Associative Pattern Recognition for Biological Regulation Data

In the last decade, bioinformatics data has been accumulated at an unprecedented rate, thanks to the advancement in sequencing technologies. Such rapid development poses both challenges and promising research topics. In this dissertation, we propose a series of associative pattern recognition algorithms in biological regulation studies. In particular, we emphasize efficiently recognizing associative patterns between genes, transcription factors, histone modifications and functional labels using heterogeneous data sources (numeric, sequences, time series data and textual labels). In protein-DNA associative pattern recognition, we introduce an efficient algorithm for affinity test by searching for over-represented DNA sequences using a hash function and modulo addition calculation. This substantially improves the efficiency of \textit{next generation sequencing} data analysis. In gene regulatory network inference, we propose a framework for refining weak networks based on transcription factor binding sites, thus improved the precision of predicted edges by up to 52%. In histone modification code analysis, we propose an approach to genome-wide combinatorial pattern recognition for histone code to function associative pattern recognition, and achieved improvement by up to $38.1\%$. We also propose a novel shape based modification pattern analysis approach, using this to successfully predict sub-classes of genes in flowering-time category. We also propose a combination to combination associative pattern recognition, and achieved better performance compared against multi-label classification and bidirectional associative memory methods. Our proposed approaches recognize associative patterns from different types of data efficiently, and provides a useful toolbox for biological regulation analysis. This dissertation presents a road-map to associative patterns recognition at genome wide level

Novel techniques of computational intelligence for analysis of astronomical structures

Gravitational forces cause the formation and evolution of a variety of cosmological structures. The detailed investigation and study of these structures is a crucial step towards our understanding of the universe. This thesis provides several solutions for the detection and classification of such structures. In the first part of the thesis, we focus on astronomical simulations, and we propose two algorithms to extract stellar structures. Although they follow different strategies (while the first one is a downsampling method, the second one keeps all samples), both techniques help to build more effective probabilistic models. In the second part, we consider observational data, and the goal is to overcome some of the common challenges in observational data such as noisy features and imbalanced classes. For instance, when not enough examples are present in the training set, two different strategies are used: a) nearest neighbor technique and b) outlier detection technique. In summary, both parts of the thesis show the effectiveness of automated algorithms in extracting valuable information from astronomical databases

Graph Analytics Methods In Feature Engineering

High-dimensional data sets can be difficult to visualize and analyze, while data in low-dimensional space tend to be more accessible. In order to aid visualization of the underlying structure of a dataset, the dimension of the dataset is reduced. The simplest approach to accomplish this task of dimensionality reduction is by a random projection of the data. Even though this approach allows some degree of visualization of the underlying structure, it is possible to lose more interesting underlying structure within the data. In order to address this concern, various supervised and unsupervised linear dimensionality reduction algorithms have been designed, such as Principal Component Analysis and Linear Discriminant Analysis. These methods can be powerful, but often miss important non-linear structure in the data. In this thesis, manifold learning approaches to dimensionality reduction are developed. These approaches combine both linear and non-linear methods of dimension reduction

Graph Theoretic Algorithms Adaptable to Quantum Computing

Computational methods are rapidly emerging as an essential tool for understanding and solving complex engineering problems, which complement the traditional tools of experimentation and theory. When considered in a discrete computational setting, many engineering problems can be reduced to a graph coloring problem. Examples range from systems design, airline scheduling, image segmentation to pattern recognition, where energy cost functions with discrete variables are extremized. However, using discrete variables over continuous variables introduces some complications when defining differential quantities, such as gradients and Hessians involved in scientific computations within solid and fluid mechanics. Consequently, graph techniques are under-utilized in this important domain. However, we have recently witnessed great developments in quantum computing where physical devices can solve discrete optimization problems faster than most well-known classical algorithms. This warrants further investigation into the re-formulation of scientific computation problems into graph-theoretic problems, thus enabling rapid engineering simulations in a soon-to-be quantum computing world. The computational techniques developed in this thesis allow the representation of surface scalars, such as perimeter and area, using discrete variables in a graph. Results from integral geometry, specifically Cauchy-Crofton relations, are used to estimate these scalars via submodular functions. With this framework, several quantities important to engineering applications can be represented in graph-based algorithms. These include the surface energy of cracks for fracture prediction, grain boundary energy to model microstructure evolution, and surface area estimates (of grains and fibers) for generating conformal meshes. Combinatorial optimization problems for these applications are presented first. The last two chapters describe two new graph coloring algorithms implemented on a physical quantum computing device: the D-wave quantum annealer. The first algorithm describes a functional minimization approach to solve differential equations. The second algorithm describes a realization of the Boltzmann machine learning algorithm on a quantum annealer. The latter allows generative and discriminative learning of data, which has vast applications in many fields. Theoretical aspects and the implementation of these problems are outlined with a focus on engineering applications.PHDAerospace EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/168116/1/sidsriva_1.pd

A Bayesian statistical analysis of behavioral facilitation associated with deep brain stimulation

Deep brain stimulation (DBS) is an established therapy for Parkinson's Disease and is being investigated as a treatment for chronic depression, obsessive compulsive disorder and for facilitating functional recovery of patients in minimally conscious states following brain injury. For all of these applications, quantitative assessments of the behavioral effects of DBS are crucial to determine whether the therapy is effective and, if so, how stimulation parameters can be optimized. Behavioral analyses for DBS are challenging because subject performance is typically assessed from only a small set of discrete measurements made on a discrete rating scale, the time course of DBS effects is unknown, and between-subject differences are often large. We demonstrate how Bayesian state-space methods can be used to characterize the relationship between DBS and behavior comparing our approach with logistic regression in two experiments: the effects of DBS on attention of a macaque monkey performing a reaction-time task, and the effects of DBS on motor behavior of a human patient in a minimally conscious state. The state-space analysis can assess the magnitude of DBS behavioral facilitation (positive or negative) at specific time points and has important implications for developing principled strategies to optimize DBS paradigms.National Institutes of Health (U.S.)(R01 MH-071847)National Institutes of Health (U.S.) (DP1 OD003646)National Institutes of Health (U.S.)(NS02172)IntElect Medical (Firm