project source code

.editorconfig

+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+insert_final_newline = false
+max_line_length = 140
+tab_width = 4

.gitignore

+# Maven stuff
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+.mvn/timing.properties
+
+# Avoid ignoring Maven wrapper jar file (.jar files are usually ignored)
+!/.mvn/wrapper/maven-wrapper.jar
+
+# Eclipse stuff
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+.recommenders
+.classpath
+.project
+
+# MacOS stuff
+*.DS_Store
+
+# IntelliJ stuff
+.idea
+*.iml
+
+# n2c2 stuff
+*.xml
+
+# Models
+models/*
+.Rproj.user

.travis.yml

+language: java
+matrix:
+  include:
+    - jdk: openjdk8
+    - jdk: openjdk11
+    - jdk: openjdk14
+addons:
+  apt:
+    packages:
+      - python3
+script: mvn test -B
+after_success:
+  - mvn clean test jacoco:report coveralls:report
+notifications:
+  email:
+    on_success: change
+    on_failure: always
+  slack:
+    rooms:
+      secure: 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
+    on_success: change
+    on_failure: always
+    on_pull_requests: false

LICENSE

+                                 Apache License
+                           Version 2.0, January 2004
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+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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+   See the License for the specific language governing permissions and
+   limitations under the License.

R/accuracy.tsv

+Criterion	Baseline	RBC	SVM	SELF-LR	PRE-LR	SELF-LSTM	PRE-LSTM
\ No newline at end of file

R/f1.tsv

+Criterion	Baseline	RBC	SVM	SELF-LR	PRE-LR	SELF-LSTM	PRE-LSTM

R/plots.R

+library(dplyr)
+library(tidyr)
+library(ggplot2)
+library(ggpubr)
+
+old_wd <- getwd()
+setwd("R")
+
+collect_data <- function(file) {
+  data <- read.delim(file)
+  
+  # We reorganize data into rows since it was created manually.
+  # May not be necessary if generated by a script.
+  data <- data %>% gather(key="method", value="value", factor_key=TRUE, -Criterion)
+  
+  # Set user friendly names.
+  levels(data$method) <- gsub("([A-Z]{3,4}).([A-Z]{2,4})", "\\1-\\2", levels(data$method))
+  
+  return(data)
+}
+
+plot_data <- function(data, title) {
+  g <- ggplot(data=data, aes(x=Criterion, y=value, fill=method)) +
+    geom_bar(stat="identity", position=position_dodge2(reverse=TRUE), color="black", size=0.25) +
+    coord_flip() +
+    scale_x_discrete(limits = rev(levels(data$Criterion))) +
+    scale_y_continuous(breaks=seq(0,1,0.1), limits=c(0,1)) +
+    ylab(title) +
+    scale_fill_brewer(palette="Set2") +
+    theme_linedraw() +
+    theme(legend.title=element_blank())
+  return(g)
+}
+
+f1_data <- collect_data("f1.tsv")
+f1_plot <- plot_data(f1_data, "F1")
+ggexport(f1_plot, filename="f1.pdf", height=10)
+
+accuracy_data <- collect_data("accuracy.tsv")
+accuracy_plot <- plot_data(accuracy_data, "Accuracy")
+ggexport(accuracy_plot, filename="accuracy.pdf", height=10)
+
+setwd(old_wd)
\ No newline at end of file

R/stats.R

+library(stats)
+
+data <- read.csv("false-analysis.csv")
+
+# Comparisons to baseline
+for (i in 3:ncol(data)) {
+  htest <- mcnemar.test(data[,2], data[,i], correct=FALSE)
+  print(htest)
+}
+
+# Pre x Self
+mcnemar.test(data[,5], data[,6], correct=FALSE)
+mcnemar.test(data[,7], data[,8], correct=FALSE)
\ No newline at end of file

