From 520801e2a0741ceea6d66ee1ae171a77aaf205e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Maja=20Jab=C5=82o=C5=84ska?= <majajjablonska@gmail.com>
Date: Tue, 7 Mar 2023 19:38:16 +0100
Subject: [PATCH] General structure
---
.idea/combolightning.iml | 2 +-
.idea/misc.xml | 2 +-
.idea/vcs.xml | 6 +
combo/checks.py | 4 -
combo/commands/__init__.py | 1 +
combo/commands/train.py | 10 +
combo/data/__init__.py | 1 +
combo/data/dataset.py | 314 +-----------------
combo/data/fields/__init__.py | 1 +
combo/data/fields/base_field.py | 5 +
.../data/fields/sequence_multilabel_field.py | 40 +--
combo/data/samplers/__init__.py | 1 +
combo/data/samplers/base_sampler.py | 5 +
combo/data/samplers/samplers.py | 5 +-
combo/data/token.py | 2 +
combo/data/token_indexers/__init__.py | 1 +
combo/data/token_indexers/base_indexer.py | 9 +
...etrained_transformer_mismatched_indexer.py | 118 +------
.../token_characters_indexer.py | 62 +---
.../token_indexers/token_features_indexer.py | 74 +----
combo/main.py | 150 +++++++++
combo/models/__init__.py | 8 +
combo/models/base.py | 6 +-
combo/models/embeddings.py | 24 ++
combo/models/encoder.py | 10 +
combo/models/graph_parser.py | 9 +
combo/models/lemma.py | 5 +
combo/models/model.py | 5 +
combo/models/morpho.py | 5 +
combo/models/parser.py | 9 +
combo/predict.py | 15 +
combo/training/__init__.py | 3 +
combo/training/checkpointer.py | 6 +
combo/training/scheduler.py | 2 +
combo/training/tensorboard_writer.py | 2 +
combo/training/trainer.py | 13 +
combo/utils/__init__.py | 0
combo/utils/checks.py | 15 +
combo/utils/download.py | 78 +++++
combo/utils/graph.py | 149 +++++++++
combo/utils/metrics.py | 17 +
requirements.txt | 6 +-
42 files changed, 607 insertions(+), 593 deletions(-)
create mode 100644 .idea/vcs.xml
delete mode 100644 combo/checks.py
create mode 100644 combo/commands/__init__.py
create mode 100644 combo/commands/train.py
create mode 100644 combo/data/fields/base_field.py
create mode 100644 combo/data/samplers/base_sampler.py
create mode 100644 combo/data/token.py
create mode 100644 combo/data/token_indexers/base_indexer.py
create mode 100644 combo/main.py
create mode 100644 combo/models/encoder.py
create mode 100644 combo/models/graph_parser.py
create mode 100644 combo/models/lemma.py
create mode 100644 combo/models/model.py
create mode 100644 combo/models/morpho.py
create mode 100644 combo/models/parser.py
create mode 100644 combo/predict.py
create mode 100644 combo/training/__init__.py
create mode 100644 combo/training/checkpointer.py
create mode 100644 combo/training/scheduler.py
create mode 100644 combo/training/tensorboard_writer.py
create mode 100644 combo/training/trainer.py
create mode 100644 combo/utils/__init__.py
create mode 100644 combo/utils/checks.py
create mode 100644 combo/utils/download.py
create mode 100644 combo/utils/graph.py
create mode 100644 combo/utils/metrics.py
diff --git a/.idea/combolightning.iml b/.idea/combolightning.iml
index 4154233..332f523 100644
--- a/.idea/combolightning.iml
+++ b/.idea/combolightning.iml
@@ -2,7 +2,7 @@
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" />
- <orderEntry type="jdk" jdkName="Python 3.9 (combolightning)" jdkType="Python SDK" />
+ <orderEntry type="jdk" jdkName="combo" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
</module>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
index fcbd09d..d1d59e6 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -1,4 +1,4 @@
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
- <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9 (combolightning)" project-jdk-type="Python SDK" />
+ <component name="ProjectRootManager" version="2" project-jdk-name="combo" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..35eb1dd
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="" vcs="Git" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/combo/checks.py b/combo/checks.py
deleted file mode 100644
index 7736e96..0000000
--- a/combo/checks.py
+++ /dev/null
@@ -1,4 +0,0 @@
-class ConfigurationError(Exception):
- def __init__(self, message: str):
- super().__init__()
- self.message = message
diff --git a/combo/commands/__init__.py b/combo/commands/__init__.py
new file mode 100644
index 0000000..83ff4f4
--- /dev/null
+++ b/combo/commands/__init__.py
@@ -0,0 +1 @@
+from .train import FinetuningTrainModel
\ No newline at end of file
diff --git a/combo/commands/train.py b/combo/commands/train.py
new file mode 100644
index 0000000..f4bb807
--- /dev/null
+++ b/combo/commands/train.py
@@ -0,0 +1,10 @@
+from pytorch_lightning import Trainer
+
+
+class FinetuningTrainModel(Trainer):
+ """
+ Class made only for finetuning,
+ the only difference is saving vocab from concatenated
+ (archive and current) datasets
+ """
+ pass
\ No newline at end of file
diff --git a/combo/data/__init__.py b/combo/data/__init__.py
index 91426e3..2d69cca 100644
--- a/combo/data/__init__.py
+++ b/combo/data/__init__.py
@@ -1,3 +1,4 @@
from .samplers import TokenCountBatchSampler
+from .token import Token
from .token_indexers import *
from .api import *
diff --git a/combo/data/dataset.py b/combo/data/dataset.py
index 0c34d3f..62ca30f 100644
--- a/combo/data/dataset.py
+++ b/combo/data/dataset.py
@@ -1,317 +1,11 @@
-import copy
import logging
-import pathlib
-from typing import Union, List, Dict, Iterable, Optional, Any, Tuple
-import conllu
-import torch
-from allennlp import data as allen_data
-from allennlp.common import checks, util
-from allennlp.data import fields as allen_fields, vocabulary
-from conllu import parser
-from dataclasses import dataclass
-from overrides import overrides
-
-from combo.data import fields
logger = logging.getLogger(__name__)
-@allen_data.DatasetReader.register("conllu")
-class UniversalDependenciesDatasetReader(allen_data.DatasetReader):
-
- def __init__(
- self,
- token_indexers: Dict[str, allen_data.TokenIndexer] = None,
- lemma_indexers: Dict[str, allen_data.TokenIndexer] = None,
- features: List[str] = None,
- targets: List[str] = None,
- use_sem: bool = False,
- **kwargs,
- ) -> None:
- super().__init__(**kwargs)
- if features is None:
- features = ["token", "char"]
- if targets is None:
- targets = ["head", "deprel", "upostag", "xpostag", "lemma", "feats"]
-
- if "token" not in features and "char" not in features:
- raise checks.ConfigurationError("There must be at least one ('char' or 'token') text-based feature!")
-
- if "deps" in targets and not ("head" in targets and "deprel" in targets):
- raise checks.ConfigurationError("Add 'head' and 'deprel' to targets when using 'deps'!")
