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conll09 output
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INSTALL
README
README_QUICK

README

1. Required data
=========================

You should provide a split of the training data on an actual training set
and a small validation set. The validation set will be used for early stopping
and automatic parameter adjustment during training. We recommend it to be at 
least 2,000 tokens or larger. You might also consider using it for tuning model
parameters. 
 

2. Preparing data
=========================

Before applying the parser you need to prepare the data. To prepare the data use
the script prepare_data provided in scripts/ directory

Usage: ./prepare_data  FREQ_CUTOFF UNKN_FREQ_CUTOFF  PROJECT_PATH  TRAINING_FILE \
 VALIDATION_FILE [other_files]*
Parameters:
  - FREQ_CUTOFF
    any feature (both atomic and composed), word form or word lemma which is
    encountered less than FREQ_CUTOFF is treated as a special 'UNKNOWN' item.
  - UNKN_FREQ_CUTOFF
    if frequency of an 'UNKNOWN' item in the training set is less than
    UNKN_FREQ_CUTOFF then it is merged with less frequent item of the same
    category. UNKN_FREQ_CUTOFF should be less or equal to FREQ_CUTOFF.
  - PROJECT_PATH
    output files are created here.  The directory should already exist.
  - TRAINING_FILE 
    training file in modified CoNLL-08 format (see my email for the format description),
    vocabulary/set of features/pos tags/etc are induced from it. This format will called
    mCoNLL-08
  - VALIDATION_FILE 
    validation file in mCoNLL-08 format. Both TRAINING_FILE and VALIDATION_FILE are 
    required to contain gold standard dependency trees.
  - other_files 
    other files (if any) to be converted in mCoNLL-08.EXT format. They can be either
    blind or with dependency structure. Even if you have gold standard files we 
    recommend providing blind files to the idp.

We recommend to use both thresholds of nor less than 5, or even 20 or higher.
Usually smaller values significantly increase vocabulary size (and, thus, 
parsing speed) without improvement in parsing accuracy.

This script:
- encodes UTF-8 in ASCII
- performs pseudo-projective transformation
- produces files with numerical values to be used by the parser 
  (we call it mCoNLL-08.EXT format)

IMPORTANT: Do not remove any created files from the PROJECT_PATH 

Possible problems and solutions:
a. If you get message like:

    `Processing file 'proj/dev.conll.utf_prj' and writing results to 'proj/dev.conll.ext'...
    Exception in thread "main" java.lang.Exception: Unknown POS 'DR''
    
It means that one of the input files (in this case dev.conll) contains a POS 
tag which does not exist in the training file (TRAINING_FILE). If this problem 
occurs with the validation set, you might consider changing split on training 
and validation set and rerunning the scripts. If this happened with an actual 
data you're going to apply your parser to (or final testing set), it indicates a
problem with data. Note, that it never happened with testing set of CoNLL-2007 
task (though happens on a language in CoNLL-X task dataset). If it happened to 
you, you will have to preprocess the final testing set replacing these 
tags.  The same applies to CPOS and atomic features of the words. 

b. You might get warnings about composed features appearing in the development or 
testing files but never appearing in training set. Ignore these warnings, or change
splits. 

Warning "Don't trust accuracy reported by idp on this file anymore", 
happens when a dependency label introduced by projectivization in a testing or
validation file has never appeared in the training file. In this case it is 
replaced with a simplified label and idp will show accuracies in 
respect to using this simplified label as gold standard. However if you measure
your accuracy as described below, this problem will never affect your results. 
For the testing files (not validation files!) we recommend that you produce 
mCoNLL-08.EXT format for blind files only and avoid this problem. 

c.  You might get warnings about new predicate senses appearing in the validation files,
 ignore this warning. However, accuracy figures given internally will not take into account
this predicates (they do not present in mCoNLL-08.EXT files)

d. You might reports about roles appearing in validation data, but not in training. Change split, or 
manually remove this roles from validation file. This situation should not happen with sufficient amount
of training data (and if bank field is set correctly everywhere).

e. Make sure that a first line in your data files is not empty. This line is 
used to decide by scripts whether files include dependency labels or not. 
E.g. projectivization won't run on files with empty first line. Otherwise you
will get an error from the projectivization software or parser.

3. Configuring the parser
=========================
 
a. Ensure that sizes of data structures match the treebank parameters

You might consider skipping this step and returning to it only if you have a 
problem with starting a parser (namely, warning that some MAX* does not match
parameters of the data) or if your parser runs out of memory during parsing.

The parser uses some fixed size data structures. You need to make sure that the
amount of memory it allocates corresponds to treebank parameters. 
To do it you can:
- either copy <project_directory>/idp_io_spec.h to parser/idp_io_spec.h
  and rebuild the parser:
  
  make clean all

- or compare <project_directory>/idp_io_spec.h  with parser/idp_io_spec.h 
and make sure that all the parameters in proj/idp_io_spec.h are not larger than
corresponding parameters in parser/idp_io_spec.h. If not, increase these 
parameters in parser/idp_io_spec.h and rebuild the parser. This option is
convenient if you plan to apply the same parser to different treebanks (or the
same treebank but with different cutoff values).

