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Exploiting Convolutional Neural Network for Risk Prediction with Medical Feature Embedding

arXiv.org Machine Learning

The widespread availability of electronic health records (EHRs) promises to usher in the era of personalized medicine. However, the problem of extracting useful clinical representations from longitudinal EHR data remains challenging. In this paper, we explore deep neural network models with learned medical feature embedding to deal with the problems of high dimensionality and temporality. Specifically, we use a multi-layer convolutional neural network (CNN) to parameterize the model and is thus able to capture complex non-linear longitudinal evolution of EHRs. Our model can effectively capture local/short temporal dependency in EHRs, which is beneficial for risk prediction. To account for high dimensionality, we use the embedding medical features in the CNN model which hold the natural medical concepts. Our initial experiments produce promising results and demonstrate the effectiveness of both the medical feature embedding and the proposed convolutional neural network in risk prediction on cohorts of congestive heart failure and diabetes patients compared with several strong baselines.


BERTSurv: BERT-Based Survival Models for Predicting Outcomes of Trauma Patients

arXiv.org Artificial Intelligence

Survival analysis is a technique to predict the times of specific outcomes, and is widely used in predicting the outcomes for intensive care unit (ICU) trauma patients. Recently, deep learning models have drawn increasing attention in healthcare. However, there is a lack of deep learning methods that can model the relationship between measurements, clinical notes and mortality outcomes. In this paper we introduce BERTSurv, a deep learning survival framework which applies Bidirectional Encoder Representations from Transformers (BERT) as a language representation model on unstructured clinical notes, for mortality prediction and survival analysis. We also incorporate clinical measurements in BERTSurv. With binary cross-entropy (BCE) loss, BERTSurv can predict mortality as a binary outcome (mortality prediction). With partial log-likelihood (PLL) loss, BERTSurv predicts the probability of mortality as a time-to-event outcome (survival analysis). We apply BERTSurv on Medical Information Mart for Intensive Care III (MIMIC III) trauma patient data. For mortality prediction, BERTSurv obtained an area under the curve of receiver operating characteristic curve (AUC-ROC) of 0.86, which is an improvement of 3.6% over baseline of multilayer perceptron (MLP) without notes. For survival analysis, BERTSurv achieved a concordance index (C-index) of 0.7. In addition, visualizations of BERT's attention heads help to extract patterns in clinical notes and improve model interpretability by showing how the model assigns weights to different inputs.


Bayesian Image Reconstruction using Deep Generative Models

arXiv.org Machine Learning

Machine learning models are commonly trained end-to-end and in a supervised setting, using paired (input, output) data. Classical examples include recent super-resolution methods that train on pairs of (low-resolution, high-resolution) images. However, these end-to-end approaches require re-training every time there is a distribution shift in the inputs (e.g., night images vs daylight) or relevant latent variables (e.g., camera blur or hand motion). In this work, we leverage state-of-the-art (SOTA) generative models (here StyleGAN2) for building powerful image priors, which enable application of Bayes' theorem for many downstream reconstruction tasks. Our method, called Bayesian Reconstruction through Generative Models (BRGM), uses a single pre-trained generator model to solve different image restoration tasks, i.e., super-resolution and in-painting, by combining it with different forward corruption models. We demonstrate BRGM on three large, yet diverse, datasets that enable us to build powerful priors: (i) 60,000 images from the Flick Faces High Quality dataset \cite{karras2019style} (ii) 240,000 chest X-rays from MIMIC III and (iii) a combined collection of 5 brain MRI datasets with 7,329 scans. Across all three datasets and without any dataset-specific hyperparameter tuning, our approach yields state-of-the-art performance on super-resolution, particularly at low-resolution levels, as well as inpainting, compared to state-of-the-art methods that are specific to each reconstruction task. We will make our code and pre-trained models available online.


Federated Uncertainty-Aware Learning for Distributed Hospital EHR Data

arXiv.org Artificial Intelligence

Recent works have shown that applying Machine Learning to Electronic Health Records (EHR) can strongly accelerate precision medicine. This requires developing models based on diverse EHR sources. Federated Learning (FL) has enabled predictive modeling using distributed training which lifted the need of sharing data and compromising privacy. Since models are distributed in FL, it is attractive to devise ensembles of Deep Neural Networks that also assess model uncertainty. We propose a new FL model called Federated Uncertainty-Aware Learning Algorithm (FUALA) that improves on Federated Averaging (FedAvg) in the context of EHR. FUALA embeds uncertainty information in two ways: It reduces the contribution of models with high uncertainty in the aggregated model. It also introduces model ensembling at prediction time by keeping the last layers of each hospital from the final round. In FUALA, the Federator (central node) sends at each round the average model to all hospitals as well as a randomly assigned hospital model update to estimate its generalization on that hospital own data. Each hospital sends back its model update as well a generalization estimation of the assigned model. At prediction time, the model outputs C predictions for each sample where C is the number of hospital models. The experimental analysis conducted on a cohort of 87K deliveries for the task of preterm-birth prediction showed that the proposed approach outperforms FedAvg when evaluated on out-of-distribution data. We illustrated how uncertainty could be measured using the proposed approach.


Biomedical Named Entity Recognition at Scale

arXiv.org Artificial Intelligence

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting meaningful chunks from clinical notes and reports, which are then fed to downstream tasks like assertion status detection, entity resolution, relation extraction, and de-identification. Reimplementing a Bi-LSTM-CNN-Char deep learning architecture on top of Apache Spark, we present a single trainable NER model that obtains new state-of-the-art results on seven public biomedical benchmarks without using heavy contextual embeddings like BERT. This includes improving BC4CHEMD to 93.72% (4.1% gain), Species800 to 80.91% (4.6% gain), and JNLPBA to 81.29% (5.2% gain). In addition, this model is freely available within a production-grade code base as part of the open-source Spark NLP library; can scale up for training and inference in any Spark cluster; has GPU support and libraries for popular programming languages such as Python, R, Scala and Java; and can be extended to support other human languages with no code changes.