-
- intersection = set(features).intersection(set(targets))
- if len(intersection) != 0:
- raise checks.ConfigurationError(
- "Features and targets cannot share elements! "
- "Remove {} from either features or targets.".format(intersection)
- )
- self.use_sem = use_sem
-
- # *.conllu readers config
- fields = list(parser.DEFAULT_FIELDS)
- fields[1] = "token" # use 'token' instead of 'form'
- field_parsers = parser.DEFAULT_FIELD_PARSERS
- # Do not make it nullable
- field_parsers.pop("xpostag", None)
- # Ignore parsing misc
- field_parsers.pop("misc", None)
- if self.use_sem:
- fields = list(fields)
- fields.append("semrel")
- field_parsers["semrel"] = lambda line, i: line[i]
- self.field_parsers = field_parsers
- self.fields = tuple(fields)
-
- self._token_indexers = token_indexers
- self._lemma_indexers = lemma_indexers
- self._targets = targets
- self._features = features
- self.generate_labels = True
- # Filter out not required token indexers to avoid
- # Mismatched token keys ConfigurationError
- for indexer_name in list(self._token_indexers.keys()):
- if indexer_name not in self._features:
- del self._token_indexers[indexer_name]
-
- @overrides
- def _read(self, file_path: str) -> Iterable[allen_data.Instance]:
- file_path = [file_path] if len(file_path.split(",")) == 0 else file_path.split(",")
-
- for conllu_file in file_path:
- file = pathlib.Path(conllu_file)
- assert conllu_file and file.exists(), f"File with path '{conllu_file}' does not exists!"
- with file.open("r", encoding="utf-8") as f:
- for annotation in conllu.parse_incr(f, fields=self.fields, field_parsers=self.field_parsers):
- yield self.text_to_instance(annotation)
-
- @overrides
- def text_to_instance(self, tree: conllu.TokenList) -> allen_data.Instance:
- fields_: Dict[str, allen_data.Field] = {}
- tree_tokens = [t for t in tree if isinstance(t["id"], int)]
- tokens = [_Token(t["token"],
- pos_=t.get("upostag"),
- tag_=t.get("xpostag"),
- lemma_=t.get("lemma"),
- feats_=t.get("feats"))
- for t in tree_tokens]
-
- # features
- text_field = allen_fields.TextField(tokens, self._token_indexers)
- fields_["sentence"] = text_field
-
- # targets
- if self.generate_labels:
- for target_name in self._targets:
- if target_name != "sent":
- target_values = [t[target_name] for t in tree_tokens]
- if target_name == "lemma":
- target_values = [allen_data.Token(v) for v in target_values]
- fields_[target_name] = allen_fields.TextField(target_values, self._lemma_indexers)
- elif target_name == "feats":
- target_values = self._feat_values(tree_tokens)
- fields_[target_name] = fields.SequenceMultiLabelField(target_values,
- self._feats_indexer,
- self._feats_as_tensor_wrapper,
- text_field,
- label_namespace="feats_labels")
- elif target_name == "head":
- target_values = [0 if v == "_" else int(v) for v in target_values]
- fields_[target_name] = allen_fields.SequenceLabelField(target_values, text_field,
- label_namespace=target_name + "_labels")
- elif target_name == "deps":
- # Graphs require adding ROOT (AdjacencyField uses sequence length from TextField).
- text_field_deps = allen_fields.TextField([_Token("ROOT")] + copy.deepcopy(tokens),
- self._token_indexers)
- enhanced_heads: List[Tuple[int, int]] = []
- enhanced_deprels: List[str] = []
- for idx, t in enumerate(tree_tokens):
- t_deps = t["deps"]
- if t_deps and t_deps != "_":
- for rel, head in t_deps:
- # EmoryNLP skips the first edge, if there are two edges between the same
- # nodes. Thanks to that one is in a tree and another in a graph.
- # This snippet follows that approach.
- if enhanced_heads and enhanced_heads[-1] == (idx, head):
- enhanced_heads.pop()
- enhanced_deprels.pop()
- enhanced_heads.append((idx, head))
- enhanced_deprels.append(rel)
- fields_["enhanced_heads"] = allen_fields.AdjacencyField(
- indices=enhanced_heads,
- sequence_field=text_field_deps,
- label_namespace="enhanced_heads_labels",
- padding_value=0,
- )
- fields_["enhanced_deprels"] = allen_fields.AdjacencyField(
- indices=enhanced_heads,
- sequence_field=text_field_deps,
- labels=enhanced_deprels,
- # Label namespace matches regular tree parsing.
- label_namespace="enhanced_deprel_labels",
- padding_value=0,
- )
- else:
- fields_[target_name] = allen_fields.SequenceLabelField(target_values, text_field,
- label_namespace=target_name + "_labels")
-
- # Restore feats fields to string representation
- # parser.serialize_field doesn't handle key without value
- for token in tree.tokens:
- if "feats" in token:
- feats = token["feats"]
- if feats:
- feats_values = []
- for k, v in feats.items():
- feats_values.append('='.join((k, v)) if v else k)
- field = "|".join(feats_values)
- else:
- field = "_"
- token["feats"] = field
-
- # metadata
- fields_["metadata"] = allen_fields.MetadataField({"input": tree,
- "field_names": self.fields,
- "tokens": tokens})
-
- return allen_data.Instance(fields_)
-
- @staticmethod
- def _feat_values(tree: List[Dict[str, Any]]):
- features = []
- for token in tree:
- token_features = []
- if token["feats"] is not None:
- for feat, value in token["feats"].items():
- if feat in ["_", "__ROOT__"]:
- pass
- else:
- # Handle case where feature is binary (doesn't have associated value)
- if value:
- token_features.append(feat + "=" + value)
- else:
- token_features.append(feat)
- features.append(token_features)
- return features
-
- @staticmethod
- def _feats_as_tensor_wrapper(field: fields.SequenceMultiLabelField):
- def as_tensor(padding_lengths):
- desired_num_tokens = padding_lengths["num_tokens"]
- assert len(field._indexed_multi_labels) > 0
- classes_count = len(field._indexed_multi_labels[0])
- default_value = [0.0] * classes_count
- padded_tags = util.pad_sequence_to_length(field._indexed_multi_labels, desired_num_tokens,
- lambda: default_value)
- tensor = torch.tensor(padded_tags, dtype=torch.long)
- return tensor
-
- return as_tensor
-
- @staticmethod
- def _feats_indexer(vocab: allen_data.Vocabulary):
- label_namespace = "feats_labels"
- vocab_size = vocab.get_vocab_size(label_namespace)
- slices = get_slices_if_not_provided(vocab)
-
- def _m_from_n_ones_encoding(multi_label: List[str], sentence_length: int) -> List[int]:
- one_hot_encoding = [0] * vocab_size
- for cat, cat_indices in slices.items():
- if cat not in ["__PAD__", "_"]:
- label_from_cat = [label for label in multi_label if cat == label.split("=")[0]]
- if label_from_cat:
- label_from_cat = label_from_cat[0]
- index = vocab.get_token_index(label_from_cat, label_namespace)
- else:
- # Get Cat=None index
- index = vocab.get_token_index(cat + "=None", label_namespace)
- one_hot_encoding[index] = 1
- return one_hot_encoding
-
- return _m_from_n_ones_encoding
-
-
-@allen_data.Vocabulary.register("from_instances_extended", constructor="from_instances_extended")
-class Vocabulary(allen_data.Vocabulary):
-
- @classmethod
- def from_instances_extended(
- cls,
- instances: Iterable[allen_data.Instance],
- min_count: Dict[str, int] = None,
- max_vocab_size: Union[int, Dict[str, int]] = None,
- non_padded_namespaces: Iterable[str] = vocabulary.DEFAULT_NON_PADDED_NAMESPACES,
- pretrained_files: Optional[Dict[str, str]] = None,
- only_include_pretrained_words: bool = False,
- min_pretrained_embeddings: Dict[str, int] = None,
- padding_token: Optional[str] = vocabulary.DEFAULT_PADDING_TOKEN,
- oov_token: Optional[str] = vocabulary.DEFAULT_OOV_TOKEN,
- ) -> "Vocabulary":
- """
- Extension to manually fill gaps in missing 'feats_labels'.
