Disease progression modeling (DPM) using longitudinal data is a challenging task in machine learning for healthcare that can provide clinicians with better tools for diagnosis and monitoring of disease. Existing DPM algorithms neglect temporal dependencies among measurements and make parametric assumptions about biomarker trajectories. In addition, they do not model multiple biomarkers jointly and need to align subjects' trajectories. In this paper, recurrent neural networks (RNNs) are utilized to address these issues. However, in many cases, longitudinal cohorts contain incomplete data, which hinders the application of standard RNNs and requires a pre-processing step such as imputation of the missing values. We, therefore, propose a generalized training rule for the most widely used RNN architecture, long short-term memory (LSTM) networks, that can handle missing values in both target and predictor variables. This algorithm is applied for modeling the progression of Alzheimer's disease (AD) using magnetic resonance imaging (MRI) biomarkers. The results show that the proposed LSTM algorithm achieves a lower mean absolute error for prediction of measurements across all considered MRI biomarkers compared to using standard LSTM networks with data imputation or using a regression-based DPM method. Moreover, applying linear discriminant analysis to the biomarkers' values predicted by the proposed algorithm results in a larger area under the receiver operating characteristic curve (AUC) for clinical diagnosis of AD compared to the same alternatives, and the AUC is comparable to state-of-the-art AUCs from a recent cross-sectional medical image classification challenge. This paper shows that built-in handling of missing values in LSTM network training paves the way for application of RNNs in disease progression modeling.
Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）
Multi-modal biological, imaging, and neuropsychological markers have demonstrated promising performance for distinguishing Alzheimer's disease (AD) patients from cognitively normal elders. However, it remains difficult to early predict when and which mild cognitive impairment (MCI) individuals will convert to AD dementia. Informed by pattern classification studies which have demonstrated that pattern classifiers built on longitudinal data could achieve better classification performance than those built on cross-sectional data, we develop a deep learning model based on recurrent neural networks…
Stony Brook University（石溪大学）；Newark Beth Israel Medical Center（纽瓦克贝丝以色列医疗中心）
COVID-19 image analysis has mostly focused on diagnostic tasks using single timepoint scans acquired upon disease presentation or admission. We present a deep learning-based approach to predict lung infiltrate progression from serial chest radiographs (CXRs) of COVID-19 patients. Our method first utilizes convolutional neural networks (CNNs) for feature extraction from patches within the concerned lung zone, and also from neighboring and remote boundary regions. The framework further incorporates a multi-scale Gated Recurrent Unit (GRU) with a correlation module for effective predictions. The …
Short-term traffic forecasting based on deep learning methods, especially recurrent neural networks (RNN), has received much attention in recent years. However, the potential of RNN-based models in traffic forecasting has not yet been fully exploited in terms of the predictive power of spatial-temporal data and the capability of handling missing data. In this paper, we focus on RNN-based models and attempt to reformulate the way to incorporate RNN and its variants into traffic prediction models. A stacked bidirectional and unidirectional LSTM network architecture (SBU-LSTM) is proposed to assi…
We propose and evaluate a new MRI reconstruction method named LORAKI that trains an autocalibrated scan-specific recurrent neural network (RNN) to recover missing k-space data. Methods like GRAPPA, SPIRiT, and AC-LORAKS assume that k-space data has shift-invariant autoregressive structure, and that the scan-specific autoregression relationships needed to recover missing samples can be learned from fully-sampled autocalibration (ACS) data. Recently, the structure of the linear GRAPPA method has been translated into a nonlinear deep learning method named RAKI. RAKI uses ACS data to train an arti…
Clemson University（克莱姆森大学）；West Virginia University（西弗吉尼亚大学）
The prediction of high-resolution hourly traffic volumes of a given roadway is essential for transportation planning. Traditionally, Automatic Traffic Recorders (ATR) are used to collect this hourly volume data. These large datasets are time series data characterized by long-term temporal dependencies and missing values. Regarding the temporal dependencies, all roadways are characterized by seasonal variations that can be weekly, monthly or yearly, depending on the cause of the variation. Regarding the missing data in a time-series sequence, traditional time series forecasting models perform p…
