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Faisal Mahmood, Ph.D.

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  1. R35GM138216 (MAHMOOD, FAISAL) Sep 15, 2020 - Jul 31, 2025
    NIH/NIGMS
    Interpretable Deep Learning Algorithms for Pathology Image Analysis
    Role: Principal Investigator

Bibliographic
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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Rahbek S, Mahmood F, Tomaszewski MR, Hanson LG, Madsen KH. Decomposition-based framework for tumor classification and prediction of treatment response from longitudinal MRI. Phys Med Biol. 2023 01 05; 68(2). PMID: 36595245.
    Citations:    Fields:    Translation:HumansAnimals
  2. Ozyoruk KB, Can S, Darbaz B, Basak K, Demir D, Gokceler GI, Serin G, Hacisalihoglu UP, Kurtulus E, Lu MY, Chen TY, Williamson DFK, Yilmaz F, Mahmood F, Turan M. A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded. Nat Biomed Eng. 2022 12; 6(12):1407-1419. PMID: 36564629.
    Citations:    Fields:    Translation:Humans
  3. Lennerz JK, Green U, Williamson DFK, Mahmood F. A unifying force for the realization of medical AI. NPJ Digit Med. 2022 Nov 15; 5(1):172. PMID: 36380011; PMCID: PMC9666657.
    Citations:    
  4. Chen C, Lu MY, Williamson DFK, Chen TY, Schaumberg AJ, Mahmood F. Fast and scalable search of whole-slide images via self-supervised deep learning. Nat Biomed Eng. 2022 12; 6(12):1420-1434. PMID: 36217022; PMCID: PMC9792371.
    Citations:    Fields:    Translation:Humans
  5. Lipkova J, Chen RJ, Chen B, Lu MY, Barbieri M, Shao D, Vaidya AJ, Chen C, Zhuang L, Williamson DFK, Shaban M, Chen TY, Mahmood F. Artificial intelligence for multimodal data integration in oncology. Cancer Cell. 2022 10 10; 40(10):1095-1110. PMID: 36220072.
    Citations: 2     Fields:    Translation:Humans
  6. Ghaffari Laleh N, Muti HS, Loeffler CML, Echle A, Saldanha OL, Mahmood F, Lu MY, Trautwein C, Langer R, Dislich B, Buelow RD, Grabsch HI, Brenner H, Chang-Claude J, Alwers E, Brinker TJ, Khader F, Truhn D, Gaisa NT, Boor P, Hoffmeister M, Schulz V, Kather JN. Erratum to 'Benchmarking weakly-supervised deep learning pipelines for whole slide classification in computational pathology' Medical Image Analysis, Volume 79, July 2022, 102474. Med Image Anal. 2022 Nov; 82:102622. PMID: 36130464.
    Citations:    Fields:    
  7. Chen RJ, Lu MY, Williamson DFK, Chen TY, Lipkova J, Noor Z, Shaban M, Shady M, Williams M, Joo B, Mahmood F. Pan-cancer integrative histology-genomic analysis via multimodal deep learning. Cancer Cell. 2022 08 08; 40(8):865-878.e6. PMID: 35944502.
    Citations: 5     Fields:    Translation:Humans
  8. Song AH, Williamson DFK, Mahmood F. Investigating Morphologic Correlates of Driver Gene Mutation Heterogeneity via Deep Learning. Cancer Res. 2022 08 03; 82(15):2672-2673. PMID: 35919991.
    Citations:    Fields:    Translation:Humans
  9. Mahmood F, Topol EJ. Digitising heart transplant rejection. Lancet. 2022 07 02; 400(10345):17. PMID: 35780784.
    Citations:    Fields:    Translation:Humans
  10. Ghaffari Laleh N, Muti HS, Loeffler CML, Echle A, Saldanha OL, Mahmood F, Lu MY, Trautwein C, Langer R, Dislich B, Buelow RD, Grabsch HI, Brenner H, Chang-Claude J, Alwers E, Brinker TJ, Khader F, Truhn D, Gaisa NT, Boor P, Hoffmeister M, Schulz V, Kather JN. Benchmarking weakly-supervised deep learning pipelines for whole slide classification in computational pathology. Med Image Anal. 2022 07; 79:102474. PMID: 35588568.
