Prediction of Overall Survival (OS) of brain cancer patients from multi-modal MRI is a challenging field of research. Most of the existing literature on survival prediction is based on Radiomic features, which does not consider either non-biological factors or the functional neurological status of the patient(s). Besides, the selection of an appropriate cut-off for survival and the presence of censored data create further problems. Application of deep learning models for OS prediction is also limited due to the lack of large annotated publicly available datasets. In this scenario we analyse the potential of two novel neuroimaging feature families, extracted from brain parcellation atlases and spatial habitats, along with classical radiomic and geometric features; to study their combined predictive power for analysing overall survival. A cross validation strategy with grid search is proposed to simultaneously select and evaluate the most predictive feature subset based on its predictive power. A Cox Proportional Hazard (CoxPH) model is employed for univariate feature selection, followed by the prediction of patient-specific survival functions by three multivariate parsimonious models viz. Coxnet, Random survival forests (RSF) and Survival SVM (SSVM). The brain cancer MRI data used for this research was taken from two open-access collections TCGA-GBM and TCGA-LGG available from The Cancer Imaging Archive (TCIA). Corresponding survival data for each patient was downloaded from The Cancer Genome Atlas (TCGA). A high cross validation $C-index$ score of $0.82\pm.10$ was achieved using RSF with the best $24$ selected features. Age was found to be the most important biological predictor. There were $9$, $6$, $6$ and $2$ features selected from the parcellation, habitat, radiomic and region-based feature groups respectively.
Imaging Biomarkers for Neurodegenerative Diseases from Detailed Segmentation of Medial Temporal Lobe Subregions on in vivo Brain MRI Using Upsampling Strategy Guided by High-resolution ex vivo MRI
University of Pennsylvania（宾夕法尼亚大学）；Siemens Healthineers（西门子医疗）；Lund University（隆德大学）；University of Castilla La Mancha（卡斯蒂利亚-拉曼恰大学）
Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）
Deep learning has a great potential for estimating biomarkers in diffusion weighted magnetic resonance imaging (dMRI). Atlases, on the other hand, are a unique tool for modeling the spatio-temporal variability of biomarkers. In this paper, we propose the first framework to exploit both deep learning and atlases for biomarker estimation in dMRI. Our framework relies on non-linear diffusion tensor registration to compute biomarker atlases and to estimate atlas reliability maps. We also use nonlinear tensor registration to align the atlas to a subject and to estimate the error of this alignment. …
This paper proposes to use deep radiomic features (DRFs) from a convolutional neural network (CNN) to model fine-grained texture signatures in the radiomic analysis of recurrent glioblastoma (rGBM). We use DRFs to predict survival of rGBM patients with preoperative T1-weighted post-contrast MR images (n=100). DRFs are extracted from regions of interest labelled by a radiation oncologist and used to compare between short-term and long-term survival patient groups. Random forest (RF) classification is employed to predict survival outcome (i.e., short or long survival), as well as to identify hig…
BioFace3D: A fully automatic pipeline for facial biomarkers extraction of 3D face reconstructions segmented from MRI
La Salle - Universitat Ramon Llull（拉蒙·柳利大学拉萨尔学院）；Universitat de Barcelona（巴塞罗那大学）；FIDMAG, Sisters Hospitallers Research Foundation（仁爱修女会研究基金会FIDMAG研究所）；CIBERSAM（精神健康生物医学研究网络）；Hospital de Sant Pau i la Santa Creu（圣保禄圣十字医院）
Clinical utility of foundation models in musculoskeletal MRI for biomarker fidelity and predictive outcomes
Center for Intelligent Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco（加利福尼亚大学旧金山分校放射与生物医学影像系智能成像中心）；Department of Bioengineering, University of California, Berkeley（加利福尼亚大学伯克利分校生物工程系）；Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco（加利福尼亚大学旧金山分校生物工程与治疗科学系）；Department of Medical Sciences and Technology, Indian Institute of Technology, Madras（印度理工学院马德拉斯分校医学科学与技术系）；Bay Area Institute of Computation, Altos Labs（Altos Labs湾区计算研究所）
Image-based brain cancer prediction models, based on radiomics, quantify the radiologic phenotype from magnetic resonance imaging (MRI). However, these features are difficult to reproduce because of variability in acquisition and preprocessing pipelines. Despite evidence of intra-tumor phenotypic heterogeneity, the spatial diversity between different slices within an MRI scan has been relatively unexplored using such methods. In this work, we propose a deep anchor attention aggregation strategy with a Vision Transformer to predict survival risk for brain cancer patients. A Deep Anchor Attentio…
