Modeling and Testing for Joint Association Using a Genetic Random Field Model

Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by the joint effect of a large number of genetic variants instead of a single variant. The joint analysis of multiple genetic variants considering linkage disequilibrium (LD) and potential interactions can further enhance the discovery process, leading to the identification of new disease-susceptibility genetic variants. Motivated by the recent development in spatial statistics, we propose a new statistical model based on the random field theory, referred to as a genetic random field model (GenRF), for joint association analysis with the consideration of possible gene-gene interactions and LD. Using a pseudo-likelihood approach, a GenRF test for the joint association of multiple genetic variants is developed, which has the following advantages: 1. considering complex interactions for improved performance; 2. natural dimension reduction; 3. boosting power in the presence of LD; 4. computationally efficient. Simulation studies are conducted under various scenarios. Compared with a commonly adopted kernel machine approach, SKAT, GenRF shows overall comparable performance and better performance in the presence of complex interactions. The method is further illustrated by an application to the Dallas Heart Study.Comment: 17 pages, 4 tables, the paper has been published on Biometric

Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

Quadratic Projection Based Feature Extraction with Its Application to Biometric Recognition

This paper presents a novel quadratic projection based feature extraction framework, where a set of quadratic matrices is learned to distinguish each class from all other classes. We formulate quadratic matrix learning (QML) as a standard semidefinite programming (SDP) problem. However, the con- ventional interior-point SDP solvers do not scale well to the problem of QML for high-dimensional data. To solve the scalability of QML, we develop an efficient algorithm, termed DualQML, based on the Lagrange duality theory, to extract nonlinear features. To evaluate the feasibility and effectiveness of the proposed framework, we conduct extensive experiments on biometric recognition. Experimental results on three representative biometric recogni- tion tasks, including face, palmprint, and ear recognition, demonstrate the superiority of the DualQML-based feature extraction algorithm compared to the current state-of-the-art algorithm

Information Theoretic Methods For Biometrics, Clustering, And Stemmatology

This thesis consists of four parts, three of which study issues related to theories and applications of biometric systems, and one which focuses on clustering. We establish an information theoretic framework and the fundamental trade-off between utility of biometric systems and security of biometric systems. The utility includes person identification and secret binding, while template protection, privacy, and secrecy leakage are security issues addressed. A general model of biometric systems is proposed, in which secret binding and the use of passwords are incorporated. The system model captures major biometric system designs including biometric cryptosystems, cancelable biometrics, secret binding and secret generating systems, and salt biometric systems. In addition to attacks at the database, information leakage from communication links between sensor modules and databases is considered. A general information theoretic rate outer bound is derived for characterizing and comparing the fundamental capacity, and security risks and benefits of different system designs. We establish connections between linear codes to biometric systems, so that one can directly use a vast literature of coding theories of various noise and source random processes to achieve good performance in biometric systems. We develop two biometrics based on laser Doppler vibrometry: LDV) signals and electrocardiogram: ECG) signals. For both cases, changes in statistics of biometric traits of the same individual is the major challenge which obstructs many methods from producing satisfactory results. We propose a ii robust feature selection method that specifically accounts for changes in statistics. The method yields the best results both in LDV and ECG biometrics in terms of equal error rates in authentication scenarios. Finally, we address a different kind of learning problem from data called clustering. Instead of having a set of training data with true labels known as in identification problems, we study the problem of grouping data points without labels given, and its application to computational stemmatology. Since the problem itself has no true answer, the problem is in general ill-posed unless some regularization or norm is set to define the quality of a partition. We propose the use of minimum description length: MDL) principle for graphical based clustering. In the MDL framework, each data partitioning is viewed as a description of the data points, and the description that minimizes the total amount of bits to describe the data points and the model itself is considered the best model. We show that in synthesized data the MDL clustering works well and fits natural intuition of how data should be clustered. Furthermore, we developed a computational stemmatology method based on MDL, which achieves the best performance level in a large dataset