## Canceled: Help Build a Watson Clone–Participants Sought for LingPipe Code Camp

January 10, 2014

Code Camp is canceled. We are late on delivering a LingPipe recipes book to our publisher and that will have to be our project for March. But we could have testers/reviewers come and hang out. Less fun I think.

Apologies.
Breck

—————————

Dates: To be absolutely clear: Dates are 3/2/2014 to 3/31/14 in Driggs Idaho. You can work remotely, we will be doing stuff before as well for setup.

New: We have setup a github repository. URL is https://github.com/watsonclone/jeopardy-.git

————————

Every year we go out west for a month of coding and skiing. Last year it was Salt Lake City Utah, this year it is Driggs Idaho for access to Grand Targhee and Jackson Hole. The house is rented for the month of March and the project selected. This year we will create a Watson clone.

I have blogged about Watson before and I totally respect what they have done. But the coverage is getting a bit breathless with the latest billion dollar effort. So how about assembling a scrappy bunch of developers and see how close we can come to recreating the Jeopardy beast?

How this works:

• We have a month of focused development. We tend to code mornings, ski afternoons. House has 3 bedrooms if you want to come stay. Prior arrangements must be made. House is paid for. Nothing else is.
• The code base will be open source. We are moving LingPipe to the AGPL so maybe that license or we could just apache license it. We want folks to be comfortable contributing.
• You don’t have to be present to contribute.
• We have a very fun time last year. We worked very hard on an email app that didn’t quite get launched but the lesson learned was to start with the project defined.

If you are interested in participating let us know at watsonclone@lingpipe.com. Let us know your background, what you want to do, do you expect to stay with us etc…. No visa situations please and we don’t have any funds to support folks. Obviously we have limited space physically and mentally so we may say no but we will do our best to be inclusive. Step 1–transcribe some Jeopardy shows.

Q: Are you frigging crazy???

A: Why, yes, yes we are. But we are also really good computational linguists….

Breck

## Lucene 4 Essentials for Text Search and Indexing

March 8, 2014

Here’s a short-ish introduction to the Lucene search engine which shows you how to use the current API to develop search over a collection of texts. Most of this post is excerpted from Text Processing in Java, Chapter 7, Text Search with Lucene.

### Lucene Overview

Apache Lucene is a search library written in Java. It’s popular in both academic and commercial settings due to its performance, configurability, and generous licensing terms. The Lucene home page is http://lucene.apache.org.

Lucene provides search over documents. A document is essentially a collection of fields. A field consists of a field name that is a string and one or more field values. Lucene does not in any way constrain document structures. Fields are constrained to store only one kind of data, either binary, numeric, or text data. There are two ways to store text data: string fields store the entire item as one string; text fields store the data as a series of tokens. Lucene provides many ways to break a piece of text into tokens as well as hooks that allow you to write custom tokenizers. Lucene has a highly expressive search API that takes a search query and returns a set of documents ranked by relevancy with documents most similar to the query having the highest score.

The Lucene API consists of a core library and many contributed libraries. The top-level package is org.apache.lucene, which is abbreviated as oal in this article. As of Lucene 4, the Lucene distribution contains approximately two dozen package-specific jars, e.g.: lucene-core-4.7.0.jar, lucene-analyzers-common-4.7.0.jar, lucene-misc-4.7.0.jar. This cuts down on the size of an application at a small cost to the complexity of the build file.

### A Lucene Index is an Inverted Index

Lucene manages an index over a dynamic collection of documents and provides very rapid updates to the index as documents are added to and deleted from the collection. An index may store a heterogeneous set of documents, with any number of different fields that may vary by document in arbitrary ways. Lucene indexes terms, which means that Lucene search is search over terms. A term combines a field name with a token. The terms created from the non-text fields in the document are pairs consisting of the field name and field value. The terms created from text fields are pairs of field name and token.

The Lucene index provides a mapping from terms to documents.  This is called an inverted index because it reverses the usual mapping of a document to the terms it contains.  The inverted index provides the mechanism for scoring search results: if a number of search terms all map to the same document, then that document is likely to be relevant.

Here are three entries from an index over part of the The Federalist Papers, a collection of 85 political essays which contains roughly 190,000 word instances over a vocabulary of about 8,000 words.  A field called text holds the contents of each essay, which have been tokenized into words, all lowercase, no punctuation.  The inverted index entries for the terms consisting of field name text and tokens abilities, able, and abolish are:

term document
text:abilities 2, 17, 21, 22, 35, 64, 76
text:able 1, 3, 4, 7, 8, 9, 10, 11, 12, 15, 16, 21, 23, 24,
25, 27, 29, 30, 33, 34, 35, 36, 37, 38, 41, 43, 46, 49,
51, 52, 58, 62, 63, 64, 67, 68, 70, 71, 75, 78, 85
text:abolish 10, 14, 26, 31, 39, 49, 45, 70, 71, 78, 81

Note that the document numbers here are Lucene’s internal references to the document.  These ids are not stable; Lucene manages the document id as it manages the index and the internal numbering may change as documents are added to and deleted from the index.