Sharif University of Technology（谢里夫理工大学）；Iranian Brain Mapping Biobank（伊朗脑图谱生物库）；National Brain Mapping Laboratory（国家脑图谱实验室）；Virtual University of Medical Sciences（虚拟医科大学）
Early detection of dementia through specific biomarkers in MR images plays a critical role in developing support strategies proactively. Fazekas scale facilitates an accurate quantitative assessment of the severity of white matter lesions and hence the disease. Imaging Biomarkers of dementia are multiple and comprehensive documentation of them is time-consuming. Therefore, any effort to automatically extract these biomarkers will be of clinical value while reducing inter-rater discrepancies. To tackle this problem, we propose to classify the disease severity based on the Fazekas scale through …
University of Tehran（德黑兰大学）；University of Nottingham（诺丁汉大学）
In this study, an automated three dimensional (3D) deep segmentation approach for detecting gliomas in 3D pre-operative MRI scans is proposed. Then, a classi-fication algorithm based on random forests, for survival prediction is presented. The objective is to segment the glioma area and produce segmentation labels for its different sub-regions, i.e. necrotic and the non-enhancing tumor core, the peri-tumoral edema, and enhancing tumor. The proposed deep architecture for the segmentation task encompasses two parallel streamlines with two different reso-lutions. One deep convolutional neural net…
Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-re…
Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）；California Institute of Technology（加州理工学院）；Massachusetts Institute of Technology（麻省理工学院）
In neuroimaging, MRI tissue properties characterize underlying neurobiology, provide quantitative biomarkers for neurological disease detection and analysis, and can be used to synthesize arbitrary MRI contrasts. Estimating tissue properties from a single scan session using a protocol available on all clinical scanners promises to reduce scan time and cost, enable quantitative analysis in routine clinical scans and provide scan-independent biomarkers of disease. However, existing tissue properties estimation methods - most often $\mathbf{T_1}$ relaxation, $\mathbf{T_2^*}$ relaxation, and proto…
Disease in the brain is often associated with subtle, spatially diffuse, or complex tissue changes that may lie beneath the level of gross visual inspection, even on magnetic resonance imaging (MRI). Unfortunately, current computer-assisted approaches that examine pre-specified features, whether anatomically-defined (i.e. thalamic volume, cortical thickness) or based on pixelwise comparison (i.e. deformation-based methods), are prone to missing a vast array of physical changes that are not well-encapsulated by these metrics. In this paper, we have developed a technique for automated pattern an…
A Machine Learning Approach for Identifying Anatomical Biomarkers of Early Mild Cognitive Impairment
Universiti Teknologi PETRONAS（国油科技大学）；Hospital Universiti Sains Malaysia（马来西亚理科大学医院）；Universiti Sains Malaysia（马来西亚理科大学）；Ulster University（阿尔斯特大学）；University of Calgary（卡尔加里大学）；University of Bath（巴斯大学）
Optimizing Prognostic Biomarker Discovery in Pancreatic Cancer Through Hybrid Ensemble Feature Selection and Multi-Omics Data
Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway（癌症遗传学系，癌症研究所，奥斯陆大学医院，奥斯陆，挪威）；Oslo Centre for Biostatistics and Epidemiology (OCBE), Department of Biostatistics, University of Oslo, Oslo, Norway（奥斯陆生物统计与流行病学中心（OCBE），生物统计学系，奥斯陆大学，奥斯陆，挪威）；Department of Informatics, University of Oslo, Oslo, Norway（信息学系，奥斯陆大学，奥斯陆，挪威）；Department of Statistics, Ludwig Maximilian University of Munich, Munich, Germany（统计学系，慕尼黑路德维希-马克西米利安大学，慕尼黑，德国）；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心（MCML））
Language-Enhanced Generative Modeling for Amyloid PET Synthesis from MRI and Blood Biomarkers
organization= Shanghai Artificial Intelligence Laboratory , city= Shanghai , postcode= 200082 , country= China；organization= School of Medicine, Xiamen University , city= Xiamen , state= Fujian , country= China；organization= Department of Nuclear Medicine \& PET Center, Huashan Hospital, Fudan University , city= Shanghai , country= China；organization= Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital , city= Shanghai , country= China；organization= Department of Computer Science, Rutgers University , city= New Brunswick , state= New Jersey , country= United States；organization= Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , city= Shenzhen , country= China
