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Fayyaz ul Amir Afsar Minhas

Fayyaz A. Afsar – Fayyaz A. Minhas – Fayyaz Minhas

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affiliation: Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan

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2025
[j35]
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Mostafa Jahanifar, Manahil Raza, Kesi Xu, Trinh Thi Le Vuong, Robert Jewsbury, Adam Shephard, Neda Zamanitajeddin, Jin Tae Kwak, Shan E Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot:
Domain Generalization in Computational Pathology: Survey and Guidelines. ACM Comput. Surv. 57(11): 285:1-285:37 (2025)
[j34]
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Piotr Keller, Muhammad Dawood, Brinder Singh Chohan, Fayyaz ul Amir Afsar Minhas:
HistoKernel: Whole slide image level Maximum Mean Discrepancy kernels for pan-cancer predictive modelling. Medical Image Anal. 101: 103491 (2025)
2024
[j33]
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Srijay Deshpande, Sokratia Georgaka, Michael Haley, Robert Sellers, James Minshull, Jayakrupakar Nallala, Martin Fergie, Nicholas Stone, Nasir M. Rajpoot, Syed Murtuza Baker, Mudassar Iqbal, Kevin Couper, Federico Roncaroli, Fayyaz Minhas:
Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling. Bioinform. 40(Supplement_2): ii174-ii181 (2024)
[j32]
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Srijay Deshpande, Muhammad Dawood, Fayyaz Minhas, Nasir M. Rajpoot:
SynCLay: Interactive synthesis of histology images from bespoke cellular layouts. Medical Image Anal. 91: 102995 (2024)
[j31]
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Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, Josef Lorenz Rumberger, Elias Baumann, Peter Hirsch, Lihao Liu, Chenyang Hong, Angelica I. Avilés-Rivero, Ayushi Jain, Heeyoung Ahn, Yiyu Hong, Hussam Azzuni, Min Xu, Mohammad Yaqub, Marie-Claire Blache, Benoît Piégu, Bertrand Vernay, Tim Scherr, Moritz Böhland, Katharina Löffler, Jiachen Li, Weiqin Ying, Chixin Wang, David R. J. Snead, Shan-E-Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot:
CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting. Medical Image Anal. 92: 103047 (2024)
[j30]
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Mostafa Jahanifar, Adam Shephard, Neda Zamanitajeddin, Simon Graham, Shan E Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot:
Mitosis detection, fast and slow: Robust and efficient detection of mitotic figures. Medical Image Anal. 94: 103132 (2024)
[j29]
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Mustafa Emre Sahin, Benjamin C. B. Symons, Pushpak Pati, Fayyaz Minhas, Declan Millar, Maria Gabrani, Stefano Mensa, Jan Lukas Robertus:
Efficient Parameter Optimisation for Quantum Kernel Alignment: A Sub-sampling Approach in Variational Training. Quantum 8: 1502 (2024)
[j28]
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Cong Wang, Zhao Chen, Fayyaz Minhas:
Physics-Informed Learning for Tropical Cyclone Intensity Prediction. IEEE Trans. Geosci. Remote. Sens. 62: 1-21 (2024)
2023
[j27]
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Mark Eastwood, Silviu Tudor Marc, Xiaohong W. Gao, Heba Sailem, Judith Offman, Emmanouil Karteris, Angeles Montero Fernandez, Danny Jonigk, William Cookson, Miriam Moffatt, Sanjay Popat, Fayyaz Minhas, Jan Lukas Robertus:
Malignant Mesothelioma subtyping via sampling driven multiple instance prediction on tissue image and cell morphology data. Artif. Intell. Medicine 143: 102628 (2023)
[j26]
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Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Shan-E-Ahmed Raza, Fayyaz A. Afsar, David R. J. Snead, Nasir M. Rajpoot:
One model is all you need: Multi-task learning enables simultaneous histology image segmentation and classification. Medical Image Anal. 83: 102685 (2023)
2022
[j25]
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Alex Foote, Amina Asif, Nasir M. Rajpoot, Fayyaz A. Minhas:
REET: robustness evaluation and enhancement toolbox for computational pathology. Bioinform. 38(12): 3312-3314 (2022)
[j24]
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Adiba Yaseen, Imran Amin, Naeem Akhter, Asa Ben-Hur, Fayyaz Minhas:
Insights into performance evaluation of compound-protein interaction prediction methods. Bioinform. 38(Supplement_2): ii75-ii81 (2022)
[j23]
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Don Neumann, Soumyadip Roy, Fayyaz ul Amir Afsar Minhas, Asa Ben-Hur:
