BioNorm: deep learning-based event normalization for the curation of reaction databases

2019 ◽  
Author(s):  
Peiliang Lou ◽  
Antonio Jimeno Yepes ◽  
Zai Zhang ◽  
Qinghua Zheng ◽  
Xiangrong Zhang ◽  
...  
Keyword(s):  
Text Mining ◽  
Natural Language ◽  
Scientific Literature ◽  
Short Term Memory ◽  
Identification Problem ◽  
Molecular Reaction ◽  
Complete Networks ◽  
Novel Method ◽  
Types Of Information ◽  
Natural Language Statement

Abstract Motivation A biochemical reaction, bio-event, depicts the relationships between participating entities. Current text mining research has been focusing on identifying bio-events from scientific literature. However, rare efforts have been dedicated to normalize bio-events extracted from scientific literature with the entries in the curated reaction databases, which could disambiguate the events and further support interconnecting events into biologically meaningful and complete networks. Results In this paper, we propose BioNorm, a novel method of normalizing bio-events extracted from scientific literature to entries in the bio-molecular reaction database, e.g. IntAct. BioNorm considers event normalization as a paraphrase identification problem. It represents an entry as a natural language statement by combining multiple types of information contained in it. Then, it predicts the semantic similarity between the natural language statement and the statements mentioning events in scientific literature using a long short-term memory recurrent neural network (LSTM). An event will be normalized to the entry if the two statements are paraphrase. To the best of our knowledge, this is the first attempt of event normalization in the biomedical text mining. The experiments have been conducted using the molecular interaction data from IntAct. The results demonstrate that the method could achieve F-score of 0.87 in normalizing event-containing statements. Availability and implementation The source code is available at the gitlab repository https://gitlab.com/BioAI/leen and BioASQvec Plus is available on figshare https://figshare.com/s/45896c31d10c3f6d857a.

scholarly journals Does higher education properly prepare graduates for the growing artificial intelligence market? Gaps identification using text mining

2021 ◽  
pp. 1-13
Author(s):  
Lamiae Benhayoun ◽  
Daniel Lang
Keyword(s):  
Artificial Intelligence ◽  
Natural Language Processing ◽  
Text Mining ◽  
Natural Language ◽  
Language Processing ◽  
Academic Training ◽  
Market Requirements ◽  
Job Advertisements ◽  
The Individual

BACKGROUND: The renewed advent of Artificial Intelligence (AI) is inducing profound changes in the classic categories of technology professions and is creating the need for new specific skills. OBJECTIVE: Identify the gaps in terms of skills between academic training on AI in French engineering and Business Schools, and the requirements of the labour market. METHOD: Extraction of AI training contents from the schools’ websites and scraping of a job advertisements’ website. Then, analysis based on a text mining approach with a Python code for Natural Language Processing. RESULTS: Categorization of occupations related to AI. Characterization of three classes of skills for the AI market: Technical, Soft and Interdisciplinary. Skills’ gaps concern some professional certifications and the mastery of specific tools, research abilities, and awareness of ethical and regulatory dimensions of AI. CONCLUSIONS: A deep analysis using algorithms for Natural Language Processing. Results that provide a better understanding of the AI capability components at the individual and the organizational levels. A study that can help shape educational programs to respond to the AI market requirements.

scholarly journals Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Chris Bauer ◽  
Ralf Herwig ◽  
Matthias Lienhard ◽  
Paul Prasse ◽  
Tobias Scheffer ◽  
...  
Keyword(s):  
Text Mining ◽  
Knowledge Base ◽  
Survival Data ◽  
Scientific Literature ◽  
Entity Recognition ◽  
Literature Mining ◽  
Cancer Drugs ◽  
Classical Text ◽  
Anti Cancer ◽  
Cancer Types

Abstract Background There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap. Conclusions Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.

A Hybrid Siamese Neural Network for Natural Language Inference in Cyber-Physical Systems

2021 ◽  
Vol 21 (2) ◽  
pp. 1-25
Author(s):  
Pin Ni ◽  
Yuming Li ◽  
Gangmin Li ◽  
Victor Chang
Keyword(s):  
Natural Language ◽  
Language Processing ◽  
Short Term Memory ◽  
Physical World ◽  
Heterogeneous Data ◽  
Cyber Physical Systems ◽  
Physical Systems ◽  
Language Data ◽  
Text Language ◽  
Different Sources