- """
- # Load manually tokens from pretrained file (using different strategy
- # - only words add all embedding file, without checking if were seen
- # in any dataset.
- tokens_to_add = None
- if pretrained_files and "tokens" in pretrained_files:
- pretrained_set = set(vocabulary._read_pretrained_tokens(pretrained_files["tokens"]))
- tokens_to_add = {"tokens": list(pretrained_set)}
- pretrained_files = None
-
- vocab = super().from_instances(
- instances=instances,
- min_count=min_count,
- max_vocab_size=max_vocab_size,
- non_padded_namespaces=non_padded_namespaces,
- pretrained_files=pretrained_files,
- only_include_pretrained_words=only_include_pretrained_words,
- tokens_to_add=tokens_to_add,
- min_pretrained_embeddings=min_pretrained_embeddings,
- padding_token=padding_token,
- oov_token=oov_token
- )
- # Extending vocab with features that does not show up explicitly.
- # To know all features we need to read full dataset first.
- # Adding auxiliary '=None' feature for each category is needed
- # to perform classification.
- get_slices_if_not_provided(vocab)
- return vocab
-
-
-def get_slices_if_not_provided(vocab: allen_data.Vocabulary):
- if hasattr(vocab, "slices"):
- return vocab.slices
-
- if "feats_labels" in vocab.get_namespaces():
- idx2token = vocab.get_index_to_token_vocabulary("feats_labels")
- for _, v in dict(idx2token).items():
- if v not in ["_", "__PAD__"]:
- empty_value = v.split("=")[0] + "=None"
- vocab.add_token_to_namespace(empty_value, "feats_labels")
-
- slices = {}
- for idx, name in vocab.get_index_to_token_vocabulary("feats_labels").items():
- # There are 2 types features: with (Case=Acc) or without assigment (None).
- # Here we group their indices by name (before assigment sign).
- name = name.split("=")[0]
- if name in slices:
- slices[name].append(idx)
- else:
- slices[name] = [idx]
- vocab.slices = slices
- return vocab.slices
-
-
-@dataclass(init=False, repr=False)
-class _Token(allen_data.Token):
- __slots__ = allen_data.Token.__slots__ + ['feats_']
-
- feats_: Optional[str]
+class DatasetReader:
+ pass
- def __init__(self, text: str = None, idx: int = None, idx_end: int = None, lemma_: str = None, pos_: str = None,
- tag_: str = None, dep_: str = None, ent_type_: str = None, text_id: int = None, type_id: int = None,
- feats_: str = None) -> None:
- super().__init__(text, idx, idx_end, lemma_, pos_, tag_, dep_, ent_type_, text_id, type_id)
- self.feats_ = feats_
+class UniversalDependenciesDatasetReader(DatasetReader):
+ pass
\ No newline at end of file
diff --git a/combo/data/fields/__init__.py b/combo/data/fields/__init__.py
index 4f8d3a2..57de344 100644
--- a/combo/data/fields/__init__.py
+++ b/combo/data/fields/__init__.py
@@ -1 +1,2 @@
+from .base_field import Field
from .sequence_multilabel_field import SequenceMultiLabelField
diff --git a/combo/data/fields/base_field.py b/combo/data/fields/base_field.py
new file mode 100644
index 0000000..83ea563
--- /dev/null
+++ b/combo/data/fields/base_field.py
@@ -0,0 +1,5 @@
+from abc import ABCMeta
+
+
+class Field(metaclass=ABCMeta):
+ pass
diff --git a/combo/data/fields/sequence_multilabel_field.py b/combo/data/fields/sequence_multilabel_field.py
index c31f78e..b7a6bbe 100644
--- a/combo/data/fields/sequence_multilabel_field.py
+++ b/combo/data/fields/sequence_multilabel_field.py
@@ -1,18 +1,16 @@
"""Sequence multilabel field implementation."""
import logging
-import textwrap
from typing import Set, List, Callable, Iterator, Union, Dict
import torch
-from allennlp import data
-from allennlp.common import checks
-from allennlp.data import fields
from overrides import overrides
+from combo.data.fields import Field
+
logger = logging.getLogger(__name__)
-class SequenceMultiLabelField(data.Field[torch.Tensor]):
+class SequenceMultiLabelField(Field):
"""
A `SequenceMultiLabelField` is an extension of the :class:`MultiLabelField` that allows for multiple labels
while keeping sequence dimension.
@@ -93,43 +91,23 @@ class SequenceMultiLabelField(data.Field[torch.Tensor]):
@overrides
def count_vocab_items(self, counter: Dict[str, Dict[str, int]]):
- if self._indexed_multi_labels is None:
- for multi_label in self.multi_labels:
- for label in multi_label:
- counter[self._label_namespace][label] += 1 # type: ignore
+ pass
@overrides
def index(self, vocab: data.Vocabulary):
- indexer = self.multi_label_indexer(vocab)
-
- indexed = []
- for multi_label in self.multi_labels:
- indexed.append(indexer(multi_label, len(self.multi_labels)))
- self._indexed_multi_labels = indexed
+ pass
@overrides
def get_padding_lengths(self) -> Dict[str, int]:
- return {"num_tokens": self.sequence_field.sequence_length()}
+ pass
@overrides
def as_tensor(self, padding_lengths: Dict[str, int]) -> torch.Tensor:
- return self.as_tensor_wrapper(padding_lengths)
+ pass
@overrides
def empty_field(self) -> "SequenceMultiLabelField":
- empty_list: List[List[str]] = [[]]
- sequence_label_field = SequenceMultiLabelField(empty_list, lambda x: lambda y: y,
- lambda x: lambda y: y,
- self.sequence_field.empty_field())
- sequence_label_field._indexed_labels = empty_list
- return sequence_label_field
+ pass
def __str__(self) -> str:
- length = self.sequence_field.sequence_length()
- formatted_labels = "".join(
- "\t\t" + labels + "\n" for labels in textwrap.wrap(repr(self.multi_labels), 100)
- )
- return (
- f"SequenceMultiLabelField of length {length} with "
- f"labels:\n {formatted_labels} \t\tin namespace: '{self._label_namespace}'."
