Ensemble learning method for hidden markov models.

For complex classification systems, data are gathered from various sources and potentially have different representations. Thus, data may have large intra-class variations. In fact, modeling each data class with a single model might lead to poor generalization. The classification error can be more severe for temporal data where each sample is represented by a sequence of observations. Thus, there is a need for building a classification system that takes into account the variations within each class in the data. This dissertation introduces an ensemble learning method for temporal data that uses a mixture of Hidden Markov Model (HMM) classifiers. We hypothesize that the data are generated by K models, each of which reacts a particular trend in the data. Model identification could be achieved through clustering in the feature space or in the parameters space. However, this approach is inappropriate in the context of sequential data. The proposed approach is based on clustering in the log-likelihood space, and has two main steps. First, one HMM is fit to each of the N individual sequences. For each fitted model, we evaluate the log-likelihood of each sequence. This will result in an N-by-N log-likelihood distance matrix that will be partitioned into K groups using a relational clustering algorithm. In the second step, we learn the parameters of one HMM per group. We propose using and optimizing various training approaches for the different K groups depending on their size and homogeneity. In particular, we investigate the maximum likelihood (ML), the minimum classification error (MCE) based discriminative, and the Variational Bayesian (VB) training approaches. Finally, to test a new sequence, its likelihood is computed in all the models and a final confidence value is assigned by combining the multiple models outputs using a decision level fusion method such as an artificial neural network or a hierarchical mixture of experts. Our approach was evaluated on two real-world applications: (1) identification of Cardio-Pulmonary Resuscitation (CPR) scenes in video simulating medical crises; and (2) landmine detection using Ground Penetrating Radar (GPR). Results on both applications show that the proposed method can identify meaningful and coherent HMM mixture components that describe different properties of the data. Each HMM mixture component models a group of data that share common attributes. The results indicate that the proposed method outperforms the baseline HMM that uses one model for each class in the data

Modeling Financial Time Series with Artificial Neural Networks

Financial time series convey the decisions and actions of a population of human actors over time. Econometric and regressive models have been developed in the past decades for analyzing these time series. More recently, biologically inspired artificial neural network models have been shown to overcome some of the main challenges of traditional techniques by better exploiting the non-linear, non-stationary, and oscillatory nature of noisy, chaotic human interactions. This review paper explores the options, benefits, and weaknesses of the various forms of artificial neural networks as compared with regression techniques in the field of financial time series analysis.CELEST, a National Science Foundation Science of Learning Center (SBE-0354378); SyNAPSE program of the Defense Advanced Research Project Agency (HR001109-03-0001

An Automatic Level Set Based Liver Segmentation from MRI Data Sets

A fast and accurate liver segmentation method is a challenging work in medical image analysis area. Liver segmentation is an important process for computer-assisted diagnosis, pre-evaluation of liver transplantation and therapy planning of liver tumors. There are several advantages of magnetic resonance imaging such as free form ionizing radiation and good contrast visualization of soft tissue. Also, innovations in recent technology and image acquisition techniques have made magnetic resonance imaging a major tool in modern medicine. However, the use of magnetic resonance images for liver segmentation has been slow when we compare applications with the central nervous systems and musculoskeletal. The reasons are irregular shape, size and position of the liver, contrast agent effects and similarities of the gray values of neighbor organs. Therefore, in this study, we present a fully automatic liver segmentation method by using an approximation of the level set based contour evolution from T2 weighted magnetic resonance data sets. The method avoids solving partial differential equations and applies only integer operations with a two-cycle segmentation algorithm. The efficiency of the proposed approach is achieved by applying the algorithm to all slices with a constant number of iteration and performing the contour evolution without any user defined initial contour. The obtained results are evaluated with four different similarity measures and they show that the automatic segmentation approach gives successful results

