Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userNeural Natural Language Processing for Unstructured Data in Electronic Health Records: a Review
139
0
0.0
(
0
)
Added by
Irene Li
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Electronic health records (EHRs), digital collections of patient healthcare events and observations, are ubiquitous in medicine and critical to healthcare delivery, operations, and research. Despite this central role, EHRs are notoriously difficult to process automatically. Well over half of the information stored within EHRs is in the form of unstructured text (e.g. provider notes, operation reports) and remains largely untapped for secondary use. Recently, however, newer neural network and deep learning approaches to Natural Language Processing (NLP) have made considerable advances, outperforming traditional statistical and rule-based systems on a variety of tasks. In this survey paper, we summarize current neural NLP methods for EHR applications. We focus on a broad scope of tasks, namely, classification and prediction, word embeddings, extraction, generation, and other topics such as question answering, phenotyping, knowledge graphs, medical dialogue, multilinguality, interpretability, etc.
rate research
Read More
Patient representation learning refers to learning a dense mathematical representation of a patient that encodes meaningful information from Electronic Health Records (EHRs). This is generally performed using advanced deep learning methods. This study presents a systematic review of this field and provides both qualitative and quantitative analyses from a methodological perspective. We identified studies developing patient representations from EHRs with deep learning methods from MEDLINE, EMBASE, Scopus, the Association for Computing Machinery (ACM) Digital Library, and Institute of Electrical and Electronics Engineers (IEEE) Xplore Digital Library. After screening 363 articles, 49 papers were included for a comprehensive data collection. We noticed a typical workflow starting with feeding raw data, applying deep learning models, and ending with clinical outcome predictions as evaluations of the learned representations. Specifically, learning representations from structured EHR data was dominant (37 out of 49 studies). Recurrent Neural Networks were widely applied as the deep learning architecture (LSTM: 13 studies, GRU: 11 studies). Disease prediction was the most common application and evaluation (31 studies). Benchmark datasets were mostly unavailable (28 studies) due to privacy concerns of EHR data, and code availability was assured in 20 studies. We show the importance and feasibility of learning comprehensive representations of patient EHR data through a systematic review. Advances in patient representation learning techniques will be essential for powering patient-level EHR analyses. Future work will still be devoted to leveraging the richness and potential of available EHR data. Knowledge distillation and advanced learning techniques will be exploited to assist the capability of learning patient representation further.
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.
Deep learning has become the dominant approach in coping with various tasks in Natural LanguageProcessing (NLP). Although text inputs are typically represented as a sequence of tokens, there isa rich variety of NLP problems that can be best expressed with a graph structure. As a result, thereis a surge of interests in developing new deep learning techniques on graphs for a large numberof NLP tasks. In this survey, we present a comprehensive overview onGraph Neural Networks(GNNs) for Natural Language Processing. We propose a new taxonomy of GNNs for NLP, whichsystematically organizes existing research of GNNs for NLP along three axes: graph construction,graph representation learning, and graph based encoder-decoder models. We further introducea large number of NLP applications that are exploiting the power of GNNs and summarize thecorresponding benchmark datasets, evaluation metrics, and open-source codes. Finally, we discussvarious outstanding challenges for making the full use of GNNs for NLP as well as future researchdirections. To the best of our knowledge, this is the first comprehensive overview of Graph NeuralNetworks for Natural Language Processing.
As the use of deep learning techniques has grown across various fields over the past decade, complaints about the opaqueness of the black-box models have increased, resulting in an increased focus on transparency in deep learning models. This work investigates various methods to improve the interpretability of deep neural networks for natural language processing (NLP) tasks, including machine translation and sentiment analysis. We provide a comprehensive discussion on the definition of the term textit{interpretability} and its various aspects at the beginning of this work. The methods collected and summarised in this survey are only associated with local interpretation and are divided into three categories: 1) explaining the models predictions through related input features; 2) explaining through natural language explanation; 3) probing the hidden states of models and word representations.
Increasing concerns and regulations about data privacy, necessitate the study of privacy-preserving methods for natural language processing (NLP) applications. Federated learning (FL) provides promising methods for a large number of clients (i.e., personal devices or organizations) to collaboratively learn a shared global model to benefit all clients, while allowing users to keep their data locally. To facilitate FL research in NLP, we present the FedNLP, a research platform for federated learning in NLP. FedNLP supports various popular task formulations in NLP such as text classification, sequence tagging, question answering, seq2seq generation, and language modeling. We also implement an interface between Transformer language models (e.g., BERT) and FL methods (e.g., FedAvg, FedOpt, etc.) for distributed training. The evaluation protocol of this interface supports a comprehensive collection of non-IID partitioning strategies. Our preliminary experiments with FedNLP reveal that there exists a large performance gap between learning on decentralized and centralized datasets -- opening intriguing and exciting future research directions aimed at developing FL methods suited to NLP tasks.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