- )
+ pass
diff --git a/combo/data/samplers/__init__.py b/combo/data/samplers/__init__.py
index ab003fe..1db58a9 100644
--- a/combo/data/samplers/__init__.py
+++ b/combo/data/samplers/__init__.py
@@ -1 +1,2 @@
+from .base_sampler import Sampler
from .samplers import TokenCountBatchSampler
diff --git a/combo/data/samplers/base_sampler.py b/combo/data/samplers/base_sampler.py
new file mode 100644
index 0000000..6e5cd40
--- /dev/null
+++ b/combo/data/samplers/base_sampler.py
@@ -0,0 +1,5 @@
+from abc import ABCMeta
+
+
+class Sampler(metaclass=ABCMeta):
+ pass
diff --git a/combo/data/samplers/samplers.py b/combo/data/samplers/samplers.py
index 5db74d9..ee32a5e 100644
--- a/combo/data/samplers/samplers.py
+++ b/combo/data/samplers/samplers.py
@@ -2,11 +2,10 @@ from typing import List
import numpy as np
-from allennlp import data as allen_data
+from combo.data.samplers import Sampler
-@allen_data.BatchSampler.register("token_count")
-class TokenCountBatchSampler(allen_data.BatchSampler):
+class TokenCountBatchSampler(Sampler):
def __init__(self, dataset, word_batch_size: int = 2500, shuffle_dataset: bool = True):
self._index = 0
diff --git a/combo/data/token.py b/combo/data/token.py
new file mode 100644
index 0000000..048fab0
--- /dev/null
+++ b/combo/data/token.py
@@ -0,0 +1,2 @@
+class Token:
+ pass
diff --git a/combo/data/token_indexers/__init__.py b/combo/data/token_indexers/__init__.py
index 550a80b..d179540 100644
--- a/combo/data/token_indexers/__init__.py
+++ b/combo/data/token_indexers/__init__.py
@@ -1,3 +1,4 @@
+from .base_indexer import TokenIndexer
from .pretrained_transformer_mismatched_indexer import PretrainedTransformerMismatchedIndexer
from .token_characters_indexer import TokenCharactersIndexer
from .token_features_indexer import TokenFeatsIndexer
diff --git a/combo/data/token_indexers/base_indexer.py b/combo/data/token_indexers/base_indexer.py
new file mode 100644
index 0000000..2fb48c0
--- /dev/null
+++ b/combo/data/token_indexers/base_indexer.py
@@ -0,0 +1,9 @@
+from abc import ABCMeta
+
+
+class TokenIndexer(metaclass=ABCMeta):
+ pass
+
+
+class PretrainedTransformerMismatchedIndexer(TokenIndexer):
+ pass
diff --git a/combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py b/combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py
index fc29896..9aa3616 100644
--- a/combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py
+++ b/combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py
@@ -1,117 +1,13 @@
-from typing import Optional, Dict, Any, List, Tuple
+from combo.data import TokenIndexer
-from allennlp import data
-from allennlp.data import token_indexers, tokenizers, IndexedTokenList, vocabulary
-from overrides import overrides
+class PretrainedTransformerMismatchedIndexer(TokenIndexer):
+ pass
-@data.TokenIndexer.register("pretrained_transformer_mismatched_fixed")
-class PretrainedTransformerMismatchedIndexer(token_indexers.PretrainedTransformerMismatchedIndexer):
- def __init__(self, model_name: str, namespace: str = "tags", max_length: int = None,
- tokenizer_kwargs: Optional[Dict[str, Any]] = None, **kwargs) -> None:
- # The matched version v.s. mismatched
- super().__init__(model_name, namespace, max_length, tokenizer_kwargs, **kwargs)
- self._matched_indexer = PretrainedTransformerIndexer(
- model_name,
- namespace=namespace,
- max_length=max_length,
- tokenizer_kwargs=tokenizer_kwargs,
- **kwargs,
- )
- self._allennlp_tokenizer = self._matched_indexer._allennlp_tokenizer
- self._tokenizer = self._matched_indexer._tokenizer
- self._num_added_start_tokens = self._matched_indexer._num_added_start_tokens
- self._num_added_end_tokens = self._matched_indexer._num_added_end_tokens
+class PretrainedTransformerIndexer(TokenIndexer):
+ pass
- @overrides
- def tokens_to_indices(self,
- tokens,
- vocabulary: vocabulary ) -> IndexedTokenList:
- """
- Method is overridden in order to raise an error while the number of tokens needed to embed a sentence exceeds the
- maximal input of a model.
- """
- self._matched_indexer._add_encoding_to_vocabulary_if_needed(vocabulary)
- wordpieces, offsets = self._allennlp_tokenizer.intra_word_tokenize(
- [t.ensure_text() for t in tokens])
-
- if len(wordpieces) > self._tokenizer.max_len_single_sentence:
- raise ValueError("Following sentence consists of more wordpiece tokens that the model can process:\n" +\
- " ".join([str(x) for x in tokens[:10]]) + " ... \n" + \
- f"Maximal input: {self._tokenizer.max_len_single_sentence}\n"+ \
- f"Current input: {len(wordpieces)}")
-
- offsets = [x if x is not None else (-1, -1) for x in offsets]
-
- output: IndexedTokenList = {
- "token_ids": [t.text_id for t in wordpieces],
- "mask": [True] * len(tokens), # for original tokens (i.e. word-level)
- "type_ids": [t.type_id for t in wordpieces],
- "offsets": offsets,
- "wordpiece_mask": [True] * len(wordpieces), # for wordpieces (i.e. subword-level)
- }
-
- return self._matched_indexer._postprocess_output(output)
-
-
-class PretrainedTransformerIndexer(token_indexers.PretrainedTransformerIndexer):
-
- def __init__(
- self,
- model_name: str,
- namespace: str = "tags",
- max_length: int = None,
- tokenizer_kwargs: Optional[Dict[str, Any]] = None,
- **kwargs,
- ) -> None:
- super().__init__(model_name, namespace, max_length, tokenizer_kwargs, **kwargs)
- self._namespace = namespace
- self._allennlp_tokenizer = PretrainedTransformerTokenizer(
- model_name, tokenizer_kwargs=tokenizer_kwargs
- )
- self._tokenizer = self._allennlp_tokenizer.tokenizer
- self._added_to_vocabulary = False
-
- self._num_added_start_tokens = len(self._allennlp_tokenizer.single_sequence_start_tokens)
- self._num_added_end_tokens = len(self._allennlp_tokenizer.single_sequence_end_tokens)
-
- self._max_length = max_length
- if self._max_length is not None:
- num_added_tokens = len(self._allennlp_tokenizer.tokenize("a")) - 1
- self._effective_max_length = ( # we need to take into account special tokens
- self._max_length - num_added_tokens
- )
- if self._effective_max_length <= 0:
- raise ValueError(
- "max_length needs to be greater than the number of special tokens inserted."
