From 16988605fe3645fc8caef5facc9ae7afbc0acb3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Maja=20Jab=C5=82o=C5=84ska?= <majajjablonska@gmail.com>
Date: Sun, 5 Mar 2023 20:07:49 +0100
Subject: [PATCH] First commit
---
.idea/.gitignore | 8 +
.idea/combolightning.iml | 8 +
.idea/inspectionProfiles/Project_Default.xml | 32 ++
.../inspectionProfiles/profiles_settings.xml | 6 +
.idea/misc.xml | 4 +
.idea/modules.xml | 8 +
combo/__init__.py | 0
combo/checks.py | 4 +
combo/config/__init__.py | 0
combo/data/__init__.py | 3 +
combo/data/api.py | 98 ++++++
combo/data/dataset.py | 317 ++++++++++++++++++
combo/data/fields/__init__.py | 1 +
.../data/fields/sequence_multilabel_field.py | 135 ++++++++
combo/data/samplers/__init__.py | 1 +
combo/data/samplers/samplers.py | 54 +++
combo/data/token_indexers/__init__.py | 3 +
...etrained_transformer_mismatched_indexer.py | 117 +++++++
.../token_characters_indexer.py | 62 ++++
.../token_indexers/token_features_indexer.py | 75 +++++
combo/data/vocabulary.py | 98 ++++++
combo/models/__init__.py | 0
combo/models/base.py | 215 ++++++++++++
combo/models/combo_nn.py | 7 +
combo/models/embeddings.py | 0
combo/models/utils.py | 7 +
docs/Configuration.md | 4 +
example.conllu | 13 +
main.py | 16 +
requirements.txt | 7 +
30 files changed, 1303 insertions(+)
create mode 100644 .idea/.gitignore
create mode 100644 .idea/combolightning.iml
create mode 100644 .idea/inspectionProfiles/Project_Default.xml
create mode 100644 .idea/inspectionProfiles/profiles_settings.xml
create mode 100644 .idea/misc.xml
create mode 100644 .idea/modules.xml
create mode 100644 combo/__init__.py
create mode 100644 combo/checks.py
create mode 100644 combo/config/__init__.py
create mode 100644 combo/data/__init__.py
create mode 100644 combo/data/api.py
create mode 100644 combo/data/dataset.py
create mode 100644 combo/data/fields/__init__.py
create mode 100644 combo/data/fields/sequence_multilabel_field.py
create mode 100644 combo/data/samplers/__init__.py
create mode 100644 combo/data/samplers/samplers.py
create mode 100644 combo/data/token_indexers/__init__.py
create mode 100644 combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py
create mode 100644 combo/data/token_indexers/token_characters_indexer.py
create mode 100644 combo/data/token_indexers/token_features_indexer.py
create mode 100644 combo/data/vocabulary.py
create mode 100644 combo/models/__init__.py
create mode 100644 combo/models/base.py
create mode 100644 combo/models/combo_nn.py
create mode 100644 combo/models/embeddings.py
create mode 100644 combo/models/utils.py
create mode 100644 docs/Configuration.md
create mode 100644 example.conllu
create mode 100644 main.py
create mode 100644 requirements.txt
diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 0000000..73f69e0
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,8 @@
+# Default ignored files
+/shelf/
+/workspace.xml
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml
+# Editor-based HTTP Client requests
+/httpRequests/
diff --git a/.idea/combolightning.iml b/.idea/combolightning.iml
new file mode 100644
index 0000000..4154233
--- /dev/null
+++ b/.idea/combolightning.iml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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="sourceFolder" forTests="false" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 0000000..11a85e3
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,32 @@
+<component name="InspectionProjectProfileManager">
+ <profile version="1.0">
+ <option name="myName" value="Project Default" />
+ <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+ <option name="ignoredPackages">
+ <value>
+ <list size="19">
+ <item index="0" class="java.lang.String" itemvalue="Click" />
+ <item index="1" class="java.lang.String" itemvalue="numpy" />
+ <item index="2" class="java.lang.String" itemvalue="importlib-metadata" />
+ <item index="3" class="java.lang.String" itemvalue="absl-py" />
+ <item index="4" class="java.lang.String" itemvalue="scipy" />
+ <item index="5" class="java.lang.String" itemvalue="transformers" />