### Lucene Versions and Version Numbers

The current Apache Lucene Java release is version 4.7, where 4 is the major version number and 7 is the minor version number.  The Apache odometer rolled over to 4.6.0 in November, 2013 and just hit 4.7.0 on February 26, 2014.  At the time that I wrote the Lucene chapter of Text Processing in Java, the current version was 4.5.  Minor version updates maintain backwards compatibility for the given major version therefore, all the example programs in the book compile and run under version 4.7 as well.

The behavior of many Lucene components has changed over time.  In particular, the index file format is subject to change from release to release as different methods of indexing and compressing the data are implemented.   To address this, the Enum class oal.util.Version was introduced in Lucene 3.  A Version instance identifies the major and minor versions of Lucene. For example, LUCENE_45 identifies version 4.5.  The Lucene version is supplied to the constructor of the components in an application.  As of Lucene 4.7, older versions have been deprecated, so the compiler issues a warning when older versions are specified.  This means that the examples from the book, which specify version 4.5, generate a compiler warning when compiled under version 4.7.

There’s no requirement that all components in an application be of the same version however, for components used for both search and indexing, it is critical that the Lucene version is the same in the code that is called at indexing time and the code that is called at search time.  A Lucene index knows what version of Lucene was used to create it (by using the Lucene Version enum constant).  Lucene is backward compatible with respect to searching and maintaining old index versions because it includes classes that can read and write all versions of the index up through the current release.

### Lucene Indexes Fields

Conceptually, Lucene provides indexing and search over documents, but implementation-wise, all indexing and search is carried out over fields.  A document is a collection of fields.  Each field has three parts: name, type, and value.  At search time, the supplied field name restricts the search to particular fields.

For example, a MEDLINE citation can be represented as a series of fields: one field for the name of the article, another field for name of the journal in which it was published, another field for the authors of the article, a pub-date field for the date of publication, a field for the text of the article’s abstract, and another field for the list of topic keywords drawn from Medical Subject Headings (MeSH).  Each of these fields is given a different name, and at search time, the client could specify that it was searching for authors or titles or both, potentially restricting to a date range and set of journals by constructing search terms for the appropriate fields and values.

The Lucene API for fields has changed across the major versions of Lucene as the functionality and organization of the underlying Lucene index have evolved.  Lucene 4 introduces a new interface oal.index.IndexableField, which is implemented by class oal.document.Field.  Lucene 4 also introduces datatype-specific subclasses of Field that encapsulate indexing and storage details for common use cases.  For example, to index integer values, use class oal.document.IntField, and to index simple unanalyzed strings (keywords), use oal.document.StringField.  These so-called sugar subclasses are all final subclasses.

The field type is an object that implements oal.index.IndexableFieldType.  Values may be text, binary, or numeric.  The value of a field can be indexed for search or stored for retrieval or both.  The value of an indexed field is processed into terms that are stored in the inverted index.  The raw value of a stored field is stored in the index in a non-inverted manner.  Storing the raw values allows you to retrieve them at search time but may consume substantial space.

Indexing and storage options are specified via setter methods on oal.document.FieldType.  These include the method setIndexed(boolean), which specifies whether or not to index a field, and the method setTokenized(boolean), which specifies whether or not the value should be tokenized.  The method setOmitNorms(boolean) controls how Lucene computes term frequency.  Lucene’s default behavior is to represent term frequency as a proportion by computing the ratio of the number of times a term occurs to the total number of terms in the document, instead of storing a simple term frequency count.  To do this calculation it stores a normalizing factor for each field that is indexed.  Calling method setOmitNorms with value true turns this off and the raw term frequency is used instead.

Some indexing choices are interdependent.  Lucene checks the values on a FieldType object at Field construction time and throws an IllegalArgumentException if the FieldType has inconsistent values.  For example, a field must be either indexed or stored or both, so indexed and/or stored must be true.  If indexed is false, then stored must be true and all other indexing options should be set to false.  The following code fragment defines a custom FieldType and then creates a Field of this type:

FieldType myFieldType = new FieldType();
myFieldType.setIndexed(true);
myFieldType.setOmitNorms(true);
myFieldType.setIndexOptions(IndexOptions.DOCS_AND_FREQS);
myFieldType.setStored(false);
myFieldType.setTokenized(true);
myFieldType.freeze();
Field myField = new Field("field name",
"field value",
myFieldType);

The source code of the subclasses of Field provides good examples of how to define a FieldType.

