scholarly journals Models and Processes to Extract Drug-like Molecules From Natural Language Text

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhi Hong ◽  
J. Gregory Pauloski ◽  
Logan Ward ◽  
Kyle Chard ◽  
Ben Blaiszik ◽  
...  
Keyword(s):  
Named Entity Recognition ◽  
New Drugs ◽  
Training Data ◽  
Entity Recognition ◽  
Free Text ◽  
Natural Language Text ◽  
Named Entity ◽  
Iterative Model ◽  
Computational Screening ◽  
Promising Source

Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of viral research. However, this literature is too large for human review and features unusual vocabularies for which existing named entity recognition (NER) models are ineffective. We report here on a project that leverages both human and artificial intelligence to detect references to such molecules in free text. We present 1) a iterative model-in-the-loop method that makes judicious use of scarce human expertise in generating training data for a NER model, and 2) the application and evaluation of this method to the problem of identifying drug-like molecules in the COVID-19 Open Research Dataset Challenge (CORD-19) corpus of 198,875 papers. We show that by repeatedly presenting human labelers only with samples for which an evolving NER model is uncertain, our human-machine hybrid pipeline requires only modest amounts of non-expert human labeling time (tens of hours to label 1778 samples) to generate an NER model with an F-1 score of 80.5%—on par with that of non-expert humans—and when applied to CORD’19, identifies 10,912 putative drug-like molecules. This enriched the computational screening team’s targets by 3,591 molecules, of which 18 ranked in the top 0.1% of all 6.6 million molecules screened for docking against the 3CLPro protein.

Developing a RadLex-based Named Entity Recognition Tool for Mining Textual Radiology Reports (Preprint)

2020 ◽  
Author(s):  
Shintaro Tsuji ◽  
Andrew Wen ◽  
Naoki Takahashi ◽  
Hongjian Zhang ◽  
Katsuhiko Ogasawara ◽  
...  
Keyword(s):  
Named Entity Recognition ◽  
Noun Phrases ◽  
General Purpose ◽  
Entity Recognition ◽  
Free Text ◽  
Clinical Text ◽  
Named Entity ◽  
Radiology Reports ◽  
Two Measures ◽  
F Measure

BACKGROUND Named entity recognition (NER) plays an important role in extracting the features of descriptions for mining free-text radiology reports. However, the performance of existing NER tools is limited because the number of entities depends on its dictionary lookup. Especially, the recognition of compound terms is very complicated because there are a variety of patterns. OBJECTIVE The objective of the study is to develop and evaluate a NER tool concerned with compound terms using the RadLex for mining free-text radiology reports. METHODS We leveraged the clinical Text Analysis and Knowledge Extraction System (cTAKES) to develop customized pipelines using both RadLex and SentiWordNet (a general-purpose dictionary, GPD). We manually annotated 400 of radiology reports for compound terms (Cts) in noun phrases and used them as the gold standard for the performance evaluation (precision, recall, and F-measure). Additionally, we also created a compound-term-enhanced dictionary (CtED) by analyzing false negatives (FNs) and false positives (FPs), and applied it for another 100 radiology reports for validation. We also evaluated the stem terms of compound terms, through defining two measures: an occurrence ratio (OR) and a matching ratio (MR). RESULTS The F-measure of the cTAKES+RadLex+GPD was 32.2% (Precision 92.1%, Recall 19.6%) and that of combined the CtED was 67.1% (Precision 98.1%, Recall 51.0%). The OR indicated that stem terms of “effusion”, "node", "tube", and "disease" were used frequently, but it still lacks capturing Cts. The MR showed that 71.9% of stem terms matched with that of ontologies and RadLex improved about 22% of the MR from the cTAKES default dictionary. The OR and MR revealed that the characteristics of stem terms would have the potential to help generate synonymous phrases using ontologies. CONCLUSIONS We developed a RadLex-based customized pipeline for parsing radiology reports and demonstrated that CtED and stem term analysis has the potential to improve dictionary-based NER performance toward expanding vocabularies.

scholarly journals Learning Task-Specific Representation for Novel Words in Sequence Labeling

2019 ◽  
Author(s):  
Minlong Peng ◽  
Qi Zhang ◽  
Xiaoyu Xing ◽  
Tao Gui ◽  
Jinlan Fu ◽  
...  
Keyword(s):  
Empirical Studies ◽  
Named Entity Recognition ◽  
Learning Task ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entity ◽  
Part Of Speech Tagging ◽  
Sequence Labeling ◽  
Part Of Speech ◽  
Word Representation

