In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce a novel, subword approach for named entity recognition (NER) that uses byte-pair encodings (BPE) in combination with convolutional and recurrent neural networks to produce byte-level tags of entities. We present experimental results on several standard biomedical datasets, namely the BioCreative VI Bio-ID, JNLPBA, and GENETAG datasets. We demonstrate competitive performance while bypassing the specialized domain expertise needed to create biomedical text tokenization rules.
Subword models have mostly been developed in the context of multilingual datasets @cite_14 , machine translation @cite_7 , and processing for character-based languages @cite_3 . develop a model that tags sequences of bytes, though they ultimately relies on word boundaries to determine appropriate tags. use characters, phonemes, and bytes as subword features, and similarly tag entities at word-level boundaries.
@cite_14 @cite_3 @cite_7
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We describe an LSTM-based model which we call Byte-to-Span (BTS) that reads text as bytes and outputs span annotations of the form [start, length, label] where start positions, lengths, and labels are separate entries in our vocabulary. Because we operate directly on unicode bytes rather than language-specific words or characters, we can analyze text in many languages with a single model. Due to the small vocabulary size, these multilingual models are very compact, but produce results similar to or better than the state-of- the-art in Part-of-Speech tagging and Named Entity Recognition that use only the provided training datasets (no external data sources). Our models are learning "from scratch" in that they do not rely on any elements of the standard pipeline in Natural Language Processing (including tokenization), and thus can run in standalone fashion on raw text. Most existing machine translation systems operate at the level of words, relying on explicit segmentation to extract tokens. We introduce a neural machine translation (NMT) model that maps a source character sequence to a target character sequence without any segmentation. We employ a character-level convolutional network with max-pooling at the encoder to reduce the length of source representation, allowing the model to be trained at a speed comparable to subword-level models while capturing local regularities. Our character-to-character model outperforms a recently proposed baseline with a subword-level encoder on WMT'15 DE-EN and CS-EN, and gives comparable performance on FI-EN and RU-EN. We then demonstrate that it is possible to share a single character-level encoder across multiple languages by training a model on a many-to-one translation task. In this multilingual setting, the character-level encoder significantly outperforms the subword-level encoder on all the language pairs. We observe that on CS-EN, FI-EN and RU-EN, the quality of the multilingual character-level translation even surpasses the models specifically trained on that language pair alone, both in terms of BLEU score and human judgment. Neural machine translation (NMT) models typically operate with a fixed vocabulary, but translation is an open-vocabulary problem. Previous work addresses the translation of out-of-vocabulary words by backing off to a dictionary. In this paper, we introduce a simpler and more effective approach, making the NMT model capable of open-vocabulary translation by encoding rare and unknown words as sequences of subword units. This is based on the intuition that various word classes are translatable via smaller units than words, for instance names (via character copying or transliteration), compounds (via compositional translation), and cognates and loanwords (via phonological and morphological transformations). We discuss the suitability of different word segmentation techniques, including simple character n-gram models and a segmentation based on the byte pair encoding compression algorithm, and empirically show that subword models improve over a back-off dictionary baseline for the WMT 15 translation tasks English-German and English-Russian by 1.1 and 1.3 BLEU, respectively. Neural machine translation (NMT) models typically operate with a fixed vocabulary, but translation is an open-vocabulary problem. Previous work addresses the translation of out-of-vocabulary words by backing off to a dictionary. In this paper, we introduce a simpler and more effective approach, making the NMT model capable of open-vocabulary translation by encoding rare and unknown words as sequences of subword units. This is based on the intuition that various word classes are translatable via smaller units than words, for instance names (via character copying or transliteration), compounds (via compositional translation), and cognates and loanwords (via phonological and morphological transformations). We discuss the suitability of different word segmentation techniques, including simple character ngram models and a segmentation based on the byte pair encoding compression algorithm, and empirically show that subword models improve over a back-off dictionary baseline for the WMT 15 translation tasks English!German and English!Russian by up to 1.1 and 1.3 BLEU, respectively.