arXiv subjects

Ehsan Adeli

Publications and source records attributed to Ehsan Adeli.

At least 109 records · Page 6Linked to original sources

arXiv2022

Bridging the Gap between Deep Learning and Hypothesis-Driven Analysis via Permutation Testing

A fundamental approach in neuroscience research is to test hypotheses based on neuropsychological and behavioral measures, i.e., whether certain factors (e.g., related to life events) are associated with an outcome (e.g., depression). In recent years, deep learning has become a potential alternative approach for conducting such analyses by predicting an outcome from a collection of factors and identifying the most "informative" ones driving the prediction. However, this approach has had limited impact as its findings are not linked to statistical significance of factors supporting hypotheses. In this article, we proposed a flexible and scalable approach based on the concept of permutation testing that integrates hypothesis testing into the data-driven deep learning analysis. We apply our approach to the yearly self-reported assessments of 621 adolescent participants of the National Consortium of Alcohol and Neurodevelopment in Adolescence (NCANDA) to predict negative valence, a symptom of major depressive disorder according to the NIMH Research Domain Criteria (RDoC). Our method successfully identifies categories of risk factors that further explain the symptom.

cs.LG↗

arXiv2022

On the Opportunities and Risks of Foundation Models

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

cs.LG↗

arXiv2022

A Penalty Approach for Normalizing Feature Distributions to Build Confounder-Free Models

Translating machine learning algorithms into clinical applications requires addressing challenges related to interpretability, such as accounting for the effect of confounding variables (or metadata). Confounding variables affect the relationship between input training data and target outputs. When we train a model on such data, confounding variables will bias the distribution of the learned features. A recent promising solution, MetaData Normalization (MDN), estimates the linear relationship between the metadata and each feature based on a non-trainable closed-form solution. However, this estimation is confined by the sample size of a mini-batch and thereby may cause the approach to be unstable during training. In this paper, we extend the MDN method by applying a Penalty approach (referred to as PDMN). We cast the problem into a bi-level nested optimization problem. We then approximate this optimization problem using a penalty method so that the linear parameters within the MDN layer are trainable and learned on all samples. This enables PMDN to be plugged into any architectures, even those unfit to run batch-level operations, such as transformers and recurrent models. We show improvement in model accuracy and greater independence from confounders using PMDN over MDN in a synthetic experiment and a multi-label, multi-site dataset of magnetic resonance images (MRIs).

cs.LG↗

arXiv2022

GaitForeMer: Self-Supervised Pre-Training of Transformers via Human Motion Forecasting for Few-Shot Gait Impairment Severity Estimation

Parkinson's disease (PD) is a neurological disorder that has a variety of observable motor-related symptoms such as slow movement, tremor, muscular rigidity, and impaired posture. PD is typically diagnosed by evaluating the severity of motor impairments according to scoring systems such as the Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS). Automated severity prediction using video recordings of individuals provides a promising route for non-intrusive monitoring of motor impairments. However, the limited size of PD gait data hinders model ability and clinical potential. Because of this clinical data scarcity and inspired by the recent advances in self-supervised large-scale language models like GPT-3, we use human motion forecasting as an effective self-supervised pre-training task for the estimation of motor impairment severity. We introduce GaitForeMer, Gait Forecasting and impairment estimation transforMer, which is first pre-trained on public datasets to forecast gait movements and then applied to clinical data to predict MDS-UPDRS gait impairment severity. Our method outperforms previous approaches that rely solely on clinical data by a large margin, achieving an F1 score of 0.76, precision of 0.79, and recall of 0.75. Using GaitForeMer, we show how public human movement data repositories can assist clinical use cases through learning universal motion representations. The code is available at https://github.com/markendo/GaitForeMer .