### Analyzing Text into Tokens

Search and indexing over text fields require processing text data into tokens.  The package oal.analysis contains the base classes for tokenizing and indexing text.  Processing may consist of a sequence  of transformations , e.g., whitespace tokenization, case normalization, stop-listing, and stemming.

The abstract class oal.analysis.TokenStream breaks the incoming text into a sequence of tokens that are retrieved using an iterator-like pattern.  TokenStream has two subclasses: oal.analysis.Tokenizer and oal.analysis.TokenFilter.   A Tokenizer takes a java.io.Reader as input whereas a TokenFilter takes another oal.analysis.TokenStream as input.  This allows us to chain together tokenizers such that the initial tokenizer gets its input from a reader and the others operate on tokens from the preceding TokenStream in the chain.

An oal.analysis.Analyzer supplies the indexing and searching processes with TokenStreams on a per-field basis.  It maps field names to tokenizers and may also supply a default analyzer for unknown field names.  Lucene includes many analysis modules that provide concrete implementations of different kinds of analyzers.  As of Lucene 4, these modules are bundled into separate jarfiles.  There are several dozen language-specific analysis packages, from oal.analysis.ar for Arabic to oal.analysis.tr for Turkish.  The package oal.analysis.core provides several general-purpose analyzers, tokenizers, and tokenizer factory classes.

The abstract class oal.analysis.Analyzer contains methods used to extract terms from input text.  Concrete subclasses of Analyzer must override the method createComponents, which returns an object of the nested class TokenStreamComponents that defines the tokenization process and provides access to initial and file components of the processing pipeline.  The initial component is a Tokenizer that handles the input source.  The final component is an instance of TokenFilter and it is the TokenStream returned by the method Analyzer.tokenStream(String,Reader).  Here is an example of a custom Analyzer that tokenizes its inputs into individual words with all letters lowercase.

Analyzer analyzer = new Analyzer() {
@Override protected TokenStreamComponents
Tokenizer source =
TokenStream filter =
new LowerCaseFilter(VERSION,source);
return new TokenStreamComponents(source, filter);
}
};

Note that the constructors for the oal.analysis.standard.StandardTokenizer and oal.analysis.core.LowerCaseFilter objects require a Version argument.  Further note that package oal.analysis.standard is distributed in the jarfile lucene-analyzers-common-4.x.y.jar, where x and y are the minor version and release number.

### Indexing Documents

Document indexing consists of first constructing a document that contains the fields to be indexed or stored, then adding that document to the index.  The key classes involved in indexing are oal.index.IndexWriter, which is responsible for adding documents to an index, and oal.store.Directory, which is the storage abstraction used for the index itself.  Directories provide an interface that’s similar to an operating system’s file system.  A Directory contains any number of sub-indexes called segments.  Maintaining the index as a set of segments allows Lucene to rapidly update and delete documents from the index.

The following example shows how to create a Lucene index given a directory containing a set of data files.  The data in this example is taking from the 20 Newsgroups corpus a set of roughly 20,000 messages posted to 20 different newsgroups.  This code is excerpted from the example program in section 7.11 of Text Processing in Java that shows how to do document classification using Lucene.  We’ll get to document classification in a later post.  Right now we just want to go over how to build the index.

void buildIndex(File indexDir, File dataDir)
throws IOException, FileNotFoundException {

Directory fsDir = FSDirectory.open(indexDir);
IndexWriterConfig iwConf
= new IndexWriterConfig(VERSION,mAnalyzer);
iwConf.setOpenMode(IndexWriterConfig.OpenMode.CREATE);
IndexWriter indexWriter
= new IndexWriter(fsDir,iwConf);

for (File group : groupsDir) {
String groupName = group.getName();
File[] posts = group.listFiles();
for (File postFile : posts) {
String number = postFile.getName();
NewsPost post = parse(postFile, groupName, number);
Document d = new Document();
post.group(),Store.YES));
post.subject(),Store.NO));
post.body(),Store.NO));
}

}
indexWriter.commit();
indexWriter.close();
}

The method buildIndex walks over the training data directory and parses the newsgroup messages into a NewsPost object, which is a simple domain model of a newsgroup post, consisting of the newsgroup name, subject, body, and filename (a string of numbers).  We treat each post as a Lucene document consisting of two fields: a StringField named category for the newsgroup name and a TextField named text that holds the message subject and message body.  Method buildIndex takes two java.io.File arguments: the directory for the Lucene index and a directory for one set of newsgroup posts where the directory name is the same as the Usenet newsgroup name, e.g.: rec.sport.baseball.

The first four statements in buildIndex create a oal.store.FSDirectory that stores the index as a file-system directory and an IndexWriter which does the work of analyzing documents and adding them to the index.  The behavior of the IndexWriter is specified by an IndexWriterConfig object.  Documents are indexed via the IndexWriter‘s default Analyzer.  At the outset of the program we define a static final Lucene Version enum constant named VERSION. and a Lucene Analyzer named mAnalyzer.  We supply these as arguments to the IndexWriterConfig constructor.  We call the setOpenMode method with the enum constant IndexWriterConfig.OpenMode.CREATE, which causes the index writer to create a new index or overwrite an existing one.

