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Deep learning models for survival analysis have gained significant attention in the literature, but they suffer from severe performance deficits when the dataset contains many irrelevant features. We give empirical evidence for this problem…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Survival analysis is a statistical framework for modeling time-to-event data, particularly valuable in healthcare for predicting outcomes like patient discharge or recurrence. This study implements and compares several survival models -…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
Experts advising decision-makers are likely to display expertise which varies as a function of the problem instance. In practice, this may lead to sub-optimal or discriminatory decisions against minority cases. In this work we model such…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Additive feature explanations using Shapley values have become popular for providing transparency into the relative importance of each feature to an individual prediction of a machine learning model. While Shapley values provide a unique…
We propose a versatile framework for survival analysis that combines advanced concepts from statistics with deep learning. The presented framework is based on piecewise exponential models and thereby supports various survival tasks, such as…
Interpretability of deep learning is widely used to evaluate the reliability of medical imaging models and reduce the risks of inaccurate patient recommendations. For models exceeding human performance, e.g. predicting RNA structure from…
Survival analysis is a hotspot in statistical research for modeling time-to-event information with data censorship handling, which has been widely used in many applications such as clinical research, information system and other fields with…
Predicting the individual risk of a clinical event using the complete patient history is still a major challenge for personalized medicine. Among the methods developed to compute individual dynamic predictions, the joint models have the…
Tree-based methods are popular nonparametric tools in studying time-to-event outcomes. In this article, we introduce a novel framework for survival trees and ensembles, where the trees partition the dynamic survivor population and can…
A new model for generating survival trajectories and data based on applying an autoencoder of a specific structure is proposed. It solves three tasks. First, it provides predictions in the form of the expected event time and the survival…
Machine and deep learning survival models demonstrate similar or even improved time-to-event prediction capabilities compared to classical statistical learning methods yet are too complex to be interpreted by humans. Several model-agnostic…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
The increasing complexity of data requires methods and models that can effectively handle intricate structures, as simplifying them would result in loss of information. While several analytical tools have been developed to work with complex…
Decision trees are prized for their interpretability and strong performance on tabular data. Yet, their reliance on simple axis-aligned linear splits often forces deep, complex structures to capture non-linear feature effects, undermining…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
Survival analysis aims at modeling the relationship between covariates and event occurrence with some untracked (censored) samples. In implementation, existing methods model the survival distribution with strong assumptions or in a discrete…
We introduce a statistical procedure that integrates survival data from multiple biomedical studies, to improve the accuracy of predictions of survival or other events, based on individual clinical and genomic profiles, compared to models…