Graph homomorphism counts, first explored by Lov\'asz in 1967, have recently garnered interest as a powerful tool in graph-based machine learning. Grohe (PODS 2020) proposed the theoretical foundations for using homomorphism counts in machine learning on graph level as well as node level tasks. By their very nature, these capture local structural information, which enables the creation of robust structural embeddings. While a first approach for graph level tasks has been made by Nguyen and Maehara (ICML 2020), we experimentally show the effectiveness of homomorphism count based node embeddings. Enriched with node labels, node weights, and edge weights, these offer an interpretable representation of graph data, allowing for enhanced explainability of machine learning models. We propose a theoretical framework for isomorphism-invariant homomorphism count based embeddings which lend themselves to a wide variety of downstream tasks. Our approach capitalises on the efficient computability of graph homomorphism counts for bounded treewidth graph classes, rendering it a practical solution for real-world applications. We demonstrate their expressivity through experiments on benchmark datasets. Although our results do not match the accuracy of state-of-the-art neural architectures, they are comparable to other advanced graph learning models. Remarkably, our approach demarcates itself by ensuring explainability for each individual feature. By integrating interpretable machine learning algorithms like SVMs or Random Forests, we establish a seamless, end-to-end explainable pipeline. Our study contributes to the advancement of graph-based techniques that offer both performance and interpretability.
The objective of this work is to develop an Electronic Medical Record (EMR) data processing tool that confers clinical context to Machine Learning (ML) algorithms for error handling, bias mitigation and interpretability. We present Trust-MAPS, an algorithm that translates clinical domain knowledge into high-dimensional, mixed-integer programming models that capture physiological and biological constraints on clinical measurements. EMR data is projected onto this constrained space, effectively bringing outliers to fall within a physiologically feasible range. We then compute the distance of each data point from the constrained space modeling healthy physiology to quantify deviation from the norm. These distances, termed "trust-scores," are integrated into the feature space for downstream ML applications. We demonstrate the utility of Trust-MAPS by training a binary classifier for early sepsis prediction on data from the 2019 PhysioNet Computing in Cardiology Challenge, using the XGBoost algorithm and applying SMOTE for overcoming class-imbalance. The Trust-MAPS framework shows desirable behavior in handling potential errors and boosting predictive performance. We achieve an AUROC of 0.91 (0.89, 0.92 : 95% CI) for predicting sepsis 6 hours before onset - a marked 15% improvement over a baseline model trained without Trust-MAPS. Trust-scores emerge as clinically meaningful features that not only boost predictive performance for clinical decision support tasks, but also lend interpretability to ML models. This work is the first to translate clinical domain knowledge into mathematical constraints, model cross-vital dependencies, and identify aberrations in high-dimensional medical data. Our method allows for error handling in EMR, and confers interpretability and superior predictive power to models trained for clinical decision support.
Machine learning methods have shown large potential for the automatic early diagnosis of Alzheimer's Disease (AD). However, some machine learning methods based on imaging data have poor interpretability because it is usually unclear how they make their decisions. Explainable Boosting Machines (EBMs) are interpretable machine learning models based on the statistical framework of generalized additive modeling, but have so far only been used for tabular data. Therefore, we propose a framework that combines the strength of EBM with high-dimensional imaging data using deep learning-based feature extraction. The proposed framework is interpretable because it provides the importance of each feature. We validated the proposed framework on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, achieving accuracy of 0.883 and area-under-the-curve (AUC) of 0.970 on AD and control classification. Furthermore, we validated the proposed framework on an external testing set, achieving accuracy of 0.778 and AUC of 0.887 on AD and subjective cognitive decline (SCD) classification. The proposed framework significantly outperformed an EBM model using volume biomarkers instead of deep learning-based features, as well as an end-to-end convolutional neural network (CNN) with optimized architecture.
New technologies have led to vast troves of large and complex datasets across many scientific domains and industries. People routinely use machine learning techniques to not only process, visualize, and make predictions from this big data, but also to make data-driven discoveries. These discoveries are often made using Interpretable Machine Learning, or machine learning models and techniques that yield human understandable insights. In this paper, we discuss and review the field of interpretable machine learning, focusing especially on the techniques as they are often employed to generate new knowledge or make discoveries from large data sets. We outline the types of discoveries that can be made using Interpretable Machine Learning in both supervised and unsupervised settings. Additionally, we focus on the grand challenge of how to validate these discoveries in a data-driven manner, which promotes trust in machine learning systems and reproducibility in science. We discuss validation from both a practical perspective, reviewing approaches based on data-splitting and stability, as well as from a theoretical perspective, reviewing statistical results on model selection consistency and uncertainty quantification via statistical inference. Finally, we conclude by highlighting open challenges in using interpretable machine learning techniques to make discoveries, including gaps between theory and practice for validating data-driven-discoveries.
