This paper presents an annotated corpora of Assamese and English short stories for event trigger detection. This marks a pioneering endeavor in short stories, contributing to developing resources for this genre, especially in the low-resource Assamese language. In the process, 200 short stories were manually annotated in both Assamese and English. The dataset was evaluated and several models were compared for predicting events that are actually happening, i.e., realis events. However, it is expensive to develop manually annotated language resources, especially when the text requires specialist knowledge to interpret. In this regard, TagIT, an automated event annotation tool, is introduced. TagIT is designed to facilitate our objective of expanding the dataset from 200 to 1,000. The best-performing model was employed in TagIT to automate the event annotation process. Extensive experiments were conducted to evaluate the quality of the expanded dataset. This study further illustrates how the combination of an automatic annotation tool and human-in-the-loop participation significantly reduces the time needed to generate a high-quality dataset.

We introduce a generic, human-out-of-the-loop pipeline, ERLKG, to perform rapid association analysis of any biomedical entity with other existing entities from a corpora of the same domain. Our pipeline consists of a Knowledge Graph (KG) created from the Open Source CORD-19 dataset by fully automating the procedure of information extraction using SciBERT. The best latent entity representations are then found by benchnmarking different KG embedding techniques on the task of link prediction using a Graph Convolution Network Auto Encoder (GCN-AE). We demonstrate the utility of ERLKG with respect to COVID-19 through multiple qualitative evaluations. Due to the lack of a gold standard, we propose a relatively large intrinsic evaluation dataset for COVID-19 and use it for validating the top two performing KG embedding techniques. We find TransD to be the best performing KG embedding technique with Pearson and Spearman correlation scores of 0.4348 and 0.4570 respectively. We demonstrate that a considerable number of ERLKG’s top protein, chemical and disease predictions are currently in consideration for COVID-19 related research.

The task of relation classification in the biomedical domain is complex due to the presence of samples obtained from heterogeneous sources such as research articles, discharge summaries, or electronic health records. It is also a constraint for classifiers which employ manual feature engineering. In this paper, we propose a convolutional recurrent neural network (CRNN) architecture that combines RNNs and CNNs in sequence to solve this problem. The rationale behind our approach is that CNNs can effectively identify coarse-grained local features in a sentence, while RNNs are more suited for long-term dependencies. We compare our CRNN model with several baselines on two biomedical datasets, namely the i2b2-2010 clinical relation extraction challenge dataset, and the SemEval-2013 DDI extraction dataset. We also evaluate an attentive pooling technique and report its performance in comparison with the conventional max pooling method. Our results indicate that the proposed model achieves state-of-the-art performance on both datasets.

Fine-grained entity type classification (FETC) is the task of classifying an entity mention to a broad set of types. Distant supervision paradigm is extensively used to generate training data for this task. However, generated training data assigns same set of labels to every mention of an entity without considering its local context. Existing FETC systems have two major drawbacks: assuming training data to be noise free and use of hand crafted features. Our work overcomes both drawbacks. We propose a neural network model that jointly learns entity mentions and their context representation to eliminate use of hand crafted features. Our model treats training data as noisy and uses non-parametric variant of hinge loss function. Experiments show that the proposed model outperforms previous state-of-the-art methods on two publicly available datasets, namely FIGER (GOLD) and BBN with an average relative improvement of 2.69% in micro-F1 score. Knowledge learnt by our model on one dataset can be transferred to other datasets while using same model or other FETC systems. These approaches of transferring knowledge further improve the performance of respective models.

Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all event extraction methods. However many of the current approaches either rely on complex hand-crafted features or consider features only within a window. In this paper we propose a method that takes the advantage of recurrent neural network (RNN) to extract higher level features present across the sentence. Thus hidden state representation of RNN along with word and entity type embedding as features avoid relying on the complex hand-crafted features generated using various NLP toolkits. Our experiments have shown to achieve state-of-art F1-score on Multi Level Event Extraction (MLEE) corpus. We have also performed category-wise analysis of the result and discussed the importance of various features in trigger identification task.