Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI
Faculty of Physics and Astronomy, Heidelberg University（海德堡大学物理与天文学学院）；Institute of Neuroinformatics, University of Zurich and ETH Zurich（苏黎世大学与苏黎世联邦理工学院神经信息学研究所）
Georgia Koppe, Hazem Toutounji, Peter Kirsch, Stefanie Lis, Daniel Durstewitz
A major tenet in theoretical neuroscience is that cognitive and behavioral processes are ultimately implemented in terms of the neural system dynamics. Accordingly, a major aim for the analysis of neurophysiological measurements should lie in the identification of the computational dynamics underlying task processing. Here we advance a state space model (SSM) based on generative piecewise-linear recurrent neural networks (PLRNN) to assess dynamics from neuroimaging data. In contrast to many other nonlinear time series models which have been proposed for reconstructing latent dynamics, our model is easily interpretable in neural terms, amenable to systematic dynamical systems analysis of the resulting set of equations, and can straightforwardly be transformed into an equivalent continuous-time dynamical system. The major contributions of this paper are the introduction of a new observation model suitable for functional magnetic resonance imaging (fMRI) coupled to the latent PLRNN, an efficient stepwise training procedure that forces the latent model to capture the 'true' underlying dynamics rather than just fitting (or predicting) the observations, and of an empirical measure based on the Kullback-Leibler divergence to evaluate from empirical time series how well this goal of approximating the underlying dynamics has been achieved. We validate and illustrate the power of our approach on simulated 'ground-truth' dynamical (benchmark) systems as well as on actual experimental fMRI time series, and demonstrate that the latent dynamics harbors task-related nonlinear structure that a linear dynamical model fails to capture. Given that fMRI is one of the most common techniques for measuring brain activity non-invasively in human subjects, this approach may provide a novel step toward analyzing aberrant (nonlinear) dynamics for clinical assessment or neuroscientific research.
Columbia University（哥伦比亚大学）；Stanford University（斯坦福大学）
We propose a hierarchical Bayesian recurrent state space model for modeling switching network connectivity in resting state fMRI data. Our model allows us to uncover shared network patterns across disease conditions. We evaluate our method on the ADNI2 dataset by inferring latent state patterns corresponding to altered neural circuits in individuals with Mild Cognitive Impairment (MCI). In addition to states shared across healthy and individuals with MCI, we discover latent states that are predominantly observed in individuals with MCI. Our model outperforms current state of the art deep learn…
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁医学院）
Recurrent neural networks (RNNs) were designed for dealing with time-series data and have recently been used for creating predictive models from functional magnetic resonance imaging (fMRI) data. However, gathering large fMRI datasets for learning is a difficult task. Furthermore, network interpretability is unclear. To address these issues, we utilize multitask learning and design a novel RNN-based model that learns to discriminate between classes while simultaneously learning to generate the fMRI time-series data. Employing the long short-term memory (LSTM) structure, we develop a discrimina…
Recent efforts to improve the interpretability of deep neural networks use saliency to characterize the importance of input features to predictions made by models. Work on interpretability using saliency-based methods on Recurrent Neural Networks (RNNs) has mostly targeted language tasks, and their applicability to time series data is less understood. In this work we analyze saliency-based methods for RNNs, both classical and gated cell architectures. We show that RNN saliency vanishes over time, biasing detection of salient features only to later time steps and are, therefore, incapable of re…
IIIT Hyderabad（海得拉巴国际信息技术学院）；University of Hyderabad（海得拉巴大学）
