Recently, there is great interest to investigate the application of deep learning models for the prediction of clinical events using electronic health records (EHR) data. In EHR data, a patient's history is often represented as a sequence of visits, and each visit contains multiple events. As a result, deep learning models developed for sequence modeling, like recurrent neural networks (RNNs) are common architecture for EHR-based clinical events predictive models. While a large variety of RNN models were proposed in the literature, it is unclear if complex architecture innovations will offer superior predictive performance. In order to move this field forward, a rigorous evaluation of various methods is needed. In this study, we conducted a thorough benchmark of RNN architectures in modeling EHR data. We used two prediction tasks: the risk for developing heart failure and the risk of early readmission for inpatient hospitalization. We found that simple gated RNN models, including GRUs and LSTMs, often offer competitive results when properly tuned with Bayesian Optimization, which is in line with similar to findings in the natural language processing (NLP) domain. For reproducibility, Our codebase is shared at //github.com/ZhiGroup/pytorch_ehr.
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The Weather4cast 2021 competition gave the participants a task of predicting the time evolution of two-dimensional fields of satellite-based meteorological data. This paper describes the author's efforts, after initial success in the first stage of the competition, to improve the model further in the second stage. The improvements consisted of a shallower model variant that is competitive against the deeper version, adoption of the AdaBelief optimizer, improved handling of one of the predicted variables where the training set was found not to represent the validation set well, and ensembling multiple models to improve the results further. The largest quantitative improvements to the competition metrics can be attributed to the increased amount of training data available in the second stage of the competition, followed by the effects of model ensembling. Qualitative results show that the model can predict the time evolution of the fields, including the motion of the fields over time, starting with sharp predictions for the immediate future and blurring of the outputs in later frames to account for the increased uncertainty.
The essence of multivariate sequential learning is all about how to extract dependencies in data. These data sets, such as hourly medical records in intensive care units and multi-frequency phonetic time series, often time exhibit not only strong serial dependencies in the individual components (the "marginal" memory) but also non-negligible memories in the cross-sectional dependencies (the "joint" memory). Because of the multivariate complexity in the evolution of the joint distribution that underlies the data generating process, we take a data-driven approach and construct a novel recurrent network architecture, termed Memory-Gated Recurrent Networks (mGRN), with gates explicitly regulating two distinct types of memories: the marginal memory and the joint memory. Through a combination of comprehensive simulation studies and empirical experiments on a range of public datasets, we show that our proposed mGRN architecture consistently outperforms state-of-the-art architectures targeting multivariate time series.
In recent years, the biggest advances in major Computer Vision tasks, such as object recognition, handwritten-digit identification, facial recognition, and many others., have all come through the use of Convolutional Neural Networks (CNNs). Similarly, in the domain of Natural Language Processing, Recurrent Neural Networks (RNNs), and Long Short Term Memory networks (LSTMs) in particular, have been crucial to some of the biggest breakthroughs in performance for tasks such as machine translation, part-of-speech tagging, sentiment analysis, and many others. These individual advances have greatly benefited tasks even at the intersection of NLP and Computer Vision, and inspired by this success, we studied some existing neural image captioning models that have proven to work well. In this work, we study some existing captioning models that provide near state-of-the-art performances, and try to enhance one such model. We also present a simple image captioning model that makes use of a CNN, an LSTM, and the beam search1 algorithm, and study its performance based on various qualitative and quantitative metrics.
RNN models have achieved the state-of-the-art performance in a wide range of text mining tasks. However, these models are often regarded as black-boxes and are criticized due to the lack of interpretability. In this paper, we enhance the interpretability of RNNs by providing interpretable rationales for RNN predictions. Nevertheless, interpreting RNNs is a challenging problem. Firstly, unlike existing methods that rely on local approximation, we aim to provide rationales that are more faithful to the decision making process of RNN models. Secondly, a flexible interpretation method should be able to assign contribution scores to text segments of varying lengths, instead of only to individual words. To tackle these challenges, we propose a novel attribution method, called REAT, to provide interpretations to RNN predictions. REAT decomposes the final prediction of a RNN into additive contribution of each word in the input text. This additive decomposition enables REAT to further obtain phrase-level attribution scores. In addition, REAT is generally applicable to various RNN architectures, including GRU, LSTM and their bidirectional versions. Experimental results demonstrate the faithfulness and interpretability of the proposed attribution method. Comprehensive analysis shows that our attribution method could unveil the useful linguistic knowledge captured by RNNs. Some analysis further demonstrates our method could be utilized as a debugging tool to examine the vulnerability and failure reasons of RNNs, which may lead to several promising future directions to promote generalization ability of RNNs.
