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- Genre: Academic theses
- Creators: Pan, Rong
- Creators: Zhou, Shuang
Description
The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to help understand the data, discover the patterns and improve the decision making. All the proposed methods can generalize to other industrial fields.
The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.
The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.
The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.
The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.
The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.
The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.
The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.
The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.
ContributorsLin, Sangdi (Author) / Runger, George C. (Thesis advisor) / Kocher, Jean-Pierre A (Committee member) / Pan, Rong (Committee member) / Escobedo, Adolfo R. (Committee member) / Arizona State University (Publisher)
Created2018
Description
The majority of research in experimental design has, to date, been focused on designs when there is only one type of response variable under consideration. In a decision-making process, however, relying on only one objective or criterion can lead to oversimplified, sub-optimal decisions that ignore important considerations. Incorporating multiple, and likely competing, objectives is critical during the decision-making process in order to balance the tradeoffs of all potential solutions. Consequently, the problem of constructing a design for an experiment when multiple types of responses are of interest does not have a clear answer, particularly when the response variables have different distributions. Responses with different distributions have different requirements of the design.
Computer-generated optimal designs are popular design choices for less standard scenarios where classical designs are not ideal. This work presents a new approach to experimental designs for dual-response systems. The normal, binomial, and Poisson distributions are considered for the potential responses. Using the D-criterion for the linear model and the Bayesian D-criterion for the nonlinear models, a weighted criterion is implemented in a coordinate-exchange algorithm. The designs are evaluated and compared across different weights. The sensitivity of the designs to the priors supplied in the Bayesian D-criterion is explored in the third chapter of this work.
The final section of this work presents a method for a decision-making process involving multiple objectives. There are situations where a decision-maker is interested in several optimal solutions, not just one. These types of decision processes fall into one of two scenarios: 1) wanting to identify the best N solutions to accomplish a goal or specific task, or 2) evaluating a decision based on several primary quantitative objectives along with secondary qualitative priorities. Design of experiment selection often involves the second scenario where the goal is to identify several contending solutions using the primary quantitative objectives, and then use the secondary qualitative objectives to guide the final decision. Layered Pareto Fronts can help identify a richer class of contenders to examine more closely. The method is illustrated with a supersaturated screening design example.
Computer-generated optimal designs are popular design choices for less standard scenarios where classical designs are not ideal. This work presents a new approach to experimental designs for dual-response systems. The normal, binomial, and Poisson distributions are considered for the potential responses. Using the D-criterion for the linear model and the Bayesian D-criterion for the nonlinear models, a weighted criterion is implemented in a coordinate-exchange algorithm. The designs are evaluated and compared across different weights. The sensitivity of the designs to the priors supplied in the Bayesian D-criterion is explored in the third chapter of this work.
The final section of this work presents a method for a decision-making process involving multiple objectives. There are situations where a decision-maker is interested in several optimal solutions, not just one. These types of decision processes fall into one of two scenarios: 1) wanting to identify the best N solutions to accomplish a goal or specific task, or 2) evaluating a decision based on several primary quantitative objectives along with secondary qualitative priorities. Design of experiment selection often involves the second scenario where the goal is to identify several contending solutions using the primary quantitative objectives, and then use the secondary qualitative objectives to guide the final decision. Layered Pareto Fronts can help identify a richer class of contenders to examine more closely. The method is illustrated with a supersaturated screening design example.
ContributorsBurke, Sarah Ellen (Author) / Montgomery, Douglas C. (Thesis advisor) / Borror, Connie M. (Thesis advisor) / Anderson-Cook, Christine M. (Committee member) / Pan, Rong (Committee member) / Silvestrini, Rachel (Committee member) / Arizona State University (Publisher)
Created2016
Description
This study concerns optimal designs for experiments where responses consist of both binary and continuous variables. Many experiments in engineering, medical studies, and other fields have such mixed responses. Although in recent decades several statistical methods have been developed for jointly modeling both types of response variables, an effective way to design such experiments remains unclear. To address this void, some useful results are developed to guide the selection of optimal experimental designs in such studies. The results are mainly built upon a powerful tool called the complete class approach and a nonlinear optimization algorithm. The complete class approach was originally developed for a univariate response, but it is extended to the case of bivariate responses of mixed variable types. Consequently, the number of candidate designs are significantly reduced. An optimization algorithm is then applied to efficiently search the small class of candidate designs for the D- and A-optimal designs. Furthermore, the optimality of the obtained designs is verified by the general equivalence theorem. In the first part of the study, the focus is on a simple, first-order model. The study is expanded to a model with a quadratic polynomial predictor. The obtained designs can help to render a precise statistical inference in practice or serve as a benchmark for evaluating the quality of other designs.
