Publications
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Peer-reviewed publications
2022
Marcolini A, Bussola N, Arbitrio E, Amgad M, Jurman G, Furlanello C. Histolab: A Python Library for Reproducible Digital Pathology Preprocessing with Automated Testing. SoftwareX . 2022 Jul;20: 101237. doi:10.1016/j.softx.2022.101237.
Elfer K, Dudgeon S, ..., Amgad M, ..., Gallas BD. Pilot study to evaluate tools to collect pathologist annotations for validating machine learning algorithms. Journal of Medical Imaging. 2022 Jul;9(4):047501. doi: 10.1117/1.JMI.9.4.047501.
Amgad M, Atteya LA, ..., Cooper LAD. NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer. GigaScience. 2022. doi: 10.1093/gigascience/giac037.
2021
Amgad M, Atteya L, Hussein H, ..., Cooper LA. Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings. Bioinformatics. 2021. doi: 10.1093/bioinformatics/btab670.
López-Pérez M, Amgad M, ..., Katsaggelos AK. Learning from crowds in digital pathology using scalable variational Gaussian processes. Scientific Reports. 2021;11(1):1-9. doi: 10.1038/s41598-021-90821-3.
Farris AB, Vizcarra J, Amgad M, ..., Hogan J. Artificial Intelligence and Algorithmic Computational Pathology: Introduction with Renal Allograft Examples. Histopathology. 2021. doi: 10.1111/his.14304
Farris AB, Vizcarra J, Amgad M, ..., Hogan J. Image Analysis Pipeline for Renal Allograft Evaluation and Fibrosis Quantification. Kidney International Reports. 2021. doi: 10.1016/j.ekir.2021.04.019.
Dudgeon SN, Wen S, ..., Amgad M, ..., Gallas BD. A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study. J Pathol Inform. 2021;12:45. doi: 10.4103/jpi.jpi_83_20.
2020
Lee S, Amgad M, ..., Cooper LAD. Interactive classification of whole-slide imaging data for cancer researchers. Cancer Research . 2020;canres.0668.2020. doi: 10.1158/0008-5472.CAN-20-0668.
Yang X, Amgad M, ..., Ivanov AA. High expression of MKK3 is associated with worse clinical outcomes in African American breast cancer patients. J Transl Med. 2020;18(334). doi: 10.1186/s12967-020-02502-w
Amgad M, …, Salgado R, Cooper LAD. Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group. Npj Breast Cancer. 2020;6(16). doi: 10.1038/s41523-020-0154-2.
Report from the TIL Working Group, an international coalition of pathologists, oncologists, and statisticians.
Kos Z, …, Amgad M, …, Salgado R. Pitfalls in assessing stromal Tumour Infiltrating Lymphocytes (sTILs) in breast cancer. Npj Breast Cancer. 2020;6(17). doi: 10.1038/s41523-020-0156-0
Hudeček J et al. Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials. Npj Breast Cancer. 2020;6(15). doi: 10.1038/s41523-020-0155-1
2019
Lee S, Amgad M, ..., Cooper L. An Ensemble-based Active Learning for Breast Cancer Classification. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA, USA, pp. 2549-2553. 2019. doi: 10.1109/BIBM47256.2019.8983317
Chandradevan R, ..., Amgad M, ..., Cooper LAD. Machine-based detection and classification for bone marrow aspirate differential counts: initial development focusing on nonneoplastic cells. Laboratory Investigations. 2019. doi: 10.1038/s41374-019-0325-7.
Amgad M, Elfandy H, …, Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083
Lead a team of 25, including 2 pathologists and 3 pathology residents. Press coverage.Released one of largest semantic segmentation datasets in histology.
Amgad M, Sarkar A, …, Cooper LAD, Barnes M. Joint region and nucleus segmentation for characterization of Tumor Infiltrating Lymphocytes in breast cancer. Medical Imaging 2019: Digital Pathology, vol. 10956, p. 109560M. International Society for Optics and Photonics, 2019. doi: 10.1117/12.2512892
2018
Elsebaie M, Amgad M, …, Elsayed Z. Management of low and intermediate risk adult rhabdomyosarcoma: A pooled survival analysis of 553 patients. Scientific Reports. 2018 Jun 19;8(1):9337. doi: 10.1038/s41598-018-27556-1.
Poster version won top spot at 2018 ACP Competition, Clinical Research Category.
Mobadersany P, Yousefi S, Amgad M, …, Cooper LAD. Predicting cancer outcomes from histology and genomics using convolutional networks. Proc. of the Nat. Acad. of Science USA. 2018;115(13):E2970-E2979. doi: 10.1073/pnas.1717139115.
Featured on PNAS journal cover. Also featured by at least 7 news outlets.
2017
Nalisnik M, Amgad M, …, Gutman DA, Cooper LAD. Interactive phenotyping of large-scale histology imaging data with HistomicsML. Scientific Reports. 2017;7(1):14588. doi: 10.1038/s41598-017-15092-3.
