seqscore 0.4.1

SeqScore: Scoring for named entity recognition and other sequence labeling tasks

SeqScore

SeqScore provides scoring for named entity recognition and other chunking tasks evaluated over sequence labels.

Installation

To install the latest official release of SeqScore, run: pip install seqscore. This will install the package and add the command seqscore in your Python environment.

SeqScore requires Python 3.7 or higher.It is tested on Python 3.7, 3.8, 3.9, and 3.10.

License

SeqScore is distributed under the MIT License.

Citation

If you use SeqScore, please cite SeqScore: Addressing Barriers to Reproducible Named Entity Recognition Evaluation.

BibTeX:

@inproceedings{palen-michel-etal-2021-seqscore,
    title = "{S}eq{S}core: Addressing Barriers to Reproducible Named Entity Recognition Evaluation",
    author = "Palen-Michel, Chester  and
      Holley, Nolan  and
      Lignos, Constantine",
    booktitle = "Proceedings of the 2nd Workshop on Evaluation and Comparison of NLP Systems",
    month = nov,
    year = "2021",
    address = "Punta Cana, Dominican Republic",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2021.eval4nlp-1.5",
    pages = "40--50",
}

Usage

Overview

For a list of commands, run seqscore --help:

$ seqscore --help
Usage: seqscore [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  convert
  count
  repair
  score
  validate

Scoring

The most common application of SeqScore is scoring CoNLL-format NER predictions. Let's assume you have two files, one containing the correct labels (annotation) and the other containing the predictions (system output).

The correct labels are in the file samples/reference.bio:

This O
is O
a O
sentence O
. O

University B-ORG
of I-ORG
Pennsylvania I-ORG
is O
in O
West B-LOC
Philadelphia I-LOC
, O
Pennsylvania B-LOC
. O

The predictions are in the file samples/predicted.bio:

This O
is O
a O
sentence O
. O

University B-ORG
of I-ORG
Pennsylvania I-ORG
is O
in O
West B-LOC
Philadelphia B-LOC
, O
Pennsylvania B-LOC
. O

To score the predictions, run: seqscore score --labels BIO --reference samples/reference.bio samples/predicted.bio

| Type   |   Precision |   Recall |     F1 |   Reference |   Predicted |   Correct |
|--------|-------------|----------|--------|-------------|-------------|-----------|
| ALL    |       50.00 |    66.67 |  57.14 |           3 |           4 |         2 |
| LOC    |       33.33 |    50.00 |  40.00 |           2 |           3 |         1 |
| ORG    |      100.00 |   100.00 | 100.00 |           1 |           1 |         1 |

A few things to note:

• The reference file must be specifed with the --reference flag.
• The chunk encoding (BIO, BIOES, etc.) must be specified using the --labels flag.
• Both files need to use the same chunk encoding. If you have files that use different chunk encodings, use the convert command.
• You can get output in different formats using the --score-format flag. Using --score-format delim will produce tab-delimited output.

The above scoring command will work for files that do not have any invalid transitions, that is, those that perfectly follow what the encoding allows. However, consider this BIO-encoded file, samples/invalid.bio:

This O
is O
a O
sentence O
. O

University I-ORG
of I-ORG
Pennsylvania I-ORG
is O
in O
West B-LOC
Philadelphia I-LOC
, O
Pennsylvania B-LOC
. O

Note that the token University has the label I-ORG, but there is no preceding B-ORG. If we score it as before with seqscore score --labels BIO --reference samples/reference.bio samples/invalid.bio, scoring will fail:

seqscore.encoding.EncodingError: Stopping due to validation errors in invalid.bio:
Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7

To score output with invalid transitions, we need to specify a repair method which can correct them. We can tell SeqScore to use the same approach that conlleval uses (which we refer to as "begin" repair in our paper): seqscore score --labels BIO --repair-method conlleval --reference samples/reference.bio samples/invalid.bio:

Validation errors in sequence at line 7 of invalid.bio:
Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7
Used method conlleval to repair:
Old: ('I-ORG', 'I-ORG', 'I-ORG', 'O', 'O', 'B-LOC', 'I-LOC', 'O', 'B-LOC', 'O')
New: ('B-ORG', 'I-ORG', 'I-ORG', 'O', 'O', 'B-LOC', 'I-LOC', 'O', 'B-LOC', 'O')
| Type   |   Precision |   Recall |     F1 |   Reference |   Predicted |   Correct |
|--------|-------------|----------|--------|-------------|-------------|-----------|
| ALL    |      100.00 |   100.00 | 100.00 |           3 |           3 |         3 |
| LOC    |      100.00 |   100.00 | 100.00 |           2 |           2 |         2 |
| ORG    |      100.00 |   100.00 | 100.00 |           1 |           1 |         1 |

You can use the -q flag to suppress the logging of all of the repairs applied. For example, running the command seqscore score -q --labels BIO --repair-method conlleval --reference samples/reference.bio samples/invalid.bio will hide the repairs:

| Type   |   Precision |   Recall |     F1 |   Reference |   Predicted |   Correct |
|--------|-------------|----------|--------|-------------|-------------|-----------|
| ALL    |      100.00 |   100.00 | 100.00 |           3 |           3 |         3 |
| LOC    |      100.00 |   100.00 | 100.00 |           2 |           2 |         2 |
| ORG    |      100.00 |   100.00 | 100.00 |           1 |           1 |         1 |

You may want to also explore the discard repair, which can produce higher scores for output from models without a CRF/constrained decoding as they are more likely to produce invalid transitions.