Stanford University（斯坦福大学）；Stanford School of Medicine（斯坦福医学院）；University of California San Diego（加州大学圣地亚哥分校）；SRI International（斯坦福国际研究院）
Many neurological diseases are characterized by gradual deterioration of brain structure and function. Large longitudinal MRI datasets have revealed such deterioration, in part, by applying machine and deep learning to predict diagnosis. A popular approach is to apply Convolutional Neural Networks (CNN) to extract informative features from each visit of the longitudinal MRI and then use those features to classify each visit via Recurrent Neural Networks (RNNs). Such modeling neglects the progressive nature of the disease, which may result in clinically implausible classifications across visits…
Alzheimer's disease (AD) is known as one of the major causes of dementia and is characterized by slow progression over several years, with no treatments or available medicines. In this regard, there have been efforts to identify the risk of developing AD in its earliest time. While many of the previous works considered cross-sectional analysis, more recent studies have focused on the diagnosis and prognosis of AD with longitudinal or time series data in a way of disease progression modeling (DPM). Under the same problem settings, in this work, we propose a novel computational framework that ca…
Systems are commonly monitored for health and security through collection and streaming of multivariate time series. Advances in time series forecasting due to adoption of multilayer recurrent neural network architectures make it possible to forecast in high-dimensional time series, and identify and classify novelties early, based on subtle changes in the trends. However, mainstream approaches to multi-variate time series predictions do not handle well cases when the ongoing forecast must include uncertainty, nor they are robust to missing data. We introduce a new architecture for time series …
Biofisika Institute (CSIC, UPV/EHU)（生物物理研究所（西班牙国家研究委员会、巴斯克大学））；University of the Basque Country (UPV/EHU)（巴斯克大学）；IKERBASQUE, Basque Foundation for Science（巴斯克科学基金会（IKERBASQUE））
This paper provides a description of the approach and methodology I used in winning the European Union Big Data Technologies Horizon Prize on data-driven prediction of electricity grid traffic. The methodology relies on identifying typical short-term recurrent fluctuations, which is subsequently refined through a regression-of-fluctuations approach. The key points and strategic considerations that led to selecting or discarding different methodological aspects are also discussed. The criteria include adaptability to changing conditions, reliability with outliers and missing data, robustness to…
Australian National University（澳大利亚国立大学）；Data61, CSIRO（联邦科学与工业研究组织数据61所）
We propose a new model for networks of time series that influence each other. Graph structures among time series are found in diverse domains, such as web traffic influenced by hyperlinks, product sales influenced by recommendation, or urban transport volume influenced by road networks and weather. There has been recent progress in graph modeling and in time series forecasting, respectively, but an expressive and scalable approach for a network of series does not yet exist. We introduce Radflow, a novel model that embodies three key ideas: a recurrent neural network to obtain node embeddings t…
Pennsylvania State University（宾夕法尼亚州立大学）；IBM T.J. Watson（IBM托马斯·J·沃森研究中心）
Multivariate time series (MTS) forecasting is widely used in various domains, such as meteorology and traffic. Due to limitations on data collection, transmission, and storage, real-world MTS data usually contains missing values, making it infeasible to apply existing MTS forecasting models such as linear regression and recurrent neural networks. Though many efforts have been devoted to this problem, most of them solely rely on local dependencies for imputing missing values, which ignores global temporal dynamics. Local dependencies/patterns would become less useful when the missing ratio is h…
Biomediq A/S（Biomediq公司）；Cerebriu A/S（Cerebriu公司）；University of Copenhagen（哥本哈根大学）；University College London（伦敦大学学院）；King’s College London（伦敦国王学院）
Disease progression modeling (DPM) using longitudinal data is a challenging machine learning task. Existing DPM algorithms neglect temporal dependencies among measurements, make parametric assumptions about biomarker trajectories, do not model multiple biomarkers jointly, and need an alignment of subjects' trajectories. In this paper, recurrent neural networks (RNNs) are utilized to address these issues. However, in many cases, longitudinal cohorts contain incomplete data, which hinders the application of standard RNNs and requires a pre-processing step such as imputation of the missing values…
Beyond Random Missingness: Clinically Rethinking for Healthcare Time Series Imputation
King’s College London（伦敦国王学院）；PyPOTS Research（PyPOTS研究中心）；University of Oxford（牛津大学）；Hong Kong University of Science and Technology（香港科技大学）；University College London（伦敦大学学院）
UNICORN: A Deep Learning Model for Integrating Multi-Stain Data in Histopathology
