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.
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.  Deep Neural Networks (DNNs) are powerful models that have achieved excellent performance on difficult learning tasks. Although DNNs work well whenever large labeled training sets are available, they cannot be used to map sequences to sequences. In this paper, we present a general end-to-end approach to sequence learning that makes minimal assumptions on the sequence structure. Our method uses a multilayered Long Short-Term Memory (LSTM) to map the input sequence to a vector of a fixed dimensionality, and then another deep LSTM to decode the target sequence from the vector. Our main result is that on an English to French translation task from the WMT'14 dataset, the translations produced by the LSTM achieve a BLEU score of 34.8 on the entire test set, where the LSTM's BLEU score was penalized on out-of-vocabulary words. Additionally, the LSTM did not have difficulty on long sentences. For comparison, a phrase-based SMT system achieves a BLEU score of 33.3 on the same dataset. When we used the LSTM to rerank the 1000 hypotheses produced by the aforementioned SMT system, its BLEU score increases to 36.5, which is close to the previous best result on this task. The LSTM also learned sensible phrase and sentence representations that are sensitive to word order and are relatively invariant to the active and the passive voice. Finally, we found that reversing the order of the words in all source sentences (but not target sentences) improved the LSTM's performance markedly, because doing so introduced many short term dependencies between the source and the target sentence which made the optimization problem easier.