chaine 3.13.1__cp311-cp311-macosx_11_0_arm64.whl

chaine/training.py

@@ -0,0 +1,184 @@
+"""
+chaine.training
+~~~~~~~~~~~~~~~
+
+This module implements the high-level API to train a conditional random field.
+"""
+
+
+from chaine.crf import HyperparameterOptimizer, Model, Trainer
+from chaine.logging import Logger, set_verbosity
+from chaine.typing import Filepath, Iterable, Labels, Sequence
+
+LOGGER = Logger(__name__)
+
+
+def train(
+    dataset: Iterable[Sequence],
+    labels: Iterable[Labels],
+    *,
+    model_filepath: Filepath = "model.chaine",
+    optimize_hyperparameters: bool = False,
+    optimization_sample_size: int | None = None,
+    verbose: int = 1,
+    **hyperparameters,
+) -> Model:
+    """Train a conditional random field.
+
+    Parameters
+    ----------
+    dataset : Iterable[Sequence]
+        Data set consisting of sequences of feature sets.
+    labels : Iterable[Labels]
+        Labels corresponding to each instance in the data set.
+    model_filepath : Filepath, optional (default=model.chaine)
+        Path to model location.
+    optimize_hyperparameters : bool
+        If True, optimize hyperparameters first.
+    optimization_sample_size : int | None
+        Number of instances to sample from the data set for hyperparameter optimization.
+    verbose : int
+        Controls the verbosity: the higher, the more messages.
+    algorithm : str
+        The following optimization algorithms are available:
+            * lbfgs: Limited-memory BFGS with L1/L2 regularization
+            * l2sgd: Stochastic gradient descent with L2 regularization
+            * ap: Averaged perceptron
+            * pa: Passive aggressive
+            * arow: Adaptive regularization of weights
+
+    Limited-memory BFGS Parameters (lbfgs)
+    --------------------------------------
+    min_freq : float, optional (default=0)
+        Threshold value for minimum frequency of a feature occurring in training data.
+    all_possible_states : bool, optional (default=False)
+        Generate state features that do not even occur in the training data.
+    all_possible_transitions : bool, optional (default=False)
+        Generate transition features that do not even occur in the training data.
+    max_iterations : int, optional (default=None)
+        Maximum number of iterations (unlimited by default).
+    num_memories : int, optional (default=6)
+        Number of limited memories for approximating the inverse hessian matrix.
+    c1 : float, optional (default=0)
+        Coefficient for L1 regularization.
+    c2 : float, optional (default=1.0)
+        Coefficient for L2 regularization.
+    epsilon : float, optional (default=1e-5)
+        Parameter that determines the condition of convergence.
+    period : int, optional (default=10)
+        Threshold value for iterations to test the stopping criterion.
+    delta : float, optional (default=1e-5)
+        Top iteration when log likelihood is not greater than this.
+    linesearch : str, optional (default="MoreThuente")
+        Line search algorithm used in updates:
+            * MoreThuente: More and Thuente's method
+            * Backtracking: Backtracking method with regular Wolfe condition
+            * StrongBacktracking: Backtracking method with strong Wolfe condition
+    max_linesearch : int, optional (default=20)
+        Maximum number of trials for the line search algorithm.
+
+    SGD with L2 Parameters (l2sgd)
+    ------------------------------
+    min_freq : float, optional (default=0)
+        Threshold value for minimum frequency of a feature occurring in training data.
+    all_possible_states : bool, optional (default=False)
+        Generate state features that do not even occur in the training data.
+    all_possible_transitions : bool, optional (default=False)
+        Generate transition features that do not even occur in the training data.
+    max_iterations : int, optional (default=None)
+        Maximum number of iterations (1000 by default).
+    c2 : float, optional (default=1.0)
+        Coefficient for L2 regularization.
+    period : int, optional (default=10)
+        Threshold value for iterations to test the stopping criterion.
+    delta : float, optional (default=1e-5)
+        Top iteration when log likelihood is not greater than this.
+    calibration_eta : float, optional (default=0.1)
+        Initial value of learning rate (eta) used for calibration.
+    calibration_rate : float, optional (default=2.0)
+        Rate of increase/decrease of learning rate for calibration.
+    calibration_samples : int, optional (default=1000)
+        Number of instances used for calibration.
+    calibration_candidates : int, optional (default=10)
+        Number of candidates of learning rate.
+    calibration_max_trials : int, optional (default=20)
+        Maximum number of trials of learning rates for calibration.
+
+    Averaged Perceptron Parameters (ap)
+    -----------------------------------
+    min_freq : float, optional (default=0)
+        Threshold value for minimum frequency of a feature occurring in training data.
+    all_possible_states : bool, optional (default=False)
+        Generate state features that do not even occur in the training data.
+    all_possible_transitions : bool, optional (default=False)
+        Generate transition features that do not even occur in the training data.
+    max_iterations : int, optional (default=None)
+        Maximum number of iterations (100 by default).
+    epsilon : float, optional (default=1e-5)
+        Parameter that determines the condition of convergence.
+
+    Passive Aggressive Parameters (pa)
+    ----------------------------------
+    min_freq : float, optional (default=0)
+        Threshold value for minimum frequency of a feature occurring in training data.
+    all_possible_states : bool, optional (default=False)
+        Generate state features that do not even occur in the training data.
+    all_possible_transitions : bool, optional (default=False)
+        Generate transition features that do not even occur in the training data.
+    max_iterations : int, optional (default=None)
+        Maximum number of iterations (100 by default).
+    epsilon : float, optional (default=1e-5)
+        Parameter that determines the condition of convergence.
+    pa_type : int, optional (default=1)
+        Strategy for updating feature weights:
+            * 0: PA without slack variables
+            * 1: PA type I
+            * 2: PA type II
+    c : float, optional (default=1)
+        Aggressiveness parameter (used only for PA-I and PA-II).
+    error_sensitive : bool, optional (default=True)
+        Include square root of predicted incorrect labels into optimization routine.
+    averaging : bool, optional (default=True)
+        Compute average of feature weights at all updates.
+
+    Adaptive Regularization of Weights Parameters (arow)
+    ----------------------------------------------------
+    min_freq : float, optional (default=0)
+        Threshold value for minimum frequency of a feature occurring in training data.
+    all_possible_states : bool, optional (default=False)
+        Generate state features that do not even occur in the training data.
+    all_possible_transitions : bool, optional (default=False)
+        Generate transition features that do not even occur in the training data.
+    max_iterations : int, optional (default=None)
+        Maximum number of iterations (100 by default).
+    epsilon : float, optional (default=1e-5)
+        Parameter that determines the condition of convergence.
+    variance : float, optional (default=1)
+        Initial variance of every feature weight.
+    gamma : float, optional (default=1)
+        Trade-off between loss function and changes of feature weights.
+
+    Returns
+    -------
+    Model
+        A conditional random field trained on the dataset.
+    """
+    set_verbosity(verbose)
+
+    if optimize_hyperparameters:
+        if hyperparameters:
+            LOGGER.warning(f"Specified hyperparameters will be overwritten: {hyperparameters}")
+
+        # optionally tune hyperparameters first
+        optimizer = HyperparameterOptimizer()
+        results = optimizer.optimize_hyperparameters(dataset, labels, optimization_sample_size)
+
+        # use hyperparameters of the best run
+        hyperparameters = results[0]["hyperparameters"]
+
+    # initialize trainer and start training
+    trainer = Trainer(**hyperparameters)
+    trainer.train(dataset, labels, model_filepath=str(model_filepath))
+
+    # load and return the trained model
+    return Model(model_filepath)

