Publications

Application-driven validation of posteriors in inverse problems
January 2025 Elsevier
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Understanding metric-related pitfalls in image analysis validation
January 2024 Nature methods
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Through the Eyes of the Expert: Aligning Human and Machine Attention for Industrial AI
January 2024 International Conference on Human-Computer Interaction
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Provably Better Explanations with Optimized Aggregation of Feature Attributions
January 2024 International Conference on Machine Learning
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Metrics reloaded: recommendations for image analysis validation
January 2024 Nature Publishing Group US New York
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How to Leverage Predictive Uncertainty Estimates for Reducing Catastrophic Forgetting in Online Continual Learning
January 2024 arXiv preprint arXiv:2407.07668
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Federated Continual Learning Goes Online: Leveraging Uncertainty for Modality-Agnostic Class-Incremental Learning
January 2024 arXiv preprint arXiv:2405.18925
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Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings
January 2024 Nature Publishing Group UK London
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Explanatory Model Monitoring to Understand the Effects of Feature Shifts on Performance
January 2024 Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining
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Disentangling Mean Embeddings for Better Diagnostics of Image Generators
January 2024
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Consistent and Asymptotically Unbiased Estimation of Proper Calibration Errors
January 2024 International Conference on Artificial Intelligence and Statistics
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A Bias-Variance-Covariance Decomposition of Kernel Scores for Generative Models
January 2024 International Conference on Machine Learning
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Uncertainty Estimates of Predictions via a General Bias-Variance Decomposition
January 2023 International Conference on Artificial Intelligence and Statistics
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Test Time Augmentation Meets Post-hoc Calibration: Uncertainty Quantification under Real-World Conditions
January 2023 Proceedings of the AAAI Conference on Artificial Intelligence
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Multimodal analysis methods in predictive biomedicine
January 2023 Computational and structural biotechnology journal
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Encoding domain knowledge in multi-view latent variable models: A bayesian approach with structured sparsity
January 2023 International Conference on Artificial Intelligence and Statistics
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The proteogenomic subtypes of acute myeloid leukemia
January 2022 Cancer Cell
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Single cell analyses identify a highly regenerative and homogenous human CD34+ hematopoietic stem cell population
January 2022 Nature communications
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Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer
January 2022 Cancer Cell
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Better uncertainty calibration via proper scores for classification and beyond
January 2022
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Towards trustworthy predictions from deep neural networks with fast adversarial calibration
January 2021 Thirty-Fifth AAAI Conference on Artificial Intelligence
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Parameterized Temperature Scaling for Boosting the Expressive Power in Post-Hoc Uncertainty Calibration
January 2021 arXiv preprint arXiv:2102.12182
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Multi-output Gaussian Processes for uncertainty-aware recommender systems
January 2021 Uncertainty in Artificial Intelligence
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Hierarchical Domain Invariant Variational Auto-Encoding with weak domain supervision
January 2021 arXiv preprint arXiv:2101.09436
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TIMELY: Improving Labeling Consistency in Medical Imaging for Cell Type Classification
January 2020 arXiv preprint arXiv:2007.05307
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
January 2020 Nature communications
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Post-hoc Uncertainty Calibration for Domain Drift Scenarios
January 2020 arXiv preprint arXiv:2012.10988
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Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification
January 2019 BioRxiv
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Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate
January 2019 The EMBO journal
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Document informed neural autoregressive topic models with distributional prior
January 2019 Proceedings of the AAAI Conference on Artificial Intelligence
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Ano-rectal wall dose-surface maps localize the dosimetric benefit of hydrogel rectum spacers in prostate cancer radiotherapy
January 2019 Clinical and translational radiation oncology
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Texttovec: Deep contextualized neural autoregressive topic models of language with distributed compositional prior
January 2018 arXiv preprint arXiv:1810.03947
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texttovec: Deep contextualized neural autoregressive models of language with distributed compositional prior
January 2018 Preprint arxiv
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Multi-Omics Factor Analysis—a framework for unsupervised integration of multi-omics data sets
January 2018 Molecular systems biology
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Document informed neural autoregressive topic models
January 2018 arXiv preprint arXiv:1808.03793
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Design and selection of machine learning methods using radiomics and dosiomics for normal tissue complication probability modeling of xerostomia
January 2018 Frontiers in oncology
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Vitamin A-retinoic acid signaling regulates hematopoietic stem cell dormancy
January 2017 Cell
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Prospective identification of hematopoietic lineage choice by deep learning
January 2017 Nature methods
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Parotid gland mean dose as a xerostomia predictor in low-dose domains
January 2017 Acta Oncologica
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Non-targeted metabolomic approach reveals two distinct types of metabolic responses to telomerase dysfunction in S. cerevisiae
January 2017 Metabolomics
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f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq
January 2017 Genome biology
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cgcorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics
January 2017 Physical biology
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A divergent population of autoantigen-responsive CD4+ T cells in infants prior to β cell autoimmunity
January 2017 Science translational medicine
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Unbiased prediction and feature selection in high-dimensional survival regression
January 2016 Journal of Computational Biology
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destiny: diffusion maps for large-scale single-cell data in R
January 2016 Bioinformatics
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Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells
January 2015 Genome biology
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RAMONA: a Web application for gene set analysis on multilevel omics data
January 2015 Bioinformatics
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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
January 2015 Jama
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Diffusion maps for high-dimensional single-cell analysis of differentiation data
January 2015 Bioinformatics
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Decoding the regulatory network of early blood development from single-cell gene expression measurements
January 2015 Nature biotechnology
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Computational assignment of cell-cycle stage from single-cell transcriptome data
January 2015 Methods
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Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
January 2015 Nature biotechnology
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Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations
January 2015 Cell stem cell
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Two non-parametric methods for derivation of constraints from radiotherapy dose–histogram data
January 2014 Physics in Medicine & Biology
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Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
January 2014 Bioinformatics
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Molecular phenotypic profiling of a Saccharomyces cerevisiae strain at the single-cell level
January 2014 Analyst
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Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes
January 2014
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Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
January 2013 Nature cell biology
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A modular framework for gene set analysis integrating multilevel omics data
January 2013 Nucleic acids research
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The dose–response of the anal sphincter region–an analysis of data from the MRC RT01 trial
January 2012 Radiotherapy and Oncology
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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
January 2012 Radiotherapy and Oncology
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A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
January 2012 Bioinformatics
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Modeling late rectal toxicities based on a parameterized representation of the 3D dose distribution
January 2011 Physics in Medicine & Biology
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Using Bayesian logistic regression to evaluate a new type of dosimetric constraint for prostate radiotherapy treatment planning
January 2010 Medical physics
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Using dose-surface maps to predict radiation-induced rectal bleeding: a neural network approach
January 2009 Physics in Medicine & Biology
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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)
January 2009 Physics in Medicine & Biology
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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
January 2008 Medical physics
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Optical trapping dynamics for cell identification
January 2006 Optical Trapping and Optical Micromanipulation III
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