arXiv subjects

Mostafa Mehdipour Ghazi

Publications and source records attributed to Mostafa Mehdipour Ghazi.

30 records · Page 2Linked to original sources

arXiv2023

Data Augmentation-Based Unsupervised Domain Adaptation In Medical Imaging

Deep learning-based models in medical imaging often struggle to generalize effectively to new scans due to data heterogeneity arising from differences in hardware, acquisition parameters, population, and artifacts. This limitation presents a significant challenge in adopting machine learning models for clinical practice. We propose an unsupervised method for robust domain adaptation in brain MRI segmentation by leveraging MRI-specific augmentation techniques. To evaluate the effectiveness of our method, we conduct extensive experiments across diverse datasets, modalities, and segmentation tasks, comparing against the state-of-the-art methods. The results show that our proposed approach achieves high accuracy, exhibits broad applicability, and showcases remarkable robustness against domain shift in various tasks, surpassing the state-of-the-art performance in the majority of cases.

eess.IV↗

arXiv2023

Deep Learning-Based Assessment of Cerebral Microbleeds in COVID-19

Cerebral Microbleeds (CMBs), typically captured as hypointensities from susceptibility-weighted imaging (SWI), are particularly important for the study of dementia, cerebrovascular disease, and normal aging. Recent studies on COVID-19 have shown an increase in CMBs of coronavirus cases. Automatic detection of CMBs is challenging due to the small size and amount of CMBs making the classes highly imbalanced, lack of publicly available annotated data, and similarity with CMB mimics such as calcifications, irons, and veins. Hence, the existing deep learning methods are mostly trained on very limited research data and fail to generalize to unseen data with high variability and cannot be used in clinical setups. To this end, we propose an efficient 3D deep learning framework that is actively trained on multi-domain data. Two public datasets assigned for normal aging, stroke, and Alzheimer's disease analysis as well as an in-house dataset for COVID-19 assessment are used to train and evaluate the models. The obtained results show that the proposed method is robust to low-resolution images and achieves 78% recall and 80% precision on the entire test set with an average false positive of 1.6 per scan.

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arXiv2022

FAST-AID Brain: Fast and Accurate Segmentation Tool using Artificial Intelligence Developed for Brain

Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols are different. Methods robust to these variations are most needed. A novel deep learning method is proposed for fast and accurate segmentation of the human brain into 132 regions. The proposed model uses an efficient U-Net-like network and benefits from the intersection points of different views and hierarchical relations for the fusion of the orthogonal 2D planes and brain labels during the end-to-end training. Weakly supervised learning is deployed to take the advantage of partially labeled data for the whole brain segmentation and estimation of the intracranial volume (ICV). Moreover, data augmentation is used to expand the magnetic resonance imaging (MRI) data by generating realistic brain scans with high variability for robust training of the model while preserving data privacy. The proposed method can be applied to brain MRI data including skull or any other artifacts without preprocessing the images or a drop in performance. Several experiments using different atlases are conducted to evaluate the segmentation performance of the trained model compared to the state-of-the-art, and the results show higher segmentation accuracy and robustness of the proposed model compared to the existing methods across different intra- and inter-domain datasets.

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arXiv2022

Learning spatiotemporal features from incomplete data for traffic flow prediction using hybrid deep neural networks

Urban traffic flow prediction using data-driven models can play an important role in route planning and preventing congestion on highways. These methods utilize data collected from traffic recording stations at different timestamps to predict the future status of traffic. Hence, data collection, transmission, storage, and extraction techniques can have a significant impact on the performance of the traffic flow model. On the other hand, a comprehensive database can provide the opportunity for using complex, yet reliable predictive models such as deep learning methods. However, most of these methods have difficulties in handling missing values and outliers. This study focuses on hybrid deep neural networks to predict traffic flow in the California Freeway Performance Measurement System (PeMS) with missing values. The proposed networks are based on a combination of recurrent neural networks (RNNs) to consider the temporal dependencies in the data recorded in each station and convolutional neural networks (CNNs) to take the spatial correlations in the adjacent stations into account. Various architecture configurations with series and parallel connections are considered based on RNNs and CNNs, and several prevalent data imputation techniques are used to examine the robustness of the hybrid networks to missing values. A comprehensive analysis performed on two different datasets from PeMS indicates that the proposed series-parallel hybrid network with the mean imputation technique achieves the lowest error in predicting the traffic flow and is robust to missing values up until 21% missing ratio in both complete and incomplete training data scenarios when applied to an incomplete test data.

