relationFactory.py

from itertools import islice
from typing import Tuple, List, Iterable, Optional, Dict, Callable, Any

from spacy.scorer import PRFScore
from thinc.types import Floats2d
import numpy
from spacy.training.example import Example
from thinc.api import Model, Optimizer
from spacy.tokens.doc import Doc
from spacy.pipeline.trainable_pipe import TrainablePipe
from spacy.vocab import Vocab
from spacy import Language
from thinc.model import set_dropout_rate
from wasabi import Printer

from typing import List, Tuple, Callable

import spacy
from spacy.tokens import Doc, Span
from thinc.types import Floats2d, Ints1d, Ragged, cast
from thinc.api import Model, Linear, chain, Logistic

import json
import os
import time
from pathlib import Path

from sklearn.metrics import precision_recall_fscore_support, f1_score
import plotly.express as px
import plotly.graph_objects as go

@spacy.registry.architectures("rel_model.v1")
def create_relation_model(

    create_instance_tensor: Model[List[Doc], Floats2d],

    classification_layer: Model[Floats2d, Floats2d],

) -> Model[List[Doc], Floats2d]:
    with Model.define_operators({">>": chain}):
        model = create_instance_tensor >> classification_layer
        model.attrs["get_instances"] = create_instance_tensor.attrs["get_instances"]
    return model


@spacy.registry.architectures("rel_classification_layer.v1")
def create_classification_layer(

    nO: int = None, nI: int = None

) -> Model[Floats2d, Floats2d]:
    with Model.define_operators({">>": chain}):
        return Linear(nO=nO, nI=nI) >> Logistic()


@spacy.registry.misc("rel_instance_generator.v1")
def create_instances(max_length: int) -> Callable[[Doc], List[Tuple[Span, Span]]]:
    def get_instances(doc: Doc) -> List[Tuple[Span, Span]]:
        instances = []
        for ent1 in doc.ents:
            for ent2 in doc.ents:
                if ent1 != ent2:
                    if max_length and abs(ent2.start - ent1.start) <= max_length:
                        instances.append((ent1, ent2))
        return instances

    return get_instances


@spacy.registry.architectures("rel_instance_tensor.v1")
def create_tensors(

    tok2vec: Model[List[Doc], List[Floats2d]],

    pooling: Model[Ragged, Floats2d],

    get_instances: Callable[[Doc], List[Tuple[Span, Span]]],

) -> Model[List[Doc], Floats2d]:

    return Model(
        "instance_tensors",
        instance_forward,
        layers=[tok2vec, pooling],
        refs={"tok2vec": tok2vec, "pooling": pooling},
        attrs={"get_instances": get_instances},
        init=instance_init,
    )


def instance_forward(model: Model[List[Doc], Floats2d], docs: List[Doc], is_train: bool) -> Tuple[Floats2d, Callable]:
    pooling = model.get_ref("pooling")
    tok2vec = model.get_ref("tok2vec")
    get_instances = model.attrs["get_instances"]
    all_instances = [get_instances(doc) for doc in docs]
    tokvecs, bp_tokvecs = tok2vec(docs, is_train)

    ents = []
    lengths = []

    for doc_nr, (instances, tokvec) in enumerate(zip(all_instances, tokvecs)):
        token_indices = []
        for instance in instances:
            for ent in instance:
                token_indices.extend([i for i in range(ent.start, ent.end)])
                lengths.append(ent.end - ent.start)
        ents.append(tokvec[token_indices])
    lengths = cast(Ints1d, model.ops.asarray(lengths, dtype="int32"))
    entities = Ragged(model.ops.flatten(ents), lengths)
    pooled, bp_pooled = pooling(entities, is_train)

