Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision (KRISS) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces KRISSBERT, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy. We released KRISSBERT at https://aka.ms/krissbert
Scientific literature analysis needs fine-grained named entity recognition (NER) to provide a wide range of information for scientific discovery. For example, chemistry research needs to study dozens to hundreds of distinct, fine-grained entity types, making consistent and accurate annotation difficult even for crowds of domain experts. On the other hand, domain-specific ontologies and knowledge bases (KBs) can be easily accessed, constructed, or integrated, which makes distant supervision realistic for fine-grained chemistry NER. In distant supervision, training labels are generated by matching mentions in a document with the concepts in the knowledge bases (KBs). However, this kind of KB-matching suffers from two major challenges: incomplete annotation and noisy annotation. We propose ChemNER, an ontology-guided, distantly-supervised method for fine-grained chemistry NER to tackle these challenges. It leverages the chemistry type ontology structure to generate distant labels with novel methods of flexible KB-matching and ontology-guided multi-type disambiguation. It significantly improves the distant label generation for the subsequent sequence labeling model training. We also provide an expert-labeled, chemistry NER dataset with 62 fine-grained chemistry types (e.g., chemical compounds and chemical reactions). Experimental results show that ChemNER is highly effective, outperforming substantially the state-of-the-art NER methods (with .25 absolute F1 score improvement).
Open-domain question answering aims at locating the answers to user-generated questions in massive collections of documents. Retriever-readers and knowledge graph approaches are two big families of solutions to this task. A retriever-reader first applies information retrieval techniques to locate a few passages that are likely to be relevant, and then feeds the retrieved text to a neural network reader to extract the answer. Alternatively, knowledge graphs can be constructed and queried to answer users’ questions. We propose an algorithm with a novel reader-retriever design that differs from both families. Our reader-retriever first uses an offline reader to read the corpus and generate collections of all answerable questions associated with their answers, and then uses an online retriever to respond to user queries by searching the pre-constructed question spaces for answers that are most likely to be asked in the given way. We further combine one retriever-reader and two reader-retrievers into a hybrid model called R6 for the best performance. Experiments with two large-scale public datasets show that R6 achieves state-of-the-art accuracy.