A for loop iterates over all files in the data directory.  Each file is first parsed into a Java NewsPost and a corresponding Lucene document is created and fields are added to the document.  This document has two fields: category and text.  Newsgroup names are stored as simple unanalyzed strings.  The field named text stores both the message subject and message body.  A document may have multiple values for a given field.  Search over that field will be over all values for that field, however phrase search over that field will not match across different field values.  When theIndexWriter.addDocument(Document) method is called, the document is added to the index and the constituent fields are indexed and stored accordingly.

The final two statements invoke the IndexWriter‘s commit and close methods, respectively.  The commit method writes all pending changes to the directory and syncs all referenced index files so that the changes are visible to index readers.  Lucene now implements a two-phase commit so that if the commit succeeds, the changes to the index will survive a crash or power loss.  A commit may be expensive, and part of performance tuning is determining when to commit as well as how often and how aggressively to merge the segments of the index.

### Document Search and Search Ranking

The Lucene search API takes a search query and returns a set of documents ranked by relevancy with documents most similar to the query having the highest score.  Lucene provides a highly configurable hybrid form of search that combines exact boolean searches with softer, more relevance-ranking-oriented vector-space search methods.  All searches are field specific, because Lucene indexes terms and a term is composed of a field name and a token.

#### Search Queries

Lucene specifies a language in which queries may be expressed.  For instance, computer NOT java produces a query that specifies the term computer must appear in the default field and the term java must not appear.  Queries may specify fields, as in text:java, which requires the term java to appear in the text field of a document.

The query syntax includes basic term and field specifications, modifiers for wildcard, fuzzy, proximity, or range searches, and boolean operators for requiring a term to be present, absent, or for combining queries with logical operators.  Finally, sub-queries may be boosted by providing numeric values to raise or lower their prominence relative to other parts of the query. The full syntax specification is in the package level javadoc for package oal.queryparser.classic.  A bonus feature of Text Processing in Java is a quick one-page reference guide to Lucene’s search query syntax (see Figure 7.2).

Queries may be constructed programmatically using the dozen or so built-in implementations of the oal.search.Query abstract base class.  The most basic kind of query is a search for a single token on a single field, i.e., a single term.  This query is implemented in Lucene’s oal.search.TermQuery class.  A term query is constructed from a Term object, which is constructed from a field name and text for the term, both specified as strings.

#### Search Scoring

Lucene’s default search scoring algorithm weights results using TF—IDF, term frequency—inverse document frequency.  Term frequency means that high-frequency terms within a document have higher weight than do low-frequency terms.  Inverse document frequency means that terms that occur frequently across many documents in a collection of documents are less likely to be meaningful descriptors of any given document in a corpus and are therefore down-weighted.  This filters out common words.

As of Lucene 4, the API provides alternative scoring algorithms and a pluggable architecture that allows developers to build their own custom scoring models.

#### Search Example

The following program illustrates the basic sequence of search operations.  This program is a simplified version of the Lucene search example program included with the book.  When run from the command line, this program takes three arguments: the path to a Lucene index; a query string; the maximum number of results to return.  It runs the specified query against the specified index and prints out the rank, score, and internal document id for all documents that match the query.

import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.standard.StandardAnalyzer;
import org.apache.lucene.index.CorruptIndexException;
import org.apache.lucene.queryparser.classic.ParseException;
import org.apache.lucene.queryparser.classic.QueryParser;
import org.apache.lucene.search.IndexSearcher;
import org.apache.lucene.search.Query;
import org.apache.lucene.search.ScoreDoc;
import org.apache.lucene.search.TopDocs;
import org.apache.lucene.store.Directory;
import org.apache.lucene.store.FSDirectory;
import org.apache.lucene.util.Version;

import java.io.File;
import java.io.IOException;

public class LuceneSearch {
public static void main(String[] args)
throws ParseException, CorruptIndexException,
IOException {

File indexDir = new File(args[0]);
String query = args[1];
int maxHits = Integer.parseInt(args[2]);

Directory fsDir = FSDirectory.open(indexDir);

Analyzer stdAn
= new StandardAnalyzer(Version.LUCENE_45);
QueryParser parser
= new QueryParser(Version.LUCENE_45,"text",stdAn);
Query q= parser.parse(query);

TopDocs hits = searcher.search(q,maxHits);
ScoreDoc[] scoreDocs = hits.scoreDocs;
System.out.println("hits=" + scoreDocs.length);
System.out.println("Hits (rank,score,docId)");
for (int n = 0; n < scoreDocs.length; ++n) {
ScoreDoc sd = scoreDocs[n];
float score = sd.score;
int docId = sd.doc;
System.out.printf("%3d %4.2f %d\n",
n, score, docId);
}
}
}

The main method is declared to throw a Lucene corrupt index exception if the index isn’t well formed, a Lucene parse exception if the query isn’t well formed, and a general Java I/O exception if there is a problem reading from or writing to the index directory.  It starts off by reading in command-line arguments, then it creates a Lucene directory, index reader, index searcher, and query parser, and then it uses the query parser to parse the query.