Word representation is a key component in neural-network-based sequence labeling systems. However, representations of unseen or rare words trained on the end task are usually poor for appreciable performance. This is commonly referred to as the out-of-vocabulary (OOV) problem. In this work, we address the OOV problem in sequence labeling using only training data of the task. To this end, we propose a novel method to predict representations for OOV words from their surface-forms (e.g., character sequence) and contexts. The method is specifically designed to avoid the error propagation problem suffered by existing approaches in the same paradigm. To evaluate its effectiveness, we performed extensive empirical studies on four part-of-speech tagging (POS) tasks and four named entity recognition (NER) tasks. Experimental results show that the proposed method can achieve better or competitive performance on the OOV problem compared with existing state-of-the-art methods.

scholarly journals BioALBERT: A Simple and Effective Pre-trained Language Model for Biomedical Named Entity Recognition

2020 ◽  
Author(s):  
Usman Naseem ◽  
Matloob Khushi ◽  
Vinay Reddy ◽  
Sakthivel Rajendran ◽  
Imran Razzak ◽  
...  
Keyword(s):  
State Of The Art ◽  
Language Model ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Future Research ◽  
Named Entity ◽  
Domain Specific ◽  
Context Dependent ◽  
Biomedical Named Entity Recognition

Abstract Background: In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER research is challenging as NER in the biomedical domain are: (i) often restricted due to limited amount of training data, (ii) an entity can refer to multiple types and concepts depending on its context and, (iii) heavy reliance on acronyms that are sub-domain specific. Existing BioNER approaches often neglect these issues and directly adopt the state-of-the-art (SOTA) models trained in general corpora which often yields unsatisfactory results. Results: We propose biomedical ALBERT (A Lite Bidirectional Encoder Representations from Transformers for Biomedical Text Mining) - bioALBERT - an effective domain-specific pre-trained language model trained on huge biomedical corpus designed to capture biomedical context-dependent NER. We adopted self-supervised loss function used in ALBERT that targets on modelling inter-sentence coherence to better learn context-dependent representations and incorporated parameter reduction strategies to minimise memory usage and enhance the training time in BioNER. In our experiments, BioALBERT outperformed comparative SOTA BioNER models on eight biomedical NER benchmark datasets with four different entity types. The performance is increased for; (i) disease type corpora by 7.47% (NCBI-disease) and 10.63% (BC5CDR-disease); (ii) drug-chem type corpora by 4.61% (BC5CDR-Chem) and 3.89 (BC4CHEMD); (iii) gene-protein type corpora by 12.25% (BC2GM) and 6.42% (JNLPBA); and (iv) Species type corpora by 6.19% (LINNAEUS) and 23.71% (Species-800) is observed which leads to a state-of-the-art results. Conclusions: The performance of proposed model on four different biomedical entity types shows that our model is robust and generalizable in recognizing biomedical entities in text. We trained four different variants of BioALBERT models which are available for the research community to be used in future research.

scholarly journals Named Entity Recognition for a Low Resource Language

2019 ◽  
Vol 8 (3) ◽  
pp. 587-590
Keyword(s):  
Machine Learning ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Linguistic Knowledge ◽  
Rule Based ◽  
Low Resource ◽  
Named Entity ◽  
The North ◽  
Rule Based Approach

Kokborok named entity recognition using the rules based approach is being studied in this paper. Named entity recognition is one of the applications of natural language processing. It is considered a subtask for information extraction. Named entity recognition is the means of identifying the named entity for some specific task. We have studied the named entity recognition system for the Kokborok language. Kokborok is the official language of the state of Tripura situated in the north eastern part of India. It is also widely spoken in other part of the north eastern state of India and adjoining areas of Bangladesh. The named entities are like the name of person, organization, location etc. Named entity recognitions are studied using the machine learning approach, rule based approach or the hybrid approach combining the machine learning and rule based approaches. Rule based named entity recognitions are influence by the linguistic knowledge of the language. Machine learning approach requires a large number of training data. Kokborok being a low resource language has very limited number of training data. The rule based approach requires linguistic rules and the results are not depended on the size of data available. We have framed a heuristic rules for identifying the named entity based on linguistic knowledge of the language. An encouraging result is obtained after we test our data with the rule based approach. We also tried to study and frame the rules for the counting system in Kokborok in this paper. The rule based approach to named entity recognition is found suitable for low resource language with limited digital work and absence of named entity tagged data. We have framed a suitable algorithm using the rules for solving the named entity recognition task for obtaining a desirable result.

scholarly journals Ensemble of deep masked language models for effective named entity recognition in multi-domain corpora

2021 ◽  
Author(s):  
Nona Naderi ◽  
Julien Knafou ◽  
Jenny Copara ◽  
Patrick Ruch ◽  
Douglas Teodoro
Keyword(s):  
Named Entity Recognition ◽  
Entity Recognition ◽  
Language Models ◽  
Free Text ◽  
Percentage Point Increase ◽  
Named Entity ◽  
Secondary Use ◽  
Point Increase ◽  
Wet Lab ◽  
Multiple Domains