+ <item index="6" class="java.lang.String" itemvalue="pytest" />
+ <item index="7" class="java.lang.String" itemvalue="scikit-learn" />
+ <item index="8" class="java.lang.String" itemvalue="allennlp" />
+ <item index="9" class="java.lang.String" itemvalue="torch" />
+ <item index="10" class="java.lang.String" itemvalue="requests" />
+ <item index="11" class="java.lang.String" itemvalue="conllu" />
+ <item index="12" class="java.lang.String" itemvalue="tqdm" />
+ <item index="13" class="java.lang.String" itemvalue="jsonnet" />
+ <item index="14" class="java.lang.String" itemvalue="filelock" />
+ <item index="15" class="java.lang.String" itemvalue="pylint" />
+ <item index="16" class="java.lang.String" itemvalue="urllib3" />
+ <item index="17" class="java.lang.String" itemvalue="pylint-quotes" />
+ <item index="18" class="java.lang.String" itemvalue="jsonnet-binary" />
+ </list>
+ </value>
+ </option>
+ </inspection_tool>
+ </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 0000000..105ce2d
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+ <settings>
+ <option name="USE_PROJECT_PROFILE" value="false" />
+ <version value="1.0" />
+ </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..fcbd09d
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +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" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..89bf708
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectModuleManager">
+ <modules>
+ <module fileurl="file://$PROJECT_DIR$/.idea/combolightning.iml" filepath="$PROJECT_DIR$/.idea/combolightning.iml" />
+ </modules>
+ </component>
+</project>
\ No newline at end of file
diff --git a/combo/__init__.py b/combo/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/combo/checks.py b/combo/checks.py
new file mode 100644
index 0000000..7736e96
--- /dev/null
+++ b/combo/checks.py
@@ -0,0 +1,4 @@
+class ConfigurationError(Exception):
+ def __init__(self, message: str):
+ super().__init__()
+ self.message = message
diff --git a/combo/config/__init__.py b/combo/config/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/combo/data/__init__.py b/combo/data/__init__.py
new file mode 100644
index 0000000..91426e3
--- /dev/null
+++ b/combo/data/__init__.py
@@ -0,0 +1,3 @@
+from .samplers import TokenCountBatchSampler
+from .token_indexers import *
+from .api import *
diff --git a/combo/data/api.py b/combo/data/api.py
new file mode 100644
index 0000000..308e9e4
--- /dev/null
+++ b/combo/data/api.py
@@ -0,0 +1,98 @@
+import collections
+import dataclasses
+import json
+from dataclasses import dataclass, field
+from typing import Optional, List, Dict, Any, Union, Tuple
+
+import conllu
+from overrides import overrides
+
+
+@dataclass
+class Token:
+ id: Optional[Union[int, Tuple]] = None
+ token: Optional[str] = None
+ lemma: Optional[str] = None
+ upostag: Optional[str] = None
+ xpostag: Optional[str] = None
+ feats: Optional[str] = None
+ head: Optional[int] = None
+ deprel: Optional[str] = None
+ deps: Optional[str] = None
+ misc: Optional[str] = None
+ semrel: Optional[str] = None
+ embeddings: Dict[str, List[float]] = field(default_factory=list, repr=False)
+
+
+@dataclass
+class Sentence:
+ tokens: List[Token] = field(default_factory=list)
+ sentence_embedding: List[float] = field(default_factory=list, repr=False)
+ metadata: Dict[str, Any] = field(default_factory=collections.OrderedDict)
+
+ def to_json(self):
+ return json.dumps({
+ "tokens": [dataclasses.asdict(t) for t in self.tokens],
+ "sentence_embedding": self.sentence_embedding,
+ "metadata": self.metadata,
+ })
+
+ def __len__(self):
+ return len(self.tokens)
+
+
+class _TokenList(conllu.TokenList):
+
+ @overrides
+ def __repr__(self):
+ return 'TokenList<' + ', '.join(token['token'] for token in self) + '>'
+
+
+def sentence2conllu(sentence: Sentence, keep_semrel: bool = True) -> conllu.TokenList:
+ tokens = []
+ for token in sentence.tokens:
+ token_dict = collections.OrderedDict(dataclasses.asdict(token))
+ # Remove semrel to have default conllu format.
