We present Disease Network Constructor (DNC), a system that extracts and visualizes a disease network, in which nodes are entities such as diseases, proteins, and genes, and edges represent regulation relation. We focused on the disease network derived through regulation events found in scientific articles on idiopathic pulmonary fibrosis (IPF). The front-end web-base user interface of DNC includes two-dimensional (2D) and 3D visualizations of the constructed disease network. The back-end system of DNC includes several natural language processing (NLP) techniques to process biomedical text including BERT-based tokenization on the basis of Bidirectional Encoder Representations from Transformers (BERT), flat and nested named entity recognition (NER), candidate generation and candidate ranking for entity linking (EL) or, relation extraction (RE), and event extraction (EE) tasks. We evaluated the end-to-end EL and end-to-end nested EE systems to determine the DNC’s back-endimplementation performance. To the best of our knowledge, this is the first attempt that addresses neural NER, EL, RE, and EE tasks in an end-to-end manner that constructs a path-way visualization from events, which we name Disease Network Constructor. The demonstration video can be accessed from https://youtu.be/rFhWwAgcXE8. We release an online system for end users and the source code is available at https://github.com/aistairc/PRISM-APIs/.

We present BiomedCurator1, a web application that extracts the structured data from scientific articles in PubMed and ClinicalTrials.gov. BiomedCurator uses state-of-the-art natural language processing techniques to fill the fields pre-selected by domain experts in the relevant biomedical area. The BiomedCurator web application includes: text generation based model for relation extraction, entity detection and recognition, text classification model for extracting several fields, information retrieval from external knowledge base to retrieve IDs, and a pattern-based extraction approach that can extract several fields using regular expressions over the PubMed and ClinicalTrials.gov datasets. Evaluation results show that different approaches of BiomedCurator web application system are effective for automatic data curation in the biomedical domain.

We present a biomedical entity linking (EL) system BENNERD that detects named enti- ties in text and links them to the unified medical language system (UMLS) knowledge base (KB) entries to facilitate the corona virus disease 2019 (COVID-19) research. BEN- NERD mainly covers biomedical domain, es- pecially new entity types (e.g., coronavirus, vi- ral proteins, immune responses) by address- ing CORD-NER dataset. It includes several NLP tools to process biomedical texts includ- ing tokenization, flat and nested entity recog- nition, and candidate generation and rank- ing for EL that have been pre-trained using the CORD-NER corpus. To the best of our knowledge, this is the first attempt that ad- dresses NER and EL on COVID-19-related entities, such as COVID-19 virus, potential vaccines, and spreading mechanism, that may benefit research on COVID-19. We release an online system to enable real-time entity annotation with linking for end users. We also release the manually annotated test set and CORD-NERD dataset for leveraging EL task. The BENNERD system is available at https://aistairc.github.io/BENNERD/.

We present a neural exhaustive approach that addresses named entity recognition (NER) and relation recognition (RE), for the entity and re- lation recognition over the wet-lab protocols shared task. We introduce BERT-based neural exhaustive approach that enumerates all pos- sible spans as potential entity mentions and classifies them into entity types or no entity with deep neural networks to address NER. To solve relation extraction task, based on the NER predictions or given gold mentions we create all possible trigger-argument pairs and classify them into relation types or no relation. In NER task, we achieved 76.60% in terms of F-score as third rank system among the partic- ipated systems. In relation extraction task, we achieved 80.46% in terms of F-score as the top system in the relation extraction or recognition task. Besides we compare our model based on the wet lab protocols corpus (WLPC) with the WLPC baseline and dynamic graph-based in- formation extraction (DyGIE) systems.

We present a neural pipeline approach that performs named entity recognition (NER) and concept indexing (CI), which links them to concept unique identifiers (CUIs) in a knowledge base, for the PharmaCoNER shared task on pharmaceutical drugs and chemical entities. We proposed a neural NER model that captures the surrounding semantic information of a given sequence by capturing the forward- and backward-context of bidirectional LSTM (Bi-LSTM) output of a target span using contextual span representation-based exhaustive approach. The NER model enumerates all possible spans as potential entity mentions and classify them into entity types or no entity with deep neural networks. For representing span, we compare several different neural network architectures and their ensembling for the NER model. We then perform dictionary matching for CI and, if there is no matching, we further compute similarity scores between a mention and CUIs using entity embeddings to assign the CUI with the highest score to the mention. We evaluate our approach on the two sub-tasks in the shared task. Among the five submitted runs, the best run for each sub-task achieved the F-score of 86.76% on Sub-task 1 (NER) and the F-score of 79.97% (strict) on Sub-task 2 (CI).

We propose a simple deep neural model for nested named entity recognition (NER). Most NER models focused on flat entities and ignored nested entities, which failed to fully capture underlying semantic information in texts. The key idea of our model is to enumerate all possible regions or spans as potential entity mentions and classify them with deep neural networks. To reduce the computational costs and capture the information of the contexts around the regions, the model represents the regions using the outputs of shared underlying bidirectional long short-term memory. We evaluate our exhaustive model on the GENIA and JNLPBA corpora in biomedical domain, and the results show that our model outperforms state-of-the-art models on nested and flat NER, achieving 77.1% and 78.4% respectively in terms of F-score, without any external knowledge resources.