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Gaser C, Kalc P, Cole JH. A perspective on brain-age estimation and its clinical promise. NATURE COMPUTATIONAL SCIENCE 2024; 4:744-751. [PMID: 39048692 DOI: 10.1038/s43588-024-00659-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Brain-age estimation has gained increased attention in the neuroscientific community owing to its potential use as a biomarker of brain health. The difference between estimated and chronological age based on neuroimaging data enables a unique perspective on brain development and aging, with multiple open questions still remaining in the brain-age research field. This Perspective presents an overview of current advancements in the field and envisions the future evolution of the brain-age framework before its potential deployment in hospital settings.
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Affiliation(s)
- Christian Gaser
- Structural Brain Mapping Group, Department of Neurology, Jena University Hospital, Jena, Germany.
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany.
- German Centre for Mental Health (DZPG), Jena-Halle-Magdeburg, Jena, Germany.
| | - Polona Kalc
- Structural Brain Mapping Group, Department of Neurology, Jena University Hospital, Jena, Germany
| | - James H Cole
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
- Dementia Research Centre, Queen Square Institute of Neurology, University College London, London, UK
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2
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Guo X, Ding Y, Xu W, Wang D, Yu H, Lin Y, Chang S, Zhang Q, Zhang Y. Predicting brain age gap with radiomics and automl: A Promising approach for age-Related brain degeneration biomarkers. J Neuroradiol 2024; 51:265-273. [PMID: 37722591 DOI: 10.1016/j.neurad.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
The Brain Age Gap (BAG), which refers to the difference between chronological age and predicted neuroimaging age, is proposed as a potential biomarker for age-related brain degeneration. However, existing brain age prediction models usually rely on a single marker and can not discover meaningful hidden information in radiographic images. This study focuses on the application of radiomics, an advanced imaging analysis technique, combined with automated machine learning to predict BAG. Our methods achieve a promising result with a mean absolute error of 1.509 using the Alzheimer's Disease Neuroimaging Initiative dataset. Furthermore, we find that the hippocampus and parahippocampal gyrus play a significant role in predicting age with interpretable method called SHapley Additive exPlanations. Additionally, our investigation of age prediction discrepancies between patients with Alzheimer's disease (AD) and those with mild cognitive impairment (MCI) reveals a notable correlation with clinical cognitive assessment scale scores. This suggests that BAG has the potential to serve as a biomarker to support the diagnosis of AD and MCI. Overall, this study presents valuable insights into the application of neuroimaging models in the diagnosis of neurodegenerative diseases.
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Affiliation(s)
- Xiaoliang Guo
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Yanhui Ding
- School of Information Science and Engineering, Shandong Normal University, Jinan, China.
| | - Weizhi Xu
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Dong Wang
- School of Artificial Intelligence, Beijing University of Posts and Telecommunication, Beijing, China
| | - Huiying Yu
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Yongkang Lin
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Shulei Chang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Qiqi Zhang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Yongxin Zhang
- School of Mathematics and Statistics, Shandong Normal University, Jinan, China.
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3
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Hu L, Wan Q, Huang L, Tang J, Huang S, Chen X, Bai X, Kong L, Deng J, Liang H, Liu G, Liu H, Lu L. MRI-based brain age prediction model for children under 3 years old using deep residual network. Brain Struct Funct 2023; 228:1771-1784. [PMID: 37603065 DOI: 10.1007/s00429-023-02686-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Early identification and intervention of abnormal brain development individual subjects are of great significance, especially during the earliest and most active stage of brain development in children aged under 3. Neuroimage-based brain's biological age has been associated with health, ability, and remaining life. However, the existing brain age prediction models based on neuroimage are predominantly adult-oriented. Here, we collected 658 T1-weighted MRI scans from 0 to 3 years old healthy controls and developed an accurate brain age prediction model for young children using deep learning techniques with high accuracy in capturing age-related changes. The performance of the deep learning-based model is comparable to that of the SVR-based model, showcasing remarkable precision and yielding a noteworthy correlation of 91% between the predicted brain age and the chronological age. Our results demonstrate the accuracy of convolutional neural network (CNN) brain-predicted age using raw T1-weighted MRI data with minimum preprocessing necessary. We also applied our model to children with low birth weight, premature delivery history, autism, and ADHD, and discovered that the brain age was delayed in children with extremely low birth weight (less than 1000 g) while ADHD may cause accelerated aging of the brain. Our child-specific brain age prediction model can be a valuable quantitative tool to detect abnormal brain development and can be helpful in the early identification and intervention of age-related brain disorders.
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Affiliation(s)
- Lianting Hu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, China
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, 510080, Guangdong, China
| | - Qirong Wan
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, 4330060, Hubei, China
| | - Li Huang
- School of Information Management, Wuhan University, Wuhan, 430072, Hubei, China
| | - Jiajie Tang
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, China
- School of Information Management, Wuhan University, Wuhan, 430072, Hubei, China
| | - Shuai Huang
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, 510080, Guangdong, China
| | - Xuanhui Chen
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, 510080, Guangdong, China
| | - Xiaohe Bai
- School of Physical Sciences, University of California San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Lingcong Kong
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
| | - Jingyi Deng
- School of Information Management, Wuhan University, Wuhan, 430072, Hubei, China
| | - Huiying Liang
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, 510080, Guangdong, China
| | - Guangjian Liu
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, 510080, Guangdong, China
| | - Hongsheng Liu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, China.
| | - Long Lu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, China.
- School of Information Management, Wuhan University, Wuhan, 430072, Hubei, China.
