To combat COVID-19, both clinicians and scientists need to digest the vast amount of relevant biomedical knowledge in literature to understand the disease mechanism and the related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports.

Named Entity Recognition (NER) and Entity Linking (EL) play an essential role in voice assistant interaction, but are challenging due to the special difficulties associated with spoken user queries. In this paper, we propose a novel architecture that jointly solves the NER and EL tasks by combining them in a joint reranking module. We show that our proposed framework improves NER accuracy by up to 3.13% and EL accuracy by up to 3.6% in F1 score. The features used also lead to better accuracies in other natural language understanding tasks, such as domain classification and semantic parsing.

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).

We study the problem of training named entity recognition (NER) models using only distantly-labeled data, which can be automatically obtained by matching entity mentions in the raw text with entity types in a knowledge base. The biggest challenge of distantly-supervised NER is that the distant supervision may induce incomplete and noisy labels, rendering the straightforward application of supervised learning ineffective. In this paper, we propose (1) a noise-robust learning scheme comprised of a new loss function and a noisy label removal step, for training NER models on distantly-labeled data, and (2) a self-training method that uses contextualized augmentations created by pre-trained language models to improve the generalization ability of the NER model. On three benchmark datasets, our method achieves superior performance, outperforming existing distantly-supervised NER models by significant margins.

Traditional search engines for life sciences (e.g., PubMed) are designed for document retrieval and do not allow direct retrieval of specific statements. Some of these statements may serve as textual evidence that is key to tasks such as hypothesis generation and new finding validation. We present EVIDENCEMINER, a web-based system that lets users query a natural language statement and automatically retrieves textual evidence from a background corpora for life sciences. EVIDENCEMINER is constructed in a completely automated way without any human effort for training data annotation. It is supported by novel data-driven methods for distantly supervised named entity recognition and open information extraction. The entities and patterns are pre-computed and indexed offline to support fast online evidence retrieval. The annotation results are also highlighted in the original document for better visualization. EVIDENCEMINER also includes analytic functionalities such as the most frequent entity and relation summarization. EVIDENCEMINER can help scientists uncover important research issues, leading to more effective research and more in-depth quantitative analysis. The system of EVIDENCEMINER is available at https://evidenceminer.firebaseapp.com/.

Combining the virtues of probability graphic models and neural networks, Conditional Variational Auto-encoder (CVAE) has shown promising performance in applications such as response generation. However, existing CVAE-based models often generate responses from a single latent variable which may not be sufficient to model high variability in responses. To solve this problem, we propose a novel model that sequentially introduces a series of latent variables to condition the generation of each word in the response sequence. In addition, the approximate posteriors of these latent variables are augmented with a backward Recurrent Neural Network (RNN), which allows the latent variables to capture long-term dependencies of future tokens in generation. To facilitate training, we supplement our model with an auxiliary objective that predicts the subsequent bag of words. Empirical experiments conducted on Opensubtitle and Reddit datasets show that the proposed model leads to significant improvement on both relevance and diversity over state-of-the-art baselines.

Temporality is crucial in understanding the course of clinical events from a patient’s electronic health recordsand temporal processing is becoming more and more important for improving access to content.SemEval 2017 Task 12 (Clinical TempEval) addressed this challenge using the THYME corpus, a corpus of clinical narratives annotated with a schema based on TimeML2 guidelines. We developed and evaluated approaches for: extraction of temporal expressions (TIMEX3) and EVENTs; EVENT attributes; document-time relations. Our approach is a hybrid model which is based on rule based methods, semi-supervised learning, and semantic features with addition of manually crafted rules.