scholarly journals An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

2008 ◽  
Vol 3 (1) ◽  
pp. 1 ◽  
Author(s):  
William A Baumgartner ◽  
K Bretonnel Cohen ◽  
Lawrence Hunter
Keyword(s):  
Text Mining ◽  
Open Source ◽  
Large Scale ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Open Source Framework

scholarly journals The BioLexicon: a large-scale terminological resource for biomedical text mining

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Thompson ◽  
John McNaught ◽  
Simonetta Montemagni ◽  
Nicoletta Calzolari ◽  
Riccardo del Gratta ◽  
...  
Keyword(s):  
Text Mining ◽  
Large Scale ◽  
Biomedical Text ◽  
Biomedical Text Mining

scholarly journals Biomedical Text Mining for Research Rigor and Integrity: Tasks, Challenges, Directions

2017 ◽  
Author(s):  
Halil Kilicoglu
Keyword(s):  
Text Mining ◽  
Biomedical Research ◽  
Large Scale ◽  
Research Output ◽  
Guideline Development ◽  
Research Integrity ◽  
Supplementary Information ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Supplementary Material

AbstractAn estimated quarter of a trillion US dollars is invested in the biomedical research enterprise annually. There is growing alarm that a significant portion of this investment is wasted, due to problems in reproducibility of research findings and in the rigor and integrity of research conduct and reporting. Recent years have seen a flurry of activities focusing on standardization and guideline development to enhance the reproducibility and rigor of biomedical research. Research activity is primarily communicated via textual artifacts, ranging from grant applications to journal publications. These artifacts can be both the source and the end result of practices leading to research waste. For example, an article may describe a poorly designed experiment, or the authors may reach conclusions not supported by the evidence presented. In this article, we pose the question of whether biomedical text mining techniques can assist the stakeholders in the biomedical research enterprise in doing their part towards enhancing research integrity and rigor. In particular, we identify four key areas in which text mining techniques can make a significant contribution: plagiarism/fraud detection, ensuring adherence to reporting guidelines, managing information overload, and accurate citation/enhanced bibliometrics. We review the existing methods and tools for specific tasks, if they exist, or discuss relevant research that can provide guidance for future work. With the exponential increase in biomedical research output and the ability of text mining approaches to perform automatic tasks at large scale, we propose that such approaches can add checks and balances that promote responsible research practices and can provide significant benefits for the biomedical research enterprise.Supplementary informationSupplementary material is available at BioRxiv.

scholarly journals PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mohammadreza Yaghoobi ◽  
Krzysztof S. Stopka ◽  
Aaditya Lakshmanan ◽  
Veera Sundararaghavan ◽  
John E. Allison ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Metals And Alloys ◽  
Analysis Tool ◽  
Computational Framework ◽  
Crystal Plasticity Finite Element ◽  
Polycrystalline Metals ◽  
Simulation Based ◽  
Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

scholarly journals Biomedical Text Mining and Its Applications

2009 ◽  
Vol 5 (12) ◽  
pp. e1000597 ◽  
Author(s):  
Raul Rodriguez-Esteban
Keyword(s):  
Text Mining ◽  
Biomedical Text ◽  
Biomedical Text Mining

scholarly journals ParaBTM: A Parallel Processing Framework for Biomedical Text Mining on Supercomputers

Molecules ◽  
2018 ◽  
Vol 23 (5) ◽  
pp. 1028 ◽  
Author(s):  
Yuting Xing ◽  
Chengkun Wu ◽  
Xi Yang ◽  
Wei Wang ◽  
En Zhu ◽  
...  
Keyword(s):  
Parallel Processing ◽  
Text Mining ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Processing Framework
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