Saurabh Johri

Albert Buchard, Baptiste Bouvier, Giulia Prando et al.

Medical Triage is of paramount importance to healthcare systems, allowing for the correct orientation of patients and allocation of the necessary resources to treat them adequately. While reliable decision-tree methods exist to triage patients based on their presentation, those trees implicitly require human inference and are not immediately applicable in a fully automated setting. On the other hand, learning triage policies directly from experts may correct for some of the limitations of hard-coded decision-trees. In this work, we present a Deep Reinforcement Learning approach (a variant of DeepQ-Learning) to triage patients using curated clinical vignettes. The dataset, consisting of 1374 clinical vignettes, was created by medical doctors to represent real-life cases. Each vignette is associated with an average of 3.8 expert triage decisions given by medical doctors relying solely on medical history. We show that this approach is on a par with human performance, yielding safe triage decisions in 94% of cases, and matching expert decisions in 85% of cases. The trained agent learns when to stop asking questions, acquires optimized decision policies requiring less evidence than supervised approaches, and adapts to the novelty of a situation by asking for more information. Overall, we demonstrate that a Deep Reinforcement Learning approach can learn effective medical triage policies directly from expert decisions, without requiring expert knowledge engineering. This approach is scalable and can be deployed in healthcare settings or geographical regions with distinct triage specifications, or where trained experts are scarce, to improve decision making in the early stage of care.

Divya Gautam, Maria Lomeli, Kostis Gourgoulias et al.

We consider the effect of structure-agnostic and structure-dependent masking schemes when training a universal marginaliser (arXiv:1711.00695) in order to learn conditional distributions of the form $P(x_i |\mathbf x_{\mathbf b})$, where $x_i$ is a given random variable and $\mathbf x_{\mathbf b}$ is some arbitrary subset of all random variables of the generative model of interest. In other words, we mimic the self-supervised training of a denoising autoencoder, where a dataset of unlabelled data is used as partially observed input and the neural approximator is optimised to minimise reconstruction loss. We focus on studying the underlying process of the partially observed data---how good is the neural approximator at learning all conditional distributions when the observation process at prediction time differs from the masking process during training? We compare networks trained with different masking schemes in terms of their predictive performance and generalisation properties.

Ciarán M. Lee, Christopher Hart, Jonathan G. Richens et al.

The discovery of causal relationships is a fundamental problem in science and medicine. In recent years, many elegant approaches to discovering causal relationships between two variables from observational data have been proposed. However, most of these deal only with purely directed causal relationships and cannot detect latent common causes. Here, we devise a general heuristic which takes a causal discovery algorithm that can only distinguish purely directed causal relations and modifies it to also detect latent common causes. We apply our method to two directed causal discovery algorithms, the Information Geometric Causal Inference of (Daniusis et al., 2010) and the Kernel Conditional Deviance for Causal Inference of (Mitrovic, Sejdinovic, & Teh, 2018), and extensively test on synthetic data -- detecting latent common causes in additive, multiplicative and complex noise regimes -- and on real data, where we are able to detect known common causes. In addition to detecting latent common causes, our experiments demonstrate that both the modified algorithms preserve the performance of the original in distinguishing directed causal relations.

Yura Perov, Logan Graham, Kostis Gourgoulias et al.

We elaborate on using importance sampling for causal reasoning, in particular for counterfactual inference. We show how this can be implemented natively in probabilistic programming. By considering the structure of the counterfactual query, one can significantly optimise the inference process. We also consider design choices to enable further optimisations. We introduce MultiVerse, a probabilistic programming prototype engine for approximate causal reasoning. We provide experimental results and compare with Pyro, an existing probabilistic programming framework with some of causal reasoning tools.

Robert Walecki, Kostis Gourgoulias, Adam Baker et al.

Probabilistic programming languages (PPLs) are powerful modelling tools which allow to formalise our knowledge about the world and reason about its inherent uncertainty. Inference methods used in PPL can be computationally costly due to significant time burden and/or storage requirements; or they can lack theoretical guarantees of convergence and accuracy when applied to large scale graphical models. To this end, we present the Universal Marginaliser (UM), a novel method for amortised inference, in PPL. We show how combining samples drawn from the original probabilistic program prior with an appropriate augmentation method allows us to train one neural network to approximate any of the corresponding conditional marginal distributions, with any separation into latent and observed variables, and thus amortise the cost of inference. Finally, we benchmark the method on multiple probabilistic programs, in Pyro, with different model structure.