chaine/typing.py

@@ -0,0 +1,18 @@
+"""
+chaine.typing
+~~~~~~~~~~~~~
+
+A collection of type hints.
+"""
+
+from os import PathLike
+from pathlib import Path
+from typing import Any, Iterable, Iterator
+
+Sequence = Iterable[dict[str, str | int | float | bool]]
+Labels = Iterable[str]
+Filepath = Path | PathLike | str
+Sentence = list[str]
+Tags = list[str]
+Features = dict[str, float | int | str | bool]
+Dataset = dict[str, dict[str, Any]]

chaine/validation.py

@@ -0,0 +1,43 @@
+"""
+chaine.validation
+~~~~~~~~~~~~~~~~~
+
+This module implements functions to validate input sequences (either for training or inference).
+"""
+
+from chaine.typing import Sequence
+
+# supported feature value data types
+TYPES = (str, int, float, bool)
+
+
+def is_valid_sequence(sequence: Sequence) -> bool:
+    """Check if the given sequence has valid input format.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        Sequence to validate.
+
+    Returns
+    -------
+    bool
+        True if sequence is valid, False otherwise.
+    """
+    return isinstance(sequence, list) and all(is_valid_token(token) for token in sequence)
+
+
+def is_valid_token(token: dict) -> bool:
+    """Check if the given token has valid input format.
+
+    Parameters
+    ----------
+    token : dict
+        Token to validate.
+
+    Returns
+    -------
+    bool
+        True if sequence is valid, False otherwise.
+    """
+    return isinstance(token, dict) and all(isinstance(value, TYPES) for value in token.values())

