Formal Concept Analysis Applications in Bioinformatics

Bioinformatics is an important field that seeks to solve biological problems with the help of computation. One specific field in bioinformatics is that of genomics, the study of genes and their functions. Genomics can provide valuable analysis as to the interaction between how genes interact with their environment. One such way to measure the interaction is through gene expression data, which determines whether (and how much) a certain gene activates in a situation. Analyzing this data can be critical for predicting diseases or other biological reactions. One method used for analysis is Formal Concept Analysis (FCA), a computing technique based in partial orders that allows the user to examine the structural properties of binary data based on which subsets of the data set depend on each other. This thesis surveys, in breadth and depth, the current literature related to the use of FCA for bioinformatics, with particular focus on gene expression data. This includes descriptions of current data management techniques specific to FCA, such as lattice reduction, discretization, and variations of FCA to account for different data types. Advantages and shortcomings of using FCA for genomic investigations, as well as the feasibility of using FCA for this application are addressed. Finally, several areas for future doctoral research are proposed. Adviser: Jitender S. Deogu

Modeling group assessments by means of hesitant fuzzy linguistic term sets

Hesitant linguistic term sets have been introduced to capture the human way of reasoning using linguistic expressions involving different levels of precision. In this paper, a lattice structure is provided to the set of hesitant fuzzy linguistic term sets by means of the operations intersection and connected union. In addition, in a group decision making framework, hesitant fuzzy linguistic descriptions are defined to manage situations in which decision makers are assessing different alternatives by means of hesitant fuzzy linguistic term sets. Based on the introduced lattice structure, two distances between hesitant fuzzy linguistic descriptions are defined. These metric structures allow distances between decision makers to be computed. A centroid of the decision making group is proposed for each distance to model group representatives in the considered group decision making framework.Peer ReviewedPostprint (author's final draft

A Hierarchical Approach to Anomalous Subgroup Discovery

Understanding peculiar and anomalous behavior of machine learning models for specific data subgroups is a fundamental building block of model performance and fairness evaluation. The analysis of these data subgroups can provide useful insights into model inner working and highlight its potentially discriminatory behavior. Current approaches to subgroup exploration ignore the presence of hierarchies in the data, and can only be applied to discretized attributes. The discretization process required for continuous attributes may significantly affect the identification of relevant subgroups. We propose a hierarchical subgroup exploration technique to identify anomalous subgroup behavior at multiple granularity levels, along with a technique for the hierarchical discretization of data attributes. The hierarchical discretization produces, for each continuous attribute, a hierarchy of intervals. The subsequent hierarchical exploration can exploit data hierarchies, selecting for each attribute the optimal granularity to identify subgroups that are both anomalous, and with enough elements to be statistically and practically significant. Compared to nonhierarchical approaches, we show that our hierarchical approach is more powerful in identifying anomalous subgroups and more stable with respect to discretization and exploration parameters

Deployment, Coverage And Network Optimization In Wireless Video Sensor Networks For 3D Indoor Monitoring

As a result of extensive research over the past decade or so, wireless sensor networks (wsns) have evolved into a well established technology for industry, environmental and medical applications. However, traditional wsns employ such sensors as thermal or photo light resistors that are often modeled with simple omni-directional sensing ranges, which focus only on scalar data within the sensing environment. In contrast, the sensing range of a wireless video sensor is directional and capable of providing more detailed video information about the sensing field. Additionally, with the introduction of modern features in non-fixed focus cameras such as the pan, tilt and zoom (ptz), the sensing range of a video sensor can be further regarded as a fan-shape in 2d and pyramid-shape in 3d. Such uniqueness attributed to wireless video sensors and the challenges associated with deployment restrictions of indoor monitoring make the traditional sensor coverage, deployment and networked solutions in 2d sensing model environments for wsns ineffective and inapplicable in solving the wireless video sensor network (wvsn) issues for 3d indoor space, thus calling for novel solutions. In this dissertation, we propose optimization techniques and develop solutions that will address the coverage, deployment and network issues associated within wireless video sensor networks for a 3d indoor environment. We first model the general problem in a continuous 3d space to minimize the total number of required video sensors to monitor a given 3d indoor region. We then convert it into a discrete version problem by incorporating 3d grids, which can achieve arbitrary approximation precision by adjusting the grid granularity. Due in part to the uniqueness of the visual sensor directional sensing range, we propose to exploit the directional feature to determine the optimal angular-coverage of each deployed visual sensor. Thus, we propose to deploy the visual sensors from divergent directional angles and further extend k-coverage to ``k-angular-coverage\u27\u27, while ensuring connectivity within the network. We then propose a series of mechanisms to handle obstacles in the 3d environment. We develop efficient greedy heuristic solutions that integrate all these aforementioned considerations one by one and can yield high quality results. Based on this, we also propose enhanced depth first search (dfs) algorithms that can not only further improve the solution quality, but also return optimal results if given enough time. Our extensive simulations demonstrate the superiority of both our greedy heuristic and enhanced dfs solutions. Finally, this dissertation discusses some future research directions such as in-network traffic routing and scheduling issues

Multi Sentence Description of Complex Manipulation Action Videos

Automatic video description requires the generation of natural language statements about the actions, events, and objects in the video. An important human trait, when we describe a video, is that we are able to do this with variable levels of detail. Different from this, existing approaches for automatic video descriptions are mostly focused on single sentence generation at a fixed level of detail. Instead, here we address video description of manipulation actions where different levels of detail are required for being able to convey information about the hierarchical structure of these actions relevant also for modern approaches of robot learning. We propose one hybrid statistical and one end-to-end framework to address this problem. The hybrid method needs much less data for training, because it models statistically uncertainties within the video clips, while in the end-to-end method, which is more data-heavy, we are directly connecting the visual encoder to the language decoder without any intermediate (statistical) processing step. Both frameworks use LSTM stacks to allow for different levels of description granularity and videos can be described by simple single-sentences or complex multiple-sentence descriptions. In addition, quantitative results demonstrate that these methods produce more realistic descriptions than other competing approaches