Since the development of high-throughput technologies, we can capture large quantities of gene¡¦s expression data from DNA microarray data, so there are some technologies have been proposed to model gene regulatory networks. Gene regulatory networks is mainly used to express the relationship between the genes, but only can express a simple relationship, and can¡¦t clearly show how the operation between genes regulatory. In the simulation method of gene regulation, the mathematical methods are more often used. In the mathematical methods, S-system is the most widely used in non-linear differential equations. When the use of mathematical simulation of gene regulatory networks, there are mainly two aspects¡G(1) deciding on the model structure and (2) estimating the involved parameter values. However, when using S-system simulated the gene regulatory networks, we can only know the gene profiles, and there is no way to know the regulatory relationships between genes, but in order to understand the relationship between genes, we must clearly understand how genes work. Therefore, we propose to encode parameter values to infer the regulatory parameter values between genes. We propose the method of encoding parameter values, and using six artificial genetic datasets, and assuming 100% parameter values are known, 90% known, 70% known, 50% known, 30% known, 10% known. The experimental results show, besides it can infer a high proportion of non-regulation, positive regulation and negative regulation, also can infer more precise parameter values, and also has a clear understanding of the regulatory relationship between genes.

<p>The mental workload for fighter pilots in modern air combat is extremely high. The pilot has to make fast dynamic decisions under high uncertainty and high time pressure. This is hard to perform in close encounters, but gets even harder when operating beyond visual range when the sensors of an aircraft become the pilot's eyes and ears. Although sensors provide good estimates for position and speed of an opponent, there is a big loss in the assessment of a situation. Important tactical events or situations can occur without the pilot noticing, which can change the outcome of a mission completely. This makes the development of an automated situation assessment system very important for future fighter aircraft. </p><p>This Master Thesis investigates the possibilities to design and implement an automated situation assessment system in a fighter aircraft. A Fuzzy-Bayesian hybrid technique is used in order to cope with the stochastic environment and making the development of the tactical situations library as clear and simple as possible.</p>

Probabilistic graphical models (PGMs) provide the capability of evaluating uncertainty and variability of product use in addition to correlating the results with aspects of the usage context. Although energy consumption during use can cause a majority of a product's environmental impact, common practice is to neglect operational variability in life cycle inventories (LCIs). Therefore, the relationship between a product's usage context and its environmental performance is rarely considered in design evaluations. This dissertation demonstrates a method for describing the usage context as a set of factors and representing the usage context through a PGM. The application to LCIs is demonstrated through the use of a lightweight vehicle design example. Although replacing steel vehicle parts with aluminum parts reduces the weight and can increase fuel economy, the energy invested in production of aluminum parts is much larger than that of steel parts. The tradeoff between energy investment and fuel savings is highly dependent upon the vehicle fuel economy and lifetime mileage. The demonstration PGM is constructed from relating factors such as driver behavior, alternative driving schedules, and residential density with local conditional probability distributions derived from publicly available data sources. Unique scenarios are then assembled from sets of conditions on these factors to provide insight for sources of variance. The vehicle example demonstrated that implementation of realistic usage scenarios via a PGM can provide a much higher fidelity investigation of energy savings during use and that distinct scenarios can have significantly different implications for the effectiveness of lightweight vehicle designs. Scenarios with large families, for example, yield high energy savings, especially if the vehicle is used for commuting or stop-and-go traffic conditions. Scenarios of small families and efficient driving schedules yield lower energy savings for lightweight vehicle designs. / text

