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The influx of deep learning (DL) techniques into the field of survival analysis in recent years has led to substantial methodological progress; for instance, learning from unstructured or high-dimensional data such as images, text or omics data. In this work, we conduct a comprehensive systematic review of DL-based methods for time-to-event analysis, characterizing them according to both survival- and DL-related attributes. In summary, the reviewed methods often address only a small subset of tasks relevant to time-to-event data—e.g., single-risk right-censored data—and neglect to incorporate more complex settings. Our findings are summarized in an editable, open-source, interactive table: https://survival-org.github.io/DL4Survival . As this research area is advancing rapidly, we encourage community contribution in order to keep this database up to date.

Interpretable machine learning has become a very active area of research due to the rising popularity of machine learning algorithms and their inherently challenging interpretability. Most work in this area has been focused on the interpretation of single features in a model. However, for researchers and practitioners, it is often equally important to quantify the importance or visualize the effect of feature groups. To address this research gap, we provide a comprehensive overview of how existing model-agnostic techniques can be defined for feature groups to assess the grouped feature importance, focusing on permutation-based, refitting, and Shapley-based methods. We also introduce an importance-based sequential procedure that identifies a stable and well-performing combination of features in the grouped feature space. Furthermore, we introduce the combined features effect plot, which is a technique to visualize the effect of a group of features based on a sparse, interpretable linear combination of features. We used simulation studies and real data examples to analyze, compare, and discuss these methods.

Patients with advanced Parkinson’s disease regularly experience unstable motor states. Objective and reliable monitoring of these fluctuations is an unmet need. We used deep learning to classify motion data from a single wrist-worn IMU sensor recording in unscripted environments. For validation purposes, patients were accompanied by a movement disorder expert, and their motor state was passively evaluated every minute. We acquired a dataset of 8,661 minutes of IMU data from 30 patients, with annotations about the motor state (OFF,ON, DYSKINETIC) based on MDS-UPDRS global bradykinesia item and the AIMS upper limb dyskinesia item. Using a 1-minute window size as an input for a convolutional neural network trained on data from a subset of patients, we achieved a three-class balanced accuracy of 0.654 on data from previously unseen subjects. This corresponds to detecting the OFF, ON, or DYSKINETIC motor state at a sensitivity/specificity of 0.64/0.89, 0.67/0.67 and 0.64/0.89, respectively. On average, the model outputs were highly correlated with the annotation on a per subject scale (r = 0.83/0.84; p < 0.0001), and sustained so for the highly resolved time windows of 1 minute (r = 0.64/0.70; p < 0.0001). Thus, we demonstrate the feasibility of long-term motor-state detection in a free-living setting with deep learning using motion data from a single IMU.

Handwriting is one of the most frequently occurring patterns in everyday life and with it comes challenging applications such as handwriting recognition, writer identification and signature verification. In contrast to offline HWR that only uses spatial information (i.e., images), online HWR uses richer spatio-temporal information (i.e., trajectory data or inertial data). While there exist many offline HWR datasets, there are only little data available for the development of OnHWR methods on paper as it requires hardware-integrated pens. This paper presents data and benchmark models for real-time sequence-to-sequence learning and single character-based recognition. Our data are recorded by a sensor-enhanced ballpoint pen, yielding sensor data streams from triaxial accelerometers, a gyroscope, a magnetometer and a force sensor at 100 Hz. We propose a variety of datasets including equations and words for both the writer-dependent and writer-independent tasks. Our datasets allow a comparison between classical OnHWR on tablets and on paper with sensor-enhanced pens. We provide an evaluation benchmark for seq2seq and single character-based HWR using recurrent and temporal convolutional networks and transformers combined with a connectionist temporal classification (CTC) loss and cross-entropy (CE) losses. Our convolutional network combined with BiLSTMs outperforms transformer-based architectures, is on par with InceptionTime for sequence-based classification tasks and yields better results compared to 28 state-of-the-art techniques. Time-series augmentation methods improve the sequence-based task, and we show that CE variants can improve the single classification task. Our implementations together with the large benchmark of state-of-the-art techniques of novel OnHWR datasets serve as a baseline for future research in the area of OnHWR on paper.

This study analyzed highly correlated, feature-rich datasets from hyperspectral remote sensing data using multiple statistical and machine-learning methods. The effect of filter-based feature selection methods on predictive performance was compared. In addition, the effect of multiple expert-based and data-driven feature sets, derived from the reflectance data, was investigated. Defoliation of trees (%), derived from in situ measurements from fall 2016, was modeled as a function of reflectance. Variable importance was assessed using permutation-based feature importance. Overall, the support vector machine (SVM) outperformed other algorithms, such as random forest (RF), extreme gradient boosting (XGBoost), and lasso (L1) and ridge (L2) regressions by at least three percentage points. The combination of certain feature sets showed small increases in predictive performance, while no substantial differences between individual feature sets were observed. For some combinations of learners and feature sets, filter methods achieved better predictive performances than using no feature selection. Ensemble filters did not have a substantial impact on performance. The most important features were located around the red edge. Additional features in the near-infrared region (800–1000 nm) were also essential to achieve the overall best performances. Filter methods have the potential to be helpful in high-dimensional situations and are able to improve the interpretation of feature effects in fitted models, which is an essential constraint in environmental modeling studies. Nevertheless, more training data and replication in similar benchmarking studies are needed to be able to generalize the results.

