diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..1cde967
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+# Project source #
+###################
+*.project
+*.classpath
+
+# Package Files #
+#################
+*.jar
diff --git a/arff/triage0_50_ngrams_size1_stopwords.arff b/arff/triage0_50_ngrams_size1_stopwords.arff
new file mode 100644
index 0000000..c7525b4
--- /dev/null
+++ b/arff/triage0_50_ngrams_size1_stopwords.arff
@@ -0,0 +1,38 @@
+% Weka training file - HIV triage - 2015
+
+@RELATION triage
+@ATTRIBUTE docID REAL %PMID of paper
+@ATTRIBUTE Ngram0trees REAL %trees
+@ATTRIBUTE Ngram1model REAL %model
+@ATTRIBUTE Ngram2triage REAL %triage
+@ATTRIBUTE Ngram3genes REAL %genes
+@ATTRIBUTE Ngram4sampling REAL %sampling
+@ATTRIBUTE Ngram5classification REAL %classification
+@ATTRIBUTE Ngram6processing REAL %processing
+@ATTRIBUTE Ngram7fungal REAL %fungal
+@ATTRIBUTE Ngram8enzymes REAL %enzymes
+@ATTRIBUTE Ngram9manual REAL %manual
+@ATTRIBUTE Ngram10literature REAL %literature
+@ATTRIBUTE Ngram11annotation REAL %annotation
+@ATTRIBUTE Ngram12mycoclapfungalgenomicsca REAL %mycoclapfungalgenomicsca
+@ATTRIBUTE Ngram13machine REAL %machine
+@ATTRIBUTE Ngram14first REAL %first
+@ATTRIBUTE Ngram15features REAL %features
+@ATTRIBUTE Ngram16mycoclap REAL %mycoclap
+@ATTRIBUTE Ngram17results REAL %results
+@ATTRIBUTE Ngram18abstracttext REAL %abstracttext
+@ATTRIBUTE Ngram19task REAL %task
+@ATTRIBUTE Ngram20http REAL %http
+@ATTRIBUTE Ngram21support REAL %support
+@ATTRIBUTE Ngram22learning REAL %learning
+@ATTRIBUTE Ngram23database REAL %database
+@ATTRIBUTE Ngram24curation REAL %curation
+@ATTRIBUTE Ngram25logistic REAL %logistic
+@ATTRIBUTE Ngram26applications REAL %applications
+@ATTRIBUTE Ngram27articletitle REAL %articletitle
+@ATTRIBUTE class {positive, negative}
+@DATA
+
+25754864,0,0,0,2,0,0,2,5,3,1,1,2,2,0,1,0,6,1,0,0,2,2,0,4,2,0,2,0,negative
+25551575,2,4,3,0,2,2,0,0,0,1,2,0,0,4,1,2,0,1,0,2,0,2,3,0,1,2,0,0,negative
+
diff --git a/arff/triage1_50_ngrams_size1_stopwords.arff b/arff/triage1_50_ngrams_size1_stopwords.arff
new file mode 100644
index 0000000..ddfc07d
--- /dev/null
+++ b/arff/triage1_50_ngrams_size1_stopwords.arff
@@ -0,0 +1,38 @@
+% Weka test file - HIV triage - 2015
+
+@RELATION triage
+@ATTRIBUTE docID REAL %PMID of paper
+@ATTRIBUTE Ngram0trees REAL %trees
+@ATTRIBUTE Ngram1model REAL %model
+@ATTRIBUTE Ngram2triage REAL %triage
+@ATTRIBUTE Ngram3genes REAL %genes
+@ATTRIBUTE Ngram4sampling REAL %sampling
+@ATTRIBUTE Ngram5classification REAL %classification
+@ATTRIBUTE Ngram6processing REAL %processing
+@ATTRIBUTE Ngram7fungal REAL %fungal
+@ATTRIBUTE Ngram8enzymes REAL %enzymes
+@ATTRIBUTE Ngram9manual REAL %manual
+@ATTRIBUTE Ngram10literature REAL %literature
+@ATTRIBUTE Ngram11annotation REAL %annotation
+@ATTRIBUTE Ngram12mycoclapfungalgenomicsca REAL %mycoclapfungalgenomicsca
+@ATTRIBUTE Ngram13machine REAL %machine
+@ATTRIBUTE Ngram14first REAL %first
+@ATTRIBUTE Ngram15features REAL %features
+@ATTRIBUTE Ngram16mycoclap REAL %mycoclap
+@ATTRIBUTE Ngram17results REAL %results
+@ATTRIBUTE Ngram18abstracttext REAL %abstracttext