As CMOS scaling faces a technological barrier in the near future, novel design paradigms are being proposed to keep up with the ever growing need for computation power and speed. Most of these novel technologies have device sizes comparable to atomic and molecular scales. At these levels the quantum mechanical effects play a dominant role in device performance, thus inducing uncertainty. The wave nature of particle matter and the uncertainty associated with device operation make a case for probabilistic modeling of the device. As the dimensions go down to a molecular scale, functioning of a nano-device will be governed primarily by the atomic level device physics. Modeling a device at such a small scale will require taking into account the quantum mechanical phenomenon inherent to the device. In this dissertation, we studied one such nano-device: Quantum-Dot Cellular Automata (QCA). We used probabilistic modeling to perform a fast approximation based method to estimate error, power and reliability in large QCA circuits. First, we associate the quantum mechanical probabilities associated with each QCA cell to design and build a probabilistic Bayesian network. Our proposed modeling is derived from density matrix-based quantum modeling, and it takes into account dependency patterns induced by clocking. Our modeling scheme is orders of magnitude faster than the coherent vector simulation method that uses quantum mechanical simulations. Furthermore, our output node polarization values match those obtained from the state of the art simulations. Second, we use this model to approximate power dissipated in a QCA circuit during a non-adiabatic switching event and also to isolate the thermal hotspots in a design. Third, we also use a hierarchical probabilistic macromodeling scheme to model QCA designs at circuit level to isolate weak spots early in the design process. It can also be used to compare two functionally equivalent logic designs without performing the expensive quantum mechanical simulations. Finally, we perform optimization studies on different QCA layouts by analyzing the designs for error and power over a range of kink energies.To the best of our knowledge the non-adiabatic power model presented in this dissertation is the first work that uses abrupt clocking scheme to estimate realistic power dissipation. All prior works used quasi-adiabatic power dissipation models. The hierarchical macromodel design is also the first work in QCA design that uses circuit level modeling and is faithful to the underlying layout level design. The effect of kink energy to study power-error tradeoffs will be of great use to circuit designers and fabrication scientists in choosing the most suitable design parameters such as cell size and grid spacing.

Reliability is one of the most serious issues confronted by microelectronics industry as feature sizes scale down from deep submicron to sub-100-nanometer and nanometer regime. Due to processing defects and increased noise effects, it is almost impractical to come up with error-free circuits. As we move beyond 22nm, devices will be operating very close to their thermal limit making the gates error-prone and every gate will have a finite propensity of providing erroneous outputs. Additional factors increasing the erroneous behaviors are low operating voltages and extremely high frequencies. These types of errors are not captured by current defect and fault tolerant mechanisms as they might not be present during the testing and reconfiguration. Hence Reliability-centric CAD analysis tool is becoming more essential not only to combat defect and hard faults but also errors that are transient and probabilistic in nature.In this dissertation, we address three broad categories of errors. First, we focus on random pattern testability of logic circuits with respect to hard or permanent faults. Second, we model the effect of single-event-upset (SEU) at an internal node to primary outputs. We capture the temporal nature of SEUs by adding timing information to our model. Finally, we model the dynamic error in nano-domain computing, where reliable computation has to be achieved with "systemic" unreliable devices, thus making the entire computation process probabilistic rather than deterministic in nature.Our central theoretical scheme relies on Bayesian Belief networks that are compact efficient models representing joint probability distribution in a minimal graphical structure that not only uses conditional independencies to model the underlying probabilistic dependence but also uses them for computational advantage. We used both exact and approximate inference which has let us achieve order of magnitude improvements in both accuracy and speed and have enabled us t o study larger benchmarks than the state-of-the-art. We are also able to study error sensitivities, explore design space, and characterize the input space with respect to errors and finally, evaluate the effect of redundancy schemes.