Lucene uses instances of the aptly named IndexReader to read data from an index, in this example, we use an instance of class oal.index.DirectoryReader.  The oal.search.IndexSearcher class performs the actual search.  Every index searcher wraps an index reader to get a handle on the indexed data.  Once we have an index searcher, we can supply queries to it and enumerate results in order of their score.

The class oal.queryparser.classic.QueryParserBase provides methods to parse a query string into a oal.search.Query object or throw a oal.queryparser.classic.ParseException if it is not.  All tokens are analyzed using the specified Analyzer.  This example is designed to search an index for Lucene version 4.5 that was created using an analyzer of class oal.analysis.standard.StandardAnalyzer which contains text a field named text.

It is important to use the same analyzer in the query parser as is used in the creation of the index.  If they don’t match, queries that should succeed will fail should the different analyzers produce differing tokenizations given the same input.  For instance, if we apply stemming to the contents of text field text during indexing and reduce the word codes to code, but we don’t apply stemming to the query, then a search for the word codes in field text will fail. The search term is text:codes but the index contains only the term text:code.  Note that package oal.queryparser.classic is distributed in the jarfile lucene-queryparser-4.x.y.jar.

The actual search is done via a call to the IndexSearcher‘s search method, which takes two arguments: the query and an upper bound on the number of hits to return.  It returns an instance of the Lucene class oal.search.TopDocs.  The TopDocs result provides access to an array of search results.  Each result is an instance of the Lucene class oal.search.ScoreDoc, which encapsulates a document reference with a floating point score.  The array of search results is sorted in decreasing order of score, with higher scores representing better matches.  For each ScoreDoc object, we get the score from the public member variable score.  We get the document reference number (Lucene’s internal identifier for the doc) from the public member variable doc.  The document identifier is used to retrieve the document from the searcher.  Here, we’re just using the id as a diagnostic to illustrate the basics of search and so we just print the number, even though it is only an internal reference.  Finally, we close the IndexReader.

This post tries to cover the essentials of Lucene 4 in a very short amount of space.  In order to do this, this post contains minimal amounts of examples, and links to the Lucene javadocs have been substituted for detailed explanation of how classes and methods behave.  Putting these code fragments together into a full application is left as an exercise to the reader.

Back when Lucene was at version 2.4 I wrote my first blog post titled “Lucene 2.4 in 60 Seconds.”  A more accurate title would have been “Lucene 2.4 in 60 Seconds or More.”  Likewise, a more accurate title for this post would be “The Essential Essentials of Text Search and Indexing with Lucene 4″ but that’s just not very snappy.  For more on the essentials of search and indexing with Lucene, please check out Chapter Seven of Text Processing in Java, (and all the other chapters as well).

To cover all of Lucene would take an entire book, and there are many good ones out there. My favorite is Lucene in Action, Second Edition, which, alas, only covers version 3.

## New Book: Text Processing in Java

January 31, 2014

I’m pleased to announce the publication of Text Processing in Java !

This book teaches you how to master the subtle art of multilingual text processing and prevent text data corruption.  Data corruption is the all-too-common problem of words that are garbled into strings of question marks, black diamonds, or random glyphs.  In Japanese this is called mojibake (“character change”), written 文字化け, but on your browser it might look like this: �����  or this: æ–‡å­—åŒ–ã‘. When this happens, pinpointing the source of error can be surprisingly difficult and time-consuming. The information and example programs in this book make it easy.

This book also provides an introduction to natural language processing using Lucene and Solr. It covers the tools and techniques necessary for managing large collections of text data, whether they come from news feeds, databases, or legacy documents. Each chapter contains executable programs that can also be used for text data forensics.

Topics covered:

• Unicode code points
• Character encodings from ASCII and Big5 to UTF-8 and UTF-32LE
• Character normalization using International Components for Unicode (ICU)
• Java I/O, including working directly with zip, gzip, and tar files
• Regular expressions in Java
• Transporting text data via HTTP
• Parsing and generating XML, HTML, and JSON
• Using Lucene 4 for natural language search and text classification
• Search, spelling correction, and clustering with Solr 4

Other books on text processing presuppose much of the material covered in this book. They gloss over the details of transforming text from one format to another and assume perfect input data. The messy reality of raw text will have you reaching for this book again and again.

