Dementia risk scores are commonly used tools to estimate the risk of developing Alzheimer's disease and dementia. We lack an overview of what risk scores are used for, what is claimed they ought to be used for, and whether they are suitable for these applications. To address this, we use the ‘Lifestyle for Brain Health’ (LIBRA) score as a representative example risk score and conduct a literature review to study its applications. The goals of this study are (1) to create an overview of how the LIBRA score has been utilized in scientific articles, (2) to record other applications that these same articles mention, and (3) to critically assess whether LIBRA is suitable for these applications. Of the 66 articles included in our review, 36 involved analyzing associations of LIBRA with dementia, cognition, or other outcomes. We also identified several other applications, with 32 articles mentioning LIBRA as an estimate of ‘dementia prevention potential’, 6 articles used LIBRA as a surrogate outcome for their trial or intervention, and 7 articles mentioned that it could help support clinician decisions in practice. Although there is a clear need for tools that can be used for these applications, the amount of evidence supporting the suitability of dementia risk scores for many of these applications is limited. We recommend that researchers transparently report the purposes of these dementia risk scores, which may include causal tasks, and that research is done to evaluate whether it is valid to use these scores in this way.

Neural networks are typically initialized such that the hidden pre-activations’ theoretical variance remains constant to avoid the vanishing and exploding gradient problem. This condition is necessary to train very deep networks, but numerous analyses show this to be insufficient. We explain this behavior by analyzing the empirical variance, which is more meaningful in the practical setting that deals with data sets of finite size. We demonstrate its discrepancy with the theoretical variance, which grows with depth. We study the output distribution of neural networks at initialization and find that its kurtosis grows to infinity with increasing depth, even if the theoretical variance stays constant. As a result, the empirical variance vanishes: its asymptotic distribution converges in probability to zero. Our analysis focuses on fully connected ReLU networks with He-initialization, but we hypothesize that many more random weight initialization methods suffer from vanishing or exploding empirical variance. We support this hypothesis experimentally and demonstrate the failure of state-of-the-art random initialization methods in very deep regimes.

Learning curves show the expected performance with respect to training set size. This is often used to evaluate and compare models, tune hyper-parameters and determine how much data is needed for a specific performance. However, the distributional properties of performance are frequently overlooked on learning curves. Generally, only an average with standard error or standard deviation is used. In this paper, we analyze the distributions of generalization performance on the learning curves. We compile a high-fidelity learning curve database, both with respect to training set size and repetitions of the sampling for a fixed training set size. Our investigation reveals that generalization performance rarely follows a Gaussian distribution for classical classifiers, regardless of dataset balance, loss function, sampling method, or hyper-parameter tuning along learning curves. Furthermore, we show that the choice of statistical summary, mean versus measures like quantiles affect the top model rankings. Our findings highlight the importance of considering different statistical measures and use of non-parametric approaches when evaluating and selecting machine learning models with learning curves.

Learning curves depict how a model’s expected performance changes with varying training set sizes, unlike training curves, showing a gradient-based model’s performance with respect to training epochs. Extrapolating learning curves can be useful for determining the performance gain with additional data. Parametric functions, that assume monotone behaviour of the curves, are a prevalent methodology to model and extrapolate learning curves. However, learning curves do not necessarily follow a specific parametric shape: they can have peaks, dips, and zigzag patterns. These unconventional shapes can hinder the extrapolation performance of commonly used parametric curve-fitting models. In addition, the objective functions for fitting such parametric models are non-convex, making them initialization-dependent and brittle. In response to these challenges, we propose a convex, data-driven approach that extracts information from available learning curves to guide the extrapolation of another targeted learning curve. Our method achieves this through using a learning curve database. Using the initial segment of the observed curve, we determine a group of similar curves from the database and reduce the dimensionality via Functional Principle Component Analysis FPCA. These principal components are used in a semi-parametric kernel ridge regression (SPKR) model to extrapolate targeted curves. The solution of the SPKR can be obtained analytically and does not suffer from initialization issues. To evaluate our method, we create a new database of diverse learning curves that do not always adhere to typical parametric shapes. Our method performs better than parametric non-parametric learning curve-fitting methods on this database for the learning curve extrapolation task.

Estimating uncertainty of machine learning models is essential to assess the quality of the predictions that these models provide. However, there are several factors that influence the quality of uncertainty estimates, one of which is the amount of model misspecification. Model misspecification always exists as models are mere simplifications or approximations to reality. The question arises whether the estimated uncertainty under model misspecification is reliable or not. In this paper, we argue that model misspecification should receive more attention, by providing thought experiments and contextualizing these with relevant literature.

