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Register a new userBootstrapping Your Own Positive Sample: Contrastive Learning With Electronic Health Record Data
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Added by
Tingyi Wanyan
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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).
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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%.
State-of-the-art methods for self-supervised learning (SSL) build representations by maximizing the similarity between different augmented views of a sample. Because these approaches try to match views of the same sample, they can be too myopic and fail to produce meaningful results when augmentations are not sufficiently rich. This motivates the use of the dataset itself to find similar, yet distinct, samples to serve as views for one another. In this paper, we introduce Mine Your Own vieW (MYOW), a new approach for building across-sample prediction into SSL. The idea behind our approach is to actively mine views, finding samples that are close in the representation space of the network, and then predict, from one samples latent representation, the representation of a nearby sample. In addition to showing the promise of MYOW on standard datasets used in computer vision, we highlight the power of this idea in a novel application in neuroscience where rich augmentations are not already established. When applied to neural datasets, MYOW outperforms other self-supervised approaches in all examples (in some cases by more than 10%), and surpasses the supervised baseline for most datasets. By learning to predict the latent representation of similar samples, we show that it is possible to learn good representations in new domains where augmentations are still limited.
We study Policy-extended Value Function Approximator (PeVFA) in Reinforcement Learning (RL), which extends conventional value function approximator (VFA) to take as input not only the state (and action) but also an explicit policy representation. Such an extension enables PeVFA to preserve values of multiple policies at the same time and brings an appealing characteristic, i.e., emph{value generalization among policies}. We formally analyze the value generalization under Generalized Policy Iteration (GPI). From theoretical and empirical lens, we show that generalized value estimates offered by PeVFA may have lower initial approximation error to true values of successive policies, which is expected to improve consecutive value approximation during GPI. Based on above clues, we introduce a new form of GPI with PeVFA which leverages the value generalization along policy improvement path. Moreover, we propose a representation learning framework for RL policy, providing several approaches to learn effective policy embeddings from policy network parameters or state-action pairs. In our experiments, we evaluate the efficacy of value generalization offered by PeVFA and policy representation learning in several OpenAI Gym continuous control tasks. For a representative instance of algorithm implementation, Proximal Policy Optimization (PPO) re-implemented under the paradigm of GPI with PeVFA achieves about 40% performance improvement on its vanilla counterpart in most environments.
Advancements in machine learning algorithms have had a beneficial impact on representation learning, classification, and prediction models built using electronic health record (EHR) data. Effort has been put both on increasing models overall performance as well as improving their interpretability, particularly regarding the decision-making process. In this study, we present a temporal deep learning model to perform bidirectional representation learning on EHR sequences with a transformer architecture to predict future diagnosis of depression. This model is able to aggregate five heterogenous and high-dimensional data sources from the EHR and process them in a temporal manner for chronic disease prediction at various prediction windows. We applied the current trend of pretraining and fine-tuning on EHR data to outperform the current state-of-the-art in chronic disease prediction, and to demonstrate the underlying relation between EHR codes in the sequence. The model generated the highest increases of precision-recall area under the curve (PRAUC) from 0.70 to 0.76 in depression prediction compared to the best baseline model. Furthermore, the self-attention weights in each sequence quantitatively demonstrated the inner relationship between various codes, which improved the models interpretability. These results demonstrate the models ability to utilize heterogeneous EHR data to predict depression while achieving high accuracy and interpretability, which may facilitate constructing clinical decision support systems in the future for chronic disease screening and early detection.
Motivation: Electronic health record (EHR) data provides a new venue to elucidate disease comorbidities and latent phenotypes for precision medicine. To fully exploit its potential, a realistic data generative process of the EHR data needs to be modelled. We present MixEHR-S to jointly infer specialist-disease topics from the EHR data. As the key contribution, we model the specialist assignments and ICD-coded diagnoses as the latent topics based on patients underlying disease topic mixture in a novel unified supervised hierarchical Bayesian topic model. For efficient inference, we developed a closed-form collapsed variational inference algorithm to learn the model distributions of MixEHR-S. We applied MixEHR-S to two independent large-scale EHR databases in Quebec with three targeted applications: (1) Congenital Heart Disease (CHD) diagnostic prediction among 154,775 patients; (2) Chronic obstructive pulmonary disease (COPD) diagnostic prediction among 73,791 patients; (3) future insulin treatment prediction among 78,712 patients diagnosed with diabetes as a mean to assess the disease exacerbation. In all three applications, MixEHR-S conferred clinically meaningful latent topics among the most predictive latent topics and achieved superior target prediction accuracy compared to the existing methods, providing opportunities for prioritizing high-risk patients for healthcare services. MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS
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