An Automated Radiomics Framework for Postoperative Survival Prediction in Colorectal Liver Metastases using Preoperative MRI
Department of Medical Biophysics, University of Toronto（多伦多大学医学生物物理学系）；Physical Sciences Platform, Sunnybrook Research Institute（阳光医疗研究学院物理科学平台）；UCL Cancer Institute, University College London（伦敦大学学院癌症研究所）；Systems and Biomedical Engineering Department, Cairo University（开罗大学系统与生物医学工程系）；Department of Surgery, University of Toronto（多伦多大学外科医学系）；Department of Laboratory Medicine and Pathobiology, University of Toronto（多伦多大学实验室医学与病理学系）；Sunnybrook Health Sciences Centre（阳光健康科学中心）；Department of Medical Imaging, University of Toronto（多伦多大学医学影像学系）
Beihang University（北京航空航天大学）；University of Sydney（悉尼大学）；Beijing TianTan Hospital（北京天坛医院）；University of New South Wales（新南威尔士大学）
Chronological age of healthy people is able to be predicted accurately using deep neural networks from neuroimaging data, and the predicted brain age could serve as a biomarker for detecting aging-related diseases. In this paper, a novel 3D convolutional network, called two-stage-age-network (TSAN), is proposed to estimate brain age from T1-weighted MRI data. Compared with existing methods, TSAN has the following improvements. First, TSAN uses a two-stage cascade network architecture, where the first-stage network estimates a rough brain age, then the second-stage network estimates the brain a…
University of New South Wales（新南威尔士大学）；CSIRO（联邦科学与工业研究组织）；Prince of Wales Hospital（威尔士亲王医院）
Cerebral small vessel disease (CSVD) is a major vascular contributor to cognitive impairment in ageing, including dementias. Imaging remains the most promising method for in vivo studies of CSVD. To replace the subjective and laborious visual rating approaches, emerging studies have applied state-of-the-art artificial intelligence to extract imaging biomarkers of CSVD from MRI scans. We aimed to summarise published computer-aided methods to examine three imaging biomarkers of CSVD, namely cerebral microbleeds (CMB), dilated perivascular spaces (PVS), and lacunes of presumed vascular origin. Se…
University of Bath（巴斯大学）；University of Cambridge（剑桥大学）
Glioblastoma is profoundly heterogeneous in regional microstructure and vasculature. Characterizing the spatial heterogeneity of glioblastoma could lead to more precise treatment. With unsupervised learning techniques, glioblastoma MRI-derived radiomic features have been widely utilized for tumor sub-region segmentation and survival prediction. However, the reliability of algorithm outcomes is often challenged by both ambiguous intermediate process and instability introduced by the randomness of clustering algorithms, especially for data from heterogeneous patients. In this paper, we propose a…
Clinical Graph-Mediated Distillation for Unpaired MRI-to-CFI Hypertension Prediction
Department of Computer Science and Engineering（计算机科学与工程系）；Research Convergence Institute（研究融合院）；Department of AI Systems Engineering（人工智能系统工程系）；Department of Electrical and Computer Engineering（电气与计算机工程系）
Erasmus MC（伊拉斯谟医学中心）；Delft University of Technology（代尔夫特理工大学）；University of Copenhagen（哥本哈根大学）
To measure the volume of specific image structures, a typical approach is to first segment those structures using a neural network trained on voxel-wise (strong) labels and subsequently compute the volume from the segmentation. A more straightforward approach would be to predict the volume directly using a neural network based regression approach, trained on image-level (weak) labels indicating volume. In this article, we compared networks optimized with weak and strong labels, and study their ability to generalize to other datasets. We experimented with white matter hyperintensity (WMH) volum…
Quantitative mapping from conventional MRI using self-supervised physics-guided deep learning: applications to a large-scale, clinically heterogeneous dataset
Australian Institute for Machine Learning, The University of Adelaide（阿德莱德大学澳大利亚机器学习研究所）；Institute for Systems and Robotics, Instituto Superior Tecnico（高等理工学院系统与机器人研究所）
Overall survival (OS) time prediction is one of the most common estimates of the prognosis of gliomas and is used to design an appropriate treatment planning. State-of-the-art (SOTA) methods for OS time prediction follow a pre-hoc approach that require computing the segmentation map of the glioma tumor sub-regions (necrotic, edema tumor, enhancing tumor) for estimating OS time. However, the training of the segmentation methods require ground truth segmentation labels which are tedious and expensive to obtain. Given that most of the large-scale data sets available from hospitals are unlikely to…
Biomediq A/S（Biomediq公司）；University of Copenhagen（哥本哈根大学）；University College London（伦敦大学学院）