README.md

+# National NLP Clinical Challenges (n2c2)
+
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/61f8f04b341a482f95b9a38073575860)](https://app.codacy.com/app/michelole/n2c2?utm_source=github.com&utm_medium=referral&utm_content=bst-mug/n2c2&utm_campaign=badger)
+[![Build Status](https://travis-ci.org/bst-mug/n2c2.svg?branch=master)](https://travis-ci.org/bst-mug/n2c2)
+[![Coverage Status](https://coveralls.io/repos/github/bst-mug/n2c2/badge.svg?branch=master)](https://coveralls.io/github/bst-mug/n2c2?branch=master)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
+A repository containing support code and resources developed at the [Institute for Medical Informatics, Statistics and Documentation at the Medical University of Graz (Austria)](https://www.medunigraz.at/imi/en/) for participation at the [2018 n2c2 Shared-Task Track 1](https://n2c2.dbmi.hms.harvard.edu/) organized by the Department of Biomedical Informatics at the Harvard Medical School.
+
+## Citing
+
+If you use data or code in your work, please cite our [JAMIA paper](https://academic.oup.com/jamia/advance-article/doi/10.1093/jamia/ocz149/5568257):
+
+```
+@article{oleynik2019evaluating,
+  title={Evaluating shallow and deep learning strategies for the 2018 n2c2 shared-task on clinical text classification},
+  author={Michel Oleynik and Amila Kugic and Zdenko Kasáč and Markus Kreuzthaler},
+  journal={Journal of the American Medical Informatics Association},
+  publisher={Oxford University Press},
+  year={2019}
+}
+```
+
+Also of interest:
+- Our [n2c2 presentation slides](https://www.medunigraz.at/imi/de/n2c2.Presentation_V6.pdf)
+
+## Code Dependencies
+- JDK8+
+- python3 (to run official evaluation scripts)
+- make (to compile fastText)
+- gcc/clang (to compile fastText)