    # Reshape so that pairs of rows are concatenated
    relations = model.ops.reshape2f(pooled, -1, pooled.shape[1] * 2)

    def backprop(d_relations: Floats2d) -> List[Doc]:
        d_pooled = model.ops.reshape2f(d_relations, d_relations.shape[0] * 2, -1)
        d_ents = bp_pooled(d_pooled).data
        d_tokvecs = []
        ent_index = 0
        for doc_nr, instances in enumerate(all_instances):
            shape = tokvecs[doc_nr].shape
            d_tokvec = model.ops.alloc2f(*shape)
            count_occ = model.ops.alloc2f(*shape)
            for instance in instances:
                for ent in instance:
                    d_tokvec[ent.start : ent.end] += d_ents[ent_index]
                    count_occ[ent.start : ent.end] += 1
                    ent_index += ent.end - ent.start
            d_tokvec /= count_occ + 0.00000000001
            d_tokvecs.append(d_tokvec)

        d_docs = bp_tokvecs(d_tokvecs)
        return d_docs

    return relations, backprop


def instance_init(model: Model, X: List[Doc] = None, Y: Floats2d = None) -> Model:
    tok2vec = model.get_ref("tok2vec")
    if X is not None:
        tok2vec.initialize(X)
    return model

Doc.set_extension("rel", default={}, force=True)
msg = Printer()


@Language.factory(

    "relation_extractor",

    requires=["doc.ents", "token.ent_iob", "token.ent_type"],

    assigns=["doc._.rel"],

    default_score_weights={

        "rel_micro_p": 0.0,

        "rel_micro_r": 0.0,

        "rel_micro_f": 1.0,

        "rel_macro_f": 1.0,

        "rel_weighted_f": 1.0,

        "f1_PART-OF": 1.0,

        "f1_LOCATED-AT": 1.0,

        "f1_CONNECTED-WITH": 1.0,

        "f1_IN-MANNER-OF": 1.0,

        "f1_ATTRIBUTE-FOR": 1.0

    },

)
def make_relation_extractor(

    nlp: Language, name: str, model: Model, eval_frequency, *, threshold: float

):
    """Construct a RelationExtractor component."""
    return RelationExtractor(nlp.vocab, model, name, threshold=threshold, eval_frequency=eval_frequency)


class RelationExtractor(TrainablePipe):
    def __init__(

        self,

        vocab: Vocab,

        model: Model,

        name: str = "rel",

        *,

        threshold: float,

        eval_frequency = 100

    ) -> None:
        """Initialize a relation extractor."""
        self.vocab = vocab
        self.model = model
        self.name = name
        self.cfg = {"labels": [], "threshold": threshold}
        self.eval_frequency = eval_frequency
        self.start_learning_time = None
        self.metric_history = []
        self.max_f1 = 0
        self.max_f1_step = 0

    @property
    def labels(self) -> Tuple[str]:
        """Returns the labels currently added to the component."""
        return tuple(self.cfg["labels"])

    @property
    def threshold(self) -> float:
        """Returns the threshold above which a prediction is seen as 'True'."""
        return self.cfg["threshold"]

    def add_label(self, label: str) -> int:
        """Add a new label to the pipe."""
        if not isinstance(label, str):
            raise ValueError("Only strings can be added as labels to the RelationExtractor")
        if label in self.labels:
            return 0
        self.cfg["labels"] = list(self.labels) + [label]
        return 1

    def __call__(self, doc: Doc) -> Doc:
        """Apply the pipe to a Doc."""
        # check that there are actually any candidate instances in this batch of examples
        total_instances = len(self.model.attrs["get_instances"](doc))
        if total_instances == 0:
            msg.info("Could not determine any instances in doc - returning doc as is.")
            return doc

        predictions = self.predict([doc])
        self.set_annotations([doc], predictions)
        return doc

    def predict(self, docs: Iterable[Doc]) -> Floats2d:
        """Apply the pipeline's model to a batch of docs, without modifying them."""
        get_instances = self.model.attrs["get_instances"]
        total_instances = sum([len(get_instances(doc)) for doc in docs])
        if total_instances == 0:
            msg.info("Could not determine any instances in any docs - can not make any predictions.")
        scores = self.model.predict(docs)
        return self.model.ops.asarray(scores)

    def set_annotations(self, docs: Iterable[Doc], scores: Floats2d) -> None:
        """Modify a batch of `Doc` objects, using pre-computed scores."""
        c = 0
        get_instances = self.model.attrs["get_instances"]
        for doc in docs:
            for (e1, e2) in get_instances(doc):
                offset = (e1.start, e2.start)
                if offset not in doc._.rel:
                    doc._.rel[offset] = {}
                for j, label in enumerate(self.labels):
                    doc._.rel[offset][label] = scores[c, j]
                c += 1

    def update(

        self,

        examples: Iterable[Example],

        *,

        drop: float = 0.0,

        set_annotations: bool = False,

        sgd: Optional[Optimizer] = None,

        losses: Optional[Dict[str, float]] = None,

    ) -> Dict[str, float]:
        """Learn from a batch of documents and gold-standard information,

        updating the pipe's model. Delegates to predict and get_loss."""
        if losses is None:
            losses = {}
        losses.setdefault(self.name, 0.0)
        set_dropout_rate(self.model, drop)