This empirical study proposes a novel methodology to measure users' perceived trust in an Explainable Artificial Intelligence (XAI) model. To do so, users' mental models are elicited using Fuzzy Cognitive Maps (FCMs). First, we exploit an interpretable Machine Learning (ML) model to classify suspected COVID-19 patients into positive or negative cases. Then, Medical Experts' (MEs) conduct a diagnostic decision-making task based on their knowledge and then prediction and interpretations provided by the XAI model. In order to evaluate the impact of interpretations on perceived trust, explanation satisfaction attributes are rated by MEs through a survey. Then, they are considered as FCM's concepts to determine their influences on each other and, ultimately, on the perceived trust. Moreover, to consider MEs' mental subjectivity, fuzzy linguistic variables are used to determine the strength of influences. After reaching the steady state of FCMs, a quantified value is obtained to measure the perceived trust of each ME. The results show that the quantified values can determine whether MEs trust or distrust the XAI model. We analyze this behavior by comparing the quantified values with MEs' performance in completing diagnostic tasks.
Explainable Deep Learning has gained significant attention in the field of artificial intelligence (AI), particularly in domains such as medical imaging, where accurate and interpretable machine learning models are crucial for effective diagnosis and treatment planning. Grad-CAM is a baseline that highlights the most critical regions of an image used in a deep learning model's decision-making process, increasing interpretability and trust in the results. It is applied in many computer vision (CV) tasks such as classification and explanation. This study explores the principles of Explainable Deep Learning and its relevance to medical imaging, discusses various explainability techniques and their limitations, and examines medical imaging applications of Grad-CAM. The findings highlight the potential of Explainable Deep Learning and Grad-CAM in improving the accuracy and interpretability of deep learning models in medical imaging. The code is available in (will be available).
Part-prototype models are explainable-by-design image classifiers, and a promising alternative to black box AI. This paper explores the applicability and potential of interpretable machine learning, in particular PIP-Net, for automated diagnosis support on real-world medical imaging data. PIP-Net learns human-understandable prototypical image parts and we evaluate its accuracy and interpretability for fracture detection and skin cancer diagnosis. We find that PIP-Net's decision making process is in line with medical classification standards, while only provided with image-level class labels. Because of PIP-Net's unsupervised pretraining of prototypes, data quality problems such as undesired text in an X-ray or labelling errors can be easily identified. Additionally, we are the first to show that humans can manually correct the reasoning of PIP-Net by directly disabling undesired prototypes. We conclude that part-prototype models are promising for medical applications due to their interpretability and potential for advanced model debugging.
The tongue surface houses a range of papillae that are integral to the mechanics and chemistry of taste and textural sensation. Although gustatory function of papillae is well investigated, the uniqueness of papillae within and across individuals remains elusive. Here, we present the first machine learning framework on 3D microscopic scans of human papillae (n = 2092), uncovering the uniqueness of geometric and topological features of papillae. The finer differences in shapes of papillae are investigated computationally based on a number of features derived from discrete differential geometry and computational topology. Interpretable machine learning techniques show that persistent homology features of the papillae shape are the most effective in predicting the biological variables. Models trained on these features with small volumes of data samples predict the type of papillae with an accuracy of 85%. The papillae type classification models can map the spatial arrangement of filiform and fungiform papillae on a surface. Remarkably, the papillae are found to be distinctive across individuals and an individual can be identified with an accuracy of 48% among the 15 participants from a single papillae. Collectively, this is the first unprecedented evidence demonstrating that tongue papillae can serve as a unique identifier inspiring new research direction for food preferences and oral diagnostics.
Explainable Artificial Intelligence (XAI) has gained significant attention recently as the demand for transparency and interpretability of machine learning models has increased. In particular, XAI for time series data has become increasingly important in finance, healthcare, and climate science. However, evaluating the quality of explanations, such as attributions provided by XAI techniques, remains challenging. This paper provides an in-depth analysis of using perturbations to evaluate attributions extracted from time series models. A perturbation analysis involves systematically modifying the input data and evaluating the impact on the attributions generated by the XAI method. We apply this approach to several state-of-the-art XAI techniques and evaluate their performance on three time series classification datasets. Our results demonstrate that the perturbation analysis approach can effectively evaluate the quality of attributions and provide insights into the strengths and limitations of XAI techniques. Such an approach can guide the selection of XAI methods for time series data, e.g., focusing on return time rather than precision, and facilitate the development of more reliable and interpretable machine learning models for time series analysis.
