Abdalla Ibrahim

Dr. Abdalla Ibrahim

Columbia University Irving Medical Center, New York, USA
orcid

Research Focus & Metrics

Academic Career Length

10Years (2017-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.

1 April 2021 in Methods
Verified
Journal Article
Open access
AIAbdalla Ibrahim
Abdalla Ibrahim
SPS. Primakov
S. Primakov
MBM. Beuque
M. Beuque
HWH.C. Woodruff
H.C. Woodruff
IHI. Halilaj
I. Halilaj
Philippe LambinPhilippe Lambin
Philippe Lambin
The advancement of artificial intelligence concurrent with the development of medical imaging techniques provided a unique opportunity to turn medical imaging from mostly qualitative, to further quantitative and mineable data that can be explored for the development of clinical decision support systems (cDSS). Radiomics, a method for the high throughput extraction of hand-crafted features from medical images, and deep learning -the data driven modeling techniques based on the principles of simplified brain neuron interactions, are the most researched quantitative imaging techniques. Many studies reported on the potential of such techniques in the context of cDSS. Such techniques could be highly appealing due to the reuse of existing data, automation of clinical workflows, minimal invasiveness, three-dimensional volumetric characterization, and the promise of high accuracy and reproducibility of results and cost-effectiveness. Nevertheless, there are several challenges that quantitative imaging techniques face, and need to be addressed before the translation to clinical use. These challenges include, but are not limited to, the explainability of the models, the reproducibility of the quantitative imaging features, and their sensitivity to variations in image acquisition and reconstruction parameters. In this narrative review, we report on the status of quantitative medical image analysis using radiomics and deep learning, the challenges the field is facing, propose a framework for robust radiomics analysis, and discuss future prospects.

Verified
Journal Article
Open access
PDF file
SMShruti Atul Mali
Shruti Atul Mali
AIAbdalla Ibrahim
Abdalla Ibrahim
Henry C WoodruffHenry C Woodruff
Henry C Woodruff
VAVincent Andrearczyk
Vincent Andrearczyk
HMHenning Müller
Henning Müller
Philippe LambinPhilippe Lambin
Philippe Lambin
Radiomics converts medical images into mineable data via a high-throughput extraction of quantitative features used for clinical decision support. However, these radiomic features are susceptible to variation across scanners, acquisition protocols, and reconstruction settings. Various investigations have assessed the reproducibility and validation of radiomic features across these discrepancies. In this narrative review, we combine systematic keyword searches with prior domain knowledge to discuss various harmonization solutions to make the radiomic features more reproducible across various scanners and protocol settings. Different harmonization solutions are discussed and divided into two main categories: image domain and feature domain. The image domain category comprises methods such as the standardization of image acquisition, post-processing of raw sensor-level image data, data augmentation techniques, and style transfer. The feature domain category consists of methods such as the identification of reproducible features and normalization techniques such as statistical normalization, intensity harmonization, ComBat and its derivatives, and normalization using deep learning. We also reflect upon the importance of deep learning solutions for addressing variability across multi-centric radiomic studies especially using generative adversarial networks (GANs), neural style transfer (NST) techniques, or a combination of both. We cover a broader range of methods especially GANs and NST methods in more detail than previous reviews.

2 February 2018 in Journal of Public Health
Verified
Journal Article
Open access
PDF file
AIAbdalla Ibrahim
Abdalla Ibrahim
SASalma M Abdalla
Salma M Abdalla
MJMohammed Jafer
Mohammed Jafer
JAJihad Abdelgadir
Jihad Abdelgadir
NVNanne de Vries
Nanne de Vries
To summarize current evidence on the impacts of child labor on physical and mental health. We searched PubMed and ScienceDirect for studies that included participants aged 18 years or less, conducted in low- and middle-income countries (LMICs), and reported quantitative data. Two independent reviewers conducted data extraction and assessment of study quality. A total of 25 studies were identified, the majority of which were cross-sectional. Child labor was found to be associated with a number of adverse health outcomes, including but not limited to poor growth, malnutrition, higher incidence of infectious and system-specific diseases, behavioral and emotional disorders, and decreased coping efficacy. Quality of included studies was rated as fair to good. Child labor remains a major public health concern in LMICs, being associated with adverse physical and mental health outcomes. Current efforts against child labor need to be revisited, at least in LMICs. Further studies following a longitudinal design, and using common methods to assess the health impact of child labor in different country contexts would inform policy making.

13 January 2020 in Acta Orthopaedica
Verified
Journal Article
Open access
PKPishtiwan H S Kalmet
Pishtiwan H S Kalmet
SSSebastian Sanduleanu
Sebastian Sanduleanu
SPSergey Primakov
Sergey Primakov
GWGuangyao Wu
Guangyao Wu
AJArthur Jochems
Arthur Jochems
MPMartijn Poeze
Martijn Poeze
Artificial intelligence (AI) is a general term that implies the use of a computer to model intelligent behavior with minimal human intervention. AI, particularly deep learning, has recently made substantial strides in perception tasks allowing machines to better represent and interpret complex data. Deep learning is a subset of AI represented by the combination of artificial neuron layers. In the last years, deep learning has gained great momentum. In the field of orthopaedics and traumatology, some studies have been done using deep learning to detect fractures in radiographs. Deep learning studies to detect and classify fractures on computed tomography (CT) scans are even more limited. In this narrative review, we provide a brief overview of deep learning technology: we (1) describe the ways in which deep learning until now has been applied to fracture detection on radiographs and CT examinations; (2) discuss what value deep learning offers to this field; and finally (3) comment on future directions of this technology.

14 June 2022 in Nature Communications
Verified
Journal Article
Open access
PDF file
SPSergey P. Primakov
Sergey P. Primakov
AIAbdalla Ibrahim
Abdalla Ibrahim
JTJanita E. van Timmeren
Janita E. van Timmeren
GWGuangyao Wu
Guangyao Wu
SKSimon A. Keek
Simon A. Keek
Philippe LambinPhilippe Lambin
Philippe Lambin
Detection and segmentation of abnormalities on medical images is highly important for patient management including diagnosis, radiotherapy, response evaluation, as well as for quantitative image research. We present a fully automated pipeline for the detection and volumetric segmentation of non-small cell lung cancer (NSCLC) developed and validated on 1328 thoracic CT scans from 8 institutions. Along with quantitative performance detailed by image slice thickness, tumor size, image interpretation difficulty, and tumor location, we report an in-silico prospective clinical trial, where we show that the proposed method is faster and more reproducible compared to the experts. Moreover, we demonstrate that on average, radiologists & radiation oncologists preferred automatic segmentations in 56% of the cases. Additionally, we evaluate the prognostic power of the automatic contours by applying RECIST criteria and measuring the tumor volumes. Segmentations by our method stratified patients into low and high survival groups with higher significance compared to those methods based on manual contours.