scholarly journals Ablations over transformer models for biomedical relationship extraction

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 710 ◽  
Author(s):  
Richard G Jackson ◽  
Erik Jansson ◽  
Aron Lagerberg ◽  
Elliot Ford ◽  
Vladimir Poroshin ◽  
...  
Keyword(s):  
Language Processing ◽  
Protein Interactions ◽  
Recent Model ◽  
Training Data ◽  
General Domain ◽  
Domain Specific ◽  
Relationship Extraction ◽  
Language Modelling ◽  
Model Training ◽  
Order Of Training

Background: Masked language modelling approaches have enjoyed success in improving benchmark performance across many general and biomedical domain natural language processing tasks, including biomedical relationship extraction (RE). However, the recent surge in both the number of novel architectures and the volume of training data they utilise may lead us to question whether domain specific pretrained models are necessary. Additionally, recent work has proposed novel classification heads for RE tasks, further improving performance. Here, we perform ablations over several pretrained models and classification heads to try to untangle the perceived benefits of each. Methods: We use a range of string preprocessing strategies, combined with Bidirectional Encoder Representations from Transformers (BERT), BioBERT and RoBERTa architectures to perform ablations over three RE datasets pertaining to drug-drug and chemical protein interactions, and general domain relationship extraction. We explore the use of the RBERT classification head, compared to a simple linear classification layer across all architectures and datasets. Results: We observe a moderate performance benefit in using the BioBERT pretrained model over the BERT base cased model, although there appears to be little difference when comparing BioBERT to RoBERTa large. In addition, we observe a substantial benefit of using the RBERT head on the general domain RE dataset, but this is not consistently reflected in the biomedical RE datasets. Finally, we discover that randomising the token order of training data does not result in catastrophic performance degradation in our selected tasks. Conclusions: We find a recent general domain pretrained model performs approximately the same as a biomedical specific one, suggesting that domain specific models may be of limited use given the tendency of recent model pretraining regimes to incorporate ever broader sets of data. In addition, we suggest that care must be taken in RE model training, to prevent fitting to non-syntactic features of datasets.

scholarly journals DeIDNER Corpus: Annotation of Clinical Discharge Summary Notes for Named Entity Recognition Using BRAT Tool

2021 ◽  
Author(s):  
Mahanazuddin Syed ◽  
Shaymaa Al-Shukri ◽  
Shorabuddin Syed ◽  
Kevin Sexton ◽  
Melody L. Greer ◽  
...  
Keyword(s):  
Language Processing ◽  
Named Entity Recognition ◽  
Discharge Summary ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entities ◽  
Named Entity ◽  
Domain Specific ◽  
Model Training ◽  
Clinical Domain

Named Entity Recognition (NER) aims to identify and classify entities into predefined categories is a critical pre-processing task in Natural Language Processing (NLP) pipeline. Readily available off-the-shelf NER algorithms or programs are trained on a general corpus and often need to be retrained when applied on a different domain. The end model’s performance depends on the quality of named entities generated by these NER models used in the NLP task. To improve NER model accuracy, researchers build domain-specific corpora for both model training and evaluation. However, in the clinical domain, there is a dearth of training data because of privacy reasons, forcing many studies to use NER models that are trained in the non-clinical domain to generate NER feature-set. Thus, influencing the performance of the downstream NLP tasks like information extraction and de-identification. In this paper, our objective is to create a high quality annotated clinical corpus for training NER models that can be easily generalizable and can be used in a downstream de-identification task to generate named entities feature-set.

scholarly journals Word embeddings for application in geosciences: development, evaluation and examples of soil-related concepts

2019 ◽  
Author(s):  
José Padarian ◽  
Ignacio Fuentes
Keyword(s):  
Language Processing ◽  
Dimensional Space ◽  
Language Model ◽  
Test Suite ◽  
Word Embeddings ◽  
General Domain ◽  
Domain Specific ◽  
Descriptive Information ◽  
Development Evaluation ◽  
Numerical Representations

Abstract. A large amount of descriptive information is available in most disciplines of geosciences. This information is usually considered subjective and ill-favoured compared with its numerical counterpart. Considering the advances in natural language processing and machine learning, it is possible to utilise descriptive information and encode it as dense vectors. These word embeddings lay on a multi-dimensional space where angles and distances have a linguistic interpretation. We used 280 764 full-text scientific articles related to geosciences to train a domain-specific language model capable of generating such embeddings. To evaluate the quality of the numerical representations, we performed three intrinsic evaluations, namely: the capacity to generate analogies, term relatedness compared with the opinion of a human subject, and categorisation of different groups of words. Since this is the first attempt to evaluate word embedding for tasks in the geosciences domain, we created a test suite specific for geosciences. We compared our results with general domain embeddings commonly used in other disciplines. As expected, our domain-specific embeddings (GeoVec) outperformed general domain embeddings in all tasks, with an overall performance improvement of 107.9 %. The resulting embedding and test suite will be made available for other researchers to use an expand.

