Time-to-event prediction, e.g. cancer survival analysis or hospital length of stay, is a highly prominent machine learning task in medical and healthcare applications. However, only a few interpretable machine learning methods comply with its challenges. To facilitate a comprehensive explanatory analysis of survival models, we formally introduce time-dependent feature effects and global feature importance explanations. We show how post-hoc interpretation methods allow for finding biases in AI systems predicting length of stay using a novel multi-modal dataset created from 1235 X-ray images with textual radiology reports annotated by human experts. Moreover, we evaluate cancer survival models beyond predictive performance to include the importance of multi-omics feature groups based on a large-scale benchmark comprising 11 datasets from The Cancer Genome Atlas (TCGA). Model developers can use the proposed methods to debug and improve machine learning algorithms, while physicians can discover disease biomarkers and assess their significance. We hope the contributed open data and code resources facilitate future work in the emerging research direction of explainable survival analysis.
Appendicitis is among the most frequent reasons for pediatric abdominal surgeries. Previous decision support systems for appendicitis have focused on clinical, laboratory, scoring, and computed tomography data and have ignored abdominal ultrasound, despite its noninvasive nature and widespread availability. In this work, we present interpretable machine learning models for predicting the diagnosis, management and severity of suspected appendicitis using ultrasound images. Our approach utilizes concept bottleneck models (CBM) that facilitate interpretation and interaction with high-level concepts understandable to clinicians. Furthermore, we extend CBMs to prediction problems with multiple views and incomplete concept sets. Our models were trained on a dataset comprising 579 pediatric patients with 1709 ultrasound images accompanied by clinical and laboratory data. Results show that our proposed method enables clinicians to utilize a human-understandable and intervenable predictive model without compromising performance or requiring time-consuming image annotation when deployed. For predicting the diagnosis, the extended multiview CBM attained an AUROC of 0.80 and an AUPR of 0.92, performing comparably to similar black-box neural networks trained and tested on the same dataset.
Prototypical part network (ProtoPNet) methods have been designed to achieve interpretable classification by associating predictions with a set of training prototypes, which we refer to as trivial prototypes because they are trained to lie far from the classification boundary in the feature space. Note that it is possible to make an analogy between ProtoPNet and support vector machine (SVM) given that the classification from both methods relies on computing similarity with a set of training points (i.e., trivial prototypes in ProtoPNet, and support vectors in SVM). However, while trivial prototypes are located far from the classification boundary, support vectors are located close to this boundary, and we argue that this discrepancy with the well-established SVM theory can result in ProtoPNet models with inferior classification accuracy. In this paper, we aim to improve the classification of ProtoPNet with a new method to learn support prototypes that lie near the classification boundary in the feature space, as suggested by the SVM theory. In addition, we target the improvement of classification results with a new model, named ST-ProtoPNet, which exploits our support prototypes and the trivial prototypes to provide more effective classification. Experimental results on CUB-200-2011, Stanford Cars, and Stanford Dogs datasets demonstrate that ST-ProtoPNet achieves state-of-the-art classification accuracy and interpretability results. We also show that the proposed support prototypes tend to be better localised in the object of interest rather than in the background region.
This work introduces a novel interpretable machine learning method called Mixture of Decision Trees (MoDT). It constitutes a special case of the Mixture of Experts ensemble architecture, which utilizes a linear model as gating function and decision trees as experts. Our proposed method is ideally suited for problems that cannot be satisfactorily learned by a single decision tree, but which can alternatively be divided into subproblems. Each subproblem can then be learned well from a single decision tree. Therefore, MoDT can be considered as a method that improves performance while maintaining interpretability by making each of its decisions understandable and traceable to humans. Our work is accompanied by a Python implementation, which uses an interpretable gating function, a fast learning algorithm, and a direct interface to fine-tuned interpretable visualization methods. The experiments confirm that the implementation works and, more importantly, show the superiority of our approach compared to single decision trees and random forests of similar complexity.
