nlstruct 0.0.2

Main features

Pandas-based preprocessing

Most of the input or infered data can be expressed as a DataFrame of features, ids and span indices.

This library therefore takes advantage of pandas advanced frame indexing and combining features to make the preprocessing fast and explicit.

Easy nested/relational batching

In structuring problems (and for text data all the more), features can be highly relational.

This library introduces a flexible, yet performant batching structure that allows to switch between numpy, scipy and torch matrices and easily split relational data.

Caching

Every procedure can be easily cached using and explicit, flexible and performant caching mecanism. Smart parameter hashing functions have been written to handle numpy, pandas and torch (cuda/cpu) data structures and models seamlessly, and return unique hashes across multiple machines.

This caching mecanism is useful for checkpointing models, restarting trainings from a given epoch, and instantly preprocessing often used data. Log saving and replay during cache loading is also possible.

Other features

• relative shareable paths
• split and transform texts, record the transformations and apply them to spans or reverse them on predictions
• "many" dataloaders to facilitate access to nlp datasets and improve reproducibility
• training helpers to seamlessly restart trainings from the last checkpoint if any
• random seed helpers to ensure reproducibility (handles builtin, numpy and torch random functions)
• colored pretty tables to monitor training
• multiple tokenizers (spacy, transformers, regex)
• brat/conll exporters
• linear tagging CRFs that automatically handle mention spans <-> token tags conversion

Example

The following shows an example of a custom preprocessing of the NCBI dataset.

We split documents into sentences, apply substitutions to the text and transform mentions spans accordingly. Finally, we create a batching structure to iterate through documents and automatically query relevant sentences, tokens and mentions.

>>> from nlstruct.dataloaders import load_ncbi_disease
>>> from nlstruct.utils import normalize_vocabularies, encode_ids, df_to_csr, assign_sorted_id
>>> from nlstruct.text import huggingface_tokenize, split_into_spans, regex_sentencize, apply_substitutions, apply_deltas, partition_spans
>>> from nlstruct.collections import Batcher
>>> from transformers import AutoTokenizer

>>> ncbi = load_ncbi_disease()
>>> docs, mentions, fragments = ncbi[["docs", "mentions", "fragments"]]
>>> mentions = mentions.merge(fragments)
>>> print(ncbi)
Dataset(
  (docs):       792 * ('doc_id', 'text', 'split')
  (mentions):  6881 * ('doc_id', 'mention_id', 'category')
  (labels):    7059 * ('label_id', 'doc_id', 'mention_id', 'label')
  (fragments): 6881 * ('doc_id', 'mention_id', 'begin', 'end', 'fragment_id')
)

>>> sentences = regex_sentencize(docs, reg_split='((?<=\.)[\n ](?:[A-Z]))')
>>> [mentions] = partition_spans([mentions], sentences, overlap_policy=False)[0]
>>> print(sentences.head(5))
   sentence_idx  begin  end                           text    doc_id  split sentence_id
0             0      0   77  A common human skin tumour...  10192393  train         0/0
1             1     78  141  WNT signalling orchestrate...  10192393  train         0/1
2             2    142  312  In response to this stimul...  10192393  train         0/2
3             3    313  477  One of the target genes fo...  10192393  train         0/3
4             4    478  742  Most colon cancers arise f...  10192393  train         0/4
>>> print(mentions.head(5))
     doc_id sentence_id  mention_id fragment_id         category  begin  end
0  10192393         0/0  10192393-0  10192393-0     DiseaseClass     15   26
1  10192393         0/3  10192393-1  10192393-1     DiseaseClass    130  136
2  10192393         0/4  10192393-2  10192393-2     DiseaseClass      5   18
3  10192393         0/4  10192393-3  10192393-3  SpecificDisease     61   87
4  10192393         0/4  10192393-4  10192393-4  SpecificDisease     89   92

>>> # Get substitutions `deltas` to shift train mentions and restored true char positions on predictions
>>> sentences, deltas = apply_substitutions(sentences, [r"sk(.)n"], [r"sk\1\1\1\1\1\1n"], doc_cols=("doc_id", "sentence_id"), apply_unidecode=True)
>>> mentions = apply_deltas(mentions, deltas, on="sentence_id")
>>> print(sentences.head(5))
                            text  sentence_idx    doc_id  split sentence_id
0  A common human skiiiiiin t...             0  10192393  train         0/0
1  WNT signalling orchestrate...             1  10192393  train         0/1
2  In response to this stimul...             2  10192393  train         0/2
3  One of the target genes fo...             3  10192393  train         0/3
4  Most colon cancers arise f...             4  10192393  train         0/4
>>> print(mentions.head(5))
     doc_id sentence_id  mention_id fragment_id         category  begin    end
0  10192393         0/0  10192393-0  10192393-0     DiseaseClass   15.0   31.0  <-- notice that the end has moved due to the substitution
1  10192393         0/3  10192393-1  10192393-1     DiseaseClass  130.0  136.0
2  10192393         0/4  10192393-2  10192393-2     DiseaseClass    5.0   18.0
3  10192393         0/4  10192393-3  10192393-3  SpecificDisease   61.0   87.0
4  10192393         0/4  10192393-4  10192393-4  SpecificDisease   89.0   92.0

