A reusable benchmark of brain-age prediction from M/EEG resting-state signals

Population-level modeling can define quantitative measures of individual aging by applying machine learning to large volumes of brain images. These measures of brain age, obtained from the general population, helped characterize disease severity in neurological populations, improving estimates of diagnosis or prognosis. Magnetoencephalography (MEG) and Electroencephalography (EEG) have the potential to further generalize this approach towards prevention and public health by enabling assessments of brain health at large scales in socioeconomically diverse environments. However, more research is needed to define methods that can handle the complexity and diversity of M/EEG signals across diverse real-world contexts. To catalyse this effort, here we propose reusable benchmarks of competing machine learning approaches for brain age modeling. We benchmarked popular classical machine learning pipelines and deep learning architectures previously used for pathology decoding or brain age estimation in 4 international M/EEG cohorts from diverse countries and cultural contexts, including recordings from more than 2500 participants. Our benchmarks were built on top of the M/EEG adaptations of the BIDS standard, providing tools that can be applied with minimal modification on any M/EEG dataset provided in the BIDS format. Our results suggest that, regardless of whether classical machine learning or deep learning was used, the highest performance was reached by pipelines and architectures involving spatially aware representations of the M/EEG signals, leading to R^2 scores between 0.60-0.71. Hand-crafted features paired with random forest regression provided robust benchmarks even in situations in which other approaches failed. Taken together, this set of benchmarks, accompanied by open-source software and high-level Python scripts, can serve as a starting point and quantitative reference for future efforts at developing M/EEG-based measures of brain aging. The generality of the approach renders this benchmark reusable for other related objectives such as modeling specific cognitive variables or clinical endpoints.

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From a deep learning model back to the brain - inferring morphological markers and their relation to aging

10.1101/803742 ◽

2019 ◽

Author(s):

Gidon Levakov ◽

Gideon Rosenthal ◽

Ilan Shelef ◽

Tammy Riklin Raviv ◽

Galia Avidan

Keyword(s):

Deep Learning ◽

Brain Aging ◽

Absolute Error ◽

Structural Mri ◽

Brain Regions ◽

Population Based ◽

List Type ◽

Brain Images ◽

Brain Age ◽

Age Prediction

AbstractWe present a Deep Learning framework for the prediction of chronological age from structural MRI scans. Previous findings associate an overestimation of brain age with neurodegenerative diseases and higher mortality rates. However, the importance of brain age prediction goes beyond serving as biomarkers for neurological disorders. Specifically, utilizing convolutional neural network (CNN) analysis to identify brain regions contributing to the prediction can shed light on the complex multivariate process of brain aging. Previous work examined methods to attribute pixel/voxel-wise contributions to the prediction in a single image, resulting in ‘explanation maps’ that were found noisy and unreliable. To address this problem, we developed an inference framework for combining these maps across subjects, thus creating a population-based rather than a subject-specific map. We applied this method to a CNN ensemble trained on predicting subjects’ age from raw T1 brain images of 10,176 subjects. Evaluating the model on an untouched test set resulted in mean absolute error of 3.07 years and a correlation between chronological and predicted age of r=0.98. Using the inference method, we revealed that cavities containing CSF, previously found as general atrophy markers, had the highest contribution for age prediction. Comparing maps derived from different models within the ensemble allowed to assess differences and similarities in brain regions utilized by the model. We showed that this method substantially increased the replicability of explanation maps, converged with results from voxel-based morphometry age studies and highlighted brain regions whose volumetric variability contributed the most to the prediction.HighlightsCNNs ensemble is shown to estimate “brain age” from sMRI with an MAE of ∼3.1 yearsA novel framework enables to highlight brain regions contributing to the predictionThis framework results in explanation maps showing consistency with the literatureAs sample size increases, these maps show higher inter-sample replicabilityCSF cavities reflecting general atrophy were found as a prominent aging biomarker

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Towards the Interpretability of Deep Learning Models for Human Neuroimaging

10.1101/2021.06.25.449906 ◽

2021 ◽

Author(s):

Simon M. Hofmann ◽

Frauke Beyer ◽

Sebastian Lapuschkin ◽

Loeffler Markus ◽

Klaus-Robert Mueller ◽

...