checkstyle.xml

+<?xml version="1.0"?>
+<!DOCTYPE module PUBLIC
+          "-//Checkstyle//DTD Checkstyle Configuration 1.3//EN"
+          "https://checkstyle.org/dtds/configuration_1_3.dtd">
+
+<!--
+    Checkstyle configuration that checks the Google coding conventions from Google Java Style
+    that can be found at https://google.github.io/styleguide/javaguide.html
+
+    Checkstyle is very configurable. Be sure to read the documentation at
+    http://checkstyle.sf.net (or in your downloaded distribution).
+
+    To completely disable a check, just comment it out or delete it from the file.
+
+    Authors: Max Vetrenko, Ruslan Diachenko, Roman Ivanov.
+ -->
+
+<module name = "Checker">
+    <property name="charset" value="UTF-8"/>
+
+    <property name="severity" value="warning"/>
+
+    <property name="fileExtensions" value="java, properties, xml"/>
+    <!-- Excludes all 'module-info.java' files              -->
+    <!-- See https://checkstyle.org/config_filefilters.html -->
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="module\-info\.java$"/>
+    </module>
+    <!-- Checks for whitespace                               -->
+    <!-- See http://checkstyle.sf.net/config_whitespace.html -->
+    <module name="FileTabCharacter">
+        <property name="eachLine" value="true"/>
+    </module>
+
+    <module name="TreeWalker">
+        <module name="OuterTypeFilename"/>
+        <module name="IllegalTokenText">
+            <property name="tokens" value="STRING_LITERAL, CHAR_LITERAL"/>
+            <property name="format"
+             value="\\u00(09|0(a|A)|0(c|C)|0(d|D)|22|27|5(C|c))|\\(0(10|11|12|14|15|42|47)|134)"/>
+            <property name="message"
+             value="Consider using special escape sequence instead of octal value or Unicode escaped value."/>
+        </module>
+        <module name="AvoidEscapedUnicodeCharacters">
+            <property name="allowEscapesForControlCharacters" value="true"/>
+            <property name="allowByTailComment" value="true"/>
+            <property name="allowNonPrintableEscapes" value="true"/>
+        </module>
+        <module name="LineLength">
+            <property name="max" value="140"/>
+            <property name="ignorePattern" value="^package.*|^import.*|a href|href|http://|https://|ftp://"/>
+        </module>
+        <module name="OneTopLevelClass"/>
+        <module name="NoLineWrap"/>
+        <module name="EmptyBlock">
+            <property name="option" value="TEXT"/>
+            <property name="tokens"
+             value="LITERAL_TRY, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE, LITERAL_SWITCH"/>
+        </module>
+        <module name="NeedBraces"/>
+        <module name="LeftCurly"/>
+        <module name="RightCurly">
+            <property name="id" value="RightCurlySame"/>
+            <property name="tokens"
+             value="LITERAL_TRY, LITERAL_CATCH, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE,
+                    LITERAL_DO"/>
+        </module>
+        <module name="RightCurly">
+            <property name="id" value="RightCurlyAlone"/>
+            <property name="option" value="alone"/>
+            <property name="tokens"
+             value="CLASS_DEF, METHOD_DEF, CTOR_DEF, LITERAL_FOR, LITERAL_WHILE, STATIC_INIT,
+                    INSTANCE_INIT"/>
+        </module>
+        <module name="WhitespaceAround">
+            <property name="allowEmptyConstructors" value="true"/>
+            <property name="allowEmptyLambdas" value="true"/>
+            <property name="allowEmptyMethods" value="true"/>
+            <property name="allowEmptyTypes" value="true"/>
+            <property name="allowEmptyLoops" value="true"/>
+            <message key="ws.notFollowed"
+             value="WhitespaceAround: ''{0}'' is not followed by whitespace. Empty blocks may only be represented as '{}' when not part of a multi-block statement (4.1.3)"/>
+            <message key="ws.notPreceded"
+             value="WhitespaceAround: ''{0}'' is not preceded with whitespace."/>
+        </module>
+        <module name="OneStatementPerLine"/>
+        <module name="MultipleVariableDeclarations"/>
+        <module name="ArrayTypeStyle"/>
+        <module name="MissingSwitchDefault"/>
+        <module name="FallThrough"/>
+        <module name="UpperEll"/>
+        <module name="ModifierOrder"/>
+        <module name="EmptyLineSeparator">
+            <property name="allowNoEmptyLineBetweenFields" value="true"/>
+        </module>
+        <module name="SeparatorWrap">
+            <property name="id" value="SeparatorWrapDot"/>
+            <property name="tokens" value="DOT"/>
+            <property name="option" value="nl"/>
+        </module>
+        <module name="SeparatorWrap">
+            <property name="id" value="SeparatorWrapComma"/>
+            <property name="tokens" value="COMMA"/>
+            <property name="option" value="EOL"/>
+        </module>
+        <module name="SeparatorWrap">
+            <!-- ELLIPSIS is EOL until https://github.com/google/styleguide/issues/258 -->
+            <property name="id" value="SeparatorWrapEllipsis"/>
+            <property name="tokens" value="ELLIPSIS"/>
+            <property name="option" value="EOL"/>
+        </module>
+        <module name="SeparatorWrap">
+            <!-- ARRAY_DECLARATOR is EOL until https://github.com/google/styleguide/issues/259 -->
+            <property name="id" value="SeparatorWrapArrayDeclarator"/>
+            <property name="tokens" value="ARRAY_DECLARATOR"/>
+            <property name="option" value="EOL"/>
+        </module>
+        <module name="SeparatorWrap">
+            <property name="id" value="SeparatorWrapMethodRef"/>
+            <property name="tokens" value="METHOD_REF"/>
+            <property name="option" value="nl"/>
+        </module>
+        <module name="PackageName">
+            <property name="format" value="^[a-z]+(\.[a-z][a-z0-9]*)*$"/>
+            <message key="name.invalidPattern"
+             value="Package name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="TypeName">
+            <message key="name.invalidPattern"
