INTERPRETION OF RADIOMIC FEATURES: ROLE OF DATA

SCIENCE FOR SURVIVAL PREDICTION

Aounaiza Ahmed

L20-2055

PhD CS
Abstract:

Precision health care involves the individualization of clinical solutions as a cardinal phase and is

part of a mechanism which generally relies on many factors. The foundation is the compilation

and collection of data over time to determine the condition of the patient and to monitor

therapeutic responses. A very important part of this method is Radiomics. Its key aim is to

introduce a protocol to first manipulate and then remove the most representative features for the

quantification of image informative information. Further research attempts to classify probable

phenotypes of diseases by signs and heterogeneity marks. As multimodal images can be

embedded into care schedules and follow-up information and are dependent on diverse data

source databases, Radiomics naturally focuses on the complex tracking of disease development

or patient's health pathway. Radiomics, however, still generates essential needs. A short list

includes: (a) effective harmonization of radiation measures intra/intermodal to promote

association with additional fields of data (genetic, therapeutic, lifestyle); (b) the capacity of data

analysis to re-examine models and computational methods for addressing various data forms and

systems (electronic medical history, human histories, hospital data, and genomics.
Contents

Abstract:...........................................................................................................................................1

Introduction:....................................................................................................................................1

Research Objectives:.......................................................................................................................1

Literature Review:...........................................................................................................................2

Image Bio Banking:.........................................................................................................................5

Image to Data Driven Research:......................................................................................................5

Radiomic Profiles:...........................................................................................................................6

Data Acquisition and mining:......................................................................................................6

Data Preprocessing:......................................................................................................................6

Feature Extraction:.......................................................................................................................6

Feature Ranking:..........................................................................................................................6

Modelling:....................................................................................................................................6

Validation:....................................................................................................................................7

Images to Network:..........................................................................................................................7

Impact Domains:..............................................................................................................................8

Conclusion:....................................................................................................................................11

References:....................................................................................................................................12
Introduction:

Radiomics is commonly correlated with medical research on artificial (AI) and machine learning

(ML) and includes research covering any form of medical imaging. There are approximately

1450 publications on a quest for PubMed with the word "Radiomics." Oncological applications

are the most common research. For example, the following significant paragraph of O' Connor

for describing Radiomics is stated as follows: "Radiomics uses computer algorithms to process

the data obtained by various techniques in medical imaging and is increasingly common in

cancer imaging research. One of the main aspects of Radiography is that digital medical pictures

do not only reflect images, but are also complicated details. Radiomic studies extract and

quantify an assortment of ‘features’ that identify the image texture and distributions of individual

voxel values—the units that make up a 3D image—within a tumor. Each voxel comprises a tiny

amount of tissue and comprises about 105 to 107 neoplastic and stromal cells, based on tumor

form and voxel dimensions.” Our special interest focuses on cancer and the multiple phenotypes

that can be selected for human cancer, and on patients that can be used in medical imaging

without invasion (MIM). While MIM becomes increasingly important in clinical practice, its

findings are not regularly combined with those from genomic, clinical and forecast information.

Therefore an information gap may be related to proof that such data could result, partial

unrevealed or unexplored. Radiography provides a transition in this direction (RAD). It only

occurs a few years after, and suggests a computational approach to collecting photographs by

characteristics. These can either provide training settings for different automated learning

algorithms or can be used to allow methods of diagnosis and outcomes prediction after particular

treatment to be robust.
Research Objectives:

This research in aimed at achieving following stated objectives:

1. To study background and emergence of Radiomics in Medical Research.

2. To explore various phases involved in the interpreting radiomic features of any

disease specifically Brain Tumor Data.