+@ATTRIBUTE Ngram19task REAL %task
+@ATTRIBUTE Ngram20http REAL %http
+@ATTRIBUTE Ngram21support REAL %support
+@ATTRIBUTE Ngram22learning REAL %learning
+@ATTRIBUTE Ngram23database REAL %database
+@ATTRIBUTE Ngram24curation REAL %curation
+@ATTRIBUTE Ngram25logistic REAL %logistic
+@ATTRIBUTE Ngram26applications REAL %applications
+@ATTRIBUTE Ngram27articletitle REAL %articletitle
+@ATTRIBUTE class {positive, negative}
+@DATA
+
+25754864,0,0,0,2,0,0,2,5,3,1,1,2,2,0,1,0,6,1,0,0,2,2,0,4,2,0,2,0,negative
+25551575,2,4,3,0,2,2,0,0,0,1,2,0,0,4,1,2,0,1,0,2,0,2,3,0,1,2,0,0,negative
+
diff --git a/build.xml b/build.xml
new file mode 100644
index 0000000..efbea36
--- /dev/null
+++ b/build.xml
@@ -0,0 +1,153 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/corpus/mycoSORTSampleTriagecorpus_test.xml b/corpus/mycoSORTSampleTriagecorpus_test.xml
new file mode 100644
index 0000000..bdd6cf2
--- /dev/null
+++ b/corpus/mycoSORTSampleTriagecorpus_test.xml
@@ -0,0 +1,468 @@
+
+
+
+ 25754864
+
+ 2015
+ 03
+ 10
+
+
+ 2015
+ 03
+ 18
+
+
+
+ 1758-0463
+
+ 2015
+
+ 2015
+
+
+ Database : the journal of biological databases and curation
+ Database (Oxford)
+
+ mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.
+
+
+
+ 10.1093/database/bav008
+ bav008
+
+ Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and oxidoreductases. Fungi are prolific producers of these enzymes, spurring fungal genome sequencing efforts to identify and catalogue the genes that encode them. To facilitate the functional annotation of these genes, biochemical data on over 800 fungal lignocellulose-degrading enzymes have been collected from the literature and organized into the searchable database, mycoCLAP (http://mycoclap.fungalgenomics.ca). First implemented in 2011, and updated as described here, mycoCLAP is capable of ranking search results according to closest biochemically characterized homologues: this improves the quality of the annotation, and significantly decreases the time required to annotate novel sequences. The database is freely available to the scientific community, as are the open source applications based on natural language processing developed to support the manual curation of mycoCLAP. Database URL: http://mycoclap.fungalgenomics.ca.
+ © The Author(s) 2015. Published by Oxford University Press.
+
+
+
+ Strasser
+ Kimchi
+ K
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ McDonnell
+ Erin
+ E
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Nyaga
+ Carol
+ C
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Wu
+ Min
+ M
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Wu
+ Sherry
+ S
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Almeida
+ Hayda
+ H
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Meurs
+ Marie-Jean
+ MJ
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Kosseim
+ Leila
+ L
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Powlowski
+ Justin
+ J
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Butler
+ Greg
+ G
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA gregb@encs.concordia.ca.