fMRI semantic category understanding using linguistic encoding models attempt to learn a forward mapping that relates stimuli to the corresponding brain activation. Classical encoding models use linear multi-variate methods to predict the brain activation (all voxels) given the stimulus. However, these methods essentially assume multiple regions as one large uniform region or several independent regions, ignoring connections among them. In this paper, we present a mixture of experts-based model where a group of experts captures brain activity patterns related to particular regions of interest …
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁大学医学院）
Heterogeneous presentation of a neurological disorder suggests potential differences in the underlying pathophysiological changes that occur in the brain. We propose to model heterogeneous patterns of functional network differences using a demographic-guided attention (DGA) mechanism for recurrent neural network models for prediction from functional magnetic resonance imaging (fMRI) time-series data. The context computed from the DGA head is used to help focus on the appropriate functional networks based on individual demographic information. We demonstrate improved classification on 3 subsets…
Functional Magnetic Resonance Imaging (fMRI) is a neuroimaging technique with pivotal importance due to its scientific and clinical applications. As with any widely used imaging modality, there is a need to ensure the quality of the same, with missing values being highly frequent due to the presence of artifacts or sub-optimal imaging resolutions. Our work focus on missing values imputation on multivariate signal data. To do so, a new imputation method is proposed consisting on two major steps: spatial-dependent signal imputation and time-dependent regularization of the imputed signal. A novel…
Functional Magnetic Resonance Imaging (fMRI) is a primary modality for studying brain activity. Modeling spatial dependence of imaging data at different scales is one of the main challenges of contemporary neuroimaging, and it could allow for accurate testing for significance in neural activity. The high dimensionality of this type of data (on the order of hundreds of thousands of voxels) poses serious modeling challenges and considerable computational constraints. For the sake of feasibility, standard models typically reduce dimensionality by modeling covariance among regions of interest (ROI…
Yale School of Medicine（耶鲁大学医学院）；Yale University（耶鲁大学）
We propose a method for estimating more reproducible functional networks that are more strongly associated with dynamic task activity by using recurrent neural networks with long short term memory (LSTMs). The LSTM model is trained in an unsupervised manner to learn to generate the functional magnetic resonance imaging (fMRI) time-series data in regions of interest. The learned functional networks can then be used for further analysis, e.g., correlation analysis to determine functional networks that are strongly associated with an fMRI task paradigm. We test our approach and compare to other m…
Resting-state fMRI Analysis using Quantum Time-series Transformer
Interdisciplinary Program in Artificial Intelligence（人工智能交叉学科项目）；Department of Brain and Cognitive Sciences（脑科学与认知科学系）；Wells Fargo（沃伦·巴菲特）；Artificial Intelligence Department（人工智能部门）；Brookhaven National Laboratory（布鲁赫斯林国家实验室）；Department of Psychology（心理学系）
Technische Universität Berlin（柏林工业大学）；Freie Universität Berlin（柏林自由大学）；Korea University（高丽大学）；Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）；Fraunhofer Heinrich Hertz Institute（弗劳恩霍夫海因里希·赫兹研究所）
The application of deep learning (DL) models to neuroimaging data poses several challenges, due to the high dimensionality, low sample size and complex temporo-spatial dependency structure of these datasets. Even further, DL models act as as black-box models, impeding insight into the association of cognitive state and brain activity. To approach these challenges, we introduce the DeepLight framework, which utilizes long short-term memory (LSTM) based DL models to analyze whole-brain functional Magnetic Resonance Imaging (fMRI) data. To decode a cognitive state (e.g., seeing the image of a hou…
Shaanxi Normal University（陕西师范大学）；University of Georgia（佐治亚大学）；Northwestern Polytechnical University（西北工业大学）；University of Texas at Arlington（德克萨斯大学阿灵顿分校）
Using deep learning models to recognize functional brain networks (FBNs) in functional magnetic resonance imaging (fMRI) has been attracting increasing interest recently. However, most existing work focuses on detecting static FBNs from entire fMRI signals, such as correlation-based functional connectivity. Sliding-window is a widely used strategy to capture the dynamics of FBNs, but it is still limited in representing intrinsic functional interactive dynamics at each time step. And the number of FBNs usually need to be set manually. More over, due to the complexity of dynamic interactions in …
