Pre-training large language models has become a standard in the natural language processing community. Such models are pre-trained on generic data (e.g. BookCorpus and English Wikipedia) and often fine-tuned on tasks in the same domain. However, in order to achieve state-of-the-art performance on out of domain tasks such as clinical named entity recognition and relation extraction, additional in domain pre-training is required. In practice, staged multi-domain pre-training presents performance deterioration in the form of catastrophic forgetting (CF) when evaluated on a generic benchmark such as GLUE. In this paper we conduct an empirical investigation into known methods to mitigate CF. We find that elastic weight consolidation provides best overall scores yielding only a 0.33% drop in performance across seven generic tasks while remaining competitive in bio-medical tasks. Furthermore, we explore gradient and latent clustering based data selection techniques to improve coverage when using elastic weight consolidation and experience replay methods.

In this paper, we propose a neural architecture and a set of training methods for ordering events by predicting temporal relations. Our proposed models receive a pair of events within a span of text as input and they identify temporal relations (Before, After, Equal, Vague) between them. Given that a key challenge with this task is the scarcity of annotated data, our models rely on either pretrained representations (i.e. RoBERTa, BERT or ELMo), transfer and multi-task learning (by leveraging complementary datasets), and self-training techniques. Experiments on the MATRES dataset of English documents establish a new state-of-the-art on this task.

Negative medical findings are prevalent in clinical reports, yet discriminating them from positive findings remains a challenging task for in-formation extraction. Most of the existing systems treat this task as a pipeline of two separate tasks, i.e., named entity recognition (NER)and rule-based negation detection. We consider this as a multi-task problem and present a novel end-to-end neural model to jointly extract entities and negations. We extend a standard hierarchical encoder-decoder NER model and first adopt a shared encoder followed by separate decoders for the two tasks. This architecture performs considerably better than the previous rule-based and machine learning-based systems. To overcome the problem of increased parameter size especially for low-resource settings, we propose the Conditional Softmax Shared Decoder architecture which achieves state-of-art results for NER and negation detection on the 2010 i2b2/VA challenge dataset and a proprietary de-identified clinical dataset.

Relation extraction (RE) aims to label relations between groups of marked entities in raw text. Most current RE models learn context-aware representations of the target entities that are then used to establish relation between them. This works well for intra-sentence RE, and we call them first-order relations. However, this methodology can sometimes fail to capture complex and long dependencies. To address this, we hypothesize that at times the target entities can be connected via a context token. We refer to such indirect relations as second-order relations, and describe an efficient implementation for computing them. These second-order relation scores are then combined with first-order relation scores to obtain final relation scores. Our empirical results show that the proposed method leads to state-of-the-art performance over two biomedical datasets.

Highlighting is a powerful tool to pick out important content and emphasize. Creating summary highlights at the sub-sentence level is particularly desirable, because sub-sentences are more concise than whole sentences. They are also better suited than individual words and phrases that can potentially lead to disfluent, fragmented summaries. In this paper we seek to generate summary highlights by annotating summary-worthy sub-sentences and teaching classifiers to do the same. We frame the task as jointly selecting important sentences and identifying a single most informative textual unit from each sentence. This formulation dramatically reduces the task complexity involved in sentence compression. Our study provides new benchmarks and baselines for generating highlights at the sub-sentence level.