+
+
+
+ Tsang
+ Adrian
+ A
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ eng
+
+ Journal Article
+ Research Support, Non-U.S. Gov't
+
+
+ 2015
+ 03
+ 08
+
+
+
+ England
+ Database (Oxford)
+ 101517697
+ 1758-0463
+
+ IM
+
+
+ Nat Biotechnol. 2004 Jun;22(6):695-700
+ 15122302
+
+
+ Appl Environ Microbiol. 2013 Aug;79(15):4620-34
+ 23709508
+
+
+ J Mol Biol. 1990 Oct 5;215(3):403-10
+ 2231712
+
+
+ Nature. 2008 Sep 4;455(7209):47-50
+ 18769432
+
+
+ Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8
+ 18838391
+
+
+ Nucleic Acids Res. 2009 Jan;37(Database issue):D588-92
+ 18984617
+
+
+ Database (Oxford). 2011;2011:bar020
+ 21622642
+
+
+ Genome Res. 2011 Jun;21(6):885-97
+ 21543515
+
+
+ Nat Methods. 2011;8(10):785-6
+ 21959131
+
+
+ Nat Biotechnol. 2011 Oct;29(10):922-7
+ 21964414
+
+
+ Enzyme Microb Technol. 2011 Apr 7;48(4-5):397-403
+ 22112956
+
+
+ BMC Med Inform Decis Mak. 2012;12 Suppl 1:S5
+ 22595090
+
+
+ Science. 2012 Jun 29;336(6089):1715-9
+ 22745431
+
+
+ Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7
+ 23161681
+
+
+ Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42
+ 23193287
+
+
+ Nat Genet. 2000 May;25(1):25-9
+ 10802651
+
+
+ PLoS One. 2014;9(12):e115892
+ 25551575
+
+
+ PMC4352688
+
+
+
+
+ 2015
+
+
+
+
+ 2015
+ 3
+ 11
+ 6
+ 0
+
+
+ 2015
+ 3
+ 11
+ 6
+ 0
+
+
+ 2015
+ 3
+ 11
+ 6
+ 0
+
+
+ epublish
+
+ bav008
+ 10.1093/database/bav008
+ 25754864
+ PMC4352688
+
+
+
+
+
+
+ 25551575
+
+ 2015
+ 01
+ 01
+
+
+ 2015
+ 01
+ 13
+
+
+
+ 1932-6203
+
+ 9
+ 12
+
+ 2014
+
+
+ PloS one
+ PLoS ONE
+
+ Machine learning for biomedical literature triage.
+
+ e115892
+
+ 10.1371/journal.pone.0115892
+
+ This paper presents a machine learning system for supporting the first task of the biological literature manual curation process, called triage. We compare the performance of various classification models, by experimenting with dataset sampling factors and a set of features, as well as three different machine learning algorithms (Naive Bayes, Support Vector Machine and Logistic Model Trees). The results show that the most fitting model to handle the imbalanced datasets of the triage classification task is obtained by using domain relevant features, an under-sampling technique, and the Logistic Model Trees algorithm.
+
+
+
+ Almeida
+ Hayda
+ H
+
+ Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada.
+
+
+
+ Meurs
+ Marie-Jean
+ MJ
+
+ Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
+
+
+
+ Kosseim
+ Leila
+ L
+
+ Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada.