Deep neural networks have shown promising results for various clinical prediction tasks such as diagnosis, mortality prediction, predicting duration of stay in hospital, etc. However, training deep networks -- such as those based on Recurrent Neural Networks (RNNs) -- requires large labeled data, high computational resources, and significant hyperparameter tuning effort. In this work, we investigate as to what extent can transfer learning address these issues when using deep RNNs to model multivariate clinical time series. We consider transferring the knowledge captured in an RNN trained on se…
Surrogate testing techniques have been used widely to investigate the presence of dynamical nonlinearities, an essential ingredient of deterministic chaotic processes. Traditional surrogate testing subscribes to statistical hypothesis testing and investigates potential differences in discriminant statistics between the given empirical sample and its surrogate counterparts. The choice and estimation of the discriminant statistics can be challenging across short time series. Also, conclusion based on a single empirical sample is an inherent limitation. The present study proposes a recurrent neur…
Heidelberg University（海德堡大学）；Central Institute of Mental Health（中央心理健康研究所）
A main theoretical interest in biology and physics is to identify the nonlinear dynamical system (DS) that generated observed time series. Recurrent Neural Networks (RNNs) are, in principle, powerful enough to approximate any underlying DS, but in their vanilla form suffer from the exploding vs. vanishing gradients problem. Previous attempts to alleviate this problem resulted either in more complicated, mathematically less tractable RNN architectures, or strongly limited the dynamical expressiveness of the RNN. Here we address this issue by suggesting a simple regularization scheme for vanilla…
Recurrent Quantum Feature Maps for Reservoir Computing
Department of Physics, University of Ottawa（渥太华大学物理系）；National Research Council of Canada（加拿大国家研究委员会）；Institute for Quantum Science and Technology, Department of Physics and Astronomy, University of Calgary（卡尔加里大学物理与天文学系量子科学与技术研究所）；Hotchkiss Brain Institute, University of Calgary（卡尔加里大学霍奇基斯脑研究所）
Okinawa Institute of Science and Technology Graduate University（冲绳科学技术大学院大学）；Advanced Telecommunications Research Institutes International（国际先进电信研究所）；RIKEN（理化学研究所）；Nara Institute of Science and Technology（奈良先端科学技术大学院大学）
In neuroscience, the functional magnetic resonance imaging (fMRI) is a vital tool to non-invasively access brain activity. Using fMRI, the functional connectivity (FC) between brain regions can be inferred, which has contributed to a number of findings of the fundamental properties of the brain. As an important clinical application of FC, clustering of subjects based on FC recently draws much attention, which can potentially reveal important heterogeneity in subjects such as subtypes of psychiatric disorders. In particular, a multiple-view clustering method is a powerful analytical tool, which…
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁医学院）
Finding the biomarkers associated with ASD is helpful for understanding the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. A promising approach to identify biomarkers is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, i.e. brain networks constructed by fMRI. One way to interpret important features is through looking at how the classification probability changes if the features are occluded or replaced. The major limitation of this approach is that replacing values may change the distribution of the data an…
Direct Estimation of Pediatric Heart Rate Variability from BOLD-fMRI: A Machine Learning Approach Using Dynamic Connectivity
University of Calgary（卡尔加里大学）；Cumming School of Medicine, University of Calgary（卡尔加里大学卡明医学院）；Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary（卡尔加里大学卡明医学院霍奇基斯脑研究所）；University of New England（新英格兰大学）
School of Computer Science, Tel Aviv University（特拉维夫大学计算机科学学院）；School of Psychological Sciences, Tel Aviv University（特拉维夫大学心理科学学院）；Sackler Faculty of Medicine, Tel Aviv University（特拉维夫大学萨克勒医学院）；Sagol School of Neuroscience, Tel Aviv University（特拉维夫大学萨戈尔神经科学学院）