ContributorsKim, Soohyun (Author) / Kao, Ming-Hung (Thesis advisor) / Dueck, Amylou (Committee member) / Pan, Rong (Committee member) / Reiser, Mark R. (Committee member) / Stufken, John (Committee member) / Arizona State University (Publisher)
Created2017
Description
In accelerated life tests (ALTs), complete randomization is hardly achievable because of economic and engineering constraints. Typical experimental protocols such as subsampling or random blocks in ALTs result in a grouped structure, which leads to correlated lifetime observations. In this dissertation, generalized linear mixed model (GLMM) approach is proposed to analyze ALT data and find the optimal ALT design with the consideration of heterogeneous group effects.
Two types of ALTs are demonstrated for data analysis. First, constant-stress ALT (CSALT) data with Weibull failure time distribution is modeled by GLMM. The marginal likelihood of observations is approximated by the quadrature rule; and the maximum likelihood (ML) estimation method is applied in iterative fashion to estimate unknown parameters including the variance component of random effect. Secondly, step-stress ALT (SSALT) data with random group effects is analyzed in similar manner but with an assumption of exponentially distributed failure time in each stress step. Two parameter estimation methods, from the frequentist’s and Bayesian points of view, are applied; and they are compared with other traditional models through simulation study and real example of the heterogeneous SSALT data. The proposed random effect model shows superiority in terms of reducing bias and variance in the estimation of life-stress relationship.
The GLMM approach is particularly useful for the optimal experimental design of ALT while taking the random group effects into account. In specific, planning ALTs under nested design structure with random test chamber effects are studied. A greedy two-phased approach shows that different test chamber assignments to stress conditions substantially impact on the estimation of unknown parameters. Then, the D-optimal test plan with two test chambers is constructed by applying the quasi-likelihood approach. Lastly, the optimal ALT planning is expanded for the case of multiple sources of random effects so that the crossed design structure is also considered, along with the nested structure.
Two types of ALTs are demonstrated for data analysis. First, constant-stress ALT (CSALT) data with Weibull failure time distribution is modeled by GLMM. The marginal likelihood of observations is approximated by the quadrature rule; and the maximum likelihood (ML) estimation method is applied in iterative fashion to estimate unknown parameters including the variance component of random effect. Secondly, step-stress ALT (SSALT) data with random group effects is analyzed in similar manner but with an assumption of exponentially distributed failure time in each stress step. Two parameter estimation methods, from the frequentist’s and Bayesian points of view, are applied; and they are compared with other traditional models through simulation study and real example of the heterogeneous SSALT data. The proposed random effect model shows superiority in terms of reducing bias and variance in the estimation of life-stress relationship.
The GLMM approach is particularly useful for the optimal experimental design of ALT while taking the random group effects into account. In specific, planning ALTs under nested design structure with random test chamber effects are studied. A greedy two-phased approach shows that different test chamber assignments to stress conditions substantially impact on the estimation of unknown parameters. Then, the D-optimal test plan with two test chambers is constructed by applying the quasi-likelihood approach. Lastly, the optimal ALT planning is expanded for the case of multiple sources of random effects so that the crossed design structure is also considered, along with the nested structure.
ContributorsSeo, Kangwon (Author) / Pan, Rong (Thesis advisor) / Montgomery, Douglas C. (Committee member) / Villalobos, J. Rene (Committee member) / Rigdon, Steven E (Committee member) / Arizona State University (Publisher)
Created2017
Description
Distributed Renewable energy generators are now contributing a significant amount of energy into the energy grid. Consequently, reliability adequacy of such energy generators will depend on making accurate forecasts of energy produced by them. Power outputs of Solar PV systems depend on the stochastic variation of environmental factors (solar irradiance, ambient temperature & wind speed) and random mechanical failures/repairs. Monte Carlo Simulation which is typically used to model such problems becomes too computationally intensive leading to simplifying state-space assumptions. Multi-state models for power system reliability offer a higher flexibility in providing a description of system state evolution and an accurate representation of probability. In this study, Universal Generating Functions (UGF) were used to solve such combinatorial problems. 8 grid connected Solar PV systems were analyzed with a combined capacity of about 5MW located in a hot-dry climate (Arizona) and accuracy of 98% was achieved when validated with real-time data. An analytics framework is provided to grid operators and utilities to effectively forecast energy produced by distributed energy assets and in turn, develop strategies for effective Demand Response in times of increased share of renewable distributed energy assets in the grid. Second part of this thesis extends the environmental modelling approach to develop an aging test to be run in conjunction with an accelerated test of Solar PV modules. Accelerated Lifetime Testing procedures in the industry are used to determine the dominant failure modes which the product undergoes in the field, as well as predict the lifetime of the product. UV stressor is one of the ten stressors which a PV module undergoes in the field. UV exposure causes browning of modules leading to drop in Short Circuit Current. This thesis presents an environmental modelling approach for the hot-dry climate and extends it to develop an aging test methodology. This along with the accelerated tests would help achieve the goal of correlating field failures with accelerated tests and obtain acceleration factor. This knowledge would help predict PV module degradation in the field within 30% of the actual value and help in knowing the PV module lifetime accurately.
