Vinh Nguyen

Goonmeet Bajaj, Vinh Nguyen, Thilini Wijesiriwardene et al.

The current UMLS (Unified Medical Language System) Metathesaurus construction process for integrating over 200 biomedical source vocabularies is expensive and error-prone as it relies on the lexical algorithms and human editors for deciding if the two biomedical terms are synonymous. Recent advances in Natural Language Processing such as Transformer models like BERT and its biomedical variants with contextualized word embeddings have achieved state-of-the-art (SOTA) performance on downstream tasks. We aim to validate if these approaches using the BERT models can actually outperform the existing approaches for predicting synonymy in the UMLS Metathesaurus. In the existing Siamese Networks with LSTM and BioWordVec embeddings, we replace the BioWordVec embeddings with the biomedical BERT embeddings extracted from each BERT model using different ways of extraction. In the Transformer architecture, we evaluate the use of the different biomedical BERT models that have been pre-trained using different datasets and tasks. Given the SOTA performance of these BERT models for other downstream tasks, our experiments yield surprisingly interesting results: (1) in both model architectures, the approaches employing these biomedical BERT-based models do not outperform the existing approaches using Siamese Network with BioWordVec embeddings for the UMLS synonymy prediction task, (2) the original BioBERT large model that has not been pre-trained with the UMLS outperforms the SapBERT models that have been pre-trained with the UMLS, and (3) using the Siamese Networks yields better performance for synonymy prediction when compared to using the biomedical BERT models.

Vinh Nguyen, Amit Sheth

Logical inference, an integral feature of the Semantic Web, is the process of deriving new triples by applying entailment rules on knowledge bases. The entailment rules are determined by the model-theoretic semantics. Incorporating context of an RDF triple (e.g., provenance, time, and location) into the inferencing process requires the formal semantics to be capable of describing the context of RDF triples also in the form of triples, or in other words, RDF contextual triples about triples. The formal semantics should also provide the rules that could entail new contextual triples about triples. In this paper, we propose the first inferencing mechanism that allows context of RDF triples, represented in the form of RDF triples about triples, to be the first-class citizens in the model-theoretic semantics and in the logical rules. Our inference mechanism is well-formalized with all new concepts being captured in the model-theoretic semantics. This formal semantics also allows us to derive a new set of entailment rules that could entail new contextual triples about triples. To demonstrate the feasibility and the scalability of the proposed mechanism, we implement a new tool in which we transform the existing knowledge bases to our representation of RDF triples about triples and provide the option for this tool to compute the inferred triples for the proposed rules. We evaluate the computation of the proposed rules on a large scale using various real-world knowledge bases such as Bio2RDF NCBI Genes and DBpedia. The results show that the computation of the inferred triples can be highly scalable. On average, one billion inferred triples adds 5-6 minutes to the overall transformation process. NCBI Genes, with 20 billion triples in total, took only 232 minutes for the transformation of 12 billion triples and added 42 minutes for inferring 8 billion triples to the overall process.

Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan et al.

The Singleton Property (SP) approach has been proposed for representing and querying metadata about RDF triples such as provenance, time, location, and evidence. In this approach, one singleton property is created to uniquely represent a relationship in a particular context, and in general, generates a large property hierarchy in the schema. It has become the subject of important questions from Semantic Web practitioners. Can an existing reasoner recognize the singleton property triples? And how? If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples? Or would the large property hierarchy affect the reasoners in some way? We address these questions in this paper and present our study about the reasoning aspects of the singleton properties. We propose a simple mechanism to enable existing reasoners to recognize the singleton property triples, as well as to infer the data triples described by the singleton property triples. We evaluate the effect of the singleton property triples in the reasoning processes by comparing the performance on RDF datasets with and without singleton properties. Our evaluation uses as benchmark the LUBM datasets and the LUBM-SP datasets derived from LUBM with temporal information added through singleton properties.