This paper presents an upgraded, real world application oriented version of gym-gazebo, the Robot Operating System (ROS) and Gazebo based Reinforcement Learning (RL) toolkit, which complies with OpenAI Gym. The content discusses the new ROS 2 based software architecture and summarizes the results obtained using Proximal Policy Optimization (PPO). Ultimately, the output of this work presents a benchmarking system for robotics that allows different techniques and algorithms to be compared using the same virtual conditions. We have evaluated environments with different levels of complexity of the Modular Articulated Robotic Arm (MARA), reaching accuracies in the millimeter scale. The converged results show the feasibility and usefulness of the gym-gazebo 2 toolkit, its potential and applicability in industrial use cases, using modular robots.
Time Series Classification (TSC) is an important and challenging problem in data mining. With the increase of time series data availability, hundreds of TSC algorithms have been proposed. Among these methods, only a few have considered Deep Neural Networks (DNNs) to perform this task. This is surprising as deep learning has seen very successful applications in the last years. DNNs have indeed revolutionized the field of computer vision especially with the advent of novel deeper architectures such as Residual and Convolutional Neural Networks. Apart from images, sequential data such as text and audio can also be processed with DNNs to reach state-of-the-art performance for document classification and speech recognition. In this article, we study the current state-of-the-art performance of deep learning algorithms for TSC by presenting an empirical study of the most recent DNN architectures for TSC. We give an overview of the most successful deep learning applications in various time series domains under a unified taxonomy of DNNs for TSC. We also provide an open source deep learning framework to the TSC community where we implemented each of the compared approaches and evaluated them on a univariate TSC benchmark (the UCR/UEA archive) and 12 multivariate time series datasets. By training 8,730 deep learning models on 97 time series datasets, we propose the most exhaustive study of DNNs for TSC to date.
Deep Convolutional Neural Networks (CNNs) are a special type of Neural Networks, which have shown state-of-the-art results on various competitive benchmarks. The powerful learning ability of deep CNN is largely achieved with the use of multiple non-linear feature extraction stages that can automatically learn hierarchical representation from the data. Availability of a large amount of data and improvements in the hardware processing units have accelerated the research in CNNs and recently very interesting deep CNN architectures are reported. The recent race in deep CNN architectures for achieving high performance on the challenging benchmarks has shown that the innovative architectural ideas, as well as parameter optimization, can improve the CNN performance on various vision-related tasks. In this regard, different ideas in the CNN design have been explored such as use of different activation and loss functions, parameter optimization, regularization, and restructuring of processing units. However, the major improvement in representational capacity is achieved by the restructuring of the processing units. Especially, the idea of using a block as a structural unit instead of a layer is gaining substantial appreciation. This survey thus focuses on the intrinsic taxonomy present in the recently reported CNN architectures and consequently, classifies the recent innovations in CNN architectures into seven different categories. These seven categories are based on spatial exploitation, depth, multi-path, width, feature map exploitation, channel boosting and attention. Additionally, it covers the elementary understanding of the CNN components and sheds light on the current challenges and applications of CNNs.
The previous work for event extraction has mainly focused on the predictions for event triggers and argument roles, treating entity mentions as being provided by human annotators. This is unrealistic as entity mentions are usually predicted by some existing toolkits whose errors might be propagated to the event trigger and argument role recognition. Few of the recent work has addressed this problem by jointly predicting entity mentions, event triggers and arguments. However, such work is limited to using discrete engineering features to represent contextual information for the individual tasks and their interactions. In this work, we propose a novel model to jointly perform predictions for entity mentions, event triggers and arguments based on the shared hidden representations from deep learning. The experiments demonstrate the benefits of the proposed method, leading to the state-of-the-art performance for event extraction.
Memory-based neural networks model temporal data by leveraging an ability to remember information for long periods. It is unclear, however, whether they also have an ability to perform complex relational reasoning with the information they remember. Here, we first confirm our intuitions that standard memory architectures may struggle at tasks that heavily involve an understanding of the ways in which entities are connected -- i.e., tasks involving relational reasoning. We then improve upon these deficits by using a new memory module -- a \textit{Relational Memory Core} (RMC) -- which employs multi-head dot product attention to allow memories to interact. Finally, we test the RMC on a suite of tasks that may profit from more capable relational reasoning across sequential information, and show large gains in RL domains (e.g. Mini PacMan), program evaluation, and language modeling, achieving state-of-the-art results on the WikiText-103, Project Gutenberg, and GigaWord datasets.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
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