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…
To deform or not: treatment-aware longitudinal registration for breast DCE-MRI during neoadjuvant chemotherapy via unsupervised keypoints detection
Radboud University Medical Centre（拉德堡德大学医学中心）；The Netherlands Cancer Institute（荷兰癌症研究所）；Macao Polytechnic University（澳门理工大学）；Maastricht University Medical Centre（马斯特里赫特大学医学中心）
Treatment-wise Glioblastoma Survival Inference with Multi-parametric Preoperative MRI
Gordon Center for Medical Imaging, Massachusetts General Hospital and Harvard Medical School（戈登医学影像中心，麻省总医院和哈佛医学院）；University of Southern California（南加州大学）；Yale University（耶鲁大学）
Comparative evaluation of training strategies using partially labelled datasets for segmentation of white matter hyperintensities and stroke lesions in FLAIR MRI
Institute of Medical Technology and Intelligent Systems, Hamburg University of Technology（汉堡工业大学医疗技术与智能系统研究所）；jung diagnostics GmbH（jung diagnostics GmbH公司）；Hamburg University of Technology（汉堡工业大学）
Lesion detection in brain Magnetic Resonance Images (MRIs) remains a challenging task. MRIs are typically read and interpreted by domain experts, which is a tedious and time-consuming process. Recently, unsupervised anomaly detection (UAD) in brain MRI with deep learning has shown promising results to provide a quick, initial assessment. So far, these methods only rely on the visual appearance of healthy brain anatomy for anomaly detection. Another biomarker for abnormal brain development is the deviation between the brain age and the chronological age, which is unexplored in combination with …
Boston Children's Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）
Brain age prediction based on children's brain MRI is an important biomarker for brain health and brain development analysis. In this paper, we consider the 3D brain MRI volume as a sequence of 2D images and propose a new framework using the recurrent neural network for brain age estimation. The proposed method is named as 2D-ResNet18+Long short-term memory (LSTM), which consists of four parts: 2D ResNet18 for feature extraction on 2D images, a pooling layer for feature reduction over the sequences, an LSTM layer, and a final regression layer. We apply the proposed method on a public multisite…
University of Rochester（罗切斯特大学）；Ludwig Maximilian University（路德维希·马克西米利安大学）
It has been shown in the literature that marijuana use is associated with changes in brain network connectivity. We propose large-scale Extended Granger Causality (lsXGC) and investigate whether it can capture such changes using resting-state fMRI. This method combines dimension reduction with source time-series augmentation and uses predictive time-series modeling for estimating directed causal relationships among fMRI time-series. It is a multivariate approach, since it is capable of identifying the interdependence of time-series in the presence of all other time-series of the underlying dyn…
Case Western Reserve University（凯斯西储大学）；Picture Health（Picture Health公司）；Stony Brook University（石溪大学）；University Hospitals Cleveland Medical Center（克利夫兰大学医院医学中心）；Yale School of Medicine（耶鲁医学院）；The Cleveland Clinic Foundation (CCF)（克利夫兰诊所基金会（CCF））；New York University (NYU) Langone Medical Center（纽约大学（NYU）朗格尼医学中心）；Louis Stokes Cleveland Veterans Medical Center（路易斯·斯托克斯克利夫兰退伍军人医学中心）
Purpose: Tumor-associated vasculature differs from healthy blood vessels by its chaotic architecture and twistedness, which promotes treatment resistance. Measurable differences in these attributes may help stratify patients by likely benefit of systemic therapy (e.g. chemotherapy). In this work, we present a new category of radiomic biomarkers called quantitative tumor-associated vasculature (QuanTAV) features, and demonstrate their ability to predict response and survival across multiple cancers, imaging modalities, and treatment regimens. Experimental Design: We segmented tumor vessels and …
As shown in computer vision, the power of deep learning lies in automatically learning relevant and powerful features for any perdition task, which is made possible through end-to-end architectures. However, deep learning approaches applied for classifying medical images do not adhere to this architecture as they rely on several pre- and post-processing steps. This shortcoming can be explained by the relatively small number of available labeled subjects, the high dimensionality of neuroimaging data, and difficulties in interpreting the results of deep learning methods. In this paper, we propos…
Concordia Institute for Information Systems Engineering, Concordia University（康考迪亚大学康考迪亚信息系统工程研究所）；University of Toronto（多伦多大学）