- )
-
-
-class PretrainedTransformerTokenizer(tokenizers.PretrainedTransformerTokenizer):
-
- def _intra_word_tokenize(
- self, string_tokens: List[str]
- ) -> Tuple[List[data.Token], List[Optional[Tuple[int, int]]]]:
- tokens: List[data.Token] = []
- offsets: List[Optional[Tuple[int, int]]] = []
- for token_string in string_tokens:
- wordpieces = self.tokenizer.encode_plus(
- token_string,
- add_special_tokens=False,
- return_tensors=None,
- return_offsets_mapping=False,
- return_attention_mask=False,
- )
- wp_ids = wordpieces["input_ids"]
-
- if len(wp_ids) > 0:
- offsets.append((len(tokens), len(tokens) + len(wp_ids) - 1))
- tokens.extend(
- data.Token(text=wp_text, text_id=wp_id)
- for wp_id, wp_text in zip(wp_ids, self.tokenizer.convert_ids_to_tokens(wp_ids))
- )
- else:
- offsets.append(None)
- return tokens, offsets
+class PretrainedTransformerTokenizer(TokenIndexer):
+ pass
diff --git a/combo/data/token_indexers/token_characters_indexer.py b/combo/data/token_indexers/token_characters_indexer.py
index ea7a3ea..6f5dbf0 100644
--- a/combo/data/token_indexers/token_characters_indexer.py
+++ b/combo/data/token_indexers/token_characters_indexer.py
@@ -1,62 +1,6 @@
-"""Custom character token indexer."""
-import itertools
-from typing import List, Dict
+from combo.data import TokenIndexer
-import torch
-from allennlp import data
-from allennlp.common import util
-from allennlp.data import tokenizers
-from allennlp.data.token_indexers import token_characters_indexer
-from overrides import overrides
-
-@data.TokenIndexer.register("characters_const_padding")
-class TokenCharactersIndexer(token_characters_indexer.TokenCharactersIndexer):
+class TokenCharactersIndexer(TokenIndexer):
"""Wrapper around allennlp token indexer with const padding."""
-
- def __init__(self,
- namespace: str = "token_characters",
- character_tokenizer: tokenizers.CharacterTokenizer = tokenizers.CharacterTokenizer(),
- start_tokens: List[str] = None,
- end_tokens: List[str] = None,
- min_padding_length: int = 0,
- token_min_padding_length: int = 0):
- super().__init__(namespace, character_tokenizer, start_tokens, end_tokens, min_padding_length,
- token_min_padding_length)
-
- @overrides
- def get_padding_lengths(self, indexed_tokens: data.IndexedTokenList) -> Dict[str, int]:
- padding_lengths = {"token_characters": len(indexed_tokens["token_characters"]),
- "num_token_characters": self._min_padding_length}
- return padding_lengths
-
- @overrides
- def as_padded_tensor_dict(
- self, tokens: data.IndexedTokenList, padding_lengths: Dict[str, int]
- ) -> Dict[str, torch.Tensor]:
- # Pad the tokens.
- padded_tokens = util.pad_sequence_to_length(
- tokens["token_characters"],
- padding_lengths["token_characters"],
- default_value=lambda: [],
- )
-
- # Pad the characters within the tokens.
- desired_token_length = padding_lengths["num_token_characters"]
- longest_token: List[int] = max(tokens["token_characters"], key=len, default=[]) # type: ignore
- padding_value = 0
- if desired_token_length > len(longest_token):
- # Since we want to pad to greater than the longest token, we add a
- # "dummy token" so we can take advantage of the fast implementation of itertools.zip_longest.
- padded_tokens.append([padding_value] * desired_token_length)
- # pad the list of lists to the longest sublist, appending 0's
- padded_tokens = list(zip(*itertools.zip_longest(*padded_tokens, fillvalue=padding_value)))
- if desired_token_length > len(longest_token):
- # Removes the "dummy token".
- padded_tokens.pop()
- # Truncates all the tokens to the desired length, and return the result.
- return {
- "token_characters": torch.LongTensor(
- [list(token[:desired_token_length]) for token in padded_tokens]
- )
- }
+ pass
diff --git a/combo/data/token_indexers/token_features_indexer.py b/combo/data/token_indexers/token_features_indexer.py
index 7c59124..b6267a4 100644
--- a/combo/data/token_indexers/token_features_indexer.py
+++ b/combo/data/token_indexers/token_features_indexer.py
@@ -1,75 +1,7 @@
"""Features indexer."""
-import collections
-from typing import List, Dict
-import torch
-from allennlp import data
-from allennlp.common import util
-from overrides import overrides
+from combo.data import TokenIndexer
-@data.TokenIndexer.register("feats_indexer")
-class TokenFeatsIndexer(data.TokenIndexer):
-
- def __init__(
- self,
- namespace: str = "feats",
- feature_name: str = "feats_",
- token_min_padding_length: int = 0,
- ) -> None:
- super().__init__(token_min_padding_length)
- self.namespace = namespace
- self._feature_name = feature_name
-
- @overrides
- def count_vocab_items(self, token: data.Token, counter: Dict[str, Dict[str, int]]):
- feats = self._feat_values(token)
- for feat in feats:
- counter[self.namespace][feat] += 1
-
- @overrides
- def tokens_to_indices(self, tokens: List[data.Token], vocabulary: data.Vocabulary) -> data.IndexedTokenList:
- indices: List[List[int]] = []
- vocab_size = vocabulary.get_vocab_size(self.namespace)
- for token in tokens:
- token_indices = []
- feats = self._feat_values(token)
- for feat in feats:
- token_indices.append(vocabulary.get_token_index(feat, self.namespace))
- indices.append(util.pad_sequence_to_length(token_indices, vocab_size))
- return {"tokens": indices}
-
- @overrides
- def get_empty_token_list(self) -> data.IndexedTokenList:
- return {"tokens": [[]]}
-
- def _feat_values(self, token):
- feats = getattr(token, self._feature_name)
- if feats is None:
- feats = collections.OrderedDict()
- features = []
- for feat, value in feats.items():
- if feat in ["_", "__ROOT__"]:
- pass
- else:
- # Handle case where feature is binary (doesn't have associated value)
- if value:
- features.append(feat + "=" + value)
- else:
- features.append(feat)
- return features
-
- @overrides
- def as_padded_tensor_dict(
- self, tokens: data.IndexedTokenList, padding_lengths: Dict[str, int]
- ) -> Dict[str, torch.Tensor]:
- tensor_dict = {}
- for key, val in tokens.items():
- vocab_size = len(val[0])
- tensor = torch.tensor(util.pad_sequence_to_length(val,
- padding_lengths[key],
- default_value=lambda: [0] * vocab_size,
- )
- )
- tensor_dict[key] = tensor
- return tensor_dict
+class TokenFeatsIndexer(TokenIndexer):
+ pass
diff --git a/combo/main.py b/combo/main.py
new file mode 100644
index 0000000..1d4d945
--- /dev/null
+++ b/combo/main.py
@@ -0,0 +1,150 @@
+import logging
+import os
+import pathlib
+import tempfile
+from typing import Dict
+
+import torch
+from absl import app
+from absl import flags
+
+from combo import models
+from combo.models.base import Predictor
+from combo.utils import checks
+
+logger = logging.getLogger(__name__)
+_FEATURES = ["token", "char", "upostag", "xpostag", "lemma", "feats"]
+_TARGETS = ["deprel", "feats", "head", "lemma", "upostag", "xpostag", "semrel", "sent", "deps"]
+
+FLAGS = flags.FLAGS
+flags.DEFINE_enum(name="mode", default=None, enum_values=["train", "predict"],
+ help="Specify COMBO mode: train or predict")
+
+# Common flags
+flags.DEFINE_integer(name="cuda_device", default=-1,
+ help="Cuda device id (default -1 cpu)")
+flags.DEFINE_string(name="output_file", default="output.log",
+ help="Predictions result file.")