3. To analyze the role of Data Science in revolutionizing Health Precision Solutions.

4. To further highlight and interpret the efficiency of Data Science as a milestone in

Survival

Literature Review:

Medical imaging has traditionally been a qualitative or semi-quantitative process. What can be

seen in a picture is difficult to measure and translate into useful predictive data. Computers take

great strides in collecting and correlating quantitative knowledge through imagery through

developments in both computer hardware and machine learning algorithms. In its two forms,

"handcrafted and deep," radiomics is a developing domain that transforms medical images into

quantitative data to produce biological data and allow for the diagnosis, treatment, decision

support, and tracking of radiological phenotypes. Handcrafted Radiomics is a multi-stage method

that removes features dependent on form, pixel strength and texture from x-rays. They explain in

the analysis the steps: beginning with quantitative imagery, how it can be collected, how to

compare this evidence with clinical and biological results, leading to models for forecasting,

such as survival and for the diagnostic identification and classification. Application and its

advantages and disadvantages of deep learning, the second arm of radiomics and its role in the

working flux of radiomic are discussed.

We provide real-world clinical implementations of radiomics in oncology to help demonstrate

the methods used, highlight literature on radiomics' uses and cover the drawbacks of radiomics

and their possible course (Rogers et al., 2020). Radiomics is an emerging field for quantitative

image analysis which aims at relevant large-scale knowledge extracted from images to clinical

and organic endpoints. In combination with machine learning, the advancement of computational

imaging techniques has provided the opportunity to transform data science analysis into more

targeted cancer therapies. Cumulative data indeed shown that sophisticated noninvasive imaging

analytics, i.e. radiomics, will expose main tumor phenotype components at many occasions

during and above the treatment process in several three-dimensional lesions. Those advances in

the use of CT, PET, US and MR imaging could allow patients to stratify and predict clinical

approaches to emergence. Deep learning algorithms have shown their enormous ability to

segment, recreate, recognize and identify the image in recent years. There are currently several

important open-source and commercial tools for embarking on new radiomics research fields.

However, quantitative imaging analysis is nuanced and basic mathematical criteria should be

pursued in order to reach its maximum potential. In particular, the area of Radiomics needs a

renewed emphasis on optimum design and reporting and standardization of image acquisition,

estimation of feature characteristics and rigorous statistical analysis in order for the area to move

forward. In this article, examples taken mainly from oncology are explored on the role of the

engine and deep learning as the major computational vehicle to develop advanced RCS models

and various clinical applications, working concepts, research opportunities, and computational

platforms for Radiomics. We also tackle problems related to typical medical applications, such

as standardization, extraction of features, model construction and validation (Park et al., 2020).

About a decade has elapsed since Lambing et al first invented Radiomics in the beginning of
2012. The idea was at the time exciting and still evident developments in the field of medical

imagery and automatic image processing. Radiomics analysis processes radiological image

images in order to extract vast quantities of quantitative image properties and then analyses them

in order to recognize meaningful trends and novel biomarkers for imaging. Radiomics was

mainly used in oncology, e.g. to encourage prejudice against histological subtypes of tumors, to

forecast patient responses and thus encourage more individualized treatment regimes. Since then,

the priorities of science have been uninterrupted and several articles on the application of

Radiomics have been conducted in different environments. In the near future, it will be worth

reviewing the findings and what have been converted into therapeutic use in nearly a decade of

studies in Radiomics (Dos et al., 2020). The aggregation of data from different centers is a big

problem in Radiomics. Legal and ethical regulations restrict the sharing of data among hospitals.

Distributed learning is a method which enables multi-center training models without leaving the

hospitals (distributed learning "privacy preserving"). This research tested the viability of

dispersed Radiomics learning in predictive patients with Head and Neck (HNC) for two years of

overall survival and HPV.

Pretreatment CT images were obtained from 1174 HNC patients in 6 separate cohorts. The

implementation of Red programme extracted 981 radiomic characteristics. Clustering

hierarchical to pick features has been done. Logistic regression was used to classify. The

validation data collection compared the receiver operating features (ROC) between centralized

and distributed models (Bogowicz et al., 2020). The assessment of standard machine learning

diagnostic efficiency and generalizability and deeper learning models to differentiate

glioblastoma from single brain metastasis using radiomics. 166 (109 glioblastomas and 57

metastases, respectively) and 82 (50 glioblastomas and 32 metastases), respectively were cohorts
in preparation and external confirmation. The 265 radiomic properties of contrast-enhancing and

peritumoral T2 hyperintense masks were derived from semiautomatically segmented regions and

were used as input data.