The use of learning curves for decision making in supervised machine learning is standard practice, yet understanding of their behavior is rather limited. To facilitate a deepening of our knowledge, we introduce the Learning Curve Database (LCDB), which contains empirical learning curves of 20 classification algorithms on 246 datasets. One of the LCDB’s unique strength is that it contains all (probabilistic) predictions, which allows for building learning curves of arbitrary metrics. Moreover, it unifies the properties of similar high quality databases in that it (i) defines clean splits between training, validation, and test data, (ii) provides training times, and (iii) provides an API for convenient access (pip install lcdb). We demonstrate the utility of LCDB by analyzing some learning curve phenomena, such as convexity, monotonicity, peaking, and curve shapes. Improving our understanding of these matters is essential for efficient use of learning curves for model selection, speeding up model training, and to determine the value of more training data.

Arguably, a desirable feature of a learner is that its performance gets better with an increasing amount of training data, at least in expectation. This issue has received renewed attention in recent years and some curious and surprising findings have been reported on. In essence, these results show that more data does actually not necessarily lead to improved performance—worse even, performance can deteriorate. Clustering, however, has not been subjected to such kind of study up to now. This paper shows that k-means clustering, a ubiquitous technique in machine learning and data mining, suffers from the same lack of so-called monotonicity and can display deterioration in expected performance with increasing training set sizes. Our main, theoretical contributions prove that 1-means clustering is monotonic, while 2-means is not even weakly monotonic, i.e., the occurrence of nonmonotonic behavior persists indefinitely, beyond any training sample size. For larger k, the question remains open.

Motivation: Anti-cancer drugs may elicit resistance or sensitivity through mechanisms which involve several genomic layers. Nevertheless, we have demonstrated that gene expression contains most of the predictive capacity compared to the remaining omic data types. Unfortunately, this comes at a price: gene expression biomarkers are often hard to interpret and show poor robustness. Results: To capture the best of both worlds, i.e. the accuracy of gene expression and the robustness of other genomic levels, such as mutations, copy-number or methylation, we developed Percolate, a computational approach which extracts the joint signal between gene expression and the other omic data types. We developed an out-of-sample extension of Percolate which allows predictions on unseen samples without the necessity to recompute the joint signal on all data. We employed Percolate to extract the joint signal between gene expression and either mutations, copy-number or methylation, and used the out-of sample extension to perform response prediction on unseen samples. We showed that the joint signal recapitulates, and sometimes exceeds, the predictive performance achieved with each data type individually. Importantly, molecular signatures created by Percolate do not require gene expression to be evaluated, rendering them suitable to clinical applications where only one data type is available. Availability: Percolate is available as a Python 3.7 package and the scripts to reproduce the results are available here.

Learning curves provide insight into the dependence of a learner's generalization performance on the training set size. This important tool can be used for model selection, to predict the effect of more training data, and to reduce the computational complexity of model training and hyperparameter tuning. This review recounts the origins of the term, provides a formal definition of the learning curve, and briefly covers basics such as its estimation. Our main contribution is a comprehensive overview of the literature regarding the shape of learning curves. We discuss empirical and theoretical evidence that supports well-behaved curves that often have the shape of a power law or an exponential. We consider the learning curves of Gaussian processes, the complex shapes they can display, and the factors influencing them. We draw specific attention to examples of learning curves that are ill-behaved, showing worse learning performance with more training data. To wrap up, we point out various open problems that warrant deeper empirical and theoretical investigation. All in all, our review underscores that learning curves are surprisingly diverse and no universal model can be identified.

Free-standing social conversations constitute a yet underexplored setting for human behavior forecasting. While the task of predicting pedestrian trajectories has received much recent attention, an intrinsic difference between these settings is how groups form and disband. Evidence from social psychology suggests that group members in a conversation explicitly self-organize to sustain the interaction by adapting to one another’s behaviors. Crucially, the same individual is unlikely to adapt similarly across different groups; contextual factors such as perceived relationships, attraction, rapport, etc., influence the entire spectrum of participants’ behaviors. A question arises: how can we jointly forecast the mutually dependent futures of conversation partners by modeling the dynamics unique to every group? In this paper, we propose the Social Process (SP) models, taking a novel meta-learning and stochastic perspective of group dynamics. Training group-specific forecasting models hinders generalization to unseen groups and is challenging given limited conversation data. In contrast, our SP models treat interaction sequences from a single group as a meta-dataset: we condition forecasts for a sequence from a given group on other observed-future sequence pairs from the same group. In this way, an SP model learns to adapt its forecasts to the unique dynamics of the interacting partners, generalizing to unseen groups in a data-efficient manner. Additionally, we first rethink the task formulation itself, motivating task requirements from social science literature that prior formulations have overlooked. For our formulation of Social Cue Forecasting, we evaluate the empirical performance of our SP models against both non-meta-learning and meta-learning approaches with similar assumptions. The SP models yield improved performance on synthetic and real-world behavior datasets.