+
+# Training flags
+flags.DEFINE_list(name="training_data_path", default=[],
+ help="Training data path(s)")
+flags.DEFINE_alias(name="training_data", original_name="training_data_path")
+flags.DEFINE_list(name="validation_data_path", default="",
+ help="Validation data path(s)")
+flags.DEFINE_alias(name="validation_data", original_name="validation_data_path")
+flags.DEFINE_string(name="pretrained_tokens", default="",
+ help="Pretrained tokens embeddings path")
+flags.DEFINE_integer(name="embedding_dim", default=300,
+ help="Embeddings dim")
+flags.DEFINE_integer(name="num_epochs", default=400,
+ help="Epochs num")
+flags.DEFINE_integer(name="word_batch_size", default=2500,
+ help="Minimum words in batch")
+flags.DEFINE_string(name="pretrained_transformer_name", default="",
+ help="Pretrained transformer model name (see transformers from HuggingFace library for list of "
+ "available models) for transformers based embeddings.")
+flags.DEFINE_list(name="features", default=["token", "char"],
+ help=f"Features used to train model (required 'token' and 'char'). Possible values: {_FEATURES}.")
+flags.DEFINE_list(name="targets", default=["deprel", "feats", "head", "lemma", "upostag", "xpostag"],
+ help=f"Targets of the model (required `deprel` and `head`). Possible values: {_TARGETS}.")
+flags.DEFINE_string(name="serialization_dir", default=None,
+ help="Model serialization directory (default - system temp dir).")
+flags.DEFINE_boolean(name="tensorboard", default=False,
+ help="When provided model will log tensorboard metrics.")
+
+# Finetune after training flags
+flags.DEFINE_list(name="finetuning_training_data_path", default="",
+ help="Training data path(s)")
+flags.DEFINE_list(name="finetuning_validation_data_path", default="",
+ help="Validation data path(s)")
+flags.DEFINE_string(name="config_path", default=str(pathlib.Path(__file__).parent / "config.template.jsonnet"),
+ help="Config file path.")
+
+# Test after training flags
+flags.DEFINE_string(name="test_path", default=None,
+ help="Test path file.")
+
+# Experimental
+flags.DEFINE_boolean(name="use_pure_config", default=False,
+ help="Ignore ext flags (experimental).")
+
+# Prediction flags
+flags.DEFINE_string(name="model_path", default=None,
+ help="Pretrained model path.")
+flags.DEFINE_string(name="input_file", default=None,
+ help="File to predict path")
+flags.DEFINE_boolean(name="conllu_format", default=True,
+ help="Prediction based on conllu format (instead of raw text).")
+flags.DEFINE_integer(name="batch_size", default=1,
+ help="Prediction batch size.")
+flags.DEFINE_boolean(name="silent", default=True,
+ help="Silent prediction to file (without printing to console).")
+flags.DEFINE_enum(name="predictor_name", default="combo-spacy",
+ enum_values=["combo", "combo-spacy"],
+ help="Use predictor with whitespace or spacy tokenizer.")
+
+
+def run(_):
+ pass
+
+
+def _get_predictor() -> Predictor:
+ # Check for GPU
+ # allen_checks.check_for_gpu(FLAGS.cuda_device)
+ checks.file_exists(FLAGS.model_path)
+ # load model from archive
+ # archive = models.load_archive(
+ # FLAGS.model_path,
+ # cuda_device=FLAGS.cuda_device,
+ # )
+ # return predictors.Predictor.from_archive(
+ # archive, FLAGS.predictor_name
+ # )
+ return Predictor()
+
+
+def _get_ext_vars(finetuning: bool = False) -> Dict:
+ if FLAGS.use_pure_config:
+ return {}
+ return {
+ "training_data_path": (
+ ",".join(FLAGS.training_data_path if not finetuning else FLAGS.finetuning_training_data_path)),
+ "validation_data_path": (
+ ",".join(FLAGS.validation_data_path if not finetuning else FLAGS.finetuning_validation_data_path)),
+ "pretrained_tokens": FLAGS.pretrained_tokens,
+ "pretrained_transformer_name": FLAGS.pretrained_transformer_name,
+ "features": " ".join(FLAGS.features),
+ "targets": " ".join(FLAGS.targets),
+ "type": "finetuning" if finetuning else "default",
+ "embedding_dim": str(FLAGS.embedding_dim),
+ "cuda_device": str(FLAGS.cuda_device),
+ "num_epochs": str(FLAGS.num_epochs),
+ "word_batch_size": str(FLAGS.word_batch_size),
+ "use_tensorboard": str(FLAGS.tensorboard),
+ }
+
+
+def main():
+ """Parse flags."""
+ flags.register_validator(
+ "features",
+ lambda values: all(
+ value in _FEATURES for value in values),
+ message="Flags --features contains unknown value(s)."
+ )
+ flags.register_validator(
+ "mode",
+ lambda value: value is not None,
+ message="Flag --mode must be set with either `predict` or `train` value")
+ flags.register_validator(
+ "targets",
+ lambda values: all(
+ value in _TARGETS for value in values),
+ message="Flag --targets contains unknown value(s)."
