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List of works by Ole Winther

A Deep Learning Approach to Identify Local Structures in Atomic-Resolution Transmission Electron Microscopy Images

article

A Disentangled Recognition and Nonlinear Dynamics Model for Unsupervised Learning ⬇️

article

A Mean Field Algorithm for Bayes Learning in Large Feed-forward Neural Networks ⬇️

article

A QUANTITATIVE STUDY OF PRUNING BY OPTIMAL BRAIN DAMAGE

scientific article (publication date: June 1993)

A Theory of Solving TAP Equations for Ising Models with General Invariant Random Matrices ⬇️

scientific article published on 28 March 2016

A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

scientific article published on 9 December 2015

A hierarchical model for ordinal matrix factorization

scientific article published on 23 June 2011

Adaptive and self-averaging Thouless-Anderson-Palmer mean-field theory for probabilistic modeling

scientific article published on 30 October 2001

Addressing caveats of neural persistence with deep graph persistence ⬇️

scientific article published on 20 July 2023

Airway Inflammation in Chronic Rhinosinusitis with Nasal Polyps and Asthma: The United Airways Concept Further Supported

scientific article published on July 2015

Aligning Optimization Trajectories with Diffusion Models for Constrained Design Generation ⬇️

scientific article published on 29 May 2023

An Adaptive Resample-Move Algorithm for Estimating Normalizing Constants ⬇️

scientific article published on 15 August 2016

An automated approach for annual layer counting in ice cores

An automated approach for annual layer counting in ice cores

An introduction to Deep learning on biological sequence data - Examples and solutions

scientific article published on 23 August 2017

Angiotensinogen and HLA class II predict bevacizumab response in recurrent glioblastoma patients

scientific article published on 26 May 2016

Autoencoding beyond pixels using a learned similarity metric ⬇️

Auxiliary Deep Generative Models ⬇️

scientific article (publication date: 16 June 2016)

BIVA: A Very Deep Hierarchy of Latent Variables for Generative Modeling ⬇️

BayesMD: flexible biological modeling for motif discovery

scientific article published in December 2008

Bayesian Inference for Structured Spike and Slab Priors ⬇️

scientific article 2014 NIPS version

Bayesian Non-negative Matrix Factorization

scientific article published on 2009

Bayesian Sparse Factor Models and DAGs Inference and Comparison ⬇️

Bayesian Structure Learning for Dynamic Brain Connectivity ⬇️

scientific article published in April 2018

Bayesian independent component analysis: Variational methods and non-negative decompositions

Bayesian inference for spatio-temporal spike and slab priors ⬇️

long version on 48 pages

Bayesian leave-one-out cross-validation approximations for Gaussian latent variable models ⬇️

scientific article published on 23 May 2016

Binning microbial genomes using deep learning

scholarly article published 10 December 2018

Bioinformatics for cancer immunotherapy target discovery

scientific article

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

scientific article published on 26 October 2015

Bloodspot: A Web Resource Facilitating the Analysis of Transcriptional Programs in Normal and Malignant Hematopoiesis ⬇️

scholarly article

Bone signaling in middle ear development: a genome-wide differential expression analysis.

scientific article published on 16 July 2014

COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes

scientific article (preprint)

Calibrated uncertainty for molecular property prediction using ensembles of message passing neural networks

scientific article published on 22 December 2021

Can large language models reason about medical questions? ⬇️

scientific article published on 17 July 2022

Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin

scientific article published on 19 March 2015

Cellular origin of prognostic chromosomal aberrations in AML patients

scientific article published on 11 February 2015

Closing the Dequantization Gap: PixelCNN as a Single-Layer Flow ⬇️

scientific article published in November 2020

CloudScan - A configuration-free invoice analysis system using recurrent neural networks ⬇️

scientific article published on 24 August 2017

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

scientific article

Comparison of Neural Network Error Measures for Simulation of Slender Marine Structures

Competence Classification of Cumulus and Granulosa Cell Transcriptome in Embryos Matched by Morphology and Female Age.

scientific article

Computing the Minimum-Phase Filter Using the QL-Factorization

Computing with Finite and Infinite Networks ⬇️

Convolutional LSTM Networks for Subcellular Localization of Proteins ⬇️

scientific article (publication date: 2015)

Daily estimates of clinical severity of symptoms in bipolar disorder from smartphone-based self-assessments

scientific article published on 18 June 2020

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data

scientific article published on 08 July 2019

Deep Belief Nets for Topic Modeling ⬇️

scientific article published on 18 January 2015

Deep Generative Models for Molecular Science

scientific article

Deep Learning for Diagnostic Binary Classification of Multiple-Lesion Skin Diseases

scientific article published on 22 September 2020

Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction

scholarly article by Alexander Rosenberg Johansen et al published 2017 in Proceedings of the 8th ACM International Conference on Bioinformatics

