Muhammad Dawood

Piotr Keller, Muhammad Dawood, Brinder Singh Chohan et al.

Machine learning in computational pathology (CPath) often aggregates patch-level predictions from multi-gigapixel Whole Slide Images (WSIs) to generate WSI-level prediction scores for crucial tasks such as survival prediction and drug effect prediction. However, current methods do not explicitly characterize distributional differences between patch sets within WSIs. We introduce HistoKernel, a novel Maximum Mean Discrepancy (MMD) kernel that measures distributional similarity between WSIs for enhanced prediction performance on downstream prediction tasks. Our comprehensive analysis demonstrates HistoKernel's effectiveness across various machine learning tasks, including retrieval (n = 9,362), drug sensitivity regression (n = 551), point mutation classification (n = 3,419), and survival analysis (n = 2,291), outperforming existing deep learning methods. Additionally, HistoKernel seamlessly integrates multi-modal data and offers a novel perturbation-based method for patch-level explainability. This work pioneers the use of kernel-based methods for WSI-level predictive modeling, opening new avenues for research. Code is available at https://github.com/pkeller00/HistoKernel.

Amina Asif, Muhammad Dawood, Fayyaz ul Amir Afsar Minhas

Learning using privileged information (LUPI) is a powerful heterogenous feature space machine learning framework that allows a machine learning model to learn from highly informative or privileged features which are available during training only to generate test predictions using input space features which are available both during training and testing. LUPI can significantly improve prediction performance in a variety of machine learning problems. However, existing large margin and neural network implementations of learning using privileged information are mostly designed for classification tasks. In this work, we have proposed a simple yet effective formulation that allows us to perform regression using privileged information through a custom loss function. Apart from regression, our formulation allows general application of LUPI to classification and other related problems as well. We have verified the correctness, applicability and effectiveness of our method on regression and classification problems over different synthetic and real-world problems. To test the usefulness of the proposed model in real-world problems, we have evaluated our method on the problem of protein binding affinity prediction. The proposed LUPI regression-based model has shown to outperform the current state-of-the-art predictor.