edwardt / processors

Natural Language Processors

What is it

The edu.arizona.sista.processors package aims to be a one-stop place for natural language (NL) processors. We currently provide three APIs: one for Stanford's CoreNLP, one for a faster processor (FastNLPProcessor) that cherry picks fast components from multiple sources (Stanford and MaltParser), and, lastly, one for biomedical texts (BioNLPProcessor), which integrates resources trained for this domain (Stanford and BANNER). If you plan to use BioNLPProcessor, please install the data resources from our fork of BANNER first!

Both CoreNLPProcessor and FastNLPProcessor now include a full-fledged Rhetorical Structure Theory (RST) discourse parser. The version in CoreNLPProcessor relies on constituent syntax, whereas the one in FastNLPProcessor uses dependency syntax. The latter is marginally worse (~2 F1 points lower for the complete task) but it is two orders of magnitude faster.

Furthermore, this code contains a machine learning (ML) package (edu.arizona.sista.learning), which includes implementations for common ML algorithms (e.g., Perceptron, Logistic Regression, Support Vector Machines, Random Forests) for both classification and ranking.

This software requires Java 1.6, Scala 2.9 or higher, and CoreNLP 1.3.4 or higher.

This code is licensed under Apache License Version 2.0. However, some of the libraries used here, most notably CoreNLP, are GPL.

(c) Mihai Surdeanu, 2013 -

Contributors: Peter Jansen, Marco Valenzuela, Gustave Hanh-Powell, Daniel Fried

Changes

• 4.0 - added BioNLPProcessor. Install our fork of the BANNER named entity recognizer before!
• 3.3 - bug fix: make sure DocumentSerializer.load() works when multiple documents are serialized into the same file.
• 3.2 - Added a discourse parser to FastNLPProcessor. This performs marginally worse than the one in CoreNLPProcessor, but it is much faster for end-to-end processing, due to the shift-reduce syntactic parser.
• 3.1 - Minimal functionality added to the learning package. Changed to CoreNLP 3.3.1.
• 3.0 - Added a RST discourse parser to CoreNLPProcessor. Added the edu.arizona.sista.learning package. Utils classes are now under edu.arizona.sista.utils rather than edu.arizona.sista.processors.utils.
• 2.2 - Various bug fixes. Added support for basic dependencies to CoreNLPProcessor.
• 2.1 - Bug fix in FastNLPProcessor: better root detection algorithm, robust to malt inconsistencies.
• 2.0 - We now support two processors: CoreNLPProcessor and FastNLPProcessor. Changed the package name from e.a.s.processor to e.a.s.processors. Added Java usage example to README. Updated to CoreNLP 3.3.0. Added better unit tests to check for thread safetiness.
• 1.5 - Bug fixing. Made the string interning process (see Processor.in) local to each thread to avoid concurrency issues in multi-threaded programs. Added new unit tests. Added minor functionality to Lexicon.
• 1.4 - Code cleanup. Added some minor new functionality such as finding base NPs in the Trees class.
• 1.3 - Reverted back to the 1.x version numbers, since we will add other software here not just CoreNLP. Added correct mvn dependencies for the CoreNLP jars. Removed the install*.sh scripts, which are no longer needed.
• 3.2.0 - Updated to Scala 2.10.1 and CoreNLP 3.2.0. Changed versioning system to be identical to CoreNLP's, so it's clear which CoreNLP version is used.
• 1.0 - Initial release

Maven

This software is available on Maven Central as well. Add the following dependencies to your pom.xml to use it:

<dependency>
   <groupId>edu.arizona.sista</groupId>
   <artifactId>processors</artifactId>
   <version>3.3</version>
</dependency>
<dependency>
   <groupId>edu.arizona.sista</groupId>
   <artifactId>processors</artifactId>
   <version>3.3</version>
   <classifier>models</classifier>
</dependency>

