Post on 24-Jan-2021
Unsupervised patient representationswith interpretable classification decisions
Madhumita Sushil, Simon Šuster, Kim Luyckx, Walter Daelemans
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Patient Representations Task-independent generalized semantic representations of patients, s.t.
Similar patients - similar representations
Patient similarity encompasses holistic patient condition
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Patient Similarity
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Pipeline - Representation Learning and Evaluation
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Data
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icons by pictohaven, LAFS, ProSymbols, Lucas Almeida, Juraj Sedlák; thenounproject.com
MIMIC-III adult patient; min. 1 non-discharge note
25k-3k-3k(train-val-test)
1-879 notes, 14 categories
PATIENT DOCUMENT
PATIENTTOKENS
Avg. 13k tokens
UCTO
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Unsupervised Representation Learning
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PATIENTTOKENS
BAG-OF-WORDS (BoW)
MEDICAL CONCEPTS
+ ASSERTION
BAG-OF-CONCEPTS (BoCUI)
SDAE-BoW / SDAE-BoCUI
Vectors
CLAMP
Stacked Denoising Autoencoder
(SDAE)
SDAE
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Unsupervised Representation Learning
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PATIENTTOKENS
DOC2VEC Vectors
DOC2VEC
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Unsupervised Representation Learning
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DOC2VEC Vectors SDAE-BoW
Vectors
SDAE-BoW +
DOC2VECVectors
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Supervised Representation Evaluation
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13% PATIENT DEATH
4% PATIENTDEATH
12% PATIENT DEATH
FEEDFORWARD NEURAL NETWORKS
IN-HOSPITALMORTALITY
30 DAYSMORTALITY
1 YEARMORTALITY
PRIMARYDIAGNOSTICCATEGORY
PRIMARYPROCEDURAL
CATEGORYGENDER
57% MALE40% MAJORITY 39% MAJORITY
Patient Representations
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Results - Representation Evaluation
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All generalized representation models significantly outperform sparse models when no. of positive instances is low (30 days mortality).
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Results - Representation Evaluation
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For all tasks except distant patient mortality, BoW model is a strong baseline (strong lexical features present).
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Results - Representation Evaluation
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Recommended to combine SDAE and doc2vec vectors for unknown tasks.
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Model InterpretabilityCritical for
● Error analysis● Exploratory analysis
Goal: Quantitative explanation of a trained model without retraining
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Feature Extraction - Pretraining AutoencodersRank features according to mean squared feature reconstruction error across all instances
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Feature Extraction - Pretraining AutoencodersRank features according to mean squared feature reconstruction error across all instances
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Feature Extraction - Pretraining AutoencodersRank features according to mean squared feature reconstruction error across all instances
0.87-0.88 Spearman correlation coefficient between feature reconstruction error and frequency
Feature entropy too high?
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Finding Influential features - Classification PhaseGradient-based feature sensitivity calculation across two neural networks
For arbitrary number of instances and output classes
Transferable to different representation learning architectures
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Feature Extraction - Classification Phase
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i1
i2r1
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Collecting all encoder layers of SDAE
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Supervised classifier
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Feature Extraction - Classification Phase
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i2r1
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Collecting all encoder layers of SDAE
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Supervised classifier
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So1, i1(1) =
Sensitivity
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Feature Extraction - Classification Phase
Feature influence = Maximum root mean squared sensitivity across all instances
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Collecting all encoder layers of SDAE
o1
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Supervised classifier
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So1, i1(1) =
Sensitivity
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Most influential features for one instance each
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ConclusionsGeneralized patient representations help for low number of positive instances
Recommended to combine autoencoder and doc2vec representations
During representation learning, autoencoder has high reconstruction error for frequent terms, perhaps due to their high entropy
The most influential features for classification however are frequent terms, and context of features plays a role.
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Unsupervised patient representations from clinical notes with interpretable classification decisions
Madhumita Sushil, Simon Šuster, Kim Luyckx, Walter Daelemans
Workshop on Machine Learning for Health, NIPS 2017.
THANK YOU!
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Results
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