Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis

Four-Fold Formal Concept Analysis Based on Complete Idempotent Semifields

Formal Concept Analysis (FCA) is a well-known supervised boolean data-mining technique rooted in Lattice and Order Theory, that has several extensions to, e.g., fuzzy and idempotent semirings. At the heart of FCA lies a Galois connection between two powersets. In this paper we extend the FCA formalism to include all four Galois connections between four different semivectors spaces over idempotent semifields, at the same time. The result is K¯-four-fold Formal Concept Analysis (K¯-4FCA) where K¯ is the idempotent semifield biasing the analysis. Since complete idempotent semifields come in dually-ordered pairs—e.g., the complete max-plus and min-plus semirings—the basic construction shows dual-order-, row–column- and Galois-connection-induced dualities that appear simultaneously a number of times to provide the full spectrum of variability. Our results lead to a fundamental theorem of K¯-four-fold Formal Concept Analysis that properly defines quadrilattices as 4-tuples of (order-dually) isomorphic lattices of vectors and discuss its relevance vis-à-vis previous formal conceptual analyses and some affordances of their results.

Screening and Identification of Differentially Expressed Genes Expressed among Left and Right Colon Adenocarcinoma

Purpose

Colon adenocarcinoma (COAD) is the third most common malignancy globally and is further categorized as left colon adenocarcinoma (LCOAD) or right colon adenocarcinoma (RCOAD) depending on the location of the primary tumor. The therapeutic outcome and long-term prognosis for patients with COAD are less than satisfactory, and this may be associated with tumor location. Therefore, it is important to investigate the genetic differences in COAD at different sites. Patients and Methods. Public data associated with COAD were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using R software (version 3.5.3), and functional annotation of DEGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A protein-protein interaction network was constructed, hub genes were identified and analyzed, and data mining using Gene Expression Profiling Interactive Analysis (GEPIA) was conducted.

Results

A total of 286 DEGs were identified between LCOAD and RCOAD. Additionally, 10 hub genes associated with COAD at different locations were screened, namely, CDKN2A, IGF1R, MDM2, SMAD3, SLC2A1, GRM5, PLCB4, FGFR1, UBE2V2, and TNFRSF10B. The expression of cyclin-dependent kinase inhibitor 2A (CDKN2A) and solute carrier family 2 member 1 (SLC2A1) was significantly associated with pathological stage (P < 0.05). COAD patients with high expression levels of CDKN2A exhibited poorer overall survival (OS) times than those with low expression levels (P < 0.05).

Conclusion

CDKN2A expression was significantly different between LCOAD and RCOAD and was closely related to the prognosis of COAD. It is of great value for further understanding of the pathogenesis of LCOAD and RCOAD.

Extracting Conceptual Relationships and Inducing Concept Lattices from Unstructured Text

Concept and relationship extraction from unstructured text data plays a key role in meaning aware computing paradigms, which make computers intelligent by helping them learn, interpret, and synthesis information. These concepts and relationships leverage knowledge in the form of ontological structures, which is the backbone of semantic web. This paper proposes a framework that extracts concepts and relationships from unstructured text data and then learns lattices that connect concepts and relationships. The proposed framework uses an off-the-shelf tool for identifying common concepts from a plain text corpus and then implements machine learning algorithms for classifying common relations that connect those concepts. Formal concept analysis is then used for generating concept lattices, which is a proven and principled method of creating formal ontologies that aid machines to learn things. A rigorous and structured experimental evaluation of the proposed method on real-world datasets has been conducted. The results show that the newly proposed framework outperforms state-of-the-art approaches in concept extraction and lattice generation.