scholarly journals Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing

2022 ◽  
Vol 3 (1) ◽  
pp. 1-23
Author(s):  
Yu Gu ◽  
Robert Tinn ◽  
Hao Cheng ◽  
Michael Lucas ◽  
Naoto Usuyama ◽  
...  

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this article, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition. To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB .

2019 ◽  
Author(s):  
Auss Abbood ◽  
Alexander Ullrich ◽  
Rüdiger Busche ◽  
Stéphane Ghozzi

AbstractAccording to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of epidemiologists sift through numerous articles and newsletters to detect relevant events. This media screening is one important part of event-based surveillance (EBS). Reading the articles, discussing their relevance, and putting key information into a database is a time-consuming process. To support EBS, but also to gain insights into what makes an article and the event it describes relevant, we developed a natural-language-processing framework for automated information extraction and relevance scoring. First, we scraped relevant sources for EBS as done at RKI (WHO Disease Outbreak News and ProMED) and automatically extracted the articles’ key data: disease, country, date, and confirmed-case count. For this, we performed named entity recognition in two steps: EpiTator, an open-source epidemiological annotation tool, suggested many different possibilities for each. We trained a naive Bayes classifier to find the single most likely one using RKI’s EBS database as labels. Then, for relevance scoring, we defined two classes to which any article might belong: The article is relevant if it is in the EBS database and irrelevant otherwise. We compared the performance of different classifiers, using document and word embeddings. Two of the tested algorithms stood out: The multilayer perceptron performed best overall, with a precision of 0.19, recall of 0.50, specificity of 0.89, F1 of 0.28, and the highest tested index balanced accuracy of 0.46. The support-vector machine, on the other hand, had the highest recall (0.88) which can be of higher interest for epidemiologists. Finally, we integrated these functionalities into a web application called EventEpi where relevant sources are automatically analyzed and put into a database. The user can also provide any URL or text, that will be analyzed in the same way and added to the database. Each of these steps could be improved, in particular with larger labeled datasets and fine-tuning of the learning algorithms. The overall framework, however, works already well and can be used in production, promising improvements in EBS. The source code is publicly available at https://github.com/aauss/EventEpi.


2021 ◽  
Author(s):  
Oscar Nils Erik Kjell ◽  
H. Andrew Schwartz ◽  
Salvatore Giorgi

The language that individuals use for expressing themselves contains rich psychological information. Recent significant advances in Natural Language Processing (NLP) and Deep Learning (DL), namely transformers, have resulted in large performance gains in tasks related to understanding natural language such as machine translation. However, these state-of-the-art methods have not yet been made easily accessible for psychology researchers, nor designed to be optimal for human-level analyses. This tutorial introduces text (www.r-text.org), a new R-package for analyzing and visualizing human language using transformers, the latest techniques from NLP and DL. Text is both a modular solution for accessing state-of-the-art language models and an end-to-end solution catered for human-level analyses. Hence, text provides user-friendly functions tailored to test hypotheses in social sciences for both relatively small and large datasets. This tutorial describes useful methods for analyzing text, providing functions with reliable defaults that can be used off-the-shelf as well as providing a framework for the advanced users to build on for novel techniques and analysis pipelines. The reader learns about six methods: 1) textEmbed: to transform text to traditional or modern transformer-based word embeddings (i.e., numeric representations of words); 2) textTrain: to examine the relationships between text and numeric/categorical variables; 3) textSimilarity and 4) textSimilarityTest: to computing semantic similarity scores between texts and significance test the difference in meaning between two sets of texts; and 5) textProjection and 6) textProjectionPlot: to examine and visualize text within the embedding space according to latent or specified construct dimensions (e.g., low to high rating scale scores).


2021 ◽  
Author(s):  
Tong Guo

Recently, the development of pre-trained language models has brought natural language processing (NLP) tasks to the new state-of-the-art. In this paper we explore the efficiency of various pre-trained language models. We pre-train a list of transformer-based models with the same amount of text and the same training steps. The experimental results shows that the most improvement upon the origin BERT is adding the RNN-layer to capture more contextual information for the transformer-encoder layers.


Author(s):  
Rinalds Vīksna ◽  
Inguna Skadiņa

Transformer-based language models pre-trained on large corpora have demonstrated good results on multiple natural language processing tasks for widely used languages including named entity recognition (NER). In this paper, we investigate the role of the BERT models in the NER task for Latvian. We introduce the BERT model pre-trained on the Latvian language data. We demonstrate that the Latvian BERT model, pre-trained on large Latvian corpora, achieves better results (81.91 F1-measure on average vs 78.37 on M-BERT for a dataset with nine named entity types, and 79.72 vs 78.83 on another dataset with seven types) than multilingual BERT and outperforms previously developed Latvian NER systems.


1990 ◽  
Vol 5 (4) ◽  
pp. 225-249 ◽  
Author(s):  
Ann Copestake ◽  
Karen Sparck Jones

AbstractThis paper reviews the current state of the art in natural language access to databases. This has been a long-standing area of work in natural language processing. But though some commercial systems are now available, providing front ends has proved much harder than was expected, and the necessary limitations on front ends have to be recognized. The paper discusses the issues, both general to language and task-specific, involved in front end design, and the way these have been addressed, concentrating on the work of the last decade. The focus is on the central process of translating a natural language question into a database query, but other supporting functions are also covered. The points are illustrated by the use of a single example application. The paper concludes with an evaluation of the current state, indicating that future progress will depend on the one hand on general advances in natural language processing, and on the other on expanding the capabilities of traditional databases.


