Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology

2006 ◽  
pp. 39-56
Author(s):  
Xiaohua Hu
Keyword(s):  
Natural Language Processing ◽  
Systems Biology ◽  
Natural Language ◽  
Language Processing ◽  
Biomedical Literature ◽  
Literature Mining ◽  
Biomedical Literature Mining

Preprocessing in Biomedical Literature Mining Using Natural Language Processing

2014 ◽  
Vol 687-691 ◽  
pp. 1149-1152
Author(s):  
Jing Peng ◽  
Hong Min Sun
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Biomedical Literature ◽  
Literature Mining ◽  
Noise Data ◽  
Text Preprocessing ◽  
Biomedical Literature Mining ◽  
The Web

The number of biomedical literatures is growing rapidly, and biomedical literature mining is becoming essential. An approach for article processing in text preprocessing is proposed in order to improve the performance of biomedical literature mining. This approach combines the Web and corpus counts in order to eliminate the limitations of noise data of the Web. We experimentally showed that the performance of the combination models is the best comparing to the pure Web and corpus models. We achieve the best precision of 89.1% on all article forms and 88.7% article loss class.

scholarly journals Using distant supervision to augment manually annotated data for relation extraction

2019 ◽  
Author(s):  
Peng Su ◽  
Gang Li ◽  
Cathy Wu ◽  
K. Vijay-Shanker
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Relation Extraction ◽  
Biomedical Literature ◽  
Training Data ◽  
Distant Supervision ◽  
Large Size ◽  
Domain Expertise

AbstractSignificant progress has been made in applying deep learning on natural language processing tasks recently. However, deep learning models typically require a large amount of annotated training data while often only small labeled datasets are available for many natural language processing tasks in biomedical literature. Building large-size datasets for deep learning is expensive since it involves considerable human effort and usually requires domain expertise in specialized fields. In this work, we consider augmenting manually annotated data with large amounts of data using distant supervision. However, data obtained by distant supervision is often noisy, we first apply some heuristics to remove some of the incorrect annotations. Then using methods inspired from transfer learning, we show that the resulting models outperform models trained on the original manually annotated sets.

Natural Language Processing–Assisted Literature Retrieval and Analysis for Combination Therapy in Cancer

2022 ◽  
Author(s):  
Jia Zeng ◽  
Christian X. Cruz-Pico ◽  
Turçin Saridogan ◽  
Md Abu Shufean ◽  
Michael Kahle ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Combination Therapy ◽  
Natural Language ◽  
Search Engine ◽  
Language Processing ◽  
Biomedical Literature ◽  
Antitumor Efficacy ◽  
Domain Specific ◽  
Validation Experiment

PURPOSE Despite advances in molecular therapeutics, few anticancer agents achieve durable responses. Rational combinations using two or more anticancer drugs have the potential to achieve a synergistic effect and overcome drug resistance, enhancing antitumor efficacy. A publicly accessible biomedical literature search engine dedicated to this domain will facilitate knowledge discovery and reduce manual search and review. METHODS We developed RetriLite, an information retrieval and extraction framework that leverages natural language processing and domain-specific knowledgebase to computationally identify highly relevant papers and extract key information. The modular architecture enables RetriLite to benefit from synergizing information retrieval and natural language processing techniques while remaining flexible to customization. We customized the application and created an informatics pipeline that strategically identifies papers that describe efficacy of using combination therapies in clinical or preclinical studies. RESULTS In a small pilot study, RetriLite achieved an F 1 score of 0.93. A more extensive validation experiment was conducted to determine agents that have enhanced antitumor efficacy in vitro or in vivo with poly (ADP-ribose) polymerase inhibitors: 95.9% of the papers determined to be relevant by our application were true positive and the application's feature of distinguishing a clinical paper from a preclinical paper achieved an accuracy of 97.6%. Interobserver assessment was conducted, which resulted in a 100% concordance. The data derived from the informatics pipeline have also been made accessible to the public via a dedicated online search engine with an intuitive user interface. CONCLUSION RetriLite is a framework that can be applied to establish domain-specific information retrieval and extraction systems. The extensive and high-quality metadata tags along with keyword highlighting facilitate information seekers to more effectively and efficiently discover knowledge in the combination therapy domain.

scholarly journals Similarity corpus on microbial transcriptional regulation

2017 ◽  
Author(s):  
Lithgow-Serrano Oscar ◽  
Gama-Castro Socorro ◽  
Ishida-Gutiérrez Cecilia ◽  
Mejía-Almonte Citlali ◽  
Tierrafría Víctor ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcriptional Regulation ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Selection Criteria ◽  
Statistical Power ◽  
Biomedical Literature ◽  
Automatic Processes ◽  
Valuable Resource

AbstractThe ability to express the same meaning in different ways is a well known property of natural language. This amazing property is the source of major difficulties in natural language processing. Given the constant increase in published literature, its curation and information extraction would strongly benefit by efficient automatic processes, for which, corpora of sentences evaluated by experts is a valuable resource. Given our interest in applying such approaches to the benefit of curation of the biomedical literature, specifically about gene regulation in microbial organisms, we decided to build a corpus with graded textual similarity evaluated by curators, and designed specifically oriented to our purposes. Based on the predefined statistical power of future analyses, we defined features of the design including sampling, selection criteria, balance, and size among others. A non-fully crossed-design was performed for each pair of sentences by 3 evaluators from 7 different groups, adapting the SEMEVAL scale to our goals in four successive iterative sessions with a clear improvement in the consensuated guidelines and inter-rater-reliability results. Alternatives for the corpus evaluation are widely discussed. To the best of our knowledge this is the first similarity corpus in this domain of knowledge. We have initiated its incorporation in our research towards high throughput curation strategies based in natural language processing.

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