Why you should use this code

• Simple API - the APIs provided are, at least in my opinion, simpler than those provided for the original code. For example, when using CoreNLP you won't have to deal with hash maps that take class objects as keys. Instead, we use mostly arrays of integers or strings, which are self explanatory.
• Memory efficient - arrays are more memory efficient than hash maps. Furthermore, we used our own implementation to intern strings (i.e., avoiding to store duplicated strings multiple times). Due to these changes, I measured up to 99% decrease in memory for the annotations corresponding to a typical natural language text, when compared to the original CoreNLP code. (Note: this reduction takes effect only after CoreNLP finishes its work.)
• Faster access - again, because we use arrays instead of hash maps, access to the NL annotations (once constructed) is considerably faster than in the original Stanford code.
• Tool-independent API - we support multiple NL and machine learning tools. If you use this code, you will have to change your code only minimally (i.e., only the constructor for the Processor object).
• Discourse parsing - we include a complete RST parser; simply instantiate CoreNLPProcessor with withDiscourse = true.
• Biomedical tools - we now include tools to process biomedical texts, which can be used under the same simple interface.

How to compile the source code

This is a standard sbt project, so use the usual commands, e.g., sbt compile, sbt assembly, to compile. Add the generated jar files under target/ to your $CLASSPATH, along with the other necessary dependency jars. Take a look at build.sbt to see which dependencies are necessary at runtime.

How to use it

Common scenarios

Most of the examples here use Scala. However, this software can be used as is from Java as well! Scroll down towards the end of this document to see a Java usage example.

Annotating entire documents

// create the processor
// any processor works here! Try FastNLPProcessor or BioNLPProcessor.
val proc:Processor = new CoreNLPProcessor(withDiscourse = true)

// the actual work is done here
val doc = proc.annotate("John Smith went to China. He visited Beijing, on January 10th, 2013.")

// you are basically done. the rest of this code simply prints out the annotations

// let's print the sentence-level annotations
var sentenceCount = 0
for (sentence <- doc.sentences) {
  println("Sentence #" + sentenceCount + ":")
  println("Tokens: " + sentence.words.mkString(" "))
  println("Start character offsets: " + sentence.startOffsets.mkString(" "))
  println("End character offsets: " + sentence.endOffsets.mkString(" "))

  // these annotations are optional, so they are stored using Option objects, hence the foreach statement
  sentence.lemmas.foreach(lemmas => println("Lemmas: " + lemmas.mkString(" ")))
  sentence.tags.foreach(tags => println("POS tags: " + tags.mkString(" ")))
  sentence.entities.foreach(entities => println("Named entities: " + entities.mkString(" ")))
  sentence.norms.foreach(norms => println("Normalized entities: " + norms.mkString(" ")))
  sentence.dependencies.foreach(dependencies => {
    println("Syntactic dependencies:")
    val iterator = new DirectedGraphEdgeIterator[String](dependencies)
    while(iterator.hasNext) {
      val dep = iterator.next
      // note that we use offsets starting at 0 (unlike CoreNLP, which uses offsets starting at 1)
      println(" head:" + dep._1 + " modifier:" + dep._2 + " label:" + dep._3)
    }
  })
  sentence.syntacticTree.foreach(tree => {
    println("Constituent tree: " + tree)
    // see the edu.arizona.sista.utils.Tree class for more information
    // on syntactic trees, including access to head phrases/words
  })

  sentenceCount += 1
  println("\n")
}

// let's print the coreference chains
doc.coreferenceChains.foreach(chains => {
  for (chain <- chains.getChains) {
    println("Found one coreference chain containing the following mentions:")
    for (mention <- chain) {
      // note that all these offsets start at 0 too
      println("\tsentenceIndex:" + mention.sentenceIndex +
        " headIndex:" + mention.headIndex +
        " startTokenOffset:" + mention.startOffset +
        " endTokenOffset:" + mention.endOffset +
        " text: " + doc.sentences(mention.sentenceIndex).words.slice(mention.startOffset, mention.endOffset).mkString("[", " ", "]"))
    }
  }
})

// let's print the discourse tree
doc.discourseTree.foreach(dt => {
  println("Document-wide discourse tree:")
  println(dt.toString())
})

The above code generates the following output:

Sentence #0:
Tokens: John Smith went to China .
Start character offsets: 0 5 11 16 19 24
End character offsets: 4 10 15 18 24 25
Lemmas: John Smith go to China .
POS tags: NNP NNP VBD TO NNP .
Named entities: PERSON PERSON O O LOCATION O
Normalized entities: O O O O O O
Syntactic dependencies:
  head:1 modifier:0 label:nn
  head:2 modifier:1 label:nsubj
  head:2 modifier:4 label:prep_to
Constituent tree: (ROOT (S (NP (NNP John) (NNP Smith)) (VP (VBD went) (PP (TO to) (NP (NNP China)))) (. .)))