chaine-3.13.1.dist-info/METADATA

@@ -0,0 +1,348 @@
+Metadata-Version: 2.1
+Name: chaine
+Version: 3.13.1
+Summary: Linear-chain conditional random fields for natural language processing
+Author: Severin Simmler
+Author-email: s.simmler@snapaddy.com
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Description-Content-Type: text/markdown
+
+# Chaine
+
+[![downloads](https://static.pepy.tech/personalized-badge/chaine?period=total&units=international_system&left_color=black&right_color=black&left_text=downloads)](https://pepy.tech/project/chaine)
+[![downloads/month](https://static.pepy.tech/personalized-badge/chaine?period=month&units=abbreviation&left_color=black&right_color=black&left_text=downloads/month)](https://pepy.tech/project/chaine)
+[![downloads/week](https://static.pepy.tech/personalized-badge/chaine?period=week&units=abbreviation&left_color=black&right_color=black&left_text=downloads/week)](https://pepy.tech/project/chaine)
+
+Chaine is a modern, fast and lightweight Python library implementing **linear-chain conditional random fields**. Use it for sequence labeling tasks like [named entity recognition](https://en.wikipedia.org/wiki/Named-entity_recognition) or [part-of-speech tagging](https://en.wikipedia.org/wiki/Part-of-speech_tagging).
+
+The main goals of this project are:
+
+- **Usability**: Designed with special focus on usability and a beautiful high-level API.
+- **Efficiency**: Performance critical parts are written in C and thus [blazingly fast](http://www.chokkan.org/software/crfsuite/benchmark.html). Loading a model from disk and retrieving feature weights for inference is optimized for both [speed and memory](http://www.chokkan.org/software/cqdb/).
+- **Persistency**: No `pickle` or `joblib` is used for serialization. A trained model will be compatible with all versions for eternity, because the underlying C library will not change. I promise.
+- **Compatibility**: There are wheels for Linux, macOS and Windows. No compiler needed.
+- **Minimalism**: No code bloat, no external dependencies.
+
+Install the latest stable version from [PyPI](https://pypi.org/project/chaine):
+
+```
+pip install chaine
+```
+
+### Table of contents
+
+- [Algorithms](#algorithms)
+- [Usage](#usage)
+  - [Features](#features)
+  - [Training](#training)
+  - [Hyperparameters](#hyperparameters)
+  - [Inference](#inference)
+  - [Weights](#weights)
+- [Credits](#credits)
+
+## Algorithms
+
+You can train models using the following methods:
+
+- Limited-Memory BFGS ([Nocedal 1980](https://www.jstor.org/stable/2006193))
+- Orthant-Wise Limited-Memory Quasi-Newton ([Andrew et al. 2007](https://www.microsoft.com/en-us/research/publication/scalable-training-of-l1-regularized-log-linear-models/))
+- Stochastic Gradient Descent ([Shalev et al. 2007](https://www.google.com/url?q=https://www.cs.huji.ac.il/~shais/papers/ShalevSiSr07.pdf))
+- Averaged Perceptron ([Collins 2002](https://aclanthology.org/W02-1001.pdf))
+- Passive Aggressive ([Crammer et al. 2006](https://jmlr.csail.mit.edu/papers/v7/crammer06a.html))
+- Adaptive Regularization of Weight Vectors ([Mejer et al. 2010](https://aclanthology.org/D10-1095.pdf))
+
+Please refer to the paper by [Lafferty et al.](https://repository.upenn.edu/cgi/viewcontent.cgi?article=1162&context=cis_papers) for a general introduction to **conditional random fields** or the respective chapter in [Speech and Language Processing](https://web.stanford.edu/~jurafsky/slp3/8.pdf).
+
+## Usage
+
+Training and using a **conditional random field** for inference is easy as:
+
+```python
+>>> import chaine
+>>> tokens = [[{"index": 0, "text": "John"}, {"index": 1, "text": "Lennon"}]]
+>>> labels = [["B-PER", "I-PER"]]
+>>> model = chaine.train(tokens, labels)
+>>> model.predict(tokens)
+[['B-PER', 'I-PER']]
+```
+
+> You can control verbosity with the argument `verbose`, where `0` will set the log level to `ERROR`, `1` to `INFO` (which is the default) and `2` to `DEBUG`.
+
+### Features
+
+One token in a sequence is represented as a dictionary with describing feature names as keys and respective values of type string, integer, float or boolean:
+
+```python
+{
+    "text": "John",
+    "num_characters": 4,
+    "relative_index": 0.0,
