Alternative articles processing flavors

build.gradle

@@ -186,11 +186,11 @@ subprojects {
 
     test {
         useJUnitPlatform()
-        
+
         testLogging.showStandardStreams = true
         // enable for having separate test executor for different tests
         forkEvery = 1
-        maxHeapSize = "1024m"        
+        maxHeapSize = "1024m"
 
         def libraries = ""
         if (Os.isFamily(Os.FAMILY_MAC)) {
@@ -199,7 +199,7 @@ subprojects {
             } else {
                 libraries = "${file("./grobid-home/lib/mac-64").absolutePath}"
             }
-        } else if (Os.isFamily(Os.FAMILY_UNIX)) {            
+        } else if (Os.isFamily(Os.FAMILY_UNIX)) {
             def jepDir = rootProject.rootDir.getAbsolutePath() + "/grobid-home/lib/lin-64/jep"
             libraries = jepDir
             jepDir = rootProject.rootDir.getAbsolutePath() + "/grobid-home/lib/lin-64"
@@ -209,7 +209,7 @@ subprojects {
         }
 
         if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-            jvmArgs "--add-opens", "java.base/java.util.stream=ALL-UNNAMED", 
+            jvmArgs "--add-opens", "java.base/java.util.stream=ALL-UNNAMED",
             "--add-opens", "java.base/java.io=ALL-UNNAMED", "--add-opens", "java.xml/jdk.xml.internal=ALL-UNNAMED"
         }
         systemProperty "java.library.path","${System.getProperty('java.library.path')}:" + libraries
@@ -351,7 +351,7 @@ project(":grobid-service") {
         } else  {
             throw new RuntimeException("Unsupported platform!")
         }
-        
+
         if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
             jvmArgs "--add-opens", "java.base/java.lang=ALL-UNNAMED"
         }
@@ -380,7 +380,7 @@ project(":grobid-service") {
     distTar { duplicatesStrategy = DuplicatesStrategy.EXCLUDE }
 
     dependencies {
-        implementation project(':grobid-core') 
+        implementation project(':grobid-core')
         implementation project(':grobid-trainer')
 
         //Dropwizard
@@ -397,7 +397,7 @@ project(":grobid-service") {
         implementation 'io.dropwizard.metrics:metrics-core:4.2.22'
         implementation 'io.dropwizard.metrics:metrics-servlets:4.2.22'
         implementation 'io.dropwizard:dropwizard-json-logging:4.0.0'
-        
+
         implementation "org.apache.pdfbox:pdfbox:2.0.3"
         implementation "javax.activation:activation:1.1.1"
         implementation "io.prometheus:simpleclient_dropwizard:0.16.0"
@@ -500,34 +500,38 @@ project(":grobid-trainer") {
     }
 
     def trainerTasks = [
-        "train_name_header"           : "org.grobid.trainer.NameHeaderTrainer",
-        "train_name_citation"         : "org.grobid.trainer.NameCitationTrainer",
-        "train_affiliation_address"   : "org.grobid.trainer.AffiliationAddressTrainer",
-//        "train_header"                : "org.grobid.trainer.HeaderTrainer",
-        "train_fulltext"              : "org.grobid.trainer.FulltextTrainer",
-        "train_shorttext"             : "org.grobid.trainer.ShorttextTrainer",
-        "train_figure"                : "org.grobid.trainer.FigureTrainer",
-        "train_table"                 : "org.grobid.trainer.TableTrainer",
-        "train_citation"              : "org.grobid.trainer.CitationTrainer",
-        "train_date"                  : "org.grobid.trainer.DateTrainer",
-//        "train_segmentation"          : "org.grobid.trainer.SegmentationTrainer",
-        "train_reference_segmentation": "org.grobid.trainer.ReferenceSegmenterTrainer",
-        "train_ebook_model"           : "org.grobid.trainer.EbookTrainer",
-        "train_patent_citation"       : "org.grobid.trainer.PatentParserTrainer",
+        "train_name_header"             : "org.grobid.trainer.NameHeaderTrainer",
+        "train_name_citation"           : "org.grobid.trainer.NameCitationTrainer",
+        "train_affiliation_address"     : "org.grobid.trainer.AffiliationAddressTrainer",
+        "train_shorttext"               : "org.grobid.trainer.ShorttextTrainer",
+        "train_figure"                  : "org.grobid.trainer.FigureTrainer",
+        "train_table"                   : "org.grobid.trainer.TableTrainer",
+        "train_citation"                : "org.grobid.trainer.CitationTrainer",
+        "train_date"                    : "org.grobid.trainer.DateTrainer",
+        "train_reference_segmentation"  : "org.grobid.trainer.ReferenceSegmenterTrainer",
+        "train_ebook_model"             : "org.grobid.trainer.EbookTrainer",
+        "train_patent_citation"         : "org.grobid.trainer.PatentParserTrainer",
         "train_funding_acknowledgement" : "org.grobid.trainer.FundingAcknowledgementTrainer"
     ]
 
