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With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when…

Tree methods (recursive partitioning) are a popular class of nonparametric methods for analyzing data. One extension of the basic tree methodology is the survival tree, which applies recursive partitioning to censored survival data. There…

Decision-making in complex systems often relies on machine learning models, yet highly accurate models such as XGBoost and neural networks can obscure the reasoning behind their predictions. In operations research applications,…

Random survival forest and survival trees are popular models in statistics and machine learning. However, there is a lack of general understanding regarding consistency, splitting rules and influence of the censoring mechanism. In this…

Survival analysis is a critical tool for the modelling of time-to-event data, such as life expectancy after a cancer diagnosis or optimal maintenance scheduling for complex machinery. However, current neural network models provide an…

A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…

Kernel survival analysis models estimate individual survival distributions with the help of a kernel function, which measures the similarity between any two data points. Such a kernel function can be learned using deep kernel survival…

Precision oncology aims to prescribe the optimal cancer treatment to the right patients, maximizing therapeutic benefits. However, identifying patient subgroups that may benefit more from experimental cancer treatments based on randomized…

The analysis of DNA sequences has become critical in numerous fields, from evolutionary biology to understanding gene regulation and disease mechanisms. While deep neural networks can achieve remarkable predictive performance, they…

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…

Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as…

Death has long been overlooked in evolutionary algorithms. Recent research has shown that death (when applied properly) can benefit the overall fitness of a population and can outperform sub-sections of a population that are "immortal" when…

Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

The modeling of time-to-event data, also known as survival analysis, requires specialized methods that can deal with censoring and truncation, time-varying features and effects, and that extend to settings with multiple competing events.…

This paper describes techniques for growing classification and regression trees designed to induce visually interpretable trees. This is achieved by penalizing splits that extend the subset of features used in a particular branch of the…

Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…

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…

With the advent of highly predictive but opaque deep learning models, it has become more important than ever to understand and explain the predictions of such models. Existing approaches define interpretability as the inverse of complexity…

Discrimination and calibration represent two important properties of survival analysis, with the former assessing the model's ability to accurately rank subjects and the latter evaluating the alignment of predicted outcomes with actual…

The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…