ContributorsKadloor, Nikhil (Author) / Kuitche, Joseph (Thesis advisor) / Pan, Rong (Thesis advisor) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2017
Description
Yield is a key process performance characteristic in the capital-intensive semiconductor fabrication process. In an industry where machines cost millions of dollars and cycle times are a number of months, predicting and optimizing yield are critical to process improvement, customer satisfaction, and financial success. Semiconductor yield modeling is essential to identifying processing issues, improving quality, and meeting customer demand in the industry. However, the complicated fabrication process, the massive amount of data collected, and the number of models available make yield modeling a complex and challenging task. This work presents modeling strategies to forecast yield using generalized linear models (GLMs) based on defect metrology data. The research is divided into three main parts. First, the data integration and aggregation necessary for model building are described, and GLMs are constructed for yield forecasting. This technique yields results at both the die and the wafer levels, outperforms existing models found in the literature based on prediction errors, and identifies significant factors that can drive process improvement. This method also allows the nested structure of the process to be considered in the model, improving predictive capabilities and violating fewer assumptions. To account for the random sampling typically used in fabrication, the work is extended by using generalized linear mixed models (GLMMs) and a larger dataset to show the differences between batch-specific and population-averaged models in this application and how they compare to GLMs. These results show some additional improvements in forecasting abilities under certain conditions and show the differences between the significant effects identified in the GLM and GLMM models. The effects of link functions and sample size are also examined at the die and wafer levels. The third part of this research describes a methodology for integrating classification and regression trees (CART) with GLMs. This technique uses the terminal nodes identified in the classification tree to add predictors to a GLM. This method enables the model to consider important interaction terms in a simpler way than with the GLM alone, and provides valuable insight into the fabrication process through the combination of the tree structure and the statistical analysis of the GLM.
ContributorsKrueger, Dana Cheree (Author) / Montgomery, Douglas C. (Thesis advisor) / Fowler, John (Committee member) / Pan, Rong (Committee member) / Pfund, Michele (Committee member) / Arizona State University (Publisher)
Created2011
Description
Longitudinal data involving multiple subjects is quite popular in medical and social science areas. I consider generalized linear mixed models (GLMMs) applied to such longitudinal data, and the optimal design searching problem under such models. In this case, based on optimal design theory, the optimality criteria depend on the estimated parameters, which leads to local optimality. Moreover, the information matrix under a GLMM doesn't have a closed-form expression. My dissertation includes three topics related to this design problem. The first part is searching for locally optimal designs under GLMMs with longitudinal data. I apply penalized quasi-likelihood (PQL) method to approximate the information matrix and compare several approximations to show the superiority of PQL over other approximations. Under different local parameters and design restrictions, locally D- and A- optimal designs are constructed based on the approximation. An interesting finding is that locally optimal designs sometimes apply different designs to different subjects. Finally, the robustness of these locally optimal designs is discussed. In the second part, an unknown observational covariate is added to the previous model. With an unknown observational variable in the experiment, expected optimality criteria are considered. Under different assumptions of the unknown variable and parameter settings, locally optimal designs are constructed and discussed. In the last part, Bayesian optimal designs are considered under logistic mixed models. Considering different priors of the local parameters, Bayesian optimal designs are generated. Bayesian design under such a model is usually expensive in time. The running time in this dissertation is optimized to an acceptable amount with accurate results. I also discuss the robustness of these Bayesian optimal designs, which is the motivation of applying such an approach.