+ if not keep_semrel:
+ del token_dict["semrel"]
+ del token_dict["embeddings"]
+ tokens.append(token_dict)
+ # Range tokens must be tuple not list, this is conllu library requirement
+ for t in tokens:
+ if type(t["id"]) == list:
+ t["id"] = tuple(t["id"])
+ if t["deps"]:
+ for dep in t["deps"]:
+ if len(dep) > 1 and type(dep[1]) == list:
+ dep[1] = tuple(dep[1])
+ return _TokenList(tokens=tokens,
+ metadata=sentence.metadata)
+
+
+def tokens2conllu(tokens: List[str]) -> conllu.TokenList:
+ return _TokenList(
+ [collections.OrderedDict({"id": idx, "token": token}) for
+ idx, token
+ in enumerate(tokens, start=1)],
+ metadata=collections.OrderedDict()
+ )
+
+
+def conllu2sentence(conllu_sentence: conllu.TokenList,
+ sentence_embedding=None, embeddings=None) -> Sentence:
+ if embeddings is None:
+ embeddings = {}
+ if sentence_embedding is None:
+ sentence_embedding = []
+ tokens = []
+ for token in conllu_sentence.tokens:
+ tokens.append(
+ Token(
+ **token, embeddings=embeddings[token["id"]]
+ )
+ )
+ return Sentence(
+ tokens=tokens,
+ sentence_embedding=sentence_embedding,
+ metadata=conllu_sentence.metadata
+ )
diff --git a/combo/data/dataset.py b/combo/data/dataset.py
new file mode 100644
index 0000000..0c34d3f
--- /dev/null
+++ b/combo/data/dataset.py
@@ -0,0 +1,317 @@
+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]
+
+ 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_
diff --git a/combo/data/fields/__init__.py b/combo/data/fields/__init__.py
new file mode 100644
index 0000000..4f8d3a2
--- /dev/null
+++ b/combo/data/fields/__init__.py
@@ -0,0 +1 @@
+from .sequence_multilabel_field import SequenceMultiLabelField
diff --git a/combo/data/fields/sequence_multilabel_field.py b/combo/data/fields/sequence_multilabel_field.py
new file mode 100644
index 0000000..c31f78e
--- /dev/null
+++ b/combo/data/fields/sequence_multilabel_field.py
@@ -0,0 +1,135 @@
+"""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
+
+logger = logging.getLogger(__name__)
+
+
+class SequenceMultiLabelField(data.Field[torch.Tensor]):
+ """
+ A `SequenceMultiLabelField` is an extension of the :class:`MultiLabelField` that allows for multiple labels
+ while keeping sequence dimension.
+
+ To allow config to different circumstances, class takes few delegates functions.
+
+ # Parameters
+
+ multi_labels : `List[List[str]]`
+ multi_label_indexer : `Callable[[data.Vocabulary], Callable[[List[str]], List[int]]]`
+ Nested callable which based on vocab and sequence length maps values of the fields in the sequence
+ from strings to indexed, int values.
+ as_tensor: `Callable[["SequenceMultiLabelField"], Callable[[Dict[str, int]], torch.Tensor]]`
+ Nested callable which based on the field itself, maps indexed data to a tensor.
+ sequence_field : `SequenceField`
+ A field containing the sequence that this `SequenceMultiLabelField` is labeling. Most often, this is a
+ `TextField`, for tagging individual tokens in a sentence.
+ label_namespace : `str`, optional (default="labels")
+ The namespace to use for converting label strings into integers. We map label strings to
+ integers for you (e.g., "entailment" and "contradiction" get converted to 0, 1, ...),
+ and this namespace tells the `Vocabulary` object which mapping from strings to integers
+ to use (so "entailment" as a label doesn't get the same integer id as "entailment" as a
+ word). If you have multiple different label fields in your data, you should make sure you
+ use different namespaces for each one, always using the suffix "labels" (e.g.,
+ "passage_labels" and "question_labels").