     def complexTrainerTasks = [
-        "train_header"                : ["org.grobid.trainer.HeaderTrainer", ""],
-        "train_header_ietf"           : ["org.grobid.trainer.HeaderTrainer", "sdo/ietf"],
-        "train_segmentation"          : ["org.grobid.trainer.SegmentationTrainer", ""],
-        "train_segmentation_ietf"     : ["org.grobid.trainer.SegmentationTrainer", "sdo/ietf"]
+        "train_header"                          : ["org.grobid.trainer.HeaderTrainer", ""],
+        "train_header_article_light"            : ["org.grobid.trainer.HeaderTrainer", "article/light"],
+        "train_header_article_light_ref"        : ["org.grobid.trainer.HeaderTrainer", "article/light-ref"],
+        "train_header_ietf"                     : ["org.grobid.trainer.HeaderTrainer", "sdo/ietf"],
+        "train_segmentation"                    : ["org.grobid.trainer.SegmentationTrainer", ""],
+        "train_segmentation_article_light"      : ["org.grobid.trainer.SegmentationTrainer", "article/light"],
+        "train_segmentation_article_light_ref"  : ["org.grobid.trainer.SegmentationTrainer", "article/light-ref"],
+        "train_segmentation_ietf"               : ["org.grobid.trainer.SegmentationTrainer", "sdo/ietf"],
+        "train_fulltext"                        : ["org.grobid.trainer.FulltextTrainer", ""],
+        "train_fulltext_article_light"          : ["org.grobid.trainer.FulltextTrainer", "article/light"],
+        "train_fulltext_article_light_ref"      : ["org.grobid.trainer.FulltextTrainer", "article/light-ref"],
     ]
 
     def libraries = ""
     if (Os.isFamily(Os.FAMILY_MAC)) {
         if (Os.OS_ARCH.equals("aarch64")) {
-            libraries = "${file("../grobid-home/lib/mac_arm-64").absolutePath}"    
+            libraries = "${file("../grobid-home/lib/mac_arm-64").absolutePath}"
         } else {
             libraries = "${file("../grobid-home/lib/mac-64").absolutePath}"
         }
@@ -537,13 +541,16 @@ project(":grobid-trainer") {
     } else  {
         throw new RuntimeException("Unsupported platform!")
     }
-    
+
     trainerTasks.each { taskName, mainClassName ->
         tasks.create(name: taskName, type: JavaExec, group: 'modeltraining') {
             main = mainClassName
             classpath = sourceSets.main.runtimeClasspath
-            if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0)
+            if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
                 jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.lang=ALL-UNNAMED"
+            } else {
+                jvmArgs '-Xmx3072m'
+            }
             systemProperty "java.library.path","${System.getProperty('java.library.path')}:" + libraries
         }
     }
@@ -552,10 +559,11 @@ project(":grobid-trainer") {
         tasks.create(name: taskName, type: JavaExec, group: 'modeltraining') {
             main = mainClassNameAndArgs[0]
             classpath = sourceSets.main.runtimeClasspath
-            if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0)
+            if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
                 jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.lang=ALL-UNNAMED"
-            if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0)
-                jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.lang=ALL-UNNAMED"    
+            } else {
+                jvmArgs '-Xmx3072m'
+            }
             args mainClassNameAndArgs[1]
         }
     }
@@ -574,7 +582,7 @@ project(":grobid-trainer") {
     task(jatsEval, dependsOn: 'classes', type: JavaExec, group: 'modelevaluation') {
         main = 'org.grobid.trainer.evaluation.EndToEndEvaluation'
         classpath = sourceSets.main.runtimeClasspath
-        args 'nlm', getArg('p2t', '.'), getArg('run', '0'), getArg('fileRatio', '1.0')
+        args 'nlm', getArg('p2t', '.'), getArg('run', '0'), getArg('fileRatio', '1.0'), getArg('flavor', '')
         if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
             jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.lang=ALL-UNNAMED"
         } else {
@@ -586,7 +594,7 @@ project(":grobid-trainer") {
     task(teiEval, dependsOn: 'classes', type: JavaExec, group: 'modelevaluation') {
         main = 'org.grobid.trainer.evaluation.EndToEndEvaluation'
         classpath = sourceSets.main.runtimeClasspath
-        args 'tei', getArg('p2t', '.'), getArg('run', '0'), getArg('fileRatio', '1.0')
+        args 'tei', getArg('p2t', '.'), getArg('run', '0'), getArg('fileRatio', '1.0'), getArg('flavor', '')
         if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
             jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.lang=ALL-UNNAMED"
         } else {

