In this paper, a new perspective is suggested for unsupervised Ontology Matching (OM) or Ontology Alignment (OA) by treating it as a translation task. Ontologies are represented as graphs, and the translation is performed from a node in the source ontology graph to a path in the target ontology graph. The proposed framework, Truveta Mapper (TM), leverages a multi-task sequence-to-sequence transformer model to perform alignment across multiple ontologies in a zero-shot, unified and end-to-end manner. Multi-tasking enables the model to implicitly learn the relationship between different ontologies via transfer-learning without requiring any explicit cross-ontology manually labeled data. This also enables the formulated framework to outperform existing solutions for both runtime latency and alignment quality. The model is pre-trained and fine-tuned only on publicly available text corpus and inner-ontologies data. The proposed solution outperforms state-of-the-art approaches, Edit-Similarity, LogMap, AML, BERTMap, and the recently presented new OM frameworks in Ontology Alignment Evaluation Initiative (OAEI22), offers log-linear complexity, and overall makes the OM task efficient and more straightforward without much post-processing involving mapping extension or mapping repair. We are open sourcing our solution.

Medical entity retrieval is an integral component for understanding and communicating information across various health systems. Current approaches tend to work well on specific medical domains but generalize poorly to unseen sub-specialties. This is of increasing concern under a public health crisis as new medical conditions and drug treatments come to light frequently. Zero-shot retrieval is challenging due to the high degree of ambiguity and variability in medical corpora, making it difficult to build an accurate similarity measure between mentions and concepts. Medical knowledge graphs (KG), however, contain rich semantics including large numbers of synonyms as well as its curated graphical structures. To take advantage of this valuable information, we propose a suite of learning tasks designed for training efficient zero-shot entity retrieval models. Without requiring any human annotation, our knowledge graph enriched architecture significantly outperforms common zero-shot benchmarks including BM25 and Clinical BERT with 7% to 30% higher recall across multiple major medical ontologies, such as UMLS, SNOMED, and ICD-10.

In graphs with rich text information, constructing expressive graph representations requires incorporating textual information with structural information. Graph embedding models are becoming more and more popular in representing graphs, yet they are faced with two issues: sampling efficiency and text utilization. Through analyzing existing models, we find their training objectives are composed of pairwise proximities, and there are large amounts of redundant node pairs in Random Walk-based methods. Besides, inferring graph structures directly from texts (also known as zero-shot scenario) is a problem that requires higher text utilization. To solve these problems, we propose a novel Text-driven Graph Embedding with Pairs Sampling (TGE-PS) framework. TGE-PS uses Pairs Sampling (PS) to generate training samples which reduces ~99% training samples and is competitive compared to Random Walk. TGE-PS uses Text-driven Graph Embedding (TGE) which adopts word- and character-level embeddings to generate node embeddings. We evaluate TGE-PS on several real-world datasets, and experimental results demonstrate that TGE-PS produces state-of-the-art results in traditional and zero-shot link prediction tasks.