+ """
+ _already_warned_namespaces: Set[str] = set()
+
+ def __init__(
+ self,
+ multi_labels: List[List[str]],
+ multi_label_indexer: Callable[[data.Vocabulary], Callable[[List[str], int], List[int]]],
+ as_tensor: Callable[["SequenceMultiLabelField"], Callable[[Dict[str, int]], torch.Tensor]],
+ sequence_field: fields.SequenceField,
+ label_namespace: str = "labels",
+ ) -> None:
+ self.multi_labels = multi_labels
+ self.sequence_field = sequence_field
+ self.multi_label_indexer = multi_label_indexer
+ self._label_namespace = label_namespace
+ self._indexed_multi_labels = None
+ self._maybe_warn_for_namespace(label_namespace)
+ self.as_tensor_wrapper = as_tensor(self)
+ if len(multi_labels) != sequence_field.sequence_length():
+ raise checks.ConfigurationError(
+ "Label length and sequence length "
+ "don't match: %d and %d" % (len(multi_labels), sequence_field.sequence_length())
+ )
+
+ if not all([isinstance(x, str) for multi_label in multi_labels for x in multi_label]):
+ raise checks.ConfigurationError(
+ "SequenceMultiLabelField must be passed either all "
+ "strings or all ints. Found labels {} with "
+ "types: {}.".format(multi_labels, [type(x) for multi_label in multi_labels for x in multi_label])
+ )
+
+ def _maybe_warn_for_namespace(self, label_namespace: str) -> None:
+ if not (self._label_namespace.endswith("labels") or self._label_namespace.endswith("tags")):
+ if label_namespace not in self._already_warned_namespaces:
+ logger.warning(
+ "Your label namespace was '%s'. We recommend you use a namespace "
+ "ending with 'labels' or 'tags', so we don't add UNK and PAD tokens by "
+ "default to your vocabulary. See documentation for "
+ "`non_padded_namespaces` parameter in Vocabulary.",
+ self._label_namespace,
+ )
+ self._already_warned_namespaces.add(label_namespace)
+
+ # Sequence methods
+ def __iter__(self) -> Iterator[Union[List[str], int]]:
+ return iter(self.multi_labels)
+
+ def __getitem__(self, idx: int) -> Union[List[str], int]:
+ return self.multi_labels[idx]
+
+ def __len__(self) -> int:
+ return len(self.multi_labels)
+
+ @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
+
+ @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
+
+ @overrides
+ def get_padding_lengths(self) -> Dict[str, int]:
+ return {"num_tokens": self.sequence_field.sequence_length()}
+
+ @overrides
+ def as_tensor(self, padding_lengths: Dict[str, int]) -> torch.Tensor:
+ return self.as_tensor_wrapper(padding_lengths)
+
+ @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
+
+ 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}'."
+ )
diff --git a/combo/data/samplers/__init__.py b/combo/data/samplers/__init__.py
new file mode 100644
index 0000000..ab003fe
--- /dev/null
+++ b/combo/data/samplers/__init__.py
@@ -0,0 +1 @@
+from .samplers import TokenCountBatchSampler
diff --git a/combo/data/samplers/samplers.py b/combo/data/samplers/samplers.py
new file mode 100644
index 0000000..5db74d9
--- /dev/null
+++ b/combo/data/samplers/samplers.py
@@ -0,0 +1,54 @@
+from typing import List
+
+import numpy as np
+
+from allennlp import data as allen_data
+
+
+@allen_data.BatchSampler.register("token_count")
+class TokenCountBatchSampler(allen_data.BatchSampler):
+
+ def __init__(self, dataset, word_batch_size: int = 2500, shuffle_dataset: bool = True):
+ self._index = 0
+ self.shuffle_dataset = shuffle_dataset
+ self.batch_dataset = self._batchify(dataset, word_batch_size)
+ if shuffle_dataset:
+ self._shuffle()
+
+ @staticmethod
+ def _batchify(dataset, word_batch_size) -> List[List[int]]:
+ dataset = list(dataset)
+ batches = []
+ batch = []
+ words_count = 0
+ lengths = [len(instance.fields["sentence"].tokens) for instance in dataset]
+ argsorted_lengths = np.argsort(lengths)
+ for idx in argsorted_lengths:
+ words_count += lengths[idx]
+ batch.append(idx)
+ if words_count > word_batch_size:
+ batches.append(batch)
+ words_count = 0
+ batch = []
+ return batches
+
+ def __iter__(self):
+ return self
+
+ def __next__(self):
+ if self._index >= len(self.batch_dataset):
+ if self.shuffle_dataset:
+ self._index = 0
+ self._shuffle()
+ raise StopIteration()
+
+ batch = self.batch_dataset[self._index]
+ self._index += 1
+ return batch
+
+ def _shuffle(self):
+ indices = np.random.permutation(range(len(self.batch_dataset)))
+ self.batch_dataset = np.array(self.batch_dataset)[indices].tolist()
+
+ def __len__(self):
+ return len(self.batch_dataset)
diff --git a/combo/data/token_indexers/__init__.py b/combo/data/token_indexers/__init__.py
new file mode 100644
index 0000000..550a80b
--- /dev/null
+++ b/combo/data/token_indexers/__init__.py
@@ -0,0 +1,3 @@
+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/pretrained_transformer_mismatched_indexer.py b/combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py
new file mode 100644
index 0000000..fc29896
--- /dev/null
+++ b/combo/data/token_indexers/pretrained_transformer_mismatched_indexer.py
@@ -0,0 +1,117 @@
+from typing import Optional, Dict, Any, List, Tuple
+
+from allennlp import data
+from allennlp.data import token_indexers, tokenizers, IndexedTokenList, vocabulary
+from overrides import overrides
+
+
+@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
+
+ @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
diff --git a/combo/data/token_indexers/token_characters_indexer.py b/combo/data/token_indexers/token_characters_indexer.py
new file mode 100644
index 0000000..ea7a3ea
--- /dev/null
+++ b/combo/data/token_indexers/token_characters_indexer.py
@@ -0,0 +1,62 @@
+"""Custom character token indexer."""