Yousefi S, Amrollahi F, Amgad M, …, Cooper LAD. Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models. Scientific Reports. 2017 Sep 15;7(1):11707. doi: 10.1038/s41598-017-11817-6.
Featured as 3rd top article in Oncology published in Nature Scientific Reports.
2016
Tsui MM, Itoh A, Amgad M, et al. Vectors for genetically-encoded tags for Electron Microscopy contrast in Drosophila. Biol Proced Online. 2016 Feb 1;18:5. doi: 10.1186/s12575-016-0034-1.
Abdelfattah NS, Amgad M, et al. Molecular underpinnings of corneal angiogenesis: advances over the past decade. International Journal of Ophthalmology. 2016 May; 9(1). doi: 10.18240/ijo.2016.05.24.
Abdelfattah NS, Amgad M, et al. Host immune cellular reactions in corneal neovascularization: Review. International Journal of Ophthalmology. 2016 Apr; 9(1). doi: 10.18240/ijo.2016.04.25.
2015
Amgad M, Itoh A, Tsui MM. Extending Ripley’s K-function to quantify aggregation in 2-D grayscale images. PLoS One. 2015;10(12):e0144404. doi: 10.1371/journal.pone.0144404.
Amgad M, Tsui MMK, …, Shash E. Medical Student Research: An Integrated Mixed-Methods Systematic Review and Meta-Analysis. PLoS One. 2015; 10(6): e0127470. doi: 10.1371/journal.pone.0127470.
Abdelfattah NS, Amgad M, et al. Clinical correlates of common corneal neovascular diseases: a literature review. International Journal of Ophthalmology. 2015; 8(1):182-93. doi: 10.3980/j.issn.2222-3959.2015.01.32.
Amgad M, Shash E. The evolution of undergraduate medical student research activities: Personal experience of a developing nation’s up-rise. J Cancer Education. 2015 Dec;30(4):813-4. doi: 10.1007/s13187-015-0923-z.
2014
Amgad M, AlFaar AS. Integrating web 2.0 in clinical research education in a developing country. J Cancer Education. 2014 Sep;29(3):536-40. doi: 10.1007/s13187-013-0595-5.
Nageeb A, Amgad M,…, Emara K. Is the ISKD a safe measure for bone lengthening? A systematic literature review. J Orthopedic Trauma and Rehabilitation. 2014 Dec;18(2):69-78. doi: 10.1016/j.jotr.2014.01.002.
Abdelfattah NS, Amgad M, et al. Development of an Arabic version of the National Eye Institute Visual Function Questionnaire as a tool to study eye diseases patients in Egypt. International Journal of Ophthalmology. 2014 Oct 18;7(5):891-7. doi: 10.3980/j.issn.2222-3959.2014.05.27.
2012
Amgad M, Shash E, Gaafar R. Cancer education for medical students in developing countries – Where do we stand and how to improve? Critical Reviews in Oncology Hematology. 2012 Oct;84(1):122-9. doi: 10.1016/j.critrevonc.2012.01.003.
Other publications
Preprints
Amgad M, Salgado R, Cooper LAD. MuTILs: explainable, multiresolution computational scoring of Tumor-Infiltrating Lymphocytes in breast carcinomas using clinical guidelines. medRxiv 2022.01.08.22268814. 2021 Jan.
Zhang L, Amgad M, Cooper LAD. A Histopathology Study Comparing Contrastive Semi-Supervised and Fully Supervised Learning. arXiv:2111.05882. 2021 Nov 10.
Yousefi S, Shaban A, Amgad M, Cooper LAD. Learning Cancer Outcomes from Heterogeneous Genomic Data Sources: An Adversarial Multi-task Learning Approach. ICML 2019 Workshop AMTL (Open Review). 2019.
Yousefi S, Shaban A, Amgad M, …, Cooper LAD. Learning Clinical Outcomes from Heterogeneous Genomic Data Sources. arXiv:1904.01637 [q-bio.QM]. 2019.
Amgad M, Fouad YA, Elsebaie MA. Approach to a highly-virulent emerging viral epidemic: A thought experiment and literature review. PeerJ Preprints. 2019. 7:e27518v1. doi: 10.7287/peerj.preprints.27518v1.
Patents
Tageldin MA, Cooper LAD, Kurkure U, Martin J. Image processing-based object classification bootstrapping of region-level annotations. Application US20220262145. Filing date: 10/31/2019. [PDF].
Sarkar A, Tageldin MA, Srinivas C. Deep-learning systems and methods for joint cell and region classification in biological images. Application WO-2019110583-A1. Legal status: Granted. 06/13/2019. [Google patents] [PDF].
Book chapters
Shash E, Amgad M. Global Perspectives on Cancer: Incidence, Care, and Experience. (Vol. 2, Ch. 20: Egypt). Feb 2015. Publisher: ABC-CLIO (Praeger). ISBN: 978-1-4408-2857-7. Book can be found here.