cs.CV↗

arXiv2022

Combining Counterfactuals With Shapley Values To Explain Image Models

With the widespread use of sophisticated machine learning models in sensitive applications, understanding their decision-making has become an essential task. Models trained on tabular data have witnessed significant progress in explanations of their underlying decision making processes by virtue of having a small number of discrete features. However, applying these methods to high-dimensional inputs such as images is not a trivial task. Images are composed of pixels at an atomic level and do not carry any interpretability by themselves. In this work, we seek to use annotated high-level interpretable features of images to provide explanations. We leverage the Shapley value framework from Game Theory, which has garnered wide acceptance in general XAI problems. By developing a pipeline to generate counterfactuals and subsequently using it to estimate Shapley values, we obtain contrastive and interpretable explanations with strong axiomatic guarantees.

cs.LG↗

arXiv2022

Explaining Image Classifiers Using Contrastive Counterfactuals in Generative Latent Spaces

Despite their high accuracies, modern complex image classifiers cannot be trusted for sensitive tasks due to their unknown decision-making process and potential biases. Counterfactual explanations are very effective in providing transparency for these black-box algorithms. Nevertheless, generating counterfactuals that can have a consistent impact on classifier outputs and yet expose interpretable feature changes is a very challenging task. We introduce a novel method to generate causal and yet interpretable counterfactual explanations for image classifiers using pretrained generative models without any re-training or conditioning. The generative models in this technique are not bound to be trained on the same data as the target classifier. We use this framework to obtain contrastive and causal sufficiency and necessity scores as global explanations for black-box classifiers. On the task of face attribute classification, we show how different attributes influence the classifier output by providing both causal and contrastive feature attributions, and the corresponding counterfactual images.

cs.CV↗

arXiv2022

An advanced spatio-temporal convolutional recurrent neural network for storm surge predictions

In this research paper, we study the capability of artificial neural network models to emulate storm surge based on the storm track/size/intensity history, leveraging a database of synthetic storm simulations. Traditionally, Computational Fluid Dynamics solvers are employed to numerically solve the storm surge governing equations that are Partial Differential Equations and are generally very costly to simulate. This study presents a neural network model that can predict storm surge, informed by a database of synthetic storm simulations. This model can serve as a fast and affordable emulator for the very expensive CFD solvers. The neural network model is trained with the storm track parameters used to drive the CFD solvers, and the output of the model is the time-series evolution of the predicted storm surge across multiple nodes within the spatial domain of interest. Once the model is trained, it can be deployed for further predictions based on new storm track inputs. The developed neural network model is a time-series model, a Long short-term memory, a variation of Recurrent Neural Network, which is enriched with Convolutional Neural Networks. The convolutional neural network is employed to capture the correlation of data spatially. Therefore, the temporal and spatial correlations of data are captured by the combination of the mentioned models, the ConvLSTM model. As the problem is a sequence to sequence time-series problem, an encoder-decoder ConvLSTM model is designed. Some other techniques in the process of model training are also employed to enrich the model performance. The results show the proposed convolutional recurrent neural network outperforms the Gaussian Process implementation for the examined synthetic storm database.

cs.LG↗

arXiv2022

Rethinking Architecture Design for Tackling Data Heterogeneity in Federated Learning

Federated learning is an emerging research paradigm enabling collaborative training of machine learning models among different organizations while keeping data private at each institution. Despite recent progress, there remain fundamental challenges such as the lack of convergence and the potential for catastrophic forgetting across real-world heterogeneous devices. In this paper, we demonstrate that self-attention-based architectures (e.g., Transformers) are more robust to distribution shifts and hence improve federated learning over heterogeneous data. Concretely, we conduct the first rigorous empirical investigation of different neural architectures across a range of federated algorithms, real-world benchmarks, and heterogeneous data splits. Our experiments show that simply replacing convolutional networks with Transformers can greatly reduce catastrophic forgetting of previous devices, accelerate convergence, and reach a better global model, especially when dealing with heterogeneous data. We release our code and pretrained models at https://github.com/Liangqiong/ViT-FL-main to encourage future exploration in robust architectures as an alternative to current research efforts on the optimization front.

