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Natural language processing (NLP) of clinical trial documents can be useful in new trial design. Here we identify entity types relevant to clinical trial design and propose a framework called CT-BERT for information extraction from clinical…

Quantitative Methods · Quantitative Biology 2021-10-20 Xiong Liu , Greg L. Hersch , Iya Khalil , Murthy Devarakonda

In an era of widespread influence of Natural Language Processing (NLP), there have been multiple research efforts to supplant traditional manual coding techniques with automated systems capable of generating solutions autonomously. With…

Computation and Language · Computer Science 2024-12-10 Namrata Das , Rakshya Panta , Neelam Karki , Ruchi Manandhar , Dinesh Baniya Kshatri

Although the International Classification of Diseases (ICD) has been adopted worldwide, manually assigning ICD codes to clinical text is time-consuming, error-prone, and expensive, motivating the development of automated approaches. This…

Computation and Language · Computer Science 2024-02-06 Gonçalo Gomes , Isabel Coutinho , Bruno Martins

Transfer learning, where a model is first pre-trained on a data-rich task before being fine-tuned on a downstream task, has emerged as a powerful technique in natural language processing (NLP). The effectiveness of transfer learning has…

Machine Learning · Computer Science 2023-09-20 Colin Raffel , Noam Shazeer , Adam Roberts , Katherine Lee , Sharan Narang , Michael Matena , Yanqi Zhou , Wei Li , Peter J. Liu

Bidirectional Encoder Representations from Transformers (BERT) has recently achieved state-of-the-art performance on a broad range of NLP tasks including sentence classification, machine translation, and question answering. The BERT model…

Computation and Language · Computer Science 2020-03-17 Zhiheng Huang , Peng Xu , Davis Liang , Ajay Mishra , Bing Xiang

Models based on bidirectional encoder representations from transformers (BERT) produce state of the art (SOTA) results on many natural language processing (NLP) tasks such as named entity recognition (NER), part-of-speech (POS) tagging etc.…

Computation and Language · Computer Science 2023-07-25 Shubham Vatsal , Adam Meyers , John E. Ortega

Attention-based models have shown significant improvement over traditional algorithms in several NLP tasks. The Transformer, for instance, is an illustrative example that generates abstract representations of tokens inputted to an encoder…

Computation and Language · Computer Science 2019-11-15 Dhanasekar Sundararaman , Vivek Subramanian , Guoyin Wang , Shijing Si , Dinghan Shen , Dong Wang , Lawrence Carin

Transformer-based machine learning models have become an essential tool for many natural language processing (NLP) tasks since the introduction of the method. A common objective of these projects is to classify text data. Classification…

Computation and Language · Computer Science 2025-02-18 Zoltán Kmetty , Bence Kollányi , Krisztián Boros

The Transformer model is widely successful on many natural language processing tasks. However, the quadratic complexity of self-attention limit its application on long text. In this paper, adopting a fine-to-coarse attention mechanism on…

Computation and Language · Computer Science 2019-11-12 Zihao Ye , Qipeng Guo , Quan Gan , Xipeng Qiu , Zheng Zhang

Obtaining large-scale annotated data for NLP tasks in the scientific domain is challenging and expensive. We release SciBERT, a pretrained language model based on BERT (Devlin et al., 2018) to address the lack of high-quality, large-scale…

Computation and Language · Computer Science 2019-09-12 Iz Beltagy , Kyle Lo , Arman Cohan

Lengthy documents pose a unique challenge to neural language models due to substantial memory consumption. While existing state-of-the-art (SOTA) models segment long texts into equal-length snippets (e.g., 128 tokens per snippet) or deploy…

Computation and Language · Computer Science 2024-05-14 Guangzeng Han , Jack Tsao , Xiaolei Huang

Several methods have been proposed for classifying long textual documents using Transformers. However, there is a lack of consensus on a benchmark to enable a fair comparison among different approaches. In this paper, we provide a…

Computation and Language · Computer Science 2022-03-23 Hyunji Hayley Park , Yogarshi Vyas , Kashif Shah

Pre-training a transformer-based model for the language modeling task in a large dataset and then fine-tuning it for downstream tasks has been found very useful in recent years. One major advantage of such pre-trained language models is…

Computation and Language · Computer Science 2020-11-17 Md Tahmid Rahman Laskar , Enamul Hoque , Jimmy Xiangji Huang

Pretrained language models such as BERT, GPT have shown great effectiveness in language understanding. The auxiliary predictive tasks in existing pretraining approaches are mostly defined on tokens, thus may not be able to capture…

Computation and Language · Computer Science 2020-06-19 Hongchao Fang , Sicheng Wang , Meng Zhou , Jiayuan Ding , Pengtao Xie

Although BERT and its variants have reshaped the NLP landscape, it still remains unclear how best to derive sentence embeddings from such pre-trained Transformers. In this work, we propose a contrastive learning method that utilizes…

Computation and Language · Computer Science 2021-06-15 Taeuk Kim , Kang Min Yoo , Sang-goo Lee

In recent years, the fields of natural language processing (NLP) and information retrieval (IR) have made tremendous progress thanksto deep learning models like Recurrent Neural Networks (RNNs), Gated Recurrent Units (GRUs) and Long…

Computation and Language · Computer Science 2021-06-15 Manish Gupta , Puneet Agrawal

The effectiveness of the BERT model on multiple linguistic tasks has been well documented. On the other hand, its potentials for narrow and specific domains such as Legal, have not been fully explored. In this paper, we examine how BERT can…

Computation and Language · Computer Science 2022-10-18 Muhammad AL-Qurishi , Sarah AlQaseemi , Riad Soussi

Large scale contextual representation models, such as BERT, have significantly advanced natural language processing (NLP) in recently years. However, in certain area like healthcare, accessing diverse large scale text data from multiple…

Computation and Language · Computer Science 2020-02-21 Dianbo Liu , Tim Miller

Language is an outcome of our complex and dynamic human-interactions and the technique of natural language processing (NLP) is hence built on human linguistic activities. Bidirectional Encoder Representations from Transformers (BERT) has…

Computation and Language · Computer Science 2022-12-06 Katsuma Inoue , Soh Ohara , Yasuo Kuniyoshi , Kohei Nakajima

Non-hierarchical sparse attention Transformer-based models, such as Longformer and Big Bird, are popular approaches to working with long documents. There are clear benefits to these approaches compared to the original Transformer in terms…

Computation and Language · Computer Science 2022-10-12 Ilias Chalkidis , Xiang Dai , Manos Fergadiotis , Prodromos Malakasiotis , Desmond Elliott
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