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4
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Musigmann M, Nacul NG, Kasap DN, Heindel W, Mannil M. Use Test of Automated Machine Learning in Cancer Diagnostics. Diagnostics (Basel) 2023; 13:2315. [PMID: 37510059 PMCID: PMC10378334 DOI: 10.3390/diagnostics13142315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Our aim is to investigate the added value of automated machine learning (AutoML) for potential future applications in cancer diagnostics. Using two important diagnostic questions, the non-invasive determination of IDH mutation status and ATRX status, we analyze whether it is possible to use AutoML to develop models that are comparable in performance to conventional machine learning models (ML) developed by experts. For this purpose, we develop AutoML models using different feature preselection methods and compare the results with previously developed conventional ML models. The cohort used for our study comprises T2-weighted MRI images of 124 patients with histologically confirmed gliomas. Using AutoML, we were able to develop sophisticated models in a very short time with only a few lines of computer code. In predicting IDH mutation status, we obtained a mean AUC of 0.7400 and a mean AUPRC of 0.8582. ATRX mutation status was predicted with very similar discriminatory power, with a mean AUC of 0.7810 and a mean AUPRC of 0.8511. In both cases, AutoML was even able to achieve a discriminatory power slightly above that of the respective conventionally developed models in a very short computing time, thus making such methods accessible to non-experts in the near future.
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Affiliation(s)
- Manfred Musigmann
- University Clinic for Radiology, University Hospital Muenster, WWU Muenster, Albert-Schweitzer-Campus 1, DE-48149 Muenster, Germany
| | - Nabila Gala Nacul
- University Clinic for Radiology, University Hospital Muenster, WWU Muenster, Albert-Schweitzer-Campus 1, DE-48149 Muenster, Germany
| | - Dilek N Kasap
- University Clinic for Radiology, University Hospital Muenster, WWU Muenster, Albert-Schweitzer-Campus 1, DE-48149 Muenster, Germany
| | - Walter Heindel
- University Clinic for Radiology, University Hospital Muenster, WWU Muenster, Albert-Schweitzer-Campus 1, DE-48149 Muenster, Germany
| | - Manoj Mannil
- University Clinic for Radiology, University Hospital Muenster, WWU Muenster, Albert-Schweitzer-Campus 1, DE-48149 Muenster, Germany
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Cumplido-Mayoral I, García-Prat M, Operto G, Falcon C, Shekari M, Cacciaglia R, Milà-Alomà M, Lorenzini L, Ingala S, Meije Wink A, Mutsaerts HJMM, Minguillón C, Fauria K, Molinuevo JL, Haller S, Chetelat G, Waldman A, Schwarz AJ, Barkhof F, Suridjan I, Kollmorgen G, Bayfield A, Zetterberg H, Blennow K, Suárez-Calvet M, Vilaplana V, Gispert JD. Biological brain age prediction using machine learning on structural neuroimaging data: Multi-cohort validation against biomarkers of Alzheimer's disease and neurodegeneration stratified by sex. eLife 2023; 12:e81067. [PMID: 37067031 PMCID: PMC10181824 DOI: 10.7554/elife.81067] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 04/10/2023] [Indexed: 04/18/2023] Open
Abstract
Brain-age can be inferred from structural neuroimaging and compared to chronological age (brain-age delta) as a marker of biological brain aging. Accelerated aging has been found in neurodegenerative disorders like Alzheimer's disease (AD), but its validation against markers of neurodegeneration and AD is lacking. Here, imaging-derived measures from the UK Biobank dataset (N=22,661) were used to predict brain-age in 2,314 cognitively unimpaired (CU) individuals at higher risk of AD and mild cognitive impaired (MCI) patients from four independent cohorts with available biomarker data: ALFA+, ADNI, EPAD, and OASIS. Brain-age delta was associated with abnormal amyloid-β, more advanced stages (AT) of AD pathology and APOE-ε4 status. Brain-age delta was positively associated with plasma neurofilament light, a marker of neurodegeneration, and sex differences in the brain effects of this marker were found. These results validate brain-age delta as a non-invasive marker of biological brain aging in non-demented individuals with abnormal levels of biomarkers of AD and axonal injury.
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Affiliation(s)
- Irene Cumplido-Mayoral
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
| | - Marina García-Prat
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
| | - Grégory Operto
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Carles Falcon
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)MadridSpain
| | - Mahnaz Shekari
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
| | - Raffaele Cacciaglia
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Marta Milà-Alomà
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Luigi Lorenzini
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Silvia Ingala
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Alle Meije Wink
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Henk JMM Mutsaerts
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Carolina Minguillón
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Karine Fauria
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - José Luis Molinuevo
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
| | - Sven Haller
- CIRD Centre d'Imagerie Rive DroiteGenevaSwitzerland
| | - Gael Chetelat
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and BrainCyceronFrance
| | - Adam Waldman
- Centre for Dementia Prevention, Edinburgh Imaging, and UK Dementia Research Institute at The University of EdinburghEdinburghUnited Kingdom
| | | | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Institutes of Neurology and Healthcare Engineering, University College LondonLondonUnited Kingdom
| | | | | | | | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, University of GothenburgMölndalSweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University HospitalMölndalSweden
- Department of Neurodegenerative Disease, UCL Queen Square Institute of NeurologyLondonUnited Kingdom
- Hong Kong Center for Neurodegenerative DiseasesHong KongChina
- UK Dementia Research Institute at UCLLondonUnited Kingdom
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, University of GothenburgMölndalSweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University HospitalMölndalSweden
| | - Marc Suárez-Calvet
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
- Servei de Neurologia, Hospital del MarBarcelonaSpain
| | - Verónica Vilaplana
- Department of Signal Theory and Communications, Universitat Politècnica de CatalunyaBarcelonaSpain
| | - Juan Domingo Gispert
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)MadridSpain
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Hossain E, Rana R, Higgins N, Soar J, Barua PD, Pisani AR, Turner K. Natural Language Processing in Electronic Health Records in relation to healthcare decision-making: A systematic review. Comput Biol Med 2023; 155:106649. [PMID: 36805219 DOI: 10.1016/j.compbiomed.2023.106649] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/04/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. METHODOLOGY After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: (1) medical note classification, (2) clinical entity recognition, (3) text summarisation, (4) deep learning (DL) and transfer learning architecture, (5) information extraction, (6) Medical language translation and (7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. RESULT AND DISCUSSION EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. CONCLUSION We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.