+    "is_number": False,
+}
+```
+
+One sequence is represented as a list of feature dictionaries:
+
+```python
+[
+    {"text": "John", "num_characters": 4}, 
+    {"text": "Lennon", "num_characters": 6}
+]
+```
+
+One data set is represented as an iterable of a list of feature dictionaries:
+
+```python
+[
+    [
+        {"text": "John", "num_characters": 4}, 
+        {"text": "Lennon", "num_characters": 6}
+    ],
+    [
+        {"text": "Paul", "num_characters": 4}, 
+        {"text": "McCartney", "num_characters": 9}
+    ],
+    ...
+]
+```
+
+This is the expected input format for training. For inference, you can also process a single sequence rather than a batch of multiple sequences.
+
+#### Generators
+
+Depending on the size of your data set, it probably makes sense to use generators. Something like this would be totally fine for both training and inference:
+
+```python
+([extract_features(token) for token in tokens] for tokens in dataset)
+```
+
+Assuming `dataset` is a generator as well, only one sequence is loaded into memory at a time.
+
+### Training
+
+You can either use the high-level function to train a model (which also loads and returns it):
+
+```python
+>>> import chaine
+>>> chaine.train(tokens, labels)
+```
+
+or the lower-level `Trainer` class:
+
+```python
+>>> from chaine import Trainer
+>>> trainer = Trainer()
+```
+
+A `Trainer` object has a method `train()` to learn states and transitions from the given data set. You have to provide a filepath to serialize the model to:
+
+```python
+>>> trainer.train(tokens, labels, model_filepath="model.chaine")
+```
+
+### Hyperparameters
+
+Before training a model, you might want to find out the ideal hyperparameters first. You can just set the respective argument to `True`:
+
+```python
+>>> import chaine
+>>> model = chaine.train(tokens, labels, optimize_hyperparameters=True)
+```
+
+> This might be very memory and time consuming, because 5-fold cross validation for each of the 10 trials for each of the algorithms is performed.
+
+or use the `HyperparameterOptimizer` class and have more control over the optimization process:
+
+```python
+>>> from chaine import HyperparameterOptimizer
+>>> from chaine.optimization import L2SGDSearchSpace
+>>> optimizer = HyperparameterOptimizer(trials=50, folds=3, spaces=[L2SGDSearchSpace()])
+>>> optimizer.optimize_hyperparameters(tokens, labels, sample_size=1000)
+```
+
+This will make 50 trials with 3-fold cross validation for the Stochastic Gradient Descent algorithm and return a sorted list of hyperparameters with evaluation stats. The given data set is downsampled to 1000 instances.
+
+<details>
+<summary>Example of a hyperparameter optimization report</summary>
+
+```json
+[
+    {
+        "hyperparameters": {
+            "algorithm": "lbfgs",
+            "min_freq": 0,
+            "all_possible_states": true,
+            "all_possible_transitions": true,
+            "num_memories": 8,
+            "c1": 0.9,
+            "c2": 0.31,
+            "epsilon": 0.00011,
+            "period": 17,
+            "delta": 0.00051,
+            "linesearch": "Backtracking",
+            "max_linesearch": 31
+        },
+        "stats": {
+            "mean_precision": 0.4490952380952381,
+            "stdev_precision": 0.16497993418839532,
+            "mean_recall": 0.4554858934169279,
+            "stdev_recall": 0.20082402876210334,
+            "mean_f1": 0.45041435392087253,
+            "stdev_f1": 0.17914435056760908,
+            "mean_time": 0.3920876979827881,
+            "stdev_time": 0.0390961164333519
+        }
+    },
+    {
+        "hyperparameters": {
+            "algorithm": "lbfgs",
+            "min_freq": 5,
+            "all_possible_states": true,
+            "all_possible_transitions": false,
+            "num_memories": 9,
+            "c1": 1.74,
+            "c2": 0.09,
+            "epsilon": 0.0008600000000000001,
+            "period": 1,
+            "delta": 0.00045000000000000004,
+            "linesearch": "StrongBacktracking",
+            "max_linesearch": 34
+        },
+        "stats": {
+            "mean_precision": 0.4344436335328176,
+            "stdev_precision": 0.15542689556199216,
+            "mean_recall": 0.4385174258109041,