scholarly journals Optimising biomedical relationship extraction with BioBERT

2020 ◽  
Author(s):  
Oliver Giles ◽  
Anneli Karlsson ◽  
Spyroula Masiala ◽  
Simon White ◽  
Gianni Cesareni ◽  
...  
Keyword(s):  
Text Mining ◽  
Protein Interactions ◽  
Language Model ◽  
Fine Tuning ◽  
Domain Specific Language ◽  
Protein Protein Interactions ◽  
Domain Specific ◽  
Manual Curation ◽  
Relationship Extraction ◽  
Biological Entities

AbstractText mining is widely used within the life sciences as an evidence stream for inferring relationships between biological entities. In most cases, conventional string matching is used to identify cooccurrences of given entities within sentences. This limits the utility of text mining results, as they tend to contain significant noise due to weak inclusion criteria. We show that, in the indicative case of protein-protein interactions (PPIs), the majority of sentences containing cooccurrences (∽75%) do not describe any causal relationship. We further demonstrate the feasibility of fine tuning a strong domain-specific language model, BioBERT, to analyse sentences containing cooccurrences and accurately (F1 score: 88.95%) identify functional links between proteins. These strong results come in spite of the deep complexity of the language involved, which limits the accuracy even of expert curators. We establish guidelines for best practices in data creation to this end, including an examination of inter-annotator agreement, of semisupervision, and of rules based alternatives to manual curation, and explore the potential for downstream use of the model to accelerate curation of interactions in the SIGNOR database of causal protein interactions and the IntAct database of experimental evidence for physical protein interactions.

scholarly journals FinBERT: A Pre-trained Financial Language Representation Model for Financial Text Mining

2020 ◽  
Author(s):  
Zhuang Liu ◽  
Degen Huang ◽  
Kaiyu Huang ◽  
Zhuang Li ◽  
Jun Zhao
Keyword(s):  
Deep Learning ◽  
Text Mining ◽  
Language Processing ◽  
Large Scale ◽  
Language Model ◽  
Training Data ◽  
Domain Specific ◽  
Current State ◽  
Language Representation ◽  
Financial Domain

There is growing interest in the tasks of financial text mining. Over the past few years, the progress of Natural Language Processing (NLP) based on deep learning advanced rapidly. Significant progress has been made with deep learning showing promising results on financial text mining models. However, as NLP models require large amounts of labeled training data, applying deep learning to financial text mining is often unsuccessful due to the lack of labeled training data in financial fields. To address this issue, we present FinBERT (BERT for Financial Text Mining) that is a domain specific language model pre-trained on large-scale financial corpora. In FinBERT, different from BERT, we construct six pre-training tasks covering more knowledge, simultaneously trained on general corpora and financial domain corpora, which can enable FinBERT model better to capture language knowledge and semantic information. The results show that our FinBERT outperforms all current state-of-the-art models. Extensive experimental results demonstrate the effectiveness and robustness of FinBERT. The source code and pre-trained models of FinBERT are available online.

scholarly journals Word embeddings for application in geosciences: development, evaluation, and examples of soil-related concepts

SOIL ◽  
2019 ◽  
Vol 5 (2) ◽  
pp. 177-187 ◽  
Author(s):  
José Padarian ◽  
Ignacio Fuentes
Keyword(s):  
Language Processing ◽  
Language Model ◽  
Numerical Data ◽  
Test Suite ◽  
Multidimensional Space ◽  
Word Embeddings ◽  
General Domain ◽  
Domain Specific ◽  
Descriptive Information ◽  
Development Evaluation

Abstract. A large amount of descriptive information is available in geosciences. This information is usually considered subjective and ill-favoured compared with its numerical counterpart. Considering the advances in natural language processing and machine learning, it is possible to utilise descriptive information and encode it as dense vectors. These word embeddings, which encode information about a word and its linguistic relationships with other words, lay on a multidimensional space where angles and distances have a linguistic interpretation. We used 280 764 full-text scientific articles related to geosciences to train a domain-specific language model capable of generating such embeddings. To evaluate the quality of the numerical representations, we performed three intrinsic evaluations: the capacity to generate analogies, term relatedness compared with the opinion of a human subject, and categorisation of different groups of words. As this is the first attempt to evaluate word embedding for tasks in the geosciences domain, we created a test suite specific for geosciences. We compared our results with general domain embeddings commonly used in other disciplines. As expected, our domain-specific embeddings (GeoVec) outperformed general domain embeddings in all tasks, with an overall performance improvement of 107.9 %. We also presented an example were we successfully emulated part of a taxonomic analysis of soil profiles that was originally applied to soil numerical data, which would not be possible without the use of embeddings. The resulting embedding and test suite will be made available for other researchers to use and expand upon.

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 ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
State Of The Art ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Language Models ◽  
General Domain ◽  
Domain Specific ◽  
And Task

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 .