2020 ◽  
Vol 16 (11) ◽  
pp. e1008277
Author(s):  
Auss Abbood ◽  
Alexander Ullrich ◽  
Rüdiger Busche ◽  
Stéphane Ghozzi

According to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of public health agents sift through numerous articles and newsletters to detect relevant events. This media screening is one important part of event-based surveillance (EBS). Reading the articles, discussing their relevance, and putting key information into a database is a time-consuming process. To support EBS, but also to gain insights into what makes an article and the event it describes relevant, we developed a natural language processing framework for automated information extraction and relevance scoring. First, we scraped relevant sources for EBS as done at the RKI (WHO Disease Outbreak News and ProMED) and automatically extracted the articles’ key data: disease, country, date, and confirmed-case count. For this, we performed named entity recognition in two steps: EpiTator, an open-source epidemiological annotation tool, suggested many different possibilities for each. We extracted the key country and disease using a heuristic with good results. We trained a naive Bayes classifier to find the key date and confirmed-case count, using the RKI’s EBS database as labels which performed modestly. Then, for relevance scoring, we defined two classes to which any article might belong: The article is relevant if it is in the EBS database and irrelevant otherwise. We compared the performance of different classifiers, using bag-of-words, document and word embeddings. The best classifier, a logistic regression, achieved a sensitivity of 0.82 and an index balanced accuracy of 0.61. Finally, we integrated these functionalities into a web application called EventEpi where relevant sources are automatically analyzed and put into a database. The user can also provide any URL or text, that will be analyzed in the same way and added to the database. Each of these steps could be improved, in particular with larger labeled datasets and fine-tuning of the learning algorithms. The overall framework, however, works already well and can be used in production, promising improvements in EBS. The source code and data are publicly available under open licenses.


Author(s):  
Claudia Kittask ◽  
Kirill Milintsevich ◽  
Kairit Sirts

Recently, large pre-trained language models, such as BERT, have reached state-of-the-art performance in many natural language processing tasks, but for many languages, including Estonian, BERT models are not yet available. However, there exist several multilingual BERT models that can handle multiple languages simultaneously and that have been trained also on Estonian data. In this paper, we evaluate four multilingual models—multilingual BERT, multilingual distilled BERT, XLM and XLM-RoBERTa—on several NLP tasks including POS and morphological tagging, NER and text classification. Our aim is to establish a comparison between these multilingual BERT models and the existing baseline neural models for these tasks. Our results show that multilingual BERT models can generalise well on different Estonian NLP tasks outperforming all baselines models for POS and morphological tagging and text classification, and reaching the comparable level with the best baseline for NER, with XLM-RoBERTa achieving the highest results compared with other multilingual models.


2021 ◽  
Author(s):  
Tong Guo

Recently, the development of pre-trained language models has brought natural language processing (NLP) tasks to the new state-of-the-art. In this paper we explore the efficiency of various pre-trained language models. We pre-train a list of transformer-based models with the same amount of text and the same training steps. The experimental results shows that the most improvement upon the origin BERT is adding the RNN-layer to capture more contextual information for the transformer-encoder layers.


2020 ◽  
Vol 10 (21) ◽  
pp. 7711
Author(s):  
Arthur Flor de Sousa Neto ◽  
Byron Leite Dantas Bezerra ◽  
Alejandro Héctor Toselli

The increasing portability of physical manuscripts to the digital environment makes it common for systems to offer automatic mechanisms for offline Handwritten Text Recognition (HTR). However, several scenarios and writing variations bring challenges in recognition accuracy, and, to minimize this problem, optical models can be used with language models to assist in decoding text. Thus, with the aim of improving results, dictionaries of characters and words are generated from the dataset and linguistic restrictions are created in the recognition process. In this way, this work proposes the use of spelling correction techniques for text post-processing to achieve better results and eliminate the linguistic dependence between the optical model and the decoding stage. In addition, an encoder–decoder neural network architecture in conjunction with a training methodology are developed and presented to achieve the goal of spelling correction. To demonstrate the effectiveness of this new approach, we conducted an experiment on five datasets of text lines, widely known in the field of HTR, three state-of-the-art Optical Models for text recognition and eight spelling correction techniques, among traditional statistics and current approaches of neural networks in the field of Natural Language Processing (NLP). Finally, our proposed spelling correction model is analyzed statistically through HTR system metrics, reaching an average sentence correction of 54% higher than the state-of-the-art method of decoding in the tested datasets.


2021 ◽  
Author(s):  
Tong Guo

Recently, the development of pre-trained language models has brought natural language processing (NLP) tasks to the new state-of-the-art. In this paper we explore the efficiency of various pre-trained language models. We pre-train a list of transformer-based models with the same amount of text and the same training steps. The experimental results shows that the most improvement upon the origin BERT is adding the RNN-layer to capture more contextual information for the transformer-encoder layers.


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