Helmholtz Munich - German Research Center for Environmental Health（亥姆霍兹慕尼黑中心——德国环境健康研究中心）；School of Computation and Information Technology, Technical University of Munich（慕尼黑工业大学计算与信息技术学院）；Department of Cardiology, German Heart Centre Munich, TUM University Hospital（慕尼黑工业大学医院德国心脏中心心脏病学系）；DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance（德国心血管研究中心慕尼黑心脏联盟合作站点）；School of Biomedical Engineering and Imaging Sciences, King’s College London（伦敦国王学院生物医学工程与影像科学学院）；MLL Munich Leukemia Laboratory（MLL慕尼黑白血病实验室）
Flexible Multimodal Neuroimaging Fusion for Alzheimer's Disease Progression Prediction
Department of Computer Science and Engineering（计算机科学与工程系）；Department of Biomedical Informatics（生物医学信息学系）；Department of Neurology（神经病学系）；Translational Data Analytics Institute（转化数据分析研究所）
Technical University of Denmark（丹麦技术大学）；Niras（尼拉斯公司）
In the digitization of energy systems, sensors and smart meters are increasingly being used to monitor production, operation and demand. Detection of anomalies based on smart meter data is crucial to identify potential risks and unusual events at an early stage, which can serve as a reference for timely initiation of appropriate actions and improving management. However, smart meter data from energy systems often lack labels and contain noise and various patterns without distinctively cyclical. Meanwhile, the vague definition of anomalies in different energy scenarios and highly complex tempor…
Given a gallery of face images of missing children, state-of-the-art face recognition systems fall short in identifying a child (probe) recovered at a later age. We propose an age-progression module that can age-progress deep face features output by any commodity face matcher. For time lapses larger than 10 years (the missing child is found after 10 or more years), the proposed age-progression module improves the closed-set identification accuracy of FaceNet from 40% to 49.56% and CosFace from 56.88% to 61.25% on a child celebrity dataset, namely ITWCC. The proposed method also outperforms sta…
Handling Missing Modalities in Multimodal Survival Prediction for Non-Small Cell Lung Cancer
Unit of Artificial Intelligence and Computer Systems, Department of Engineering（人工智能与计算机系统单位，工程系）；Università Campus Bio-Medico di Roma（罗马生物医学大学）；Department of Diagnostics and Intervention, Radiation Physics, Biomedical Engineering（诊断与介入部门，辐射物理，生物医学工程）；Umeå University（乌梅学院）；Research Unit of Radiation Oncology, Department of Medicine and Surgery（放射肿瘤研究单位，医学与外科部门）；Fondazione Policlinico Universitario Campus Bio-Medico（生物医学大学附属医院基金会）；Anatomical Pathology Operative Research Unit（解剖病理学操作研究单位）；Research Unit of Anatomical Pathology, Department of Medicine and Surgery（解剖病理学研究单位，医学与外科部门）；Department of Medicine and Surgery（医学与外科部门）
Given a gallery of face images of missing children, state-of-the-art face recognition systems fall short in identifying a child (probe) recovered at a later age. We propose a feature aging module that can age-progress deep face features output by a face matcher. In addition, the feature aging module guides age-progression in the image space such that synthesized aged faces can be utilized to enhance longitudinal face recognition performance of any face matcher without requiring any explicit training. For time lapses larger than 10 years (the missing child is found after 10 or more years), the …
Idiopathic Pulmonary Fibrosis (IPF) is an inexorably progressive fibrotic lung disease with a variable and unpredictable rate of progression. CT scans of the lungs inform clinical assessment of IPF patients and contain pertinent information related to disease progression. In this work, we propose a multi-modal method that uses neural networks and memory banks to predict the survival of IPF patients using clinical and imaging data. The majority of clinical IPF patient records have missing data (e.g. missing lung function tests). To this end, we propose a probabilistic model that captures the de…
Alzheimers Disease Progression Prediction Based on Manifold Mapping of Irregularly Sampled Longitudinal Data
College of Computer Science and Technology, Huaqiao University（华侨大学计算机科学与技术学院）；Key Laboratory of Computer Vision and Machine Learning in Fujian Province（福建省计算机视觉与机器学习重点实验室）；College of Information Science and Engineering,Ritsumeikan University（立命馆大学信息科学与工程学院）
Peking University（北京大学）；Microsoft Research Asia（微软亚洲研究院）；Capital Medical University（首都医科大学）；Deepwise AI Lab（深睿医疗AI实验室）；Beijing Stars Universal Technology Co Ltd（北京星辰万联科技有限公司）
Forecasting Parapapillary atrophy (PPA), i.e., a symptom related to most irreversible eye diseases, provides an alarm for implementing an intervention to slow down the disease progression at early stage. A key question for this forecast is: how to fully utilize the historical data (e.g., retinal image) up to the current stage for future disease prediction? In this paper, we provide an answer with a novel framework, namely \textbf{D}isease \textbf{F}orecast via \textbf{P}rogression \textbf{L}earning (\textbf{DFPL}), which exploits the irreversibility prior (i.e., cannot be reversed once diagnos…
