nervaluate 1.1.0
NER evaluation considering partial match scoring
License: MIT License
Requires Python: >=3.11
Keywords: named-entity-recognition, ner, evaluation-metrics, partial-match-scoring, nlp

[![python](https://img.shields.io/badge/Python-3.11-3776AB.svg?style=flat&logo=python&logoColor=white)](https://www.python.org)
&nbsp;
[![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
&nbsp;
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
&nbsp;
![GitHub](https://img.shields.io/github/license/ivyleavedtoadflax/nervaluate)
&nbsp;
![Pull Requests Welcome](https://img.shields.io/badge/pull%20requests-welcome-brightgreen.svg)
&nbsp;
![PyPI](https://img.shields.io/pypi/v/nervaluate)

# nervaluate

`nervaluate` is a module for evaluating Named Entity Recognition (NER) models as defined in the SemEval 2013 - 9.1 task.

The evaluation metrics output by nervaluate go beyond a simple token/tag based schema, and consider different scenarios 
based on whether all the tokens that belong to a named entity were classified or not, and also whether the correct 
entity type was assigned.

This full problem is described in detail in the [original blog](http://www.davidsbatista.net/blog/2018/05/09/Named_Entity_Evaluation/) 
post by [David Batista](https://github.com/davidsbatista), and this package extends the code in the [original repository](https://github.com/davidsbatista/NER-Evaluation) 
which accompanied the blog post.

The code draws heavily on the papers:

* [SemEval-2013 Task 9 : Extraction of Drug-Drug Interactions from Biomedical Texts (DDIExtraction 2013)](https://www.aclweb.org/anthology/S13-2056)

* [SemEval-2013 Task 9.1 - Evaluation Metrics](https://davidsbatista.net/assets/documents/others/semeval_2013-task-9_1-evaluation-metrics.pdf)

# Usage example

```
pip install nervaluate
```

A possible input format are lists of NER labels, where each list corresponds to a sentence and each label is a token label.
Initialize the `Evaluator` class with the true labels and predicted labels, and specify the entity types we want to evaluate.

```python
from nervaluate.evaluator import Evaluator

true = [
    ['O', 'B-PER', 'I-PER', 'O', 'O', 'O', 'B-ORG', 'I-ORG'],  # "The John Smith who works at Google Inc"
    ['O', 'B-LOC', 'B-PER', 'I-PER', 'O', 'O', 'B-DATE'],      # "In Paris Marie Curie lived in 1895"
]
  
pred = [
    ['O', 'O', 'B-PER', 'I-PER', 'O', 'O', 'B-ORG', 'I-ORG'],
    ['O', 'B-LOC', 'I-LOC', 'B-PER', 'O', 'O', 'B-DATE'],
]
   
evaluator = Evaluator(true, pred, tags=['PER', 'ORG', 'LOC', 'DATE'], loader="list")
```

Print the summary report for the evaluation, which will show the metrics for each entity type and evaluation scenario:

```python

print(evaluator.summary_report())

Scenario: all

              correct   incorrect     partial      missed    spurious   precision      recall    f1-score

ent_type            5           0           0           0           0        1.00        1.00        1.00
   exact            2           3           0           0           0        0.40        0.40        0.40
 partial            2           0           3           0           0        0.40        0.40        0.40
  strict            2           3           0           0           0        0.40        0.40        0.40
```  

or aggregated by entity type under a specific evaluation scenario:

```python
print(evaluator.summary_report(mode='entities'))  
  
Scenario: strict

             correct   incorrect     partial      missed    spurious   precision      recall    f1-score

   DATE            1           0           0           0           0        1.00        1.00        1.00
    LOC            0           1           0           0           0        0.00        0.00        0.00
    ORG            1           0           0           0           0        1.00        1.00        1.00
    PER            0           2           0           0           0        0.00        0.00        0.00
```

# Evaluation Scenarios

## Token level evaluation for NER is too simplistic

When running machine learning models for NER, it is common to report metrics at the individual token level. This may 
not be the best approach, as a named entity can be made up of multiple tokens, so a full-entity accuracy would be 
desirable.

When comparing the golden standard annotations with the output of a NER system different scenarios might occur:

__I. Surface string and entity type match__

| Token | Gold  | Prediction |
|-------|-------|------------|
| in    | O     | O          |
| New   | B-LOC | B-LOC      |
| York  | I-LOC | I-LOC      |
| .     | O     | O          |

__II. System hypothesized an incorrect entity__

| Token    | Gold | Prediction |
|----------|------|------------|
| an       | O    | O          |
| Awful    | O    | B-ORG      |
| Headache | O    | I-ORG      |
| in       | O    | O          |

__III. System misses an entity__

| Token | Gold  | Prediction |
|-------|-------|------------|
| in    | O     | O          |
| Palo  | B-LOC | O          |
| Alto  | I-LOC | O          |
| ,     | O     | O          |

Based on these three scenarios we have a simple classification evaluation that can be measured in terms of false 
positives, true positives, false negatives and false positives, and subsequently compute precision, recall and 
F1-score for each named-entity type.

However, this simple schema ignores the possibility of partial matches or other scenarios when the NER system gets
the named-entity surface string correct but the type wrong. We might also want to evaluate these scenarios 
again at a full-entity level.