+
+
+
+ Butler
+ Greg
+ G
+
+ Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
+
+
+
+ Tsang
+ Adrian
+ A
+
+ Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
+
+
+
+ eng
+
+ Journal Article
+ Research Support, Non-U.S. Gov't
+
+
+ 2014
+ 12
+ 31
+
+
+
+ United States
+ PLoS One
+ 101285081
+ 1932-6203
+
+ IM
+
+
+ Proc AMIA Symp. 2001;:17-21
+ 11825149
+
+
+ Artif Intell Med. 2005 Sep-Oct;35(1-2):121-34
+ 16024240
+
+
+ Mol Cell. 2006 Mar 3;21(5):589-94
+ 16507357
+
+
+ Bioinformatics. 2006 Mar 15;22(6):658-64
+ 16287934
+
+
+ Artif Intell Med. 2006 May;37(1):7-18
+ 16233974
+
+
+ Nature. 2008 Sep 4;455(7209):47-50
+ 18769432
+
+
+ IEEE Trans Syst Man Cybern B Cybern. 2009 Feb;39(1):281-8
+ 19068445
+
+
+ Database (Oxford). 2011;2011:bar020
+ 21622642
+
+
+ J Integr Bioinform. 2011;8(3):176
+ 21926439
+
+
+ Database (Oxford). 2012;2012:bas020
+ 22513129
+
+
+ BMC Med Inform Decis Mak. 2012;12 Suppl 1:S5
+ 22595090
+
+
+ PLoS One. 2013;8(6):e65848
+ 23785456
+
+
+ PLoS One. 2013;8(12):e80503
+ 24312478
+
+
+ PLoS One. 2014;9(4):e91315
+ 24705246
+
+
+ PLoS One. 2014;9(7):e102039
+ 25036529
+
+
+ PMC4281078
+
+
+
+
+ 2014
+
+
+
+
+ 2014
+ 9
+ 4
+
+
+ 2014
+ 11
+ 27
+
+
+ 2014
+ 12
+ 31
+
+
+ 2015
+ 1
+ 1
+ 6
+ 0
+
+
+ 2015
+ 1
+ 1
+ 6
+ 0
+
+
+ 2015
+ 1
+ 1
+ 6
+ 0
+
+
+ epublish
+
+ 10.1371/journal.pone.0115892
+ PONE-D-14-39858
+ 25551575
+ PMC4281078
+
+
+
+
+
diff --git a/corpus/mycoSORTSampleTriagecorpus_train_50.xml b/corpus/mycoSORTSampleTriagecorpus_train_50.xml
new file mode 100644
index 0000000..bdd6cf2
--- /dev/null
+++ b/corpus/mycoSORTSampleTriagecorpus_train_50.xml
@@ -0,0 +1,468 @@
+
+
+
+ 25754864
+
+ 2015
+ 03
+ 10
+
+
+ 2015
+ 03
+ 18
+
+
+
+ 1758-0463
+
+ 2015
+
+ 2015
+
+
+ Database : the journal of biological databases and curation
+ Database (Oxford)
+
+ mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.
+
+
+
+ 10.1093/database/bav008
+ bav008
+
+ Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and oxidoreductases. Fungi are prolific producers of these enzymes, spurring fungal genome sequencing efforts to identify and catalogue the genes that encode them. To facilitate the functional annotation of these genes, biochemical data on over 800 fungal lignocellulose-degrading enzymes have been collected from the literature and organized into the searchable database, mycoCLAP (http://mycoclap.fungalgenomics.ca). First implemented in 2011, and updated as described here, mycoCLAP is capable of ranking search results according to closest biochemically characterized homologues: this improves the quality of the annotation, and significantly decreases the time required to annotate novel sequences. The database is freely available to the scientific community, as are the open source applications based on natural language processing developed to support the manual curation of mycoCLAP. Database URL: http://mycoclap.fungalgenomics.ca.
+ © The Author(s) 2015. Published by Oxford University Press.
+
+
+
+ Strasser
+ Kimchi
+ K
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ McDonnell
+ Erin
+ E
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Nyaga
+ Carol
+ C
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Wu
+ Min
+ M
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Wu
+ Sherry
+ S
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Almeida
+ Hayda
+ H
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Meurs
+ Marie-Jean
+ MJ
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Kosseim
+ Leila
+ L
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Powlowski
+ Justin
+ J
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ Butler
+ Greg
+ G
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA gregb@encs.concordia.ca.
+
+
+
+ Tsang
+ Adrian
+ A
+
+ Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA Centre for Structural and Functional Genomics, Department of Computer Science and Software Engineering, Department of Chemistry and Biochemistry, and Department of Biology Concordia University, Montréal, QC, USA.
