Related papers: BERT might be Overkill: A Tiny but Effective Biome…

Transformer-based models, specifically BERT, have propelled research in various NLP tasks. However, these models are limited to a maximum token limit of 512 tokens. Consequently, this makes it non-trivial to apply it in a practical setting…

The availability of biomedical text data and advances in natural language processing (NLP) have made new applications in biomedical NLP possible. Language models trained or fine tuned using domain specific corpora can outperform general…

Large pre-trained language models help to achieve state of the art on a variety of natural language processing (NLP) tasks, nevertheless, they still suffer from forgetting when incrementally learning a sequence of tasks. To alleviate this…

Recent advancements in the NLP field showed that transfer learning helps with achieving state-of-the-art results for new tasks by tuning pre-trained models instead of starting from scratch. Transformers have made a significant improvement…

A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical…

Recently, there is an effort to extend fine-grained entity typing by using a richer and ultra-fine set of types, and labeling noun phrases including pronouns and nominal nouns instead of just named entity mentions. A key challenge for this…

Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of…

Recognizing spans of biomedical concepts and their types (e.g., drug or gene) in free text, often called biomedical named entity recognition (NER), is a basic component of information extraction (IE) pipelines. Without a strong NER…

This paper describes a system submitted by team BigGreen to LCP 2021 for predicting the lexical complexity of English words in a given context. We assemble a feature engineering-based model with a deep neural network model founded on BERT.…

Motivation: Named Entity Recognition (NER) is a key task to support biomedical research. In Biomedical Named Entity Recognition (BioNER), obtaining high-quality expert annotated data is laborious and expensive, leading to the development of…

We propose an autoregressive entity linking model, that is trained with two auxiliary tasks, and learns to re-rank generated samples at inference time. Our proposed novelties address two weaknesses in the literature. First, a recent method…

State-of-the-art performance on language understanding tasks is now achieved with increasingly large networks; the current record holder has billions of parameters. Given a language model pre-trained on massive unlabeled text corpora, only…

This paper presents new state-of-the-art models for three tasks, part-of-speech tagging, syntactic parsing, and semantic parsing, using the cutting-edge contextualized embedding framework known as BERT. For each task, we first replicate and…

Models based on the transformer architecture, such as BERT, have marked a crucial step forward in the field of Natural Language Processing. Importantly, they allow the creation of word embeddings that capture important semantic information…

Contextualized word embeddings derived from pre-trained language models (LMs) show significant improvements on downstream NLP tasks. Pre-training on domain-specific corpora, such as biomedical articles, further improves their performance.…

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…

Contextual word representations, typically trained on unstructured, unlabeled text, do not contain any explicit grounding to real world entities and are often unable to remember facts about those entities. We propose a general method to…

Recently, multilingual BERT works remarkably well on cross-lingual transfer tasks, superior to static non-contextualized word embeddings. In this work, we provide an in-depth experimental study to supplement the existing literature of…

Transformer-based masked language models such as BERT, trained on general corpora, have shown impressive performance on downstream tasks. It has also been demonstrated that the downstream task performance of such models can be improved by…

Building named entity recognition (NER) models for languages that do not have much training data is a challenging task. While recent work has shown promising results on cross-lingual transfer from high-resource languages to low-resource…