Graph Embedded Nonparametric Mutual Information For Supervised Dimensionality Reduction

In this paper, we propose a novel algorithm for dimensionality reduction that uses as a criterion the mutual information (MI) between the transformed data and their cor- responding class labels. The MI is a powerful criterion that can be used as a proxy to the Bayes error rate. Further- more, recent quadratic nonparametric implementations of MI are computationally efficient and do not require any prior assumptions about the class densities. We show that the quadratic nonparametric MI can be formulated as a kernel objective in the graph embedding framework. Moreover, we propose its linear equivalent as a novel linear dimensionality reduction algorithm. The derived methods are compared against the state-of-the-art dimensionality reduction algorithms with various classifiers and on various benchmark and real-life datasets. The experimental results show that nonparametric MI as an optimization objective for dimensionality reduction gives comparable and in most of the cases better results compared with other dimensionality reduction methods

Graph Embedding with Data Uncertainty

spectral-based subspace learning is a common data preprocessing step in many machine learning pipelines. The main aim is to learn a meaningful low dimensional embedding of the data. However, most subspace learning methods do not take into consideration possible measurement inaccuracies or artifacts that can lead to data with high uncertainty. Thus, learning directly from raw data can be misleading and can negatively impact the accuracy. In this paper, we propose to model artifacts in training data using probability distributions; each data point is represented by a Gaussian distribution centered at the original data point and having a variance modeling its uncertainty. We reformulate the Graph Embedding framework to make it suitable for learning from distributions and we study as special cases the Linear Discriminant Analysis and the Marginal Fisher Analysis techniques. Furthermore, we propose two schemes for modeling data uncertainty based on pair-wise distances in an unsupervised and a supervised contexts.Comment: 20 pages, 4 figure

Mitotic cell detection in H&E stained meningioma histopathology slides

Indiana University-Purdue University Indianapolis (IUPUI)Meningioma represent more than one-third of all primary central nervous system (CNS) tumors, and it can be classified into three grades according to WHO (World Health Organization) in terms of clinical aggressiveness and risk of recurrence. A key component of meningioma grades is the mitotic count, which is defined as quantifying the number of cells in the process of dividing (i.e., undergoing mitosis) at a specific point in time. Currently, mitosis counting is done manually by a pathologist looking at 10 consecutive high-power fields (HPF) on a glass slide under a microscope, which is an extremely laborious and time-consuming process. The goal of this thesis is to investigate the use of computerized methods to automate the detection of mitotic nuclei with limited labeled data. We built computational methods to detect and quantify the histological features of mitotic cells on a whole slides image which mimic the exact process of pathologist workflow. Since we do not have enough training data from meningioma slide, we learned the mitotic cell features through public available breast cancer datasets, and predicted on meingioma slide for accuracy. We use either handcrafted features that capture certain morphological, statistical, or textural attributes of mitoses or features learned with convolutional neural networks (CNN). Hand crafted features are inspired by the domain knowledge, while the data-driven VGG16 models tend to be domain agnostic and attempt to learn additional feature bases that cannot be represented through any of the handcrafted features. Our work on detection of mitotic cells shows 100% recall , 9% precision and 0.17 F1 score. The detection using VGG16 performs with 71% recall, 73% precision, and 0.77 F1 score. Finally, this research of automated image analysis could drastically increase diagnostic efficiency and reduce inter-observer variability and errors in pathology diagnosis, which would allow fewer pathologists to serve more patients while maintaining diagnostic accuracy and precision. And all these methodologies will increasingly transform practice of pathology, allowing it to mature toward a quantitative science