We present a deep neural network method for learning a personal representation for individuals that are performing a self neuromodulation task, guided by functional MRI (fMRI). This neurofeedback task (watch vs. regulate) provides the subjects with a continuous feedback contingent on down regulation of their Amygdala signal and the learning algorithm focuses on this region's time-course of activity. The representation is learned by a self-supervised recurrent neural network, that predicts the Amygdala activity in the next fMRI frame given recent fMRI frames and is conditioned on the learned in…
Wayne State University（韦恩州立大学）；New York University（纽约大学）
Understanding human fetal neurodevelopment is of great clinical importance as abnormal development is linked to adverse neuropsychiatric outcomes after birth. Recent advances in functional Magnetic Resonance Imaging (fMRI) have provided new insight into development of the human brain before birth, but these studies have predominately focused on brain functional connectivity (i.e. Fisher z-score), which requires manual processing steps for feature extraction from fMRI images. Deep learning approaches (i.e., Convolutional Neural Networks) have achieved remarkable success on learning directly fro…
Xi'an Jiaotong University（西安交通大学）；Shanghai University of Finance and Economics（上海财经大学）；Fourth Military Medical University（第四军医大学）；Air Force Medical University（空军军医大学）；Xijing Hospital（西京医院）
Major depressive disorder (MDD) requires study of brain functional connectivity alterations for patients, which can be uncovered by resting-state functional magnetic resonance imaging (rs-fMRI) data. We consider the problem of identifying alterations of brain functional connectivity for a single MDD patient. This is particularly difficult since the amount of data collected during an fMRI scan is too limited to provide sufficient information for individual analysis. Additionally, rs-fMRI data usually has the characteristics of incompleteness, sparsity, variability, high dimensionality and high …
Identifying Neural Signatures from fMRI using Hybrid Principal Components Regression
Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus（生物统计学与信息学系，科罗拉多大学安施图茨医疗校区）；Department of Biostatistics and Bioinformatics, Emory University（生物统计学与生物信息学系，埃默里大学）；Department of Radiology, University of Colorado Anschutz Medical Campus（放射学系，科罗拉多大学安施图茨医疗校区）；Laureate Institute for Brain Research, Tulsa, OK, USA（脑研究拉奥尔特研究所，俄克拉荷马州塔尔萨市）；Department of Community Medicine, University of Tulsa（社区医学系，塔尔萨大学）；Department of Internal Medicine, Carver College of Medicine, University of Iowa（内科学系，卡弗医学院，爱荷华大学）
University of Rochester（罗切斯特大学）；Ludwig Maximilian University（路德维希·马克西米利安大学）
We introduce large-scale Augmented Granger Causality (lsAGC) as a method for connectivity analysis in complex systems. The lsAGC algorithm combines dimension reduction with source time-series augmentation and uses predictive time-series modeling for estimating directed causal relationships among time-series. This method is a multivariate approach, since it is capable of identifying the influence of each time-series on any other time-series in the presence of all other time-series of the underlying dynamic system. We quantitatively evaluate the performance of lsAGC on synthetic directional time…
University Paderborn（帕德博恩大学）；Heinz Nixdorf Institute（海因茨·尼克斯多夫研究所）；Paderborn University（帕德博恩大学）
While trade-offs between modeling effort and model accuracy remain a major concern with system identification, resorting to data-driven methods often leads to a complete disregard for physical plausibility. To address this issue, we propose a physics-guided hybrid approach for modeling non-autonomous systems under control. Starting from a traditional physics-based model, this is extended by a recurrent neural network and trained using a sophisticated multi-objective strategy yielding physically plausible models. While purely data-driven methods fail to produce satisfying results, experiments c…
Contrastive Graph Pooling for Explainable Classification of Brain Networks
School of Computer Science and Engineering, Nanyang Technological University（南洋理工大学计算机科学与工程学院）；Department of Computer Science and Technology, Tsinghua University（清华大学计算机科学与技术系）；School of Computer Science, the University of Auckland（奥克兰大学计算机学院）；Lee Kong Chian School of Medicine, Nanyang Technological University（南洋理工大学李光前医学院）