cs.LG↗

arXiv2021

CARRNN: A Continuous Autoregressive Recurrent Neural Network for Deep Representation Learning from Sporadic Temporal Data

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 learning architecture based on a recurrent neural network (RNN) unit and a continuous-time autoregressive (CAR) model. The proposed model, called CARRNN, uses a generalized discrete-time autoregressive model that is trainable end-to-end using neural networks modulated by time lags to describe the changes caused by the irregularity and asynchronicity. It is applied to multivariate time-series regression tasks using data provided for Alzheimer's disease progression modeling and intensive care unit (ICU) mortality rate prediction, where the proposed model based on a gated recurrent unit (GRU) achieves the lowest prediction errors among the proposed RNN-based models and state-of-the-art methods using GRUs and long short-term memory (LSTM) networks in their architecture.

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arXiv2020

Robust parametric modeling of Alzheimer's disease progression

Quantitative characterization of disease progression using longitudinal data can provide long-term predictions for the pathological stages of individuals. This work studies the robust modeling of Alzheimer's disease progression using parametric methods. The proposed method linearly maps the individual's age to a disease progression score (DPS) and jointly fits constrained generalized logistic functions to the longitudinal dynamics of biomarkers as functions of the DPS using M-estimation. Robustness of the estimates is quantified using bootstrapping via Monte Carlo resampling, and the estimated inflection points of the fitted functions are used to temporally order the modeled biomarkers in the disease course. Kernel density estimation is applied to the obtained DPSs for clinical status classification using a Bayesian classifier. Different M-estimators and logistic functions, including a novel type proposed in this study, called modified Stannard, are evaluated on the data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) for robust modeling of volumetric MRI and PET biomarkers, CSF measurements, as well as cognitive tests. The results show that the modified Stannard function fitted using the logistic loss achieves the best modeling performance with an average normalized MAE of 0.991 across all biomarkers and bootstraps. Applied to the ADNI test set, this model achieves a multiclass AUC of 0.934 in clinical status classification. The obtained results for the proposed model outperform almost all state-of-the-art results in predicting biomarker values and classifying clinical status. Finally, the experiments show that the proposed model, trained using abundant ADNI data, generalizes well to data from the National Alzheimer's Coordinating Center (NACC) with an average normalized MAE of 1.182 and a multiclass AUC of 0.929.

stat.AP↗

arXiv2019

On the Initialization of Long Short-Term Memory Networks

Weight initialization is important for faster convergence and stability of deep neural networks training. In this paper, a robust initialization method is developed to address the training instability in long short-term memory (LSTM) networks. It is based on a normalized random initialization of the network weights that aims at preserving the variance of the network input and output in the same range. The method is applied to standard LSTMs for univariate time series regression and to LSTMs robust to missing values for multivariate disease progression modeling. The results show that in all cases, the proposed initialization method outperforms the state-of-the-art initialization techniques in terms of training convergence and generalization performance of the obtained solution.

cs.LG↗

arXiv2019

Training recurrent neural networks robust to incomplete data: application to Alzheimer's disease progression modeling