On the choice of negative examples for prediction of host-pathogen protein interactions. Frontiers Bioinform. 2 (2022)
[j22]
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Srijay Deshpande, Fayyaz A. Minhas, Simon Graham, Nasir M. Rajpoot:
SAFRON: Stitching Across the Frontier Network for Generating Colorectal Cancer Histology Images. Medical Image Anal. 77: 102337 (2022)
[j21]
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Wenqi Lu, Michael Toss, Muhammad Dawood, Emad Rakha, Nasir M. Rajpoot, Fayyaz A. Minhas:
SlideGraph+: Whole slide image level graphs to predict HER2 status in breast cancer. Medical Image Anal. 80: 102486 (2022)
[j20]
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Sadaf Gull, Fayyaz A. Minhas:
AMP₀: Species-Specific Prediction of Anti-microbial Peptides Using Zero and Few Shot Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 275-283 (2022)
2021
[j19]
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Kelvin K. F. Li, Stephen A. Jarvis, Fayyaz A. Minhas:
Elementary effects analysis of factors controlling COVID-19 infections in computational simulation reveals the importance of social distancing and mask usage. Comput. Biol. Medicine 134: 104369 (2021)
[j18]
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Adiba Yaseen, Sadaf Gull, Naeem Akhtar, Imran Amin, Fayyaz A. Minhas:
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning. J. Bioinform. Comput. Biol. 19(5): 2150021:1-2150021:20 (2021)
[j17]
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  - journals/nar/HuangYYAWLZMY21
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Le Huang, Bowen Yang, Haidong Yi, Amina Asif, Jiawei Wang, Trevor Lithgow, Han Zhang, Fayyaz ul Amir Afsar Minhas, Yanbin Yin:
AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. Nucleic Acids Res. 49(Database-Issue): D622-D629 (2021)
[j16]
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Farzeen Munir, Sadaf Gull, Amina Asif, Fayyaz ul Amir Afsar Minhas:
MILAMP: Multiple Instance Prediction of Amyloid Proteins. IEEE ACM Trans. Comput. Biol. Bioinform. 18(3): 1142-1150 (2021)
2020
[j15]
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  - journals/biodatamining/AbbasiYHAM20
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Wajid Arshad Abbasi, Adiba Yaseen, Fahad Ul Hassan, Saiqa Andleeb, Fayyaz ul Amir Afsar Minhas:
ISLAND: in-silico proteins binding affinity prediction using sequence information. BioData Min. 13(1): 20 (2020)
[j14]
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Amina Asif, Muhammad Dawood, Bismillah Jan, Javaid Khurshid, Mark DeMaria, Fayyaz ul Amir Afsar Minhas:
PHURIE: hurricane intensity estimation from infrared satellite imagery using machine learning. Neural Comput. Appl. 32(9): 4821-4834 (2020)
[j13]
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Muhammad Dawood, Amina Asif, Fayyaz ul Amir Afsar Minhas:
Deep-PHURIE: deep learning based hurricane intensity estimation from infrared satellite imagery. Neural Comput. Appl. 32(13): 9009-9017 (2020)
2019
[j12]
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Sadaf Gull, Nauman Shamim, Fayyaz ul Amir Afsar Minhas:
AMAP: Hierarchical multi-label prediction of biologically active and antimicrobial peptides. Comput. Biol. Medicine 107: 172-181 (2019)
[j11]
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Amina Asif, Fayyaz ul Amir Afsar Minhas:
An embarrassingly simple approach to neural multiple instance classification. Pattern Recognit. Lett. 128: 474-479 (2019)
2018
[j10]
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Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas:
Learning protein binding affinity using privileged information. BMC Bioinform. 19(1): 425:1-425:12 (2018)
[j9]
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Abdul Hannan Basit, Wajid Arshad Abbasi, Amina Asif, Sadaf Gull, Fayyaz ul Amir Afsar Minhas:
Training host-pathogen protein-protein interaction predictors. J. Bioinform. Comput. Biol. 16(4): 1850014:1-1850014:18 (2018)
[j8]
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Asif Ahmad, Amina Asif, Nasir M. Rajpoot, Muhammad Arif, Fayyaz ul Amir Afsar Minhas:
Correlation Filters for Detection of Cellular Nuclei in Histopathology Images. J. Medical Syst. 42(1): 7:1-7:8 (2018)
2017
[j7]
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Fayyaz ul Amir Afsar Minhas, Eric D. Ross, Asa Ben-Hur:
Amino acid composition predicts prion activity. PLoS Comput. Biol. 13(4) (2017)
2016
[j6]
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Fayyaz ul Amir Afsar Minhas, Amina Asif, Muhammad Arif:
CAFÉ-Map: Context Aware Feature Mapping for mining high dimensional biomedical data. Comput. Biol. Medicine 79: 68-79 (2016)
[j5]
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Wajid Arshad Abbasi, Fayyaz ul Amir Afsar Minhas:
Issues in performance evaluation for host-pathogen protein interaction prediction. J. Bioinform. Comput. Biol. 14(3): 1650011:1-1650011:17 (2016)
2012
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Fayyaz ul Amir Afsar Minhas, Asa Ben-Hur:
Multiple instance learning of Calmodulin binding sites. Bioinform. 28(18): 416-422 (2012)
[j3]
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Muhammad Arif, Ijaz A. Malagore, Fayyaz A. Afsar:
Detection and Localization of Myocardial Infarction using K-nearest Neighbor Classifier. J. Medical Syst. 36(1): 279-289 (2012)
[j2]
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Fayyaz ul Amir Afsar Minhas, Durre Sabih, Mutawarra Hussain:
Automated Classification of Liver Disorders using Ultrasound Images. J. Medical Syst. 36(5): 3163-3172 (2012)
2011
[j1]
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Fayyaz ul Amir Afsar Minhas, Muhammad Arif:
MOX: A novel global optimization algorithm inspired from Oviposition site selection and egg hatching inhibition in mosquitoes. Appl. Soft Comput. 11(8): 4614-4625 (2011)

Conference and Workshop Papers

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2025
[c26]
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Ethar Alzaid, Fayyaz Minhas:
Transductive Survival Ranking for Pan-Cancer Automatic Risk Stratification Using Whole Slide Images. MIUA (1) 2025: 3-15
[c25]
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George Wright, Paul Brighton, Hiroyuki Yoshihara, Joe Thornton, Joanne Muter, Jan Brosens, Fayyaz Minhas:
ASTER: Automated Segmentation of Endometrial Histology Images for Reproductive Health Assessment. MIUA (1) 2025: 43-57
[c24]
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Lucan DSilva, Fayyaz Minhas:
Learnable Moran's Index for Modeling Spatial Autocorrelation in Whole Slide Images to Predict Breast Cancer Outcomes. MIUA (1) 2025: 118-130
2024
[c23]
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Cong Wang, Zhao Chen, Fayyaz Minhas:
Physical Structure Representation and Environmental Data Fusion for Cyclone Intensity Prediction. IGARSS 2024: 7316-7319
[c22]
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Tudor Ducaru, Stefan Stoica, Vlad Holban, Fayyaz Minhas:
A Two-Stage Neural Network Model for Automatic Detection of Skiffs from Satellite Imagery. IJCNN 2024: 1-7
2023
[c21]
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Piotr Keller, Muhammad Dawood, Fayyaz ul Amir Afsar Minhas:
Maximum Mean Discrepancy Kernels for Predictive and Prognostic Modeling of Whole Slide Images. ISBI 2023: 1-5
[c20]
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Ethar Alzaid, Muhammad Dawood, Fayyaz Minhas:
A Transductive Approach to Survival Ranking for Cancer Risk Stratification. MLCB 2023: 101-109
[c19]
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Piotr Keller, Muhammad Dawood, Fayyaz ul Amir Afsar Minhas:
Do Tissue Source Sites Leave Identifiable Signatures in Whole Slide Images Beyond Staining? TML4H 2023: 1-10
2022
[c18]
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Mark Eastwood, Silviu Tudor Marc, Xiaohong W. Gao, Heba Sailem, Judith Offman, Emmanouil Karteris, Angeles Montero Fernandez, Danny Jonigk, William Cookson, Miriam Moffatt, Sanjay Popat, Fayyaz A. Minhas, Jan Lukas Robertus:
Malignant Mesothelioma Subtyping of Tissue Images via Sampling Driven Multiple Instance Prediction. AIME 2022: 263-272
[c17]
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Callum Christopher Mackenzie, Muhammad Dawood, Simon Graham, Mark Eastwood, Fayyaz ul Amir Afsar Minhas:
Neural Graph Modelling of Whole Slide Images for Survival Ranking. LoG 2022: 48
[c16]
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Quoc Dang Vu, Robert Jewsbury, Simon Graham, Mostafa Jahanifar, Shan-E-Ahmed Raza, Fayyaz Minhas, Abhir Bhalerao, Nasir M. Rajpoot:
Nuclear Segmentation and Classification: On Color and Compression Generalization. MLMI@MICCAI 2022: 249-258
2021
[c15]
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  - conf/icann/AsifDM21
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Amina Asif, Muhammad Dawood, Fayyaz ul Amir Afsar Minhas:
A Generalized Meta-loss Function for Distillation Based Learning Using Privileged Information for Classification and Regression. ICANN (3) 2021: 534-545