ContributorsShi, Yao (Author) / Stufken, John (Thesis advisor) / Kao, Ming-Hung (Thesis advisor) / Lan, Shiwei (Committee member) / Pan, Rong (Committee member) / Reiser, Mark (Committee member) / Arizona State University (Publisher)
Created2022
Description
This dissertation covers several topics in machine learning and causal inference. First, the question of “feature selection,” a common byproduct of regularized machine learning methods, is investigated theoretically in the context of treatment effect estimation. This involves a detailed review and extension of frameworks for estimating causal effects and in-depth theoretical study. Next, various computational approaches to estimating causal effects with machine learning methods are compared with these theoretical desiderata in mind. Several improvements to current methods for causal machine learning are identified and compelling angles for further study are pinpointed. Finally, a common method used for “explaining” predictions of machine learning algorithms, SHAP, is evaluated critically through a statistical lens.
ContributorsHerren, Andrew (Author) / Hahn, P Richard (Thesis advisor) / Kao, Ming-Hung (Committee member) / Lopes, Hedibert (Committee member) / McCulloch, Robert (Committee member) / Zhou, Shuang (Committee member) / Arizona State University (Publisher)
Created2023
Description
This dissertation develops versatile modeling tools to estimate causal effects when conditional unconfoundedness is not immediately satisfied. Chapter 2 provides a brief overview ofcommon techniques in causal inference, with a focus on models relevant to the data explored
in later chapters. The rest of the dissertation focuses on the development of novel “reduced
form” models which are designed to assess the particular challenges of different datasets.
Chapter 3 explores the question of whether or not forecasts of bankruptcy cause bankruptcy.
The question arises from the observation that companies issued going concern opinions were
more likely to go bankrupt in the following year, leading people to speculate that the opinions themselves caused the bankruptcy via a “self-fulfilling prophecy”. A Bayesian machine
learning sensitivity analysis is developed to answer this question. In exchange for additional
flexibility and fewer assumptions, this approach loses point identification of causal effects
and thus a sensitivity analysis is developed to study a wide range of plausible scenarios of
the causal effect of going concern opinions on bankruptcy. Reported in the simulations are
different performance metrics of the model in comparison with other popular methods and a
robust analysis of the sensitivity of the model to mis-specification. Results on empirical data
indicate that forecasts of bankruptcies likely do have a small causal effect.
Chapter 4 studies the effects of vaccination on COVID-19 mortality at the state level in
the United States. The dynamic nature of the pandemic complicates more straightforward
regression adjustments and invalidates many alternative models. The chapter comments on
the limitations of mechanistic approaches as well as traditional statistical methods to epidemiological data. Instead, a state space model is developed that allows the study of the
ever-changing dynamics of the pandemic’s progression. In the first stage, the model decomposes the observed mortality data into component surges, and later uses this information in
a semi-parametric regression model for causal analysis. Results are investigated thoroughly
for empirical justification and stress-tested in simulated settings.
ContributorsPapakostas, Demetrios (Author) / Hahn, Paul (Thesis advisor) / McCulloch, Robert (Committee member) / Zhou, Shuang (Committee member) / Kao, Ming-Hung (Committee member) / Lan, Shiwei (Committee member) / Arizona State University (Publisher)
Created2023
Description
Tracking disease cases is an essential task in public health; however, tracking the number of cases of a disease may be difficult not every infection can be recorded by public health authorities. Notably, this may happen with whole country measles case reports, even such countries with robust registration systems. Eilertson et al. (2019) propose using a state-space model combined with maximum likelihood methods for estimating measles transmission. A Bayesian approach that uses particle Markov Chain Monte Carlo (pMCMC) is proposed to estimate the parameters of the non-linear state-space model developed in Eilertson et al. (2019) and similar previous studies. This dissertation illustrates the performance of this approach by calculating posterior estimates of the model parameters and predictions of the unobserved states in simulations and case studies. Also, Iteration Filtering (IF2) is used as a support method to verify the Bayesian estimation and to inform the selection of prior distributions. In the second half of the thesis, a birth-death process is proposed to model the unobserved population size of a disease vector. This model studies the effect of a disease vector population size on a second affected population. The second population follows a non-homogenous Poisson process when conditioned on the vector process with a transition rate given by a scaled version of the vector population. The observation model also measures a potential threshold event when the host species population size surpasses a certain level yielding a higher transmission rate. A maximum likelihood procedure is developed for this model, which combines particle filtering with the Minorize-Maximization (MM) algorithm and extends the work of Crawford et al. (2014).
ContributorsMartinez Rivera, Wilmer Osvaldo (Author) / Fricks, John (Thesis advisor) / Reiser, Mark (Committee member) / Zhou, Shuang (Committee member) / Cheng, Dan (Committee member) / Lan, Shiwei (Committee member) / Arizona State University (Publisher)
Created2022