RFID technologies are being recently adopted in the retail space tracking consumer in-store movements. The RFID-collected data are location sensitive and constantly updated as a consumer moves inside a store. By capturing the entire shopping process including the movement path rather than analyzing merely the shopping basket at check-out, the RFID-collected data provide unique and exciting opportunities to study consumer purchase behavior and thus lead to actionable marketing applications.This dissertation research focuses on (a) advancing the representation and management of the RFID-collected shopping path data; (b) analyzing, modeling and predicting customer shopping activities with a spatial pattern discovery approach and a dynamic probabilistic modeling based methodology to enable advanced spatial business intelligence. The spatial pattern discovery approach identifies similar consumers based on a similarity metric between consumer shopping paths. The direct applications of this approach include a novel consumer segmentation methodology and an in-store real-time product recommendation algorithm. A hierarchical decision-theoretic model based on dynamic Bayesian networks (DBN) is developed to model consumer in-store shopping activities. This model can be used to predict a shopper's purchase goal in real time, infer her shopping actions, and estimate the exact product she is viewing at a time. We develop an approximate inference algorithm based on particle filters and a learning procedure based on the Expectation-Maximization (EM) algorithm to perform filtering and prediction for the network model. The developed models are tested on a real RFID-collected shopping trip dataset with promising results in terms of prediction accuracies of consumer purchase interests.This dissertation contributes to the marketing and information systems literature in several areas. First, it provides empirical insights about the correlation between spatial movement patterns and consumer purchase interests. Such correlation is demonstrated with in-store shopping data, but can be generalized to other marketing contexts such as store visit decisions by consumers and location and category management decisions by a retailer. Second, our study shows the possibility of utilizing consumer in-store movement to predict consumer purchase. The predictive models we developed have the potential to become the base of an intelligent shopping environment where store managers customize marketing efforts to provide location-aware recommendations to consumers as they travel through the store.

Boolean propositional satisfiability (SAT) and probabilistic reasoning represent two core problems in AI. Backtracking based algorithms have been applied in both problems. In this thesis, I investigate structure-based techniques for solving real world SAT and Bayesian networks, such as software testing and medical diagnosis instances. When solving a SAT instance using backtracking search, a sequence of decisions must be made as to which variable to branch on or instantiate next. Real world problems are often amenable to a divide-and-conquer strategy where the original instance is decomposed into independent sub-problems. Existing decomposition techniques are based on pre-processing the static structure of the original problem. I propose a dynamic decomposition method based on hypergraph separators. Integrating this dynamic separator decomposition into the variable ordering of a modern SAT solver leads to speedups on large real world SAT problems. Encoding a Bayesian network into a CNF formula and then performing weighted model counting is an effective method for exact probabilistic inference. I present two encodings for improving this approach with noisy-OR and noisy-MAX relations. In our experiments, our new encodings are more space efficient and can speed up the previous best approaches over two orders of magnitude. The ability to solve similar problems incrementally is critical for many probabilistic reasoning problems. My aim is to exploit the similarity of these instances by forwarding structural knowledge learned during the analysis of one instance to the next instance in the sequence. I propose dynamic model counting and extend the dynamic decomposition and caching technique to multiple runs on a series of problems with similar structure. This allows us to perform Bayesian inference incrementally as the evidence, parameter, and structure of the network change. Experimental results show that my approach yields significant improvements over previous model counting approaches on multiple challenging Bayesian network instances.

Capturing the mechanism of gene regulation in a living cell is essential to predict the behavior of cell in response to intercellular or extra cellular factors. Such prediction capability can potentially lead to development of improved diagnostic tests and therapeutics [21]. Amongst reverse engineering approaches that aim to model gene regulation are Dynamic Bayesian Networks (DBNs). DBNs are of particular interest as these models are capable of discovering the causal relationships between genes while dealing with noisy gene expression data. At the same time, the problem of discovering the optimum DBN model, makes structure learning of DBN a challenging topic. This is mainly due to the high dimensionality of the search space of gene expression data that makes exhaustive search strategies for identifying the best DBN structure, not practical. In this work, for the first time the application of a covariance-based evolutionary search algorithm is proposed for structure learning of DBNs. In addition, the convergence time of the proposed algorithm is improved compared to the previously reported covariance-based evolutionary search approaches. This is achieved by keeping a fixed number of good sample solutions from previous iterations. Finally, the proposed approach, M-CMA-ES, unlike gradient-based methods has a high probability to converge to a global optimum. To assess how efficient this approach works, a temporal synthetic dataset is developed. The proposed approach is then applied to this dataset as well as Brainsim dataset, a well known simulated temporal gene expression data [58]. The results indicate that the proposed method is quite efficient in reconstructing the networks in both the synthetic and Brainsim datasets. Furthermore, it outperforms other algorithms in terms of both the predicted structure accuracy and the mean square error of the reconstructed time series of gene expression data. For validation purposes, the proposed approach is also applied to a biological dataset composed of 14 cell-cycle regulated genes in yeast Saccharomyces Cerevisiae. Considering the KEGG1 pathway as the target network, the efficiency of the proposed reverse engineering approach significantly improves on the results of two previous studies of yeast cell cycle data in terms of capturing the correct interactions. / Thesis (Master, Computing) -- Queen's University, 2008-09-09 11:35:33.312