[c14]
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Muhammad Dawood, Kim Branson, Nasir M. Rajpoot, Fayyaz ul Amir Afsar Minhas:
ALBRT: Cellular Composition Prediction in Routine Histology Images. ICCVW 2021: 664-673
[c13]
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Simon Graham, Mostafa Jahanifar, Ayesha Azam, Mohammed Nimir, Yee-Wah Tsang, Katherine Dodd, Emily Hero, Harvir Sahota, Atisha Tank, Ksenija Benes, Noorul Wahab, Fayyaz A. Minhas, Shan-E-Ahmed Raza, Hesham Eldaly, Kishore Gopalakrishnan, David R. J. Snead, Nasir M. Rajpoot:
Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification. ICCVW 2021: 684-693
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Mostafa Jahanifar, Adam J. Shephard, Neda Zamanitajeddin, Raja Muhammad Saad Bashir, Mohsin Bilal, Syed Ali Khurram, Fayyaz A. Minhas, Nasir M. Rajpoot:
Stain-Robust Mitotic Figure Detection for the Mitosis Domain Generalization Challenge. MIDOG/MOOD/Learn2Reg@MICCAI 2021: 48-52
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Rawan Albusayli, J. Dinny Graham, Nirmala Pathmanathan, Muhammad Shaban, Fayyaz Minhas, Jane E. Armes, Nasir M. Rajpoot:
Simple non-iterative clustering and CNNs for coarse segmentation of breast cancer whole-slide images. Digital Pathology 2021
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Fayyaz A. Minhas, Michael S. Toss, Noor ul Wahab, Emad Rakha, Nasir M. Rajpoot:
L₁-Regularized Neural Ranking for Risk Stratification and Its Application to Prediction of Time to Distant Metastasis in Luminal Node Negative Chemotherapy Naïve Breast Cancer Patients. PKDD/ECML Workshops (2) 2021: 390-400
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Muhammad Dawood, Kim Branson, Nasir M. Rajpoot, Fayyaz ul Amir Afsar Minhas:
All You Need is Color: Image Based Spatial Gene Expression Prediction Using Neural Stain Learning. PKDD/ECML Workshops (2) 2021: 437-450
2020
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Wenqi Lu, Simon Graham, Mohsin Bilal, Nasir M. Rajpoot, Fayyaz A. Minhas:
Capturing Cellular Topology in Multi-Gigapixel Pathology Images. CVPR Workshops 2020: 1049-1058
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Asfand Yaar, Amina Asif, Shan E Ahmed Raza, Nasir M. Rajpoot, Fayyaz A. Minhas:
Cross-Domain Knowledge Transfer for Prediction of Chemosensitivity in Ovarian Cancer Patients. CVPR Workshops 2020: 4020-4025
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Amina Asif, Fayyaz ul Amir Afsar Minhas:
Generalized Neural Framework for Learning with Rejection. IJCNN 2020: 1-8
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Srijay Deshpande, Fayyaz A. Minhas, Nasir M. Rajpoot:
Train Small, Generate Big: Synthesis of Colorectal Cancer Histology Images. SASHIMI@MICCAI 2020: 164-173
2017
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Fahad Ul Hassan, Fayyaz ul Amir Afsar Minhas:
Deep and Self-Taught Learning for Protein Accessible Surface Area Prediction. FIT 2017: 264-269
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Kanza Hamid, Amina Asif, Wajid Arshad Abbasi, Durre Sabih, Fayyaz ul Amir Afsar Minhas:
Machine Learning with Abstention for Automated Liver Disease Diagnosis. FIT 2017: 356-361
2009
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Muhammad Arif, Fayyaz A. Afsar, Muhammad Usman Akram, Adnan Fida:
Arif Index for Predicting the Classification Accuracy of Features and Its Application in Heart Beat Classification Problem. PAKDD 2009: 491-498
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Muhammad Arif, Muhammad Usman Akram, Fayyaz A. Afsar:
Arrhythmia Beat Classification Using Pruned Fuzzy K-Nearest Neighbor Classifier. SoCPaR 2009: 37-42

Editorship

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2024
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Francesco Ciompi, Nadieh Khalili, Linda Studer, Milda Poceviciute, Amjad Khan, Mitko Veta, Yiping Jiao, Neda Haj-Hosseini, Hao Chen, Shan Raza, Fayyaz Minhas, Inti Zlobec, Nikolay Burlutskiy, Veronica Vilaplana, Biagio Brattoli, Henning Müller, Manfredo Atzori:
Proceedings of the MICCAI Workshop on Computational Pathology, Marrakesh, Morocco, 6 October 2024. Proceedings of Machine Learning Research 254, PMLR 2024 [contents]
2021
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Manfredo Atzori, Nikolay Burlutskiy, Francesco Ciompi, Zhang Li, Fayyaz A. Minhas, Henning Müller, Tingying Peng, Nasir M. Rajpoot, Ben Torben-Nielsen, Jeroen van der Laak, Mitko Veta, Yinyin Yuan, Inti Zlobec:
MICCAI Workshop on Computational Pathology, COMPAY@MICCAI 2021, 27 September 2021, Virtual Event. Proceedings of Machine Learning Research 156, PMLR 2021 [contents]

Data and Artifacts

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2024
[d14]
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Johnathan Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version v1.6.0. Zenodo, 2024 [all versions]
2023
[d13]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version v1.3.2. Zenodo, 2023 [all versions]
[d12]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version v1.3.3. Zenodo, 2023 [all versions]
[d11]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version v1.4.0. Zenodo, 2023 [all versions]
[d10]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version v1.4.1. Zenodo, 2023 [all versions]
2022
[d9]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.0.1. Zenodo, 2022 [all versions]
[d8]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.1.0. Zenodo, 2022 [all versions]
[d7]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.2.0. Zenodo, 2022 [all versions]
[d6]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.2.0. Zenodo, 2022 [all versions]
[d5]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.2.0. Zenodo, 2022 [all versions]
[d4]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.2.1. Zenodo, 2022 [all versions]
[d3]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version 1.3.0. Zenodo, 2022 [all versions]
[d2]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox as an end-to-end library for advanced tissue image analytics. Version 1.3.1. Zenodo, 2022 [all versions]
2021
[d1]
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John Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David B. A. Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza:
TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics. Version 1.0.0. Zenodo, 2021 [all versions]

Informal and Other Publications

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2026
[i40]
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  - journals/corr/abs-2601-11336
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Mark Eastwood, Thomas Alexander McKee, Zedong Hu, Sabine Tejpar, Fayyaz Minhas:
Beer-Lambert Autoencoder for Unsupervised Stain Representation Learning and Deconvolution in Multi-immunohistochemical Brightfield Histology Images. CoRR abs/2601.11336 (2026)
2025
[i39]
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George Wright, Slawomir Michniewski, Eleanor Jameson, Fayyaz ul Amir Afsar Minhas:
DepoRanker: A Web Tool to predict Klebsiella Depolymerases using Machine Learning. CoRR abs/2501.16405 (2025)
[i38]
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  - journals/corr/abs-2502-19123
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Behnaz Elhaminia, Abdullah Alsalemi, Esha Nasir, Mostafa Jahanifar, Ruqayya Awan, Lawrence Young, Nasir M. Rajpoot, Fayyaz Minhas, Shan E Ahmed Raza:
From Traditional to Deep Learning Approaches in Whole Slide Image Registration: A Methodological Review. CoRR abs/2502.19123 (2025)
[i37]
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  - journals/corr/abs-2512-22262
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Piotr Keller, Mark Eastwood, Zedong Hu, Aimée Selten, Ruqayya Awan, Gertjan Rasschaert, Sara Verbandt, Vlad Popovici, Hubert Piessevaux, Hayley T. Morris, Petros Tsantoulis, Thomas Alexander McKee, André D'Hoore, Cédric Schraepen, Xavier Sagaert, Gert De Hertogh, Sabine Tejpar, Fayyaz Minhas:
INSIGHT: Spatially resolved survival modelling from routine histology crosslinked with molecular profiling reveals prognostic epithelial-immune axes in stage II/III colorectal cancer. CoRR abs/2512.22262 (2025)
2024
[i36]
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  - journals/corr/abs-2401-02879
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Mustafa Emre Sahin, Benjamin C. B. Symons, Pushpak Pati, Fayyaz Minhas, Declan Millar, Maria Gabrani, Jan Lukas Robertus, Stefano Mensa:
Efficient Parameter Optimisation for Quantum Kernel Alignment: A Sub-sampling Approach in Variational Training. CoRR abs/2401.02879 (2024)
[i35]
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  - journals/corr/abs-2402-09990
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Mark Eastwood, John Pocock, Mostafa Jahanifar, Adam Shephard, Skiros Habib, Ethar Alzaid, Abdullah Alsalemi, Jan Lukas Robertus, Nasir M. Rajpoot, Shan E Ahmed Raza, Fayyaz Minhas:
TIAViz: A Browser-based Visualization Tool for Computational Pathology Models. CoRR abs/2402.09990 (2024)