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Affiliation(s)
- Elias Hossain
- School of Engineering & Physical Sciences, North South University, Dhaka 1229, Bangladesh.
| | - Rajib Rana
- School of Mathematics, Physics and Computing, University of Southern Queensland, Springfield Central QLD 4300, Australia
| | - Niall Higgins
- School of Management and Enterprise, University of Southern Queensland, Darling Heights QLD 4350, Australia; School of Nursing, Queensland University of Technology, Kelvin Grove, Brisbane, QLD 4000, Australia; Metro North Mental Health, Herston QLD 4029, Australia
| | - Jeffrey Soar
- School of Business, University of Southern Queensland, Springfield Central QLD 4300, Australia
| | - Prabal Datta Barua
- School of Business, University of Southern Queensland, Springfield Central QLD 4300, Australia
| | - Anthony R Pisani
- Center for the Study and Prevention of Suicide, University of Rochester, Rochester, NY, United States
| | - Kathryn Turner
- School of Nursing, Queensland University of Technology, Kelvin Grove, Brisbane, QLD 4000, Australia
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Schumann A, Gaser C, Sabeghi R, Schulze PC, Festag S, Spreckelsen C, Bär KJ. Using machine learning to estimate the calendar age based on autonomic cardiovascular function. Front Aging Neurosci 2023; 14:899249. [PMID: 36755773 PMCID: PMC9899796 DOI: 10.3389/fnagi.2022.899249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Introduction Aging is accompanied by physiological changes in cardiovascular regulation that can be evaluated using a variety of metrics. In this study, we employ machine learning on autonomic cardiovascular indices in order to estimate participants' age. Methods We analyzed a database including resting state electrocardiogram and continuous blood pressure recordings of healthy volunteers. A total of 884 data sets met the inclusion criteria. Data of 72 other participants with an BMI indicating obesity (>30 kg/m²) were withheld as an evaluation sample. For all participants, 29 different cardiovascular indices were calculated including heart rate variability, blood pressure variability, baroreflex function, pulse wave dynamics, and QT interval characteristics. Based on cardiovascular indices, sex and device, four different approaches were applied in order to estimate the calendar age of healthy subjects, i.e., relevance vector regression (RVR), Gaussian process regression (GPR), support vector regression (SVR), and linear regression (LR). To estimate age in the obese group, we drew normal-weight controls from the large sample to build a training set and a validation set that had an age distribution similar to the obesity test sample. Results In a five-fold cross validation scheme, we found the GPR model to be suited best to estimate calendar age, with a correlation of r=0.81 and a mean absolute error of MAE=5.6 years. In men, the error (MAE=5.4 years) seemed to be lower than that in women (MAE=6.0 years). In comparison to normal-weight subjects, GPR and SVR significantly overestimated the age of obese participants compared with controls. The highest age gap indicated advanced cardiovascular aging by 5.7 years in obese participants. Discussion In conclusion, machine learning can be used to estimate age on cardiovascular function in a healthy population when considering previous models of biological aging. The estimated age might serve as a comprehensive and readily interpretable marker of cardiovascular function. Whether it is a useful risk predictor should be investigated in future studies.
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Affiliation(s)
- Andy Schumann
- Lab for Autonomic Neuroscience, Imaging and Cognition (LANIC), Department of Psychosomatic Medicine and Psychotherapy, Jena University Hospital, Jena, Germany
| | - Christian Gaser
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
| | - Rassoul Sabeghi
- Lab for Autonomic Neuroscience, Imaging and Cognition (LANIC), Department of Psychosomatic Medicine and Psychotherapy, Jena University Hospital, Jena, Germany
| | - P. Christian Schulze
- Department of Internal Medicine I, Division of Cardiology, Jena University Hospital, Jena, Germany
| | - Sven Festag
- Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Jena, Germany
- SMITH Consortium of the German Medical Informatics Initiative, Leipzig, Germany
| | - Cord Spreckelsen
- Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Jena, Germany
- SMITH Consortium of the German Medical Informatics Initiative, Leipzig, Germany
| | - Karl-Jürgen Bär
- Lab for Autonomic Neuroscience, Imaging and Cognition (LANIC), Department of Psychosomatic Medicine and Psychotherapy, Jena University Hospital, Jena, Germany
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8
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Cai H, Li A, Yu G, Yang X, Liu M. Brain Age Prediction in Developing Childhood with Multimodal Magnetic Resonance Images. Neuroinformatics 2023; 21:5-19. [PMID: 35962180 DOI: 10.1007/s12021-022-09596-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
It is well known that brain development is very fast and complex in the early childhood with age-based neurological and physiological changes of brain structure and function. The brain maturity is an important indicator for evaluating the normal development of children. In this paper, we propose a multimodal regression framework to combine the features from structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) data for age prediction of children. First, three types of features are extracted from sMRI and DTI data. Second, we propose to combine the sparse coding and Q-Learning for feature selection from each modality. Finally, the ensemble regression is performed by random forest based on proximity measures to fuse multimodal features for age prediction. The proposed method is evaluated on 212 participants, including 76 young children less than 2 years old and 136 children aged from 2-15 years old recruited from Shanghai Children's Hospital. The results show that integrating multimodal features has achieved the highest accuracies with the root mean squared error (RMSE) of 0.208 years and mean absolute error (MAE) of 0.150 years for age prediction of young children (0-2), and RMSE of 1.666 years and MAE of 1.087 years for older children (2-15). We have shown that the selected features by Q-Learning can consistently improve the prediction accuracy. The comparison of prediction results demonstrates that the proposed method performs better than other competing methods.