+import itertools
+from typing import List, Dict
+
+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):
+ """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]
+ )
+ }
diff --git a/combo/data/token_indexers/token_features_indexer.py b/combo/data/token_indexers/token_features_indexer.py
new file mode 100644
index 0000000..7c59124
--- /dev/null
+++ b/combo/data/token_indexers/token_features_indexer.py
@@ -0,0 +1,75 @@
+"""Features indexer."""
+import collections
+from typing import List, Dict
+
+import torch
+from allennlp import data
+from allennlp.common import util
+from overrides import overrides
+
+
+@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
diff --git a/combo/data/vocabulary.py b/combo/data/vocabulary.py
new file mode 100644
index 0000000..d482b6c
--- /dev/null
+++ b/combo/data/vocabulary.py
@@ -0,0 +1,98 @@
+from collections import defaultdict, OrderedDict
+from typing import Dict, Union, Optional, Iterable, Callable, Any, Set
+
+from torchtext.vocab import Vocab as TorchtextVocab
+from torchtext.vocab import vocab as torchtext_vocab
+
+DEFAULT_NON_PADDED_NAMESPACES = ("*tags", "*labels")
+DEFAULT_PADDING_TOKEN = "@@PADDING@@"
+DEFAULT_OOV_TOKEN = "@@UNKNOWN@@"
+NAMESPACE_PADDING_FILE = "non_padded_namespaces.txt"
+DEFAULT_NAMESPACE = "tokens"
+
+
+def match_namespace(pattern: str, namespace: str):
+ if not isinstance(pattern, str):
+ raise ValueError("Pattern and namespace must be string types, got %s and %s." %
+ (type(pattern), type(namespace)))
+ if pattern == namespace:
+ return True
+ if len(pattern)>2 and pattern[0] == '*' and namespace.endswith(pattern[1:]):
+ return True
+ return False
+
+
+class _NamespaceDependentDefaultDict(defaultdict[str, TorchtextVocab]):
+ def __init__(self,
+ non_padded_namespaces: Iterable[str],
+ padding_token: str,
+ oov_token: str):
+ self._non_padded_namespaces = set(non_padded_namespaces)
+ self._padding_token = padding_token
+ self._oov_token = oov_token
+ super().__init__()
+
+ def __missing__(self, namespace: str):
+ # Non-padded namespace
+ if any([match_namespace(namespace, npn) for npn in self._non_padded_namespaces]):
+ value = torchtext_vocab(
+ OrderedDict([
+ (self._padding_token, 0),
+ (self._oov_token, 1)])
+ )
+ else:
+ value = torchtext_vocab(OrderedDict([]))
+ dict.__setitem__(self, namespace, value)
+ return value
+
+ def add_non_padded_namespaces(self, non_padded_namespaces: Set[str]):
+ self._non_padded_namespaces.update(non_padded_namespaces)
+
+
+class Vocabulary:
+ def __init__(self,
+ counter: Dict[str, Dict[str, int]] = None,
+ min_count: Dict[str, int] = None,
+ max_vocab_size: Union[int, Dict[str, int]] = None,
+ non_padded_namespaces: Iterable[str] = DEFAULT_NON_PADDED_NAMESPACES,
+ padding_token: Optional[str] = DEFAULT_PADDING_TOKEN,
+ oov_token: Optional[str] = DEFAULT_OOV_TOKEN):
+
+ # ordered_dict – Ordered Dictionary mapping tokens to their corresponding occurance frequencies.
+ #
+ # min_freq – The minimum frequency needed to include a token in the vocabulary.
+ #
+ # specials – Special symbols to add. The order of supplied tokens will be preserved.