Hyper parameters have been optimized in the cohort by ten-fold cross-validation for any deep

neural network (DNN) and seven conventional computer classifiers in conjunction with one of

five feature selection approaches. In the validation cohort, glioblastoma from metastasis was

diagnosed as the optimized models and two neuroradiologists. The most prominent malignant

brain tumors in adults are glioblastoma and brain metastasis. In order to prepare more diagnostic

work and treatment, distinction between these two types of tumors is critical. In the event of a

possible brain metastasis, the main tumor and its dissemination status must be thoroughly

identified. In addition, the methods of care vary with these tumors; Metastatic and stereotypical

radiation resections are favored in blocks, while glioblastomas should be considered with

optimum protection and molecular grading accompanied by concomitant chemo radiation.

Usually, definitive diagnosis is based on histopathology for glioblastoma or metastasis. This

pose, however, a risk of morbidity, particularly in tumors in the vicinity of eloquent areas or in

advanced patients. Precise noninvasive diagnosis of radiology will also be highly useful.

Computer-assisted medical imaging (CAD-MIM) is not a novel concept for treating diagnosis or

therapeutic issues. The first approach to converge the CAD-MIM into a RAD function is by ad

hoc imaging procedures and show techniques, to provide evidence on clinical use. In the effort to

extract biomarkers consistent with illness, it will then combine quantitative measures of

characteristics into diagnostic values. The emphasis now has, however, been on designing

integrated technologies that can help clinical decisions through both software tools or data-driven

analyzes. A rich area of operation for deep learning (DEL) or an ideal general basis for using ML
and computational approaches, ensemble templates (EMs), visualisation or big data analytics has

recently been established in RAD. The data-science computer community has RAD's biggest

effect, owing to its affiliation with therapeutic endpoints, is clearly predicted at medical group

level. Each individual eventually generates a health pattern which represents an individualized

risk profile and/or reacts to therapy differently, requiring tailored intervention and time

monitoring.

Researches on dynamic connections between cancer genetics, genomics and clinical influences

have been encouraged by the RAD work. The current situation was distinguished by three major

numerical factors: (1) the reduced criticality of the size factor: data length, atmosphere and width

can be handled now in unparalleled amounts. (2) Improvement in depth or resolution: dynamic

hierarchies of image data may be exposed in an effective manner. (3) The desire to learn, verify

and generalize: it exists on a machine basis and cross-culturally. These aspects contribute to both

the contextualization and understanding of clinically applicable data patterns, thereby promoting

decision making and raising the scope of clinical practice change. In order to take decisions

about individual therapies and disease prediction, support for radiation oncologists is particularly

important to identify patient prognostic pathways. RAD uses the two-stage method to forecast

the effect of therapy (1) to retrieve the features and (2) to use them in a simulation model for

success/failure prediction (even personalized therapy, as the ultimate goal). This method includes

a complex model system for the combined study of many data forms recorded along the course

of the patient result (POT). The information obtained from integrated data modeling will allow

superior predictive ability while providing better discrimination between tumor phenotypes.

RAD has to be fully assimilated by engaged science groups, but is structured to bring accuracy to

value intrinsically. In turn, this means that more objective criteria and metrics for data analysis
are required. Both comparison data and systematic methodologies must strive for optimal

reproducibility and generalization, including multi-center development and testing of future

clinical trials. In clinical settings, repetitive imaging tools are currently being used mainly

concentrated on structural tests, with only little connection with physiological effects or early

knowledge about the responses to particular targeted therapies or on the pursuit of exploratory

end punctures in the design of so-called integral cancer markers. These limits are partially

affected by improvements in infrastructure affecting photography or by variations of imaging

techniques. Quality metrics provide both diagnostic and forecasting tests. MIM facilitates non-

invasive disease assessment, including transient progression tests (i.e., disease trajectories). It is

important that therapeutic response is established at an early stage in many complex diseases,

since this ensures the patient has the potential to assess the best possible prognosis course. Using

tests for biomarker expression values, stratifications of patients are anticipated when unique

targeted therapies are activated.