Discriminate Chinese Word Segmenter with Global and Context Features

2012 ◽  
Vol 198-199 ◽  
pp. 267-272
Author(s):  
Cong Hui Zhu ◽  
Shi Liang Wang ◽  
De Quan Zheng
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Training Data ◽  
Chinese Word ◽  
Global Features ◽  
Feature Sets ◽  
Model Training ◽  
Context Features ◽  
Original Feature

Chinese Word segmenter is the basis for all subsequent applications of natural language processing. The Corpus-based statistic method has become the predominant method. However, the training corpora are not enough especially in certain areas. Therefore, we introduce some global features and context features in order to get almost the same performance only with much smaller scale corpus. The experiments results show that our approach significantly outperforms the original feature sets in the same training data. Meanwhile, the time-consuming of model training is also reduced. In addition, these features do not depend on classifiers, so our method can easily be changed to other models.

scholarly journals Collecting specialty-related medical terms: Development and evaluation of a resource for Spanish

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pilar López-Úbeda ◽  
Alexandra Pomares-Quimbaya ◽  
Manuel Carlos Díaz-Galiano ◽  
Stefan Schulz
Keyword(s):  
Language Processing ◽  
Classification Problem ◽  
Snomed Ct ◽  
Language Resources ◽  
Clinical Specialty ◽  
Controlled Vocabularies ◽  
Clinical Text ◽  
Domain Specific ◽  
Medical Terms ◽  
Core Vocabulary

Abstract Background Controlled vocabularies are fundamental resources for information extraction from clinical texts using natural language processing (NLP). Standard language resources available in the healthcare domain such as the UMLS metathesaurus or SNOMED CT are widely used for this purpose, but with limitations such as lexical ambiguity of clinical terms. However, most of them are unambiguous within text limited to a given clinical specialty. This is one rationale besides others to classify clinical text by the clinical specialty to which they belong. Results This paper addresses this limitation by proposing and applying a method that automatically extracts Spanish medical terms classified and weighted per sub-domain, using Spanish MEDLINE titles and abstracts as input. The hypothesis is biomedical NLP tasks benefit from collections of domain terms that are specific to clinical subdomains. We use PubMed queries that generate sub-domain specific corpora from Spanish titles and abstracts, from which token n-grams are collected and metrics of relevance, discriminatory power, and broadness per sub-domain are computed. The generated term set, called Spanish core vocabulary about clinical specialties (SCOVACLIS), was made available to the scientific community and used in a text classification problem obtaining improvements of 6 percentage points in the F-measure compared to the baseline using Multilayer Perceptron, thus demonstrating the hypothesis that a specialized term set improves NLP tasks. Conclusion The creation and validation of SCOVACLIS support the hypothesis that specific term sets reduce the level of ambiguity when compared to a specialty-independent and broad-scope vocabulary.

Fully automated contrast and non-contrast cardiac view detection in echocardiography a multi-centre, multi-vendor study

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Gao ◽  
D Stojanovski ◽  
A Parker ◽  
P Marques ◽  
S Heitner ◽  
...  
Keyword(s):  
Neural Network ◽  
Training Data ◽  
Classification Model ◽  
Validation Dataset ◽  
Funding Source ◽  
Private Company ◽  
Validation Data ◽  
Independent Test ◽  
Model Training ◽  
Confusion Matrices

Abstract Background Correctly identifying views acquired in a 2D echocardiographic examination is paramount to post-processing and quantification steps often performed as part of most clinical workflows. In many exams, particularly in stress echocardiography, microbubble contrast is used which greatly affects the appearance of the cardiac views. Here we present a bespoke, fully automated convolutional neural network (CNN) which identifies apical 2, 3, and 4 chamber, and short axis (SAX) views acquired with and without contrast. The CNN was tested in a completely independent, external dataset with the data acquired in a different country than that used to train the neural network. Methods Training data comprised of 2D echocardiograms was taken from 1014 subjects from a prospective multisite, multi-vendor, UK trial with the number of frames in each view greater than 17,500. Prior to view classification model training, images were processed using standard techniques to ensure homogenous and normalised image inputs to the training pipeline. A bespoke CNN was built using the minimum number of convolutional layers required with batch normalisation, and including dropout for reducing overfitting. Before processing, the data was split into 90% for model training (211,958 frames), and 10% used as a validation dataset (23,946 frames). Image frames from different subjects were separated out entirely amongst the training and validation datasets. Further, a separate trial dataset of 240 studies acquired in the USA was used as an independent test dataset (39,401 frames). Results Figure 1 shows the confusion matrices for both validation data (left) and independent test data (right), with an overall accuracy of 96% and 95% for the validation and test datasets respectively. The accuracy for the non-contrast cardiac views of >99% exceeds that seen in other works. The combined datasets included images acquired across ultrasound manufacturers and models from 12 clinical sites. Conclusion We have developed a CNN capable of automatically accurately identifying all relevant cardiac views used in “real world” echo exams, including views acquired with contrast. Use of the CNN in a routine clinical workflow could improve efficiency of quantification steps performed after image acquisition. This was tested on an independent dataset acquired in a different country to that used to train the model and was found to perform similarly thus indicating the generalisability of the model. Figure 1. Confusion matrices Funding Acknowledgement Type of funding source: Private company. Main funding source(s): Ultromics Ltd.

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