Cyber-Physical Systems (CPS), as a multi-dimensional complex system that connects the physical world and the cyber world, has a strong demand for processing large amounts of heterogeneous data. These tasks also include Natural Language Inference (NLI) tasks based on text from different sources. However, the current research on natural language processing in CPS does not involve exploration in this field. Therefore, this study proposes a Siamese Network structure that combines Stacked Residual Long Short-Term Memory (bidirectional) with the Attention mechanism and Capsule Network for the NLI module in CPS, which is used to infer the relationship between text/language data from different sources. This model is mainly used to implement NLI tasks and conduct a detailed evaluation in three main NLI benchmarks as the basic semantic understanding module in CPS. Comparative experiments prove that the proposed method achieves competitive performance, has a certain generalization ability, and can balance the performance and the number of trained parameters.

scholarly journals How Do Subway Signs Affect Pedestrians’ Wayfinding Behavior through Visual Short-Term Memory?

2021 ◽  
Vol 13 (12) ◽  
pp. 6866
Author(s):  
Haoru Li ◽  
Jinliang Xu ◽  
Xiaodong Zhang ◽  
Fangchen Ma
Keyword(s):  
Public Transportation ◽  
Short Term Memory ◽  
Memory Capacity ◽  
Cognitive Test ◽  
Subway Station ◽  
Short Term ◽  
Term Memory ◽  
Visual Short Term Memory ◽  
The Difference ◽  
Types Of Information

Recently, subways have become an important part of public transportation and have developed rapidly in China. In the subway station setting, pedestrians mainly rely on visual short-term memory to obtain information on how to travel. This research aimed to explore the short-term memory capacities and the difference in short-term memory for different information for Chinese passengers regarding subway signs. Previous research has shown that people’s general short-term memory capacity is approximately four objects and that, the more complex the information, the lower people’s memory capacity. However, research on the short-term memory characteristics of pedestrians for subway signs is scarce. Hence, based on the STM theory and using 32 subway signs as stimuli, we recruited 120 subjects to conduct a cognitive test. The results showed that passengers had a different memory accuracy for different types of information in the signs. They were more accurate regarding line number and arrow, followed by location/text information, logos, and orientation. Meanwhile, information type, quantity, and complexity had significant effects on pedestrians’ short-term memory capacity. Finally, according to our results that outline the characteristics of short-term memory for subway signs, we put forward some suggestions for subway signs. The findings will be effective in helping designers and managers improve the quality of subway station services as well as promoting the development of pedestrian traffic in such a setting.

scholarly journals Efficient natural language classification algorithm for detecting duplicate unsupervised features

2021 ◽  
Vol 20 (3) ◽  
pp. 623-653
Author(s):  
Saud Altaf ◽  
Sofia Iqbal ◽  
Muhammad Waseem Soomro
Keyword(s):  
Natural Language ◽  
Short Term Memory ◽  
Short Term ◽  
Vocabulary Size ◽  
Language Understanding ◽  
Inverse Document Frequency ◽  
Classification Technique ◽  
Document Frequency ◽  
Text Features ◽  
Long Short Term Memory

This paper focuses on capturing the meaning of Natural Language Understanding (NLU) text features to detect the duplicate unsupervised features. The NLU features are compared with lexical approaches to prove the suitable classification technique. The transfer-learning approach is utilized to train the extraction of features on the Semantic Textual Similarity (STS) task. All features are evaluated with two types of datasets that belong to Bosch bug and Wikipedia article reports. This study aims to structure the recent research efforts by comparing NLU concepts for featuring semantics of text and applying it to IR. The main contribution of this paper is a comparative study of semantic similarity measurements. The experimental results demonstrate the Term Frequency–Inverse Document Frequency (TF-IDF) feature results on both datasets with reasonable vocabulary size. It indicates that the Bidirectional Long Short Term Memory (BiLSTM) can learn the structure of a sentence to improve the classification.

scholarly journals BO-LSTM: Classifying relations via long short-term memory networks along biomedical ontologies

2018 ◽  
Author(s):  
Andre Lamurias ◽  
Luka A. Clarke ◽  
Francisco M. Couto
Keyword(s):  
Deep Learning ◽  
Text Mining ◽  
Drug Interactions ◽  
Short Term Memory ◽  
Biomedical Ontologies ◽  
Short Term ◽  
Term Memory ◽  
Domain Specific ◽  
Learning Techniques ◽  
Long Short Term Memory

