Evaluation of Word and Paragraph Embeddings and Analogical Reasoning as an Alternative to Term Frequency-Inverse Document Frequency-based Classification in Support of Biocuration

This research addresses the problem, can unsupervised learning generate a representation that improves on the commonly used term frequency-inverse document frequency (TF-IDF ) representation by capturing semantic relations? The analysis measures the quality of sentence classification using term TF-IDF representations, and finds a practical upper limit to precision and recall in a biomedical text classification task (F1-score of 0.85). Arguably, one could use ontologies to supplement TF-IDF, but ontologies are sparse in coverage and costly to create. This prompts a correlated question: can unsupervised learning capture semantic relations at least as well as existing ontologies, and thus supplement existing sparse ontologies? A shallow neural network implementing the Skip-Gram algorithm is used to generate semantic vectors using a corpus of approximately 2.4 billion words. The ability to capture meaning is assessed by comparing semantic vectors generated with MESH. Results indicate that semantic vectors trained by unsupervised methods capture comparable levels of semantic features in some cases, such as amino acid (92% of similarity represented in MESH), but perform substantially poorer in more expansive topics, such as pathogenic bacteria (37.8% similarity represented in MESH). Possible explanations for this difference in performance are proposed along with a method to combine manually curated ontologies with semantic vector spaces to produce a more comprehensive representation than either alone. Semantic vectors are also used as representations for paragraphs, which, when used for classification, achieve an F1-score of 0.92. The results of classification and analogical reasoning tasks are promising but a formal model of semantic vectors, subject to the constraints of known linguistic phenomenon, is needed. This research includes initial steps for developing a formal model of semantic vectors based on a combination of linear algebra and fuzzy set theory subject to the semantic molecularism linguistic model. This research is novel in its analysis of semantic vectors applied to the biomedical domain, analysis of different performance characteristics in biomedical analogical reasoning tasks, comparison semantic relations captured by between vectors and MESH, and the initial development of a formal model of semantic vectors.

Name thesis:degree_name

Ph. D.

Level thesis:degree_level

doctoral

Discipline thesis:degree_discipline

Genetics, Bioinformatics, and Computational Biology

Department dc:contributor.department

Animal and Poultry Sciences

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2016

Author dc:creator

• Sullivan, Daniel Edward

Chair dc:contributor.committeechair

• Wattam, Alice Rebecca

Committee members dc:contributor.committeemember

• Bevan, David R.
• Hoops, Stefan
• Marathe, Madhav Vishnu

• text mining
• Machine learning
• biocuration
• linguistics
• natural language processing

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Dc Identifier Other

vt_gsexam:7665

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/80572