Sentence #1:
Tokens: He visited Beijing , on January 10th , 2013 .
Start character offsets: 26 29 37 44 46 49 57 61 63 67
End character offsets: 28 36 44 45 48 56 61 62 67 68
Lemmas: he visit Beijing , on January 10th , 2013 .
POS tags: PRP VBD NNP , IN NNP JJ , CD .
Named entities: O O LOCATION O O DATE DATE DATE DATE O
Normalized entities: O O O O O 2013-01-10 2013-01-10 2013-01-10 2013-01-10 O
Syntactic dependencies:
  head:1 modifier:0 label:nsubj
  head:1 modifier:2 label:dobj
  head:1 modifier:8 label:tmod
  head:2 modifier:5 label:prep_on
  head:5 modifier:6 label:amod
Constituent tree: (ROOT (S (NP (PRP He)) (VP (VBD visited) (NP (NP (NNP Beijing)) (, ,) (PP (IN on) (NP (NNP January) (JJ 10th))) (, ,)) (NP-TMP (CD 2013))) (. .)))


Found one coreference chain containing the following mentions:
  sentenceIndex:1 headIndex:2 startTokenOffset:2 endTokenOffset:3 text: [Beijing]
Found one coreference chain containing the following mentions:
  sentenceIndex:1 headIndex:0 startTokenOffset:0 endTokenOffset:1 text: [He]
  sentenceIndex:0 headIndex:1 startTokenOffset:0 endTokenOffset:2 text: [John Smith]
Found one coreference chain containing the following mentions:
  sentenceIndex:1 headIndex:5 startTokenOffset:5 endTokenOffset:9 text: [January 10th , 2013]
Found one coreference chain containing the following mentions:
  sentenceIndex:0 headIndex:4 startTokenOffset:4 endTokenOffset:5 text: [China]
  
Document-wide discourse tree:
elaboration (LeftToRight)
  TEXT:John Smith went to China .
  TEXT:He visited Beijing , on January 10th , 2013 .

For more details about the annotation data structures, please see the edu/arizona/sista/processor/Document.scala file.

Changing processors is trivial: just replace the first line in the above example with:

val proc:Processor = new FastNLPProcessor()
// everything else stays the same

FastNLPProcessor uses the Stanford tokenizer, POS tagger, and NER, but replaces its parser with maltparser, trained to generated Stanford "basic" (rather than "collapsed") dependencies. This means that this annotator does not produce constituent trees and coreference chains. However, because of the faster parser, you should see a speedup increase of at least one order of magnitude. The output of the above code with FastNLPProcessor is:

Sentence #0:
Tokens: John Smith went to China .
Start character offsets: 0 5 11 16 19 24
End character offsets: 4 10 15 18 24 25
Lemmas: John Smith go to China .
POS tags: NNP NNP VBD TO NNP .
Named entities: PERSON PERSON O O LOCATION O
Normalized entities: O O O O O O
Syntactic dependencies:
 head:1 modifier:0 label:nn
 head:2 modifier:1 label:nsubj
 head:2 modifier:3 label:prep
 head:2 modifier:5 label:punct
 head:3 modifier:4 label:pobj


Sentence #1:
Tokens: He visited Beijing , on January 10th , 2013 .
Start character offsets: 26 29 37 44 46 49 57 61 63 67
End character offsets: 28 36 44 45 48 56 61 62 67 68
Lemmas: he visit Beijing , on January 10th , 2013 .
POS tags: PRP VBD NNP , IN NNP JJ , CD .
Named entities: O O LOCATION O O DATE DATE DATE DATE O
Normalized entities: O O O O O 2013-01-10 2013-01-10 2013-01-10 2013-01-10 O
Syntactic dependencies:
 head:1 modifier:0 label:nsubj
 head:1 modifier:2 label:dobj
 head:1 modifier:3 label:punct
 head:1 modifier:4 label:prep
 head:1 modifier:9 label:punct
 head:4 modifier:5 label:pobj
 head:5 modifier:6 label:amod
 head:5 modifier:7 label:punct
 head:5 modifier:8 label:num