## Limits of Floating Point and the Asymmetry of 0 and 1

December 19, 2013

If we are representing probabilities, we are interested in numbers between 0 and 1. It turns out these have very different properties in floating-point arithmetic. And it’s not as easy to solve as just working on the log scale.

### Smallest Gaps between Floating Point Numbers of Different Magnitudes

The difference between 0 and the next biggest number representable in double-precision floating point (Java or C++ double) is on the order of 1e-300. In constrast, the difference between 1 and the next smallest number representable is around 1e-15. The reason is that to exploit the maximum number of significant digits, the mantissa for the number near 1 has to be scaled roughly like 0.999999999999999 or 1.0000000000001 and the exponent has to be scaled like 0.

### CDFs and Complementary CDFs

This is why there are two differently translated error functions in math libs, erf() and erfc(), which are rescaled cumulative and complementary cumulative distribution functions. That is, you can use erf() to calculate the cumulative unit normal distribution function (cdf), written Phi(x); erfc() can be used to calculate the complementary cumulative unit normal distribution function (ccdf), written (1 – Phi(x)).

### Log Scale no Panacea

Switching to the log scale doesn’t sove the problem. If you have a number very close to 1, you need to be careful in taking its log. If you write log(1-x), you run into the problem that x can only be so close to 1. That’s why standard math libraries provide a log1p() function defined by log1p(x) = log(1 + x). This gives you back the precision you lose by subtraction two numbers close to each other (what’s called “catastrophic cancellation” in the arithmetic processing literature).

### A Little Quiz

I’ll end with a little quiz to get you thinking about floating point a little more closely. Suppose you set the bits in a floating point number randomly, say by flipping a coin for each bit.

Junior Varsity:  What’s the approximate probability that the random floating point number has an absolute value less than 1?

Varsity:  What is the event probability of drawing a number in the range (L,U). Or, equivalently, what’s the density function to which the draws are proportional?

## Fokkens et al. on Replication Failure

September 25, 2013

After ACL, Becky Passonneau said I should read this:

You should, too. Or if you’d rather watch, there’s a video of their ACL presentation.

### The Gist

The gist of the paper is that the authors tried to reproduce some results found in the literature for word sense identification and named-entity detection, and had a rather rough go of it. In particular, they found that every little decision they made impacted the evaluation error they got, including how to evaluate the error. As the narrative of their paper unfolded, all I could do was nod along. I loved that their paper was in narrative form — it made it very easy to follow.

The authors stress that we need more information for reproducibility and that reproducing known results should get more respect. No quibble there. A secondary motivation (after the pedagogical one) of the LingPipe tutorials was to show that we could reproduce existing results in the literature.

### The Minor Fall

Although they’re riding one of my favorite hobby horses, they don’t quite lead it in the direction I would have. In fact, they stray into serious discussion of the point estimates of performance that their experiments yielded, despite the variation they see under cross-validation folds. So while they note that rankings of approaches changes based on what seem like minor details, they stop short of calling into question the whole idea of trying to assign a simple ranking. Instead, they stress getting to the bottom of why the rankings differ.

### A Slightly Different Take on the Issue

What I would’ve liked to have seen in this paper is more emphasis on two key statistical concepts:

1. the underlying sample variation problem, and
2. the overfitting problem with evaluations.

Sample Variation

The authors talk about sample variation a bit when they consider different folds, etc., in cross-validation. For reasons I don’t understand they call it “experimental setup.” But they don’t put it in terms of estimation variance. That is, independently of getting the features to all line up, the performance and hence rankings of various approaches vary to a large extent because of sample variation. The easiest way to see this is to run cross-validation.

I would have stressed that the bootstrap method should be used to get at sample variation. The bootstrap differs from cross-validation in that it samples training and test subsets with replacement. The bootstrap effectively evaluates within-sample sampling variation, even in the face of non-i.i.d. samples (usually there is correlation among the items in a corpus due to choosing multiple sentences from a single document or even multiple words from the same sentence). The picture is even worse in that the data set at hand is rarely truly representative of the intended out-of-sample application, which is typically to new text. The authors touch on these issues with discussions of “robustness.”

Overfitting

The authors don’t really address the overfitting problem, though it is tangential to what they call the “versioning” problem (when mismatched versions of corpora such as WordNet produce different results).

Overfitting is a huge problem in the current approach to evaluation in NLP and machine learning research. I don’t know why anyone cares about the umpteenth evaluation on the same fold of the Penn Treebank that produces a fraction of a percentage gain. When the variation across folds is higher than your estimated gain on a single fold, it’s time to pack the papers in the file drawer, not in the proceedings of ACL. At least until we also get a journal of negative results to go with our journal of reproducibility.

### The Major Lift

Perhaps hill-climbing error on existing data sets is not the best way forward methdologically. Maybe, just maybe, we can make the data better. It’s certainly what Breck and I tell customers who want to build an application.