+ )
+ app.run(run)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/combo/models/__init__.py b/combo/models/__init__.py
index e69de29..9ad341a 100644
--- a/combo/models/__init__.py
+++ b/combo/models/__init__.py
@@ -0,0 +1,8 @@
+from .base import FeedForwardPredictor
+from .graph_parser import GraphDependencyRelationModel
+from .parser import DependencyRelationModel
+from .embeddings import CharacterBasedWordEmbeddings
+from .encoder import ComboEncoder
+from .lemma import LemmatizerModel
+from .model import ComboModel
+from .morpho import MorphologicalFeatures
diff --git a/combo/models/base.py b/combo/models/base.py
index 11df601..016ef85 100644
--- a/combo/models/base.py
+++ b/combo/models/base.py
@@ -4,7 +4,11 @@ import torch
import torch.nn as nn
import utils
import combo.models.combo_nn as combo_nn
-import combo.checks as checks
+import combo.utils.checks as checks
+
+
+class Model:
+ pass
class Predictor(nn.Module):
diff --git a/combo/models/embeddings.py b/combo/models/embeddings.py
index e69de29..e5ebff8 100644
--- a/combo/models/embeddings.py
+++ b/combo/models/embeddings.py
@@ -0,0 +1,24 @@
+class Embedding:
+ pass
+
+class TokenEmbedder:
+ pass
+
+class CharacterBasedWordEmbeddings(TokenEmbedder):
+ pass
+
+
+class ProjectedWordEmbedder(TokenEmbedder):
+ pass
+
+
+class PretrainedTransformerMismatchedEmbedder(TokenEmbedder):
+ pass
+
+
+class TransformersWordEmbedder(PretrainedTransformerMismatchedEmbedder):
+ pass
+
+
+class FeatsTokenEmbedder(TokenEmbedder):
+ pass
\ No newline at end of file
diff --git a/combo/models/encoder.py b/combo/models/encoder.py
new file mode 100644
index 0000000..f25f4a1
--- /dev/null
+++ b/combo/models/encoder.py
@@ -0,0 +1,10 @@
+class Encoder:
+ pass
+
+
+class StackedBidirectionalLstm(Encoder):
+ pass
+
+
+class ComboEncoder(Encoder):
+ pass
diff --git a/combo/models/graph_parser.py b/combo/models/graph_parser.py
new file mode 100644
index 0000000..82eefde
--- /dev/null
+++ b/combo/models/graph_parser.py
@@ -0,0 +1,9 @@
+from combo.models.base import Predictor
+
+
+class GraphHeadPredictionModel(Predictor):
+ pass
+
+
+class GraphDependencyRelationModel(Predictor):
+ pass
diff --git a/combo/models/lemma.py b/combo/models/lemma.py
new file mode 100644
index 0000000..77254f6
--- /dev/null
+++ b/combo/models/lemma.py
@@ -0,0 +1,5 @@
+from combo.models.base import Predictor
+
+
+class LemmatizerModel(Predictor):
+ pass
diff --git a/combo/models/model.py b/combo/models/model.py
new file mode 100644
index 0000000..134a606
--- /dev/null
+++ b/combo/models/model.py
@@ -0,0 +1,5 @@
+from combo.models.base import Model
+
+
+class ComboModel(Model):
+ pass
\ No newline at end of file
diff --git a/combo/models/morpho.py b/combo/models/morpho.py
new file mode 100644
index 0000000..4d65686
--- /dev/null
+++ b/combo/models/morpho.py
@@ -0,0 +1,5 @@
+from combo.models.base import Predictor
+
+
+class MorphologicalFeatures(Predictor):
+ pass
diff --git a/combo/models/parser.py b/combo/models/parser.py
new file mode 100644
index 0000000..46e3766
--- /dev/null
+++ b/combo/models/parser.py
@@ -0,0 +1,9 @@
+from combo.models.base import Predictor
+
+
+class HeadPredictionModel(Predictor):
+ pass
+
+
+class DependencyRelationModel(Predictor):
+ pass
diff --git a/combo/predict.py b/combo/predict.py
new file mode 100644
index 0000000..bdf9797
--- /dev/null
+++ b/combo/predict.py
@@ -0,0 +1,15 @@
+import logging
+import os
+import sys
+from typing import List, Union, Dict, Any
+
+from combo import data
+from combo.data import sentence2conllu, tokens2conllu, conllu2sentence
+from combo.models.base import Predictor
+from combo.utils import download, graph
+
+logger = logging.getLogger(__name__)
+
+
+class COMBO(Predictor):
+ pass
diff --git a/combo/training/__init__.py b/combo/training/__init__.py
new file mode 100644
index 0000000..94da4e6
--- /dev/null
+++ b/combo/training/__init__.py
@@ -0,0 +1,3 @@
+from .checkpointer import FinishingTrainingCheckpointer
+from .scheduler import Scheduler
+from .trainer import GradientDescentTrainer
diff --git a/combo/training/checkpointer.py b/combo/training/checkpointer.py
new file mode 100644
index 0000000..9823f14
--- /dev/null
+++ b/combo/training/checkpointer.py
@@ -0,0 +1,6 @@
+class Checkpointer:
+ pass
+
+
+class FinishingTrainingCheckpointer:
+ pass
diff --git a/combo/training/scheduler.py b/combo/training/scheduler.py
new file mode 100644
index 0000000..eff71b9
--- /dev/null
+++ b/combo/training/scheduler.py
@@ -0,0 +1,2 @@
+class Scheduler:
+ pass
diff --git a/combo/training/tensorboard_writer.py b/combo/training/tensorboard_writer.py
new file mode 100644
index 0000000..f56966c
--- /dev/null
+++ b/combo/training/tensorboard_writer.py
@@ -0,0 +1,2 @@
+class NullTensorboardWriter:
+ pass
\ No newline at end of file
diff --git a/combo/training/trainer.py b/combo/training/trainer.py
new file mode 100644
index 0000000..ebb8ff0
--- /dev/null
+++ b/combo/training/trainer.py
@@ -0,0 +1,13 @@
+from pytorch_lightning import Trainer
+
+
+class Callback:
+ pass
+
+
+class TransferPatienceEpochCallback:
+ pass
+
+
+class GradientDescentTrainer(Trainer):
+ pass
diff --git a/combo/utils/__init__.py b/combo/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/combo/utils/checks.py b/combo/utils/checks.py
new file mode 100644
index 0000000..ea76ac1
--- /dev/null
+++ b/combo/utils/checks.py
@@ -0,0 +1,15 @@
+import torch
+
+
+class ConfigurationError(Exception):
+ def __init__(self, message: str):
+ super().__init__()
+ self.message = message
+
+
+def file_exists(*paths):
+ pass
+
+
+def check_size_match(size_1: torch.Size, size_2: torch.Size, tensor_1_name: str, tensor_2_name: str):
+ pass
diff --git a/combo/utils/download.py b/combo/utils/download.py
new file mode 100644
index 0000000..5c7ce6f
--- /dev/null
+++ b/combo/utils/download.py
@@ -0,0 +1,78 @@
+import errno
+import logging
+import os
+
+import requests
+import tqdm
+import urllib3
+from requests import adapters, exceptions
+
+logger = logging.getLogger(__name__)
+
+DATA_TO_PATH = {
+ "enhanced" : "iwpt_2020",
+ "iwpt2021" : "iwpt_2021",
+ "ud25" : "ud_25",
+ "ud27" : "ud_27",
+ "ud29" : "ud_29"}
+_URL = "http://s3.clarin-pl.eu/dspace/combo/{data}/{model}.tar.gz"
+_HOME_DIR = os.getenv("HOME", os.curdir)
+_CACHE_DIR = os.getenv("COMBO_DIR", os.path.join(_HOME_DIR, ".combo"))
+
+
+def download_file(model_name, force=False):
+ _make_cache_dir()
+ data = model_name.split("-")[-1]
+ url = _URL.format(model=model_name, data=DATA_TO_PATH[data])
+ local_filename = url.split("/")[-1]
+ location = os.path.join(_CACHE_DIR, local_filename)
+ if os.path.exists(location) and not force:
+ logger.debug("Using cached model.")
+ return location
+ chunk_size = 1024
+ logger.info(url)
+ try:
+ with _requests_retry_session(retries=2).get(url, stream=True) as r:
+ pbar = tqdm.tqdm(unit="B", total=int(r.headers.get("content-length")),
+ unit_divisor=chunk_size, unit_scale=True)
+ with open(location, "wb") as f:
+ with pbar:
+ for chunk in r.iter_content(chunk_size):
+ if chunk:
+ f.write(chunk)
+ pbar.update(len(chunk))
+ except exceptions.RetryError:
+ raise ConnectionError(f"Couldn't find or download model {model_name}.tar.gz. "
+ "Check if model name is correct or try again later!")