+             value="Type name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="MemberName">
+            <property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9]*$"/>
+            <message key="name.invalidPattern"
+             value="Member name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="ParameterName">
+            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
+            <message key="name.invalidPattern"
+             value="Parameter name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="LambdaParameterName">
+            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
+            <message key="name.invalidPattern"
+                     value="Lambda parameter name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="CatchParameterName">
+            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
+            <message key="name.invalidPattern"
+             value="Catch parameter name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="LocalVariableName">
+            <property name="tokens" value="VARIABLE_DEF"/>
+            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
+            <message key="name.invalidPattern"
+             value="Local variable name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="ClassTypeParameterName">
+            <property name="format" value="(^[A-Z][0-9]?)$|([A-Z][a-zA-Z0-9]*[T]$)"/>
+            <message key="name.invalidPattern"
+             value="Class type name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="MethodTypeParameterName">
+            <property name="format" value="(^[A-Z][0-9]?)$|([A-Z][a-zA-Z0-9]*[T]$)"/>
+            <message key="name.invalidPattern"
+             value="Method type name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="InterfaceTypeParameterName">
+            <property name="format" value="(^[A-Z][0-9]?)$|([A-Z][a-zA-Z0-9]*[T]$)"/>
+            <message key="name.invalidPattern"
+             value="Interface type name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="NoFinalizer"/>
+        <module name="GenericWhitespace">
+            <message key="ws.followed"
+             value="GenericWhitespace ''{0}'' is followed by whitespace."/>
+            <message key="ws.preceded"
+             value="GenericWhitespace ''{0}'' is preceded with whitespace."/>
+            <message key="ws.illegalFollow"
+             value="GenericWhitespace ''{0}'' should followed by whitespace."/>
+            <message key="ws.notPreceded"
+             value="GenericWhitespace ''{0}'' is not preceded with whitespace."/>
+        </module>
+        <module name="Indentation">
+            <property name="basicOffset" value="4"/>
+            <property name="braceAdjustment" value="0"/>
+            <property name="caseIndent" value="4"/>
+            <property name="throwsIndent" value="4"/>
+            <property name="lineWrappingIndentation" value="4"/>
+            <property name="arrayInitIndent" value="4"/>
+        </module>
+        <module name="OverloadMethodsDeclarationOrder"/>
+        <module name="VariableDeclarationUsageDistance"/>
+        <module name="CustomImportOrder">
+            <property name="separateLineBetweenGroups" value="true"/>
+            <property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE"/>
+        </module>
+        <module name="MethodParamPad"/>
+        <module name="NoWhitespaceBefore">
+            <property name="tokens"
+             value="COMMA, SEMI, POST_INC, POST_DEC, DOT, ELLIPSIS, METHOD_REF"/>
+            <property name="allowLineBreaks" value="true"/>
+        </module>
+        <module name="ParenPad"/>
+        <module name="OperatorWrap">
+            <property name="option" value="NL"/>
+            <property name="tokens"
+             value="BAND, BOR, BSR, BXOR, DIV, EQUAL, GE, GT, LAND, LE, LITERAL_INSTANCEOF, LOR,
+                    LT, MINUS, MOD, NOT_EQUAL, PLUS, QUESTION, SL, SR, STAR, METHOD_REF "/>
+        </module>
+        <module name="AnnotationLocation">
+            <property name="id" value="AnnotationLocationMostCases"/>
+            <property name="tokens"
+             value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF"/>
+        </module>
+        <module name="AnnotationLocation">
+            <property name="id" value="AnnotationLocationVariables"/>
+            <property name="tokens" value="VARIABLE_DEF"/>
+            <property name="allowSamelineMultipleAnnotations" value="true"/>
+        </module>
+        <module name="InvalidJavadocPosition"/>
+        <module name="JavadocTagContinuationIndentation"/>
+        <module name="SummaryJavadoc">
+            <property name="forbiddenSummaryFragments"
+             value="^@return the *|^This method returns |^A [{]@code [a-zA-Z0-9]+[}]( is a )"/>
+        </module>
+        <module name="JavadocParagraph"/>
+        <module name="AtclauseOrder">
+            <property name="tagOrder" value="@param, @return, @throws, @deprecated"/>
+            <property name="target"
+             value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>
+        </module>
+        <module name="JavadocMethod">
+            <property name="scope" value="public"/>
+            <property name="allowMissingParamTags" value="true"/>
+            <property name="allowMissingThrowsTags" value="true"/>
+            <property name="allowMissingReturnTag" value="true"/>
+            <property name="allowedAnnotations" value="Override, Test"/>
+            <property name="allowThrowsTagsForSubclasses" value="true"/>
+        </module>
+        <module name="MethodName">
+            <property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9_]*$"/>
+            <message key="name.invalidPattern"
+             value="Method name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="SingleLineJavadoc">
+            <property name="ignoreInlineTags" value="false"/>
+        </module>
+        <module name="EmptyCatchBlock">
+            <property name="exceptionVariableName" value="expected"/>
+        </module>
+    </module>
+</module>

