Thomas P Quinn

Thomas P Quinn, Sunil Gupta, Svetha Venkatesh et al.

Deep learning has become popular because of its potential to achieve high accuracy in prediction tasks. However, accuracy is not always the only goal of statistical modelling, especially for models developed as part of scientific research. Rather, many scientific models are developed to facilitate scientific discovery, by which we mean to abstract a human-understandable representation of the natural world. Unfortunately, the opacity of deep neural networks limit their role in scientific discovery, creating a new demand for models that are transparently interpretable. This article is a field guide to transparent model design. It provides a taxonomy of transparent model design concepts, a practical workflow for putting design concepts into practice, and a general template for reporting design choices. We hope this field guide will help researchers more effectively design transparently interpretable models, and thus enable them to use deep learning for scientific discovery.

Thomas P Quinn, Simon Coghlan

Medical students will almost inevitably encounter powerful medical AI systems early in their careers. Yet, contemporary medical education does not adequately equip students with the basic clinical proficiency in medical AI needed to use these tools safely and effectively. Education reform is urgently needed, but not easily implemented, largely due to an already jam-packed medical curricula. In this article, we propose an education reform framework as an effective and efficient solution, which we call the Embedded AI Ethics Education Framework. Unlike other calls for education reform to accommodate AI teaching that are more radical in scope, our framework is modest and incremental. It leverages existing bioethics or medical ethics curricula to develop and deliver content on the ethical issues associated with medical AI, especially the harms of technology misuse, disuse, and abuse that affect the risk-benefit analyses at the heart of healthcare. In doing so, the framework provides a simple tool for going beyond the "What?" and the "Why?" of medical AI ethics education, to answer the "How?", giving universities, course directors, and/or professors a broad road-map for equipping their students with the necessary clinical proficiency in medical AI.

Tri Minh Nguyen, Thomas P Quinn, Thin Nguyen et al.

Motivation: Many high-performance DTA models have been proposed, but they are mostly black-box and thus lack human interpretability. Explainable AI (XAI) can make DTA models more trustworthy, and can also enable scientists to distill biological knowledge from the models. Counterfactual explanation is one popular approach to explaining the behaviour of a deep neural network, which works by systematically answering the question "How would the model output change if the inputs were changed in this way?". Most counterfactual explanation methods only operate on single input data. It remains an open problem how to extend counterfactual-based XAI methods to DTA models, which have two inputs, one for drug and one for target, that also happen to be discrete in nature. Methods: We propose a multi-agent reinforcement learning framework, Multi-Agent Counterfactual Drug target binding Affinity (MACDA), to generate counterfactual explanations for the drug-protein complex. Our proposed framework provides human-interpretable counterfactual instances while optimizing both the input drug and target for counterfactual generation at the same time. Results: We benchmark the proposed MACDA framework using the Davis dataset and find that our framework produces more parsimonious explanations with no loss in explanation validity, as measured by encoding similarity and QED. We then present a case study involving ABL1 and Nilotinib to demonstrate how MACDA can explain the behaviour of a DTA model in the underlying substructure interaction between inputs in its prediction, revealing mechanisms that align with prior domain knowledge.