cs.LG↗

arXiv2022

Intervertebral Disc Labeling With Learning Shape Information, A Look Once Approach

Accurate and automatic segmentation of intervertebral discs from medical images is a critical task for the assessment of spine-related diseases such as osteoporosis, vertebral fractures, and intervertebral disc herniation. To date, various approaches have been developed in the literature which routinely relies on detecting the discs as the primary step. A disadvantage of many cohort studies is that the localization algorithm also yields false-positive detections. In this study, we aim to alleviate this problem by proposing a novel U-Net-based structure to predict a set of candidates for intervertebral disc locations. In our design, we integrate the image shape information (image gradients) to encourage the model to learn rich and generic geometrical information. This additional signal guides the model to selectively emphasize the contextual representation and suppress the less discriminative features. On the post-processing side, to further decrease the false positive rate, we propose a permutation invariant 'look once' model, which accelerates the candidate recovery procedure. In comparison with previous studies, our proposed approach does not need to perform the selection in an iterative fashion. The proposed method was evaluated on the spine generic public multi-center dataset and demonstrated superior performance compared to previous work. We have provided the implementation code in https://github.com/rezazad68/intervertebral-lookonce

cs.CV↗

arXiv2021

Convolutional generative adversarial imputation networks for spatio-temporal missing data in storm surge simulations

Imputation of missing data is a task that plays a vital role in a number of engineering and science applications. Often such missing data arise in experimental observations from limitations of sensors or post-processing transformation errors. Other times they arise from numerical and algorithmic constraints in computer simulations. One such instance and the application emphasis of this paper are numerical simulations of storm surge. The simulation data corresponds to time-series surge predictions over a number of save points within the geographic domain of interest, creating a spatio-temporal imputation problem where the surge points are heavily correlated spatially and temporally, and the missing values regions are structurally distributed at random. Very recently, machine learning techniques such as neural network methods have been developed and employed for missing data imputation tasks. Generative Adversarial Nets (GANs) and GAN-based techniques have particularly attracted attention as unsupervised machine learning methods. In this study, the Generative Adversarial Imputation Nets (GAIN) performance is improved by applying convolutional neural networks instead of fully connected layers to better capture the correlation of data and promote learning from the adjacent surge points. Another adjustment to the method needed specifically for the studied data is to consider the coordinates of the points as additional features to provide the model more information through the convolutional layers. We name our proposed method as Convolutional Generative Adversarial Imputation Nets (Conv-GAIN). The proposed method's performance by considering the improvements and adaptations required for the storm surge data is assessed and compared to the original GAIN and a few other techniques. The results show that Conv-GAIN has better performance than the alternative methods on the studied data.

cs.LG↗

arXiv2021

TRiPOD: Human Trajectory and Pose Dynamics Forecasting in the Wild

Joint forecasting of human trajectory and pose dynamics is a fundamental building block of various applications ranging from robotics and autonomous driving to surveillance systems. Predicting body dynamics requires capturing subtle information embedded in the humans' interactions with each other and with the objects present in the scene. In this paper, we propose a novel TRajectory and POse Dynamics (nicknamed TRiPOD) method based on graph attentional networks to model the human-human and human-object interactions both in the input space and the output space (decoded future output). The model is supplemented by a message passing interface over the graphs to fuse these different levels of interactions efficiently. Furthermore, to incorporate a real-world challenge, we propound to learn an indicator representing whether an estimated body joint is visible/invisible at each frame, e.g. due to occlusion or being outside the sensor field of view. Finally, we introduce a new benchmark for this joint task based on two challenging datasets (PoseTrack and 3DPW) and propose evaluation metrics to measure the effectiveness of predictions in the global space, even when there are invisible cases of joints. Our evaluation shows that TRiPOD outperforms all prior work and state-of-the-art specifically designed for each of the trajectory and pose forecasting tasks.

