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Register a new userFew-Shot Electronic Health Record Coding through Graph Contrastive Learning
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Shanshan Wang
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Electronic health record (EHR) coding is the task of assigning ICD codes to each EHR. Most previous studies either only focus on the frequent ICD codes or treat rare and frequent ICD codes in the same way. These methods perform well on frequent ICD codes but due to the extremely unbalanced distribution of ICD codes, the performance on rare ones is far from satisfactory. We seek to improve the performance for both frequent and rare ICD codes by using a contrastive graph-based EHR coding framework, CoGraph, which re-casts EHR coding as a few-shot learning task. First, we construct a heterogeneous EHR word-entity (HEWE) graph for each EHR, where the words and entities extracted from an EHR serve as nodes and the relations between them serve as edges. Then, CoGraph learns similarities and dissimilarities between HEWE graphs from different ICD codes so that information can be transferred among them. In a few-shot learning scenario, the model only has access to frequent ICD codes during training, which might force it to encode features that are useful for frequent ICD codes only. To mitigate this risk, CoGraph devises two graph contrastive learning schemes, GSCL and GECL, that exploit the HEWE graph structures so as to encode transferable features. GSCL utilizes the intra-correlation of different sub-graphs sampled from HEWE graphs while GECL exploits the inter-correlation among HEWE graphs at different clinical stages. Experiments on the MIMIC-III benchmark dataset show that CoGraph significantly outperforms state-of-the-art methods on EHR coding, not only on frequent ICD codes, but also on rare codes, in terms of several evaluation indicators. On frequent ICD codes, GSCL and GECL improve the classification accuracy and F1 by 1.31% and 0.61%, respectively, and on rare ICD codes CoGraph has more obvious improvements by 2.12% and 2.95%.
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Aiming at expanding few-shot relations coverage in knowledge graphs (KGs), few-shot knowledge graph completion (FKGC) has recently gained more research interests. Some existing models employ a few-shot relations multi-hop neighbor information to enhance its semantic representation. However, noise neighbor information might be amplified when the neighborhood is excessively sparse and no neighbor is available to represent the few-shot relation. Moreover, modeling and inferring complex relations of one-to-many (1-N), many-to-one (N-1), and many-to-many (N-N) by previous knowledge graph completion approaches requires high model complexity and a large amount of training instances. Thus, inferring complex relations in the few-shot scenario is difficult for FKGC models due to limited training instances. In this paper, we propose a few-shot relational learning with global-local framework to address the above issues. At the global stage, a novel gated and attentive neighbor aggregator is built for accurately integrating the semantics of a few-shot relations neighborhood, which helps filtering the noise neighbors even if a KG contains extremely sparse neighborhoods. For the local stage, a meta-learning based TransH (MTransH) method is designed to model complex relations and train our model in a few-shot learning fashion. Extensive experiments show that our model outperforms the state-of-the-art FKGC approaches on the frequently-used benchmark datasets NELL-One and Wiki-One. Compared with the strong baseline model MetaR, our model achieves 5-shot FKGC performance improvements of 8.0% on NELL-One and 2.8% on Wiki-One by the metric Hits@10.
Electronic Health Record (EHR) data has been of tremendous utility in Artificial Intelligence (AI) for healthcare such as predicting future clinical events. These tasks, however, often come with many challenges when using classical machine learning models due to a myriad of factors including class imbalance and data heterogeneity (i.e., the complex intra-class variances). To address some of these research gaps, this paper leverages the exciting contrastive learning framework and proposes a novel contrastive regularized clinical classification model. The contrastive loss is found to substantially augment EHR-based prediction: it effectively characterizes the similar/dissimilar patterns (by its push-and-pull form), meanwhile mitigating the highly skewed class distribution by learning more balanced feature spaces (as also echoed by recent findings). In particular, when naively exporting the contrastive learning to the EHR data, one hurdle is in generating positive samples, since EHR data is not as amendable to data augmentation as image data. To this end, we have introduced two unique positive sampling strategies specifically tailored for EHR data: a feature-based positive sampling that exploits the feature space neighborhood structure to reinforce the feature learning; and an attribute-based positive sampling that incorporates pre-generated patient similarity metrics to define the sample proximity. Both sampling approaches are designed with an awareness of unique high intra-class variance in EHR data. Our overall framework yields highly competitive experimental results in predicting the mortality risk on real-world COVID-19 EHR data with a total of 5,712 patients admitted to a large, urban health system. Specifically, our method reaches a high AUROC prediction score of 0.959, which outperforms other baselines and alternatives: cross-entropy(0.873) and focal loss(0.931).
Few-shot learning aims to transfer information from one task to enable generalization on novel tasks given a few examples. This information is present both in the domain and the class labels. In this work we investigate the complementary roles of these two sources of information by combining instance-discriminative contrastive learning and supervised learning in a single framework called Supervised Momentum Contrastive learning (SUPMOCO). Our approach avoids a problem observed in supervised learning where information in images not relevant to the task is discarded, which hampers their generalization to novel tasks. We show that (self-supervised) contrastive learning and supervised learning are mutually beneficial, leading to a new state-of-the-art on the META-DATASET - a recently introduced benchmark for few-shot learning. Our method is based on a simple modification of MOCO and scales better than prior work on combining supervised and self-supervised learning. This allows us to easily combine data from multiple domains leading to further improvements.
Contrastive learning is a discriminative approach that aims at grouping similar samples closer and diverse samples far from each other. It it an efficient technique to train an encoder generating distinguishable and informative representations, and it may even increase the encoders transferability. Most current applications of contrastive learning benefit only a single representation from the last layer of an encoder.In this paper, we propose a multi-level contrasitive learning approach which applies contrastive losses at different layers of an encoder to learn multiple representations from the encoder. Afterward, an ensemble can be constructed to take advantage of the multiple representations for the downstream tasks. We evaluated the proposed method on few-shot learning problems and conducted experiments using the mini-ImageNet and the tiered-ImageNet datasets. Our model achieved the new state-of-the-art results for both datasets, comparing to previous regular, ensemble, and contrastive learing (single-level) based approaches.
Most recent few-shot learning (FSL) methods are based on meta-learning with episodic training. In each meta-training episode, a discriminative feature embedding and/or classifier are first constructed from a support set in an inner loop, and then evaluated in an outer loop using a query set for model updating. This query set sample centered learning objective is however intrinsically limited in addressing the lack of training data problem in the support set. In this paper, a novel contrastive prototype learning with augmented embeddings (CPLAE) model is proposed to overcome this limitation. First, data augmentations are introduced to both the support and query sets with each sample now being represented as an augmented embedding (AE) composed of concatenated embeddings of both the original and augment
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