Staartjes have contributed equally to this series, and share first authorship. Abstract As analytical machine learning tools become readily available for clinicians to use, the understanding of key concepts and the awareness of analytical pitfalls are increasingly required for clinicians, investigators, reviewers and editors, who even as experts in their clinical field, sometimes find themselves insufficiently equipped to evaluate machine learning methodologies. In this section, we provide explanations on the general principles of machine learning, as well as analytical steps required for successful machine learning-based predictive modelling, which is the focus of this series. In particular, we define the terms machine learning, artificial intelligence, as well as supervised and unsupervised learning, continuing by introducing optimization, thus, the minimization of an objective error function as the central dogma of machine learning. In addition, we discuss why it is important to separate predictive and explanatory modelling, and most importantly state that a prediction model should not be used to make inferences. Lastly, we broadly describe a classical workflow for training a machine learning model, starting with data pre-processing and feature engineering and selection, continuing on with a training structure consisting of a resampling method, hyperparameter tuning, and model selection, and ending with evaluation of model discrimination and calibration as well as robust internal or external validation of the fully developed model. Methodological rigor and clarity as well as understanding of the underlying reasoning of the internal workings of a machine learning approach are required, otherwise predictive applications despite being strong analytical tools are not well accepted into the clinical routine.

Counterfactual explanations are usually obtained by identifying the smallest change made to an input to change a prediction made by a fixed model (hereafter called sparse methods). Recent work, however, has revitalized an old insight: there often does not exist one superior solution to a prediction problem with respect to commonly used measures of interest (e.g. error rate). In fact, often multiple different classifiers give almost equal solutions. This phenomenon is known as predictive multiplicity (Breiman, 2001; Marx et al., 2019). In this work, we derive a general upper bound for the costs of counterfactual explanations under predictive multiplicity. Most notably, it depends on a discrepancy notion between two classifiers, which describes how differently they treat negatively predicted individuals. We then compare sparse and data support approaches empirically on real-world data. The results show that data support methods are more robust to multiplicity of different models. At the same time, we show that those methods have provably higher cost of generating counterfactual explanations under one fixed model. In summary, our theoretical and empiricaln results challenge the commonly held view that counterfactual recommendations should be sparse in general.

With the abundance of machine learning methods available and the temptation of using them all in an ensemble method, having a model-agnostic method of feature selection is incredibly alluring. Principal component analysis was developed in 1901 and has been a strong contender in this role since, but in the end is an unsupervised method. It offers no guarantee that the features that are selected have good predictive power because it does not know what is being predicted. To this end, Peng et al. developed the minimum redundancy-maximum relevance (mRMR) method in 2005. It uses the mutual information not only between predictors but also includes the mutual information with the response in its calculation. Estimating mutual information and entropy tend to be expensive and problematic endeavors, which leads to excessive processing times even for dataset that is approximately 750 by 750 in a Leave-One-Subject-Out jackknife situation. To remedy this, we use a method from 2012 called Distance Correlation Sure Independence Screening (DC-SIS) which uses the distance correlation measure of Sz\'ekely et al. to select features that have the greatest dependence with the response. We show that this method produces statistically indistinguishable results to the mRMR selection method on Parkinson's Disease vocal diagnosis data 90 times faster.

A large body of research has focused on adversarial attacks which require to modify all input features with small $l_2$- or $l_\infty$-norms. In this paper we instead focus on query-efficient sparse attacks in the black-box setting. Our versatile framework, Sparse-RS, based on random search achieves state-of-the-art success rate and query efficiency for different sparse attack models such as $l_0$-bounded perturbations (outperforming established white-box methods), adversarial patches, and adversarial framing. We show the effectiveness of Sparse-RS on different datasets considering problems from image recognition and malware detection and multiple variations of sparse threat models, including targeted and universal perturbations. In particular Sparse-RS can be used for realistic attacks such as universal adversarial patch attacks without requiring a substitute model. The code of our framework is available at https://github.com/fra31/sparse-rs.

Machine learning is a powerful tool for predicting human-related outcomes, from credit scores to heart attack risks. But when deployed, learned models also affect how users act in order to improve outcomes, whether predicted or real. The standard approach to learning is agnostic to induced user actions and provides no guarantees as to the effect of actions. We provide a framework for learning predictors that are both accurate and promote good actions. For this, we introduce look-ahead regularization which, by anticipating user actions, encourages predictive models to also induce actions that improve outcomes. This regularization carefully tailors the uncertainty estimates governing confidence in this improvement to the distribution of model-induced actions. We report the results of experiments on real and synthetic data that show the effectiveness of this approach.