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Affiliation(s)
- Hongjie Cai
- School of EIEE, Shanghai Jiao Tong University, Shanghai, China
| | - Aojie Li
- School of EIEE, Shanghai Jiao Tong University, Shanghai, China
| | - Guangjun Yu
- Department of Child Health Care, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China
| | - Xiujun Yang
- Department of Radiology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
| | - Manhua Liu
- School of EIEE, Shanghai Jiao Tong University, Shanghai, China. .,MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, Shanghai, 200240, China.
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9
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Mouches P, Wilms M, Aulakh A, Langner S, Forkert ND. Multimodal brain age prediction fusing morphometric and imaging data and association with cardiovascular risk factors. Front Neurol 2022; 13:979774. [PMID: 36588902 PMCID: PMC9794870 DOI: 10.3389/fneur.2022.979774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction The difference between the chronological and biological brain age, called the brain age gap (BAG), has been identified as a promising biomarker to detect deviation from normal brain aging and to indicate the presence of neurodegenerative diseases. Moreover, the BAG has been shown to encode biological information about general health, which can be measured through cardiovascular risk factors. Current approaches for biological brain age estimation, and therefore BAG estimation, either depend on hand-crafted, morphological measurements extracted from brain magnetic resonance imaging (MRI) or on direct analysis of brain MRI images. The former can be processed with traditional machine learning models while the latter is commonly processed with convolutional neural networks (CNNs). Using a multimodal setting, this study aims to compare both approaches in terms of biological brain age prediction accuracy and biological information captured in the BAG. Methods T1-weighted MRI, containing brain tissue information, and magnetic resonance angiography (MRA), providing information about brain arteries, from 1,658 predominantly healthy adults were used. The volumes, surface areas, and cortical thickness of brain structures were extracted from the T1-weighted MRI data, while artery density and thickness within the major blood flow territories and thickness of the major arteries were extracted from MRA data. Independent multilayer perceptron and CNN models were trained to estimate the brain age from the hand-crafted features and image data, respectively. Next, both approaches were fused to assess the benefits of combining image data and hand-crafted features for brain age prediction. Results The combined model achieved a mean absolute error of 4 years between the chronological and predicted biological brain age. Among the independent models, the lowest mean absolute error was observed for the CNN using T1-weighted MRI data (4.2 years). When evaluating the BAGs obtained using the different approaches and imaging modalities, diverging associations between cardiovascular risk factors were found. For example, BAGs obtained from the CNN models showed an association with systolic blood pressure, while BAGs obtained from hand-crafted measurements showed greater associations with obesity markers. Discussion In conclusion, the use of more diverse sources of data can improve brain age estimation modeling and capture more diverse biological deviations from normal aging.
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Affiliation(s)
- Pauline Mouches
- Biomedical Engineering Program, University of Calgary, Calgary, AB, Canada,Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada,Department of Radiology, University of Calgary, Calgary, AB, Canada,*Correspondence: Pauline Mouches
| | - Matthias Wilms
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Agampreet Aulakh
- Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
| | - Sönke Langner
- Institute for Diagnostic Radiology and Neuroradiology, Rostock University Medical Center, Rostock, Germany
| | - Nils D. Forkert
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada,Department of Radiology, University of Calgary, Calgary, AB, Canada,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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10
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Wang H, Zhang S, Xing X, Yue Q, Feng W, Chen S, Zhang J, Xie D, Chen N, Liu Y. Radiomic study on preoperative multi-modal magnetic resonance images identifies IDH-mutant TERT promoter-mutant gliomas. Cancer Med 2022; 12:2524-2537. [PMID: 36176070 PMCID: PMC9939206 DOI: 10.1002/cam4.5097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Gliomas with comutations of isocitrate dehydrogenase (IDH) genes and telomerase reverse transcriptase (TERT) gene promoter (IDHmut pTERTmut) show distinct biological features and respond to first-line treatment differently in comparison with other gliomas. This study aimed to characterize the IDHmut pTERTmut gliomas in multimodal MRI using the radiomic method and establish a precise diagnostic model identifying this group of gliomas. METHODS A total of 140 patients with untreated primary gliomas were admitted between 2016 and 2020 to West China Hospital as a discovery cohort, including 22 IDHmut pTERTmut patients. Thirty-four additional cases from a different hospital were included in the study as an independent validation cohort. A total of 3654 radiomic features were extracted from the preoperative multimodal MRI images (T1c, FLAIR, and ADC maps) and filtered in a data-driven approach. The discovery cohort was split into training and test sets by a 4:1 ratio. A diagnostic model (multilayer perceptron classifier) for detecting the IDHmut pTERTmut gliomas was trained using an automatic machine-learning algorithm named tree-based pipeline optimization tool (TPOT). The most critical radiomic features in the model were identified and visualized. RESULTS The model achieved an area under the receiver-operating curve (AUROC) of 0.971 (95% CI, 0.902-1.000), the sensitivity of 0.833 (95% CI, 0.333-1.000), and the specificity of 0.966 (95% CI, 0.931-1.000) in the test set. The area under the precision-recall curve (AUCPR) was 0.754 (95% CI, 0.572-0.833) and the F1 score was 0.833 (95% CI, 0.500-1.000). In the independent validation set, the model reached 0.952 AUROC, 0.714 sensitivity, 0.963 specificity, 0.841 AUCPR, and 0.769 F1 score. MR radiomic features of the IDHmut pTERTmut gliomas represented homogenous low-complexity texture in three modalities. CONCLUSIONS An accurate diagnostic model was constructed for detecting IDHmut pTERTmut gliomas using multimodal radiomic features. The most important features were associated with the homogenous simple texture of IDHmut pTERTmut gliomas in MRI images transformed using Laplacian of Gaussian and wavelet filters.