+ #
+ # special_first – Indicates whether to insert symbols at the beginning or at the end.
+ self._padding_token = padding_token if padding_token is not None else DEFAULT_PADDING_TOKEN
+ self._oov_token = oov_token if oov_token is not None else DEFAULT_OOV_TOKEN
+ self._non_padded_namespaces = set(non_padded_namespaces)
+ self._vocab = _NamespaceDependentDefaultDict(self._non_padded_namespaces,
+ self._padding_token,
+ self._oov_token)
+
+ def _extend(self,
+ tokens_to_add: Dict[str, Dict[str, int]]):
+ for namespace, tokens in tokens_to_add.items():
+ for token in tokens:
+ self._vocab[namespace].append_token(token)
+
+ # def add_token_to_namespace(self, token: str, namespace: str = DEFAULT_NAMESPACE):
+ # """
+ # Add the token if not present and return the index even if token was already in the namespace.
+ #
+ # :param token: token to be added
+ # :param namespace: namespace to add the token to
+ # :return: index of the token in the namespace
+ # """
+ #
+ # if not isinstance(token, str):
+ # raise ValueError("Vocabulary tokens must be strings. Got %s with type %s" % (repr(token), type(token)))
+ #
+
+
+ @classmethod
+ def empty(cls):
+ return cls()
+
diff --git a/combo/models/__init__.py b/combo/models/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/combo/models/base.py b/combo/models/base.py
new file mode 100644
index 0000000..11df601
--- /dev/null
+++ b/combo/models/base.py
@@ -0,0 +1,215 @@
+from typing import Dict, Optional, List, Union, Tuple
+
+import torch
+import torch.nn as nn
+import utils
+import combo.models.combo_nn as combo_nn
+import combo.checks as checks
+
+
+class Predictor(nn.Module):
+ def forward(self,
+ x: Union[torch.Tensor, List[torch.Tensor]],
+ mask: Optional[torch.BoolTensor] = None,
+ labels: Optional[Union[torch.Tensor, List[torch.Tensor]]] = None,
+ sample_weights: Optional[Union[torch.Tensor, List[torch.Tensor]]] = None) -> Dict[str, torch.Tensor]:
+ raise NotImplementedError()
+
+
+class Linear(nn.Linear):
+
+ def __init__(self,
+ in_features: int,
+ out_features: int,
+ activation: Optional[combo_nn.Activation] = None,
+ dropout_rate: Optional[float] = 0.0):
+ super().__init__(in_features, out_features)
+ self.activation = activation if activation else self.identity
+ self.dropout = nn.Dropout(p=dropout_rate) if dropout_rate else self.identity
+
+ def forward(self, x: torch.FloatTensor) -> torch.FloatTensor:
+ x = super().forward(x)
+ x = self.activation(x)
+ return self.dropout(x)
+
+ def get_output_dim(self) -> int:
+ return self.out_features
+
+ @staticmethod
+ def identity(x):
+ return x
+
+
+class FeedForward(torch.nn.Module):
+ """
+ Modified copy of allennlp.modules.feedforward.FeedForward
+
+ This `Module` is a feed-forward neural network, just a sequence of `Linear` layers with
+ activation functions in between.
+
+ # Parameters
+
+ input_dim : `int`, required
+ The dimensionality of the input. We assume the input has shape `(batch_size, input_dim)`.
+ num_layers : `int`, required
+ The number of `Linear` layers to apply to the input.
+ hidden_dims : `Union[int, List[int]]`, required
+ The output dimension of each of the `Linear` layers. If this is a single `int`, we use
+ it for all `Linear` layers. If it is a `List[int]`, `len(hidden_dims)` must be
+ `num_layers`.
+ activations : `Union[Activation, List[Activation]]`, required
+ The activation function to use after each `Linear` layer. If this is a single function,
+ we use it after all `Linear` layers. If it is a `List[Activation]`,
+ `len(activations)` must be `num_layers`. Activation must have torch.nn.Module type.
+ dropout : `Union[float, List[float]]`, optional (default = `0.0`)
+ If given, we will apply this amount of dropout after each layer. Semantics of `float`
+ versus `List[float]` is the same as with other parameters.
