The robust selection of predictive genes via a simple classifier

Identifying genes that direct the mechanism of a disease from expression data is extremely useful in understanding how that mechanism works. This in turn may lead to better diagnoses and potentially can lead to a cure for that disease. This task becomes extremely challenging when the data are characterised by only a small number of samples and a high number of dimensions, as it is often the case with gene expression data. Motivated by this challenge, we present a general framework that focuses on simplicity and data perturbation. These are the keys for the robust identification of the most predictive features in such data. Within this framework, we propose a simple selective na¨ıve Bayes classifier discovered using a global search technique, and combine it with data perturbation to increase its robustness to small sample sizes. An extensive validation of the method was carried out using two applied datasets from the field of microarrays and a simulated dataset, all confounded by small sample sizes and high dimensionality. The method has been shown capable of identifying genes previously confirmed or associated with prostate cancer and viral infections

Mathematics at the eve of a historic transition in biology

A century ago physicists and mathematicians worked in tandem and established quantum mechanism. Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. Currently, biology is undergoing a historic transition from qualitative, phenomenological and descriptive to quantitative, analytical and predictive. Mathematics, again, becomes a driving force behind this new transition in biology.Comment: 5 pages, 2 figure

EXPLAINABLE FEATURE- AND DECISION-LEVEL FUSION

Information fusion is the process of aggregating knowledge from multiple data sources to produce more consistent, accurate, and useful information than any one individual source can provide. In general, there are three primary sources of data/information: humans, algorithms, and sensors. Typically, objective data---e.g., measurements---arise from sensors. Using these data sources, applications such as computer vision and remote sensing have long been applying fusion at different levels (signal, feature, decision, etc.). Furthermore, the daily advancement in engineering technologies like smart cars, which operate in complex and dynamic environments using multiple sensors, are raising both the demand for and complexity of fusion. There is a great need to discover new theories to combine and analyze heterogeneous data arising from one or more sources. The work collected in this dissertation addresses the problem of feature- and decision-level fusion. Specifically, this work focuses on fuzzy choquet integral (ChI)-based data fusion methods. Most mathematical approaches for data fusion have focused on combining inputs relative to the assumption of independence between them. However, often there are rich interactions (e.g., correlations) between inputs that should be exploited. The ChI is a powerful aggregation tool that is capable modeling these interactions. Consider the fusion of m sources, where there are 2m unique subsets (interactions); the ChI is capable of learning the worth of each of these possible source subsets. However, the complexity of fuzzy integral-based methods grows quickly, as the number of trainable parameters for the fusion of m sources scales as 2m. Hence, we require a large amount of training data to avoid the problem of over-fitting. This work addresses the over-fitting problem of ChI-based data fusion with novel regularization strategies. These regularization strategies alleviate the issue of over-fitting while training with limited data and also enable the user to consciously push the learned methods to take a predefined, or perhaps known, structure. Also, the existing methods for training the ChI for decision- and feature-level data fusion involve quadratic programming (QP). The QP-based learning approach for learning ChI-based data fusion solutions has a high space complexity. This has limited the practical application of ChI-based data fusion methods to six or fewer input sources. To address the space complexity issue, this work introduces an online training algorithm for learning ChI. The online method is an iterative gradient descent approach that processes one observation at a time, enabling the applicability of ChI-based data fusion on higher dimensional data sets. In many real-world data fusion applications, it is imperative to have an explanation or interpretation. This may include providing information on what was learned, what is the worth of individual sources, why a decision was reached, what evidence process(es) were used, and what confidence does the system have on its decision. However, most existing machine learning solutions for data fusion are black boxes, e.g., deep learning. In this work, we designed methods and metrics that help with answering these questions of interpretation, and we also developed visualization methods that help users better understand the machine learning solution and its behavior for different instances of data