If making the data better sounds appealing, check out

I find the two ideas so compelling that it’s the only area of NLP I’m actively researching. More on that later (or sooner if you want to read ahead).

(My apologies to Leonard Cohen for stealing his lyrics.)

## LingPipe Incubator Welcomes Seer

September 9, 2013

We have started an incubator program for start-ups with natural language processing (NLP) needs. Seer is our first egg. The company creates productivity apps based on unstructured data sources–that is where LingPIpe fits in. The guys (Conall and Joe) fit a pattern that we see quite often–smart people with a good idea that presupposes NLP but they don’t have much experience with it.

The GetSeer guys were on the ball right away because they had a bunch of data annotated and had cobbled together a regular expression based classifier that served as an excellent starting point. We had machine learning based classifiers up and running within two hours of starting. That included an evaluation harness. Nice.

The great thing about our working setup is that I get to teach/advise which keeps my time commitment manageable and they get to do most of the heavy lifting which is how they learn to build and maintain NLP systems. I have had to learn some Scala since I co-code most of the time when we work together and that is their implementation language. Scala is a hip extension of Java with a less verbose syntax and stronger type inference.

I’ll keep the blog updated with developments. Current status:

• There is a small amount of training data.
• Current results are awful (no surprise).
• We have been roughing in the solution with Naive Bayes. Next steps will be opening a can of logistic regression for more interesting feature extraction.

## Token Lumpers and Splitters: Spider-Man vs. Superman

August 21, 2013

One of the perennial problems in tokenization for search, classification, or clustering of natural language data is which words and phrases are spelled as compounds and which are separate words. For instance consider “dodgeball” (right) vs. “dodge ball” (wrong) and “golfball” (wrong) vs. “golf ball” (right)?

It’s a classic lumpers vs. splitters problem. Alas, the “right” answer can change over time and some words are listed as both lumped and split in some dictionaries.

This point was first brought home to me and Breck when we were browsing Comcast’s query logs for TV search queries, where users seemed to arbitrarily insert or delete spaces in queries. Who can blame them with the inconsistencies of English in this regard?

This token lumping vs. splitting problem is one of the reasons LingPipe’s spelling correction is not token-based like Lucene’s (though Lucene has other ways to handle combining and splitting compounds — more on that from Mitzi in the near future). And it’s one of the reasons (along with morphological affixes) that character n-grams provide a better basis for classification than hard tokenization.

My favorite examples are comic book superhero names. It turns out that the editors at Marvel Comics are splitters, whereas those at DC Comics are lumpers. Hence we have on the Marvel roster,

Ant-Man, Iron Man, and Spider-Man.

They’re not consistent on hyphenation, which is another issue if you don’t throw away punctuation.

DC, on the other hand, employs men, women, and children, but doesn’t have the budget for spaces:

Aquaman, Batman, Catwoman, Hawkman, Martian Manhunter, Superboy, Supergirl, and Superman.

The exception that proves the rule (I’m open-minded enough to use a phrase that’s a pet peeve of mine), DC gives us:

Wonder Woman

## VerbCorner: Another Game with Words

July 4, 2013

Games with Words continues to roll out new games, releasing VerbCorner.

VerbCorner contains a series of sub-games with titles like “Philosophical Zombie Hunter” and questions that sound like they’re straight of an SAT reading comprehension test, starting with a long story I won’t repeat and then questions like:

Michelle smashed the gauble into quaps. Which of the following is *definitely* a real human?

1. Michelle
2. None of the above
3. Can’t tell because in this context ‘smash’ has more than one meaning.
4. Can’t tell because the sentence is ungrammatical.
5. Can’t tell because I don’t know that verb.

Josh Hartshorne, one of the developers, writes that Verbcorner is “a new project I’m doing in collaboration with Martha Palmer at CU-Boulder, which is aimed at getting human judgments to inform the semantics assigned to verbs in VerbNet. You can find a press release about the project … You’ll see we’ve incorporated a lot of gamification elements in order to make the task more engaging (and also to improve annotation quality).”

This note from the press release harkens back to my philosophical semantics days, “If we do not want to define words in terms of other words, what should they be defined in terms of? This remains an open research question…”. I’ll say! The project has a generative semantics feel; in the press release, Josh is quoted as saying “There are a few dozen core components of meaning and there are tens of thousands of verbs in English.” Now I’m left hanging as to what a “core component of meaning” is!

## All Bayesian Models are Generative (in Theory)

May 23, 2013

[This post is a followup to my previous post, Generative vs. discriminative; Bayesian vs. frequentist.]