>>> tokens = huggingface_tokenize(sentences, AutoTokenizer.from_pretrained('camembert-base'))
>>> # Express mentions as token spans instead of char spans
>>> mentions = split_into_spans(mentions, tokens, pos_col="token_idx")
>>> mentions = assign_sorted_id(mentions, "mention_idx", groupby=["doc_id", "sentence_id"], sort_on="begin")
>>> print(tokens.head(5))
   id  token_id  token_idx  token  begin  end  sentence_idx    doc_id  split sentence_id
0   0         0          0    <s>      0    0             0  10192393  train         0/0
1   0         1          1     ▁A      0    1             0  10192393  train         0/0
2   0         2          2  ▁comm      2    6             0  10192393  train         0/0
3   0         3          3     on      6    8             0  10192393  train         0/0
4   0         4          4      ▁      9    9             0  10192393  train         0/0
>>> print(mentions.head(5))
     doc_id sentence_id  mention_id fragment_id         category  begin  end  mention_idx
0  10094559       234/1  10094559-1  10094559-1  SpecificDisease      1    7            0
1   3258663       548/1   3258663-2   3258663-2  SpecificDisease      1   10            0
2  10633128       465/1  10633128-1  10633128-1  SpecificDisease      1    7            0
3   8252631       268/7  8252631-11  8252631-11         Modifier      1    4            0
4   7437512       417/0   7437512-0   7437512-0  SpecificDisease      1    9            0

>>> # Encode object / strings etc that is not an id as a pandas categories
>>> [sentences, tokens, mentions], vocabularies = normalize_vocabularies([sentences, tokens, mentions], train_vocabularies={"text": False})

>>> # Encode doc/sentence/mention ids as integers
>>> unique_mention_ids = encode_ids([mentions], ("doc_id", "mention_id"), inplace=True)
>>> unique_sentence_ids = encode_ids([sentences, mentions, tokens], ("doc_id", "sentence_id"), inplace=True)
>>> unique_doc_ids = encode_ids([docs, sentences, mentions, tokens], "doc_id", inplace=True)

>>> # Create the batcher collection
>>> batcher = Batcher({
>>>     "doc": {
>>>         "doc_id": docs["doc_id"],
>>>         "sentence_id": df_to_csr(sentences["doc_id"], sentences["sentence_idx"], sentences["sentence_id"]),
>>>         "sentence_mask": df_to_csr(sentences["doc_id"], sentences["sentence_idx"]),
>>>     },
>>>     "sentence": {
>>>         "sentence_id": sentences["sentence_id"],
>>>         "token": df_to_csr(tokens["sentence_id"], tokens["token_idx"], tokens["token"].cat.codes),
>>>         "token_mask": df_to_csr(tokens["sentence_id"], tokens["token_idx"]),
>>>         "mention_id": df_to_csr(mentions["sentence_id"], mentions["mention_idx"], mentions["mention_id"]),
>>>         "mention_mask": df_to_csr(mentions["sentence_id"], mentions["mention_idx"]),
>>>     },
>>>     "mention": {
>>>         "mention_id": mentions["mention_id"],
>>>         "begin": mentions["begin"],
>>>         "end": mentions["end"],
>>>         "category": mentions["category"].cat.codes,
>>>     },
>>> }, masks={"sentence": {"mention_id": "mention_mask", "token": "token_mask"}, "doc": {"sentence_id": "sentence_mask"}})
>>> print(batcher)
Batcher(
  [doc]:
    (doc_id): ndarray[int64](792,)
    (sentence_id): csr_matrix[int64](792, 44)
    (sentence_mask): csr_matrix[bool](792, 44)
  [sentence]:
    (sentence_id): ndarray[int64](6957,)
    (token): csr_matrix[int16](6957, 211)
    (token_mask): csr_matrix[bool](6957, 211)
    (mention_id): csr_matrix[int64](6957, 13)
    (mention_mask): csr_matrix[bool](6957, 13)
  [mention]:
    (mention_id): ndarray[int64](6881,)
    (begin): ndarray[int64](6881,)
    (end): ndarray[int64](6881,)
    (category): ndarray[int8](6881,)
)

>>> # Query some documents and convert them to torch
>>> batch = batcher["doc"][[3,4,5]].densify(torch.device('cpu'))
>>> print(batch)
Batcher(
  [doc]:
    (doc_id): tensor[torch.int64](3,)
    (sentence_id): tensor[torch.int64](3, 9)
    (sentence_mask): tensor[torch.bool](3, 9)
    (@sentence_id): tensor[torch.int64](3, 9) <-- indices relative to the batch have been created
    (@sentence_mask): tensor[torch.bool](3, 9)
  [sentence]:
    (sentence_id): tensor[torch.int64](22,)
    (token): tensor[torch.int64](22, 74)
    (token_mask): tensor[torch.bool](22, 74) <-- token tensor has been resized to remove excess pad tokens
    (mention_id): tensor[torch.int64](22, 3)
    (mention_mask): tensor[torch.bool](22, 3)
    (@mention_id): tensor[torch.int64](22, 3)
    (@mention_mask): tensor[torch.bool](22, 3)
  [mention]:
    (mention_id): tensor[torch.int64](22,)
    (begin): tensor[torch.int64](22,)
    (end): tensor[torch.int64](22,)
    (category): tensor[torch.int64](22,)
)

>>> # Easily access tensors in the batch
>>> print(batch["sentence", "token"].shape)
torch.Size([22, 74])

Install

This project is still under development and subject to changes.

pip install nlstruct