Data about the spatial variation of soil attributes is required to address a great number of environmental issues, such as improving water quality, flood mitigation, and determining the effects of the terrestrial carbon cycle. The need for a continuum of soils data is problematic, as it is only possible to observe soil attributes at a limited number of locations, beyond which, prediction is required. There is, however, disparity between the way in which much of the existing information about soil is recorded and the format in which the data is required. There are two primary methods of representing the variation in soil properties, as a set of distinct classes or as a continuum. The former is how the variation in soils has been recorded historically by the soil survey, whereas the latter is how soils data is typically required. One solution to this issue is to use a soil-landscape modelling approach which relates the soil to the wider landscape (including topography, land-use, geology and climatic conditions) using a statistical model. In this study, the soil-landscape modelling approach has been applied to the prediction of soil bulk density (Db). The original contribution to knowledge of the study is demonstrating that producing a continuous surface of Db using a soil-landscape modelling approach is that a viable alternative to the ‘classification’ approach which is most frequently used. The benefit of this method is shown in relation to the prediction of soil carbon stocks, which can be predicted more accurately and with less uncertainty. The second part of this study concerns the inclusion of expert knowledge within the soil-landscape modelling approach. The statistical modelling approaches used to predict Db are data driven, hence it is difficult to interpret the processes which the model represents. In this study, expert knowledge is used to predict Db within a Bayesian network modelling framework, which structures knowledge in terms of probability. This approach creates models which can be more easily interpreted and consequently facilitate knowledge discovery, it also provides a method for expert knowledge to be used as a proxy for empirical data. The contribution to knowledge of this section of the study is twofold, firstly, that Bayesian networks can be used as tools for data-mining to predict a continuous soil attribute such as Db and that in lieu of data, expert knowledge can be used to accurately predict landscape-scale trends in the variation of Db using a Bayesian modelling approach.

The main theme of this dissertation is the study of polytopes arising from binary multi-way contingency tables and characteristic imsets for Bayesian networks. Firstly, we study on three-way tables whose entries are independent Bernoulli ran- dom variables with canonical parameters under no three-way interaction generalized linear models. Here, we use the sequential importance sampling (SIS) method with the conditional Poisson (CP) distribution to sample binary three-way tables with the sufficient statistics, i.e., all two-way marginal sums, fixed. Compared with Monte Carlo Markov Chain (MCMC) approach with a Markov basis (MB), SIS procedure has the advantage that it does not require expensive or prohibitive pre-computations. Note that this problem can also be considered as estimating the number of lattice points inside the polytope defined by the zero-one and two-way marginal constraints. The theorems in Chapter 2 give the parameters for the CP distribution on each column when it is sampled. In this chapter, we also present the algorithms, the simulation results, and the results for Samson’s monks data. Bayesian networks, a part of the family of probabilistic graphical models, are widely applied in many areas and much work has been done in model selections for Bayesian networks. The second part of this dissertation investigates the problem of finding the optimal graph by using characteristic imsets, where characteristic imsets are defined as 0-1 vector representations of Bayesian networks which are unique up to Markov equivalence. Characteristic imset polytopes are defined as the convex hull of all characteristic imsets we consider. It was proven that the problem of finding optimal Bayesian network for a specific dataset can be converted to a linear programming problem over the characteristic imset polytope [51]. In Chapter 3, we first consider characteristic imset polytopes for all diagnosis models and show that these polytopes are direct product of simplices. Then we give the combinatorial description of all edges and all facets of these polytopes. At the end of this chapter, we generalize these results to the characteristic imset polytopes for all Bayesian networks with a fixed underlying ordering of nodes. Chapter 4 includes discussion and future work on these two topics.