search

greenelab / deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine
https://greenelab.github.io/deep-review/
Other
1.25k stars 271 forks source link

Bidirectional LSTM-CRF for Clinical Concept Extraction #150

Closed agitter closed 7 years ago

agitter commented 7 years ago

https://arxiv.org/abs/1611.08373

Automated extraction of concepts from patient clinical records is an essential facilitator of clinical research. For this reason, the 2010 i2b2/VA Natural Language Processing Challenges for Clinical Records introduced a concept extraction task aimed at identifying and classifying concepts into predefined categories (i.e., treatments, tests and problems). State-of-the-art concept extraction approaches heavily rely on handcrafted features and domain-specific resources which are hard to collect and define. For this reason, this paper proposes an alternative, streamlined approach: a recurrent neural network (the bidirectional LSTM with CRF decoding) initialized with general-purpose, off-the-shelf word embeddings. The experimental results achieved on the 2010 i2b2/VA reference corpora using the proposed framework outperform all recent methods and ranks closely to the best submission from the original 2010 i2b2/VA challenge.

cgreene commented 7 years ago

This is a short paper that employs an LTSM network with random, Word2Vec, and GloVe embeddings. Performance is generally strong without hand-tuning or hand-constructed features applied on top of embeddings, though even the best LTSM method was pareto dominated by existing methods (i.e. there are methods that are better in both precision and recall). I'll probably mention it but it's definitely not transformative over existing approaches. Of note, the authors provide source code for the analyses.

gwaybio commented 7 years ago

Of note, the authors provide source code for the analyses.

This could be something we stress heavily in the discussion about progressing the field. Made me think of a tweet I saw today about #159

cgreene commented 7 years ago

@gwaygenomics : I like the idea of noting exactly which contributions have provided source code. That might be loads of work though...

cgreene commented 7 years ago

@gwaygenomics : can you also note that tweet in the #159 discussion?

cgreene commented 7 years ago

Might as well provide the link to the code here in case someone comes along later and wants it:

https://github.com/raghavchalapathy/Bidirectional-LSTM-CRF-for-Clinical-Concept-Extraction

cgreene commented 7 years ago

I guess this means we can tag @raghavchalapathy also!

cgreene commented 7 years ago

Discussed in #167