Model distillation has been a popular method for producing interpretable machine learning. It uses an interpretable "student" model to mimic the predictions made by the black box "teacher" model. However, when the student model is sensitive to the variability of the data sets used for training even when keeping the teacher fixed, the corresponded interpretation is not reliable. Existing strategies stabilize model distillation by checking whether a large enough corpus of pseudo-data is generated to reliably reproduce student models, but methods to do so have so far been developed for a specific student model. In this paper, we develop a generic approach for stable model distillation based on central limit theorem for the average loss. We start with a collection of candidate student models and search for candidates that reasonably agree with the teacher. Then we construct a multiple testing framework to select a corpus size such that the consistent student model would be selected under different pseudo samples. We demonstrate the application of our proposed approach on three commonly used intelligible models: decision trees, falling rule lists and symbolic regression. Finally, we conduct simulation experiments on Mammographic Mass and Breast Cancer datasets and illustrate the testing procedure throughout a theoretical analysis with Markov process. The code is publicly available at https://github.com/yunzhe-zhou/GenericDistillation.
Big streams of Earth images from satellites or other platforms (e.g., drones and mobile phones) are becoming increasingly available at low or no cost and with enhanced spatial and temporal resolution. This thesis recognizes the unprecedented opportunities offered by the high quality and open access Earth observation data of our times and introduces novel machine learning and big data methods to properly exploit them towards developing applications for sustainable and resilient agriculture. The thesis addresses three distinct thematic areas, i.e., the monitoring of the Common Agricultural Policy (CAP), the monitoring of food security and applications for smart and resilient agriculture. The methodological innovations of the developments related to the three thematic areas address the following issues: i) the processing of big Earth Observation (EO) data, ii) the scarcity of annotated data for machine learning model training and iii) the gap between machine learning outputs and actionable advice. This thesis demonstrated how big data technologies such as data cubes, distributed learning, linked open data and semantic enrichment can be used to exploit the data deluge and extract knowledge to address real user needs. Furthermore, this thesis argues for the importance of semi-supervised and unsupervised machine learning models that circumvent the ever-present challenge of scarce annotations and thus allow for model generalization in space and time. Specifically, it is shown how merely few ground truth data are needed to generate high quality crop type maps and crop phenology estimations. Finally, this thesis argues there is considerable distance in value between model inferences and decision making in real-world scenarios and thereby showcases the power of causal and interpretable machine learning in bridging this gap.
Counterfactual Explanations are becoming a de-facto standard in post-hoc interpretable machine learning. For a given classifier and an instance classified in an undesired class, its counterfactual explanation corresponds to small perturbations of that instance that allows changing the classification outcome. This work aims to leverage Counterfactual Explanations to detect the important decision boundaries of a pre-trained black-box model. This information is used to build a supervised discretization of the features in the dataset with a tunable granularity. Using the discretized dataset, an optimal Decision Tree can be trained that resembles the black-box model, but that is interpretable and compact. Numerical results on real-world datasets show the effectiveness of the approach in terms of accuracy and sparsity.
Explainable artificial intelligence (XAI) provides explanations for not interpretable machine learning (ML) models. While many technical approaches exist, there is a lack of validation of these techniques on real-world datasets. In this work, we present a use-case of XAI: an ML model which is trained to estimate electrification rates based on mobile phone data in Senegal. The data originate from the Data for Development challenge by Orange in 2014/15. We apply two model-agnostic, local explanation techniques and find that while the model can be verified, it is biased with respect to the population density. We conclude our paper by pointing to the two main challenges we encountered during our work: data processing and model design that might be restricted by currently available XAI methods, and the importance of domain knowledge to interpret explanations.