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Affiliation(s)
- Haoyu Wang
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina,Department of NeurosurgeryXinhua Hospital, Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Shuxin Zhang
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina,Department of Head and Neck Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of MedicineUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xiang Xing
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
| | - Qiang Yue
- Department of RadiologyWest China Hospital of Sichuan UniversityChengduChina
| | - Wentao Feng
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
| | - Siliang Chen
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
| | - Jun Zhang
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Dan Xie
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Ni Chen
- Department of Pathology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yanhui Liu
- Department of NeurosurgeryWest China Hospital of Sichuan UniversityChengduChina
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11
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Accelerated functional brain aging in major depressive disorder: evidence from a large scale fMRI analysis of Chinese participants. Transl Psychiatry 2022; 12:397. [PMID: 36130921 PMCID: PMC9492670 DOI: 10.1038/s41398-022-02162-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/12/2022] Open
Abstract
Major depressive disorder (MDD) is one of the most common mental health conditions that has been intensively investigated for its association with brain atrophy and mortality. Recent studies suggest that the deviation between the predicted and the chronological age can be a marker of accelerated brain aging to characterize MDD. However, current conclusions are usually drawn based on structural MRI information collected from Caucasian participants. The universality of this biomarker needs to be further validated by subjects with different ethnic/racial backgrounds and by different types of data. Here we make use of the REST-meta-MDD, a large scale resting-state fMRI dataset collected from multiple cohort participants in China. We develop a stacking machine learning model based on 1101 healthy controls, which estimates a subject's chronological age from fMRI with promising accuracy. The trained model is then applied to 1276 MDD patients from 24 sites. We observe that MDD patients exhibit a +4.43 years (p < 0.0001, Cohen's d = 0.31, 95% CI: 2.23-3.88) higher brain-predicted age difference (brain-PAD) compared to controls. In the MDD subgroup, we observe a statistically significant +2.09 years (p < 0.05, Cohen's d = 0.134525) brain-PAD in antidepressant users compared to medication-free patients. The statistical relationship observed is further checked by three different machine learning algorithms. The positive brain-PAD observed in participants in China confirms the presence of accelerated brain aging in MDD patients. The utilization of functional brain connectivity for age estimation verifies existing findings from a new dimension.
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12
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Automated Classification of Atherosclerotic Radiomics Features in Coronary Computed Tomography Angiography (CCTA). Diagnostics (Basel) 2022; 12:diagnostics12071660. [PMID: 35885564 PMCID: PMC9318450 DOI: 10.3390/diagnostics12071660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
Radiomics is the process of extracting useful quantitative features of high-dimensional data that allows for automated disease classification, including atherosclerotic disease. Hence, this study aimed to quantify and extract the radiomic features from Coronary Computed Tomography Angiography (CCTA) images and to evaluate the performance of automated machine learning (AutoML) model in classifying the atherosclerotic plaques. In total, 202 patients who underwent CCTA examination at Institut Jantung Negara (IJN) between September 2020 and May 2021 were selected as they met the inclusion criteria. Three primary coronary arteries were segmented on axial sectional images, yielding a total of 606 volume of interest (VOI). Subsequently, the first order, second order, and shape order of radiomic characteristics were extracted for each VOI. Model 1, Model 2, Model 3, and Model 4 were constructed using AutoML-based Tree-Pipeline Optimization Tools (TPOT). The heatmap confusion matrix, recall (sensitivity), precision (PPV), F1 score, accuracy, receiver operating characteristic (ROC), and area under the curve (AUC) were analysed. Notably, Model 1 with the first-order features showed superior performance in classifying the normal coronary arteries (F1 score: 0.88; Inverse F1 score: 0.94), as well as in classifying the calcified (F1 score: 0.78; Inverse F1 score: 0.91) and mixed plaques (F1 score: 0.76; Inverse F1 score: 0.86). Moreover, Model 2 consisting of second-order features was proved useful, specifically in classifying the non-calcified plaques (F1 score: 0.63; Inverse F1 score: 0.92) which are a key point for prediction of cardiac events. Nevertheless, Model 3 comprising the shape-based features did not contribute to the classification of atherosclerotic plaques. Overall, TPOT shown promising capabilities in terms of finding the best pipeline and tailoring the model using CCTA-based radiomic datasets.
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13
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Liu Y, Li T, Fan Z, Li Y, Sun Z, Li S, Liang Y, Zhou C, Zhu Q, Zhang H, Liu X, Wang L, Wang Y. Image-Based Differentiation of Intracranial Metastasis From Glioblastoma Using Automated Machine Learning. Front Neurosci 2022; 16:855990. [PMID: 35645718 PMCID: PMC9133479 DOI: 10.3389/fnins.2022.855990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose The majority of solitary brain metastases appear similar to glioblastomas (GBMs) on magnetic resonance imaging (MRI). This study aimed to develop and validate an MRI-based model to differentiate intracranial metastases from GBMs using automated machine learning. Materials and Methods Radiomics features from 354 patients with brain metastases and 354 with GBMs were used to build prediction algorithms based on T2-weighted images, contrast-enhanced (CE) T1-weighted images, or both. The data of these subjects were subjected to a nested 10-fold split in the training and testing groups to build the best algorithms using the tree-based pipeline optimization tool (TPOT). The algorithms were independently validated using data from 124 institutional patients with solitary brain metastases and 103 patients with GBMs from the cancer genome atlas. Results Three groups of models were developed. The average areas under the receiver operating characteristic curve (AUCs) were 0.856 for CE T1-weighted images, 0.976 for T2-weighted images, and 0.988 for a combination in the testing groups, and the AUCs of the groups of models in the independent validation were 0.687, 0.831, and 0.867, respectively. A total of 149 radiomics features were considered as the most valuable features for the differential diagnosis of GBMs and metastases. Conclusion The models established by TPOT can distinguish glioblastoma from solitary brain metastases well, and its non-invasiveness, convenience, and robustness make it potentially useful for clinical applications.