Image Bio Banking:

The development of IB is quite clearly expected to begin alongside the increase of the field of

imagery bio banking. The use of high-performance computing to extract radiomic features can

gradually leverage diagnostic multimodal images created by different technologies, but

translation gaps still need to be resolved before validement has been achieved in medical

settings. The development of biologic samples, omics and clinical information for patients

constitutes a new boundary whose ultimate step is the next generation of integrated biobanks

whereby radiomic information is paired with genomic, proteomic or metabolomics outcomes, in

order to allow for creative and tailored approach to the treatment of illnesses. The scenario will

be centered on data science to assembling a first layer of raw and processed data, metadata,
composite measurements of characteristics and bio-markers obtained from medical photographs,

whilst other disease-related considerations such as patient prognostics, pathological observations

and genomic profiling will lead to another layer. The outcome of this dynamic mixture of

structured, harmonized and synchronized data should become an enriching genotype structure

connected with other deposits and subject to complete technological validity and additional

qualifications for optimum clinical routine use. A final purpose should therefore be considered,

in compliance with the clinical guidelines, to assimilate multilevel knowledge into a prediction

model with selected main characteristics. Although validation is the necessary step to be taken to

render the model predictions clinically relevant, calibration of the models used will continue to

be necessary in order to determine a forecast matching.

Image to Data Driven Research:

In general, and in view of the above initiatives, data science is totally crucial to RAD processes,

including validation and calibration stages, from the collection and assimilation of various data,

to the extraction and the selection of information for exploration, through modeling. The clinical

testing model is reviewed in this case. Imaging is not only instrumental in showing a clinical

proof theory, it is also a medium that provides objective results that can be explained by models.

In order for physicians to understand data-driven outcomes, concrete targets to define patient

needs need to be met. In order to provide complementary knowledge of interest in patient health

and covering diverse data sets, annotations and spatial/temporal combination of multiomic data,

MMIM with various data modalities must, for example, be analyzed in detail. The functional

usefulness can be referred to the cancer sector, in which cancer types vary considerably with

respect to reference datasets and clinical/molecular annotations.

Two big advancements are now highly useful from a simulation point of view: transfer learning

(TL) and ensemble modelling (EM). TL assumes that functionality that has been learned in a

given application area can be extended successfully to another similar field. Since this approach

seeks to solve problems by leveraging solutions that resolve similar problems, it is normal to

assess the rating of features for accuracy and robustness (across domains) (significance). In

comparison, TL will inherently use similarity that traditional methods can hardly hypothesize.

EM is a rational weighting technique or projections derived from multiple models that are

implemented over identical or different data sets. The key explanation for the use of EM is to

reconcile proof that not enough knowledge may otherwise be given at the person level.

Radiomic Profiles:

RAD provides a range of computational approaches to resolve health challenges and primarily

focuses on studies that classify phenotypes of diseases. Ideally, those phenotypes could align

with other kinds of clinical information, electronic health reports, therapy response,

genomic/proteomic/metabolomics studies, and other information for biomarker identification and

quantitative support of decision making.

Data Acquisition and mining:

Data gathered from various sites, centers and imaging modalities have various characteristics,

criteria and procedures that could affect outcomes efficiency, comparability and productivity.

Data Preprocessing:

This generally decreases the uncertainty and increases the robustness of the interesting radiomic

data characteristics. The key goal here is to mine and clean data from incompatibilities and

mistakes, which can confuse the following moves.

Feature Extraction:

Data characteristics consist of the syntheses between the MIM material and the clinical ends to

be derived, partly empirically and partly computationally, from the available data. This second

class includes the use of a range of methods, among other tools, from statistics to ML.

Feature Ranking:

You need to concentrate on the highest predictive performance functions, usually a package.

Redundancies and incorrect similarities can be removed so that a sufficient number of

characteristics will reduce the likelihood of duplication.

Modelling:

Providing a wide variety of variably tracked alternatives the proper models should be developed

to calculate the function prediction capacity to clinical outcome.

Validation:

This is the last crucial step of the importance that can be applied in patient clinical work. The

models are tested first in their separate facets of success and then tuned such that the match

between clinical findings and model forecasts is always tailored iterative.