Classical artificial neural networks have witnessed widespread successes in machine-learning applications. Here, we propose fermion neural networks (FNNs) whose physical properties, such as local density of states or conditional conductance, serve as outputs, once the inputs are incorporated as an initial layer. Comparable to back-propagation, we establish an efficient optimization, which entitles FNNs to competitive performance on challenging machine-learning benchmarks. FNNs also directly apply to quantum systems, including hard ones with interactions, and offer in-situ analysis without preprocessing or presumption. Following machine learning, FNNs precisely determine topological phases and emergent charge orders. Their quantum nature also brings various advantages: quantum correlation entitles more general network connectivity and insight into the vanishing gradient problem, quantum entanglement opens up novel avenues for interpretable machine learning, etc.
In intensive care units (ICUs), critically ill patients are monitored with electroencephalograms (EEGs) to prevent serious brain injury. The number of patients who can be monitored is constrained by the availability of trained physicians to read EEGs, and EEG interpretation can be subjective and prone to inter-observer variability. Automated deep learning systems for EEG could reduce human bias and accelerate the diagnostic process. However, black box deep learning models are untrustworthy, difficult to troubleshoot, and lack accountability in real-world applications, leading to a lack of trust and adoption by clinicians. To address these challenges, we propose a novel interpretable deep learning model that not only predicts the presence of harmful brainwave patterns but also provides high-quality case-based explanations of its decisions. Our model performs better than the corresponding black box model, despite being constrained to be interpretable. The learned 2D embedded space provides the first global overview of the structure of ictal-interictal-injury continuum brainwave patterns. The ability to understand how our model arrived at its decisions will not only help clinicians to diagnose and treat harmful brain activities more accurately but also increase their trust and adoption of machine learning models in clinical practice; this could be an integral component of the ICU neurologists' standard workflow.
In recent years, there has been growing attention to interpretable machine learning models which can give explanatory insights on their behaviour. Thanks to their interpretability, decision trees have been intensively studied for classification tasks and, due to the remarkable advances in mixed integer programming (MIP), various approaches have been proposed to formulate the problem of training an Optimal Classification Tree (OCT) as a MIP model. We present a novel mixed integer quadratic formulation for the OCT problem, which exploits the generalization capabilities of Support Vector Machines for binary classification. Our model, denoted as Margin Optimal Classification Tree (MARGOT), encompasses maximum margin multivariate hyperplanes nested in a binary tree structure. To enhance the interpretability of our approach, we analyse two alternative versions of MARGOT, which include feature selection constraints inducing sparsity of the hyperplanes' coefficients. First, MARGOT has been tested on non-linearly separable synthetic datasets in a 2-dimensional feature space to provide a graphical representation of the maximum margin approach. Finally, the proposed models have been tested on benchmark datasets from the UCI repository. The MARGOT formulation turns out to be easier to solve than other OCT approaches, and the generated tree better generalizes on new observations. The two interpretable versions effectively select the most relevant features, maintaining good prediction quality.
Interpretable machine learning plays a key role in healthcare because it is challenging in understanding feature importance in deep learning model predictions. We propose a novel framework that uses deep learning to study feature sensitivity for model predictions. This work combines sensitivity analysis with heterogeneous time-series deep learning model prediction, which corresponds to the interpretations of spatio-temporal features. We forecast county-level COVID-19 infection using the Temporal Fusion Transformer. We then use the sensitivity analysis extending Morris Method to see how sensitive the outputs are with respect to perturbation to our static and dynamic input features. The significance of the work is grounded in a real-world COVID-19 infection prediction with highly non-stationary, finely granular, and heterogeneous data. 1) Our model can capture the detailed daily changes of temporal and spatial model behaviors and achieves high prediction performance compared to a PyTorch baseline. 2) By analyzing the Morris sensitivity indices and attention patterns, we decipher the meaning of feature importance with observational population and dynamic model changes. 3) We have collected 2.5 years of socioeconomic and health features over 3142 US counties, such as observed cases and deaths, and a number of static (age distribution, health disparity, and industry) and dynamic features (vaccination, disease spread, transmissible cases, and social distancing). Using the proposed framework, we conduct extensive experiments and show our model can learn complex interactions and perform predictions for daily infection at the county level. Being able to model the disease infection with a hybrid prediction and description accuracy measurement with Morris index at the county level is a central idea that sheds light on individual feature interpretation via sensitivity analysis.
