Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications, where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on the existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this article, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art GNNs into four categories, namely, recurrent GNNs, convolutional GNNs, graph autoencoders, and spatial–temporal GNNs. We further discuss the applications of GNNs across various domains and summarize the open-source codes, benchmark data sets, and model evaluation of GNNs. Finally, we propose potential research directions in this rapidly growing field.

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A Comprehensive Survey on Graph Neural Networks

We investigate conditions sufficient for identification of average treatment effects using instrumental variables. First we show that the existence of valid instruments is not sufficient to identify any meaningful average treatment effect. We then establish that the combination of an instrument and a condition on the relation between the instrument and the participation status is sufficient for identification of a local average treatment effect for those who can be induced to change their participation status by changing the value of the instrument. Finally we derive the probability limit of the standard IV estimator under these conditions. It is seen to be a weighted average of local average treatment effects.

Evolution and Rationality Some Recent Game-Theoretic Results. Identification and Estimation of Local Average Treatment Effects

Explainable Artificial Intelligence (XAI): Concepts, Taxonomies, Opportunities and Challenges toward Responsible AI

Here we present deep-learning techniques for healthcare, centering our discussion on deep learning in computer vision, natural language processing, reinforcement learning, and generalized methods. We describe how these computational techniques can impact a few key areas of medicine and explore how to build end-to-end systems. Our discussion of computer vision focuses largely on medical imaging, and we describe the application of natural language processing to domains such as electronic health record data. Similarly, reinforcement learning is discussed in the context of robotic-assisted surgery, and generalized deep-learning methods for genomics are reviewed.

A guide to deep learning in healthcare.

In the last years, Artificial Intelligence (AI) has achieved a notable momentum that may deliver the best of expectations over many application sectors across the field. For this to occur, the entire community stands in front of the barrier of explainability, an inherent problem of AI techniques brought by sub-symbolism (e.g. ensembles or Deep Neural Networks) that were not present in the last hype of AI. Paradigms underlying this problem fall within the so-called eXplainable AI (XAI) field, which is acknowledged as a crucial feature for the practical deployment of AI models. This overview examines the existing literature in the field of XAI, including a prospect toward what is yet to be reached. We summarize previous efforts to define explainability in Machine Learning, establishing a novel definition that covers prior conceptual propositions with a major focus on the audience for which explainability is sought. We then propose and discuss about a taxonomy of recent contributions related to the explainability of different Machine Learning models, including those aimed at Deep Learning methods for which a second taxonomy is built. This literature analysis serves as the background for a series of challenges faced by XAI, such as the crossroads between data fusion and explainability. Our prospects lead toward the concept of Responsible Artificial Intelligence, namely, a methodology for the large-scale implementation of AI methods in real organizations with fairness, model explainability and accountability at its core. Our ultimate goal is to provide newcomers to XAI with a reference material in order to stimulate future research advances, but also to encourage experts and professionals from other disciplines to embrace the benefits of AI in their activity sectors, without any prior bias for its lack of interpretability.

Explainable Artificial Intelligence (XAI): Concepts, Taxonomies, Opportunities and Challenges toward Responsible AI.

Leveraging large historical data in electronic health record (EHR), we developed Doctor AI, a generic predictive model that covers observed medical conditions and medication uses. Doctor AI is a temporal model using recurrent neural networks (RNN) and was developed and applied to longitudinal time stamped EHR data from 260K patients over 8 years. Encounter records (e.g. diagnosis codes, medication codes or procedure codes) were input to RNN to predict (all) the diagnosis and medication categories for a subsequent visit. Doctor AI assesses the history of patients to make multilabel predictions (one label for each diagnosis or medication category). Based on separate blind test set evaluation, Doctor AI can perform differential diagnosis with up to 79% recall@30, significantly higher than several baselines. Moreover, we demonstrate great generalizability of Doctor AI by adapting the resulting models from one institution to another without losing substantial accuracy.

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Doctor AI: Predicting Clinical Events via Recurrent Neural Networks

Accuracy and interpretability are two dominant features of successful predictive models. Typically, a choice must be made in favor of complex black box models such as recurrent neural networks (RNN) for accuracy versus less accurate but more interpretable traditional models such as logistic regression. This tradeoff poses challenges in medicine where both accuracy and interpretability are important. We addressed this challenge by developing the REverse Time AttentIoN model (RETAIN) for application to Electronic Health Records (EHR) data. RETAIN achieves high accuracy while remaining clinically interpretable and is based on a two-level neural attention model that detects influential past visits and significant clinical variables within those visits (e.g. key diagnoses). RETAIN mimics physician practice by attending the EHR data in a reverse time order so that recent clinical visits are likely to receive higher attention. RETAIN was tested on a large health system EHR dataset with 14 million visits completed by 263K patients over an 8 year period and demonstrated predictive accuracy and computational scalability comparable to state-of-the-art methods such as RNN, and ease of interpretability comparable to traditional models.

RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism

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RETAIN: An interpretable predictive model for healthcare using reverse time attention mechanism

Deep learning methods exhibit promising performance for predictive modeling in healthcare, but two important challenges remain: - Data insufficiency: Often in healthcare predictive modeling, the sample size is insufficient for deep learning methods to achieve satisfactory results. Interpretation: The representations learned by deep learning methods should align with medical knowledge. To address these challenges, we propose GRaph-based Attention Model (GRAM) that supplements electronic health records (EHR) with hierarchical information inherent to medical ontologies. Based on the data volume and the ontology structure, GRAM represents a medical concept as a combination of its ancestors in the ontology via an attention mechanism. We compared predictive performance (i.e. accuracy, data needs, interpretability) of GRAM to various methods including the recurrent neural network (RNN) in two sequential diagnoses prediction tasks and one heart failure prediction task. Compared to the basic RNN, GRAM achieved 10% higher accuracy for predicting diseases rarely observed in the training data and 3% improved area under the ROC curve for predicting heart failure using an order of magnitude less training data. Additionally, unlike other methods, the medical concept representations learned by GRAM are well aligned with the medical ontology. Finally, GRAM exhibits intuitive attention behaviors by adaptively generalizing to higher level concepts when facing data insufficiency at the lower level concepts.

https://dl.acm.org/doi/pdf/10.1145/3097983.3098126

GRAM: Graph-based Attention Model for Healthcare Representation Learning

Proper representations of medical concepts such as diagnosis, medication, procedure codes and visits from Electronic Health Records (EHR) has broad applications in healthcare analytics. Patient EHR data consists of a sequence of visits over time, where each visit includes multiple medical concepts, e.g., diagnosis, procedure, and medication codes. This hierarchical structure provides two types of relational information, namely sequential order of visits and co-occurrence of the codes within a visit. In this work, we propose Med2Vec, which not only learns the representations for both medical codes and visits from large EHR datasets with over million visits, but also allows us to interpret the learned representations confirmed positively by clinical experts. In the experiments, Med2Vec shows significant improvement in prediction accuracy in clinical applications compared to baselines such as Skip-gram, GloVe, and stacked autoencoder, while providing clinically meaningful interpretation.

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Mohammad Taha Bahadori

Papers

Doctor AI: Predicting Clinical Events via Recurrent Neural Networks

RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism

RETAIN: An interpretable predictive model for healthcare using reverse time attention mechanism

GRAM: Graph-based Attention Model for Healthcare Representation Learning

Multi-layer Representation Learning for Medical Concepts