    Citations: 6     Fields:    Translation:Humans
  11. Chen RJ, Lu MY, Wang J, Williamson DFK, Rodig SJ, Lindeman NI, Mahmood F. Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis. IEEE Trans Med Imaging. 2022 04; 41(4):757-770. PMID: 32881682.
    Citations: 37     Fields:    Translation:Humans
  12. Lipkova J, Chen TY, Lu MY, Chen RJ, Shady M, Williams M, Wang J, Noor Z, Mitchell RN, Turan M, Coskun G, Yilmaz F, Demir D, Nart D, Basak K, Turhan N, Ozkara S, Banz Y, Odening KE, Mahmood F. Deep learning-enabled assessment of cardiac allograft rejection from endomyocardial biopsies. Nat Med. 2022 03; 28(3):575-582. PMID: 35314822; PMCID: PMC9353336.
    Citations: 4     Fields:    Translation:Humans
  13. Lu MY, Chen RJ, Kong D, Lipkova J, Singh R, Williamson DFK, Chen TY, Mahmood F. Federated learning for computational pathology on gigapixel whole slide images. Med Image Anal. 2022 02; 76:102298. PMID: 34911013; PMCID: PMC9340569.
    Citations: 14     Fields:    Translation:Humans
  14. Lu MY, Sater HA, Mahmood F. Multiplex computational pathology for treatment response predication. Cancer Cell. 2021 08 09; 39(8):1053-1055. PMID: 34375608.
    Citations: 3     Fields:    Translation:Humans
  15. Chen RJ, Lu MY, Chen TY, Williamson DFK, Mahmood F. Synthetic data in machine learning for medicine and healthcare. Nat Biomed Eng. 2021 06; 5(6):493-497. PMID: 34131324; PMCID: PMC9353344.
    Citations: 35     Fields:    Translation:Humans
  16. Lu MY, Chen TY, Williamson DFK, Zhao M, Shady M, Lipkova J, Mahmood F. AI-based pathology predicts origins for cancers of unknown primary. Nature. 2021 06; 594(7861):106-110. PMID: 33953404.
    Citations: 57     Fields:    Translation:Humans
  17. Ozyoruk KB, Gokceler GI, Bobrow TL, Coskun G, Incetan K, Almalioglu Y, Mahmood F, Curto E, Perdigoto L, Oliveira M, Sahin H, Araujo H, Alexandrino H, Durr NJ, Gilbert HB, Turan M. EndoSLAM dataset and an unsupervised monocular visual odometry and depth estimation approach for endoscopic videos. Med Image Anal. 2021 07; 71:102058. PMID: 33930829.
    Citations: 10     Fields:    Translation:Animals
  18. Speight R, Tyyger M, Schmidt MA, Liney G, Johnstone R, Eccles CL, Dubec M, George B, Henry A, Herbert T, Nyholm T, Mahmood F, Korhonen J, Sims R, Tijssen RHN, Vanhoutte F, Busoni S, Lacornerie T, McCallum H. IPEM Topical Report: an international IPEM survey of MRI use for external beam radiotherapy treatment planning. Phys Med Biol. 2021 03 23; 66(7). PMID: 33631729.
    Citations: 7     Fields:    Translation:Humans
  19. Lu MY, Williamson DFK, Chen TY, Chen RJ, Barbieri M, Mahmood F. Data-efficient and weakly supervised computational pathology on whole-slide images. Nat Biomed Eng. 2021 06; 5(6):555-570. PMID: 33649564; PMCID: PMC8711640.