n2c2.properties

+# SVM cost values per class
+svm.cost.makes_decisions=1
+svm.cost.hba1c=1
+svm.cost.asp_for_mi=1
+svm.cost.alcohol_abuse=1
+svm.cost.advanced_cad=1
+svm.cost.creatinine=1
+svm.cost.english=1
+svm.cost.mi_6mos=1
+svm.cost.drug_abuse=1
+svm.cost.major_diabetes=1
+svm.cost.keto_1yr=1
+svm.cost.abdominal=1
+svm.cost.dietsupp_2mos=1
+
+nn.samplesTraining=data/train/
+nn.models=models/
+nn.samplesTrainingBDT=Z:/n2c2/data/models/samplesTrainingBDT
+nn.samplesTestBDT=Z:/n2c2/data/models/samplesTestBDT/
+nn.samplesPredictedBDT=out/
\ No newline at end of file

pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<groupId>at.medunigraz.imi.bst</groupId>
+	<artifactId>n2c2</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<packaging>jar</packaging>
+
+	<name>n2c2</name>
+	<url>http://maven.apache.org</url>
+
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+
+		<!-- BEGIN added for deeplearning4j -->
+		<!-- .............................. -->
+		<!-- Generic properties -->
+		<java.version>1.8</java.version>
+		<!-- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> -->
+		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
+
+		<!-- Change the nd4j.backend property to nd4j-cuda-7.5-platform or nd4j-cuda-8.0-platform 
+			to use CUDA GPUs -->
+		<nd4j.backend>nd4j-native-platform</nd4j.backend>
+		<!-- <nd4j.backend>nd4j-cuda-8.0-platform</nd4j.backend> -->
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<shadedClassifier>bin</shadedClassifier>
+
+		<nd4j.version>0.9.1</nd4j.version>
+		<dl4j.version>0.9.1</dl4j.version>
+		<datavec.version>0.9.1</datavec.version>
+		<arbiter.version>0.9.1</arbiter.version>
+		<rl4j.version>0.9.1</rl4j.version>
+
+		<!-- For Spark examples: change the _1 to _2 to switch between Spark 1 
+			and Spark 2 -->
+		<dl4j.spark.version>0.9.1_spark_1</dl4j.spark.version>
+		<datavec.spark.version>0.9.1_spark_1</datavec.spark.version>
+
+		<!-- Scala binary version: DL4J's Spark and UI functionality are released 
+			with both Scala 2.10 and 2.11 support -->
+		<scala.binary.version>2.11</scala.binary.version>
+
+		<logback.version>1.1.7</logback.version>
+		<jfreechart.version>1.0.13</jfreechart.version>
+		<jcommon.version>1.0.23</jcommon.version>
+		<maven-shade-plugin.version>2.4.3</maven-shade-plugin.version>
+		<maven-compiler-plugin.version>3.6.1</maven-compiler-plugin.version>
+		<exec-maven-plugin.version>1.4.0</exec-maven-plugin.version>
+		<maven.minimum.version>3.3.1</maven.minimum.version>
+		<!--<javafx.version>2.2.3</javafx.version>-->
+		<!--<javafx.runtime.lib.jar>${env.JAVAFX_HOME}/jfxrt.jar</javafx.runtime.lib.jar>-->
+		<aws.sdk.version>1.11.109</aws.sdk.version>
+		<jackson.version>2.6.6</jackson.version>
+		<scala.plugin.version>3.2.2</scala.plugin.version>
+
+		<!-- END added for deeplearning4j -->
+		<!-- ............................ -->
+
+	</properties>
+
+	<build>
+		<filters>
+			<filter>n2c2.properties</filter>
+		</filters>
+		<resources>
+			<resource>
+				<directory>src/main/resources</directory>
+				<filtering>true</filtering>
+			</resource>
+		</resources>
+		<plugins>
+			<plugin>
+				<artifactId>maven-antrun-plugin</artifactId>
+				<version>1.8</version>
+				<executions>
+					<execution>
+						<phase>generate-sources</phase>
+						<configuration>
+							<target>
+								<!-- fastText -->
+								<mkdir dir="${project.build.directory}/lib" />
+								<get
+										src="https://github.com/facebookresearch/fastText/archive/v0.2.0.zip"
+										dest="${project.build.directory}/lib/fastText-0.2.0.zip"
+										verbose="false" usetimestamp="true"/>
+								<unzip
+										src="${project.build.directory}/lib/fastText-0.2.0.zip"
+										dest="${project.build.directory}/lib/" />
+								<exec executable="make" failonerror="true"
+									  dir="${project.build.directory}/lib/fastText-0.2.0/"/>
+								<move file="${project.build.directory}/lib/fastText-0.2.0/fasttext"
+									  tofile="${project.build.directory}/lib/fasttext"/>
+                                <!-- Evaluation script -->
+                                <get
+                                        src="https://raw.githubusercontent.com/filannim/2018_n2c2_evaluation_scripts/master/track1_eval.py"
+                                        dest="${project.build.directory}/track1_eval.py"
+                                        verbose="false" usetimestamp="true"/>
+                                <!-- Sample file -->
+								<get
+									src="https://n2c2.dbmi.hms.harvard.edu/files/n2c2_sample_file_annotations.zip"
+									dest="${project.build.directory}/n2c2_sample_file_annotations.zip"
+									verbose="false" usetimestamp="true" />
+								<unzip
+									src="${project.build.directory}/n2c2_sample_file_annotations.zip"
+									dest="${project.build.directory}" />
+								<copy
+									file="${project.build.directory}/n2c2_sample_file_annotations/sample.xml"
+									tofile="${basedir}/src/test/resources/gold-standard/sample.xml" />
+								<copy
+									file="${project.build.directory}/n2c2_sample_file_annotations/sample.xml"
+									tofile="${basedir}/src/test/resources/results/sample.xml" />
+							</target>
+						</configuration>
+						<goals>
+							<goal>run</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.7.0</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+			<!--<plugin>-->
+			<!--<groupId>org.codehaus.mojo</groupId>-->
+			<!--<artifactId>exec-maven-plugin</artifactId>-->
+			<!--<version>1.6.0</version>-->
+			<!--<configuration>-->
+			<!--<mainClass>at.medunigraz.imi.bst.n2c2.SVMClassifierRunner/mainClass>-->
+			<!--</configuration>-->
+			<!--</plugin>-->
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<version>0.8.5</version>
+				<executions>
+					<execution>
+						<id>prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.eluder.coveralls</groupId>
+				<artifactId>coveralls-maven-plugin</artifactId>
+				<version>4.3.0</version>
+			</plugin>
+
+
+			<!-- BEGIN added for deeplearning4j -->
