com.wcohen.ss

Class AbbreviationAlignment

java.lang.Object

com.wcohen.ss.AbstractStringDistance

com.wcohen.ss.AbstractTokenizedStringDistance

com.wcohen.ss.AbstractStatisticalTokenDistance

com.wcohen.ss.AbbreviationAlignment

All Implemented Interfaces:

StringDistance, StringDistanceLearner

public class AbbreviationAlignment
extends AbstractStatisticalTokenDistance

Abbreviation distance metric which evaluates the probability of a short-form string being an abbreviation/acronym of another long-form string. The probability is given by an HMM-based alignment between the two strings.

Sample command line:
java com.wcohen.ss.AbbreviationAlignment "DNA" "Deoxyribonucleic acid"
Expected output:

 M        |M      |M|M   |
 D        |N      | |A   |
 Deoxyribo|nucleic| |acid|
 
 Probability = 3.674595157620664E-6
 

where, the rows of the alignment contain: (1) the states of the Viterbi path in the Alignment-HMM, (2) the short form characters, and (3) the long form characters. The probability of the Viterbi path is also given.

Citation: Dana Movshovitz-Attias and William Cohen, Alignment-HMM-based Extraction of Abbreviations from Biomedical Text, 2012, BioNLP in NAACL

Author:

Dana Movshovitz-Attias

See Also:

ExtractAbbreviations

Field Summary

Fields inherited from class com.wcohen.ss.AbstractStatisticalTokenDistance

collectionSize, documentFrequency, totalTokenCount

Fields inherited from class com.wcohen.ss.AbstractTokenizedStringDistance

tokenizer

Constructor Summary

Constructors

Constructor and Description
AbbreviationAlignment()

Method Summary

Modifier and Type	Method and Description
String	explainScore(StringWrapper s, StringWrapper t) This method needs to be implemented by subclasses.
static String[]	init(String[] argv)
protected AlignmentPredictionModel	loadPredictor()
static void	main(String[] argv) Evaluates the probability of the short-form string (string1) being an abbreviation/acronym of the long-form string (string2). Usage: AbbreviationAlignment short_form_string long_form_string [train_data_dir]
double	score(StringWrapper s, StringWrapper t) This method needs to be implemented by subclasses.
void	setTrainDir(String trainDir)

Methods inherited from class com.wcohen.ss.AbstractStatisticalTokenDistance

checkTrainingHasHappened, getDocumentFrequency, tokenIterator, train

Methods inherited from class com.wcohen.ss.AbstractTokenizedStringDistance

asBagOfTokens, prepare, setStringWrapperPool

Methods inherited from class com.wcohen.ss.AbstractStringDistance

addExample, doMain, explainScore, getDistance, hasNextQuery, nextQuery, prepare, prepare, score, setDistanceInstancePool

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbbreviationAlignment

public AbbreviationAlignment()

Method Detail

main

public static void main(String[] argv)

Evaluates the probability of the short-form string (string1) being an abbreviation/acronym of the long-form string (string2).
Usage: AbbreviationAlignment short_form_string long_form_string [train_data_dir]

init

public static String[] init(String[] argv)

setTrainDir

public void setTrainDir(String trainDir)

loadPredictor

protected AlignmentPredictionModel loadPredictor()

score

public double score(StringWrapper s,
                    StringWrapper t)

Description copied from class: AbstractStringDistance

This method needs to be implemented by subclasses.

Specified by:

score in interface StringDistance

Specified by:

score in class AbstractStringDistance

explainScore

public String explainScore(StringWrapper s,
                           StringWrapper t)

Description copied from class: AbstractStringDistance

This method needs to be implemented by subclasses.

Specified by:

explainScore in interface StringDistance

Specified by:

explainScore in class AbstractStringDistance