[i34]
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  - journals/corr/abs-2405-02040
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Ethar Alzaid, Gabriele Pergola, Harriet Evans, David R. J. Snead, Fayyaz Minhas:
Large Multimodal Model based Standardisation of Pathology Reports with Confidence and their Prognostic Significance. CoRR abs/2405.02040 (2024)
[i33]
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  - journals/corr/abs-2408-05195
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Piotr Keller, Muhammad Dawood, Brinder Singh Chohan, Fayyaz ul Amir Afsar Minhas:
HistoKernel: Whole Slide Image Level Maximum Mean Discrepancy Kernels for Pan-Cancer Predictive Modelling. CoRR abs/2408.05195 (2024)
2023
[i32]
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  - journals/corr/abs-2301-03418
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Quoc Dang Vu, Robert Jewsbury, Simon Graham, Mostafa Jahanifar, Shan E Ahmed Raza, Fayyaz Minhas, Abhir Bhalerao, Nasir M. Rajpoot:
Nuclear Segmentation and Classification: On Color & Compression Generalization. CoRR abs/2301.03418 (2023)
[i31]
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  - journals/corr/abs-2301-09624
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Piotr Keller, Muhammad Dawood, Fayyaz ul Amir Afsar Minhas:
Maximum Mean Discrepancy Kernels for Predictive and Prognostic Modeling of Whole Slide Images. CoRR abs/2301.09624 (2023)
[i30]
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  - journals/corr/abs-2302-12653
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Mark Eastwood, Heba Sailem, Silviu Tudor Marc, Xiaohong W. Gao, Judith Offman, Emmanouil Karteris, Angeles Montero Fernandez, Danny Jonigk, William Cookson, Miriam Moffatt, Sanjay Popat, Fayyaz ul Amir Afsar Minhas, Jan Lukas Robertus:
MesoGraph: Automatic Profiling of Malignant Mesothelioma Subtypes from Histological Images. CoRR abs/2302.12653 (2023)
[i29]
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  - journals/corr/abs-2303-06274
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Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, Josef Lorenz Rumberger, Elias Baumann, Peter Hirsch, Lihao Liu, Chenyang Hong, Angelica I. Avilés-Rivero, Ayushi Jain, Heeyoung Ahn, Yiyu Hong, Hussam Azzuni, Min Xu, Mohammad Yaqub, Marie-Claire Blache, Benoît Piégu, Bertrand Vernay, Tim Scherr, Moritz Böhland, Katharina Löffler, Jiachen Li, Weiqin Ying, Chixin Wang, Dagmar Kainmueller, Carola-Bibiane Schönlieb, Shuolin Liu, Dhairya Talsania, Yughender Meda, Prakash Mishra, Muhammad Ridzuan, Oliver Neumann, Marcel P. Schilling, Markus Reischl, Ralf Mikut, Banban Huang, Hsiang-Chin Chien, Ching-Ping Wang, Chia-Yen Lee, Hong-Kun Lin, Zaiyi Liu, Xipeng Pan, Chu Han, Jijun Cheng, Muhammad Dawood, Srijay Deshpande, Raja Muhammad Saad Bashir, Adam Shephard, Pedro Costa, João D. Nunes, Aurélio Campilho, Jaime S. Cardoso, Hrishikesh P. S, Densen Puthussery, Devika R. G, Jiji C V, Ye Zhang, Zijie Fang, Zhifan Lin, Yongbing Zhang, Chunhui Lin, Liukun Zhang, Lijian Mao, Min Wu, Thi Tuong Vi Vo, Soo-Hyung Kim, Taebum Lee, Satoshi Kondo, Satoshi Kasai, Pranay Dumbhare, Vedant Phuse, Yash Dubey, Ankush Jamthikar, Trinh Thi Le Vuong, Jin Tae Kwak, Dorsa Ziaei, Hyun Jung, Tianyi Miao, David R. J. Snead, Shan-E-Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot:
CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting. CoRR abs/2303.06274 (2023)
[i28]
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Srijay Deshpande, Fayyaz Minhas, Nasir M. Rajpoot:
Synthesis of Annotated Colorectal Cancer Tissue Images from Gland Layout. CoRR abs/2305.05006 (2023)
[i27]
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Adam J. Shephard, Raja Muhammad Saad Bashir, Hanya Mahmood, Mostafa Jahanifar, Fayyaz Minhas, Shan E Ahmed Raza, Kris D. McCombe, Stephanie G. Craig, Jacqueline A. James, Jill Brooks, Paul Nankivell, Hisham Mehanna, Syed Ali Khurram, Nasir M. Rajpoot:
A Fully Automated and Explainable Algorithm for the Prediction of Malignant Transformation in Oral Epithelial Dysplasia. CoRR abs/2307.03757 (2023)
[i26]
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  - journals/corr/abs-2310-19656
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Mostafa Jahanifar, Manahil Raza, Kesi Xu, Trinh Thi Le Vuong, Robert Jewsbury, Adam Shephard, Neda Zamanitajeddin, Jin Tae Kwak, Shan E Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot:
Domain Generalization in Computational Pathology: Survey and Guidelines. CoRR abs/2310.19656 (2023)
