Cary Oberije

Mrs. Cary Oberije

orcid

Research Focus & Metrics

Academic Career Length

21Years (2006-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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26 February 2020 in British Journal of Radiology
Verified
Journal Article
Closed access
WRWilliam Rogers
William Rogers
SSSithin Thulasi Seetha
Sithin Thulasi Seetha
TRTurkey Refaee
Turkey Refaee
RLRelinde I. Y. Lieverse
Relinde I. Y. Lieverse
Renée GranzierRenée Granzier
Renée Granzier
Philippe LambinPhilippe Lambin
Philippe Lambin
Historically, medical imaging has been a qualitative or semi-quantitative modality. It is difficult to quantify what can be seen in an image, and to turn it into valuable predictive outcomes. As a result of advances in both computational hardware and machine learning algorithms, computers are making great strides in obtaining quantitative information from imaging and correlating it with outcomes. Radiomics, in its two forms “handcrafted and deep,” is an emerging field that translates medical images into quantitative data to yield biological information and enable radiologic phenotypic profiling for diagnosis, theragnosis, decision support, and monitoring. Handcrafted radiomics is a multistage process in which features based on shape, pixel intensities, and texture are extracted from radiographs. Within this review, we describe the steps: starting with quantitative imaging data, how it can be extracted, how to correlate it with clinical and biological outcomes, resulting in models that can be used to make predictions, such as survival, or for detection and classification used in diagnostics. The application of deep learning, the second arm of radiomics, and its place in the radiomics workflow is discussed, along with its advantages and disadvantages. To better illustrate the technologies being used, we provide real-world clinical applications of radiomics in oncology, showcasing research on the applications of radiomics, as well as covering its limitations and its future direction.

15 May 2018 in Medical Physics
Verified
Journal Article
Open access
PDF file
TDTimo M. Deist
Timo M. Deist
FDFrank J. W. M. Dankers
Frank J. W. M. Dankers
GVGilmer Valdes
Gilmer Valdes
RWRobin Wijsman
Robin Wijsman
IHI‐Chow Hsu
I‐Chow Hsu
Philippe LambinPhilippe Lambin
Philippe Lambin
Purpose: Machine learning classification algorithms (classifiers) for prediction of treatment response are becoming more popular in radiotherapy literature. General Machine learning literature provides evidence in favor of some classifier families (random forest, support vector machine, gradient boosting) in terms of classification performance. The purpose of this study is to compare such classifiers specifically for (chemo)radiotherapy datasets and to estimate their average discriminative performance for radiation treatment outcome prediction.Methods: We collected 12 datasets (3496 patients) from prior studies on post‐(chemo)radiotherapy toxicity, survival, or tumor control with clinical, dosimetric, or blood biomarker features from multiple institutions and for different tumor sites, that is, (non‐)small‐cell lung cancer, head and neck cancer, and meningioma. Six common classification algorithms with built‐in feature selection (decision tree, random forest, neural network, support vector machine, elastic net logistic regression, LogitBoost) were applied on each dataset using the popular open‐source R package caret. The R code and documentation for the analysis are available online (https://github.com/timodeist/classifier_selection_code). All classifiers were run on each dataset in a 100‐repeated nested fivefold cross‐validation with hyperparameter tuning. Performance metrics (AUC, calibration slope and intercept, accuracy, Cohen's kappa, and Brier score) were computed. We ranked classifiers by AUC to determine which classifier is likely to also perform well in future studies. We simulated the benefit for potential investigators to select a certain classifier for a new dataset based on our study (pre‐selection based on other datasets) or estimating the best classifier for a dataset (set‐specific selection based on information from the new dataset) compared with uninformed classifier selection (random selection).Results: Random forest (best in 6/12 datasets) and elastic net logistic regression (best in 4/12 datasets) showed the overall best discrimination, but there was no single best classifier across datasets. Both classifiers had a median AUC rank of 2. Preselection and set‐specific selection yielded a significant average AUC improvement of 0.02 and 0.02 over random selection with an average AUC rank improvement of 0.42 and 0.66, respectively.Conclusion: Random forest and elastic net logistic regression yield higher discriminative performance in (chemo)radiotherapy outcome and toxicity prediction than other studied classifiers. Thus, one of these two classifiers should be the first choice for investigators when building classification models or to benchmark one's own modeling results against. Our results also show that an informed preselection of classifiers based on existing datasets can improve discrimination over random selection.

1 July 2007 in International Journal of Radiation Oncology, Biology, Physics
Verified
Journal Article
Closed access
PDF file
ABAngela van Baardwijk
Angela van Baardwijk
GBGeert Bosmans
Geert Bosmans
LBLiesbeth Boersma
Liesbeth Boersma
JBJeroen Buijsen
Jeroen Buijsen
SWStofferinus Wanders
Stofferinus Wanders
DRDirk De Ruysscher
Dirk De Ruysscher

1 September 2006 in International Journal of Radiation Oncology, Biology, Physics
Verified
Journal Article
Closed access
BBBrigitta Baumert
Brigitta Baumert
IRIsabelle Rutten
Isabelle Rutten
COCary Oberije
Cary Oberije
ATAlbert Twijnstra
Albert Twijnstra
MDMiranda J.M. Dirx
Miranda J.M. Dirx
BKBela Kubat
Bela Kubat

1 October 2013 in Radiotherapy and Oncology
Verified
Journal Article
Open access
PLPhilippe Lambin
Philippe Lambin
ERErik Roelofs
Erik Roelofs
BRBart Reymen
Bart Reymen
EVEmmanuel Rios Velazquez
Emmanuel Rios Velazquez
JBJeroen Buijsen
Jeroen Buijsen
ADAndré Dekker
André Dekker
An overview of the Rapid Learning methodology, its results, and the potential impact on radiotherapy. Rapid Learning methodology is divided into four phases. In the data phase, diverse data are collected about past patients, treatments used, and outcomes. Innovative information technologies that support semantic interoperability enable distributed learning and data sharing without additional burden on health care professionals and without the need for data to leave the hospital. In the knowledge phase, prediction models are developed for new data and treatment outcomes by applying machine learning methods to data. In the application phase, this knowledge is applied in clinical practice via novel decision support systems or via extensions of existing models such as Tumour Control Probability models. In the evaluation phase, the predictability of treatment outcomes allows the new knowledge to be evaluated by comparing predicted and actual outcomes. Personalised or tailored cancer therapy ensures not only that patients receive an optimal treatment, but also that the right resources are being used for the right patients. Rapid Learning approaches combined with evidence based medicine are expected to improve the predictability of outcome and radiotherapy is the ideal field to study the value of Rapid Learning. The next step will be to include patient preferences in the decision making.

1 June 2007 in European Journal of Cancer
Verified
Journal Article
Closed access
ABAngela van Baardwijk
Angela van Baardwijk
CDChristophe Dooms
Christophe Dooms
RSRobert Jan van Suylen
Robert Jan van Suylen
EVErik Verbeken
Erik Verbeken
MHMonique Hochstenbag
Monique Hochstenbag
DRDirk De Ruysscher
Dirk De Ruysscher