Smartphone applications designed to track human motion in combination with wearable sensors, e.g., during physical exercising, raised huge attention recently. Commonly, they provide quantitative services, such as personalized training instructions or the counting of distances. But qualitative monitoring and assessment is still missing, e.g., to detect malpositions, to prevent injuries, or to optimize training success. We address this issue by presenting a concept for qualitative as well as generic assessment of recurrent human motion by processing multi-dimensional, continuous time series trac…
University College London（伦敦大学学院）；Biomediq A/S（Biomediq公司）；University of Copenhagen（哥本哈根大学）；Cerebriu A/S（Cerebriu公司）
Learning temporal patterns from multivariate longitudinal data is challenging especially in cases when data is sporadic, as often seen in, e.g., healthcare applications where the data can suffer from irregularity and asynchronicity as the time between consecutive data points can vary across features and samples, hindering the application of existing deep learning models that are constructed for complete, evenly spaced data with fixed sequence lengths. In this paper, a novel deep learning-based model is developed for modeling multiple temporal features in sporadic data using an integrated deep …
Cornell（康奈尔大学）；Electrical and Computer Eng, Cornell（康奈尔大学电气与计算机工程学院）
In this work, we consider the problem of predicting the course of a progressive disease, such as cancer or Alzheimer's. Progressive diseases often start with mild symptoms that might precede a diagnosis, and each patient follows their own trajectory. Patient trajectories exhibit wild variability, which can be associated with many factors such as genotype, age, or sex. An additional layer of complexity is that, in real life, the amount and type of data available for each patient can differ significantly. For example, for one patient we might have no prior history, whereas for another patient we…
Medical Video Generation for Disease Progression Simulation
University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；University of Texas at Austin（德克萨斯大学奥斯汀分校）；SambaNova System, Inc（SambaNova系统公司）；Objective, Inc（Objective公司）；Microsoft（微软公司）；University of Virginia（弗吉尼亚大学）；Shenzhen Nanshan People’s Hospital（深圳市南山区人民医院）；Shenzhen Children’s Hospital（深圳市儿童医院）
Télécom SudParis, Institut Polytechnique de Paris（巴黎电信 SudParis，巴黎综合理工学院）；University College London（伦敦大学学院）；Digital Technologies and Artificial Intelligence Development Research Institute (AIRI)（数字技术与人工智能发展研究院（AIRI））
Recurrent neural networks are powerful tools for handling incomplete data problems in computer vision, thanks to their significant generative capabilities. However, the computational demand for these algorithms is too high to work in real time, without specialized hardware or software solutions. In this paper, we propose a framework for augmenting recurrent processing capabilities into a feedforward network without sacrificing much from computational efficiency. We assume a mixture model and generate samples of the last hidden layer according to the class decisions of the output layer, modify …
College of Information Science & Technology, Beijing University of Chemical Technology（北京化工大学信息科学与技术学院）；National Research Center for High-Performance Computing Engineering Technology, Sugon Information Industry Co., Ltd（曙光信息产业股份有限公司高性能计算工程技术国家研究中心）；Sichuan Provincial Key Laboratory of Information Coding and Transmission, Southwest Jiaotong University（西南交通大学信息编码与传输四川省重点实验室）；Institute of Electronics, Chinese Academy of Sciences（中国科学院电子学研究所）
The outstanding pattern recognition performance of deep learning brings new vitality to the synthetic aperture radar (SAR) automatic target recognition (ATR). However, there is a limitation in current deep learning based ATR solution that each learning process only handle one SAR image, namely learning the static scattering information, while missing the space-varying information. It is obvious that multi-aspect joint recognition introduced space-varying scattering information should improve the classification accuracy and robustness. In this paper, a novel multi-aspect-aware method is propose…
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；California Nano Systems Institute (CNSI)（加州纳米系统研究所）；David Geffen School of Medicine, University of California, Los Angeles（加利福尼亚大学洛杉矶分校大卫·格芬医学院）
Digital holography is one of the most widely used label-free microscopy techniques in biomedical imaging. Recovery of the missing phase information of a hologram is an important step in holographic image reconstruction. Here we demonstrate a convolutional recurrent neural network (RNN) based phase recovery approach that uses multiple holograms, captured at different sample-to-sensor distances to rapidly reconstruct the phase and amplitude information of a sample, while also performing autofocusing through the same network. We demonstrated the success of this deep learning-enabled holography me…
IIT Bombay（印度理工学院孟买分校）；Cornell University（康奈尔大学）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Adobe Research（Adobe研究院）