cs.CV↗

arXiv2021

3D CNNs with Adaptive Temporal Feature Resolutions

While state-of-the-art 3D Convolutional Neural Networks (CNN) achieve very good results on action recognition datasets, they are computationally very expensive and require many GFLOPs. While the GFLOPs of a 3D CNN can be decreased by reducing the temporal feature resolution within the network, there is no setting that is optimal for all input clips. In this work, we therefore introduce a differentiable Similarity Guided Sampling (SGS) module, which can be plugged into any existing 3D CNN architecture. SGS empowers 3D CNNs by learning the similarity of temporal features and grouping similar features together. As a result, the temporal feature resolution is not anymore static but it varies for each input video clip. By integrating SGS as an additional layer within current 3D CNNs, we can convert them into much more efficient 3D CNNs with adaptive temporal feature resolutions (ATFR). Our evaluations show that the proposed module improves the state-of-the-art by reducing the computational cost (GFLOPs) by half while preserving or even improving the accuracy. We evaluate our module by adding it to multiple state-of-the-art 3D CNNs on various datasets such as Kinetics-600, Kinetics-400, mini-Kinetics, Something-Something V2, UCF101, and HMDB51.

cs.CV↗

arXiv2021

Longitudinal Correlation Analysis for Decoding Multi-Modal Brain Development

Starting from childhood, the human brain restructures and rewires throughout life. Characterizing such complex brain development requires effective analysis of longitudinal and multi-modal neuroimaging data. Here, we propose such an analysis approach named Longitudinal Correlation Analysis (LCA). LCA couples the data of two modalities by first reducing the input from each modality to a latent representation based on autoencoders. A self-supervised strategy then relates the two latent spaces by jointly disentangling two directions, one in each space, such that the longitudinal changes in latent representations along those directions are maximally correlated between modalities. We applied LCA to analyze the longitudinal T1-weighted and diffusion-weighted MRIs of 679 youths from the National Consortium on Alcohol and Neurodevelopment in Adolescence. Unlike existing approaches that focus on either cross-sectional or single-modal modeling, LCA successfully unraveled coupled macrostructural and microstructural brain development from morphological and diffusivity features extracted from the data. A retesting of LCA on raw 3D image volumes of those subjects successfully replicated the findings from the feature-based analysis. Lastly, the developmental effects revealed by LCA were inline with the current understanding of maturational patterns of the adolescent brain.

q-bio.NC↗

arXiv2021

Spatio-Temporal Graph Convolution for Resting-State fMRI Analysis

The Blood-Oxygen-Level-Dependent (BOLD) signal of resting-state fMRI (rs-fMRI) records the temporal dynamics of intrinsic functional networks in the brain. However, existing deep learning methods applied to rs-fMRI either neglect the functional dependency between different brain regions in a network or discard the information in the temporal dynamics of brain activity. To overcome those shortcomings, we propose to formulate functional connectivity networks within the context of spatio-temporal graphs. We train a spatio-temporal graph convolutional network (ST-GCN) on short sub-sequences of the BOLD time series to model the non-stationary nature of functional connectivity. Simultaneously, the model learns the importance of graph edges within ST-GCN to gain insight into the functional connectivities contributing to the prediction. In analyzing the rs-fMRI of the Human Connectome Project (HCP, N=1,091) and the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA, N=773), ST-GCN is significantly more accurate than common approaches in predicting gender and age based on BOLD signals. Furthermore, the brain regions and functional connections significantly contributing to the predictions of our model are important markers according to the neuroscience literature.

cs.LG↗

arXiv2021

Truncated Gaussian-Mixture Variational AutoEncoder

Variation Autoencoder (VAE) has become a powerful tool in modeling the non-linear generative process of data from a low-dimensional latent space. Recently, several studies have proposed to use VAE for unsupervised clustering by using mixture models to capture the multi-modal structure of latent representations. This strategy, however, is ineffective when there are outlier data samples whose latent representations are meaningless, yet contaminating the estimation of key major clusters in the latent space. This exact problem arises in the context of resting-state fMRI (rs-fMRI) analysis, where clustering major functional connectivity patterns is often hindered by heavy noise of rs-fMRI and many minor clusters (rare connectivity patterns) of no interest to analysis. In this paper we propose a novel generative process, in which we use a Gaussian-mixture to model a few major clusters in the data, and use a non-informative uniform distribution to capture the remaining data. We embed this truncated Gaussian-Mixture model in a Variational AutoEncoder framework to obtain a general joint clustering and outlier detection approach, called tGM-VAE. We demonstrated the applicability of tGM-VAE on the MNIST dataset and further validated it in the context of rs-fMRI connectivity analysis.

