Computer Science and Engineering, Department of


First Advisor

Jitender S. Deogun

Date of this Version

Winter 11-10-2020


Roscoe, S. (2020). Formal Concept Analysis Applications in Bioinformatics. M.S. thesis. University of Nebraska-Lincoln


A THESIS. Presented to the Faculty of The Graduate College at the University of Nebraska. In Partial Fulfilment of Requirements for the Degree of Master of Science. Major: Computer Science. Under the Supervision of Professor Jitender S. Deogun. Lincoln, Nebraska. November, 2020

Copyright © 2020 Sarah R. Roscoe


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. Deogun