A study on developing novel methods for relation extraction

Relation Extraction (RE) is a task of Natural Language Processing (NLP) to detect and classify the relations between two entities. Relation extraction in the biomedical and scientific literature domain is challenging as text can contain multiple pairs of entities in the same instance. During the course of this research, we developed an RE framework (RelEx), which consists of five main RE paradigms: rule-based, machine learning-based, Convolutional Neural Network (CNN)-based, Bidirectional Encoder Representations from Transformers (BERT)-based, and Graph Convolutional Networks (GCNs)-based approaches. RelEx\u27s rule-based approach uses co-location information of the entities to determine whether a relation exists between a selected entity and the other entities. RelEx\u27s machine learning-based approach consists of traditional feature representations into traditional machine learning algorithms. RelEx\u27s CNN-based approach consists of three CNN architectures: Segment-CNN, single-label Sentence-CNN, and multi-label Sentence-CNN. RelEx\u27s BERT-based approach utilizes BERT\u27s contextualized word embeddings into a feed-forward neural network. Finally, RelEx\u27s GCN-based approach consists of two GCN-based architectures: GCN-Vanilla, GCN-BERT. We evaluated variations of these approaches in two different domains across four distinct relation types. Overall our findings showed that the rule-based approach is applicable for data with fewer instances in the training data. In contrast, the CNN-based, BERT-based, and GCN-based approaches perform better with labeled data with many training instances. These approaches automatically identify patterns in the data efficiently, whereas rule-based approaches require expert knowledge to generate rules. The CNN-based, BERT-based approaches capture the local contextual information within a sentence or document by embedding both semantic and syntactic information in a learned representation. However, their ability to capture the long-range dependency global information in a text is limited. GCN-based approaches capture the global association information by performing convolution operations on neighbor nodes in a graph and incorporating information from neighbors. Combining GCN with BERT integrates the local contextual and global association information of the words and generates better representations for the words

Table Search Using a Deep Contextualized Language Model

Pretrained contextualized language models such as BERT have achieved impressive results on various natural language processing benchmarks. Benefiting from multiple pretraining tasks and large scale training corpora, pretrained models can capture complex syntactic word relations. In this paper, we use the deep contextualized language model BERT for the task of ad hoc table retrieval. We investigate how to encode table content considering the table structure and input length limit of BERT. We also propose an approach that incorporates features from prior literature on table retrieval and jointly trains them with BERT. In experiments on public datasets, we show that our best approach can outperform the previous state-of-the-art method and BERT baselines with a large margin under different evaluation metrics.Comment: Accepted at SIGIR 2020 (Long

Named Entity Recognition in Spanish Biomedical Literature: Short Review and Bert Model

Named Entity Recognition (NER) is the rst step for knowledge acquisition when we deal with an unknown corpus of texts. Having received these entities, we have an opportunity to form parameters space and to solve problems of text mining as concept normalization, speech recognition, etc. The recent advances in NER are related to the technology of word embeddings, which transforms text to the form being effective for Deep Learning. In the paper, we show how NER detects pharmacological substances, compounds, and proteins in the dataset obtained from the Spanish Clinical Case Corpus (SPACCC). To achieve this goal, we use contextualized word embeddings based on BERT language representation, which shows better results than the standard word embeddings