Despite the popularity of feature importance (FI) measures in interpretable machine learning, the statistical adequacy of these methods is rarely discussed. From a statistical perspective, a major distinction is between analyzing a variable's importance before and after adjusting for covariates - i.e., between $\textit{marginal}$ and $\textit{conditional}$ measures. Our work draws attention to this rarely acknowledged, yet crucial distinction and showcases its implications. Further, we reveal that for testing conditional FI, only few methods are available and practitioners have hitherto been severely restricted in method application due to mismatching data requirements. Most real-world data exhibits complex feature dependencies and incorporates both continuous and categorical data (mixed data). Both properties are oftentimes neglected by conditional FI measures. To fill this gap, we propose to combine the conditional predictive impact (CPI) framework with sequential knockoff sampling. The CPI enables conditional FI measurement that controls for any feature dependencies by sampling valid knockoffs - hence, generating synthetic data with similar statistical properties - for the data to be analyzed. Sequential knockoffs were deliberately designed to handle mixed data and thus allow us to extend the CPI approach to such datasets. We demonstrate through numerous simulations and a real-world example that our proposed workflow controls type I error, achieves high power and is in line with results given by other conditional FI measures, whereas marginal FI metrics result in misleading interpretations. Our findings highlight the necessity of developing statistically adequate, specialized methods for mixed data.
Shapley values are ubiquitous in interpretable Machine Learning due to their strong theoretical background and efficient implementation in the SHAP library. Computing these values previously induced an exponential cost with respect to the number of input features of an opaque model. Now, with efficient implementations such as Interventional TreeSHAP, this exponential burden is alleviated assuming one is explaining ensembles of decision trees. Although Interventional TreeSHAP has risen in popularity, it still lacks a formal proof of how/why it works. We provide such proof with the aim of not only increasing the transparency of the algorithm but also to encourage further development of these ideas. Notably, our proof for Interventional TreeSHAP is easily adapted to Shapley-Taylor indices and one-hot-encoded features.
Black-box models, such as deep neural networks, exhibit superior predictive performances, but understanding their behavior is notoriously difficult. Many explainable artificial intelligence methods have been proposed to reveal the decision-making processes of black box models. However, their applications in high-stakes domains remain limited. Recently proposed neural additive models (NAM) have achieved state-of-the-art interpretable machine learning. NAM can provide straightforward interpretations with slight performance sacrifices compared with multi-layer perceptron. However, NAM can only model 1$^{\text{st}}$-order feature interactions; thus, it cannot capture the co-relationships between input features. To overcome this problem, we propose a novel interpretable machine learning method called higher-order neural additive models (HONAM) and a feature interaction method for high interpretability. HONAM can model arbitrary orders of feature interactions. Therefore, it can provide the high predictive performance and interpretability that high-stakes domains need. In addition, we propose a novel hidden unit to effectively learn sharp-shape functions. We conducted experiments using various real-world datasets to examine the effectiveness of HONAM. Furthermore, we demonstrate that HONAM can achieve fair AI with a slight performance sacrifice. The source code for HONAM is publicly available.
Interpretable machine learning seeks to understand the reasoning process of complex black-box systems that are long notorious for lack of explainability. One flourishing approach is through counterfactual explanations, which provide suggestions on what a user can do to alter an outcome. Not only must a counterfactual example counter the original prediction from the black-box classifier but it should also satisfy various constraints for practical applications. Diversity is one of the critical constraints that however remains less discussed. While diverse counterfactuals are ideal, it is computationally challenging to simultaneously address some other constraints. Furthermore, there is a growing privacy concern over the released counterfactual data. To this end, we propose a feature-based learning framework that effectively handles the counterfactual constraints and contributes itself to the limited pool of private explanation models. We demonstrate the flexibility and effectiveness of our method in generating diverse counterfactuals of actionability and plausibility. Our counterfactual engine is more efficient than counterparts of the same capacity while yielding the lowest re-identification risks.
