Sparse, interpretable and transparent predictive model identification for healthcare data analysis

Data-driven modelling approaches play an indispensable role in analyzing and understanding complex processes. This study proposes a type of sparse, interpretable and transparent (SIT) machine learning model, which can be used to understand the dependent relationship of a response variable on a set of potential explanatory variables. An ideal candidate for such a SIT representation is the well-known NARMAX (nonlinear autoregressive moving average with exogenous inputs) model, which can be established from measured input and output data of the system of interest, and the final refined model is usually simple, parsimonious and easy to interpret. The performance of the proposed SIT models is evaluated through two real healthcare datasets

Learning Difference Equations with Structured Grammatical Evolution for Postprandial Glycaemia Prediction

People with diabetes must carefully monitor their blood glucose levels, especially after eating. Blood glucose regulation requires a proper combination of food intake and insulin boluses. Glucose prediction is vital to avoid dangerous post-meal complications in treating individuals with diabetes. Although traditional methods, such as artificial neural networks, have shown high accuracy rates, sometimes they are not suitable for developing personalised treatments by physicians due to their lack of interpretability. In this study, we propose a novel glucose prediction method emphasising interpretability: Interpretable Sparse Identification by Grammatical Evolution. Combined with a previous clustering stage, our approach provides finite difference equations to predict postprandial glucose levels up to two hours after meals. We divide the dataset into four-hour segments and perform clustering based on blood glucose values for the twohour window before the meal. Prediction models are trained for each cluster for the two-hour windows after meals, allowing predictions in 15-minute steps, yielding up to eight predictions at different time horizons. Prediction safety was evaluated based on Parkes Error Grid regions. Our technique produces safe predictions through explainable expressions, avoiding zones D (0.2% average) and E (0%) and reducing predictions on zone C (6.2%). In addition, our proposal has slightly better accuracy than other techniques, including sparse identification of non-linear dynamics and artificial neural networks. The results demonstrate that our proposal provides interpretable solutions without sacrificing prediction accuracy, offering a promising approach to glucose prediction in diabetes management that balances accuracy, interpretability, and computational efficiency

Interpretable Machine Learning Model for Clinical Decision Making

Despite machine learning models being increasingly used in medical decision-making and meeting classification predictive accuracy standards, they remain untrusted black-boxes due to decision-makers\u27 lack of insight into their complex logic. Therefore, it is necessary to develop interpretable machine learning models that will engender trust in the knowledge they generate and contribute to clinical decision-makers intention to adopt them in the field. The goal of this dissertation was to systematically investigate the applicability of interpretable model-agnostic methods to explain predictions of black-box machine learning models for medical decision-making. As proof of concept, this study addressed the problem of predicting the risk of emergency readmissions within 30 days of being discharged for heart failure patients. Using a benchmark data set, supervised classification models of differing complexity were trained to perform the prediction task. More specifically, Logistic Regression (LR), Random Forests (RF), Decision Trees (DT), and Gradient Boosting Machines (GBM) models were constructed using the Healthcare Cost and Utilization Project (HCUP) Nationwide Readmissions Database (NRD). The precision, recall, area under the ROC curve for each model were used to measure predictive accuracy. Local Interpretable Model-Agnostic Explanations (LIME) was used to generate explanations from the underlying trained models. LIME explanations were empirically evaluated using explanation stability and local fit (R2). The results demonstrated that local explanations generated by LIME created better estimates for Decision Trees (DT) classifiers

Explainable artificial intelligence for omics data: a systematic mapping study

Researchers increasingly turn to explainable artificial intelligence (XAI) to analyze omics data and gain insights into the underlying biological processes. Yet, given the interdisciplinary nature of the field, many findings have only been shared in their respective research community. An overview of XAI for omics data is needed to highlight promising approaches and help detect common issues. Toward this end, we conducted a systematic mapping study. To identify relevant literature, we queried Scopus, PubMed, Web of Science, BioRxiv, MedRxiv and arXiv. Based on keywording, we developed a coding scheme with 10 facets regarding the studies’ AI methods, explainability methods and omics data. Our mapping study resulted in 405 included papers published between 2010 and 2023. The inspected papers analyze DNA-based (mostly genomic), transcriptomic, proteomic or metabolomic data by means of neural networks, tree-based methods, statistical methods and further AI methods. The preferred post-hoc explainability methods are feature relevance (n = 166) and visual explanation (n = 52), while papers using interpretable approaches often resort to the use of transparent models (n = 83) or architecture modifications (n = 72). With many research gaps still apparent for XAI for omics data, we deduced eight research directions and discuss their potential for the field. We also provide exemplary research questions for each direction. Many problems with the adoption of XAI for omics data in clinical practice are yet to be resolved. This systematic mapping study outlines extant research on the topic and provides research directions for researchers and practitioners

Explainable AI for clinical risk prediction: a survey of concepts, methods, and modalities

Recent advancements in AI applications to healthcare have shown incredible promise in surpassing human performance in diagnosis and disease prognosis. With the increasing complexity of AI models, however, concerns regarding their opacity, potential biases, and the need for interpretability. To ensure trust and reliability in AI systems, especially in clinical risk prediction models, explainability becomes crucial. Explainability is usually referred to as an AI system's ability to provide a robust interpretation of its decision-making logic or the decisions themselves to human stakeholders. In clinical risk prediction, other aspects of explainability like fairness, bias, trust, and transparency also represent important concepts beyond just interpretability. In this review, we address the relationship between these concepts as they are often used together or interchangeably. This review also discusses recent progress in developing explainable models for clinical risk prediction, highlighting the importance of quantitative and clinical evaluation and validation across multiple common modalities in clinical practice. It emphasizes the need for external validation and the combination of diverse interpretability methods to enhance trust and fairness. Adopting rigorous testing, such as using synthetic datasets with known generative factors, can further improve the reliability of explainability methods. Open access and code-sharing resources are essential for transparency and reproducibility, enabling the growth and trustworthiness of explainable research. While challenges exist, an end-to-end approach to explainability in clinical risk prediction, incorporating stakeholders from clinicians to developers, is essential for success

Counterfactuals and Causability in Explainable Artificial Intelligence: Theory, Algorithms, and Applications

There has been a growing interest in model-agnostic methods that can make deep learning models more transparent and explainable to a user. Some researchers recently argued that for a machine to achieve a certain degree of human-level explainability, this machine needs to provide human causally understandable explanations, also known as causability. A specific class of algorithms that have the potential to provide causability are counterfactuals. This paper presents an in-depth systematic review of the diverse existing body of literature on counterfactuals and causability for explainable artificial intelligence. We performed an LDA topic modelling analysis under a PRISMA framework to find the most relevant literature articles. This analysis resulted in a novel taxonomy that considers the grounding theories of the surveyed algorithms, together with their underlying properties and applications in real-world data. This research suggests that current model-agnostic counterfactual algorithms for explainable AI are not grounded on a causal theoretical formalism and, consequently, cannot promote causability to a human decision-maker. Our findings suggest that the explanations derived from major algorithms in the literature provide spurious correlations rather than cause/effects relationships, leading to sub-optimal, erroneous or even biased explanations. This paper also advances the literature with new directions and challenges on promoting causability in model-agnostic approaches for explainable artificial intelligence