+
+
+
+ eng
+
+ Journal Article
+ Research Support, Non-U.S. Gov't
+
+
+ 2015
+ 03
+ 08
+
+
+
+ England
+ Database (Oxford)
+ 101517697
+ 1758-0463
+
+ IM
+
+
+ Nat Biotechnol. 2004 Jun;22(6):695-700
+ 15122302
+
+
+ Appl Environ Microbiol. 2013 Aug;79(15):4620-34
+ 23709508
+
+
+ J Mol Biol. 1990 Oct 5;215(3):403-10
+ 2231712
+
+
+ Nature. 2008 Sep 4;455(7209):47-50
+ 18769432
+
+
+ Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8
+ 18838391
+
+
+ Nucleic Acids Res. 2009 Jan;37(Database issue):D588-92
+ 18984617
+
+
+ Database (Oxford). 2011;2011:bar020
+ 21622642
+
+
+ Genome Res. 2011 Jun;21(6):885-97
+ 21543515
+
+
+ Nat Methods. 2011;8(10):785-6
+ 21959131
+
+
+ Nat Biotechnol. 2011 Oct;29(10):922-7
+ 21964414
+
+
+ Enzyme Microb Technol. 2011 Apr 7;48(4-5):397-403
+ 22112956
+
+
+ BMC Med Inform Decis Mak. 2012;12 Suppl 1:S5
+ 22595090
+
+
+ Science. 2012 Jun 29;336(6089):1715-9
+ 22745431
+
+
+ Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7
+ 23161681
+
+
+ Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42
+ 23193287
+
+
+ Nat Genet. 2000 May;25(1):25-9
+ 10802651
+
+
+ PLoS One. 2014;9(12):e115892
+ 25551575
+
+
+ PMC4352688
+
+
+
+
+ 2015
+
+
+
+
+ 2015
+ 3
+ 11
+ 6
+ 0
+
+
+ 2015
+ 3
+ 11
+ 6
+ 0
+
+
+ 2015
+ 3
+ 11
+ 6
+ 0
+
+
+ epublish
+
+ bav008
+ 10.1093/database/bav008
+ 25754864
+ PMC4352688
+
+
+
+
+
+
+ 25551575
+
+ 2015
+ 01
+ 01
+
+
+ 2015
+ 01
+ 13
+
+
+
+ 1932-6203
+
+ 9
+ 12
+
+ 2014
+
+
+ PloS one
+ PLoS ONE
+
+ Machine learning for biomedical literature triage.
+
+ e115892
+
+ 10.1371/journal.pone.0115892
+
+ This paper presents a machine learning system for supporting the first task of the biological literature manual curation process, called triage. We compare the performance of various classification models, by experimenting with dataset sampling factors and a set of features, as well as three different machine learning algorithms (Naive Bayes, Support Vector Machine and Logistic Model Trees). The results show that the most fitting model to handle the imbalanced datasets of the triage classification task is obtained by using domain relevant features, an under-sampling technique, and the Logistic Model Trees algorithm.
+
+
+
+ Almeida
+ Hayda
+ H
+
+ Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada.
+
+
+
+ Meurs
+ Marie-Jean
+ MJ
+
+ Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
+
+
+
+ Kosseim
+ Leila
+ L
+
+ Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada.