Keyword(s):

Deep Learning ◽

Large Scale ◽

Brain Aging ◽

Accelerated Aging ◽

Population Based ◽

Learning Models ◽

Brain Images ◽

Subarachnoid Spaces ◽

Magnetic Resonance Imaging Mri ◽

Brain Age

Brain-age (BA) estimates based on deep learning are increasingly used as neuroimaging biomarker for brain health; however, the underlying neural features have remained unclear. We combined ensembles of convolutional neural networks with Layer-wise Relevance Propagation (LRP) to detect which brain features contribute to BA. Trained on magnetic resonance imaging (MRI) data of a population-based study (n=2637, 18-82 years), our models estimated age accurately based on single and multiple modalities, regionally restricted and whole-brain images (mean absolute errors 3.38-5.07 years). We find that BA estimates capture aging at both small and large-scale changes, revealing gross enlargements of ventricles and subarachnoid spaces, as well as lesions, iron accumulations and atrophies that appear throughout the brain. Divergence from expected aging reflected cardiovascular risk factors and accelerated aging was more pronounced in the frontal lobe. Applying LRP, our study demonstrates how superior deep learning models detect brain-aging in healthy and at-risk individuals throughout adulthood.

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A Review of Recent Deep Learning Approaches in Human-Centered Machine Learning

Sensors ◽

10.3390/s21072514 ◽

2021 ◽

Vol 21 (7) ◽

pp. 2514

Author(s):

Tharindu Kaluarachchi ◽

Andrew Reis ◽

Suranga Nanayakkara

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Review Paper ◽

Learning Systems ◽

Learning Approaches ◽

Application Development ◽

Research Gaps ◽

Domain Experts ◽

Working Definition ◽

Real World Application

After Deep Learning (DL) regained popularity recently, the Artificial Intelligence (AI) or Machine Learning (ML) field is undergoing rapid growth concerning research and real-world application development. Deep Learning has generated complexities in algorithms, and researchers and users have raised concerns regarding the usability and adoptability of Deep Learning systems. These concerns, coupled with the increasing human-AI interactions, have created the emerging field that is Human-Centered Machine Learning (HCML). We present this review paper as an overview and analysis of existing work in HCML related to DL. Firstly, we collaborated with field domain experts to develop a working definition for HCML. Secondly, through a systematic literature review, we analyze and classify 162 publications that fall within HCML. Our classification is based on aspects including contribution type, application area, and focused human categories. Finally, we analyze the topology of the HCML landscape by identifying research gaps, highlighting conflicting interpretations, addressing current challenges, and presenting future HCML research opportunities.

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Detection of Malicious Software by Analyzing Distinct Artifacts Using Machine Learning and Deep Learning Algorithms

Electronics ◽

10.3390/electronics10141694 ◽

2021 ◽

Vol 10 (14) ◽

pp. 1694

Author(s):

Mathew Ashik ◽

A. Jyothish ◽

S. Anandaram ◽

P. Vinod ◽

Francesco Mercaldo ◽

...

Keyword(s):

Neural Network ◽

Machine Learning ◽

Deep Learning ◽

Support Vector ◽

Malware Analysis ◽

Learning Approaches ◽

Dynamic Features ◽

System Calls ◽

Prevention Methods ◽

Structural Aspects

Malware is one of the most significant threats in today’s computing world since the number of websites distributing malware is increasing at a rapid rate. Malware analysis and prevention methods are increasingly becoming necessary for computer systems connected to the Internet. This software exploits the system’s vulnerabilities to steal valuable information without the user’s knowledge, and stealthily send it to remote servers controlled by attackers. Traditionally, anti-malware products use signatures for detecting known malware. However, the signature-based method does not scale in detecting obfuscated and packed malware. Considering that the cause of a problem is often best understood by studying the structural aspects of a program like the mnemonics, instruction opcode, API Call, etc. In this paper, we investigate the relevance of the features of unpacked malicious and benign executables like mnemonics, instruction opcodes, and API to identify a feature that classifies the executable. Prominent features are extracted using Minimum Redundancy and Maximum Relevance (mRMR) and Analysis of Variance (ANOVA). Experiments were conducted on four datasets using machine learning and deep learning approaches such as Support Vector Machine (SVM), Naïve Bayes, J48, Random Forest (RF), and XGBoost. In addition, we also evaluate the performance of the collection of deep neural networks like Deep Dense network, One-Dimensional Convolutional Neural Network (1D-CNN), and CNN-LSTM in classifying unknown samples, and we observed promising results using APIs and system calls. On combining APIs/system calls with static features, a marginal performance improvement was attained comparing models trained only on dynamic features. Moreover, to improve accuracy, we implemented our solution using distinct deep learning methods and demonstrated a fine-tuned deep neural network that resulted in an F1-score of 99.1% and 98.48% on Dataset-2 and Dataset-3, respectively.