There are numerous examples of these applications in the literature (see for example [45] for the

RAD indicator used in ovarian cancer, for work on Parkinson's and many others). Finally, for the

screening, identification and monitorement of patient’s RAD profiles are highly beneficial. It is

necessary to summed the most useful benefits as follows: (a) time reproducibility, (b) cost-

effective data selection, (c) spatial heterogeneity assessment in greater proportion compared with

biopsies, (d) the significance of disease hallmarks, (e) recognition of the drug targets and the

biomarker roadmap, (f). The aim of this list is to be inspired by the constant developments in PM

technology and technique.

Other essential tasks reported in Figure 1 are complementing the above six stages: lesion

annotation, harmonization, reduction in dimensionality and calibration. The first task, annotation

of lesions, depends on different existing algorithms that are often protected by characteristics

(skin, lung, liver, etc.; see for instance for an algorithmic application for general discussion). The

concerns with non-common or co-occurring forms emerge. Therefore, harmonization is required

in RAD, in particular for clinical transmission, which includes reproducibility of the extracted

features. Reduction and optimization of dimensionality are primarily calculating tasks whose

scope is to improve the value and efficiency of the effects to the maximum possible

interpretability.
Images to Network:

The heterogeneity of cancer indicates a complexity that requires a comprehensive study. The first

element refers to the scale component.

Heterogeneity occurs at different

levels: hereditary, biochemical,

cellular and physiological, inter alia,

obviously contributing to the quest for

multiscale inference. A mixture of

image read back information can also

be incorporated in interpretable

models, such as a mixture of

physiological properties such as perfusion, oxygenation, pH and hypoxia; anatomy structures;

histological characterization (necrotic, viable, antigenic, etc...) The tumor stage must be

identified, calculated and quantified in a manner that represents tumor stages, taking into account

all of those facets. However, data obtained in a range of space-time resolutions are difficult to

translate into an interpretable predictive model.

In order to see what improvement is made possible in the presence of the former, the degree of

complexity reached by imaging is important not only to the tumor but also to the host. The host–

tumor interface (HTI) areas are of course given special importance as the key location for

tracking of disease development, as reciprocal dynamic infiltration/from the tumor to the hosts

and vice versa occurs. These regions also have hyper heterogeneity, based on the host association

with tumor cells, growth factors and antigenic elements, among others as immune modulators,

vascular components, and nutrients. Another factor is rehabilitation since the therapeutic
outcomes can be assessed considerably by measuring HTI regions in terms of tumor tolerance.

The distribution and frequency of therapeutic goals will also shift over the course of an illness,

indicating that more heterogeneity at the clinical level needs to be addressed.

Impact Domains:

In view of treatment and its effects (early reaction and follow-up) over time, they can be tracked

over networks through the evaluation of differential model configurations before and after

treatment and in the determination of which disruption effects can be therapeutically induced to

impact the HTI regions and/or to kill the tumor regions Figures demonstrate conditions and state

changes with examples of disease progression, simulation of surgery, optimal therapy, follow-up

therapy and contact tumor-host.

A time-consuming and tissue-involving assessment of the target expression state is typically

useful to minimize the likelihood of erroneous treatment decisions. The fundamental premise in

practice is that calculated terms are given practical significance, which due to other influences

requires caution (epigenetic, lifestyle, etc.). However, there is yet to be a potential connection

between goal expression and recurring symptoms on the basis of variables such as lack of cutoff

values, insufficient understanding of the entire degree of therapy reaction and a lack of predictive

reference values for expression.

There's a strong molecular foundation for clinical pathological heterogeneity. Such a

heterogeneity inhibits, by example, known gene signatures from recognizing robust biomarkers.

IB will be immensely beneficial here. There may be several morphologic characteristics in

different parts of the tumor, which is why pathologists are testing many pieces. Moreover, spatial

and time heterogeneity helps tumors to respond to the micro-environment and sub clones appear

either to compete or to collaborate in a complex mix. The crucial role of tumor heterogeneity in

the clinics can be emphasized by functional and metabolic images because images offer non-
invasive access to datasets whose spatial information is gathered by individual voxels: the

morphological, metabolic and physiological information collected from a restricted volume of

tissue.

It is very clear that spatial tumor heterogeneity must be identified and assessed in order to

classify subpopulations of the tumor as reagents or as therapeutic resistant. Imaging phenotypes

may represent histological and genetic characteristics which can often be linked to the outcomes

of the patient. The debate over quantitative imagery for therapeutic use and supportive judgments

relies on the capacity to formulate robust, multidimensional and multi-parametric approaches.