+
+
+
+ Butler
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+ Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
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+ Tsang
+ Adrian
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+ Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
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+ eng
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+ Journal Article
+ Research Support, Non-U.S. Gov't
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+ 2014
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+
+
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+ 2014
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+
+
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+ 2014
+ 9
+ 4
+
+
+ 2014
+ 11
+ 27
+
+
+ 2014
+ 12
+ 31
+
+
+ 2015
+ 1
+ 1
+ 6
+ 0
+
+
+ 2015
+ 1
+ 1
+ 6
+ 0
+
+
+ 2015
+ 1
+ 1
+ 6
+ 0
+
+
+ epublish
+
+ 10.1371/journal.pone.0115892
+ PONE-D-14-39858
+ 25551575
+ PMC4281078
+
+
+
+
+
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+20879840 negative
+1934116 positive
+22112956 positive
+19453169 positive
+20591661 positive
+1896470 negative
+19000618 positive
+19580870 negative
+9406381 positive
+17002602 positive
+6771030 negative
+15555940 positive
+15555941 negative
+1320186 positive
+8836148 positive
+23101390 positive
+21531609 negative
+3384334 positive
+23624166 negative
+24313660 negative
+17551789 positive
+21632240 negative
+15555935 positive
+23318568 negative
+16121561 negative
+8929394 positive
+22203550 negative
+3440521 positive
+12466887 positive
+8815461 negative
+8837470 positive
+19924304 negative
+12630320 negative
+17194495 positive
+1606968 positive
+21498763 negative
+9335167 positive
+3153146 negative
+15116339 negative
+17277884 positive
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+15784980 positive
+18661293 negative
+8085821 positive
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+12237858 positive
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+3314909 negative
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+9546185 positive
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+3290051 negative
+11553760 negative
+10584016 positive
+10586675 negative
+11319115 positive
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+16694 negative
+12506981 positive
+15749766 negative
+16362326 negative
+2450787 negative
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+15808943 positive
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+20414741 negative
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+15715951 negative
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+16330537 positive
+9756469 positive
+8529895 positive
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+10427736 negative
+16944135 positive
+16614901 positive
+15850449 negative
+7592488 positive
+23463247 positive
+16668702 negative
+17851776 negative
+19044008 negative
+16328626 positive
+16739943 negative
+8455560 negative
+19129654 positive
+15629130 positive
+12374797 positive
+9325167 negative
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+9002269 negative
+20419375 positive
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+17964183 positive
+20235799 negative
+560243 negative
+3124870 negative
+15316684 negative
+12145937 negative
+4736235 negative
+2113524 positive
+20850111 negative
+24232491 negative
+7805053 positive
+4796770 negative
+23292745 negative
+6540443 negative
+18942586 negative
+10572260 positive
+9003585 negative
+2925681 positive
+17455791 positive
+16407250 negative
+12664153 positive
+1899374 negative
+16776296 positive
+2785629 negative
+15819855 negative
+21350668 negative
+23280774 negative
+9177963 negative
+12489121 negative
+12383257 positive
+16535476 negative
+11402645 negative
+10830498 positive
+7961928 negative
+22738957 negative
+11601607 negative
+17876815 positive
+1930835 negative
+8572698 positive
+23454546 negative
+20675115 negative
+18060506 positive
+3240864 positive
+2762318 negative
+20807550 negative
+21920035 positive
+9546178 positive
+9546179 positive
+23956415 negative
+22036533 positive
+22750808 positive
+23077275 positive
+1643283 negative
+12387863 negative
+11955286 negative
+3912145 negative
+14558143 negative
+16233469 positive
+8419289 positive
+2227420 positive
+12400688 positive
+1979298 positive
+19941023 positive
+10222181 positive
+18327544 negative
+6068063 negative
+22579385 negative
+6068064 negative
\ No newline at end of file
diff --git a/src/analyse/.gitignore b/src/analyse/.gitignore
new file mode 100644
index 0000000..6b468b6
--- /dev/null
+++ b/src/analyse/.gitignore
@@ -0,0 +1 @@
+*.class
diff --git a/src/analyse/Extractor.java b/src/analyse/Extractor.java
new file mode 100644
index 0000000..dfb2d48
--- /dev/null
+++ b/src/analyse/Extractor.java
@@ -0,0 +1,455 @@
+/*
+ * The MIT License (MIT)
+
+Copyright (c) 2014
+
+Hayda Almeida
+Marie-Jean Meurs
+
+Concordia University
+Tsang Lab
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package analyse;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+
+import configure.ConfigConstants;
+/**
+ * Implements common tools to FeatureExtractor
+ * and NgramExtractor classes that are used to
+ * extract features from doc instances
+ *
+ * @author halmeida
+ *
+ */
+public class Extractor {
+
+
+ String id;
+ String endId;
+ String openFile;
+ String endFile;
+ String openAbst;
+ String closeAbst;
+ String abstractLabel;
+ String openEC;
+ String closeEC;
+ String classTag;
+ String openTitle;
+ String closeTitle;
+ String openJournal;
+ String closeJournal;
+ String copyR;
+ String closeCopyR;
+
+ /**
+ * Replaces special characters to clean
+ * text for tokenizing.