cs.LG↗

arXiv2021

Confounder-Aware Visualization of ConvNets

With recent advances in deep learning, neuroimaging studies increasingly rely on convolutional networks (ConvNets) to predict diagnosis based on MR images. To gain a better understanding of how a disease impacts the brain, the studies visualize the salience maps of the ConvNet highlighting voxels within the brain majorly contributing to the prediction. However, these salience maps are generally confounded, i.e., some salient regions are more predictive of confounding variables (such as age) than the diagnosis. To avoid such misinterpretation, we propose in this paper an approach that aims to visualize confounder-free saliency maps that only highlight voxels predictive of the diagnosis. The approach incorporates univariate statistical tests to identify confounding effects within the intermediate features learned by ConvNet. The influence from the subset of confounded features is then removed by a novel partial back-propagation procedure. We use this two-step approach to visualize confounder-free saliency maps extracted from synthetic and two real datasets. These experiments reveal the potential of our visualization in producing unbiased model-interpretation.

cs.LG↗

arXiv2021

Longitudinal Self-Supervised Learning

Machine learning analysis of longitudinal neuroimaging data is typically based on supervised learning, which requires a large number of ground-truth labels to be informative. As ground-truth labels are often missing or expensive to obtain in neuroscience, we avoid them in our analysis by combing factor disentanglement with self-supervised learning to identify changes and consistencies across the multiple MRIs acquired of each individual over time. Specifically, we propose a new definition of disentanglement by formulating a multivariate mapping between factors (e.g., brain age) associated with an MRI and a latent image representation. Then, factors that evolve across acquisitions of longitudinal sequences are disentangled from that mapping by self-supervised learning in such a way that changes in a single factor induce change along one direction in the representation space. We implement this model, named Longitudinal Self-Supervised Learning (LSSL), via a standard autoencoding structure with a cosine loss to disentangle brain age from the image representation. We apply LSSL to two longitudinal neuroimaging studies to highlight its strength in extracting the brain-age information from MRI and revealing informative characteristics associated with neurodegenerative and neuropsychological disorders. Moreover, the representations learned by LSSL facilitate supervised classification by recording faster convergence and higher (or similar) prediction accuracy compared to several other representation learning techniques.

cs.LG↗

arXiv2021

Going Beyond Saliency Maps: Training Deep Models to Interpret Deep Models

Interpretability is a critical factor in applying complex deep learning models to advance the understanding of brain disorders in neuroimaging studies. To interpret the decision process of a trained classifier, existing techniques typically rely on saliency maps to quantify the voxel-wise or feature-level importance for classification through partial derivatives. Despite providing some level of localization, these maps are not human-understandable from the neuroscience perspective as they do not inform the specific meaning of the alteration linked to the brain disorder. Inspired by the image-to-image translation scheme, we propose to train simulator networks that can warp a given image to inject or remove patterns of the disease. These networks are trained such that the classifier produces consistently increased or decreased prediction logits for the simulated images. Moreover, we propose to couple all the simulators into a unified model based on conditional convolution. We applied our approach to interpreting classifiers trained on a synthetic dataset and two neuroimaging datasets to visualize the effect of the Alzheimer's disease and alcohol use disorder. Compared to the saliency maps generated by baseline approaches, our simulations and visualizations based on the Jacobian determinants of the warping field reveal meaningful and understandable patterns related to the diseases.

eess.IV↗