Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge

Human-in-the-loop assisted de novo molecular design

A de novo molecular design workflow can be used together with technologies such as reinforcement learning to navigate the chemical space. A bottleneck in the workflow that remains to be solved is how to integrate human feedback in the exploration of the chemical space to optimize molecules. A human drug designer still needs to design the goal, expressed as a scoring function for the molecules that captures the designer's implicit knowledge about the optimization task. Little support for this task exists and, consequently, a chemist usually resorts to iteratively building the objective function of multi-parameter optimization (MPO) in de novo design. We propose a principled approach to use human-in-the-loop machine learning to help the chemist to adapt the MPO scoring function to better match their goal. An advantage is that the method can learn the scoring function directly from the user's feedback while they browse the output of the molecule generator, instead of the current manual tuning of the scoring function with trial and error. The proposed method uses a probabilistic model that captures the user's idea and uncertainty about the scoring function, and it uses active learning to interact with the user. We present two case studies for this: In the first use-case, the parameters of an MPO are learned, and in the second use-case a non-parametric component of the scoring function to capture human domain knowledge is developed. The results show the effectiveness of the methods in two simulated example cases with an oracle, achieving significant improvement in less than 200 feedback queries, for the goals of a high QED score and identifying potent molecules for the DRD2 receptor, respectively. We further demonstrate the performance gains with a medicinal chemist interacting with the system.

A Survey of Domain Knowledge Elicitation in Applied Machine Learning

Eliciting knowledge from domain experts can play an important role throughout the machine learning process, from correctly specifying the task to evaluating model results. However, knowledge elicitation is also fraught with challenges. In this work, we consider why and how machine learning researchers elicit knowledge from experts in the model development process. We develop a taxonomy to characterize elicitation approaches according to the elicitation goal, elicitation target, elicitation process, and use of elicited knowledge. We analyze the elicitation trends observed in 28 papers with this taxonomy and identify opportunities for adding rigor to these elicitation approaches. We suggest future directions for research in elicitation for machine learning by highlighting avenues for further exploration and drawing on what we can learn from elicitation research in other fields.

Progress in Nanorobotics for Advancing Biomedicine

Nanorobotics, which has long been a fantasy in the realm of science fiction, is now a reality due to the considerable developments in diverse fields including chemistry, materials, physics, information and nanotechnology in the past decades. Not only different prototypes of nanorobots whose sizes are nanoscale are invented for various biomedical applications, but also robotic nanomanipulators which are able to handle nano-objects obtain substantial achievements for applications in biomedicine. The outstanding achievements in nanorobotics have significantly expanded the field of medical robotics and yielded novel insights into the underlying mechanisms guiding life activities, remarkably showing an emerging and promising way for advancing the diagnosis & treatment level in the coming era of personalized precision medicine. In this review, the recent advances in nanorobotics (nanorobots, nanorobotic manipulations) for biomedical applications are summarized from several facets (including molecular machines, nanomotors, DNA nanorobotics, and robotic nanomanipulators), and the future perspectives are also presented.

A decision-theoretic approach for model interpretability in Bayesian framework

A salient approach to interpretable machine learning is to restrict modeling to simple models. In the Bayesian framework, this can be pursued by restricting the model structure and prior to favor interpretable models. Fundamentally, however, interpretability is about users’ preferences, not the data generation mechanism; it is more natural to formulate interpretability as a utility function. In this work, we propose an interpretability utility, which explicates the trade-off between explanation fidelity and interpretability in the Bayesian framework. The method consists of two steps. First, a reference model, possibly a black-box Bayesian predictive model which does not compromise accuracy, is fitted to the training data. Second, a proxy model from an interpretable model family that best mimics the predictive behaviour of the reference model is found by optimizing the interpretability utility function. The approach is model agnostic—neither the interpretable model nor the reference model are restricted to a certain class of models—and the optimization problem can be solved using standard tools. Through experiments on real-word data sets, using decision trees as interpretable models and Bayesian additive regression models as reference models, we show that for the same level of interpretability, our approach generates more accurate models than the alternative of restricting the prior. We also propose a systematic way to measure stability of interpretabile models constructed by different interpretability approaches and show that our proposed approach generates more stable models.