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Affiliation(s)
- Yukun Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tianshi Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ziwen Fan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhiyan Sun
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shaowu Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yuchao Liang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chunyao Zhou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hong Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xing Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Lei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Lei Wang,
| | - Yinyan Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- *Correspondence: Yinyan Wang,
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14
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Baker MR, Padmaja DL, Puviarasi R, Mann S, Panduro-Ramirez J, Tiwari M, Samori IA. Implementing Critical Machine Learning (ML) Approaches for Generating Robust Discriminative Neuroimaging Representations Using Structural Equation Model (SEM). COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:6501975. [PMID: 35465018 PMCID: PMC9023163 DOI: 10.1155/2022/6501975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/09/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022]
Abstract
Critical ML or CML is a critical approach development of the standard ML (SML) procedure. Conventional ML (ML) is being used in radiology departments where complex neuroimages are discriminated using ML technology. Radiologists and researchers found that sole decision by the ML algorithms is not accurate enough to implement the treatment procedure. Thus, an intelligent decision is required further by the radiologists after evaluating the ML outcomes. The current research is based on the critical ML, where radiologists' critical thinking ability, IQ (intelligence quotient), and experience in radiology have been examined to understand how these factors affect the accuracy of neuroimaging discrimination. A primary quantitative survey has been carried out, and the data were analysed in IBM SPSS. The results showed that experience in works has a positive impact on neuroimaging discrimination accuracy. IQ and trained ML are also responsible for improving the accuracy as well. Thus, radiologists with more experience in that field are able to improve the discriminative and diagnostic capability of CML.
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Affiliation(s)
- Mohammed Rashad Baker
- Department of Computer Techniques Engineering, College of Information Technology, Imam Ja'afar Al-Sadiq University, Baghdad, Iraq
| | - D. Lakshmi Padmaja
- Department of Information Technology, Anurag University, Hyderabad, Telangana State, India
| | - R. Puviarasi
- Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Suman Mann
- Information Technology Department, Maharaja Surajmal Institute of Technology, New Delhi, India
| | | | - Mohit Tiwari
- Department of Computer Science and Engineering, Bharati Vidyapeeth's College of Engineering, A-4, Rohtak Road, Paschim Vihar, Delhi, India
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15
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Solanes A, Radua J. Advances in Using MRI to Estimate the Risk of Future Outcomes in Mental Health - Are We Getting There? Front Psychiatry 2022; 13:fpsyt-13-826111. [PMID: 35492715 PMCID: PMC9039205 DOI: 10.3389/fpsyt.2022.826111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Aleix Solanes
- Imaging of Mood- and Anxiety-Related Disorders (IMARD) Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Department of Psychiatry and Forensic Medicine, School of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Joaquim Radua
- Imaging of Mood- and Anxiety-Related Disorders (IMARD) Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Early Psychosis: Interventions and Clinical-detection Lab, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,Department of Clinical Neuroscience, Stockholm Health Care Services, Stockholm County Council, Karolinska Institutet, Stockholm, Sweden
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16
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Automatic machine learning based on native T1 mapping can identify myocardial fibrosis in patients with hypertrophic cardiomyopathy. Eur Radiol 2021; 32:1044-1053. [PMID: 34477909 DOI: 10.1007/s00330-021-08228-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/07/2021] [Accepted: 07/23/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To investigate the feasibility of automatic machine learning (autoML) based on native T1 mapping to predict late gadolinium enhancement (LGE) status in hypertrophic cardiomyopathy (HCM). METHODS Ninety-one HCM patients and 44 healthy controls who underwent cardiovascular MRI were enrolled. The native T1 maps of HCM patients were classified as LGE ( +) or LGE (-) based on location-matched LGE images. An autoML pipeline was implemented using the tree-based pipeline optimization tool (TPOT) for 3 binary classifications: LGE ( +) and LGE (-), LGE (-) and control, and HCM and control. TPOT modeling was repeated 10 times to obtain the optimal model for each classification. The diagnostic performance of the best models by slice and by case was evaluated using sensitivity, specificity, accuracy, and microaveraged area under the curve (AUC). RESULTS Ten prediction models were generated by TPOT for each of the 3 binary classifications. The diagnostic accuracy obtained with the best pipeline in detecting LGE status in the testing cohort of HCM patients was 0.80 by slice and 0.79 by case. In addition, the TPOT model also showed discriminability between LGE (-) patients and control (accuracy: 0.77 by slice; 0.78 by case) and for all HCM patients and controls (accuracy: 0.88 for both). CONCLUSIONS Native T1 map analysis based on autoML correlates with LGE ( +) or (-) status. The TPOT machine learning algorithm could be a promising method for predicting myocardial fibrosis, as reflected by the presence of LGE in HCM patients without the need for late contrast-enhanced MRI sequences. KEY POINTS • The tree-based pipeline optimization tool (TPOT) is a machine learning algorithm that could help predict late gadolinium enhancement (LGE) status in patients with hypertrophic cardiomyopathy. • The TPOT could serve as an adjuvant method to detect LGE by using information from native T1 maps, thus avoiding the need for contrast agent. • The TPOT also detects native T1 map alterations in LGE-negative patients with hypertrophic cardiomyopathy.
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17
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Abstract
Machine learning (ML) has been slowly entering every aspect of our lives and its positive impact has been astonishing. To accelerate embedding ML in more applications and incorporating it in real-world scenarios, automated machine learning (AutoML) is emerging. The main purpose of AutoML is to provide seamless integration of ML in various industries, which will facilitate better outcomes in everyday tasks. In healthcare, AutoML has been already applied to easier settings with structured data such as tabular lab data. However, there is still a need for applying AutoML for interpreting medical text, which is being generated at a tremendous rate. For this to happen, a promising method is AutoML for clinical notes analysis, which is an unexplored research area representing a gap in ML research. The main objective of this paper is to fill this gap and provide a comprehensive survey and analytical study towards AutoML for clinical notes. To that end, we first introduce the AutoML technology and review its various tools and techniques. We then survey the literature of AutoML in the healthcare industry and discuss the developments specific to clinical settings, as well as those using general AutoML tools for healthcare applications. With this background, we then discuss challenges of working with clinical notes and highlight the benefits of developing AutoML for medical notes processing. Next, we survey relevant ML research for clinical notes and analyze the literature and the field of AutoML in the healthcare industry. Furthermore, we propose future research directions and shed light on the challenges and opportunities this emerging field holds. With this, we aim to assist the community with the implementation of an AutoML platform for medical notes, which if realized can revolutionize patient outcomes.
