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Register a new userDeveloping a Portable Natural Language Processing Based Phenotyping System
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Chengsheng Mao
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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This paper presents a portable phenotyping system that is capable of integrating both rule-based and statistical machine learning based approaches. Our system utilizes UMLS to extract clinically relevant features from the unstructured text and then facilitates portability across different institutions and data systems by incorporating OHDSIs OMOP Common Data Model (CDM) to standardize necessary data elements. Our system can also store the key components of rule-based systems (e.g., regular expression matches) in the format of OMOP CDM, thus enabling the reuse, adaptation and extension of many existing rule-based clinical NLP systems. We experimented with our system on the corpus from i2b2s Obesity Challenge as a pilot study. Our system facilitates portable phenotyping of obesity and its 15 comorbidities based on the unstructured patient discharge summaries, while achieving a performance that often ranked among the top 10 of the challenge participants. This standardization enables a consistent application of numerous rule-based and machine learning based classification techniques downstream.
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The COVID-19 pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread. Many of these difficulties are fundamentally information needs; attempts to address these needs have caused an information overload for both researchers and the public. Natural language processing (NLP), the branch of artificial intelligence that interprets human language, can be applied to address many of the information needs made urgent by the COVID-19 pandemic. This review surveys approximately 150 NLP studies and more than 50 systems and datasets addressing the COVID-19 pandemic. We detail work on four core NLP tasks: information retrieval, named entity recognition, literature-based discovery, and question answering. We also describe work that directly addresses aspects of the pandemic through four additional tasks: topic modeling, sentiment and emotion analysis, caseload forecasting, and misinformation detection. We conclude by discussing observable trends and remaining challenges.
Neural networks models for NLP are typically implemented without the explicit encoding of language rules and yet they are able to break one performance record after another. This has generated a lot of research interest in interpreting the representations learned by these networks. We propose here a novel interpretation approach that relies on the only processing system we have that does understand language: the human brain. We use brain imaging recordings of subjects reading complex natural text to interpret word and sequence embeddings from 4 recent NLP models - ELMo, USE, BERT and Transformer-XL. We study how their representations differ across layer depth, context length, and attention type. Our results reveal differences in the context-related representations across these models. Further, in the transformer models, we find an interaction between layer depth and context length, and between layer depth and attention type. We finally hypothesize that altering BERT to better align with brain recordings would enable it to also better understand language. Probing the altered BERT using syntactic NLP tasks reveals that the model with increased brain-alignment outperforms the original model. Cognitive neuroscientists have already begun using NLP networks to study the brain, and this work closes the loop to allow the interaction between NLP and cognitive neuroscience to be a true cross-pollination.
We introduce Trankit, a light-weight Transformer-based Toolkit for multilingual Natural Language Processing (NLP). It provides a trainable pipeline for fundamental NLP tasks over 100 languages, and 90 pretrained pipelines for 56 languages. Built on a state-of-the-art pretrained language model, Trankit significantly outperforms prior multilingual NLP pipelines over sentence segmentation, part-of-speech tagging, morphological feature tagging, and dependency parsing while maintaining competitive performance for tokenization, multi-word token expansion, and lemmatization over 90 Universal Dependencies treebanks. Despite the use of a large pretrained transformer, our toolkit is still efficient in memory usage and speed. This is achieved by our novel plug-and-play mechanism with Adapters where a multilingual pretrained transformer is shared across pipelines for different languages. Our toolkit along with pretrained models and code are publicly available at: https://github.com/nlp-uoregon/trankit. A demo website for our toolkit is also available at: http://nlp.uoregon.edu/trankit. Finally, we create a demo video for Trankit at: https://youtu.be/q0KGP3zGjGc.
Transformer-based pretrained language models (T-PTLMs) have achieved great success in almost every NLP task. The evolution of these models started with GPT and BERT. These models are built on the top of transformers, self-supervised learning and transfer learning. Transformed-based PTLMs learn universal language representations from large volumes of text data using self-supervised learning and transfer this knowledge to downstream tasks. These models provide good background knowledge to downstream tasks which avoids training of downstream models from scratch. In this comprehensive survey paper, we initially give a brief overview of self-supervised learning. Next, we explain various core concepts like pretraining, pretraining methods, pretraining tasks, embeddings and downstream adaptation methods. Next, we present a new taxonomy of T-PTLMs and then give brief overview of various benchmarks including both intrinsic and extrinsic. We present a summary of various useful libraries to work with T-PTLMs. Finally, we highlight some of the future research directions which will further improve these models. We strongly believe that this comprehensive survey paper will serve as a good reference to learn the core concepts as well as to stay updated with the recent happenings in T-PTLMs.
Federated Learning aims to learn machine learning models from multiple decentralized edge devices (e.g. mobiles) or servers without sacrificing local data privacy. Recent Natural Language Processing techniques rely on deep learning and large pre-trained language models. However, both big deep neural and language models are trained with huge amounts of data which often lies on the server side. Since text data is widely originated from end users, in this work, we look into recent NLP models and techniques which use federated learning as the learning framework. Our survey discusses major challenges in federated natural language processing, including the algorithm challenges, system challenges as well as the privacy issues. We also provide a critical review of the existing Federated NLP evaluation methods and tools. Finally, we highlight the current research gaps and future directions.
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