+			<!-- .............................. -->
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>exec-maven-plugin</artifactId>
+				<version>${exec-maven-plugin.version}</version>
+				<executions>
+					<execution>
+						<goals>
+							<goal>exec</goal>
+						</goals>
+					</execution>
+				</executions>
+				<configuration>
+					<executable>java</executable>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>${maven-shade-plugin.version}</version>
+				<configuration>
+					<shadedArtifactAttached>true</shadedArtifactAttached>
+					<shadedClassifierName>${shadedClassifier}</shadedClassifierName>
+					<createDependencyReducedPom>true</createDependencyReducedPom>
+					<filters>
+						<filter>
+							<artifact>*:*</artifact>
+							<excludes>
+								<exclude>org/datanucleus/**</exclude>
+								<exclude>META-INF/*.SF</exclude>
+								<exclude>META-INF/*.DSA</exclude>
+								<exclude>META-INF/*.RSA</exclude>
+							</excludes>
+						</filter>
+					</filters>
+				</configuration>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+							<transformers>
+								<transformer
+									implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+									<resource>reference.conf</resource>
+								</transformer>
+								<transformer
+									implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
+								<transformer
+									implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+								</transformer>
+							</transformers>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+
+			<!-- <plugin> -->
+			<!-- <groupId>org.apache.maven.plugins</groupId> -->
+			<!-- <artifactId>maven-compiler-plugin</artifactId> -->
+			<!-- <version>3.5.1</version> -->
+			<!-- <configuration> -->
+			<!-- <source>${java.version}</source> -->
+			<!-- <target>${java.version}</target> -->
+			<!-- </configuration> -->
+			<!-- </plugin> -->
+
+			<!-- END added for deeplearning4j -->
+			<!-- ............................ -->
+		</plugins>
+	</build>
+
+	<!-- BEGIN added for deeplearning4j -->
+	<!-- .............................. -->
+	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>org.nd4j</groupId>
+				<artifactId>nd4j-native-platform</artifactId>
+				<version>${nd4j.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.nd4j</groupId>
+				<artifactId>nd4j-cuda-7.5-platform</artifactId>
+				<version>${nd4j.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.nd4j</groupId>
+				<artifactId>nd4j-cuda-8.0-platform</artifactId>
+				<version>${nd4j.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.nd4j</groupId>
+				<artifactId>nd4j-cuda-9.0-platform</artifactId>
+				<version>${nd4j.version}</version>
+			</dependency>
+		</dependencies>
+	</dependencyManagement>
+	<!-- END added for deeplearning4j -->
+	<!-- ............................ -->
+
+	<dependencies>
+		<!-- BEGIN added for deeplearning4j -->
+		<!-- .............................. -->
+
+		<!-- ND4J backend. You need one in every DL4J project. Normally define 
+			artifactId as either "nd4j-native-platform" or "nd4j-cuda-7.5-platform" -->
+		<dependency>
+			<groupId>org.nd4j</groupId>
+			<artifactId>${nd4j.backend}</artifactId>
+		</dependency>
+
+		<!-- Core DL4J functionality -->
+		<dependency>
+			<groupId>org.deeplearning4j</groupId>
+			<artifactId>deeplearning4j-core</artifactId>
+			<version>${dl4j.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.deeplearning4j</groupId>
+			<artifactId>deeplearning4j-nlp</artifactId>
+			<version>${dl4j.version}</version>
+		</dependency>
+
+		<!-- deeplearning4j-ui is used for HistogramIterationListener + visualization: 
+			see http://deeplearning4j.org/visualization -->
+		<dependency>
+			<groupId>org.deeplearning4j</groupId>
+			<artifactId>deeplearning4j-ui_${scala.binary.version}</artifactId>
+			<version>${dl4j.version}</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.apache.lucene/lucene-analyzers-common -->
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-analyzers-common</artifactId>
+			<version>7.5.0</version>
+		</dependency>
+
+		<!-- END added for deeplearning4j -->
+		<!-- ............................ -->
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.12</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.hamcrest</groupId>
+			<artifactId>hamcrest-library</artifactId>
+			<version>1.3</version>
+		</dependency>
+		<dependency>
+			<groupId>xmlunit</groupId>
+			<artifactId>xmlunit</artifactId>
+			<version>1.6</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-api</artifactId>
+			<version>2.8.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-core</artifactId>
+			<version>2.8.1</version>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.6</version>
+		</dependency>
+		<dependency>
+			<groupId>com.opencsv</groupId>
+			<artifactId>opencsv</artifactId>
+			<version>4.1</version>
+		</dependency>
+		<dependency>
+			<groupId>com.github.haifengl</groupId>
+			<artifactId>smile-core</artifactId>
+			<version>1.5.1</version>
+		</dependency>
+		<dependency>
+			<groupId>nz.ac.waikato.cms.weka</groupId>
+			<artifactId>weka-stable</artifactId>
+			<version>3.8.2</version>
+		</dependency>
+		<dependency>
+			<groupId>nz.ac.waikato.cms.weka</groupId>
+			<artifactId>LibSVM</artifactId>
+			<version>1.0.10</version>
+		</dependency>
+		<dependency>
+			<groupId>org.projectlombok</groupId>
+			<artifactId>lombok</artifactId>
+			<version>1.18.0</version>
+			<scope>provided</scope>
+		</dependency>
+		<!-- JDK10+ https://github.com/deeplearning4j/deeplearning4j/issues/5804#issuecomment-443487090-->
+		<dependency>
+			<groupId>net.jodah</groupId>
+			<artifactId>typetools</artifactId>
+			<version>0.5.0</version>
+		</dependency>
+        <!-- May be used for Weka stemmer. Conflicts with Lucene dependencies -->
+        <!--<dependency>-->
+        <!--<groupId>com.github.rholder</groupId>-->
+        <!--<artifactId>snowball-stemmer</artifactId>-->
+        <!--<version>1.3.0.581.1</version>-->
+        <!--</dependency>-->
+	</dependencies>
+</project>

