high levels of transaction attribute, implementation performance suffers more when firms have weak relationships with technology suppliers than with moderate and low levels of transaction attributes. The implications of the study are offered for both the academic and practitioner audience. The thesis closes with reports on its limitations and suggestions for further research that would address some of these limitations.

A Bayesian modeling approach to multi-dimensional sentiment distributions prediction

Sentiment analysis has long focused on binary classification of text as either positive or negative. There has been few work on mapping sentiments or emotions into multiple dimensions. This paper studies a Bayesian modeling approach to multi-class sentiment classification and multidimensional sentiment distributions prediction. It proposes effective mechanisms to incorporate supervised information such as labeled feature constraints and document-level sentiment distributions derived from the training data into model learning. We have evaluated our approach on the datasets collected from the confession section of the Experience Project website where people share their life experiences and personal stories. Our results show that using the latent representation of the training documents derived from our approach as features to build a maximum entropy classifier outperforms other approaches on multi-class sentiment classification. In the more difficult task of multi-dimensional sentiment distributions prediction, our approach gives superior performance compared to a few competitive baselines. © 2012 ACM.

A multi-level investigation of psychological contract breach and organizational identification through the lens of perceived organizational membership:testing a moderated-mediated model

Drawing on the perceived organizational membership theoretical framework and the social identity view of dissonance theory, I examined in this study the dynamics of the relationship between psychological contract breach and organizational identification. I included group-level transformational and transactional leadership as well as procedural justice in the hypothesized model as key antecedents for organizational membership processes. I further explored the mediating role of psychological contract breach in the relationship between leadership, procedural justice climate, and organizational identification and proposed separateness–connectedness self-schema as an important moderator of the above mediated relationship. Hierarchical linear modeling results from a sample of 864 employees from 162 work units in 10 Greek organizations indicated that employees' perception of psychological contract breach negatively affected their organizational identification. I also found psychological contract breach to mediate the impact of transformational and transactional leadership on organizational identification. Results further provided support for moderated mediation and showed that the indirect effects of transformational and transactional leadership on identification through psychological contract breach were stronger for employees with a low connectedness self-schema.

Goal-based modeling of dynamically adaptive system requirements

Self-adaptation is emerging as an increasingly important capability for many applications, particularly those deployed in dynamically changing environments, such as ecosystem monitoring and disaster management. One key challenge posed by Dynamically Adaptive Systems (DASs) is the need to handle changes to the requirements and corresponding behavior of a DAS in response to varying environmental conditions. Berry et al. previously identified four levels of RE that should be performed for a DAS. In this paper, we propose the Levels of RE for Modeling that reify the original levels to describe RE modeling work done by DAS developers. Specifically, we identify four types of developers: the system developer, the adaptation scenario developer, the adaptation infrastructure developer, and the DAS research community. Each level corresponds to the work of a different type of developer to construct goal model(s) specifying their requirements. We then leverage the Levels of RE for Modeling to propose two complementary processes for performing RE for a DAS. We describe our experiences with applying this approach to GridStix, an adaptive flood warning system, deployed to monitor the River Ribble in Yorkshire, England.

How contracts and enforcement explain transaction outcomes

This study considers the influence of contracts on enforcement and the subsequent performance impact of aligned and misaligned enforcement. We define enforcement as a corrective action aimed at remedying problems occurring in the transaction. First we explain the role of contracts and show that at the component level, contracts can both increase and decrease enforcement. Building on an alignment perspective and accounting for the endogeneity of enforcement, we use these contractual components and variables related to enforcement to predict the occurrence of enforcement. We use such predictions to show that aligned enforcement results in higher performance. We also show that the performance impact of misaligned enforcement is relatively greater for transactions where enforcement is not expected. We conduct the study using a unique dataset reporting on 971 business transactions across a wide range of industries.