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. Instead, we propose a generalized training rule for the most widely used RNN architecture, long short-term memory (LSTM) networks, that can handle both missing predictor and target values. The proposed LSTM algorithm is applied to model the progression of Alzheimer's disease (AD) using six volumetric magnetic resonance imaging (MRI) biomarkers, i.e., volumes of ventricles, hippocampus, whole brain, fusiform, middle temporal gyrus, and entorhinal cortex, and it is compared to standard LSTM networks with data imputation and a parametric, regression-based DPM method. The results show that the proposed algorithm achieves a significantly lower mean absolute error (MAE) than the alternatives with p < 0.05 using Wilcoxon signed rank test in predicting values of almost all of the MRI biomarkers. Moreover, a linear discriminant analysis (LDA) classifier applied to the predicted biomarker values produces a significantly larger AUC of 0.90 vs. at most 0.84 with p < 0.001 using McNemar's test for clinical diagnosis of AD. Inspection of MAE curves as a function of the amount of missing data reveals that the proposed LSTM algorithm achieves the best performance up until more than 74% missing values. Finally, it is illustrated how the method can successfully be applied to data with varying time intervals.

cs.CV↗

arXiv2018

Robust training of recurrent neural networks to handle missing data for disease progression modeling

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.

cs.CV↗

arXiv2018

Combining Multiple Views for Visual Speech Recognition

Visual speech recognition is a challenging research problem with a particular practical application of aiding audio speech recognition in noisy scenarios. Multiple camera setups can be beneficial for the visual speech recognition systems in terms of improved performance and robustness. In this paper, we explore this aspect and provide a comprehensive study on combining multiple views for visual speech recognition. The thorough analysis covers fusion of all possible view angle combinations both at feature level and decision level. The employed visual speech recognition system in this study extracts features through a PCA-based convolutional neural network, followed by an LSTM network. Finally, these features are processed in a tandem system, being fed into a GMM-HMM scheme. The decision fusion acts after this point by combining the Viterbi path log-likelihoods. The results show that the complementary information contained in recordings from different view angles improves the results significantly. For example, the sentence correctness on the test set is increased from 76% for the highest performing single view ($30^\circ$) to up to 83% when combining this view with the frontal and $60^\circ$ view angles.

cs.CV↗

arXiv2017

Visual Speech Recognition Using PCA Networks and LSTMs in a Tandem GMM-HMM System

Automatic visual speech recognition is an interesting problem in pattern recognition especially when audio data is noisy or not readily available. It is also a very challenging task mainly because of the lower amount of information in the visual articulations compared to the audible utterance. In this work, principle component analysis is applied to the image patches - extracted from the video data - to learn the weights of a two-stage convolutional network. Block histograms are then extracted as the unsupervised learning features. These features are employed to learn a recurrent neural network with a set of long short-term memory cells to obtain spatiotemporal features. Finally, the obtained features are used in a tandem GMM-HMM system for speech recognition. Our results show that the proposed method has outperformed the baseline techniques applied to the OuluVS2 audiovisual database for phrase recognition with the frontal view cross-validation and testing sentence correctness reaching 79% and 73%, respectively, as compared to the baseline of 74% on cross-validation.

cs.CV↗

arXiv2016

A Comprehensive Analysis of Deep Learning Based Representation for Face Recognition

Deep learning based approaches have been dominating the face recognition field due to the significant performance improvement they have provided on the challenging wild datasets. These approaches have been extensively tested on such unconstrained datasets, on the Labeled Faces in the Wild and YouTube Faces, to name a few. However, their capability to handle individual appearance variations caused by factors such as head pose, illumination, occlusion, and misalignment has not been thoroughly assessed till now. In this paper, we present a comprehensive study to evaluate the performance of deep learning based face representation under several conditions including the varying head pose angles, upper and lower face occlusion, changing illumination of different strengths, and misalignment due to erroneous facial feature localization. Two successful and publicly available deep learning models, namely VGG-Face and Lightened CNN have been utilized to extract face representations. The obtained results show that although deep learning provides a powerful representation for face recognition, it can still benefit from preprocessing, for example, for pose and illumination normalization in order to achieve better performance under various conditions. Particularly, if these variations are not included in the dataset used to train the deep learning model, the role of preprocessing becomes more crucial. Experimental results also show that deep learning based representation is robust to misalignment and can tolerate facial feature localization errors up to 10% of the interocular distance.

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