+
+ return location
+
+
+def _make_cache_dir():
+ try:
+ os.makedirs(_CACHE_DIR)
+ logger.info(f"Making cache dir {_CACHE_DIR}")
+ except OSError as e:
+ if e.errno != errno.EEXIST:
+ raise
+
+
+def _requests_retry_session(
+ retries=3,
+ backoff_factor=0.3,
+ status_forcelist=(404, 500, 502, 504),
+ session=None,
+):
+ """Source: https://www.peterbe.com/plog/best-practice-with-retries-with-requests"""
+ session = session or requests.Session()
+ retry = urllib3.Retry(
+ total=retries,
+ read=retries,
+ connect=retries,
+ backoff_factor=backoff_factor,
+ status_forcelist=status_forcelist,
+ )
+ adapter = adapters.HTTPAdapter(max_retries=retry)
+ session.mount("http://", adapter)
+ session.mount("https://", adapter)
+ return session
diff --git a/combo/utils/graph.py b/combo/utils/graph.py
new file mode 100644
index 0000000..f61a68e
--- /dev/null
+++ b/combo/utils/graph.py
@@ -0,0 +1,149 @@
+"""Based on https://github.com/emorynlp/iwpt-shared-task-2020."""
+
+import numpy as np
+
+_ACL_REL_CL = "acl:relcl"
+
+
+def graph_and_tree_merge(tree_arc_scores,
+ tree_rel_scores,
+ graph_arc_scores,
+ graph_rel_scores,
+ label2idx,
+ idx2label,
+ graph_label2idx,
+ graph_idx2label,
+ tokens):
+ graph_arc_scores = np.copy(graph_arc_scores)
+ # Exclude self-loops, in-place operation.
+ np.fill_diagonal(graph_arc_scores, 0)
+ # Connection to root will be handled by tree.
+ graph_arc_scores[:, 0] = False
+ # The same with labels.
+ root_idx = graph_label2idx["root"]
+ graph_rel_scores[:, :, root_idx] = -float('inf')
+ graph_rel_pred = graph_rel_scores.argmax(-1)
+
+ # Add tree edges to graph
+ tree_heads = [0] + tree_arc_scores
+ graph = [[] for _ in range(len(tree_heads))]
+ labeled_graph = [[] for _ in range(len(tree_heads))]
+ for d, h in enumerate(tree_heads):
+ if not d:
+ continue
+ label = idx2label[tree_rel_scores[d - 1]]
+ # graph_label = graph_idx2label[graph_rel_pred[d - 1][h - 1]]
+ # if ">" in graph_label and label in graph_label:
+ # print("Using graph label instead of tree.")
+ # label = graph_label
+ if label != _ACL_REL_CL:
+ graph[h].append(d)
+ labeled_graph[h].append((d, label))
+
+ # Debug only
+ # Extract graph edges
+ graph_edges = np.argwhere(graph_arc_scores)
+
+ # Add graph edges which aren't creating a cycle
+ for (d, h) in graph_edges:
+ if not d or not h or d in graph[h]:
+ continue
+ try:
+ path = next(_dfs(graph, d, h))
+ except StopIteration:
+ # There is not path from d to h
+ label = graph_idx2label[graph_rel_pred[d][h]]
+ if label != _ACL_REL_CL:
+ graph[h].append(d)
+ labeled_graph[h].append((d, label))
+
+ # Add 'acl:relcl' without checking for cycles.
+ for d, h in enumerate(tree_heads):
+ if not d:
+ continue
+ label = idx2label[tree_rel_scores[d - 1]]
+ if label == _ACL_REL_CL:
+ graph[h].append(d)
+ labeled_graph[h].append((d, label))
+
+ assert len(labeled_graph[0]) == 1
+ d = graph[0][0]
+ graph[d].append(0)
+ labeled_graph[d].append((0, "root"))
+
+ parse_graph = [[] for _ in range(len(tree_heads))]
+ for h in range(len(tree_heads)):
+ for d, label in labeled_graph[h]:
+ parse_graph[d].append((h, label))
+ parse_graph[d] = sorted(parse_graph[d])
+
+ for i, g in enumerate(parse_graph):
+ heads = np.array([x[0] for x in g])
+ rels = np.array([x[1] for x in g])
+ indices = rels.argsort()
+ heads = heads[indices].tolist()
+ rels = rels[indices].tolist()
+ deps = '|'.join(f'{h}:{r}' for h, r in zip(heads, rels))
+ tokens[i - 1]["deps"] = deps
+ return
+
+
+def _dfs(graph, start, end):
+ fringe = [(start, [])]
+ while fringe:
+ state, path = fringe.pop()
+ if path and state == end:
+ yield path
+ continue
+ for next_state in graph[state]:
+ if next_state in path:
+ continue
+ fringe.append((next_state, path + [next_state]))
+
+
+def restore_collapse_edges(tree_tokens):
+ # https://gist.github.com/hankcs/776e7d95c19e5ff5da8469fe4e9ab050
+ empty_tokens = []
+ for token in tree_tokens:
+ deps = token["deps"].split("|")
+ for i, d in enumerate(deps):
+ if ">" in d:
+ # {head}:{empty_node_relation}>{current_node_relation}
+ # should map to
+ # For new, empty node:
+ # {head}:{empty_node_relation}
+ # For current node:
+ # {new_empty_node_id}:{current_node_relation}
+ # TODO consider where to put new_empty_node_id (currently at the end)
+ head, relation = d.split(':', 1)
+ ehead = f"{len(tree_tokens)}.{len(empty_tokens) + 1}"
+ empty_node_relation, current_node_relation = relation.split(">", 1)
+ # Edge case, double >
+ if ">" in current_node_relation:
+ second_empty_node_relation, current_node_relation = current_node_relation.split(">")
+ deps[i] = f"{ehead}:{current_node_relation}"
+ second_ehead = f"{len(tree_tokens)}.{len(empty_tokens) + 2}"
+ empty_tokens.append(
+ {
+ "id": ehead,
+ "deps": f"{second_ehead}:{empty_node_relation}"
+ }
+ )
+ empty_tokens.append(
+ {
+ "id": second_ehead,
+ "deps": f"{head}:{second_empty_node_relation}"
+ }
+ )
+
+ else:
+ deps[i] = f"{ehead}:{current_node_relation}"
+ empty_tokens.append(
+ {
+ "id": ehead,
+ "deps": f"{head}:{empty_node_relation}"
+ }
+ )
+ deps = sorted([d.split(":", 1) for d in deps], key=lambda x: float(x[0]))
+ token["deps"] = "|".join([f"{k}:{v}" for k, v in deps])
+ return empty_tokens
diff --git a/combo/utils/metrics.py b/combo/utils/metrics.py
new file mode 100644
index 0000000..9181040
--- /dev/null
+++ b/combo/utils/metrics.py
@@ -0,0 +1,17 @@
+class Metric:
+ pass
+
+class LemmaAccuracy(Metric):
+ pass
+
+
+class SequenceBoolAccuracy(Metric):
+ pass
+
+
+class AttachmentScores(Metric):
+ pass
+
+
+class SemanticMetrics(Metric):
+ pass
diff --git a/requirements.txt b/requirements.txt
index 61f0590..718d417 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,11 @@
+absl-py~=1.4.0
conllu~=4.4.1
dependency-injector~=4.41.0
overrides~=7.3.1
torch~=1.13.1
torchtext~=0.14.1
numpy~=1.24.1
-pytorch-lightning~=1.9.0
\ No newline at end of file
+pytorch-lightning~=1.9.0
+requests~=2.28.2
+tqdm~=4.64.1
+urllib3~=1.26.14
\ No newline at end of file
--
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