If you have particularly long sentences or long words you will need to update
MAX_SENT_LEN (default 400) or MAX_REC_LEN (default 100) fields in idp_io_spec.h. 

b. Create configuration files for the parser

Sample configuration files are available in directory sample/:
sample/parser.par  main configuration file
sample/parser.ih   input features of the parser, format is similar to the format 
                   used in features models of MALTParser of Nivre et al.
sample/parser.hh   interconnections between latent state vectors

Format description is inside inside these files. You can copy these files
in your project directory.
At least you will need to change the following parameters in parser.par:

- TRAIN_FILE should point to the training set file created by prepare_data 
script. It has extension .ext and it is placed by the script (prepare_data
or conll2ext) in the project directory.

- TEST_FILE during training should point to the validation set file created by
prepare_data script. It also has extension .ext and placed in the project 
directory. During actual use of the parser TEST_FILE should point to the target 
text as explained later.

3. Start training
=========================
 
To start training from the project directory type:

<idp_path>/idp -train parser.par 

Current status of the parser is saved in *.prog file. After each training and a 
validation iteration the parser saves its status and weights in  *state and 
*wgt* files. If the parser is interrupted it will resume from this point. The 
following output will indicate that:

"Resuming training  with the following parameters..."

If you want to start training from the beginning - remove *state and *wgt* files. 
When the training is finished resulting weights will be saved in 
MODEL_NAME.best.wgt file, where MODEL_NAME is as indicated in the configuration
file.

After each validation, validation accuracy is reported. Validation accuracy
is computed internally without deprojectivization and, thus, differs from the 
true score. MODEL_NAME.state also stores the last and the best achieved
validation scores. 

Possible problems:
a. Possibly but very unlikely you can get too many links connected to the 
considered state if FEAT_MODE 1 or 2 is set in parser.par.  It might happen 
if your treebank  (tagger/morph. analyzer output) has exceedingly  many distinct 
features for each  word and you defined many features of type FEATS in *ih file.
See a sample parser.ih for description of how to avoid this problem.
b. You might get warnings about non projectivity.  Fix the data or try adjusting PARSING_MODE 
(increase). PARSING_MODE effect only syntactic parsing

==================================================================
Applying the parser to data 
==================================================================

1. Converting data from mCoNLL-08 to mCoNLL-08.EXT format
=========================

You had an opportunity to convert all your data to mCoNLL-08.EXT format when
creating the project (as additional parameters of scripts/prepare_data 
script). If you did not do that, you can convert it at any point:

scripts/conll2ext  PROJECT_PATH  TRAINING_FILE.conll FILE_TO_CONVERT.conll
Parameters:
- PROJECT_PATH
    project path used for this parsing project, output file will also be created here.
- TRAINING_FILE.conll
    (IMPORTANT!) the same training file in mCoNLL-08 format as used for creation of the 
    project (was supplied as a parameter to prepare_data script)
- FILE_TO_CONVERT.conll
    file (in mCoNLL-08 format) to be converted to mCoNLL-08.EXT format

The script will produce FILE_TO_CONVERT.conll.ext in PROJECT_PATH.
 
Problems:

scripts/conll2ext uses ./prepare_data script. So, the same problems as
described in "Prepare data" section might happen.

2. Parsing 
=========================
 
You can run the parser on you test file test.conll.ext with:

<idp_path>/idp -parse parser.par TEST_FILE=test.conll.ext \
      OUT_FILE=test_res.conll.ext

where parser.par is you configuration file and OUT_FILE defines where to 
put parser output in CoNLL.ext format. You can provide other parameters
to the parser in the command line (they override parameters given in *par).
E.g. you might consider increasing search beam:

<idp_path>/idp -parse parser.par TEST_FILE=test.conll.ext \
      OUT_FILE=test_res.conll.ext BEAM=50

Alternatively, you can set testing configuration in a separate configuration
file, e.g parser_test.par:

<idp_path>/idp -parse parser_test.par 

The parser will report parsing accuracy (if test.conll.ext included gold 
standard dependencies and relation labels). This score is computed internally
and without deprojectivization. If applied to blind file it will report testing 
accuracy of 0.00%. Don't worry, just convert output and evaluate as explained
in the next section.


3. Converting results to CoNLL format and evaluation
=========================

a. Conversion 

To convert the parser output you should use the script scripts/ext_to_conll

<idp_path>/scripts/ext2conll PROJECT_PATH test.conll  parser_res.conll.ext \
     parser_res.conll

-  PROJECT_PATH
   path to the parsing project (the same as before!)
-  test.conll 
   Original test mCoNLL-08 file in utf-8 (as before processing with ./prepare_data or 
   ./convert_to_conll_ext) - blind or with gold standard dependency/srl structure
-  parser_res.conll.ext 
   Parser output on this file in mCoNLL-08.ext format
-  parser_res.conll
   Parser output converted to mCoNLL-08 format and deprojectivized will be produced 
   by the script.    Additionally parser_res.conll.proj will contain the parser 
   output in CoNLL format echo but without deprojectivization.


#This script uses Python module validateFormat.py developed by CoNLL 2007 team 
#to validate the output format  (not any more???)
and Nivre et al projectivization software.

b. Evaluation

Use the standard eval08.pl (see its credits, license (?) and description at
http://depparse.uvt.nl/depparse-wiki/SharedTaskWebsite )
To get detailed evaluation results run:

<idp_path>/scripts/eval08.pl -g gold_std.conll -s parser_res.conll 

gold_std.conll   
    gold standard for the testing set
parser_res.conll
    parsing results produced by the parser converted to CoNLL format (see 
    previous step)