Annotating documents already split into sentences

val doc = proc.annotateFromSentences(List("John Smith went to China.", "He visited Beijing."))
// everything else stays the same

Annotating documents already split into sentences and tokenized

val doc = annotateFromTokens(List(
  List("John", "Smith", "went", "to", "China", "."),
  List("There", ",", "he", "visited", "Beijing", ".")))
// everything else stays the same

Using individual annotators

You can of course use only some of the annotators provided by CoreNLP by calling them individually. To illustrate, the Processor.annotate() method is implemented as follows:

def annotate(doc:Document): Document = {
  tagPartsOfSpeech(doc)
  lemmatize(doc)
  recognizeNamedEntities(doc)
  parse(doc)
  chunking(doc)
  labelSemanticRoles(doc)
  resolveCoreference(doc)
  discourse(doc)
  doc.clear()
  doc
}

(Note that CoreNLP currently does not support chunking and semantic role labeling.) You can use just a few of these annotators. For example, if you need just POS tags, lemmas and named entities, you could use the following code:

val doc = proc.mkDocument("John Smith went to China. He visited Beijing, on January 10th, 2013.")
proc.tagPartsOfSpeech(doc)
proc.lemmatize(doc)
proc.recognizeNamedEntities(doc)
doc.clear()

Note that the last method called (doc.clear()) clears the internal structures created by the actual CoreNLP annotators. This saves a lot of memory, so, although it is not strictly necessary, I recommend you call it.

Serialization

This package also offers serialization code for the generated annotations. The two scenarios currently supported are:

Serialization to/from streams

// saving to a PrintWriter, pw
val someAnnotation = proc.annotate(someText)
val serializer = new DocumentSerializer
serializer.save(someAnnotation, pw)

// loading from an InputStream, is
val someAnnotation = serializer.load(is)

Serialization to/from Strings

// saving to a String object, savedString
val someAnnotation = proc.annotate(someText)
val serializer = new DocumentSerializer
val savedString = serializer.save(someAnnotation)

// loading from a String object, fromString
val someAnnotation = serializer.load(fromString)

Note that space required for these serialized annotations is considerably smaller (8 to 10 times) than the corresponding serialized Java objects. This is because we store only the information required to recreate these annotations (e.g., words, lemmas, etc.) without storing any of the Java/Scala objects and classes.

Cleaning up the interned strings

Classes that implement the Processor trait intern String objects to avoid allocating memory repeatedly for the same string. This is implemented by maintaining an internal dictionary of strings previously seen. This dictionary is unlikely to use a lot of memory due to the Zipfian distribution of language. But, if memory usage is a big concern, it can be cleaned by calling:

Processor.in.clear()

I recommend you do this only after you annotated all the documents you plan to keep in memory.

Although I see no good reason for doing this, you can disable the interning of strings completely by setting the internStrings = false in the CoreNLProcessor constructor, as such:

val processor = new CoreNLPProcessor(internStrings = false)

Using processors from Java

Scala is (largely) compatible with Java, so this library can be directly used from Java. Below is Java code that translates most of the functionality from the first Scala example in this document to Java:

public class ProcessorJavaExample {
    public static void main(String [] args) throws Exception {
        // create the processor
        Processor proc = new CoreNLPProcessor(true);
        // for much faster processing, use FastNLPProcessor
        // Processor proc = new FastNLPProcessor(true);
        
        // the actual work is done here
        Document doc = proc.annotate("John Smith went to China. He visited Beijing, on January 10th, 2013.");
        
        // you are basically done. the rest of this code simply prints out the annotations

        // let's print the sentence-level annotations
        int sentenceCount = 0;
        for (Sentence sentence: doc.sentences()) {
            System.out.println("Sentence #" + sentenceCount + ":");
            System.out.println("Tokens: " + mkString(sentence.words(), " "));
            System.out.println("Start character offsets: " + mkString(sentence.startOffsets(), " "));
            System.out.println("End character offsets: " + mkString(sentence.endOffsets(), " "));
            