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Analysis of the Nosema Cells Identification for Microscopic Images

Sensors ◽

10.3390/s21093068 ◽

2021 ◽

Vol 21 (9) ◽

pp. 3068

Author(s):

Soumaya Dghim ◽

Carlos M. Travieso-González ◽

Radim Burget

Keyword(s):

Neural Network ◽

Machine Learning ◽

Image Processing ◽

Deep Learning ◽

The Other ◽

Support Vector ◽

Learning Approaches ◽

Microscopic Images ◽

Trained Neural Network ◽

Nosema Disease

The use of image processing tools, machine learning, and deep learning approaches has become very useful and robust in recent years. This paper introduces the detection of the Nosema disease, which is considered to be one of the most economically significant diseases today. This work shows a solution for recognizing and identifying Nosema cells between the other existing objects in the microscopic image. Two main strategies are examined. The first strategy uses image processing tools to extract the most valuable information and features from the dataset of microscopic images. Then, machine learning methods are applied, such as a neural network (ANN) and support vector machine (SVM) for detecting and classifying the Nosema disease cells. The second strategy explores deep learning and transfers learning. Several approaches were examined, including a convolutional neural network (CNN) classifier and several methods of transfer learning (AlexNet, VGG-16 and VGG-19), which were fine-tuned and applied to the object sub-images in order to identify the Nosema images from the other object images. The best accuracy was reached by the VGG-16 pre-trained neural network with 96.25%.

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A Review of Computer-Aided Expert Systems for Breast Cancer Diagnosis

Cancers ◽

10.3390/cancers13112764 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2764

Author(s):

Xin Yu Liew ◽

Nazia Hameed ◽

Jeremie Clos

Keyword(s):

Breast Cancer ◽

Machine Learning ◽

Deep Learning ◽

Main Process ◽

Learning Approaches ◽

Learning Methods ◽

Advantages And Disadvantages ◽

Computer Aided ◽

Conventional Methods ◽

The Impact

A computer-aided diagnosis (CAD) expert system is a powerful tool to efficiently assist a pathologist in achieving an early diagnosis of breast cancer. This process identifies the presence of cancer in breast tissue samples and the distinct type of cancer stages. In a standard CAD system, the main process involves image pre-processing, segmentation, feature extraction, feature selection, classification, and performance evaluation. In this review paper, we reviewed the existing state-of-the-art machine learning approaches applied at each stage involving conventional methods and deep learning methods, the comparisons within methods, and we provide technical details with advantages and disadvantages. The aims are to investigate the impact of CAD systems using histopathology images, investigate deep learning methods that outperform conventional methods, and provide a summary for future researchers to analyse and improve the existing techniques used. Lastly, we will discuss the research gaps of existing machine learning approaches for implementation and propose future direction guidelines for upcoming researchers.

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Validating Deep Neural Networks for Online Decoding of Motor Imagery Movements from EEG Signals

Sensors ◽

10.3390/s19010210 ◽

2019 ◽

Vol 19 (1) ◽

pp. 210 ◽

Cited By ~ 32

Author(s):

Zied Tayeb ◽

Juri Fedjaev ◽

Nejla Ghaboosi ◽

Christoph Richter ◽

Lukas Everding ◽

...

Keyword(s):

Neural Network ◽

Machine Learning ◽

Deep Learning ◽

Convolutional Neural Network ◽

Motor Imagery ◽

Classification Performance ◽

Feature Engineering ◽

Learning Models ◽

Eeg Signals ◽

Learning Methods

Non-invasive, electroencephalography (EEG)-based brain-computer interfaces (BCIs) on motor imagery movements translate the subject’s motor intention into control signals through classifying the EEG patterns caused by different imagination tasks, e.g., hand movements. This type of BCI has been widely studied and used as an alternative mode of communication and environmental control for disabled patients, such as those suffering from a brainstem stroke or a spinal cord injury (SCI). Notwithstanding the success of traditional machine learning methods in classifying EEG signals, these methods still rely on hand-crafted features. The extraction of such features is a difficult task due to the high non-stationarity of EEG signals, which is a major cause by the stagnating progress in classification performance. Remarkable advances in deep learning methods allow end-to-end learning without any feature engineering, which could benefit BCI motor imagery applications. We developed three deep learning models: (1) A long short-term memory (LSTM); (2) a spectrogram-based convolutional neural network model (CNN); and (3) a recurrent convolutional neural network (RCNN), for decoding motor imagery movements directly from raw EEG signals without (any manual) feature engineering. Results were evaluated on our own publicly available, EEG data collected from 20 subjects and on an existing dataset known as 2b EEG dataset from “BCI Competition IV”. Overall, better classification performance was achieved with deep learning models compared to state-of-the art machine learning techniques, which could chart a route ahead for developing new robust techniques for EEG signal decoding. We underpin this point by demonstrating the successful real-time control of a robotic arm using our CNN based BCI.

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