Validate

To check if a file has any invalid transitions, we can run seqscore validate --labels BIO samples/reference.bio:

No errors found in 0 tokens, 2 sequences, and 1 documents in reference.bio

For the example of the samples/invalid.bio, we can run seqscore validate --labels BIO samples/invalid.bio:

Encountered 1 errors in 1 tokens, 2 sequences, and 1 documents in invalid.bio
Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7

Convert

We can convert a file from one chunk encoding to another. For example, seqscore convert --input-labels BIO --output-labels BIOES samples/reference.bio samples/reference.bioes will read samples/reference.bio in BIO encoding and write the BIOES-converted file to samples/reference_convert.bioes:

This O
is O
a O
sentence O
. O

University B-ORG
of I-ORG
Pennsylvania E-ORG
is O
in O
West B-LOC
Philadelphia E-LOC
, O
Pennsylvania S-LOC
. O

We can get a list of available chunk encodings by running seqscore convert --help:

Usage: seqscore convert [OPTIONS] FILE OUTPUT_FILE

Options:
  --file-encoding TEXT            [default: UTF-8]
  --ignore-comment-lines
  --ignore-document-boundaries / --use-document-boundaries
  --output-delim TEXT             [default: space]
  --input-labels [BIO|BIOES|BILOU|BMES|BMEOW|IO|IOB]
                                  [required]
  --output-labels [BIO|BIOES|BILOU|BMES|BMEOW|IO|IOB]
                                  [required]
  --help                          Show this message and exit.

Repair

We can also apply repair methods to a file, creating an output file with only valid transitions. For example, we can run seqscore repair --labels BIO --repair-method conlleval samples/invalid.bio samples/invalid_repair_conlleval.bio, which will apply the conlleval repair method to the samples/invalid.bio and write the repaired labels to samples/invalid_repair_conlleval.bio:

This O
is O
a O
sentence O
. O

University B-ORG
of I-ORG
Pennsylvania I-ORG
is O
in O
West B-LOC
Philadelphia I-LOC
, O
Pennsylvania B-LOC
. O

If we want to apply the discard repair method, we can run seqscore repair --labels BIO --repair-method discard samples/invalid.bio samples/invalid_repair_discard.bio and the output will be written to samples/invalid_repair_discard.bio:

This O
is O
a O
sentence O
. O

University O
of O
Pennsylvania O
is O
in O
West B-LOC
Philadelphia I-LOC
, O
Pennsylvania B-LOC
. O

Count

The count subcommand can produce the counts of chunks in the input file. For example, if we run seqscore count --labels BIO samples/reference.bio samples/reference_count.csv, tab-delimited counts would be writtn to be samples/reference_count.csv:

1	ORG	University of Pennsylvania
1	LOC	West Philadelphia
1	LOC	Pennsylvania

We can specify the repair method being used when counting. For example, running seqscore count --repair-method conlleval --labels BIO samples/invalid.bio samples/invalid_count.csv, specifies that the conlleval method should be used to repair labels before counting. The output is given in samples/invalid_count.csv:

1	ORG	University of Pennsylvania
1	LOC	West Philadelphia
1	LOC	Pennsylvania

Features coming soon!

• More documentation
• More error analysis tools

FAQ

Why can't I score output files that are in the format conlleval expects?

At this time, SeqScore intentionally does not support the "merged" format used by conlleval where each line contains a token, correct tag, and predicted tag:

University B-ORG B-ORG
of I-ORG I-ORG
Pennsylvania I-ORG I-ORG
is O O
in O O
West B-LOC B-LOC
Philadelphia I-LOC B-LOC
, O O
Pennsylvania B-LOC B-LOC
. O O

We do not support this format because we have found that creating predictions in this format is a common source of errors in scoring pipelines.

Development

For the latest development version, check out the main branch (stable, but sometimes newer than the version on PyPI), or the dev branch (latest, but less tested).

To install from a clone of this repository, use: pip install -e .

Setting up an environment for development

1. Create an environment: conda create -y -n seqscore python=3.8
2. Activate the environment: conda activate seqscore
3. Install seqscore: pip install -e .
4. Install development dependencies: pip install -r requirements.txt