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

LearnFCA: A Fuzzy FCA and Probability Based Approach for Learning and Classification

Formal concept analysis(FCA) is a mathematical theory based on lattice and order theory used for data analysis and knowledge representation. Over the past several years, many of its extensions have been proposed and applied in several domains including data mining, machine learning, knowledge management, semantic web, software development, chemistry ,biology, medicine, data analytics, biology and ontology engineering. This thesis reviews the state-of-the-art of theory of Formal Concept Analysis(FCA) and its various extensions that have been developed and well-studied in the past several years. We discuss their historical roots, reproduce the original definitions and derivations with illustrative examples. Further, we provide a literature review of it’s applications and various approaches adopted by researchers in the areas of dataanalysis, knowledge management with emphasis to data-learning and classification problems. We propose LearnFCA, a novel approach based on FuzzyFCA and probability theory for learning and classification problems. LearnFCA uses an enhanced version of FuzzyLattice which has been developed to store class labels and probability vectors and has the capability to be used for classifying instances with encoded and unlabelled features. We evaluate LearnFCA on encodings from three datasets - mnist, omniglot and cancer images with interesting results and varying degrees of success. Adviser: Dr Jitender Deogu

LEARNFCA: A FUZZY FCA AND PROBABILITY BASED APPROACH FOR LEARNING AND CLASSIFICATION

Formal concept analysis(FCA) is a mathematical theory based on lattice and order theory used for data analysis and knowledge representation. Over the past several years, many of its extensions have been proposed and applied in several domains including data mining, machine learning, knowledge management, semantic web, software development, chemistry ,biology, medicine, data analytics, biology and ontology engineering. This thesis reviews the state-of-the-art of theory of Formal Concept Analysis(FCA) and its various extensions that have been developed and well-studied in the past several years. We discuss their historical roots, reproduce the original definitions and derivations with illustrative examples. Further, we provide a literature review of it’s applications and various approaches adopted by researchers in the areas of dataanalysis, knowledge management with emphasis to data-learning and classification problems. We propose LearnFCA, a novel approach based on FuzzyFCA and probability theory for learning and classification problems. LearnFCA uses an enhanced version of FuzzyLattice which has been developed to store class labels and probability vectors and has the capability to be used for classifying instances with encoded and unlabelled features. We evaluate LearnFCA on encodings from three datasets - mnist, omniglot and cancer images with interesting results and varying degrees of success. Adviser: Jitender Deogu

Concept learning consistency under three‑way decision paradigm

Concept Mining is one of the main challenges both in Cognitive Computing and in Machine Learning. The ongoing improvement of solutions to address this issue raises the need to analyze whether the consistency of the learning process is preserved. This paper addresses a particular problem, namely, how the concept mining capability changes under the reconsideration of the hypothesis class. The issue will be raised from the point of view of the so-called Three-Way Decision (3WD) paradigm. The paradigm provides a sound framework to reconsider decision-making processes, including those assisted by Machine Learning. Thus, the paper aims to analyze the influence of 3WD techniques in the Concept Learning Process itself. For this purpose, we introduce new versions of the Vapnik-Chervonenkis dimension. Likewise, to illustrate how the formal approach can be instantiated in a particular model, the case of concept learning in (Fuzzy) Formal Concept Analysis is considered.This work is supported by State Investigation Agency (Agencia Estatal de Investigación), project PID2019-109152GB-100/AEI/10.13039/501100011033. We acknowledge the reviewers for their suggestions and guidance on additional references that have enriched our paper. Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature

Fuzzy algebras of concepts

Preconcepts are basic units of knowledge that form the basis of formal concepts in formal concept analysis (FCA). This paper investigates the relations among different kinds of preconcepts, such as protoconcepts, meet and join-semiconcepts and formal concepts. The first contribution of this paper, is to present a fuzzy powerset lattice gradation, that coincides with the preconcept lattice at its 1-cut. The second and more significant contribution, is to introduce a preconcept algebra gradation that yields different algebras for protoconcepts, semiconcepts, and concepts at different cuts. This result reveals new insights into the structure and properties of the different categories of preconcepts.Partial funding for open access charge: Universidad de Málag