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deepMINE - Natural Language Processing based Automatic Literature Mining and Research Summarization for Early Stage Comprehension in Pandemic Situations specifically for COVID-19

Joshi, B. P.; Bakrola, V. D.; Shah, P.; Krishnamurthy, R.

2020-04-02 bioinformatics
10.1101/2020.03.30.014555 bioRxiv
Show abstract

The recent pandemic created due to Novel Coronavirus (nCOV-2019) from Wuhan, China demanding a large scale of a general health emergency. This demands novel research on the vaccine to fight against this pandemic situation, re-purposing of the existing drugs, phylogenetic analysis to identify the origin and determine the similarity with other known viruses, etc. The very preliminary task from the research community is to analyze the wide verities of existing related research articles, which is very much time-consuming in such situations where each minute counts for saving hundreds of human lives. The entire manual processing is even lower down the efficiency in mining the information. We have developed a complete automatic literature mining system that delivers efficient and fast mining from existing biomedical literature databases. With the help of modern-day deep learning algorithms, our system also delivers a summarization of important research articles that provides ease and fast comprehension of critical research articles. The system is currently scanning nearly 1,46,115,136 English words from 29,315 research articles in not greater than 1.5 seconds with multiple search keywords. Our research article presents the criticality of literature mining, especially in pandemic situations with the implementation and online deployment of the system.

Matching journals

The top 8 journals account for 50% of the predicted probability mass.

1
Database
51 papers in training set
Top 0.1%
22.8%
2
Genomics, Proteomics & Bioinformatics
171 papers in training set
Top 0.7%
8.5%
3
PLOS ONE
4510 papers in training set
Top 33%
4.4%
4
Nucleic Acids Research
1128 papers in training set
Top 5%
4.0%
5
GigaScience
172 papers in training set
Top 0.5%
3.6%
6
Journal of Biomedical Informatics
45 papers in training set
Top 0.5%
3.3%
7
BMC Bioinformatics
383 papers in training set
Top 3%
2.8%
8
IEEE Journal of Biomedical and Health Informatics
34 papers in training set
Top 0.6%
2.8%
50% of probability mass above
9
Bioinformatics
1061 papers in training set
Top 6%
2.6%
10
Briefings in Bioinformatics
326 papers in training set
Top 3%
2.6%
11
Scientific Reports
3102 papers in training set
Top 49%
2.1%
12
IEEE/ACM Transactions on Computational Biology and Bioinformatics
32 papers in training set
Top 0.1%
2.1%
13
Computers in Biology and Medicine
120 papers in training set
Top 2%
1.9%
14
Computational and Structural Biotechnology Journal
216 papers in training set
Top 4%
1.7%
15
Neuroinformatics
40 papers in training set
Top 0.6%
1.5%
16
iScience
1063 papers in training set
Top 17%
1.5%
17
BioData Mining
15 papers in training set
Top 0.4%
1.3%
18
IEEE Access
31 papers in training set
Top 0.6%
1.2%
19
Bioinformatics Advances
184 papers in training set
Top 4%
0.9%
20
Nature Communications
4913 papers in training set
Top 59%
0.9%
21
NAR Genomics and Bioinformatics
214 papers in training set
Top 3%
0.9%
22
Bioengineering
24 papers in training set
Top 1%
0.8%
23
Patterns
70 papers in training set
Top 2%
0.8%
24
Informatics in Medicine Unlocked
21 papers in training set
Top 1%
0.8%
25
Journal of the American Medical Informatics Association
61 papers in training set
Top 2%
0.8%
26
Proceedings of the National Academy of Sciences
2130 papers in training set
Top 44%
0.8%
27
Frontiers in Genetics
197 papers in training set
Top 9%
0.8%
28
BMC Medical Informatics and Decision Making
39 papers in training set
Top 3%
0.7%
29
PeerJ
261 papers in training set
Top 16%
0.7%
30
Research Synthesis Methods
20 papers in training set
Top 0.2%
0.7%