doc/Benchmarking-biorxiv.md

@@ -24,7 +24,7 @@ Evaluation on 2000 PDF preprints out of 2000 (no failure).
 
 Runtime for processing 2000 PDF: **1713** seconds (0.85 seconds per PDF file) on Ubuntu 22.04, 16 CPU (32 threads), 128GB RAM and with a GeForce GTX 1080 Ti GPU.
 
-Note: with CRF only models runtime is 622s (0.31 second per PDF) with 4GPU, 8 threads. 
+Note: with CRF only models runtime is 622s (0.31 second per PDF) with 4 CPU, 8 threads. 
 
 
 ## Header metadata 
@@ -35,14 +35,14 @@ Evaluation on 2000 random PDF files out of 1998 PDF (ratio 1.0).
 
 **Field-level results**
 
-| label            |  precision |   recall  |     f1     | support |
+| label                       | precision | recall    | f1        | support |
 |---               |---         |---        |---         |---      |
 | abstract | 2.36 | 2.31 | 2.34 | 1989 |
 | authors | 84.3 | 83.58 | 83.94 | 1998 |
 | first_author | 96.97 | 96.24 | 96.61 | 1996 |
 | keywords | 58.9 | 59.95 | 59.42 | 839 |
 | title | 77.77 | 76.99 | 77.38 | 1999 |
-|                  |            |           |            |         |
+|                             |           |           |           |         |
 | **all fields (micro avg.)** | **64.95** | **64.38** | **64.66** | 8821 |
 | all fields (macro avg.) | 64.06 | 63.82 | 63.94 | 8821 |
 

doc/Benchmarking-elife.md

@@ -24,7 +24,7 @@ Evaluation on 984 PDF preprints out of 984 (no failure).
 
 Runtime for processing 984 PDF: **1131** seconds (1.15 seconds per PDF file) on Ubuntu 22.04, 16 CPU (32 threads), 128GB RAM and with a GeForce GTX 1080 Ti GPU.
 
-Note: with CRF only models runtime is 492s (0.50 seconds per PDF) with 4GPU, 8 threads. 
+Note: with CRF only models runtime is 492s (0.50 seconds per PDF) with 4 CPU, 8 threads. 
 
 
 

doc/Benchmarking-plos.md

@@ -24,7 +24,7 @@ Evaluation on 1000 PDF preprints out of 1000 (no failure).
 
 Runtime for processing 1000 PDF: **999** seconds, (0.99 seconds per PDF) on Ubuntu 22.04, 16 CPU (32 threads), 128GB RAM and with a GeForce GTX 1080 Ti GPU.
 
-Note: with CRF only models runtime is 304s (0.30 seconds per PDF) with 4GPU, 8 threads. 
+Note: with CRF only models runtime is 304s (0.30 seconds per PDF) with 4 CPU, 8 threads. 
 
 
 ## Header metadata 

doc/Benchmarking-pmc.md

@@ -24,7 +24,7 @@ Evaluation on 1943 random PDF PMC files out of 1943 PDF from 1943 different jour
 
 Runtime for processing 1943 PDF: **1467** seconds, (0.75s per PDF) on Ubuntu 22.04, 16 CPU (32 threads), 128GB RAM and with a GeForce GTX 1080 Ti GPU.
 
-Note: with CRF only models, runtime is 470s (0.24 seconds per PDF) with 4GPU, 8 threads.
+Note: with CRF only models, runtime is 470s (0.24 seconds per PDF) with 4 CPU, 8 threads.