Graph processes model a number of important problems such as identifying the epicenter of an earthquake or predicting weather. In this paper, we propose a Graph Convolutional Recurrent Neural Network (GCRNN) architecture specifically tailored to deal with these problems. GCRNNs use convolutional filter banks to keep the number of trainable parameters independent of the size of the graph and of the time sequences considered. We also put forward Gated GCRNNs, a time-gated variation of GCRNNs akin to LSTMs. When compared with GNNs and another graph recurrent architecture in experiments using both…
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used handcrafted features on human-annotated data sets. In this paper, we propose a novel tree recurrent neural network with structured attention architecture for doing PPI. Our architecture achieves state of the art results (precision, recall, and F1-score) on the AIMed and BioInfer benchmark data sets. Moreover, our models achieve a significant improvement over …
Multimodal Recurrent Ensembles for Predicting Brain Responses to Naturalistic Movies (Algonauts 2025)
Max Planck Institute for Human Cognitive and Brain Sciences（马克斯·普朗克人类认知与脑科学研究所）；TU Dresden（德累斯顿技术大学）；School for Embedded and Composite AI (SECAI)（嵌入式与复合人工智能学院）；Center for Scalable Data Analytics & AI (ScaDS.AI)（可扩展数据与人工智能中心）
University of Florida（佛罗里达大学）；UiT - The Arctic University of Norway（挪威北极圈大学）
We propose causal recurrent variational autoencoder (CR-VAE), a novel generative model that is able to learn a Granger causal graph from a multivariate time series x and incorporates the underlying causal mechanism into its data generation process. Distinct to the classical recurrent VAEs, our CR-VAE uses a multi-head decoder, in which the $p$-th head is responsible for generating the $p$-th dimension of $\mathbf{x}$ (i.e., $\mathbf{x}^p$). By imposing a sparsity-inducing penalty on the weights (of the decoder) and encouraging specific sets of weights to be zero, our CR-VAE learns a sparse adj…
ADVA Optical Networking SE（ADVA光网络公司）；Christian-Albrechts-Universität zu Kiel（基尔大学）
We propose a deep learning approach based on an autoencoder for identifying and localizing fiber faults in passive optical networks. The experimental results show that the proposed method detects faults with 97% accuracy, pinpoints them with an RMSE of 0.18 m and outperforms conventional techniques.
Electronic Medical Records (EMR) are a rich source of patient information, including measurements reflecting physiologic signs and administered therapies. Identifying which variables are useful in predicting clinical outcomes can be challenging. Advanced algorithms such as deep neural networks were designed to process high-dimensional inputs containing variables in their measured form, thus bypass separate feature selection or engineering steps. We investigated the effect of extraneous input variables on the predictive performance of Recurrent Neural Networks (RNN) by including in the input ve…
Deep learning has demonstrated success in many applications; however, their use in healthcare has been limited due to the lack of transparency into how they generate predictions. Algorithms such as Recurrent Neural Networks (RNNs) when applied to Electronic Medical Records (EMR) introduce additional barriers to transparency because of the sequential processing of the RNN and the multi-modal nature of EMR data. This work seeks to improve transparency by: 1) introducing Learned Binary Masks (LBM) as a method for identifying which EMR variables contributed to an RNN model's risk of mortality (ROM…
The use of sensors available through smart devices has pervaded everyday life in several applications including human activity monitoring, healthcare, and social networks. In this study, we focus on the use of smartwatch accelerometer sensors to recognize eating activity. More specifically, we collected sensor data from 10 participants while consuming pizza. Using this information, and other comparable data available for similar events such as smoking and medication-taking, and dissimilar activities of jogging, we developed a LSTM-ANN architecture that has demonstrated 90% success in identifyi…
Modern malware typically makes use of a domain generation algorithm (DGA) to avoid command and control domains or IPs being seized or sinkholed. This means that an infected system may attempt to access many domains in an attempt to contact the command and control server. Therefore, the automatic detection of DGA domains is an important task, both for the sake of blocking malicious domains and identifying compromised hosts. However, many DGAs use English wordlists to generate plausibly clean-looking domain names; this makes automatic detection difficult. In this work, we devise a notion of diff…
