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Researcher profile

Fayyaz Minhas

Fayyaz Minhas contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningComputer Visioneess.IVphysics.ao-phQuantitative Methods

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Published work

5 published item(s)

preprint2026arXiv

Beer-Lambert Autoencoder for Unsupervised Stain Representation Learning and Deconvolution in Multi-immunohistochemical Brightfield Histology Images

Separating the contributions of individual chromogenic stains in RGB histology whole slide images (WSIs) is essential for stain normalization, quantitative assessment of marker expression, and cell-level readouts in immunohistochemistry (IHC). Classical Beer-Lambert (BL) color deconvolution is well-established for two- or three-stain settings, but becomes under-determined and unstable for multiplex IHC (mIHC) with K>3 chromogens. We present a simple, data-driven encoder-decoder architecture that learns cohort-specific stain characteristics for mIHC RGB WSIs and yields crisp, well-separated per-stain concentration maps. The encoder is a compact U-Net that predicts K nonnegative concentration channels; the decoder is a differentiable BL forward model with a learnable stain matrix initialized from typical chromogen hues. Training is unsupervised with a perceptual reconstruction objective augmented by loss terms that discourage unnecessary stain mixing. On a colorectal mIHC panel comprising 5 stains (H, CDX2, MUC2, MUC5, CD8) we show excellent RGB reconstruction, and significantly reduced inter-channel bleed-through compared with matrix-based deconvolution. Code and model are available at https://github.com/measty/StainQuant.git.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Interpretable rainfall modelling reveals rapid reorganisation of Amazonian rainfall under vegetation loss

Understanding how vegetation loss alters rainfall remains a major challenge in climate and hydrological science, as deforestation modifies precipitation through heterogeneous, seasonal and nonlinear land-atmosphere feedbacks. Existing models struggle to capture these dynamics: convection is parameterised at coarse scales, tipping behaviour is poorly constrained, and rainfall-deforestation analyses are limited to multi-decadal timescales. Therefore, many approaches resolve correlations rather than causal effects, limiting our ability to anticipate hydrological disruption. Using a neural-network model for hourly rainfall prediction, combined with pathway diagnostics and sensitivity analyses, we examine how vegetation perturbations reorganise rainfall across space, intensity regimes, and timescales under deforestation. We assess whether the model captures physically consistent dependencies linking vegetation, atmospheric state, and precipitation, and whether sustained canopy loss induces threshold behaviour. The model accurately predicts rainfall occurrence and intensity (Spearman = 0.84, F1 = 0.93, ROC-AUC = 0.98) and learns temporally ordered dependencies aligned with ecohydrological theory. Sensitivity analyses reveal rapid, asymmetric responses to vegetation loss: heavy rainfall (20-50 mm/h) declines by up to 7% under sustained deforestation, while light rainfall (0.1-1 mm/h) increases by 4%. Rainfall entropy rises by 1.3%, and dry-season intensity increases by 0.3-0.5% per 0.5% forest-cover loss, with strongest impacts in the north-western Amazon and Andean foothills. Threshold analysis reveals a sharp decline in precipitating area fraction after 2-3 months of sustained vegetation change in sensitive regions. These results demonstrate that data-driven approaches uncover process-relevant land-atmosphere coupling and highlight growing hydrological vulnerability in the Amazon.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Nuclear Segmentation and Classification: On Color & Compression Generalization

Since the introduction of digital and computational pathology as a field, one of the major problems in the clinical application of algorithms has been the struggle to generalize well to examples outside the distribution of the training data. Existing work to address this in both pathology and natural images has focused almost exclusively on classification tasks. We explore and evaluate the robustness of the 7 best performing nuclear segmentation and classification models from the largest computational pathology challenge for this problem to date, the CoNIC challenge. We demonstrate that existing state-of-the-art (SoTA) models are robust towards compression artifacts but suffer substantial performance reduction when subjected to shifts in the color domain. We find that using stain normalization to address the domain shift problem can be detrimental to the model performance. On the other hand, neural style transfer is more consistent in improving test performance when presented with large color variations in the wild.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Insights into performance evaluation of com-pound-protein interaction prediction methods

Motivation: Machine learning based prediction of compound-protein interactions (CPIs) is important for drug design, screening and repurposing studies and can improve the efficiency and cost-effectiveness of wet lab assays. Despite the publication of many research papers reporting CPI predictors in the recent years, we have observed a number of fundamental issues in experiment design that lead to over optimistic estimates of model performance. Results: In this paper, we analyze the impact of several important factors affecting generalization perfor-mance of CPI predictors that are overlooked in existing work: 1. Similarity between training and test examples in cross-validation 2. The strategy for generating negative examples, in the absence of experimentally verified negative examples. 3. Choice of evaluation protocols and performance metrics and their alignment with real-world use of CPI predictors in screening large compound libraries. Using both an existing state-of-the-art method (CPI-NN) and a proposed kernel based approach, we have found that assessment of predictive performance of CPI predictors requires careful con-trol over similarity between training and test examples. We also show that random pairing for gen-erating synthetic negative examples for training and performance evaluation results in models with better generalization performance in comparison to more sophisticated strategies used in existing studies. Furthermore, we have found that our kernel based approach, despite its simple design, exceeds the prediction performance of CPI-NN. We have used the proposed model for compound screening of several proteins including SARS-CoV-2 Spike and Human ACE2 proteins and found strong evidence in support of its top hits. Availability: Code and raw experimental results available at https://github.com/adibayaseen/HKRCPI Contact: Fayyaz.minhas@warwick.ac.uk

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

REET: Robustness Evaluation and Enhancement Toolbox for Computational Pathology

Motivation: Digitization of pathology laboratories through digital slide scanners and advances in deep learning approaches for objective histological assessment have resulted in rapid progress in the field of computational pathology (CPath) with wide-ranging applications in medical and pharmaceutical research as well as clinical workflows. However, the estimation of robustness of CPath models to variations in input images is an open problem with a significant impact on the down-stream practical applicability, deployment and acceptability of these approaches. Furthermore, development of domain-specific strategies for enhancement of robustness of such models is of prime importance as well. Implementation and Availability: In this work, we propose the first domain-specific Robustness Evaluation and Enhancement Toolbox (REET) for computational pathology applications. It provides a suite of algorithmic strategies for enabling robustness assessment of predictive models with respect to specialized image transformations such as staining, compression, focusing, blurring, changes in spatial resolution, brightness variations, geometric changes as well as pixel-level adversarial perturbations. Furthermore, REET also enables efficient and robust training of deep learning pipelines in computational pathology. REET is implemented in Python and is available at the following URL: https://github.com/alexjfoote/reetoolbox. Contact: Fayyaz.minhas@warwick.ac.uk

0 citations0 reviewsNo code linkedOpen access