Deep learning for automated drivetrain fault detection

scholarly article by Martin Bach-Andersen et al published 5 October 2017 in Wind Energy

DeepLoc 2.1: multi-label membrane protein type prediction using protein language models

scientific article published in 2024

DeepLoc: prediction of protein subcellular localization using deep learning

scientific article published on 7 July 2017

DeepLoc: prediction of protein subcellular localization using deep learning

scientific article

DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning

scholarly article

DermX: An end-to-end framework for explainable automated dermatological diagnosis

Detecting sequence signals in targeting peptides using deep learning

scientific article published on 30 September 2019

DiffEnc: Variational Diffusion with a Learned Encoder ⬇️

scientific article published on 30 October 2023

Differential gene expression in the otic capsule and the middle ear--an annotation of bone-related signaling genes

scientific article

DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

scientific article published in 2024

Discovery of regulatory elements is improved by a discriminatory approach

scientific article

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1.

scientific article

Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma

scientific article

Dynamical Functional Theory for Compressed Sensing ⬇️

scientific article published on 11 May 2017

Dynamical functional theory for compressed sensing

Efficient approaches to Gaussian process classification ⬇️

scientific article published on 2000

End-to-End Information Extraction without Token-Level Supervision ⬇️

scientific article published on 16 July 2017

Ensemble Learning and Linear Response Theory for ICA ⬇️

Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells

scientific article

Evaluation of the Influence of Uncertain Forward Models on the EEG Source Reconstruction Problem

Expectation Consistent Free Energies for Approximate Inference ⬇️

FindZebra - the search engine for difficult medical cases.

scientific article

FindZebra Online Search Delving into Rare Disease Case Reports Using Natural Language Processing

scientific article published in January 2022

FindZebra online search delving into rare disease case reports using natural language processing

scientific article published on 29 June 2023

FindZebra: A search engine for rare diseases

scientific article (publication date: June 2013)

Flexible and efficient implementations of Bayesian independent component analysis

Forecasting Mood in Bipolar Disorder From Smartphone Self-assessments: Hierarchical Bayesian Approach

scientific article published on 01 April 2020

Gaussian Process Based Independent Analysis for Temporal Source Separation in fMRI

scientific article (publication date: February 2017)

Gene expression of the endolymphatic sac.

scientific article published on 23 October 2011

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

scientific article

Graph neural network interatomic potential ensembles with calibrated aleatoric and epistemic uncertainty on energy and forces

scientific article published in January 2023

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

scientific article

Hash Embeddings for Efficient Word Representations ⬇️

HemaExplorer: a Web server for easy and fast visualization of gene expression in normal and malignant hematopoiesis

article

HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

scientific article published on 9 November 2012

Hemaexplorer 2.0: A Free Access Internet Platform For Visualization Of Gene Expression In AML Patients and The Normal Hematopoietic Hierarchy ⬇️

scholarly article

Hierarchical Bayesian model for simultaneous EEG source and forward model reconstruction (SOFOMORE)

article

Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools ⬇️

scientific article published on 24 November 2020

Image-free Classifier Injection for Zero-Shot Classification ⬇️

scientific article published on 21 August 2023

Improved metagenome binning and assembly using deep variational autoencoders

scientific article

Improving The Analysis Of Gene Expression Profiles By Comparing AML Blasts With Their Nearest Normal Counterparts ⬇️

scholarly article

Improving on Expectation Propagation ⬇️

Incremental Gaussian Processes ⬇️

scholarly article by Joaquin Quiñonero Candela & Ole Winther published 2003 in Advances in Neural Information Processing Systems 15

Independent component analysis for understanding multimedia content

scientific article (publication date: 7 November 2002)

Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection

scientific article

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

scientific article

Joint Iterative Carrier Synchronization and Signal Detection Employing Expectation Maximization

Ladder Variational Autoencoders ⬇️

scientific article published on 27 May 2016

Large-scale Automated Analysis of High-Resolution Transmission Electron Microscopy Data Assisted by Deep Learning Neural Networks

scientific article published in 2022

Literature classification for semi-automated updating of biological knowledgebases

scientific article published on 16 October 2013

Low complexity Bayesian single channel source separation

Mean Field Methods for Classification with Gaussian Processes ⬇️

Mean-field approaches to independent component analysis

scientific article published on April 2002

MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma

scientific article published on 24 December 2013

Molecular signatures of thyroid follicular neoplasia

scientific article

Multivariate Hawkes process models of the occurrence of regulatory elements

scientific article

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

scientific article published on 09 March 2019

Neural Machine Translation with Characters and Hierarchical Encoding ⬇️

scientific article (publication date: 20 October 2016)

Neural Networks and Cellular Automata Complexity ⬇️

scientific article (publication date: 1993)

Nonlinear Impairment Compensation Using Expectation Maximization for PDM 16-QAM Systems