Background Distributed statistical analyses provide a promising approach for privacy protection when analyzing data distributed over several databases. Instead of directly operating on data, the analyst receives anonymous summary statistics, which are combined into an aggregated result. Further, in discrimination model (prognosis, diagnosis, etc.) development, it is key to evaluate a trained model w.r.t. to its prognostic or predictive performance on new independent data. For binary classification, quantifying discrimination uses the receiver operating characteristics (ROC) and its area under the curve (AUC) as aggregation measure. We are interested to calculate both as well as basic indicators of calibration-in-the-large for a binary classification task using a distributed and privacy-preserving approach. Methods We employ DataSHIELD as the technology to carry out distributed analyses, and we use a newly developed algorithm to validate the prediction score by conducting distributed and privacy-preserving ROC analysis. Calibration curves are constructed from mean values over sites. The determination of ROC and its AUC is based on a generalized linear model (GLM) approximation of the true ROC curve, the ROC-GLM, as well as on ideas of differential privacy (DP). DP adds noise (quantified by the ℓ 2 sensitivity Δ 2 ( f ^ ) ) to the data and enables a global handling of placement numbers. The impact of DP parameters was studied by simulations. Results In our simulation scenario, the true and distributed AUC measures differ by Δ AUC < 0.01 depending heavily on the choice of the differential privacy parameters. It is recommended to check the accuracy of the distributed AUC estimator in specific simulation scenarios along with a reasonable choice of DP parameters. Here, the accuracy of the distributed AUC estimator may be impaired by too much artificial noise added from DP. Conclusions The applicability of our algorithms depends on the ℓ 2 sensitivity Δ 2 ( f ^ ) of the underlying statistical/predictive model. The simulations carried out have shown that the approximation error is acceptable for the majority of simulated cases. For models with high Δ 2 ( f ^ ) , the privacy parameters must be set accordingly higher to ensure sufficient privacy protection, which affects the approximation error. This work shows that complex measures, as the AUC, are applicable for validation in distributed setups while preserving an individual’s privacy.

Increasing availability of large routinely collected datasets presents many possibilities to answer more questions about health and disease, and at a faster pace. These opportunities are exciting, but, without the necessary expertise, well intentioned researchers can unwittingly fall into traps that make their work indistinguishable from that of less well meaning researchers. This article describes important challenges that arise in the analysis of routinely collected data and offers mitigation strategies to improve the trustworthiness of experimental and observational studies with the aim of explanation or prediction using classical statistical methods or AI algorithms. It also provides a roadmap to support researchers in conducting analyses on routinely collected data that produce more reliable estimates.

Deep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting unlabeled data, self-supervised learning techniques can improve the performance of machine learning models in the presence of limited labeled data. Although many self-supervised learning methods have been suggested before, they have failed to exploit the unique characteristics of genomic data. Therefore, we introduce Self-GenomeNet , a self-supervised learning technique that is custom-tailored for genomic data. Self-GenomeNet leverages reverse-complement sequences and effectively learns short- and long-term dependencies by predicting targets of different lengths. Self-GenomeNet performs better than other self-supervised methods in data-scarce genomic tasks and outperforms standard supervised training with ~10 times fewer labeled training data. Furthermore, the learned representations generalize well to new datasets and tasks. These findings suggest that Self-GenomeNet is well suited for large-scale, unlabeled genomic datasets and could substantially improve the performance of genomic models. Self-GenomeNet, a self-supervised learning technique, is trained by predicting unlabeled reverse-complement genome sequences of different lengths and improves the performance of models substantially when a limited amount of labeled data is available.

The intentional distortion of test results presents a fundamental problem to self-report-based psychiatric assessment, such as screening for depressive symptoms. The first objective of the study was to clarify whether depressed patients like healthy controls possess both the cognitive ability and motivation to deliberately influence results of commonly used screening measures. The second objective was the construction of a method derived directly from within the test takers’ responses to systematically detect faking behavior. Supervised machine learning algorithms posit the potential to empirically learn the implicit interconnections between responses, which shape detectable faking patterns. In a standardized design, faking bad and faking good were experimentally induced in a matched sample of 150 depressed and 150 healthy subjects. Participants completed commonly used questionnaires to detect depressive and associated symptoms. Group differences throughout experimental conditions were evaluated using linear mixed-models. Machine learning algorithms were trained on the test results and compared regarding their capacity to systematically predict distortions in response behavior in two scenarios: (1) differentiation of authentic patient responses from simulated responses of healthy participants; (2) differentiation of authentic patient responses from dissimulated patient responses. Statistically significant convergence of the test scores in both faking conditions suggests that both depressive patients and healthy controls have the cognitive ability as well as the motivational compliance to alter their test results. Evaluation of the algorithmic capability to detect faking behavior yielded ideal predictive accuracies of up to 89%. Implications of the findings, as well as future research objectives are discussed. Trial Registration The study was pre-registered at the German registry for clinical trials (Deutsches Register klinischer Studien, DRKS; DRKS00007708).

In many application areas, prediction rules trained based on high-dimensional data are subsequently applied to make predictions for observations from other sources, but they do not always perform well in this setting. This is because data sets from different sources can feature (slightly) differing distributions, even if they come from similar populations. In the context of high-dimensional data and beyond, most prediction methods involve one or several tuning parameters. Their values are commonly chosen by maximizing the cross-validated prediction performance on the training data. This procedure, however, implicitly presumes that the data to which the prediction rule will be ultimately applied, follow the same distribution as the training data. If this is not the case, less complex prediction rules that slightly underfit the training data may be preferable. Indeed, a tuning parameter does not only control the degree of adjustment of a prediction rule to the training data, but also, more generally, the degree of adjustment to the distribution of the training data. On the basis of this idea, in this paper we compare various approaches including new procedures for choosing tuning parameter values that lead to better generalizing prediction rules than those obtained based on cross-validation. Most of these approaches use an external validation data set. In our extensive comparison study based on a large collection of 15 transcriptomic data sets, tuning on external data and robust tuning with a tuned robustness parameter are the two approaches leading to better generalizing prediction rules.