Semi-supervised learning is the learning setting in which we have both labeled and unlabeled data at our disposal. This survey covers theoretical results for this setting and maps out the benefits of unlabeled data in classification and regression tasks. Most methods that use unlabeled data rely on certain assumptions about the data distribution. When those assumptions are not met, including unlabeled data may actually decrease performance. For all practical purposes, it is therefore instructive to have an understanding of the underlying theory and the possible learning behavior that comes with it. This survey gathers results about the possible gains one can achieve when using semi-supervised learning as well as results about the limits of such methods. Specifically, it aims to answer the following questions: what are, in terms of improving supervised methods, the limits of semi-supervised learning? What are the assumptions of different methods? What can we achieve if the assumptions are true? As, indeed, the precise assumptions made are of the essence, this is where the survey's particular attention goes out to.

We illustrate the detrimental effect, such as overconfident decisions, that exponential behavior can have in methods like classical LDA and logistic regression. We then show how polynomiality can remedy the situation. This, among others, leads purposefully to random-level performance in the tails, away from the bulk of the training data. A directly related, simple, yet important technical novelty we subsequently present is softRmax: a reasoned alternative to the standard softmax function employed in contemporary (deep) neural networks. It is derived through linking the standard softmax to Gaussian class-conditional models, as employed in LDA, and replacing those by a polynomial alternative. We show that two aspects of softRmax, conservativeness and inherent gradient regularization, lead to robustness against adversarial attacks without gradient obfuscation.

Though much effort has been spent on designing new active learning algorithms, little attention has been paid to the initialization problem of active learning, i.e., how to find a set of labeled samples which contains at least one instance per category. This work identifies the initialization of active learning as a separate and novel research problem, reviews existing methods that can be adapted to be used for this task and, in addition, proposes a new active initialization criterion: the Nearest Neighbor Criterion. Experiments on 16 benchmark datasets verify that the novel method often finds an initialization set with fewer queried samples than other methods do.

Domain adaptation has become a prominent problem setting in machine learning and related fields. This review asks the question: How can a classifier learn from a source domain and generalize to a target domain We present a categorization of approaches, divided into, what we refer to as, sample-based, feature-based, and inference-based methods. Sample-based methods focus on weighting individual observations during training based on their importance to the target domain. Feature-based methods revolve around on mapping, projecting, and representing features such that a source classifier performs well on the target domain and inference-based methods incorporate adaptation into the parameter estimation procedure, for instance through constraints on the optimization procedure. Additionally, we review a number of conditions that allow for formulating bounds on the cross-domain generalization error. Our categorization highlights recurring ideas and raises questions important to further research.

We present ReproducedPapers.org : an open online repository for teaching and structuring machine learning reproducibility. We evaluate doing a reproduction project among students and the added value of an online reproduction repository among AI researchers. We use anonymous self-assessment surveys and obtained 144 responses. Results suggest that students who do a reproduction project place more value on scientific reproductions and become more critical thinkers. Students and AI researchers agree that our online reproduction repository is valuable.

Preclinical models have been the workhorse of cancer research, producing massive amounts of drug response data. Unfortunately, translating response biomarkers derived from these datasets to human tumors has proven to be particularly challenging. To address this challenge, we developed TRANSACT, a computational framework that builds a consensus space to capture biological processes common to preclinical models and human tumors and exploits this space to construct drug response predictors that robustly transfer from preclinical models to human tumors. TRANSACT performs favorably compared to four competing approaches, including two deep learning approaches, on a set of 23 drug prediction challenges on The Cancer Genome Atlas and 226 metastatic tumors from the Hartwig Medical Foundation. We demonstrate that response predictions deliver a robust performance for a number of therapies of high clinical importance: platinum-based chemotherapies, gemcitabine, and paclitaxel. In contrast to other approaches, we demonstrate the interpretability of the TRANSACT predictors by correctly identifying known biomarkers of targeted therapies, and we propose potential mechanisms that mediate the resistance to two chemotherapeutic agents.