2022
[i25]
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  - journals/corr/abs-2201-12311
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Alex Foote, Amina Asif, Nasir M. Rajpoot, Fayyaz A. Minhas:
REET: Robustness Evaluation and Enhancement Toolbox for Computational Pathology. CoRR abs/2201.12311 (2022)
[i24]
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  - journals/corr/abs-2202-00001
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Adiba Yaseen, Imran Amin, Naeem Akhter, Asa Ben-Hur, Fayyaz A. Minhas:
Insights into performance evaluation of com-pound-protein interaction prediction methods. CoRR abs/2202.00001 (2022)
[i23]
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  - journals/corr/abs-2203-00077
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Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Fayyaz A. Minhas, David R. J. Snead, Nasir M. Rajpoot:
One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification. CoRR abs/2203.00077 (2022)
[i22]
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  - journals/corr/abs-2212-13780
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Srijay Deshpande, Muhammad Dawood, Fayyaz A. Minhas, Nasir M. Rajpoot:
SynCLay: Interactive Synthesis of Histology Images from Bespoke Cellular Layouts. CoRR abs/2212.13780 (2022)
2021
[i21]
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  - journals/corr/abs-2106-08153
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Alex Foote, Amina Asif, Ayesha Azam, Tim Marshall-Cox, Nasir M. Rajpoot, Fayyaz A. Minhas:
Now You See It, Now You Dont: Adversarial Vulnerabilities in Computational Pathology. CoRR abs/2106.08153 (2021)
[i20]
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  - journals/corr/abs-2106-13689
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Noor ul Wahab, Islam M. Miligy, Katherine Dodd, Harvir Sahota, Michael Toss, Wenqi Lu, Mostafa Jahanifar, Mohsin Bilal, Simon Graham, Young Park, Giorgos Hadjigeorghiou, Abhir Bhalerao, Ayat Lashen, Asmaa Ibrahim, Ayaka Katayama, Henry O. Ebili, Matthew Parkin, Tom Sorell, Shan E Ahmed Raza, Emily Hero, Hesham Eldaly, Yee-Wah Tsang, Kishore Gopalakrishnan, David R. J. Snead, Emad Rakha, Nasir M. Rajpoot, Fayyaz A. Minhas:
Semantic annotation for computational pathology: Multidisciplinary experience and best practice recommendations. CoRR abs/2106.13689 (2021)
[i19]
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  - journals/corr/abs-2108-10365
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Fayyaz A. Minhas, Michael S. Toss, Noor ul Wahab, Emad Rakha, Nasir M. Rajpoot:
L1-regularized neural ranking for risk stratification and its application to prediction of time to distant metastasis in luminal node negative chemotherapy naïve breast cancer patients. CoRR abs/2108.10365 (2021)
[i18]
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  - journals/corr/abs-2108-10446
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Muhammad Dawood, Kim Branson, Nasir M. Rajpoot, Fayyaz ul Amir Afsar Minhas:
All You Need is Color: Image based Spatial Gene Expression Prediction using Neural Stain Learning. CoRR abs/2108.10446 (2021)
[i17]
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  - journals/corr/abs-2108-11195
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Simon Graham, Mostafa Jahanifar, Ayesha Azam, Mohammed Nimir, Yee-Wah Tsang, Katherine Dodd, Emily Hero, Harvir Sahota, Atisha Tank, Ksenija Benes, Noorul Wahab, Fayyaz A. Minhas, Shan-E-Ahmed Raza, Hesham Eldaly, Kishore Gopalakrishnan, David R. J. Snead, Nasir M. Rajpoot:
Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification. CoRR abs/2108.11195 (2021)
[i16]
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  - journals/corr/abs-2109-00853
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Mostafa Jahanifar, Adam J. Shephard, Neda Zamani Tajeddin, Raja Muhammad Saad Bashir, Mohsin Bilal, Syed Ali Khurram, Fayyaz A. Minhas, Nasir M. Rajpoot:
Stain-Robust Mitotic Figure Detection for the Mitosis Domain Generalization Challenge. CoRR abs/2109.00853 (2021)
[i15]
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  - journals/corr/abs-2110-06042
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Wenqi Lu, Michael Toss, Emad Rakha, Nasir M. Rajpoot, Fayyaz A. Minhas:
SlideGraph+: Whole Slide Image Level Graphs to Predict HER2Status in Breast Cancer. CoRR abs/2110.06042 (2021)
[i14]
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  - journals/corr/abs-2111-14485
