Publications

Preprints / Under Review

1. Carbon footprint driven deep learning model selection for medical imaging
   In OpenReview, 2021. (link)
   
2. Deep ensemble model for segmenting microscopy images in the presence of limited labeled data
   In OpenReview, 2021. (link)
   
3. Automatic airway segmentation from Computed Tomography using robust and efficient 3-D convolutional neural networks
   In Arxiv, 2021. (link)
   
4. Dynamic β-VAEs for quantifying biodiversity by clustering optically recorded insect signals
   In Arxiv, 2021. (link)
   
5. Locomotor deficits in ALS mice are paralleled by loss of V1-interneuron-connections onto fast motor neurons
   In BioRxiv, 2020. (link)
   

Journal Articles

1. Detection of foraging behavior from accelerometer data using U-Net type convolutional networks
   In Ecological Informatics, 2021. (link)
   
2. Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients
   In Scientific Reports, 2021. (link)
   
3. Locally orderless tensor networks for classifying two- and three-dimensional medical images
   In The Journal of Machine Learning for Biomedical Imaging, 2020. (link)
   
4. Graph Refinement based Airway Extraction using Mean-Field Networks and Graph Neural Networks
   In Medical Image Analysis, 2020. (link)
   
5. Segmentation of roots in soil with U-Net
   In Journal of Plant Methods, 2019. (link)
   
6. Increasing Accuracy of Optimal Surfaces Using Min-Marginal Energies
   In IEEE transactions on medical imaging, 2019. (link)
   
7. Extracting tree-structures in CT data by tracking multiple statistically ranked hypotheses
   In the International Journal of Medical Physics Research and Practice, 2019. (link)
   
8. A batch algorithm for estimating trajectories of point targets using expectation maximization
   In IEEE Transactions on Signal Processing, 2016. (link)
   

Refereed Conference/Workshop Papers

1. Segmenting two-dimensional structures with strided tensor networks
   In 27th international conference on Information Processing in Medical Imaging (IPMI), 2021. (link)
   
2. Multi-layered tensor networks for image classification
   In First Workshop on Quantum Tensor Networks in Machine Learning. In conjunction with 34th NeurIPS, 2020., 2020. (link)
   
3. Characterising the Atomic Structure of Mono-Metallic Nanoparticles from X-Ray Scattering Data Using Conditional Generative Models
   In 16th International Workshop on Mining and Learning with Graphs, 2020. (link)
   
4. Uncertainty quantification in medical image segmentation with Normalizing Flows
   In 11th International Workshop on Machine Learning in Medical Imaging, 2020. (link)
   
5. Carbontracker: Tracking and Predicting the Carbon Footprint of Training Deep Learning Models
   In ICML Workshop on Challenges in Deploying and monitoring Machine Learning Systems, 2020. (link)
   
6. Lung Segmentation from Chest X-rays using Variational Data Imputation
   In ICML Workshop on The Art of Learning with Missing Values (Artemiss-2020), 2020. (link)
   
7. Tensor Networks for Medical Image Classification
   In the proceedings of International Conference on Medical Imaging with Deep Learning (MIDL). Winner of Runner-up Best Paper Award., 2020. (link)
   
8. A joint 3D UNet-Graph Neural Network-based method for Airway Segmentation from chest CTs
   In the proceedings of International Workshop on Machine Learning in Medical Imaging, 2019. (link)
   
9. Mean field network based graph refinement with application to airway tree extraction
   In the proceedings of 21st Conference on Medical Image Computing & Computer Assisted Intervention (MICCAI 2018), Grenada, Spain, 2018. (link)
   
10. Extraction of Airways using Graph Neural Networks
    In the proceedings of 1st Conference on Medical Imaging with Deep Learning (MIDL 2018), Amsterdam., 2018. (link)
    
11. Extraction of airways with probabilistic state-space models and Bayesian smoothing
    In the proceedings of Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics, 2017. (link)
    
12. Extraction of airway trees using multiple hypothesis tracking and template matching
    In the proceedings of The Sixth International Workshop on Pulmonary Image Analysis. MICCAI, 2016. (link)
    

Reports

1. Extraction of Airways from Volumetric Data
   In University of Copenhagen (PhD Thesis), 2018. (link)
   
2. Bayesian tracking of multiple point targets using expectation maximization
   In Chalmers University (MSc Thesis), 2015. (link)