+ *
+ * @param str text to be cleaned
+ * @return string with cleaned text
+ */
+ public String removeSpecialChar(String str){
+ str = str.replace("}", "");
+ str = str.replace("{", "");
+ str = str.replace("]", "");
+ str = str.replace("[", "");
+ str = str.replace("\"", "");
+ str = str.replace("<", "");
+ str = str.replace(">", "");
+ str = str.replace("/", " ");
+ str = str.replace("\\", " ");
+ str = str.replace("#", "");
+ str = str.replace("*", "");
+ str = str.replace(">", "");
+ str = str.replace("&apos", "");
+ str = str.replace("%", "");
+ str = str.replace(""", "");
+ str = str.replace("&", "");
+ str = str.replace("=", "");
+ str = str.replace("?", "");
+ str = str.replace("!", "");
+ str = str.replace(";", "");
+ str = str.replace(":", "");
+// str = str.replace(",", "");
+// str = str.replace(".", "");
+ str = str.replace(")", "");
+ str = str.replace("(", "");
+ str = str.replace("\t\t", "\t");
+ //losing ngrams because of hifen between names
+ str = str.replace("-", " ");
+ str = str.replace(" ", "");
+
+ return str;
+ }
+
+ /**
+ * Handles external tags (and multiple abstract
+ * text tags) present in a single paper
+ * @param str abstract content
+ * @return string without external tags
+ */
+
+ public String processAbstract(String str){
+ str = str.replace(" ", "");
+
+ if(str.contains("Copyright") && !(str.contains(".")));
+ }
+
+ //Handling the word "Copyright" before the end of abstract
+ if(temp.contains("Copyright ")){
+ temp = "";
+ do{
+ i++;
+ //an exception here can mean that a copyright information
+ //tag content did not ended with a period
+ }while(!(remove[i]).equalsIgnoreCase("."));
+ }
+ else sb.append(remove[i]);
+ }
+
+ abstrac = sb.toString();
+ abstrac = removeAbstractTags(abstrac);
+
+ return abstrac;
+ }
+
+
+ /**
+ * Removes specific tags encountered on Abstract texts.
+ * This is used to clean the abstract text before
+ * processing the feature count on the model.
+ * @param str
+ * @return
+ */
+
+ public String removeAbstractTags(String str){
+ //this order of removing tags matters to
+ //exclude the first tag from the abstracts.
+
+ str = str.replace("", "");
+ str = str.replace("", "");
+ str = str.replace("", "");
+ str = str.replace("copyright", "");
+ str = str.replace("", "");
+ str = str.replace("", "");
+ str = str.replace("", "");
+ str = str.replace("", "");
+
+ return str;
+ }
+
+
+ /**
+ * Removes the markup annotations of a
+ * text field, and keeps its content
+ *
+ * @param str text containing markups
+ * @return string with cleaned text
+ */
+ public String removeTags(String str) {
+ String[] remove = str.split("");
+ StringBuilder sb = new StringBuilder();
+
+ for(int i = 0; i < remove.length; i++){
+
+ //iterating over the text until finding opening tag
+ if(remove[i].equalsIgnoreCase("<")){
+ do{
+ i++;
+ }
+ //skipping the content until finding closing tag
+ while(!(remove[i].equalsIgnoreCase(">")));
+ }
+ else sb.append(remove[i]);
+ }
+
+ return sb.toString();
+ }
+
+
+ /**
+ * Displays the keys and values of the
+ * maps created.
+ *
+ * @param hash HashMap containing list,
+ * values, counts
+ */
+ public void displayList(HashMap hash){
+ Iterator