We present a deep, bidirectional, recurrent framework for cleaning noisy and incomplete motion capture data. It exploits temporal coherence and joint correlations to infer adaptive filters for each joint in each frame. A single model can be trained to denoise a heterogeneous mix of action types, under substantial amounts of noise. A signal that has both noise and gaps is preprocessed with a second bidirectional network that synthesizes missing frames from surrounding context. The approach handles a wide variety of noise types and long gaps, does not rely on knowledge of the noise distribution,…
University of Southern California（南加州大学）；US Army Research Laboratory（美国陆军研究实验室）
Recent advances in convolutional neural networks have shown promising results in 3D shape completion. But due to GPU memory limitations, these methods can only produce low-resolution outputs. To inpaint 3D models with semantic plausibility and contextual details, we introduce a hybrid framework that combines a 3D Encoder-Decoder Generative Adversarial Network (3D-ED-GAN) and a Long-term Recurrent Convolutional Network (LRCN). The 3D-ED-GAN is a 3D convolutional neural network trained with a generative adversarial paradigm to fill missing 3D data in low-resolution. LRCN adopts a recurrent neura…
Fraunhofer IOSB（弗劳恩霍夫光电、系统技术及图像处理研究所）；University of Nevada, Las Vegas（内华达大学拉斯维加斯分校）
In tasks such as tracking, time-series data inevitably carry missing observations. While traditional tracking approaches can handle missing observations, recurrent neural networks (RNNs) are designed to receive input data in every step. Furthermore, current solutions for RNNs, like omitting the missing data or data imputation, are not sufficient to account for the resulting increased uncertainty. Towards this end, this paper introduces an RNN-based approach that provides a full temporal filtering cycle for motion state estimation. The Kalman filter inspired approach, enables to deal with missi…
University of Central Florida（中佛罗里达大学）；Megvii Technology（旷视科技）
In this paper, we present a new inpainting framework for recovering missing regions of video frames. Compared with image inpainting, performing this task on video presents new challenges such as how to preserving temporal consistency and spatial details, as well as how to handle arbitrary input video size and length fast and efficiently. Towards this end, we propose a novel deep learning architecture which incorporates ConvLSTM and optical flow for modeling the spatial-temporal consistency in videos. It also saves much computational resource such that our method can handle videos with larger f…
In this paper, we propose a predictive regression model for longitudinal images with missing data based on large deformation diffeomorphic metric mapping (LDDMM) and deep neural networks. Instead of directly predicting image scans, our model predicts a vector momentum sequence associated with a baseline image. This momentum sequence parameterizes the original image sequence in the LDDMM framework and lies in the tangent space of the baseline image, which is Euclidean. A recurrent network with long term-short memory (LSTM) units encodes the time-varying changes in the vector-momentum sequence, …
Multi-View Imputation and Cross-Attention Network Based on Incomplete Longitudinal and Multimodal Data for Conversion Prediction of Mild Cognitive Impairment
Cine cardiac MRI reconstruction using a convolutional recurrent network with refinement
Institute for Digital Communications, University of Edinburgh（爱丁堡大学数字通信研究所）；Institute of Information Science and Technologies “Alessandro Faedo”, National Research Council of Italy (CNR)（意大利国家研究委员会信息科学与技术研究所（亚历山德罗·法埃多））；Department of Information Engineering, University of Pisa（比萨大学信息工程系）；Institute for Infrastructure and Environment, University of Edinburgh（爱丁堡大学基础设施与环境研究所）；The Alan Turing Institute（阿兰·图灵研究所）
Video super-resolution (VSR) aims to estimate a high-resolution (HR) frame from a low-resolution (LR) frames. The key challenge for VSR lies in the effective exploitation of spatial correlation in an intra-frame and temporal dependency between consecutive frames. However, most of the previous methods treat different types of the spatial features identically and extract spatial and temporal features from the separated modules. It leads to lack of obtaining meaningful information and enhancing the fine details. In VSR, there are three types of temporal modeling frameworks: 2D convolutional neura…
Given a video and a description sentence with one missing word (we call it the "source sentence"), Video-Fill-In-the-Blank (VFIB) problem is to find the missing word automatically. The contextual information of the sentence, as well as visual cues from the video, are important to infer the missing word accurately. Since the source sentence is broken into two fragments: the sentence's left fragment (before the blank) and the sentence's right fragment (after the blank), traditional Recurrent Neural Networks cannot encode this structure accurately because of many possible variations of the missin…
