In this paper, we propose a general framework for mitigating the disparities of the predicted classes with respect to secondary attributes within the data (e.g., race, gender etc.). Our proposed method involves learning a multi-objective function that in addition to learning the primary objective of predicting the primary class labels from the data, also employs a clustering-based heuristic to minimize the disparities of the class label distribution with respect to the cluster memberships, with the assumption that each cluster should ideally map to a distinct combination of attribute values. Experiments demonstrate effective mitigation of cognitive biases on a benchmark dataset without the use of annotations of secondary attribute values (the zero-shot case) or with the use of a small number of attribute value annotations (the few-shot case).
This paper studies the end-to-end construction of an NLP Knowledge Graph (KG) from scientific papers. We focus on extracting four types of relations: evaluatedOn between tasks and datasets, evaluatedBy between tasks and evaluation metrics, as well as coreferent and related relations between the same type of entities. For instance, F1-score is coreferent with F-measure. We introduce novel methods for each of these relation types and apply our final framework (SciNLP-KG) to 30,000 NLP papers from ACL Anthology to build a large-scale KG, which can facilitate automatically constructing scientific leaderboards for the NLP community. The results of our experiments indicate that the resulting KG contains high-quality information.
Healthcare predictive analytics aids medical decision-making, diagnosis prediction and drug review analysis. Therefore, prediction accuracy is an important criteria which also necessitates robust predictive language models. However, the models using deep learning have been proven vulnerable towards insignificantly perturbed input instances which are less likely to be misclassified by humans. Recent efforts of generating adversaries using rule-based synonyms and BERT-MLMs have been witnessed in general domain, but the ever increasing biomedical literature poses unique challenges. We propose BBAEG (Biomedical BERT-based Adversarial Example Generation), a black-box attack algorithm for biomedical text classification, leveraging the strengths of both domain-specific synonym replacement for biomedical named entities and BERTMLM predictions, spelling variation and number replacement. Through automatic and human evaluation on two datasets, we demonstrate that BBAEG performs stronger attack with better language fluency, semantic coherence as compared to prior work.
Entity linking (or Normalization) is an essential task in text mining that maps the entity mentions in the medical text to standard entities in a given Knowledge Base (KB). This task is of great importance in the medical domain. It can also be used for merging different medical and clinical ontologies. In this paper, we center around the problem of disease linking or normalization. This task is executed in two phases: candidate generation and candidate scoring. In this paper, we present an approach to rank the candidate Knowledge Base entries based on their similarity with disease mention. We make use of the Triplet Network for candidate ranking. While the existing methods have used carefully generated sieves and external resources for candidate generation, we introduce a robust and portable candidate generation scheme that does not make use of the hand-crafted rules. Experimental results on the standard benchmark NCBI disease dataset demonstrate that our system outperforms the prior methods by a significant margin.
Traditional biomedical version of embeddings obtained from pre-trained language models have recently shown state-of-the-art results for relation extraction (RE) tasks in the medical domain. In this paper, we explore how to incorporate domain knowledge, available in the form of molecular structure of drugs, for predicting Drug-Drug Interaction from textual corpus. We propose a method, BERTChem-DDI, to efficiently combine drug embeddings obtained from the rich chemical structure of drugs along with off-the-shelf domain-specific BioBERT embedding-based RE architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other strong baselines architectures by 3.4\% macro F1-score.
Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language understanding tasks (NLU) in the biomedical domain. Relation Classification (RC) falls into one of the most critical tasks. In this paper, we explore how to incorporate domain knowledge of the biomedical entities (such as drug, disease, genes), obtained from Knowledge Graph (KG) Embeddings, for predicting Drug-Drug Interaction from textual corpus. We propose a new method, BERTKG-DDI, to combine drug embeddings obtained from its interaction with other biomedical entities along with domain-specific BioBERT embedding-based RC architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other baselines architectures by 4.1% macro F1-score.
An active learning (AL) algorithm seeks to construct an effective classifier with a minimal number of labeled examples in a bootstrapping manner. While standard AL heuristics, such as selecting those points for annotation for which a classification model yields least confident predictions, there has been no empirical investigation to see if these heuristics lead to models that are more interpretable to humans. In the era of data-driven learning, this is an important research direction to pursue. This paper describes our work-in-progress towards developing an AL selection function that in addition to model effectiveness also seeks to improve on the interpretability of a model during the bootstrapping steps. Concretely speaking, our proposed selection function trains an `explainer' model in addition to the classifier model, and favours those instances where a different part of the data is used, on an average, to explain the predicted class. Initial experiments exhibited encouraging trends in showing that such a heuristic can lead to developing more effective and more explainable end-to-end data-driven classifiers.