Knowledge constitutes the accumulated understanding and experience that humans use to gain insight into the world. In deep learning, prior knowledge is essential for mitigating shortcomings of data-driven models, such as data dependence, generalization ability, and compliance with constraints. To enable efficient evaluation of the worth of knowledge, we present a framework inspired by interpretable machine learning. Through quantitative experiments, we assess the influence of data volume and estimation range on the worth of knowledge. Our findings elucidate the complex relationship between data and knowledge, including dependence, synergistic, and substitution effects. Our model-agnostic framework can be applied to a variety of common network architectures, providing a comprehensive understanding of the role of prior knowledge in deep learning models. It can also be used to improve the performance of informed machine learning, as well as distinguish improper prior knowledge.
This study investigates the interplay among social demographics, built environment characteristics, and environmental hazard exposure features in determining community level cancer prevalence. Utilizing data from five Metropolitan Statistical Areas in the United States: Chicago, Dallas, Houston, Los Angeles, and New York, the study implemented an XGBoost machine learning model to predict the extent of cancer prevalence and evaluate the importance of different features. Our model demonstrates reliable performance, with results indicating that age, minority status, and population density are among the most influential factors in cancer prevalence. We further explore urban development and design strategies that could mitigate cancer prevalence, focusing on green space, developed areas, and total emissions. Through a series of experimental evaluations based on causal inference, the results show that increasing green space and reducing developed areas and total emissions could alleviate cancer prevalence. The study and findings contribute to a better understanding of the interplay among urban features and community health and also show the value of interpretable machine learning models for integrated urban design to promote public health. The findings also provide actionable insights for urban planning and design, emphasizing the need for a multifaceted approach to addressing urban health disparities through integrated urban design strategies.
Unsupervised machine learning models build an internal representation of their training data without the need for explicit human guidance or feature engineering. This learned representation provides insights into which features of the data are relevant for the task at hand. In the context of quantum physics, training models to describe quantum states without human intervention offers a promising approach to gaining insight into how machines represent complex quantum states. The ability to interpret the learned representation may offer a new perspective on non-trivial features of quantum systems and their efficient representation. We train a generative model on two-qubit density matrices generated by a parameterized quantum circuit. In a series of computational experiments, we investigate the learned representation of the model and its internal understanding of the data. We observe that the model learns an interpretable representation which relates the quantum states to their underlying entanglement characteristics. In particular, our results demonstrate that the latent representation of the model is directly correlated with the entanglement measure concurrence. The insights from this study represent proof of concept towards interpretable machine learning of quantum states. Our approach offers insight into how machines learn to represent small-scale quantum systems autonomously.
Given the increasing volume and quality of genomics data, extracting new insights requires interpretable machine-learning models. This work presents Genomic Interpreter: a novel architecture for genomic assay prediction. This model outperforms the state-of-the-art models for genomic assay prediction tasks. Our model can identify hierarchical dependencies in genomic sites. This is achieved through the integration of 1D-Swin, a novel Transformer-based block designed by us for modelling long-range hierarchical data. Evaluated on a dataset containing 38,171 DNA segments of 17K base pairs, Genomic Interpreter demonstrates superior performance in chromatin accessibility and gene expression prediction and unmasks the underlying `syntax' of gene regulation.
We propose and implement an interpretable machine learning classification model for Explainable AI (XAI) based on expressive Boolean formulas. Potential applications include credit scoring and diagnosis of medical conditions. The Boolean formula defines a rule with tunable complexity (or interpretability), according to which input data are classified. Such a formula can include any operator that can be applied to one or more Boolean variables, thus providing higher expressivity compared to more rigid rule-based and tree-based approaches. The classifier is trained using native local optimization techniques, efficiently searching the space of feasible formulas. Shallow rules can be determined by fast Integer Linear Programming (ILP) or Quadratic Unconstrained Binary Optimization (QUBO) solvers, potentially powered by special purpose hardware or quantum devices. We combine the expressivity and efficiency of the native local optimizer with the fast operation of these devices by executing non-local moves that optimize over subtrees of the full Boolean formula. We provide extensive numerical benchmarking results featuring several baselines on well-known public datasets. Based on the results, we find that the native local rule classifier is generally competitive with the other classifiers. The addition of non-local moves achieves similar results with fewer iterations, and therefore using specialized or quantum hardware could lead to a speedup by fast proposal of non-local moves.
In recent years, machine learning methods have been rapidly implemented in the medical domain. However, current state-of-the-art methods usually produce opaque, black-box models. To address the lack of model transparency, substantial attention has been given to develop interpretable machine learning methods. In the medical domain, counterfactuals can provide example-based explanations for predictions, and show practitioners the modifications required to change a prediction from an undesired to a desired state. In this paper, we propose a counterfactual explanation solution for predicting the survival of cardiovascular ICU patients, by representing their electronic health record as a sequence of medical events, and generating counterfactuals by adopting and employing a text style-transfer technique. Experimental results on the MIMIC-III dataset strongly suggest that text style-transfer methods can …
The Classification Tree (CT) is one of the most common models in interpretable machine learning. Although such models are usually built with greedy strategies, in recent years, thanks to remarkable advances in Mixer-Integer Programming (MIP) solvers, several exact formulations of the learning problem have been developed. In this paper, we argue that some of the most relevant ones among these training models can be encapsulated within a general framework, whose instances are shaped by the specification of loss functions and regularizers. Next, we introduce a novel realization of this framework: specifically, we consider the logistic loss, handled in the MIP setting by a linear piece-wise approximation, and couple it with $\ell_1$-regularization terms. The resulting Optimal Logistic Tree model numerically proves to be able to induce trees with enhanced interpretability features and competitive generalization capabilities, compared to the state-of-the-art MIP-based approaches.