            // these annotations are optional, so they are stored using Option objects, hence the isDefined checks
            if(sentence.lemmas().isDefined()){
                System.out.println("Lemmas: " + mkString(sentence.lemmas().get(), " "));
            }
            if(sentence.tags().isDefined()){
                System.out.println("POS tags: " + mkString(sentence.tags().get(), " "));
            }
            if(sentence.entities().isDefined()){
                System.out.println("Named entities: " + mkString(sentence.entities().get(), " "));
            }
            if(sentence.norms().isDefined()){
                System.out.println("Normalized entities: " + mkString(sentence.norms().get(), " "));
            }
            if(sentence.dependencies().isDefined()) {
                System.out.println("Syntactic dependencies:");
                DirectedGraphEdgeIterator<String> iterator = new        
                DirectedGraphEdgeIterator<String>(sentence.dependencies().get());
                while(iterator.hasNext()) {
                    // this is a scala Tuple3
                    Tuple3<Object, Object, String> dep = iterator.next();
                    // note that we use offsets starting at 0 (unlike CoreNLP, which uses offsets starting at 1)
                    System.out.println(" head:" + dep._1() + " modifier:" + dep._2() + " label:" + dep._3());
                }
            }
            if(sentence.syntacticTree().isDefined()) {
                System.out.println("Constituent tree: " + sentence.syntacticTree().get());
                // see the edu.arizona.sista.struct.Tree class for more information
                // on syntactic trees, including access to head phrases/words
            }

            sentenceCount += 1;
            System.out.println("\n");
        }

        // let's print the coreference chains
        if(doc.coreferenceChains().isDefined()) {
            // these are scala.collection Iterator and Iterable (not Java!)
            Iterator<Iterable<CorefMention>> chains = doc.coreferenceChains().get().getChains().iterator();
            while(chains.hasNext()) {
                Iterator<CorefMention> chain = chains.next().iterator();
                System.out.println("Found one coreference chain containing the following mentions:");
                while(chain.hasNext()) {
                    CorefMention mention = chain.next();
                    // note that all these offsets start at 0 too
                    System.out.println("\tsentenceIndex:" + mention.sentenceIndex() +
                        " headIndex:" + mention.headIndex() +
                        " startTokenOffset:" + mention.startOffset() +
                        " endTokenOffset:" + mention.endOffset());
                }
            }
        }
    }

    public static String mkString(String [] sa, String sep) {
        StringBuilder os = new StringBuilder();
        for(int i = 0; i < sa.length; i ++) {
            if(i > 0) os.append(sep);
            os.append(sa[i]);
        }
        return os.toString();
    }
    public static String mkString(int [] sa, String sep) {
        StringBuilder os = new StringBuilder();
        for(int i = 0; i < sa.length; i ++) {
            if(i > 0) os.append(sep);
            os.append(Integer.toString(sa[i]));
        }
        return os.toString();
    }
}

The output of this code is:

Sentence #0:
Tokens: John Smith went to China .
Start character offsets: 0 5 11 16 19 24
End character offsets: 4 10 15 18 24 25
Lemmas: John Smith go to China .
POS tags: NNP NNP VBD TO NNP .
Named entities: PERSON PERSON O O LOCATION O
Normalized entities: O O O O O O
Syntactic dependencies:
 head:1 modifier:0 label:nn
 head:2 modifier:1 label:nsubj
 head:2 modifier:4 label:prep_to
Constituent tree: 
(ROOT
    (S
        (NP
            (NNP John)
            (NNP Smith)
        )
        (VP
            (VBD went)
            (PP
                (TO to)
                (NP
                    (NNP China)
                )
            )
        )
        (. .)
    )
)


Sentence #1:
Tokens: He visited Beijing , on January 10th , 2013 .
Start character offsets: 26 29 37 44 46 49 57 61 63 67
End character offsets: 28 36 44 45 48 56 61 62 67 68
Lemmas: he visit Beijing , on January 10th , 2013 .
POS tags: PRP VBD NNP , IN NNP JJ , CD .
Named entities: O O LOCATION O O DATE DATE DATE DATE O
Normalized entities: O O O O O 2013-01-10 2013-01-10 2013-01-10 2013-01-10 O
Syntactic dependencies:
 head:1 modifier:0 label:nsubj
 head:1 modifier:2 label:dobj
 head:1 modifier:8 label:tmod
 head:2 modifier:5 label:prep_on
 head:5 modifier:6 label:amod
Constituent tree: 
(ROOT
    (S
        (NP
            (PRP He)
        )
        (VP
            (VBD visited)
            (NP
                (NP
                    (NNP Beijing)
                )
                (, ,)
                (PP
                    (IN on)
                    (NP
                        (NNP January)
                        (JJ 10th)
                    )
                )
                (, ,)
            )
            (NP-TMP
                (CD 2013)
            )
        )
        (. .)
    )
)