Programming-by-example technologies are being deployed in industrial products for real-time synthesis of various kinds of data transformations. These technologies rely on the user to provide few representative examples of the transformation task. Motivated by the need to find the most pertinent question to ask the user, in this paper, we introduce the {\em significant questions problem}, and show that it is hard in general. We then develop an information-theoretic greedy approach for solving the problem. We justify the greedy algorithm using the conditional entropy result, which informally says that the question that achieves the maximum information gain is the one that we know least about. In the context of interactive program synthesis, we use the above result to develop an {\em{active program learner}} that generates the significant inputs to pose as queries to the user in each iteration. The procedure requires extending a {\em{passive program learner}} to a {\em{sampling program learner}} that is able to sample candidate programs from the set of all consistent programs to enable estimation of information gain. It also uses clustering of inputs based on features in the inputs and the corresponding outputs to sample a small set of candidate significant inputs. Our active learner is able to tradeoff false negatives for false positives and converge in a small number of iterations on a real-world dataset of %around 800 string transformation tasks.

Hypergraphs provide a natural representation for many real world datasets. We propose a novel framework, HNHN, for hypergraph representation learning. HNHN is a hypergraph convolution network with nonlinear activation functions applied to both hypernodes and hyperedges, combined with a normalization scheme that can flexibly adjust the importance of high-cardinality hyperedges and high-degree vertices depending on the dataset. We demonstrate improved performance of HNHN in both classification accuracy and speed on real world datasets when compared to state of the art methods.

Many modern data analyses benefit from explicitly modeling dependence structure in data - such as measurements across time or space, ordered words in a sentence, or genes in a genome. A gold standard evaluation technique is structured cross-validation (CV), which leaves out some data subset (such as data within a time interval or data in a geographic region) in each fold. But CV here can be prohibitively slow due to the need to rerun already-expensive learning algorithms many times. Previous work has shown approximate cross-validation (ACV) methods provide a fast and provably accurate alternative in the setting of empirical risk minimization. But this existing ACV work is restricted to simpler models by the assumptions that (i) data across CV folds are independent and (ii) an exact initial model fit is available. In structured data analyses, both these assumptions are often untrue. In the present work, we address (i) by extending ACV to CV schemes with dependence structure between the folds. To address (ii), we verify - both theoretically and empirically - that ACV quality deteriorates smoothly with noise in the initial fit. We demonstrate the accuracy and computational benefits of our proposed methods on a diverse set of real-world applications.

Non-negative Matrix Factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy data sets with applications in data mining, text recognition, dimension reduction, face recognition, anomaly detection, blind source separation, and many other fields. An important input for NMF is the latent dimensionality of the data, that is, the number of hidden features, K, present in the explored data set. Unfortunately, this quantity is rarely known a priori. We utilize a supervised machine learning approach in combination with a recent method for model determination, called NMFk, to determine the number of hidden features automatically. NMFk performs a set of NMF simulations on an ensemble of matrices, obtained by bootstrapping the initial data set, and determines which K produces stable groups of latent features that reconstruct the initial data set well. We then train a Multi-Layer Perceptron (MLP) classifier network to determine the correct number of latent features utilizing the statistics and characteristics of the NMF solutions, obtained from NMFk. In order to train the MLP classifier, a training set of 58,660 matrices with predetermined latent features were factorized with NMFk. The MLP classifier in conjunction with NMFk maintains a greater than 95% success rate when applied to a held out test set. Additionally, when applied to two well-known benchmark data sets, the swimmer and MIT face data, NMFk/MLP correctly recovered the established number of hidden features. Finally, we compared the accuracy of our method to the ARD, AIC and Stability-based methods.

Beyond the possible misuses of technology, there is an increased awareness that these processes are not neutral and can reproduce and amplify past and current structural inequalities [1, 2]. Within this context, particular interest is paid to the role of machine learning (ML) with well known examples of models biased against historically discriminated groups [3, 4, 5] or the intersection of these groups [6, 7]. Fairness in ML has emerged as a community initially motivated to develop technological solutions to the disparate impact and treatment by biased algorithms [8, 9, 10, 11, 5] that also moves to a broader and multi-disciplinary understanding of the issues of socio-technological interventions [12, 13, 14, 15]. This work contribute to this field by studying how far bias mitigation can go whilst satisfying the accuracy and transparency of the models, thus providing a tool for a wider understanding of the technological boundaries of socio-technical proposals. Bias mitigation techniques can broadly be divided into three non-exclusive categories [16]: (1) preprocessing, (2) inprocessing, and (3) postprocessing. The preprocessing techniques attempt to learn new representations of data to satisfy fairness definitions. The inprocessing methods involve modifying the classifier algorithm by adding a fairness constraint to the optimization problem. The postprocessing methods aim at removing discriminatory decisions after the model is trained. Normally, in inprocessing approaches the fairness criteria are used as an optimization constraint rather than as a guide to build a more equitable prediction model.