Can language models read biomedical texts and explain the biomedical mechanisms discussed? In this work we introduce a biomedical mechanism summarization task. Biomedical studies often investigate the mechanisms behind how one entity (e.g., a protein or a chemical) affects another in a biological context. The abstracts of these publications often include a focused set of sentences that present relevant supporting statements regarding such relationships, associated experimental evidence, and a concluding sentence that summarizes the mechanism underlying the relationship. We leverage this structure and create a summarization task, where the input is a collection of sentences and the main entities in an abstract, and the output includes the relationship and a sentence that summarizes the mechanism. Using a small amount of manually labeled mechanism sentences, we train a mechanism sentence classifier to filter a large biomedical abstract collection and create a summarization dataset with 22k instances. We also introduce conclusion sentence generation as a pretraining task with 611k instances. We benchmark the performance of large bio-domain language models. We find that while the pretraining task help improves performance, the best model produces acceptable mechanism outputs in only 32% of the instances, which shows the task presents significant challenges in biomedical language understanding and summarization.
Figurative language is ubiquitous in human communication. However, current NLP models are unable to demonstrate a significant understanding of instances of this phenomena. The EMNLP 2022 shared task on figurative language understanding posed the problem of predicting and explaining the relation between a premise and a hypothesis containing an instance of the use of figurative language. We experiment with different variations of using T5-large for this task and build a model that significantly outperforms the task baseline. Treating it as a new task for T5 and simply finetuning on the data achieves the best score on the defined evaluation. Furthermore, we find that hypothesis-only models are able to achieve most of the performance.
Natural language inference (NLI) is critical in many domains requiring complex decision-making, such as the biomedical domain. We introduce a novel semi-supervised procedure that bootstraps biomedical NLI datasets from positive entailment examples present in abstracts of biomedical publications. We focus on challenging texts where the hypothesis includes mechanistic information such as biochemical interactions between two entities. A key contribution of this work is automating the creation of negative examples that are informative without being simplistic. We generate a range of negative examples using nine strategies that manipulate the structure of the underlying mechanisms both with rules, e.g., flip the roles of the entities in the interaction, and, more importantly, by imposing the perturbed conditions as logical constraints in a neuro-logical decoding system (CITATION).We use this procedure to create a novel dataset for NLI in the biomedical domain, called . The accuracy of neural classifiers on this dataset is in the mid 70s F1, which indicates that this NLI task remains to be solved. Critically, we observe that the performance on the different classes of negative examples varies widely, from 97% F1 on the simple negative examples that change the role of the entities in the hypothesis, to barely better than chance on the negative examples generated using neuro-logic decoding.
Neural Machine Translation (NMT) models are strong enough to convey semantic and syntactic information from the source language to the target language. However, these models are suffering from the need for a large amount of data to learn the parameters. As a result, for languages with scarce data, these models are at risk of underperforming. We propose to augment attention based neural network with reordering information to alleviate the lack of data. This augmentation improves the translation quality for both English to Persian and Persian to English by up to 6% BLEU absolute over the baseline models.
Predicting how events induce emotions in the characters of a story is typically seen as a standard multi-label classification task, which usually treats labels as anonymous classes to predict. They ignore information that may be conveyed by the emotion labels themselves. We propose that the semantics of emotion labels can guide a model’s attention when representing the input story. Further, we observe that the emotions evoked by an event are often related: an event that evokes joy is unlikely to also evoke sadness. In this work, we explicitly model label classes via label embeddings, and add mechanisms that track label-label correlations both during training and inference. We also introduce a new semi-supervision strategy that regularizes for the correlations on unlabeled data. Our empirical evaluations show that modeling label semantics yields consistent benefits, and we advance the state-of-the-art on an emotion inference task.
Even though sentiment analysis has been well-studied on a wide range of domains, there hasn’tbeen much work on inferring author sentiment in news articles. To address this gap, we introducePerSenT, a crowd-sourced dataset that captures the sentiment of an author towards the mainentity in a news article. Our benchmarks of multiple strong baselines show that this is a difficultclassification task. BERT performs the best amongst the baselines. However, it only achievesa modest performance overall suggesting that fine-tuning document-level representations aloneisn’t adequate for this task. Making paragraph-level decisions and aggregating over the entiredocument is also ineffective. We present empirical and qualitative analyses that illustrate thespecific challenges posed by this dataset. We release this dataset with 5.3k documents and 38kparagraphs with 3.2k unique entities as a challenge in entity sentiment analysis.