Ashish Anand


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ERLKG: Entity Representation Learning and Knowledge Graph based association analysis of COVID-19 through mining of unstructured biomedical corpora
Sayantan Basu | Sinchani Chakraborty | Atif Hassan | Sana Siddique | Ashish Anand
Proceedings of the First Workshop on Scholarly Document Processing

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.


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Learning local and global contexts using a convolutional recurrent network model for relation classification in biomedical text
Desh Raj | Sunil Sahu | Ashish Anand
Proceedings of the 21st Conference on Computational Natural Language Learning (CoNLL 2017)

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.

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Fine-Grained Entity Type Classification by Jointly Learning Representations and Label Embeddings
Abhishek Abhishek | Ashish Anand | Amit Awekar
Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 1, Long Papers

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.

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Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models
Rahul V S S Patchigolla | Sunil Sahu | Ashish Anand
BioNLP 2017

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.

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Investigating how well contextual features are captured by bi-directional recurrent neural network models
Kushal Chawla | Sunil Kumar Sahu | Ashish Anand
Proceedings of the 14th International Conference on Natural Language Processing (ICON-2017)


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Recurrent neural network models for disease name recognition using domain invariant features
Sunil Sahu | Ashish Anand
Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

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Relation extraction from clinical texts using domain invariant convolutional neural network
Sunil Sahu | Ashish Anand | Krishnadev Oruganty | Mahanandeeshwar Gattu
Proceedings of the 15th Workshop on Biomedical Natural Language Processing


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Evaluating distributed word representations for capturing semantics of biomedical concepts
Muneeb TH | Sunil Sahu | Ashish Anand
Proceedings of BioNLP 15