Genetic heterogeneity analysis using genetic algorithm and network science

Through genome-wide association studies (GWAS), disease susceptible genetic variables can be identified by comparing the genetic data of individuals with and without a specific disease. However, the discovery of these associations poses a significant challenge due to genetic heterogeneity and feature interactions. Genetic variables intertwined with these effects often exhibit lower effect-size, and thus can be difficult to be detected using machine learning feature selection methods. To address these challenges, this paper introduces a novel feature selection mechanism for GWAS, named Feature Co-selection Network (FCSNet). FCS-Net is designed to extract heterogeneous subsets of genetic variables from a network constructed from multiple independent feature selection runs based on a genetic algorithm (GA), an evolutionary learning algorithm. We employ a non-linear machine learning algorithm to detect feature interaction. We introduce the Community Risk Score (CRS), a synthetic feature designed to quantify the collective disease association of each variable subset. Our experiment showcases the effectiveness of the utilized GA-based feature selection method in identifying feature interactions through synthetic data analysis. Furthermore, we apply our novel approach to a case-control colorectal cancer GWAS dataset. The resulting synthetic features are then used to explain the genetic heterogeneity in an additional case-only GWAS dataset

A contribution to the incorporation of sociability and creativity skills to computers and robots

This dissertation contains the research and work completed by the PhD candidate on the incorporation of sociability and creativity skills to computers and robots. Both skills can be directly related with empathy, which is the ability to understand and share the feelings of another. In this form, this research can be contextualized in the framework of recent developments towards the achievement of empathy machines. The first challenge at hands refers to designing pioneering techniques based on the use of social robots to improve user experience interacting with them. In particular, research focus is on eliminating or minimizing pain and anxiety as well as loneliness and stress of long-term hospitalized child patients. This challenge is approached by developing a cloud-based robotics architecture to effectively develop complex tasks related to hospitalized children assistance. More specifically, a multiagent learning system is introduced based on a combination of machine learning and cloud computing using low-cost robots (Innvo labs's Pleo rb). Moreover, a wireless communication system is also developed for the Pleo robot in order to help the health professional who conducts therapy with the child, monitoring, understanding, and controlling Pleo behavior at any moment. As a second challenge, a new formulation of the concept of creativity is proposed in order to empower computers with. Based on previous well established theories from Boden and Wiggins, this thesis redefines the formal mechanism of exploratory and transformational creativity in a way which facilitates the computational implementation of these mechanisms in Creativity Support Systems. The proposed formalization is applied and validated on two real cases: the first, about chocolate designing, in which a novel and flavorful combination of chocolate and fruit is generated. The second case is about the composition of a single voice tune of reel using ABC notation

A contribution to the incorporation of sociability and creativity skills to computers and robots

This dissertation contains the research and work completed by the PhD candidate on the incorporation of sociability and creativity skills to computers and robots. Both skills can be directly related with empathy, which is the ability to understand and share the feelings of another. In this form, this research can be contextualized in the framework of recent developments towards the achievement of empathy machines. The first challenge at hands refers to designing pioneering techniques based on the use of social robots to improve user experience interacting with them. In particular, research focus is on eliminating or minimizing pain and anxiety as well as loneliness and stress of long-term hospitalized child patients. This challenge is approached by developing a cloud-based robotics architecture to effectively develop complex tasks related to hospitalized children assistance. More specifically, a multiagent learning system is introduced based on a combination of machine learning and cloud computing using low-cost robots (Innvo labs's Pleo rb). Moreover, a wireless communication system is also developed for the Pleo robot in order to help the health professional who conducts therapy with the child, monitoring, understanding, and controlling Pleo behavior at any moment. As a second challenge, a new formulation of the concept of creativity is proposed in order to empower computers with. Based on previous well established theories from Boden and Wiggins, this thesis redefines the formal mechanism of exploratory and transformational creativity in a way which facilitates the computational implementation of these mechanisms in Creativity Support Systems. The proposed formalization is applied and validated on two real cases: the first, about chocolate designing, in which a novel and flavorful combination of chocolate and fruit is generated. The second case is about the composition of a single voice tune of reel using ABC notation.Postprint (published version

Information Extraction on Para-Relational Data.

