Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation

Published in

Journal of Biomedical Informatics(2020)

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TL;DR

The HLAN model and label embedding initialisation can provide better or comparable results for automated coding to the state-of-the-art, CNN-based models and can provide more comprehensive explanations for each label by highlighting key words and sentences in the discharge summaries, compared to the n-grams in the CNN-based models and the downgraded baselines.

Authors

V'ictor Su'arez-Paniagua

2 papers

Honghan Wu

3 papers

Hang Dong

1 papers

W. Whiteley

1 papers

References48 items

An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels

HyperCore: Hyperbolic and Co-graph Representation for Automatic ICD Coding

Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset

5分で分かる!? 有名論文ナナメ読み：Jacob Devlin et al. : BERT : Pre-training of Deep Bidirectional Transformers for Language Understanding

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation

Published in

Journal of Biomedical Informatics(2020)

External Links:

Generate Graph DownloadPDF

TL;DR

Authors

V'ictor Su'arez-Paniagua

2 papers

Honghan Wu

3 papers

Hang Dong

1 papers

W. Whiteley

1 papers

References48 items

An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels

HyperCore: Hyperbolic and Co-graph Representation for Automatic ICD Coding

Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset

5分で分かる!? 有名論文ナナメ読み：Jacob Devlin et al. : BERT : Pre-training of Deep Bidirectional Transformers for Language Understanding

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Ontological attention ensembles for capturing semantic concepts in ICD code prediction from clinical text

Ethics of Artificial Intelligence in Radiology: Summary of the Joint European and North American Multisociety Statement

Ethics of artificial intelligence in radiology: summary of the joint European and North American multisociety statement

Medical Concept Embedding with Multiple Ontological Representations

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Few-Shot and Zero-Shot Multi-Label Learning for Structured Label Spaces

Explainable Prediction of Medical Codes from Clinical Text

Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives

Multi-Label Classification of Patient Notes a Case Study on ICD Code Assignment

Initializing neural networks for hierarchical multi-label text classification

European Union Regulations on Algorithmic Decision-Making and a "Right to Explanation"

Hierarchical Attention Networks for Document Classification

Improved Neural Network-based Multi-label Classification with Better Initialization Leveraging Label Co-occurrence

MIMIC-III, a freely accessible critical care database

A Tutorial on Multilabel Learning

Adam: A Method for Stochastic Optimization

Neural Machine Translation by Jointly Learning to Align and Translate

Convolutional Neural Networks for Sentence Classification

A Review on Multi-Label Learning Algorithms

Learning Phrase Representations using RNN Encoder–Decoder for Statistical Machine Translation

Large-Scale Multi-label Text Classification - Revisiting Neural Networks

ICD-9-CM to ICD-10-CM Codes: What? Why? How?

Distributed Representations of Words and Phrases and their Compositionality

A systematic literature review of automated clinical coding and classification systems

Software Framework for Topic Modelling with Large Corpora

Understanding the difficulty of training deep feedforward neural networks

A shared task involving multi-label classification of clinical free text

An introduction to ROC analysis

Human-in-the-Loop Machine Learning: Active learning and annotation for human-centered AI

Predicting ICD-9 Codes from Medical Notes – Does the Magic of BERT Applies Here?

BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding

Multi-Label Classification of Patient Notes: Case Study on ICD Code Assignment

ICD-11 contains nearly 4x as many codes as ICD-10: Here’s what WHO has to say

Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods

Mining Multi-label Data

Visualizing Data using t-SNE

Multilabel neural networks with applications to functional genomics and text categorization

Edinburgh Research Explorer Automated Social Text Annotation With Joint Multilabel Attention Networks

CNN with a label-wise attention mechanism

This Paper Is Included in the Proceedings of the 12th Usenix Symposium on Operating Systems Design and Implementation (osdi '16). Tensorflow: a System for Large-scale Machine Learning Tensorflow: a System for Large-scale Machine Learning