+
+ # Examples
+
+ ```python
+ FeedForward(124, 2, [64, 32], torch.nn.ReLU(), 0.2)
+ #> FeedForward(
+ #> (_activations): ModuleList(
+ #> (0): ReLU()
+ #> (1): ReLU()
+ #> )
+ #> (_linear_layers): ModuleList(
+ #> (0): Linear(in_features=124, out_features=64, bias=True)
+ #> (1): Linear(in_features=64, out_features=32, bias=True)
+ #> )
+ #> (_dropout): ModuleList(
+ #> (0): Dropout(p=0.2, inplace=False)
+ #> (1): Dropout(p=0.2, inplace=False)
+ #> )
+ #> )
+ ```
+ """
+
+ def __init__(
+ self,
+ input_dim: int,
+ num_layers: int,
+ hidden_dims: Union[int, List[int]],
+ activations: Union[combo_nn.Activation, List[combo_nn.Activation]],
+ dropout: Union[float, List[float]] = 0.0,
+ ) -> None:
+
+ super().__init__()
+ if not isinstance(hidden_dims, list):
+ hidden_dims = [hidden_dims] * num_layers # type: ignore
+ if not isinstance(activations, list):
+ activations = [activations] * num_layers # type: ignore
+ if not isinstance(dropout, list):
+ dropout = [dropout] * num_layers # type: ignore
+ if len(hidden_dims) != num_layers:
+ raise checks.ConfigurationError(
+ "len(hidden_dims) (%d) != num_layers (%d)" % (len(hidden_dims), num_layers)
+ )
+ if len(activations) != num_layers:
+ raise checks.ConfigurationError(
+ "len(activations) (%d) != num_layers (%d)" % (len(activations), num_layers)
+ )
+ if len(dropout) != num_layers:
+ raise checks.ConfigurationError(
+ "len(dropout) (%d) != num_layers (%d)" % (len(dropout), num_layers)
+ )
+ self._activations = torch.nn.ModuleList(activations)
+ input_dims = [input_dim] + hidden_dims[:-1]
+ linear_layers = []
+ for layer_input_dim, layer_output_dim in zip(input_dims, hidden_dims):
+ linear_layers.append(torch.nn.Linear(layer_input_dim, layer_output_dim))
+ self._linear_layers = torch.nn.ModuleList(linear_layers)
+ dropout_layers = [torch.nn.Dropout(p=value) for value in dropout]
+ self._dropout = torch.nn.ModuleList(dropout_layers)
+ self._output_dim = hidden_dims[-1]
+ self.input_dim = input_dim
+
+ def get_output_dim(self):
+ return self._output_dim
+
+ def get_input_dim(self):
+ return self.input_dim
+
+ def forward(self, inputs: torch.Tensor) -> Tuple[torch.Tensor, List[torch.Tensor]]:
+
+ output = inputs
+ feature_maps = []
+ for layer, activation, dropout in zip(
+ self._linear_layers, self._activations, self._dropout
+ ):
+ feature_maps.append(output)
+ output = dropout(activation(layer(output)))
+ return output, feature_maps
+
+
+
+class FeedForwardPredictor(Predictor):
+ """Feedforward predictor. Should be used on top of Seq2Seq encoder."""
+
+ def __init__(self, feedforward_network: "FeedForward"):
+ super().__init__()
+ self.feedforward_network = feedforward_network
+
+ def forward(self,
+ x: Union[torch.Tensor, List[torch.Tensor]],
+ mask: Optional[torch.BoolTensor] = None,
+ labels: Optional[Union[torch.Tensor, List[torch.Tensor]]] = None,
+ sample_weights: Optional[Union[torch.Tensor, List[torch.Tensor]]] = None) -> Dict[str, torch.Tensor]:
+ if mask is None:
+ mask = x.new_ones(x.size()[:-1])
+
+ x, feature_maps = self.feedforward_network(x)
+ output = {
+ "prediction": x.argmax(-1),
+ "probability": x,
+ "embedding": feature_maps[-1],
+ }
+
+ if labels is not None:
+ if sample_weights is None:
+ sample_weights = labels.new_ones([mask.size(0)])
+ output["loss"] = self._loss(x, labels, mask, sample_weights)
+
+ return output
+
+ def _loss(self,
+ pred: torch.Tensor,
+ true: torch.Tensor,
+ mask: torch.BoolTensor,
+ sample_weights: torch.Tensor) -> torch.Tensor:
+ BATCH_SIZE, _, CLASSES = pred.size()
+ valid_positions = mask.sum()
+ pred = pred.reshape(-1, CLASSES)
+ true = true.reshape(-1)
+ mask = mask.reshape(-1)
+ loss = utils.masked_cross_entropy(pred, true, mask)
+ loss = loss.reshape(BATCH_SIZE, -1) * sample_weights.unsqueeze(-1)
+ return loss.sum() / valid_positions
+
+ @classmethod
+ def from_vocab(cls,
+ vocab: data.Vocabulary,
+ vocab_namespace: str,
+ input_dim: int,
+ num_layers: int,
+ hidden_dims: List[int],
+ activations: Union[combo_nn.Activation, List[combo_nn.Activation]],
+ dropout: Union[float, List[float]] = 0.0,
+ ):
+ if len(hidden_dims) + 1 != num_layers:
+ raise checks.ConfigurationError(
+ f"len(hidden_dims) ({len(hidden_dims):d}) + 1 != num_layers ({num_layers:d})"
+ )
+
+ assert vocab_namespace in vocab.get_namespaces(), \
+ f"There is not {vocab_namespace} in created vocabs, check if this field has any values to predict!"