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18
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Erramuzpe A, Schurr R, Yeatman JD, Gotlib IH, Sacchet MD, Travis KE, Feldman HM, Mezer AA. A Comparison of Quantitative R1 and Cortical Thickness in Identifying Age, Lifespan Dynamics, and Disease States of the Human Cortex. Cereb Cortex 2021; 31:1211-1226. [PMID: 33095854 PMCID: PMC8485079 DOI: 10.1093/cercor/bhaa288] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/25/2020] [Accepted: 09/03/2020] [Indexed: 07/22/2023] Open
Abstract
Brain development and aging are complex processes that unfold in multiple brain regions simultaneously. Recently, models of brain age prediction have aroused great interest, as these models can potentially help to understand neurological diseases and elucidate basic neurobiological mechanisms. We test whether quantitative magnetic resonance imaging can contribute to such age prediction models. Using R1, the longitudinal rate of relaxation, we explore lifespan dynamics in cortical gray matter. We compare R1 with cortical thickness, a well-established biomarker of brain development and aging. Using 160 healthy individuals (6-81 years old), we found that R1 and cortical thickness predicted age similarly, but the regions contributing to the prediction differed. Next, we characterized R1 development and aging dynamics. Compared with anterior regions, in posterior regions we found an earlier R1 peak but a steeper postpeak decline. We replicate these findings: firstly, we tested a subset (N = 10) of the original dataset for whom we had additional scans at a lower resolution; and second, we verified the results on an independent dataset (N = 34). Finally, we compared the age prediction models on a subset of 10 patients with multiple sclerosis. The patients are predicted older than their chronological age using R1 but not with cortical thickness.
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Affiliation(s)
| | - R Schurr
- The Hebrew University of Jerusalem, The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - J D Yeatman
- Graduate School of Education, Stanford University, Stanford, CA, USA
- Division of Developmental-Behavioral Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - I H Gotlib
- Psychology, Stanford University, Stanford, CA, USA
| | - M D Sacchet
- Harvard Medical School, Center for Depression, Anxiety, and Stress Research, McLean Hospital, Belmont, MA, USA
| | - K E Travis
- Pediatrics, Stanford University, Stanford, CA, USA
| | - H M Feldman
- Development and Behavior Unit, Stanford University, Stanford, CA, USA
| | - A A Mezer
- The Hebrew University of Jerusalem, The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
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19
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Zhang S, Sun H, Su X, Yang X, Wang W, Wan X, Tan Q, Chen N, Yue Q, Gong Q. Automated machine learning to predict the co-occurrence of isocitrate dehydrogenase mutations and O 6 -methylguanine-DNA methyltransferase promoter methylation in patients with gliomas. J Magn Reson Imaging 2021; 54:197-205. [PMID: 33393131 DOI: 10.1002/jmri.27498] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 02/05/2023] Open
Abstract
Combining isocitrate dehydrogenase mutation (IDHmut) with O6 -methylguanine-DNA methyltransferase promoter methylation (MGMTmet) has been identified as a critical prognostic molecular marker for gliomas. The aim of this study was to determine the ability of glioma radiomics features from magnetic resonance imaging (MRI) to predict the co-occurrence of IDHmut and MGMTmet by applying the tree-based pipeline optimization tool (TPOT), an automated machine learning (autoML) approach. This was a retrospective study, in which 162 patients with gliomas were evaluated, including 58 patients with co-occurrence of IDHmut and MGMTmet and 104 patients with other status comprising: IDH wildtype and MGMT unmethylated (n = 67), IDH wildtype and MGMTmet (n = 36), and IDHmut and MGMT unmethylated (n = 1). Three-dimensional (3D) T1-weighted images, gadolinium-enhanced 3D T1-weighted images (Gd-3DT1WI), T2-weighted images, and fluid-attenuated inversion recovery (FLAIR) images acquired at 3.0 T were used. Radiomics features were extracted from FLAIR and Gd-3DT1WI images. The TPOT was employed to generate the best machine learning pipeline, which contains both feature selector and classifier, based on input feature sets. A 4-fold cross-validation was used to evaluate the performance of automatically generated models. For each iteration, the training set included 121 subjects, while the test set included 41 subjects. Student's t-test or a chi-square test was applied on different clinical characteristics between two groups. Sensitivity, specificity, accuracy, kappa score, and AUC were used to evaluate the performance of TPOT-generated models. Finally, we compared the above metrics of TPOT-generated models to identify the best-performing model. Patients' ages and grades between two groups were significantly different (p = 0.002 and p = 0.000, respectively). The 4-fold cross-validation showed that gradient boosting classifier trained on shape and textual features from the Laplacian-of-Gaussian-filtered Gd-3DT1 achieved the best performance (average sensitivity = 81.1%, average specificity = 94%, average accuracy = 89.4%, average kappa score = 0.76, average AUC = 0.951). Using autoML based on radiomics features from MRI, a high discriminatory accuracy was achieved for predicting co-occurrence of IDHmut and MGMTmet in gliomas. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY STAGE: 3.