AbstractRecent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific resources, such as ontologies. In Life and Health Sciences there is a vast and valuable set of such resources publicly available, which are continuously being updated. Biomedical ontologies are nowadays a mainstream approach to formalize existing knowledge about entities, such as genes, chemicals, phenotypes, and disorders. These resources contain supplementary information that may not be yet encoded in training data, particularly in domains with limited labeled data.We propose a new model, BO-LSTM, that takes advantage of domain-specific ontologies, by representing each entity as the sequence of its ancestors in the ontology. We implemented BO-LSTM as a recurrent neural network with long short-term memory units and using an open biomedical ontology, which in our case-study was Chemical Entities of Biological Interest (ChEBI). We assessed the performance of BO-LSTM on detecting and classifying drug-drug interactions in a publicly available corpus from an international challenge, composed of 792 drug descriptions and 233 scientific abstracts. By using the domain-specific ontology in addition to word embeddings and WordNet, BO-LSTM improved both the F1-score of the detection and classification of drug-drug interactions, particularly in a document set with a limited number of annotations. Our findings demonstrate that besides the high performance of current deep learning techniques, domain-specific ontologies can still be useful to mitigate the lack of labeled data.Author summaryA high quantity of biomedical information is only available in documents such as scientific articles and patents. Due to the rate at which new documents are produced, we need automatic methods to extract useful information from them. Text mining is a subfield of information retrieval which aims at extracting relevant information from text. Scientific literature is a challenge to text mining because of the complexity and specificity of the topics approached. In recent years, deep learning has obtained promising results in various text mining tasks by exploring large datasets. On the other hand, ontologies provide a detailed and sound representation of a domain and have been developed to diverse biomedical domains. We propose a model that combines deep learning algorithms with biomedical ontologies to identify relations between concepts in text. We demonstrate the potential of this model to extract drug-drug interactions from abstracts and drug descriptions. This model can be applied to other biomedical domains using an annotated corpus of documents and an ontology related to that domain to train a new classifier.

scholarly journals PaperBLAST: Text-mining papers for information about homologs

2017 ◽  
Author(s):  
Morgan N. Price ◽  
Adam P. Arkin
Keyword(s):  
Text Mining ◽  
Genome Sequencing ◽  
Full Text ◽  
Large Scale ◽  
Scientific Literature ◽  
Protein Sequences ◽  
Protein Coding ◽  
Link Protein ◽  
Protein Coding Genes ◽  
Link Type

AbstractLarge-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/.

scholarly journals Natural Language Processing for Rapid Response to Emergent Diseases: Case Study of Calcium Channel Blockers and Hypertension in the COVID-19 Pandemic

10.2196/20773 ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. e20773 ◽  
Author(s):  
Antoine Neuraz ◽  
Ivan Lerner ◽  
William Digan ◽  
Nicolas Paris ◽  
Rosy Tsopra ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Text Mining ◽  
Natural Language ◽  
Calcium Channel ◽  
Language Processing ◽  
Calcium Channel Blockers ◽  
Structured Data ◽  
Channel Blockers ◽  
Knowledge Model ◽  
Long Term Treatment

Background A novel disease poses special challenges for informatics solutions. Biomedical informatics relies for the most part on structured data, which require a preexisting data or knowledge model; however, novel diseases do not have preexisting knowledge models. In an emergent epidemic, language processing can enable rapid conversion of unstructured text to a novel knowledge model. However, although this idea has often been suggested, no opportunity has arisen to actually test it in real time. The current coronavirus disease (COVID-19) pandemic presents such an opportunity. Objective The aim of this study was to evaluate the added value of information from clinical text in response to emergent diseases using natural language processing (NLP). Methods We explored the effects of long-term treatment by calcium channel blockers on the outcomes of COVID-19 infection in patients with high blood pressure during in-patient hospital stays using two sources of information: data available strictly from structured electronic health records (EHRs) and data available through structured EHRs and text mining. Results In this multicenter study involving 39 hospitals, text mining increased the statistical power sufficiently to change a negative result for an adjusted hazard ratio to a positive one. Compared to the baseline structured data, the number of patients available for inclusion in the study increased by 2.95 times, the amount of available information on medications increased by 7.2 times, and the amount of additional phenotypic information increased by 11.9 times. Conclusions In our study, use of calcium channel blockers was associated with decreased in-hospital mortality in patients with COVID-19 infection. This finding was obtained by quickly adapting an NLP pipeline to the domain of the novel disease; the adapted pipeline still performed sufficiently to extract useful information. When that information was used to supplement existing structured data, the sample size could be increased sufficiently to see treatment effects that were not previously statistically detectable.

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