scripts/print_vectors.sh

+#!/bin/sh
+
+# First parameter is the embeddings model, either:
+# a) `n2c2-fasttext.bin` (manually generated by `train_embeddings.sh`);
+# b) `BioWordVec_PubMed_MIMICIII_d200.bin` (downloaded from https://github.com/ncbi-nlp/BioSentVec)
+#   BioWordVec_PubMed_MIMICIII_d200,  this is the link to download: https://ftp.ncbi.nlm.nih.gov/pub/lu/Suppl/BioSentVec/BioWordVec_PubMed_MIMICIII_d200.bin
+# `vocab.txt` should be first generated by `VocabularyDumper.java`
+
+# fasttext print-word-vectors n2c2-fasttext.bin < vocab.txt > vectors.tsv
+fasttext print-word-vectors BioWordVec_PubMed_MIMICIII_d200.bin < vocab.txt > vectors.tsv
+
+# The `.vec` file loaded by deeplearning4j requires an extra line with the input dimensions.
+LINES=27875
+DIM=200
+echo "$LINES $DIM" | cat - vectors.tsv > vectors.vec
\ No newline at end of file

scripts/train_embeddings.sh

+#!/bin/sh
+
+# Parameters follows https://github.com/ncbi-nlp/BioSentVec/blob/master/src/train_biowordvec.sh
+# `sentences.txt` should be first generated by `SentenceDumper.java`
+fasttext skipgram -input sentences.txt -output n2c2-fasttext -dim 200 -t 0.001 -minCount 0 -neg 10 -wordNgrams 6 -ws 20
\ No newline at end of file