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Affiliation(s)
- Simin Zhang
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China.,Huaxi Glioma Center, West China Hospital of Sichuan University, Chengdu, China
| | - Huaiqiang Sun
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaorui Su
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China.,Huaxi Glioma Center, West China Hospital of Sichuan University, Chengdu, China
| | - Xibiao Yang
- Huaxi Glioma Center, West China Hospital of Sichuan University, Chengdu, China.,Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Weina Wang
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Xinyue Wan
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Qiaoyue Tan
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China.,Division of Radiation Physics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu, China
| | - Ni Chen
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Yue
- Huaxi Glioma Center, West China Hospital of Sichuan University, Chengdu, China.,Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
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20
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Dafflon J, Pinaya WHL, Turkheimer F, Cole JH, Leech R, Harris MA, Cox SR, Whalley HC, McIntosh AM, Hellyer PJ. An automated machine learning approach to predict brain age from cortical anatomical measures. Hum Brain Mapp 2020; 41:3555-3566. [PMID: 32415917 PMCID: PMC7416036 DOI: 10.1002/hbm.25028] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 12/31/2022] Open
Abstract
The use of machine learning (ML) algorithms has significantly increased in neuroscience. However, from the vast extent of possible ML algorithms, which one is the optimal model to predict the target variable? What are the hyperparameters for such a model? Given the plethora of possible answers to these questions, in the last years, automated ML (autoML) has been gaining attention. Here, we apply an autoML library called Tree-based Pipeline Optimisation Tool (TPOT) which uses a tree-based representation of ML pipelines and conducts a genetic programming-based approach to find the model and its hyperparameters that more closely predicts the subject's true age. To explore autoML and evaluate its efficacy within neuroimaging data sets, we chose a problem that has been the focus of previous extensive study: brain age prediction. Without any prior knowledge, TPOT was able to scan through the model space and create pipelines that outperformed the state-of-the-art accuracy for Freesurfer-based models using only thickness and volume information for anatomical structure. In particular, we compared the performance of TPOT (mean absolute error [MAE]: 4.612 ± .124 years) and a relevance vector regression (MAE 5.474 ± .140 years). TPOT also suggested interesting combinations of models that do not match the current most used models for brain prediction but generalise well to unseen data. AutoML showed promising results as a data-driven approach to find optimal models for neuroimaging applications.
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Affiliation(s)
- Jessica Dafflon
- Department of NeuroimagingInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUK
| | - Walter H. L. Pinaya
- Department of Psychosis StudiesInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUK
- Center of Mathematics, Computation and CognitionUniversidade Federal do ABCSanto AndréBrazil
| | - Federico Turkheimer
- Department of NeuroimagingInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUK
| | - James H. Cole
- Department of NeuroimagingInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUK
| | - Robert Leech
- Department of NeuroimagingInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUK
| | | | - Simon R. Cox
- Lothian Birth Cohorts group, Department of PsychologyUniversity of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| | | | | | - Peter J. Hellyer
- Department of NeuroimagingInstitute of Psychiatry, Psychology and Neuroscience, King's College LondonLondonUK
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21
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Da Costa PF, Dafflon J, Pinaya WHL. Brain-Age Prediction Using Shallow Machine Learning: Predictive Analytics Competition 2019. Front Psychiatry 2020; 11:604478. [PMID: 33343431 PMCID: PMC7738323 DOI: 10.3389/fpsyt.2020.604478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023] Open
Abstract
As we age, our brain structure changes and our cognitive capabilities decline. Although brain aging is universal, rates of brain aging differ markedly, which can be associated with pathological mechanism of psychiatric and neurological diseases. Predictive models have been applied to neuroimaging data to learn patterns associated with this variability and develop a neuroimaging biomarker of the brain condition. Aiming to stimulate the development of more accurate brain-age predictors, the Predictive Analytics Competition (PAC) 2019 provided a challenge that included a dataset of 2,640 participants. Here, we present our approach which placed between the top 10 of the challenge. We developed an ensemble of shallow machine learning methods (e.g., Support Vector Regression and Decision Tree-based regressors) that combined voxel-based and surface-based morphometric data. We used normalized brain volume maps (i.e., gray matter, white matter, or both) and features of cortical regions and anatomical structures, like cortical thickness, volume, and mean curvature. In order to fine-tune the hyperparameters of the machine learning methods, we combined the use of genetic algorithms and grid search. Our ensemble had a mean absolute error of 3.7597 years on the competition, showing the potential that shallow methods still have in predicting brain-age.
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Affiliation(s)
- Pedro F Da Costa
- Centre for Neuroimaging Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.,Centre for Brain and Cognitive Development, Birkbeck College, London, United Kingdom
| | - Jessica Dafflon
- Centre for Neuroimaging Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Walter H L Pinaya
- Department of Biomedical Engineering, King's College London, London, United Kingdom
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22
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Lombardi A, Monaco A, Donvito G, Amoroso N, Bellotti R, Tangaro S. Brain Age Prediction With Morphological Features Using Deep Neural Networks: Results From Predictive Analytic Competition 2019. Front Psychiatry 2020; 11:619629. [PMID: 33551880 PMCID: PMC7854554 DOI: 10.3389/fpsyt.2020.619629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/18/2020] [Indexed: 12/05/2022] Open
Abstract
Morphological changes in the brain over the lifespan have been successfully described by using structural magnetic resonance imaging (MRI) in conjunction with machine learning (ML) algorithms. International challenges and scientific initiatives to share open access imaging datasets also contributed significantly to the advance in brain structure characterization and brain age prediction methods. In this work, we present the results of the predictive model based on deep neural networks (DNN) proposed during the Predictive Analytic Competition 2019 for brain age prediction of 2638 healthy individuals. We used FreeSurfer software to extract some morphological descriptors from the raw MRI scans of the subjects collected from 17 sites. We compared the proposed DNN architecture with other ML algorithms commonly used in the literature (RF, SVR, Lasso). Our results highlight that the DNN models achieved the best performance with MAE = 4.6 on the hold-out test, outperforming the other ML strategies. We also propose a complete ML framework to perform a robust statistical evaluation of feature importance for the clinical interpretability of the results.
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Affiliation(s)
- Angela Lombardi
- Istituto Nazionale di Fisica Nucleare, Bari, Italy.,Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | | | | | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare, Bari, Italy.,Dipartimento di Farmacia - Scienze del Farmaco, Universitá degli Studi di Bari Aldo Moro, Bari, Italy
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare, Bari, Italy.,Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Sabina Tangaro
- Istituto Nazionale di Fisica Nucleare, Bari, Italy.,Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
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