Hyperspectral-Augmented Target Tracking

With the global war on terrorism, the nature of military warfare has changed significantly. The United States Air Force is at the forefront of research and development in the field of intelligence, surveillance, and reconnaissance that provides American forces on the ground and in the air with the capability to seek, monitor, and destroy mobile terrorist targets in hostile territory. One such capability recognizes and persistently tracks multiple moving vehicles in complex, highly ambiguous urban environments. The thesis investigates the feasibility of augmenting a multiple-target tracking system with hyperspectral imagery. The research effort evaluates hyperspectral data classification using fuzzy c-means and the self-organizing map clustering algorithms for remote identification of moving vehicles. Results demonstrate a resounding 29.33% gain in performance from the baseline kinematic-only tracking to the hyperspectral-augmented tracking. Through a novel methodology, the hyperspectral observations are integrated in the MTT paradigm. Furthermore, several novel ideas are developed and implemented—spectral gating of hyperspectral observations, a cost function for hyperspectral observation-to-track association, and a self-organizing map filtering method. It appears that relatively little work in the target tracking and hyperspectral image classification literature exists that addresses these areas. Finally, two hyperspectral sensor modes are evaluated—Pushbroom and Region-of-Interest. Both modes are based on realistic technologies, and investigating their performance is the goal of performance-driven sensing. Performance comparison of the two modes can drive future design of hyperspectral sensors

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

Misty Mountain clustering: application to fast unsupervised flow cytometry gating

<p>Abstract</p> <p>Background</p> <p>There are many important clustering questions in computational biology for which no satisfactory method exists. Automated clustering algorithms, when applied to large, multidimensional datasets, such as flow cytometry data, prove unsatisfactory in terms of speed, problems with local minima or cluster shape bias. Model-based approaches are restricted by the assumptions of the fitting functions. Furthermore, model based clustering requires serial clustering for all cluster numbers within a user defined interval. The final cluster number is then selected by various criteria. These supervised serial clustering methods are time consuming and frequently different criteria result in different optimal cluster numbers. Various unsupervised heuristic approaches that have been developed such as affinity propagation are too expensive to be applied to datasets on the order of 10⁶points that are often generated by high throughput experiments.</p> <p>Results</p> <p>To circumvent these limitations, we developed a new, unsupervised density contour clustering algorithm, called Misty Mountain, that is based on percolation theory and that efficiently analyzes large data sets. The approach can be envisioned as a progressive top-down removal of clouds covering a data histogram relief map to identify clusters by the appearance of statistically distinct peaks and ridges. This is a parallel clustering method that finds every cluster after analyzing only once the cross sections of the histogram. The overall run time for the composite steps of the algorithm increases linearly by the number of data points. The clustering of 10⁶data points in 2D data space takes place within about 15 seconds on a standard laptop PC. Comparison of the performance of this algorithm with other state of the art automated flow cytometry gating methods indicate that Misty Mountain provides substantial improvements in both run time and in the accuracy of cluster assignment.</p> <p>Conclusions</p> <p>Misty Mountain is fast, unbiased for cluster shape, identifies stable clusters and is robust to noise. It provides a useful, general solution for multidimensional clustering problems. We demonstrate its suitability for automated gating of flow cytometry data.</p

A Survey of Flow Cytometry Data Analysis Methods

Flow cytometry (FCM) is widely used in health research and in treatment for a variety of tasks, such as in the diagnosis and monitoring of leukemia and lymphoma patients, providing the counts of helper-T lymphocytes needed to monitor the course and treatment of HIV infection, the evaluation of peripheral blood hematopoietic stem cell grafts, and many other diseases. In practice, FCM data analysis is performed manually, a process that requires an inordinate amount of time and is error-prone, nonreproducible, nonstandardized, and not open for re-evaluation, making it the most limiting aspect of this technology. This paper reviews state-of-the-art FCM data analysis approaches using a framework introduced to report each of the components in a data analysis pipeline. Current challenges and possible future directions in developing fully automated FCM data analysis tools are also outlined

The curvHDR Method for Gating Flow Cytometry Samples

Motivation: High-throughput flow cytometry experiments produce hundreds of large multivariate samples of cellular characteristics. These samples require specialized processing to obtain clinically meaningful measurements. A major component of this processing is a form of cell subsetting known as gating. Manual gating is time-consuming and subjective. Good automatic and semi-automatic gating algorithms are very beneficial to high-throughput flow cytometry. Results: We develop a statistical procedure, named curvHDR, for automatic and semi-automatic gating. The method combines the notions of significant high negative curvature regions and highest density regions and has the ability to adapt well to human-perceived gates. The underlying principles apply to dimension of arbitrary size, although we focus on dimensions up to three. Accompanying software, compatible with contemporary flow cytometry informatics, is developed. Availability: Software for Bioconductor within R is available