Para-relational data (such as spreadsheets and diagrams) refers to a type of nearly relational data that shares the important qualities of relational data but does not present itself in a relational format. Para-relational data often conveys highly valuable information and is widely used in many different areas. If we can convert para-relational data into the relational format, many existing tools can be leveraged for a variety of interesting applications, such as data analysis with relational query systems and data integration applications. This dissertation aims to convert para-relational data into a high-quality relational form with little user assistance. We have developed four standalone systems, each addressing a specific type of para-relational data. Senbazuru is a prototype spreadsheet database management system that extracts relational information from a large number of spreadsheets. Anthias is an extension of the Senbazuru system to convert a broader range of spreadsheets into a relational format. Lyretail is an extraction system to detect long-tail dictionary entities on webpages. Finally, DiagramFlyer is a web-based search system that obtains a large number of diagrams automatically extracted from web-crawled PDFs. Together, these four systems demonstrate that converting para-relational data into the relational format is possible today, and also suggest directions for future systems.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120853/1/chenzhe_1.pd

Automatic Extraction and Assessment of Entities from the Web

The search for information about entities, such as people or movies, plays an increasingly important role on the Web. This information is still scattered across many Web pages, making it more time consuming for a user to find all relevant information about an entity. This thesis describes techniques to extract entities and information about these entities from the Web, such as facts, opinions, questions and answers, interactive multimedia objects, and events. The findings of this thesis are that it is possible to create a large knowledge base automatically using a manually-crafted ontology. The precision of the extracted information was found to be between 75–90 % (facts and entities respectively) after using assessment algorithms. The algorithms from this thesis can be used to create such a knowledge base, which can be used in various research fields, such as question answering, named entity recognition, and information retrieval

Fine-grained Subjectivity and Sentiment Analysis: Recognizing the intensity, polarity, and attitudes of private states

Private states (mental and emotional states) are part of the information that is conveyed in many forms of discourse. News articles often report emotional responses to news stories; editorials, reviews, and weblogs convey opinions and beliefs. This dissertation investigates the manual and automatic identification of linguistic expressions of private states in a corpus of news documents from the world press. A term for the linguistic expression of private states is subjectivity.The conceptual representation of private states used in this dissertation is that of Wiebe et al. (2005). As part of this research, annotators are trained to identify expressions of private states and their properties, such as the source and the intensity of the private state. This dissertation then extends the conceptual representation of private states to better model the attitudes and targets of private states. The inter-annotator agreement studies conducted for this dissertation show that the various concepts in the original and extended representation of private states can be reliably annotated.Exploring the automatic recognition of various types of private states is also a large part of this dissertation. Experiments are conducted that focus on three types of fine-grained subjectivity analysis: recognizing the intensity of clauses and sentences, recognizing the contextual polarity of words and phrases, and recognizing the attribution levels where sentiment and arguing attitudes are expressed. Various supervised machine learning algorithms are used to train automatic systems to perform each of these tasks. These experiments result in automatic systems for performing fine-grained subjectivity analysis that significantly outperform baseline systems

Controlled self-organisation using learning classifier systems

The complexity of technical systems increases, breakdowns occur quite often. The mission of organic computing is to tame these challenges by providing degrees of freedom for self-organised behaviour. To achieve these goals, new methods have to be developed. The proposed observer/controller architecture constitutes one way to achieve controlled self-organisation. To improve its design, multi-agent scenarios are investigated. Especially, learning using learning classifier systems is addressed

Applied Cognitive Sciences

Cognitive science is an interdisciplinary field in the study of the mind and intelligence. The term cognition refers to a variety of mental processes, including perception, problem solving, learning, decision making, language use, and emotional experience. The basis of the cognitive sciences is the contribution of philosophy and computing to the study of cognition. Computing is very important in the study of cognition because computer-aided research helps to develop mental processes, and computers are used to test scientific hypotheses about mental organization and functioning. This book provides a platform for reviewing these disciplines and presenting cognitive research as a separate discipline