Conference abstracts and presentations
Oral presentations
Pathology Informatics Summit 2021 (Virtual):
Gallas BD*, Elfer K, Amgad M, ... . High Throughput Truthing (HTT): pathologist agreement from a pilot study.
Chicago Biomedical Informatics Data Jam 2020 (Chicago, IL)
Amgad M*. High-resolution mapping of the tumor microenvironment in breast carcinomas.
ACLPS 2020 (Virtual)
Drumheller B*, Amgad M, ..., Jaye D. Early Development of a Machine Learning Approach to Quantify MYC Immunohistochemical Staining in Lymphoma. American Journal of Clinical Pathology. 154(Supplement_1):S19-. 2020.
Path. Informatics 2019 (Pitt., PA)
Gallas BD*, Amgad M, et al. A Collaborative Project to Produce Regulatory-Grade Pathologist Annotations to Validate Viewers and Algorithms.
SPIE 2019 (San Diego, CA)
Amgad M*, Sarkar A, …, Cooper LAD, Barnes M. Joint region and nucleus segmentation for characterization of Tumor Infiltrating Lymphocytes in breast cancer. Medical Imaging 2019: Digital Pathology, vol. 10956, p. 109560M. 2019.
Dom. Viol. 2012 (Cairo, Egypt)
Magdy T, Amgad M*, Salama M et al. Prevalence and patterns of female genital mutilation and domestic violence among Cairo University medical students. Cairo University.
* Presenter
Poster presentations
Pathology Visions 2021 (Las Vegas, NV) || TRAVEL AWARD ||
Amgad M, Cooper LAD. Beyond saliency heatmaps: explaining deep-learning nucleus classification with intuitive decision tree approximations.
Pathology Informatics Summit 2021 (Virtual) || BEST POSTER AWARD || TRAINEE AWARD ||
Amgad M, Cooper LAD. MuTILs: a multiresolution approach for computational TILs assessment using clinical guidelines.
AACR 2020 (San Francisco, CA)
Saad AM, Elsebaie MAT, Amgad M, ..., Abdel-Rahman O. Racial disparities in pancreatic adenocarcinoma survival. Do they exist for patients who already survived their first year? [abstract]. AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2): Abstract B110.
USCAP 2020 (Los Angeles, CA)
Farris A, Vizcarra J, Amgad M, ..., Hogan J. Renal Allograft Image Analysis Pipeline Correlations with Interstitial Fibrosis Assessment. Laboratory Investigation. 2020;100(Suppl.1), 1574-1575.
ICML 2019 (Long Beach, CA)
Yousefi S, Shaban A, Amgad M, Cooper LAD. Learning cancer outcomes from heterogeneous genomic data sources: An adversarial multi-task learning approach.
AACR 2019 (Atlanta, GA)
Amgad M, Kurkure U, …, Cooper LAD. Systematic computational analysis of histologic-genomic associations in triple-negative infiltrating ductal carcinomas of the breast [abstract]. Cancer Research. 2019;79(13)-suppl.
SABCS 2018 (San Antonio, TX)
Amgad M, Sarkar A, …, Cooper LAD, Barnes M. Computational scoring of tumor infiltrating lymphocytes in triple-negative breast cancer [abstract]. Cancer Research. 2019;79(4)-suppl.
Path. Visions 2018 (San Diego, CA)
Amgad M, Elfandy H, ... , Cooper LAD. Hierarchical Crowdsourcing for Generating Large-Scale Annotations of Histopathology. J Pathology Informatics. 2019;10:10.
ACLPS 2018 (Houston, TX)
Abdulrahman A, Amgad M, Cooper LAD, Jaye D. Early Experience in Developing a Machine-Learning and Digital Pathology Approach to Automate Bone Marrow Differential Counts. American J. of Clinical Pathology. 2018;150 (suppl_1),S149-S150.
ACP 2018 (New Orleans, LA) || BEST POSTER AWARD ||
Elsebaie M, Amgad M, …, Elsayed Z. Management of low and intermediate-risk adult rhabdomyosarcoma: A pooled survival analysis of 553 patients. Sci. Rep. 2018;8(1):9337.
AANS/CNS 2017 (Houston, TX)
Halani SH, et al. Markers and Mechanisms of Disease Progression in IDH-Mutant Astrocytomas. Neurosurgery. 2017; 64(CN_suppl_1):261–262.
ARVO 2013 (Washnigton, DC)
Saleh N et al. Development of an Arabic Version of the National Eye Institute Visual Function Questionnaire as a tool to study eye diseases patients in Egypt. Invest Ophthalmol Vis Sci 2013;54: E-Abstract 5335.
ESOT 2013 (Vienna, AU)
Elkhashab SA et al. Quality of life in dialysis patients: Impact of a functioning graft. Transplant International 26 (Suppl. 2), 185–339, P021.