Found one coreference chain containing the following mentions:
	sentenceIndex:1 headIndex:2 startTokenOffset:2 endTokenOffset:7
Found one coreference chain containing the following mentions:
	sentenceIndex:0 headIndex:1 startTokenOffset:0 endTokenOffset:2
	sentenceIndex:1 headIndex:0 startTokenOffset:0 endTokenOffset:1
Found one coreference chain containing the following mentions:
	sentenceIndex:1 headIndex:5 startTokenOffset:5 endTokenOffset:7
Found one coreference chain containing the following mentions:
	sentenceIndex:0 headIndex:4 startTokenOffset:4 endTokenOffset:5
Found one coreference chain containing the following mentions:
	sentenceIndex:1 headIndex:8 startTokenOffset:8 endTokenOffset:9

The discourse parser

The discourse parser in processors is inspired by the parser of Feng and Hirst and the HILDA parser of Hernault et al., but with a different feature set. It is transparently integrated in both CoreNLPProcessor and FastNLPProcessor: just instantiate it as CoreNLPProcessor(withDiscourse = true) or FastNLPProcessor(withDiscourse = true). If discourse is enabled, Document.discourseTree stores the discourse tree for the entire document as an instance of the DiscourseTree class.

Following the conventions from other modern discourse parsing work, the discourse tree:

• Is represented as a binary tree, containing hypotactic relations (containing one nucleus and one satellite node) or paratactic relations (both nodes have equal importance).
• Stores the relation labels in the parent node (in DiscourseTree.relationLabel) rather than the satellite nodes (like the RST corpus). We use the same 18 labels as Feng and Hirst.
• Stores the relation direction in DiscourseTree.relationDirection. The direction can be LeftToRight (meaning the nucleus is the left child), RightToLeft (the right node is the nucleus), or None (for paratactic relations).

If you end up using this discourse parser, I would appreciate it if you cited this work:

Peter Jansen, Mihai Surdeanu, and Peter Clark. Discourse Complements Lexical Semantics for Non-factoid Answer Reranking. In Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (ACL), 2014. [bib]

The edu.arizona.sista.learning package

processors now contains a machine learning (ML) package (edu.arizona.sista.learning), which includes implementations for common ML algorithms (e.g., Perceptron, Logistic Regression, Support Vector Machines, Random Forests) for both classification and ranking.

The structure of this package is heavily inspired by Stanford's CoreNLP. Similar to CoreNLP, we use a Datum trait to store a single data point, which is implemented by BVFDatum to store binary-valued-feature datums, or by RVFDatum to store real-valued-feature datums. A collection of data points is stored as a Dataset, which is similarly implemented by BVFDataset or RVFDataset. All classifiers implement the Classifier trait, which has three main methods: train, which trains a model a given dataset, classOf, which returns the most likely prediction for a given datum, and scoresOf, which returns the scores for all known labels for a given datum. We currently support the following classifiers: large-margin Perceptron (PerceptronClassifier), linear SVMs and logistic regression from liblinear (LibLinearClassifier), dual SVMs from libsvm (LibSVMClassifier), and random forests from fast-random-forest (RandomForestClassifier).

A similar structure exists for ranking problems, with RankingDataset used to store a corpus of ranking examples, and RankingClassifier as the API to be implemented by all ranking classifiers. We currently support the following classifiers: ranking Perceptron (PerceptronRankingClassifier), ranking SVMs from svm-rank (SVMRankingClassifier), and boosted decision trees from jforests (JForestsRankingClassifier).

For usage examples, including how to create datums and datasets from scratch or import them from the svm-light format, please take a look at the examples under src/test/scala/edu/arizona/sista/learning.