According to official statistics, cancer is considered as the second leading cause of human fatalities. Among different types of cancer, brain tumor is seen as one of the deadliest forms due to its aggressive nature, heterogeneous characteristics, and low relative survival rate. Determining the type of brain tumor has significant impact on the treatment choice and patient's survival. Human-centered diagnosis is typically error-prone and unreliable resulting in a recent surge of interest to automatize this process using convolutional neural networks (CNNs). CNNs, however, fail to fully utilize …
Indiana University School of Medicine（印第安纳大学医学院）；Purdue University（普渡大学）；Dayton Children’s Hospital（代顿儿童医院）
Background and Purpose: Biopsy is the main determinants of glioma clinical management, but require invasive sampling that fail to detect relevant features because of tumor heterogeneity. The purpose of this study was to evaluate the accuracy of a voxel-wise, multiparametric MRI radiomic method to predict features and develop a minimally invasive method to objectively assess neoplasms. Methods: Multiparametric MRI were registered to T1-weighted gadolinium contrast-enhanced data using a 12 degree-of-freedom affine model. The retrospectively collected MRI data included T1-weighted, T1-weighted ga…
Characterization of breast parenchyma on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a challenging task owing to the complexity of underlying tissue structures. Current quantitative approaches, including radiomics and deep learning models, do not explicitly capture the complex and subtle parenchymal structures, such as fibroglandular tissue. In this paper, we propose a novel method to direct a neural network's attention to a dedicated set of voxels surrounding biologically relevant tissue structures. By extracting multi-dimensional topological structures with high salienc…
MRI-based and metabolomics-based age scores act synergetically for mortality prediction shown by multi-cohort federated learning
Maastricht University Medical Centre +（马斯特里赫特大学医学中心）；Leiden University Medical Center（莱顿大学医学中心）；Delft University of Technology（代尔夫特理工大学）；Erasmus MC - University Medical Center Rotterdam（伊拉斯姆斯大学医学中心鹿特丹分校）；Leiden University（莱顿大学）
Lady Davis Institute for Medical Research, McGill University（麦吉尔大学戴维斯夫人医学研究所）；Hudson Institute of Medical Research（哈德逊医学研究所）；Montreal Neurological Institute, McGill University（麦吉尔大学蒙特利尔神经学研究所）；Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）；The Laboratory for Imagery, Vision and Artificial Intelligence（图像、视觉与人工智能实验室）
Imaging biomarkers offer a non-invasive way to predict the response of immunotherapy prior to treatment. In this work, we propose a novel type of deep radiomic features (DRFs) computed from a convolutional neural network (CNN), which capture tumor characteristics related to immune cell markers and overall survival. Our study uses four MRI sequences (T1-weighted, T1-weighted post-contrast, T2-weighted and FLAIR) with corresponding immune cell markers of 151 patients with brain tumor. The proposed method extracts a total of 180 DRFs by aggregating the activation maps of a pre-trained 3D-CNN with…
Dictionary-based Pathology Mining with Hard-instance-assisted Classifier Debiasing for Genetic Biomarker Prediction from WSIs
Shanghai Key Laboratory of Multidimensional Information Processing, East China Normal University（华东师范大学上海市多维度信息处理重点实验室）；Department of General Surgery, Tongji Hospital, Tongji University School of Medicine（同济大学医学院附属同济医院普外科）
Our objective is the calibration of mathematical tumor growth models from a single multiparametric scan. The target problem is the analysis of preoperative Glioblastoma (GBM) scans. To this end, we present a fully automatic tumor-growth calibration methodology that integrates a single-species reaction-diffusion partial differential equation (PDE) model for tumor progression with multiparametric Magnetic Resonance Imaging (mpMRI) scans to robustly extract patient specific biomarkers i.e., estimates for (i) the tumor cell proliferation rate, (ii) the tumor cell migration rate, and (iii) the orig…
Imperial College London（帝国理工学院）；MRC London Institute of Medical Sciences（MRC伦敦医学科学研究所）
In this work, a novel approach is proposed for joint analysis of high dimensional time-resolved cardiac motion features obtained from segmented cardiac MRI and low dimensional clinical risk factors to improve survival prediction in heart failure. Different methods are evaluated to find the optimal way to insert conventional covariates into deep prediction networks. Correlation analysis between autoencoder latent codes and covariate features is used to examine how these predictors interact. We believe that similar approaches could also be used to introduce knowledge of genetic variants to such …