        # check that there are actually any candidate instances in this batch of examples
        total_instances = 0
        for eg in examples:
            total_instances += len(self.model.attrs["get_instances"](eg.predicted))
        if total_instances == 0:
            msg.info("Could not determine any instances in doc.")
            return losses

        # run the model
        docs = [eg.predicted for eg in examples]
        predictions, backprop = self.model.begin_update(docs)
        loss, gradient = self.get_loss(examples, predictions)
        backprop(gradient)
        if sgd is not None:
            self.model.finish_update(sgd)
        losses[self.name] += loss
        if set_annotations:
            self.set_annotations(docs, predictions)
        return losses

    def get_focal_loss(self, examples: Iterable[Example], scores, gamma=3.0, alpha=0.25, eps=1e-8) -> Tuple[float, float]:
        truths = self._examples_to_truth(examples)
        scores_2 = numpy.clip(scores, eps, 1. - eps)
        p_t = numpy.clip(scores_2 * truths + (1 - scores_2) * (1 - truths), eps, 1. - eps)

        focal_loss = -(1 - p_t) ** gamma * numpy.log(p_t)
        loss = numpy.mean(numpy.sum(focal_loss, axis=1))
        gradient = focal_loss * (1 - 2 * truths)
        return float(loss), gradient
    

    def get_loss(self, examples: Iterable[Example], scores) -> Tuple[float, float]:
        """Find the loss and gradient of loss for the batch of documents and

        their predicted scores."""
        truths = self._examples_to_truth(examples)
        gradient = scores - truths
        mean_square_error = (gradient ** 2).sum(axis=1).mean()
        return float(mean_square_error), gradient

    def initialize(

        self,

        get_examples: Callable[[], Iterable[Example]],

        *,

        nlp: Language = None,

        labels: Optional[List[str]] = None,

    ):
        """Initialize the pipe for training, using a representative set

        of data examples.

        """
        if labels is not None:
            for label in labels:
                self.add_label(label)
        else:
            for example in get_examples():
                relations = example.reference._.rel
                for indices, label_dict in relations.items():
                    for label in label_dict.keys():
                        self.add_label(label)
        self._require_labels()

        subbatch = list(islice(get_examples(), 10))
        doc_sample = [eg.reference for eg in subbatch]
        label_sample = self._examples_to_truth(subbatch)
        if label_sample is None:
            raise ValueError("Call begin_training with relevant entities and relations annotated in "
                             "at least a few reference examples!")
        self.model.initialize(X=doc_sample, Y=label_sample)

    def _examples_to_truth(self, examples: List[Example]) -> Optional[numpy.ndarray]:
        # check that there are actually any candidate instances in this batch of examples
        nr_instances = 0
        for eg in examples:
            nr_instances += len(self.model.attrs["get_instances"](eg.reference))
        if nr_instances == 0:
            return None

        truths = numpy.zeros((nr_instances, len(self.labels)), dtype="f")
        c = 0
        for i, eg in enumerate(examples):
            for (e1, e2) in self.model.attrs["get_instances"](eg.reference):
                gold_label_dict = eg.reference._.rel.get((e1.start, e2.start), {})
                for j, label in enumerate(self.labels):
                    truths[c, j] = gold_label_dict.get(label, 0)
                c += 1

        truths = self.model.ops.asarray(truths)
        return truths

    def score(self, examples: Iterable[Example], **kwargs) -> Dict[str, Any]:
        """Score a batch of examples."""
        scores = score_relations(examples, self.threshold)

        tmp_scores = scores.copy()
        tmp_scores["step"] = len(self.metric_history) * self.eval_frequency
        if tmp_scores["rel_macro_f"] > self.max_f1:
            self.max_f1 = tmp_scores["rel_macro_f"]
            self.max_f1_step = tmp_scores["step"]
        self.metric_history.append(tmp_scores)