Taking single modalities could over-simplify the complex dynamics under research

(heterogeneity, metabolism). However, the related tumor molecular profiles were already

effectively correlated with quantitative phenotypes (such as tumor, form of, margin and blood

stream kinetics) (DNA mutation, miRNA, protein, pathway gene expression, and copy number

variation).

Methods and Results:

Our architecture comprises of convolutional blocks that extract survival related features from the

MRI images concatenated with their corresponding segmented image (as a channel map),

concatenates age of the patient with these feature maps and finally Fully Connected layers are

applied. The final prediction has been distributed into 2 models.

1. Classification Model:

 Survival days lying in range 0 - 300

 Survival days lying in range 300 - 450

 Survival days lying in range 450+

This was the challenge BraTS had requested in 2017. The other model we try is the number of

days of regression. In classification model, the final prediction here is sigmoid. For this reason

we obey the process and divide every day in the ground by the maximum days of survival. This

implies that any simple truth is between 0 and 1. Our sigmoid production is like this. We

multiply our performance by max days finally to estimate. The classification model contains

240 / 240 / 5 inputs and Softmax inputs in the three classes. The regression model uses scale 240

to 240 to 5 and generates a chance of sigmoid.

For 163 patients, we have total data. For preparation and research we divided it into 134 and 29

respectively. Adam optimizer, categorical cross entropy as the loss function and precision as

metric was trained on 134 patients with classifications models. We practice for 80 epochs and

batch size 64 with a learning rate set to 1e-2.

Adam Optimizer, Mean squared loss as loss function and MSE as a parameter are educated on

the regression model. We train for 90 epochs and batch size 64 with learning rate 1e-2.

On 29 testing patients, our classification model produced a precision of 0.5172. In the 29 test

photos, our model of regression resulted in a mean squared 0.2107 error.

Conclusion:

In the world of clinical science, both accuracy and uncertainty change more and more. This

developments in the field of photography, which already were very remarkable, are meant to

improve the therapeutic utility of large radiological evaluations and in particular of biomarker-

based technology. Further comparison of datasets and the use of information from different

modalities would be needed. Clinical trials in which the endpoints and IB of the imaging must be
better established and checked are of vital significance. In combination with inter-patient

heterogeneity, heterogeneity in intra-patients is a source of insecurity that needs detailed

research. Therefore, a change in emphasis towards variability involves an analysis of the basic

weight of repetitiveness (repetitive testing of the same subject over time) and productivity of

measurements (measurement of the same subject with different instruments of the same type).

RAD reliability relies upon validation of stable models that are characteristics of which accuracy

and generalization have been extensively tested. The data sciences and related methods for

computer machine learning are crucial to quantifying spatial constructs that occur, for example,

in imaging and describe the tumor microenvironment.

While the use in the production of MIM and RAD fields of sophisticated machine modeled tools

is now a crucial element for translational problems, two core questions remain contentious and

still need to be addressed. The first concern is the lack of agreement as to what form of learning

or what set of functions should be used (refer to IBSI, for instance). The issue goes beyond

modelling aspects and includes high-quality data and structured processes while reliable models

can be more resilient. The second challenge is that outcomes can be misunderstood. It is fair to

assume that we should have faith or not trust in the forecasts obtained through the instruments.

As such, new strategies promise to have wide-ranging effects on the medical sector and on DL, a

particular reference goes to variation auto encoders and adverse generative networks, all capable

of unregulated learning of vast volumes of data. In addition, the study of techniques to integrate

imaging approaches to boost detection capacity and reliable diagnostics is related to these

activities.

Finally, Radiomics displays the aspects of diseases that aren't apparent just from pictures.

Researchers may, for example, recognize highly predictive characteristics for success and total
survival time as well as treatment responses in order to create valuable metrics. These results

may help to classify medium to high risk patients for disease development and recurrence. The

importance of forecasting patients' reaction therapy in advance (e.g. chemo or immunotherapy)

or suggests the need for more intensive observations and follow-up for other patients allows to

restructure treatment in other patients.

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