    Citations: 68     Fields:    Translation:Humans
  20. Bernchou U, Christiansen RL, Bertelsen A, Tilly D, Riis HL, Jensen HR, Mahmood F, Hansen CR, Hansen VN, Schytte T, Brink C. End-to-end validation of the geometric dose delivery performance of MR linac adaptive radiotherapy. Phys Med Biol. 2021 02 12; 66(4):045034. PMID: 33321475.
    Citations: 2     Fields:    Translation:Humans
  21. Incetan K, Celik IO, Obeid A, Gokceler GI, Ozyoruk KB, Almalioglu Y, Chen RJ, Mahmood F, Gilbert H, Durr NJ, Turan M. VR-Caps: A Virtual Environment for Capsule Endoscopy. Med Image Anal. 2021 05; 70:101990. PMID: 33609920.
    Citations: 8     Fields:    Translation:Humans
  22. Almalioglu Y, Bengisu Ozyoruk K, Gokce A, Incetan K, Irem Gokceler G, Ali Simsek M, Ararat K, Chen RJ, Durr NJ, Mahmood F, Turan M. EndoL2H: Deep Super-Resolution for Capsule Endoscopy. IEEE Trans Med Imaging. 2020 12; 39(12):4297-4309. PMID: 32795966.
    Citations: 4     Fields:    
  23. Mahmood F, Borders D, Chen RJ, Mckay GN, Salimian KJ, Baras A, Durr NJ. Deep Adversarial Training for Multi-Organ Nuclei Segmentation in Histopathology Images. IEEE Trans Med Imaging. 2020 11; 39(11):3257-3267. PMID: 31283474.
    Citations: 40     Fields:    Translation:Humans
  24. Mahmood F, Zhang H, Lin J, Wan C. Laser-Induced Graphene Derived from Kraft Lignin for Flexible Supercapacitors. ACS Omega. 2020 Jun 23; 5(24):14611-14618. PMID: 32596598; PMCID: PMC7315590.
    Citations: 8     
  25. Chen MT, Mahmood F, Sweer JA, Durr NJ. GANPOP: Generative Adversarial Network Prediction of Optical Properties From Single Snapshot Wide-Field Images. IEEE Trans Med Imaging. 2020 06; 39(6):1988-1999. PMID: 31899416.
    Citations: 16     Fields:    Translation:Animals
  26. Bobrow TL, Mahmood F, Inserni M, Durr NJ. DeepLSR: a deep learning approach for laser speckle reduction. Biomed Opt Express. 2019 Jun 01; 10(6):2869-2882. PMID: 31259057; PMCID: PMC6583356.
    Citations: 6     
  27. Mahmood, F., Borders, D., Chen, R., McKay, G.N., Salimian, K.J., Baras, A. and Durr, N.J., . Deep adversarial training for multi-organ nuclei segmentation in histopathology images. IEEE Transactions on Medical Imaging. 2019. View Publication.
  28. Bobrow, T.L., Mahmood, F., Inserni, M. and Durr, N.J.,. DeepLSR: Deep learning approach for laser speckle reduction. Biomedical Optics Express. 2019. View Publication.
  29. McKay GN, Mahmood F, Durr NJ. Large dynamic range autorefraction with a low-cost diffuser wavefront sensor. Biomed Opt Express. 2019 Apr 01; 10(4):1718-1735. PMID: 31061764; PMCID: PMC6484988.
    Citations: 4     
  30. McKay, G.N., Mahmood, F. and Durr, N.J. Large dynamic range autorefraction with a low-cost diffuser wavefront sensor. Biomedical Optics Express. 2019; 10(4):1718-1735. View Publication.
  31. Mahmood, F., Toots, M., Öfverstedt, L.G.W. and Skoglund, B.U. 2D discrete Fourier transform with simultaneous edge artifact removal for real-time applications US Patent US20180204313A1. 2018. View Publication.