src/main/java/at/medunigraz/imi/bst/n2c2/ClassifierRunner.java

+package at.medunigraz.imi.bst.n2c2;
+
+import at.medunigraz.imi.bst.n2c2.classifier.factory.ClassifierFactory;
+import at.medunigraz.imi.bst.n2c2.classifier.factory.FactoryProvider;
+import at.medunigraz.imi.bst.n2c2.evaluator.BasicEvaluator;
+import at.medunigraz.imi.bst.n2c2.evaluator.Evaluator;
+import at.medunigraz.imi.bst.n2c2.evaluator.OfficialEvaluator;
+import at.medunigraz.imi.bst.n2c2.model.Patient;
+import at.medunigraz.imi.bst.n2c2.model.metrics.Metrics;
+import at.medunigraz.imi.bst.n2c2.stats.CSVStatsWriter;
+import at.medunigraz.imi.bst.n2c2.stats.StatsWriter;
+import at.medunigraz.imi.bst.n2c2.util.DatasetUtil;
+import at.medunigraz.imi.bst.n2c2.validation.TestValidator;
+import at.medunigraz.imi.bst.n2c2.validation.Validator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+
+public class ClassifierRunner {
+
+    private static final Logger LOG = LogManager.getLogger();
+
+    private static final ClassifierFactory[] CLASSIFIERS = new ClassifierFactory[]{
+        FactoryProvider.getMajorityFactory(),
+        FactoryProvider.getRBCFactory(),
+        FactoryProvider.getSVMFactory(),
+        FactoryProvider.getSelfTrainedPerceptronFactory(),
+//        FactoryProvider.getPreTrainedPerceptronFactory(),
+        FactoryProvider.getLSTMSelfTrainedFactory()
+//        FactoryProvider.getLSTMPreTrainedFactory()
+    };
+
+    public static void main(String[] args) throws IOException {
+        final File trainFolder = new File("data/train");
+        final File testFolder = new File("data/test");
+        final File statsFolder = new File("stats");
+
+        List<Patient> trainPatients = DatasetUtil.loadFromFolder(trainFolder);
+        List<Patient> testPatients = DatasetUtil.loadFromFolder(testFolder);
+        Collections.sort(testPatients);
+
+        Evaluator officialEvaluator = new OfficialEvaluator();    // n2c2 official metrics
+        Evaluator basicEvaluator = new BasicEvaluator();        // accuracy and fp/fn metrics
+
+        for (ClassifierFactory factory : CLASSIFIERS) {
+            String name = factory.toString();
+            LOG.info("Running {}...", name);
+            System.out.println("Running {}..." + name);
+
+            Validator officialValidator = new TestValidator(trainPatients, testPatients, factory, officialEvaluator);
+            Validator basicValidator = new TestValidator(trainPatients, testPatients, factory, basicEvaluator);
+
+            Metrics officialMetrics = officialValidator.validate();
+            Metrics basicMetrics = basicValidator.validate();
+
+            // run FastTextFacade:
+            /*
+            ] /Users/yunfei/Documents/fastText-0.9.2/fasttext supervised -input /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/fasttext/train.txt -output /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/fasttext/model -thread 1 -epoch 100 -lr 0.50 -dim 200 -pretrainedVectors /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/target/classes/at/medunigraz/imi/bst/n2c2/classifier/self-trained-vectors.vec
+            16:39:48 DEBUG [FastTextFacade      ] /Users/yunfei/Documents/fastText-0.9.2/fasttext predict /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/fasttext/model.bin /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/fasttext/test.txt
+            16:39:50 DEBUG [FastTextFacade      ] /Users/yunfei/Documents/fastText-0.9.2/fasttext supervised -input /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/fasttext/train.txt -output /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/fasttext/model -thread 1 -epoch 100 -lr 0.50 -dim 200 -pretrainedVectors /Users/yunfei/Desktop/uiuc/598-deep-learning/project/n2c2/target/classes/at/medunigraz/imi/bst/n2c2/classifier/self-trained-vectors.vec
+            */
+
+            writeAndClose(officialMetrics, new File(statsFolder, name + "-official.csv"));
+            writeAndClose(basicMetrics, new File(statsFolder, name + "-basic.csv"));
+        }
+    }
+
+    private static void writeAndClose(Metrics metrics, File file) throws IOException {
+        StatsWriter csvWriter = new CSVStatsWriter(file);
+        csvWriter.write(metrics);
+        csvWriter.close();
+    }
+}

src/main/java/at/medunigraz/imi/bst/n2c2/classifier/Classifier.java

+package at.medunigraz.imi.bst.n2c2.classifier;
+
+import at.medunigraz.imi.bst.n2c2.model.Criterion;
+import at.medunigraz.imi.bst.n2c2.model.Eligibility;
+import at.medunigraz.imi.bst.n2c2.model.Patient;
+
+import java.util.List;
+
+public interface Classifier {
+
+    void train(List<Patient> examples);
+
+    Eligibility predict(Patient p, Criterion c);
+
+    List<Patient> predict(List<Patient> patientList);
+}

src/main/java/at/medunigraz/imi/bst/n2c2/classifier/CriterionBasedClassifier.java

+package at.medunigraz.imi.bst.n2c2.classifier;
+
+import at.medunigraz.imi.bst.n2c2.model.Criterion;
+import at.medunigraz.imi.bst.n2c2.model.Eligibility;
+import at.medunigraz.imi.bst.n2c2.model.Patient;
+
+import java.util.List;
+
+public abstract class CriterionBasedClassifier implements Classifier {
+
+    protected Criterion criterion;
+
+    public CriterionBasedClassifier(Criterion c) {
+        this.criterion = c;
+    }
+
+    @Override
+    public List<Patient> predict(List<Patient> patientList) {
+        patientList.forEach(p -> p.withCriterion(criterion, predict(p)));
+        return patientList;
+    }
+
+    @Override
+    public Eligibility predict(Patient p, Criterion c) {
+        if (!c.equals(criterion)) {
+            throw new UnsupportedOperationException("Criterion must be consistent with constructor!");
+        }
+        return predict(p);
+    }
+
+    public abstract Eligibility predict(Patient p);
+
+    @Override
+    public String toString() {
+        return getClass().getSimpleName();
+    }
+}