+            "stdev_recall": 0.19873733310765845,
+            "mean_f1": 0.43386496201052716,
+            "stdev_f1": 0.17225578421967264,
+            "mean_time": 0.12209572792053222,
+            "stdev_time": 0.0236177196325414
+        }
+    },
+    {
+        "hyperparameters": {
+            "algorithm": "lbfgs",
+            "min_freq": 2,
+            "all_possible_states": true,
+            "all_possible_transitions": true,
+            "num_memories": 1,
+            "c1": 0.91,
+            "c2": 0.4,
+            "epsilon": 0.0008400000000000001,
+            "period": 13,
+            "delta": 0.00018,
+            "linesearch": "MoreThuente",
+            "max_linesearch": 43
+        },
+        "stats": {
+            "mean_precision": 0.41963433149859447,
+            "stdev_precision": 0.16363544501259455,
+            "mean_recall": 0.4331173486012196,
+            "stdev_recall": 0.21344965207006913,
+            "mean_f1": 0.422038027332145,
+            "stdev_f1": 0.18245844823319127,
+            "mean_time": 0.2586916446685791,
+            "stdev_time": 0.04341208573100539
+        }
+    },
+    {
+        "hyperparameters": {
+            "algorithm": "l2sgd",
+            "min_freq": 5,
+            "all_possible_states": true,
+            "all_possible_transitions": true,
+            "c2": 1.68,
+            "period": 2,
+            "delta": 0.00047000000000000004,
+            "calibration_eta": 0.0006900000000000001,
+            "calibration_rate": 2.9000000000000004,
+            "calibration_samples": 1400,
+            "calibration_candidates": 25,
+            "calibration_max_trials": 23
+        },
+        "stats": {
+            "mean_precision": 0.2571428571428571,
+            "stdev_precision": 0.43330716823151716,
+            "mean_recall": 0.01,
+            "stdev_recall": 0.022360679774997897,
+            "mean_f1": 0.01702127659574468,
+            "stdev_f1": 0.038060731531911314,
+            "mean_time": 0.15442829132080077,
+            "stdev_time": 0.051750737506044905
+        }
+    }
+]
+```
+</details>
+
+### Inference
+
+The high-level function `chaine.train()` returns a `Model` object. You can load an already trained model from disk by initializing a `Model` object with the model's filepath:
+
+```python
+>>> from chaine import Model
+>>> model = Model("model.chaine")
+```
+
+You can predict labels for a batch of sequences:
+
+```python
+>>> tokens = [
+...     [{"index": 0, "text": "John"}, {"index": 1, "text": "Lennon"}],
+...     [{"index": 0, "text": "Paul"}, {"index": 1, "text": "McCartney"}],
+...     [{"index": 0, "text": "George"}, {"index": 1, "text": "Harrison"}],
+...     [{"index": 0, "text": "Ringo"}, {"index": 1, "text": "Starr"}]
+... ]
+>>> model.predict(tokens)
+[['B-PER', 'I-PER'], ['B-PER', 'I-PER'], ['B-PER', 'I-PER'], ['B-PER', 'I-PER']]
+```
+
+or only for a single sequence:
+
+```python
+>>> model.predict_single(tokens[0])
+['B-PER', 'I-PER']
+```
+
+If you are interested in the model's probability distribution for a given sequence, you can:
+
+```python
+>>> model.predict_proba_single(tokens[0])
+[[{'B-PER': 0.99, 'I-PER': 0.01}, {'B-PER': 0.01, 'I-PER': 0.99}]]
+```
+
+> Use the `model.predict_proba()` method for a batch of sequences.
+
+### Weights
+
+After loading a trained model, you can inspect the learned transition and state weights:
+
+```python
+>>> model = Model("model.chaine")
+>>> model.transitions
+[{'from': 'B-PER', 'to': 'I-PER', 'weight': 1.430506540616852e-06}]
+>>> model.states
+[{'feature': 'text:John', 'label': 'B-PER', 'weight': 9.536710877105517e-07}, ...]
+```
+
+You can also dump both transition and state weights as JSON:
+
+```python
+>>> model.dump_states("states.json")
+>>> model.dump_transitions("transitions.json")
+```
+
+## Credits
+
+This project makes use of and is partially based on:
+
+- [CRFsuite](https://github.com/chokkan/crfsuite)
+- [libLBFGS](https://github.com/chokkan/liblbfgs)
+- [python-crfsuite](https://github.com/scrapinghub/python-crfsuite)
+- [sklearn-crfsuite](https://github.com/TeamHG-Memex/sklearn-crfsuite)
+

chaine-3.13.1.dist-info/RECORD

@@ -0,0 +1,68 @@
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