The focus of this paper is a proof of concept, machine learning (ML) pipeline that extracts heart rate from pressure sensor data acquired on low-power edge devices. The ML pipeline consists an upsampler neural network, a signal quality classifier, and a 1D-convolutional neural network optimized for efficient and accurate heart rate estimation. The models were designed so the pipeline was less than 40 kB. Further, a hybrid pipeline consisting of the upsampler and classifier, followed by a peak detection algorithm was developed. The pipelines were deployed on ESP32 edge device and benchmarked against signal processing to determine the energy usage, and inference times. The results indicate that the proposed ML and hybrid pipeline reduces energy and time per inference by 82% and 28% compared to traditional algorithms. The main trade-off for ML pipeline was accuracy, with a mean absolute error (MAE) of 3.28, compared to 2.39 and 1.17 for the hybrid and signal processing pipelines. The ML models thus show promise for deployment in energy and computationally constrained devices. Further, the lower sampling rate and computational requirements for the ML pipeline could enable custom hardware solutions to reduce the cost and energy needs of wearable devices.
With the increasing application of deep learning algorithms to time series classification, especially in high-stake scenarios, the relevance of interpreting those algorithms becomes key. Although research in time series interpretability has grown, accessibility for practitioners is still an obstacle. Interpretability approaches and their visualizations are diverse in use without a unified API or framework. To close this gap, we introduce TSInterpret an easily extensible open-source Python library for interpreting predictions of time series classifiers that combines existing interpretation approaches into one unified framework. The library features (i) state-of-the-art interpretability algorithms, (ii) exposes a unified API enabling users to work with explanations consistently and provides (iii) suitable visualizations for each explanation.
ControlBurn is a Python package to construct feature-sparse tree ensembles that support nonlinear feature selection and interpretable machine learning. The algorithms in this package first build large tree ensembles that prioritize basis functions with few features and then select a feature-sparse subset of these basis functions using a weighted lasso optimization criterion. The package includes visualizations to analyze the features selected by the ensemble and their impact on predictions. Hence ControlBurn offers the accuracy and flexibility of tree-ensemble models and the interpretability of sparse generalized additive models. ControlBurn is scalable and flexible: for example, it can use warm-start continuation to compute the regularization path (prediction error for any number of selected features) for a dataset with tens of thousands of samples and hundreds of features in seconds. For larger datasets, the runtime scales linearly in the number of samples and features (up to a log factor), and the package support acceleration using sketching. Moreover, the ControlBurn framework accommodates feature costs, feature groupings, and $\ell_0$-based regularizers. The package is user-friendly and open-source: its documentation and source code appear on https://pypi.org/project/ControlBurn/ and https://github.com/udellgroup/controlburn/.
Interpretable machine learning offers insights into what factors drive a certain prediction of a black-box system. A large number of interpreting methods focus on identifying explanatory input features, which generally fall into two main categories: attribution and selection. A popular attribution-based approach is to exploit local neighborhoods for learning instance-specific explainers in an additive manner. The process is thus inefficient and susceptible to poorly-conditioned samples. Meanwhile, many selection-based methods directly optimize local feature distributions in an instance-wise training framework, thereby being capable of leveraging global information from other inputs. However, they can only interpret single-class predictions and many suffer from inconsistency across different settings, due to a strict reliance on a pre-defined number of features selected. This work exploits the strengths of both methods and proposes a framework for learning local explanations simultaneously for multiple target classes. Our model explainer significantly outperforms additive and instance-wise counterparts on faithfulness with more compact and comprehensible explanations. We also demonstrate the capacity to select stable and important features through extensive experiments on various data sets and black-box model architectures.