+ hidden_dims = hidden_dims + [vocab.get_vocab_size(vocab_namespace)]
+
+ return cls(FeedForward(
+ input_dim=input_dim,
+ num_layers=num_layers,
+ hidden_dims=hidden_dims,
+ activations=activations,
+ dropout=dropout))
+
diff --git a/combo/models/combo_nn.py b/combo/models/combo_nn.py
new file mode 100644
index 0000000..2866670
--- /dev/null
+++ b/combo/models/combo_nn.py
@@ -0,0 +1,7 @@
+import torch
+import torch.nn as nn
+
+
+class Activation(nn.Module):
+ def __cal__(self, tensor: torch.Tensor) -> torch.Tensor:
+ raise NotImplementedError
diff --git a/combo/models/embeddings.py b/combo/models/embeddings.py
new file mode 100644
index 0000000..e69de29
diff --git a/combo/models/utils.py b/combo/models/utils.py
new file mode 100644
index 0000000..0a447f9
--- /dev/null
+++ b/combo/models/utils.py
@@ -0,0 +1,7 @@
+import torch
+import torch.nn.functional as F
+
+
+def masked_cross_entropy(pred: torch.Tensor, true: torch.Tensor, mask: torch.BoolTensor) -> torch.Tensor:
+ pred = pred + (mask.float().unsqueeze(-1) + 1e-45).log()
+ return F.cross_entropy(pred, true, reduction="none") * mask
diff --git a/docs/Configuration.md b/docs/Configuration.md
new file mode 100644
index 0000000..7fb14f5
--- /dev/null
+++ b/docs/Configuration.md
@@ -0,0 +1,4 @@
+# Configuration
+
+Dependency injection is used for configuration using the ```dependency_injector``` package.
+Configuration files can be in json or ini format.
\ No newline at end of file
diff --git a/example.conllu b/example.conllu
new file mode 100644
index 0000000..32e0653
--- /dev/null
+++ b/example.conllu
@@ -0,0 +1,13 @@
+# sent_id = test-s1
+# text = Easy sentence.
+1 Verylongwordwhichmustbetruncatedbythesystemto30 easy ADJ adj AdpType=Prep|Adp 2 amod _ _
+2 Sentence verylonglemmawhichmustbetruncatedbythesystemto30 NOUN nom Number=Sing 0 root _ _
+3 . . PUNCT . _ 1 punct _ _
+
+# sent_id = test-s1
+# text = Easy sentence.
+1 Verylongwordwhichmustbetruncatedbythesystemto30 easy ADJ adj AdpType=Prep|Adp 2 amod _ _
+2 Sentence verylonglemmawhichmustbetruncatedbythesystemto30 NOUN nom Number=Sing 0 root _ _
+3 . . PUNCT . _ 1 punct 2:mod _
+4 . . PUNCT . _ 1 punct 2:xmod _
+
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..5596b44
--- /dev/null
+++ b/main.py
@@ -0,0 +1,16 @@
+# This is a sample Python script.
+
+# Press Shift+F10 to execute it or replace it with your code.
+# Press Double Shift to search everywhere for classes, files, tool windows, actions, and settings.
+
+
+def print_hi(name):
+ # Use a breakpoint in the code line below to debug your script.
+ print(f'Hi, {name}') # Press Ctrl+F8 to toggle the breakpoint.
+
+
+# Press the green button in the gutter to run the script.
+if __name__ == '__main__':
+ print_hi('PyCharm')
+
+# See PyCharm help at https://www.jetbrains.com/help/pycharm/
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..61f0590
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,7 @@
+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
--
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