Word sense disambiguation helps identifying the proper sense of ambiguous words in text. With large terminologies such as the UMLS Metathesaurus ambiguities appear and highly effective disambiguation methods are required. Supervised learning algorithm methods are used as one of the approaches to perform disambiguation. Features extracted from the context of an ambiguous word are used to identify the proper sense of such a word. The type of features have an impact on machine learning methods, thus affect disambiguation performance. In this work, we have evaluated several types of features deriv…
Behavioral malware detection aims to improve on the performance of static signature-based techniques used by anti-virus systems, which are less effective against modern polymorphic and metamorphic malware. Behavioral malware classification aims to go beyond the detection of malware by also identifying a malware's family according to a naming scheme such as the ones used by anti-virus vendors. Behavioral malware classification techniques use run-time features, such as file system or network activities, to capture the behavioral characteristic of running processes. The increasing volume of malwa…
Acoustic characterization of speech rhythm: going beyond metrics with recurrent neural networks
Purdue University（普渡大学）；Ghent University（根特大学）；Integrative Neuroscience and Cognition Center, CNRS & Université Paris Cité（整合神经科学与认知中心，法国国家科学研究中心与巴黎西岱大学）；University of Padua（帕多瓦大学）
University of Oxford（牛津大学）；University of Kent（肯特大学）
The emergence of online services in our daily lives has been accompanied by a range of malicious attempts to trick individuals into performing undesired actions, often to the benefit of the adversary. The most popular medium of these attempts is phishing attacks, particularly through emails and websites. In order to defend against such attacks, there is an urgent need for automated mechanisms to identify this malevolent content before it reaches users. Machine learning techniques have gradually become the standard for such classification problems. However, identifying common measurable feature…
IBM T.J. Watson Research Center（IBM T.J.沃森研究中心）；Massachusetts Institute of Technology（麻省理工学院）
We propose a recurrent neural network for a "model-free" simulation of a dynamical system with unknown parameters without prior knowledge. The deep learning model aims to jointly learn the nonlinear time marching operator and the effects of the unknown parameters from a time series dataset. We assume that the time series data set consists of an ensemble of trajectories for a range of the parameters. The learning task is formulated as a statistical inference problem by considering the unknown parameters as random variables. A latent variable is introduced to model the effects of the unknown par…
Brain-related disorders such as epilepsy can be diagnosed by analyzing electroencephalograms (EEG). However, manual analysis of EEG data requires highly trained clinicians, and is a procedure that is known to have relatively low inter-rater agreement (IRA). Moreover, the volume of the data and the rate at which new data becomes available make manual interpretation a time-consuming, resource-hungry, and expensive process. In contrast, automated analysis of EEG data offers the potential to improve the quality of patient care by shortening the time to diagnosis and reducing manual error. In this …
California Institute of Technology（加州理工学院）；European Organization for Nuclear Research (CERN)（欧洲核子研究组织（CERN））；Imperial College London（帝国理工学院）
This paper presents novel reconfigurable architectures for reducing the latency of recurrent neural networks (RNNs) that are used for detecting gravitational waves. Gravitational interferometers such as the LIGO detectors capture cosmic events such as black hole mergers which happen at unknown times and of varying durations, producing time-series data. We have developed a new architecture capable of accelerating RNN inference for analyzing time-series data from LIGO detectors. This architecture is based on optimizing the initiation intervals (II) in a multi-layer LSTM (Long Short-Term Memory) …