Jonathan G. Richens, Ciaran M. Lee, Saurabh Johri

Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient's symptoms by determining the diseases \emph{causing} them. However, existing diagnostic algorithms are purely associative, identifying diseases that are strongly correlated with a patients symptoms and medical history. We show that this inability to disentangle correlation from causation can result in sub-optimal or dangerous diagnoses. To overcome this, we reformulate diagnosis as a counterfactual inference task and derive new counterfactual diagnostic algorithms. We show that this approach is closer to the diagnostic reasoning of clinicians and significantly improves the accuracy and safety of the resulting diagnoses. We compare our counterfactual algorithm to the standard Bayesian diagnostic algorithm and a cohort of 44 doctors using a test set of clinical vignettes. While the Bayesian algorithm achieves an accuracy comparable to the average doctor, placing in the top 48% of doctors in our cohort, our counterfactual algorithm places in the top 25% of doctors, achieving expert clinical accuracy. This improvement is achieved simply by changing how we query our model, without requiring any additional model improvements. Our results show that counterfactual reasoning is a vital missing ingredient for applying machine learning to medical diagnosis.

Robert Walecki, Albert Buchard, Kostis Gourgoulias et al.

Probabilistic graphical models are powerful tools which allow us to formalise our knowledge about the world and reason about its inherent uncertainty. There exist a considerable number of methods for performing inference in probabilistic graphical models; however, they can be computationally costly due to significant time burden and/or storage requirements; or they lack theoretical guarantees of convergence and accuracy when applied to large scale graphical models. To this end, we propose the Universal Marginaliser Importance Sampler (UM-IS) -- a hybrid inference scheme that combines the flexibility of a deep neural network trained on samples from the model and inherits the asymptotic guarantees of importance sampling. We show how combining samples drawn from the graphical model with an appropriate masking function allows us to train a single neural network to approximate any of the corresponding conditional marginal distributions, and thus amortise the cost of inference. We also show that the graph embeddings can be applied for tasks such as: clustering, classification and interpretation of relationships between the nodes. Finally, we benchmark the method on a large graph (>1000 nodes), showing that UM-IS outperforms sampling-based methods by a large margin while being computationally efficient.

Salman Razzaki, Adam Baker, Yura Perov et al.

Online symptom checkers have significant potential to improve patient care, however their reliability and accuracy remain variable. We hypothesised that an artificial intelligence (AI) powered triage and diagnostic system would compare favourably with human doctors with respect to triage and diagnostic accuracy. We performed a prospective validation study of the accuracy and safety of an AI powered triage and diagnostic system. Identical cases were evaluated by both an AI system and human doctors. Differential diagnoses and triage outcomes were evaluated by an independent judge, who was blinded from knowing the source (AI system or human doctor) of the outcomes. Independently of these cases, vignettes from publicly available resources were also assessed to provide a benchmark to previous studies and the diagnostic component of the MRCGP exam. Overall we found that the Babylon AI powered Triage and Diagnostic System was able to identify the condition modelled by a clinical vignette with accuracy comparable to human doctors (in terms of precision and recall). In addition, we found that the triage advice recommended by the AI System was, on average, safer than that of human doctors, when compared to the ranges of acceptable triage provided by independent expert judges, with only a minimal reduction in appropriateness.

Laura Douglas, Iliyan Zarov, Konstantinos Gourgoulias et al.

We consider the problem of inference in a causal generative model where the set of available observations differs between data instances. We show how combining samples drawn from the graphical model with an appropriate masking function makes it possible to train a single neural network to approximate all the corresponding conditional marginal distributions and thus amortize the cost of inference. We further demonstrate that the efficiency of importance sampling may be improved by basing proposals on the output of the neural network. We also outline how the same network can be used to generate samples from an approximate joint posterior via a chain decomposition of the graph.