        return scores

    def preprocess_metric_history(self):
        result = {
            "metric_name": [],
            "metric_value": [],
            "step": []
        }
        for cur_metrics in self.metric_history:
            cur_step = cur_metrics["step"]
            for key, value in cur_metrics.items():
                if key != "step" and isinstance(value, float):
                    result["metric_name"].append(key)
                    result["metric_value"].append(value)
                    result["step"].append(cur_step)
        return result

    def save_metrics_history(self, path):
        if self.start_learning_time is None:
            self.start_learning_time = time.monotonic()

        if self.metric_history:

            metrics_history_to_save = self.preprocess_metric_history()
            fig = px.line(metrics_history_to_save, x="step", y="metric_value", color="metric_name")
            for trace in fig.data:
                if trace.name in ["rel_micro_f", "rel_macro_f", "rel_weighted_f"]:
                    trace.line.width = 6
                else:
                    trace.line.width = 1

                idx = list(trace.x).index(self.max_f1_step)
                highlight_y = list(trace.y)[idx]
                line_color = trace.line.color
                line_name = trace.name
                fig.add_trace(go.Scatter(
                    x=[self.max_f1_step], y=[highlight_y],
                    mode='markers+text',
                    marker=dict(
                        color=line_color, size=10),
                        text=[f"{round(highlight_y, 2)}"],
                        textposition="top center",
                        name=f"{line_name} best"
                    ))

            current_time = time.monotonic()
            current_time_of_training = current_time - self.start_learning_time
            current_time_of_training_text = f"{int(current_time_of_training // 3600)} hrs {int(current_time_of_training % 3600) // 60} min {round(current_time_of_training % 60)} sec"

            fig.update_layout(title = dict(
                text="Training statistics",
                subtitle=dict(
                    text=f"Training time amounted to {current_time_of_training_text}",
                    font=dict(color="gray", size=13),
                )
            ))

            output_dir = os.path.join(str(path), "logs")
            os.makedirs(output_dir, exist_ok=True)
            fig_path = os.path.join(output_dir, "training_metrics.html")
            json_path = os.path.join(output_dir, "training_metrics.json")
            fig.write_html(fig_path)
            with open(json_path, "w", encoding="utf-8") as f:
                json.dump({
                    "data": metrics_history_to_save,
                    "train_time_s": current_time_of_training
                }, f, indent=2, ensure_ascii=False)

    def to_disk(self, path, *args, **kwargs):
        super().to_disk(path, *args, **kwargs)
        output_dir = Path(path)
        output_dir_metrics = output_dir.parent.parent
        self.save_metrics_history(output_dir_metrics)


def score_relations(examples: Iterable[Example], threshold: float) -> Dict[str, Any]:
    """Score a batch of examples."""

    y_true = []
    y_pred = []
    for example in examples:
        gold = example.reference._.rel
        pred = example.predicted._.rel
        for key, pred_dict in pred.items():
            gold_labels = {k for (k, v) in gold.get(key, {}).items() if v == 1.0}
            for k, v in pred_dict.items():
                if v >= threshold:
                    if k in gold_labels:
                        y_true.append(k)
                        y_pred.append(k)
                    else:
                        y_true.append("O")
                        y_pred.append(k)
                else:
                    if k in gold_labels:
                        y_true.append(k)
                        y_pred.append("O")


    labels = sorted({label for label in y_true if label != "O"})

    precision, recall, f1, support = precision_recall_fscore_support(
        y_true, y_pred, labels=labels, zero_division=0, average=None
    )
    result = {}
    for l, p, r, f in zip(labels, precision, recall, f1):
        result[f"f1_{l}"] = f

    p, r, f1_micro, _ = precision_recall_fscore_support(
        y_true, y_pred, labels=labels, zero_division=0, average="micro", beta=1
    )

    result["rel_micro_p"] = p
    result["rel_micro_r"] = r
    result["rel_micro_f"] = f1_micro
    result["rel_macro_f"] = f1_score(y_true, y_pred, average="macro", labels=labels, zero_division=0)
    result["rel_weighted_f"] = f1_score(y_true, y_pred, average="weighted", labels=labels, zero_division=0)

    return result