AbstractThe health and life science domains are well known for their wealth of entities. These entities are presented as free text in large corpora, such as biomedical scientific and electronic health records. To enable the secondary use of these corpora and unlock their value, named entity recognition (NER) methods are proposed. Inspired by the success of deep masked language models, we present an ensemble approach for NER using these models. Results show statistically significant improvement of the ensemble models over baselines based on individual models in multiple domains - chemical, clinical and wet lab - and languages - English and French. The ensemble model achieves an overall performance of 79.2% macro F1-score, a 4.6 percentage point increase upon the baseline in multiple domains and languages. These results suggests that ensembles are a more effective strategy for tackling NER. We further perform a detailed analysis of their performance based on a set of entity properties.

scholarly journals Named Entity Recognition (NER) for Tibetan and Mongolian Newspapers

2021 ◽  
Author(s):  
Robert Barnett ◽  
Christian Faggionato ◽  
Marieke Meelen ◽  
Sargai Yunshaab ◽  
Tsering Samdrup ◽  
...  
Keyword(s):  
Gold Standard ◽  
Named Entity Recognition ◽  
The State ◽  
Training Data ◽  
Entity Recognition ◽  
People's Republic Of China ◽  
Republic Of China ◽  
Named Entity ◽  
Policy Analysts ◽  
Standard Training

Modern Tibetan and Vertical (Traditional) Mongolian are scripts used by c.11m people, mostly within the People’s Republic of China. In terms of publicly available tools for NLP, these languages and their scripts are extremely low-resourced and under-researched. We set out firstly to survey the state of NLP for these languages, and secondly to facilitate research by historians and policy analysts working on Tibetan newspapers. Their primary need is to be able to carry out Named Entity Recognition (NER) in Modern Tibetan, a script which has no word or sentence boundaries and for which no segmenters have been developed. Working on LightTag, an online tagger using character-based modelling, we were able to produce gold-standard training data for NER for use with Modern Tibetan.

scholarly journals NER for Tibetan and Mongolian Newspapers

2021 ◽  
Author(s):  
Robert Barnett ◽  
Christian Faggionato ◽  
Marieke Meelen ◽  
Sargai Yunshaab ◽  
Tsering Samdrup ◽  
...  
Keyword(s):  
Gold Standard ◽  
Named Entity Recognition ◽  
The State ◽  
Training Data ◽  
Entity Recognition ◽  
People's Republic Of China ◽  
Republic Of China ◽  
Named Entity ◽  
Policy Analysts ◽  
Standard Training

Modern Tibetan and Vertical (Traditional) Mongolian are scripts used by c.11m people, mostly within the People’s Republic of China. In terms of publicly available tools for NLP, these languages and their scripts are extremely low-resourced and under-researched. We set out firstly to survey the state of NLP for these languages, and secondly to facilitate research by historians and policy analysts working on Tibetan newspapers. Their primary need is to be able to carry out Named Entity Recognition (NER) in Modern Tibetan, a script which has no word or sentence boundaries and for which no segmenters have been developed. Working on LightTag, an online tagger using character-based modelling, we were able to produce gold-standard training data for NER for use with Modern Tibetan.

scholarly journals A pre-training and self-training approach for biomedical named entity recognition

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246310
Author(s):  
Shang Gao ◽  
Olivera Kotevska ◽  
Alexandre Sorokine ◽  
J. Blair Christian
Keyword(s):  
Transfer Learning ◽  
Question Answering ◽  
Named Entity Recognition ◽  
Model Performance ◽  
Training Data ◽  
Entity Recognition ◽  
Literature Mining ◽  
Unified Medical Language System ◽  
Named Entity ◽  
Training Approach

Named entity recognition (NER) is a key component of many scientific literature mining tasks, such as information retrieval, information extraction, and question answering; however, many modern approaches require large amounts of labeled training data in order to be effective. This severely limits the effectiveness of NER models in applications where expert annotations are difficult and expensive to obtain. In this work, we explore the effectiveness of transfer learning and semi-supervised self-training to improve the performance of NER models in biomedical settings with very limited labeled data (250-2000 labeled samples). We first pre-train a BiLSTM-CRF and a BERT model on a very large general biomedical NER corpus such as MedMentions or Semantic Medline, and then we fine-tune the model on a more specific target NER task that has very limited training data; finally, we apply semi-supervised self-training using unlabeled data to further boost model performance. We show that in NER tasks that focus on common biomedical entity types such as those in the Unified Medical Language System (UMLS), combining transfer learning with self-training enables a NER model such as a BiLSTM-CRF or BERT to obtain similar performance with the same model trained on 3x-8x the amount of labeled data. We further show that our approach can also boost performance in a low-resource application where entities types are more rare and not specifically covered in UMLS.

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