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Simon Graham, Mostafa Jahanifar, Quoc Dang Vu, Giorgos Hadjigeorghiou, Thomas Leech, David R. J. Snead, Shan E Ahmed Raza, Fayyaz A. Minhas, Nasir M. Rajpoot:
CoNIC: Colon Nuclei Identification and Counting Challenge 2022. CoRR abs/2111.14485 (2021)
[i13]
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  - journals/corr/abs-2112-09496
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Amina Asif, Kashif Rajpoot, David R. J. Snead, Fayyaz A. Minhas, Nasir M. Rajpoot:
Towards Launching AI Algorithms for Cellular Pathology into Clinical & Pharmaceutical Orbits. CoRR abs/2112.09496 (2021)
2020
[i12]
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  - journals/corr/abs-2008-04526
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Srijay Deshpande, Fayyaz A. Minhas, Simon Graham, Nasir M. Rajpoot:
SAFRON: Stitching Across the Frontier for Generating Colorectal Cancer Histology Images. CoRR abs/2008.04526 (2020)
[i11]
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  - journals/corr/abs-2011-11381
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Kelvin K. F. Li, Stephen A. Jarvis, Fayyaz A. Minhas:
Elementary Effects Analysis of factors controlling COVID-19 infections in computational simulation reveals the importance of Social Distancing and Mask Usage. CoRR abs/2011.11381 (2020)
2019
[i10]
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  - journals/corr/abs-1901-01686
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Fayyaz ul Amir Afsar Minhas, Amina Asif, Asa Ben-Hur:
Ten ways to fool the masses with machine learning. CoRR abs/1901.01686 (2019)
[i9]
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  - journals/corr/abs-1905-01947
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Amina Asif, Fayyaz ul Amir Afsar Minhas:
An embarrassingly simple approach to neural multiple instance classification. CoRR abs/1905.01947 (2019)
[i8]
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  - journals/corr/abs-1911-00896
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Amina Asif, Fayyaz ul Amir Afsar Minhas:
Generalized Learning with Rejection for Classification and Regression Problems. CoRR abs/1911.00896 (2019)
[i7]
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  - journals/corr/abs-1911-06106
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Sadaf Gull, Fayyaz ul Amir Afsar Minhas:
AMP0: Species-Specific Prediction of Anti-microbial Peptides using Zero and Few Shot Learning. CoRR abs/1911.06106 (2019)
[i6]
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  - journals/corr/abs-1912-12187
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Fayyaz ul Amir Afsar Minhas, Amina Asif:
Learning Neural Activations. CoRR abs/1912.12187 (2019)
2018
[i5]
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  - journals/corr/abs-1811-04463
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Kanza Hamid, Amina Asif, Wajid Arshad Abbasi, Durre Sabih, Fayyaz ul Amir Afsar Minhas:
Machine Learning with Abstention for Automated Liver Disease Diagnosis. CoRR abs/1811.04463 (2018)
[i4]
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  - journals/corr/abs-1811-06885
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Amina Asif, Muhammad Dawood, Fayyaz ul Amir Afsar Minhas:
A generalized meta-loss function for distillation and learning using privileged information for classification and regression. CoRR abs/1811.06885 (2018)
2017
[i3]
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  - journals/corr/abs-1711-04913
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Amina Asif, Wajid Arshad Abbasi, Farzeen Munir, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas:
pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications. CoRR abs/1711.04913 (2017)
[i2]
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  - journals/corr/abs-1711-07886
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Abdul Hannan Basit, Wajid Arshad Abbasi, Amina Asif, Fayyaz ul Amir Afsar Minhas:
Training large margin host-pathogen protein-protein interaction predictors. CoRR abs/1711.07886 (2017)
[i1]
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  - journals/corr/abs-1711-10540
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Wajid Arshad Abbasi, Fahad Ul Hassan, Adiba Yaseen, Fayyaz ul Amir Afsar Minhas:
ISLAND: In-Silico Prediction of Proteins Binding Affinity Using Sequence Descriptors. CoRR abs/1711.10540 (2017)

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