Building accurate and interpretable Machine Learning (ML) models for heterogeneous/mixed data is a long-standing challenge for algorithms designed for numeric data. This work focuses on developing numeric coding schemes for non-numeric attributes for ML algorithms to support accurate and explainable ML models, methods for lossless visualization of n-D non-numeric categorical data with visual rule discovery in these visualizations, and accurate and explainable ML models for categorical data. This study proposes a classification of mixed data types and analyzes their important role in Machine Learning. It presents a toolkit for enforcing interpretability of all internal operations of ML algorithms on mixed data with a visual data exploration on mixed data. A new Sequential Rule Generation (SRG) algorithm for explainable rule generation with categorical data is proposed and successfully evaluated in multiple computational experiments. This work is one of the steps to the full scope ML algorithms for mixed data supported by lossless visualization of n-D data in General Line Coordinates beyond Parallel Coordinates.
This work uses visual knowledge discovery in parallel coordinates to advance methods of interpretable machine learning. The graphic data representation in parallel coordinates made the concepts of hypercubes and hyperblocks (HBs) simple to understand for end users. It is suggested to use mixed and pure hyperblocks in the proposed data classifier algorithm Hyper. It is shown that Hyper models generalize decision trees. The algorithm is presented in several settings and options to discover interactively or automatically overlapping or non-overlapping hyperblocks. Additionally, the use of hyperblocks in conjunction with language descriptions of visual patterns is demonstrated. The benchmark data from the UCI ML repository were used to evaluate the Hyper algorithm. It enabled the discovery of mixed and pure HBs evaluated using 10-fold cross validation. Connections among hyperblocks, dimension reduction and visualization have been established. The capability of end users to find and observe hyperblocks, as well as the ability of side-by-side visualizations to make patterns evident, are among major advantages ofhyperblock technology and the Hyper algorithm. A new method to visualize incomplete n-D data with missing values is proposed, while the traditional parallel coordinates do not support it. The ability of HBs to better prevent both overgeneralization and overfitting of data over decision trees is demonstrated as another benefit of the hyperblocks. The features of VisCanvas 2.0 software tool that implements Hyper technology are presented.
In the early days of machine learning (ML), the emphasis was on developing complex algorithms to achieve best predictive performance. To understand and explain the model results, one had to rely on post hoc explainability techniques, which are known to have limitations. Recently, with the recognition that interpretability is just as important, researchers are compromising on small increases in predictive performance to develop algorithms that are inherently interpretable. While doing so, the ML community has rediscovered the use of low-order functional ANOVA (fANOVA) models that have been known in the statistical literature for some time. This paper starts with a description of challenges with post hoc explainability and reviews the fANOVA framework with a focus on main effects and second-order interactions. This is followed by an overview of two recently developed techniques: Explainable Boosting Machines or EBM (Lou et al., 2013) and GAMI-Net (Yang et al., 2021b). The paper proposes a new algorithm, called GAMI-Lin-T, that also uses trees like EBM, but it does linear fits instead of piecewise constants within the partitions. There are many other differences, including the development of a new interaction filtering algorithm. Finally, the paper uses simulated and real datasets to compare selected ML algorithms. The results show that GAMI-Lin-T and GAMI-Net have comparable performances, and both are generally better than EBM.
Cauliflower is a hand-harvested crop that must fulfill high-quality standards in sales making the timing of harvest important. However, accurately determining harvest-readiness can be challenging due to the cauliflower head being covered by its canopy. While deep learning enables automated harvest-readiness estimation, errors can occur due to field-variability and limited training data. In this paper, we analyze the reliability of a harvest-readiness classifier with interpretable machine learning. By identifying clusters of saliency maps, we derive reliability scores for each classification result using knowledge about the domain and the image properties. For unseen data, the reliability can be used to (i) inform farmers to improve their decision-making and (ii) increase the model prediction accuracy. Using RGB images of single cauliflower plants at different developmental stages from the GrowliFlower dataset, we investigate various saliency mapping approaches and find that they result in different quality of reliability scores. With the most suitable interpretation tool, we adjust the classification result and achieve a 15.72% improvement of the overall accuracy to 88.14% and a 15.44% improvement of the average class accuracy to 88.52% for the GrowliFlower dataset.