Publications

Understanding metric-related pitfalls in image analysis validation
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Through the Eyes of the Expert: Aligning Human and Machine Attention for Industrial AI
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Provably Better Explanations with Optimized Aggregation of Feature Attributions
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How to Leverage Predictive Uncertainty Estimates for Reducing Catastrophic Forgetting in Online Continual Learning
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Federated Continual Learning Goes Online: Leveraging Uncertainty for Modality-Agnostic Class-Incremental Learning
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Explanatory Model Monitoring to Understand the Effects of Feature Shifts on Performance
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Consistent and Asymptotically Unbiased Estimation of Proper Calibration Errors
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Uncertainty Estimates of Predictions via a General Bias-Variance Decomposition
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Test Time Augmentation Meets Post-hoc Calibration: Uncertainty Quantification under Real-World Conditions
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Multimodal analysis methods in predictive biomedicine
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Metrics reloaded: Recommendations for image analysis validation. arXiv 2023
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Encoding Domain Knowledge in Multi-view Latent Variable Models: A Bayesian Approach with Structured Sparsity
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A Bias-Variance-Covariance Decomposition of Kernel Scores for Generative Models
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The proteogenomic subtypes of acute myeloid leukemia
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Single cell analyses identify a highly regenerative and homogenous human CD34+ hematopoietic stem cell population
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Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer
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Better Uncertainty Calibration via Proper Scores for Classification and Beyond
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Towards trustworthy predictions from deep neural networks with fast adversarial calibration
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Parameterized Temperature Scaling for Boosting the Expressive Power in Post-Hoc Uncertainty Calibration
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Multi-output Gaussian Processes for uncertainty-aware recommender systems
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Hierarchical Domain Invariant Variational Auto-Encoding with weak domain supervision
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TIMELY: Improving Labeling Consistency in Medical Imaging for Cell Type Classification
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
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Post-hoc Uncertainty Calibration for Domain Drift Scenarios
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Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification
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Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate
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Document informed neural autoregressive topic models with distributional prior
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Ano-rectal wall dose-surface maps localize the dosimetric benefit of hydrogel rectum spacers in prostate cancer radiotherapy
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Texttovec: Deep contextualized neural autoregressive topic models of language with distributed compositional prior
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texttovec: Deep contextualized neural autoregressive models of language with distributed compositional prior
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Multi-Omics Factor Analysis—a framework for unsupervised integration of multi-omics data sets
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Document informed neural autoregressive topic models
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Design and selection of machine learning methods using radiomics and dosiomics for normal tissue complication probability modeling of xerostomia
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Vitamin A-retinoic acid signaling regulates hematopoietic stem cell dormancy
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Prospective identification of hematopoietic lineage choice by deep learning
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Parotid gland mean dose as a xerostomia predictor in low-dose domains
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Non-targeted metabolomic approach reveals two distinct types of metabolic responses to telomerase dysfunction in S. cerevisiae
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f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq
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cgcorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics
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A divergent population of autoantigen-responsive CD4+ T cells in infants prior to β cell autoimmunity
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Unbiased prediction and feature selection in high-dimensional survival regression
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destiny: diffusion maps for large-scale single-cell data in R
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Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells
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RAMONA: a Web application for gene set analysis on multilevel omics data
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Effects of high-dose oral insulin on immune responses in children at high risk for type 1 diabetes: the Pre-POINT randomized clinical trial
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Diffusion maps for high-dimensional single-cell analysis of differentiation data
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Decoding the regulatory network of early blood development from single-cell gene expression measurements
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Computational assignment of cell-cycle stage from single-cell transcriptome data
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Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
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Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations
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Two non-parametric methods for derivation of constraints from radiotherapy dose–histogram data
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Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
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Molecular phenotypic profiling of a Saccharomyces cerevisiae strain at the single-cell level
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Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes
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Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
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A modular framework for gene set analysis integrating multilevel omics data
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The dose–response of the anal sphincter region–an analysis of data from the MRC RT01 trial
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Novel approaches to improve the therapeutic index of head and neck radiotherapy: an analysis of data from the PARSPORT randomised phase III trial
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A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
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Modeling late rectal toxicities based on a parameterized representation of the 3D dose distribution
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Using Bayesian logistic regression to evaluate a new type of dosimetric constraint for prostate radiotherapy treatment planning
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Using dose-surface maps to predict radiation-induced rectal bleeding: a neural network approach
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Assessing correlations between the spatial distribution of the dose to the rectal wall and late rectal toxicity after prostate radiotherapy: an analysis of data from the MRC RT01 trial (ISRCTN 47772397)
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Dosimetric impact of motion in free-breathing and gated lung radiotherapy: A 4D Monte Carlo study of intrafraction and interfraction effects
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Optical trapping dynamics for cell identification
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