  32. Mahmood F, Chen R, Sudarsky S, Yu D, Durr NJ. Deep learning with cinematic rendering: fine-tuning deep neural networks using photorealistic medical images. Phys Med Biol. 2018 09 13; 63(18):185012. PMID: 30113015.
    Citations: 9     Fields:    Translation:HumansAnimals
  33. Mahmood F, Durr NJ. Deep learning and conditional random fields-based depth estimation and topographical reconstruction from conventional endoscopy. Med Image Anal. 2018 08; 48:230-243. PMID: 29990688.
    Citations: 26     Fields:    Translation:Animals
  34. Mahmood F, Chen R, Durr NJ. Unsupervised Reverse Domain Adaptation for Synthetic Medical Images via Adversarial Training. IEEE Trans Med Imaging. 2018 12; 37(12):2572-2581. PMID: 29993538.
    Citations: 36     Fields:    Translation:Humans
  35. Mahmood, F., Shahid, N., Skoglund, U. and Vandergheynst, P. Adaptive Graph-Based Total Variation for Tomographic Reconstructions. IEEE Signal Processing Letters. 2018; 25(5):700-704. View Publication.
  36. Mahmood, F., Öfverstedt, L.G., Toots, M., Wilken, G. and Skoglund, U. An Extended Field-Based Method for Noise Removal From Electron Tomographic Reconstructions. IEEE Access. 2018; 6:17326-17339. View Publication.
  37. Mahmood, F. and Durr, N.J., . Topographical reconstructions from monocular optical colonoscopy images via deep learning. 15th IEEE International Symposium on Biomedical Imaging. 2018; 216-219. View Publication.
  38. Mahmood, F., Toots, M., Öfverstedt, L.G. and Skoglund, U. Algorithm and Architecture Optimization for 2D Discrete Fourier Transforms with Simultaneous Edge Artifact Removal. International Journal of Reconfigurable Computing. 2017.
  39. Mahmood F, Johannesen HH, Geertsen P, Hansen RH. Repeated diffusion MRI reveals earliest time point for stratification of radiotherapy response in brain metastases. Phys Med Biol. 2017 04 21; 62(8):2990-3002. PMID: 28306548.
    Citations: 16     Fields:    Translation:Humans
  40. Mahmood, F., Öfverstedt, L.G.W. and Skoglund, B.U.,. Extended field iterative reconstruction technique (EFIRT) for correlated noise removal. US Patent US9594032B2. 2017. View Publication.
  41. Mahmood F. Algorithmic and Architectural Developments for Cryo-Electron Tomography. 2017. View Publication.
  42. Mahmood F, Shahid N, Vandergheynst P, Skoglund U. Graph-based sinogram denoising for tomographic reconstructions. Annu Int Conf IEEE Eng Med Biol Soc. 2016 Aug; 2016:3961-3664. PMID: 28269152.
    Citations:    Fields:    Translation:Humans
  43. Mohan DM, Kumar P, Mahmood F, Wong KF, Agrawal A, Elgendi M, Shukla R, Ang N, Ching A, Dauwels J, Chan AH. Effect of Subliminal Lexical Priming on the Subjective Perception of Images: A Machine Learning Approach. PLoS One. 2016; 11(2):e0148332. PMID: 26866807.
    Citations: 3     Fields:    Translation:Humans
  44. Mahmood, F., Toots, M., Öfverstedt, L.G. and Skoglund, U., . 2D discrete Fourier transform with simultaneous edge artifact removal for real-time applications. IEEE International Conference on Field Programmable Technology (FPT). 2015; 236-239. View Publication.
  45. Kumar P, Mahmood F, Mohan DM, Wong K, Agrawal A, Elgendi M, Shukla R, Dauwels J, Chan AH. On the effect of subliminal priming on subjective perception of images: a machine learning approach. Annu Int Conf IEEE Eng Med Biol Soc. 2014; 2014:5438-41. PMID: 25571224.
    Citations: 2     Fields:    Translation:HumansCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.