Hierarchical Attention bi-directional Gated Recurrent Unit, proposed in [1

Bi-GRU, Bi-directional Gated Recurrent Unit [25] for multi-label classiﬁcation

Field of Study

Computer ScienceMedicine

Journal Information

Name

Journal of biomedical informatics

Page

104769

Venue Information

Name

Journal of Biomedical Informatics

Type

journal

URL

http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description

Alternate Names

J Biomed Informatics

TL;DR

Authors

References48 items

An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels

HyperCore: Hyperbolic and Co-graph Representation for Automatic ICD Coding

Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset

5分で分かる!? 有名論文ナナメ読み：Jacob Devlin et al. : BERT : Pre-training of Deep Bidirectional Transformers for Language Understanding

PyTorch: An Imperative Style, High-Performance Deep Learning Library

TL;DR

Authors

References48 items

An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels

HyperCore: Hyperbolic and Co-graph Representation for Automatic ICD Coding

Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset

5分で分かる!? 有名論文ナナメ読み：Jacob Devlin et al. : BERT : Pre-training of Deep Bidirectional Transformers for Language Understanding

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Ontological attention ensembles for capturing semantic concepts in ICD code prediction from clinical text

Ethics of Artificial Intelligence in Radiology: Summary of the Joint European and North American Multisociety Statement

Ethics of artificial intelligence in radiology: summary of the joint European and North American multisociety statement

Medical Concept Embedding with Multiple Ontological Representations

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Few-Shot and Zero-Shot Multi-Label Learning for Structured Label Spaces

Explainable Prediction of Medical Codes from Clinical Text

Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives

Multi-Label Classification of Patient Notes a Case Study on ICD Code Assignment

Initializing neural networks for hierarchical multi-label text classification

European Union Regulations on Algorithmic Decision-Making and a "Right to Explanation"

Hierarchical Attention Networks for Document Classification

Improved Neural Network-based Multi-label Classification with Better Initialization Leveraging Label Co-occurrence

MIMIC-III, a freely accessible critical care database

A Tutorial on Multilabel Learning

Adam: A Method for Stochastic Optimization

Neural Machine Translation by Jointly Learning to Align and Translate

Convolutional Neural Networks for Sentence Classification

A Review on Multi-Label Learning Algorithms

Learning Phrase Representations using RNN Encoder–Decoder for Statistical Machine Translation

Large-Scale Multi-label Text Classification - Revisiting Neural Networks

ICD-9-CM to ICD-10-CM Codes: What? Why? How?

Distributed Representations of Words and Phrases and their Compositionality

Processing

A systematic literature review of automated clinical coding and classification systems

Software Framework for Topic Modelling with Large Corpora

Understanding the difficulty of training deep feedforward neural networks

A shared task involving multi-label classification of clinical free text

An introduction to ROC analysis

Human-in-the-Loop Machine Learning: Active learning and annotation for human-centered AI

Predicting ICD-9 Codes from Medical Notes – Does the Magic of BERT Applies Here?

BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding

Multi-Label Classification of Patient Notes: Case Study on ICD Code Assignment

ICD-11 contains nearly 4x as many codes as ICD-10: Here’s what WHO has to say

Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods

Mining Multi-label Data

Visualizing Data using t-SNE

Multilabel neural networks with applications to functional genomics and text categorization

Edinburgh Research Explorer Automated Social Text Annotation With Joint Multilabel Attention Networks

CNN with a label-wise attention mechanism

This Paper Is Included in the Proceedings of the 12th Usenix Symposium on Operating Systems Design and Implementation (osdi '16). Tensorflow: a System for Large-scale Machine Learning Tensorflow: a System for Large-scale Machine Learning

Hierarchical Attention bi-directional Gated Recurrent Unit, proposed in [1

Bi-GRU, Bi-directional Gated Recurrent Unit [25] for multi-label classiﬁcation

Field of Study

Journal Information

Name

Page

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Type

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