Nonlinear impairment compensation using expectation maximization for dispersion managed and unmanaged PDM 16-QAM transmission

scientific article

On Sphere Detection and Minimum-Phase Prefiltered Reduced-State Sequence Estimation

On the Slow Convergence of EM and VBEM in Low-Noise Linear Models

scientific article published on 01 September 2005

On the Transfer of Disentangled Representations in Realistic Settings ⬇️

scientific article published on 27 October 2020

Optimal Variance Control of the Score Function Gradient Estimator for Importance Weighted Bounds ⬇️

scientific article published on 5 August 2020

Optimal allocation of reviewers for peer feedback

Optimal online learning: a Bayesian approach

scholarly article

Optimization of neural networks for time-domain simulation of mooring lines

PASS-GP: Predictive active set selection for Gaussian processes

Particle Filter Inference in an Articulatory-Based Speech Model

Predictive active set selection methods for Gaussian processes

Protein Secondary Structure Prediction with Long Short Term Memory Networks ⬇️

scientific article published on 4 January 2015

RSK is a principal effector of the RAS-ERK pathway for eliciting a coordinate promotile/invasive gene program and phenotype in epithelial cells

scientific article

Rare Disease Diagnosis as an Information Retrieval Task

Rare disease diagnosis: A review of web search, social media and large-scale data-mining approaches

scientific article

Recurrent Relational Networks ⬇️

Reducing the rate and duration of Re-ADMISsions among patients with unipolar disorder and bipolar disorder using smartphone-based monitoring and treatment - the RADMIS trials: study protocol for two randomized controlled trials

scientific article

Reducing the rate of psychiatric Re-ADMISsions in Bipolar Disorder using smartphones The RADMIS trial

scientific article published on 23 December 2020

Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm

scientific article published on 27 October 2005

S-AMP for Non-linear Observation Models ⬇️

scientific article published on 25 January 2015

S-AMP for non-linear observation models

S-AMP: Approximate Message Passing for General Matrix Ensembles ⬇️

scientific article published on 12 May 2014

S-AMP: Approximate message passing for general matrix ensembles

SCHA-VAE: Hierarchical Context Aggregation for Few-Shot Generation ⬇️

scientific article published on 23 October 2021

SOFOMORE: Combined EEG source and forward model reconstruction

Scalable Bayesian Modelling of Paired Symbols ⬇️

scientific article published on 10 September 2014

Self-Averaging Expectation Propagation ⬇️

scientific article published on 23 August 2016

Semi-Supervised Generation with Cluster-aware Generative Models ⬇️

scientific article (publication date: 3 April 2017)

Sequential Neural Models with Stochastic Layers ⬇️

scientific article published on 13 November 2016

SignalP 5.0 improves signal peptide predictions using deep neural networks

scientific article published on 18 February 2019

Simultaneous EEG Source and Forward Model Reconstruction (SOFOMORE) Using a Hierarchical Bayesian Approach

scientific article (publication date: October 2010)

Spatio-temporal Spike and Slab Priors for Multiple Measurement Vector Problems ⬇️

scientific article published on 19 August 2015

Specialized tools are needed when searching the web for rare disease diagnoses

scientific article (publication date: 2013)

Statistical modelling for ship propulsion efficiency

SurVAE Flows: Surjections to Bridge the Gap between VAEs and Flows ⬇️

scientific article published in November 2020

Systematic review of machine learning for diagnosis and prognosis in dermatology

scientific article published on 31 October 2019

TAP Gibbs Free Energy, Belief Propagation and Sparsity ⬇️

Teaching computers to fold proteins

scientific article

The Bipolar Illness Onset study: research protocol for the BIO cohort study.

scientific article

The Effect of Correlated Input Data on the Dynamics of Learning ⬇️

article

The middle ear immune defense changes with age.

scientific article published on 07 January 2015

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

scientific article published on 4 August 2023

Tractable Approximations for Probabilistic Models: The Adaptive Thouless-Anderson-Palmer Mean Field Approach

scientific article published in Physical Review Letters

Tractable inference for probabilistic data models

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury

scientific article

Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility

Transition1x - a dataset for building generalizable reactive machine learning potentials

Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

scientific article

Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals

scientific article

Uncertainty-aware and explainable machine learning for early prediction of battery degradation trajectory

scientific article published in January 2023

Unifying Molecular and Textual Representations via Multi-task Language Modelling ⬇️

scientific article published on 29 January 2023

Using Neural Networks to Identify Atoms in HRTEM Images

scholarly article

Variational Linear Response ⬇️

Variational Open-Domain Question Answering ⬇️

scientific article published on 23 September 2022

Voice analysis as an objective state marker in bipolar disorder

scientific article (publication date: 19 July 2016)

scVAE: Variational auto-encoders for single-cell gene expression data

scientific article published on 16 May 2020

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