Stanford Topic Modeling Toolbox: Exception

Question

I'm trying to work with the Stanford Topic Modeling Toolbox. I downloaded the "tmt-0.4.0.jar"-File from here: http://nlp.stanford.edu/software/tmt/tmt-0.4/ and I tried to examples. Example 0 and 1 worked fine, but trying example 2 (no code-changes), I receive the following exception:

[cell] loading pubmed-oa-subset.csv.term-counts.cache.70108071.gz [Concurrent] 32 permits Exception in thread "Thread-3" java.lang.ArrayIndexOutOfBoundsException: -1 at scalanlp.stage.text.TermCounts$class.getDF(TermFilters.scala:64) at scalanlp.stage.text.TermCounts$$anon$2.getDF(TermFilters.scala:84) at scalanlp.stage.text.TermMinimumDocumentCountFilter$$anonfun$apply$4$$anonfun$apply$5$$anonfun$apply$6.apply(TermFilters.scala:172) at scalanlp.stage.text.TermMinimumDocumentCountFilter$$anonfun$apply$4$$anonfun$apply$5$$anonfun$apply$6.apply(TermFilters.scala:172) at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:390) at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:388) at scala.collection.Iterator$class.foreach(Iterator.scala:660) at scala.collection.Iterator$$anon$22.foreach(Iterator.scala:382) at scala.collection.IterableViewLike$Transformed$class.foreach(IterableViewLike.scala:41) at scala.collection.IterableViewLike$$anon$5.foreach(IterableViewLike.scala:82) at scala.collection.TraversableOnce$class.size(TraversableOnce.scala:104) at scala.collection.IterableViewLike$$anon$5.size(IterableViewLike.scala:82) at scalanlp.stage.text.DocumentMinimumLengthFilter.filter(DocumentFilters.scala:31) at scalanlp.stage.text.DocumentMinimumLengthFilter.filter(DocumentFilters.scala:28) at scalanlp.stage.generic.Filter$$anonfun$apply$1.apply(Filter.scala:38) at scalanlp.stage.generic.Filter$$anonfun$apply$1.apply(Filter.scala:38) at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:390) at edu.stanford.nlp.tmt.data.concurrent.Concurrent$$anonfun$map$2.apply(Concurrent.scala:100) at edu.stanford.nlp.tmt.data.concurrent.Concurrent$$anonfun$map$2.apply(Concurrent.scala:88) at edu.stanford.nlp.tmt.data.concurrent.Concurrent$$anon$4.run(Concurrent.scala:45)

Why do I receive this exception, and how can this be fixed? Thanks a lot for your help!

PS: The code is the same as in example 2 of the website:

// Stanford TMT Example 2 - Learning an LDA model
// http://nlp.stanford.edu/software/tmt/0.4/

// tells Scala where to find the TMT classes
import scalanlp.io._;
import scalanlp.stage._;
import scalanlp.stage.text._;
import scalanlp.text.tokenize._;
import scalanlp.pipes.Pipes.global._;

import edu.stanford.nlp.tmt.stage._;
import edu.stanford.nlp.tmt.model.lda._;
import edu.stanford.nlp.tmt.model.llda._;

val source = CSVFile("pubmed-oa-subset.csv") ~> IDColumn(1);

val tokenizer = {
  SimpleEnglishTokenizer() ~>            // tokenize on space and punctuation
  CaseFolder() ~>                        // lowercase everything
  WordsAndNumbersOnlyFilter() ~>         // ignore non-words and non-numbers
  MinimumLengthFilter(3)                 // take terms with >=3 characters
}

val text = {
  source ~>                              // read from the source file
  Column(4) ~>                           // select column containing text
  TokenizeWith(tokenizer) ~>             // tokenize with tokenizer above
  TermCounter() ~>                       // collect counts (needed below)
  TermMinimumDocumentCountFilter(4) ~>   // filter terms in <4 docs
  TermDynamicStopListFilter(30) ~>       // filter out 30 most common terms
  DocumentMinimumLengthFilter(5)         // take only docs with >=5 terms
}

// turn the text into a dataset ready to be used with LDA
val dataset = LDADataset(text);

// define the model parameters
val params = LDAModelParams(numTopics = 30, dataset = dataset,
  topicSmoothing = 0.01, termSmoothing = 0.01);

// Name of the output model folder to generate
val modelPath = file("lda-"+dataset.signature+"-"+params.signature);

// Trains the model: the model (and intermediate models) are written to the
// output folder.  If a partially trained model with the same dataset and
// parameters exists in that folder, training will be resumed.
TrainCVB0LDA(params, dataset, output=modelPath, maxIterations=1000);

// To use the Gibbs sampler for inference, instead use
// TrainGibbsLDA(params, dataset, output=modelPath, maxIterations=1500);

Without the code to compare it to, we have no idea how to diagonose it. — wheaties

Kajanan Kajanan · Accepted Answer · 2014-07-09T04:18:20

The answer has been posted by the author of the tool. Please have a look here.

This usually happens when you have a stale .cache file - unfortunately the error message isn't particularly useful. Try deleting cache in the run folder and running again.

https://lists.cs.princeton.edu/pipermail/topic-models/2012-July/001979.html

Stanford Topic Modeling Toolbox: Exception

1 Answers