For example:

__IV. System identifies the surface string but assigns the wrong entity type__

| Token | Gold  | Prediction |
|-------|-------|------------|
| I     | O     | O          |
| live  | O     | O          |
| in    | O     | O          |
| Palo  | B-LOC | B-ORG      |
| Alto  | I-LOC | I-ORG      |
| ,     | O     | O          |

__V. System gets the boundaries of the surface string wrong__

| Token   | Gold  | Prediction |
|---------|-------|------------|
| Unless  | O     | B-PER      |
| Karl    | B-PER | I-PER      |
| Smith   | I-PER | I-PER      |
| resigns | O     | O          |

__VI. System gets the boundaries and entity type wrong__

| Token   | Gold  | Prediction |
|---------|-------|------------|
| Unless  | O     | B-ORG      |
| Karl    | B-PER | I-ORG      |
| Smith   | I-PER | I-ORG      |
| resigns | O     | O          |


## Defining evaluation metrics

How can we incorporate these described scenarios into evaluation metrics? See the [original blog](http://www.davidsbatista.net/blog/2018/05/09/Named_Entity_Evaluation/) 
for a great explanation, a summary is included here.

We can define the following five metrics to consider different categories of errors:

| Error type      | Explanation                                                              |
|-----------------|--------------------------------------------------------------------------|
| Correct (COR)   | both are the same                                                        |
| Incorrect (INC) | the output of a system and the golden annotation don’t match             |
| Partial (PAR)   | system and the golden annotation are somewhat “similar” but not the same |
| Missing (MIS)   | a golden annotation is not captured by a system                          |
| Spurious (SPU)  | system produces a response which doesn’t exist in the golden annotation  |

These five metrics can be measured in four different ways:

| Evaluation schema | Explanation                                                                       |
|-------------------|-----------------------------------------------------------------------------------|
| Strict            | exact boundary surface string match and entity type                               |
| Exact             | exact boundary match over the surface string, regardless of the type              |
| Partial           | partial boundary match over the surface string, regardless of the type            |
| Type              | some overlap between the system tagged entity and the gold annotation is required |

These five errors and four evaluation schema interact in the following ways:

| Scenario | Gold entity | Gold string    | Pred entity | Pred string         | Type | Partial | Exact | Strict |
|----------|-------------|----------------|-------------|---------------------|------|---------|-------|--------|
| III      | BRAND       | tikosyn        |             |                     | MIS  | MIS     | MIS   | MIS    |
| II       |             |                | BRAND       | healthy             | SPU  | SPU     | SPU   | SPU    |
| V        | DRUG        | warfarin       | DRUG        | of warfarin         | COR  | PAR     | INC   | INC    |
| IV       | DRUG        | propranolol    | BRAND       | propranolol         | INC  | COR     | COR   | INC    |
| I        | DRUG        | phenytoin      | DRUG        | phenytoin           | COR  | COR     | COR   | COR    |
| VI       | GROUP       | contraceptives | DRUG        | oral contraceptives | INC  | PAR     | INC   | INC    |

Then precision, recall and f1-score are calculated for each different evaluation schema. In order to achieve data, 
two more quantities need to be calculated:

```
POSSIBLE (POS) = COR + INC + PAR + MIS = TP + FN
ACTUAL (ACT) = COR + INC + PAR + SPU = TP + FP
```

Then we can compute precision, recall, f1-score, where roughly describing precision is the percentage of correct 
named-entities found by the NER system. Recall as the percentage of the named-entities in the golden annotations 
that are retrieved by the NER system. 

This is computed in two different ways depending on whether we want an exact  match (i.e., strict and exact ) or a 
partial match (i.e., partial and type) scenario:

__Exact Match (i.e., strict and exact )__
```
Precision = (COR / ACT) = TP / (TP + FP)
Recall = (COR / POS) = TP / (TP+FN)
```

__Partial Match (i.e., partial and type)__
```
Precision = (COR + 0.5 × PAR) / ACT = TP / (TP + FP)
Recall = (COR + 0.5 × PAR)/POS = COR / ACT = TP / (TP + FN)
```

__Putting all together:__

| Measure   | Type | Partial | Exact | Strict |
|-----------|------|---------|-------|--------|
| Correct   | 3    | 3       | 3     | 2      |
| Incorrect | 2    | 0       | 2     | 3      |
| Partial   | 0    | 2       | 0     | 0      |
| Missed    | 1    | 1       | 1     | 1      |
| Spurious  | 1    | 1       | 1     | 1      |
| Precision | 0.5  | 0.66    | 0.5   | 0.33   |
| Recall    | 0.5  | 0.66    | 0.5   | 0.33   |
| F1        | 0.5  | 0.66    | 0.5   | 0.33   |


## Notes:

In scenarios IV and VI the entity type of the `true` and `pred` does not match, in both cases we only scored against 
the true entity, not the predicted one. You can argue that the predicted entity could also be scored as spurious, 
but according to the definition of `spurious`:

* Spurious (SPU) : system produces a response which does not exist in the golden annotation;

In this case there exists an annotation, but with a different entity type, so we assume it's only incorrect.


## Contributing to the `nervaluate` package

### Extending the package to accept more formats

The `Evaluator` accepts the following formats:

* Nested lists containing NER labels
* CoNLL style tab delimited strings
* [prodi.gy](https://prodi.gy) style lists of spans

Additional formats can easily be added by creating a new loader class in `nervaluate/loaders.py`. The  loader class 
should inherit from the `DataLoader` base class and implement the `load` method. 

The `load` method should return a list of entity lists, where each entity is represented as a dictionary 
with `label`, `start`, and `end` keys.

The new loader can then be added to the `_setup_loaders` method in the `Evaluator` class, and can be selected with the
 `loader` argument when instantiating the `Evaluator` class.

Here is list of formats we intend to [include](https://github.com/MantisAI/nervaluate/issues/3).

### General Contributing

Improvements, adding new features and bug fixes are welcome. If you wish to participate in the development of `nervaluate` 
please read the guidelines in the [CONTRIBUTING.md](CONTRIBUTING.md) file.

---

Give a ⭐️ if this project helped you!