I had a brief chat with Andrew Gelman about the topic of generative vs. discriminative models. It came up when I was asking him why he didn’t like the frequentist semicolon notation for variables that are not random. He said that in Bayesian analyses, all the variables are considered random. It just turns out we can sidestep having to model the predictors (i.e., covariates or features) in a regression. Andrew explains how this works in section 14.1, subsection “Formal Bayesian justification of conditional modeling” in Bayesian Data Analysis, 2nd Edition (the 3rd Edition is now complete and will be out in the foreseeable future). I’ll repeat the argument here.

Suppose we have predictor matrix $X$ and outcome vector $y$. In regression modeling, we assume a coefficient vector $\beta$ and explicitly model the outcome likelihood $p(y|\beta,X)$ and coefficient prior $p(\beta)$. But what about $X$? If we were modeling $X$, we’d have a full likelihood $p(X,y|\beta,\psi)$, where $\psi$ are the additional parameters involved in modeling $X$ and the prior is now joint, $p(\beta,\psi)$.

So how do we justify conditional modeling as Bayesians? We simply assume that $\psi$ and $\beta$ have independent priors, so that

$p(\beta,\psi) = p(\beta) \times p(\psi)$.

The posterior then neatly factors as

$p(\beta,\psi|y,X) = p(\psi|X) \times p(\beta|X,y)$.

Looking at just the inference for the regression coefficients $\beta$, we have the familiar expression

$p(\beta|y,X) \propto p(\beta) \times p(y|\beta,X)$.

Therefore, we can think of everything as a joint model under the hood. Regression models involve an independence assumption so we can ignore the inference for $\psi$. To quote BDA,

The practical advantage of using such a regression model is that it is much easier to specify a realistic conditional distribution of one variable given $k$ others than a joint distribution on all $k+1$ variables.

We knew that all along.

## The Latin1 Transcoding Trick for Ant

April 21, 2013

A while back Bob blogged about The Latin1 Transcoding Trick for Java Servlets, etc.

Suppose you have an API that insists on converting an as-yet-unseen stream of bytes to characters for you (e.g. servlets), but lets you set the character encoding if you want.

Because Latin1 (officially, ISO-8859-1) maps bytes one-to-one to Unicode code points, setting Latin1 as the character encoding means that you get a single Java char for each byte.

Another situation where this trick comes in real handy is dealing with the way that Ant compiles its logfiles.

If, like me, you’re fond of debug-by-printf and you use Ant to compile and run your programs, then you might have run into the problem that has given rise to many StackOverflow queries, that is, when you use an Ant task to run the program and instrument your code with print statements to standard out, Ant replaces non-ASCII characters with a question mark. When the problem you’re trying to debug is making sure that non-ASCII characters are being processed correctly, this is both misleading and maddening. The standard advice on StackOverflow is to set the shell environment variable ANT_OPTS using the following incantation (for bash shell):

export ANT_OPTS="-Dfile.encoding=UTF-8"

This works as long as you’re working with UTF-8 encoded character data and your terminal’s encoding is set to UTF-8 as well. Here a solution that works no matter what character encoding is in play:

export ANT_OPTS="-Dfile.encoding=Latin1"

It’s the ol’ Latin1 transcoding trick!

Of course you already know about character encodings . Do you know about Ant’s IO System? Here’s what Ant contributor Conor MacNeill says:

The Ant IO system is designed to associate any output sent to System.out and System.err with the task that generated the output and to log the output accordingly.

Ant’s Main class installs its own output streams into System.out and System.err. These streams are instances of DemuxOutputStreams

Using the source code for Ant 1.9.0, in class org.apache.tools.ant.Main we see that System.In, System.Out, and System.Err are all reassigned to Ant’s DemuxInputStream and DemuxOutputStream, which extend InputStream and OutputStream, respectively:

System.setIn(new DemuxInputStream(project));
System.setOut(new PrintStream(new DemuxOutputStream(project, false)));
System.setErr(new PrintStream(new DemuxOutputStream(project, true)));

The call to the PrintStream constructor is the one-arg constructor PrintStream(OutputStream out). Because no file encoding is specified, the encoding used is the default charset for the JVM that’s running Ant. This is specified by the system property file.encoding. This property varies depending on your platform and locale. To check this, try this on your machine:

public class GetDefaultEncoding {
public static void main(String[] args) {
System.out.println(System.getProperty("file.encoding"));
}
}

On my Mac running OS-X the default is US-ASCII (because the default locale on this machine is en_US). On my Windows XP machine the default is Cp1252 (Windows Latin1 which differs from ISO_8859-1 just enough to be noticeable).

At the point where Ant’s DemuxInputStream reads in the bytes sent to System.out by a Java task, any character outside of the default character set is replaced by a question mark. When Latin1 is the default encoding, all bytes are valid Latin1 characters and their Unicode code point value is the same as the byte value so the bytes from the Java task pass through the Ant IO system unchanged.

As long as the next process in the chain (e.g. the terminal app) is configured to handle whatever encoding your text data is in, you’re good to go.