from typing import List, Tuple, Set, Dict, cast from thinc.types import Ints2d from spacy.tokens import Doc # type alias to make writing this less tedious MentionClusters = List[List[Tuple[int, int]]] DEFAULT_CLUSTER_PREFIX = "coref_clusters" class GraphNode: def __init__(self, node_id: int): self.id = node_id self.links: Set[GraphNode] = set() self.visited = False def link(self, another: "GraphNode"): self.links.add(another) another.links.add(self) def __repr__(self) -> str: return str(self.id) def get_sentence_ids(doc): out = [] sent_id = -1 for tok in doc: if tok.is_sent_start: sent_id += 1 out.append(sent_id) return out def doc2clusters(doc: Doc, prefix=DEFAULT_CLUSTER_PREFIX) -> MentionClusters: """Given a doc, give the mention clusters. This is useful for scoring. """ out = [] for name, val in doc.spans.items(): if not name.startswith(prefix): continue cluster = [] for mention in val: cluster.append((mention.start, mention.end)) out.append(cluster) return out # from model.py, refactored to be non-member def get_predicted_antecedents(xp, antecedent_idx, antecedent_scores): """Get the ID of the antecedent for each span. -1 if no antecedent.""" predicted_antecedents = [] for i, idx in enumerate(xp.argmax(antecedent_scores, axis=1) - 1): if idx < 0: predicted_antecedents.append(-1) else: predicted_antecedents.append(antecedent_idx[i][idx]) return predicted_antecedents # from model.py, refactored to be non-member def get_predicted_clusters( xp, span_starts, span_ends, antecedent_idx, antecedent_scores ): """Convert predictions to usable cluster data. return values: clusters: a list of spans (i, j) that are a cluster Note that not all spans will be in the final output; spans with no antecedent or referrent are omitted from clusters and mention2cluster. """ # Get predicted antecedents predicted_antecedents = get_predicted_antecedents( xp, antecedent_idx, antecedent_scores ) # Get predicted clusters mention_to_cluster_id = {} predicted_clusters = [] for i, predicted_idx in enumerate(predicted_antecedents): if predicted_idx < 0: continue assert i > predicted_idx, f"span idx: {i}; antecedent idx: {predicted_idx}" # Check antecedent's cluster antecedent = (int(span_starts[predicted_idx]), int(span_ends[predicted_idx])) antecedent_cluster_id = mention_to_cluster_id.get(antecedent, -1) if antecedent_cluster_id == -1: antecedent_cluster_id = len(predicted_clusters) predicted_clusters.append([antecedent]) mention_to_cluster_id[antecedent] = antecedent_cluster_id # Add mention to cluster mention = (int(span_starts[i]), int(span_ends[i])) predicted_clusters[antecedent_cluster_id].append(mention) mention_to_cluster_id[mention] = antecedent_cluster_id predicted_clusters = [tuple(c) for c in predicted_clusters] return predicted_clusters def select_non_crossing_spans( idxs: List[int], starts: List[int], ends: List[int], limit: int ) -> List[int]: """Given a list of spans sorted in descending order, return the indexes of spans to keep, discarding spans that cross. Nested spans are allowed. """ # ported from Model._extract_top_spans selected: List[int] = [] start_to_max_end: Dict[int, int] = {} end_to_min_start: Dict[int, int] = {} for idx in idxs: if len(selected) >= limit or idx > len(starts): break start, end = starts[idx], ends[idx] cross = False for ti in range(start, end): max_end = start_to_max_end.get(ti, -1) if ti > start and max_end > end: cross = True break min_start = end_to_min_start.get(ti, -1) if ti < end and 0 <= min_start < start: cross = True break if not cross: # this index will be kept # record it so we can exclude anything that crosses it selected.append(idx) max_end = start_to_max_end.get(start, -1) if end > max_end: start_to_max_end[start] = end min_start = end_to_min_start.get(end, -1) if min_start == -1 or start < min_start: end_to_min_start[end] = start # sort idxs by order in doc selected = sorted(selected, key=lambda idx: (starts[idx], ends[idx])) # This was causing many repetitive entities in the output - removed for now # while len(selected) < limit: # selected.append(selected[0]) # this seems a bit weird? return selected def create_head_span_idxs(ops, doclen: int): """Helper function to create single-token span indices.""" aa = ops.xp.arange(0, doclen) bb = ops.xp.arange(0, doclen) + 1 return ops.asarray2i([aa, bb]).T def get_clusters_from_doc(doc) -> List[List[Tuple[int, int]]]: """Given a Doc, convert the cluster spans to simple int tuple lists.""" out = [] for key, val in doc.spans.items(): cluster = [] for span in val: # TODO check that there isn't an off-by-one error here # cluster.append((span.start, span.end)) # TODO This conversion should be happening earlier in processing head_i = span.root.i cluster.append((head_i, head_i + 1)) # don't want duplicates cluster = list(set(cluster)) out.append(cluster) return out def create_gold_scores( ments: Ints2d, clusters: List[List[Tuple[int, int]]] ) -> List[List[bool]]: """Given mentions considered for antecedents and gold clusters, construct a gold score matrix. This does not include the placeholder. In the gold matrix, the value of a true antecedent is True, and otherwise it is False. These will be converted to 1/0 values later. """ # make a mapping of mentions to cluster id # id is not important but equality will be ment2cid: Dict[Tuple[int, int], int] = {} for cid, cluster in enumerate(clusters): for ment in cluster: ment2cid[ment] = cid ll = len(ments) out = [] # The .tolist() call is necessary with cupy but not numpy mentuples = [cast(Tuple[int, int], tuple(mm.tolist())) for mm in ments] for ii, ment in enumerate(mentuples): if ment not in ment2cid: # this is not in a cluster so it has no antecedent out.append([False] * ll) continue # this might change if no real antecedent is a candidate row = [] cid = ment2cid[ment] for jj, ante in enumerate(mentuples): # antecedents must come first if jj >= ii: row.append(False) continue row.append(cid == ment2cid.get(ante, -1)) out.append(row) # caller needs to convert to array, and add placeholder return out