Protein Graph Neural Networks for Heterogeneous Cryo-EM Reconstruction.

Ozan Öktem https://openreview.net/profile?id=~Ozan_%C3%96ktem1 https://orcid.org/0000-0002-1118-6483 https://www.wikidata.org/entity/Q84870900 https://d-nb.info/gnd/1201580226

Jonathan Krook Axel Janson Joakim Andén Melanie Weber Ozan Öktem Protein Graph Neural Networks for Heterogeneous Cryo-EM Reconstruction. 2026 February abs/2602.21915 CoRR https://doi.org/10.48550/arXiv.2602.21915 db/journals/corr/corr2602.html#abs-2602-21915 streams/journals/corr

Buda Bajic Johannes A. J. Huber Benedikt Neyses Linus Olofsson Ozan Öktem Sparse view tomographic reconstruction of elongated objects using learned primal-dual networks. 112295 2025 162 Eng. Appl. Artif. Intell. https://doi.org/10.1016/j.engappai.2025.112295 db/journals/eaai/eaai162.html#BajicHNOO25 streams/journals/eaai

Erik Jansson Jonathan Krook Klas Modin Ozan Öktem Geometric Shape Matching for Recovering Protein Conformations from Single-Particle Cryo-EM Data. 2509-2546 2025 18 SIAM J. Imaging Sci. 4 https://doi.org/10.1137/24m1704336 db/journals/siamis/siamis18.html#JanssonKMO25 streams/journals/siamis

Jonathan Krook Willem Diepeveen Ozan Öktem Direct Atomistic Reconstruction in Homogeneous Cryo-EM Using Protein Geometry Regularization. 173-184 2025 SSVM (1) https://doi.org/10.1007/978-3-031-92366-1_14 conf/scalespace/2025-1 db/conf/scalespace/ssvm2025-1.html#KrookDO25 streams/conf/scalespace

Aurora Poggi Giuseppe Alessio D'Inverno Hjalmar Brismar Ozan Öktem Matthieu Barreau Kateryna Morozovska Data-driven multi-agent modelling of calcium interactions in cell culture: PINN vs Regularized Least-squares. 2025 May abs/2505.20327 CoRR https://doi.org/10.48550/arXiv.2505.20327 db/journals/corr/corr2505.html#abs-2505-20327 streams/journals/corr

Emanuel Ström Anna-Karin Tornberg Ozan Öktem Deep Micro Solvers for Rough-Wall Stokes Flow in a Heterogeneous Multiscale Method. 2025 July abs/2507.13902 CoRR https://doi.org/10.48550/arXiv.2507.13902 db/journals/corr/corr2507.html#abs-2507-13902 streams/journals/corr

Emilien Valat Ozan Öktem Improving the Generalisation of Learned Reconstruction Frameworks. 2025 November abs/2511.12730 CoRR https://doi.org/10.48550/arXiv.2511.12730 db/journals/corr/corr2511.html#abs-2511-12730 streams/journals/corr

Andreas Hauptmann Ozan Öktem Learned iterative networks: An operator learning perspective. 2025 December abs/2512.08444 CoRR https://doi.org/10.48550/arXiv.2512.08444 db/journals/corr/corr2512.html#abs-2512-08444 streams/journals/corr

Sebastian Banert Jevgenija Rudzusika Ozan Öktem Jonas Adler Accelerated Forward-Backward Optimization Using Deep Learning. 1236-1263 2024 34 SIAM J. Optim. 2 https://doi.org/10.1137/22m1532548 db/journals/siamjo/siamjo34.html#BanertROA24

Jevgenija Rudzusika Buda Bajic Thomas Köhler 0003 Ozan Öktem 3D Helical CT Reconstruction With a Memory Efficient Learned Primal-Dual Architecture. 1414-1424 2024 10 IEEE Trans. Computational Imaging https://doi.org/10.1109/TCI.2024.3463485 db/journals/tci/tci10.html#RudzusikaBKO24 streams/journals/tci

Paul Häusner Ozan Öktem Jens Sjölund Neural incomplete factorization: learning preconditioners for the conjugate gradient method. 2024 2024 Trans. Mach. Learn. Res. https://openreview.net/forum?id=FozLrZ3CI5 db/journals/tmlr/tmlr2024.html#HausnerOS24

Subhadip Mukherjee Sören Dittmer Zakhar Shumaylov Sebastian Lunz Ozan Öktem Carola B. Schönlieb Data-Driven Convex Regularizers for Inverse Problems. 13386-13390 2024 ICASSP https://doi.org/10.1109/ICASSP48485.2024.10447719 conf/icassp/2024 db/conf/icassp/icassp2024.html#MukherjeeDSLOS24

Knut Salomonsson Eric Oldgren Emanuel Ström Ozan Öktem Fast deep learning based reconstruction for limited angle tomography. 2024 abs/2402.12141 CoRR https://doi.org/10.48550/arXiv.2402.12141 db/journals/corr/corr2402.html#abs-2402-12141

Buda Bajic Johannes A. J. Huber Benedikt Neyses Linus Olofsson Ozan Öktem Reconstruction for Sparse View Tomography of Long Objects Applied to Imaging in the Wood Industry. 2024 abs/2403.02820 CoRR https://doi.org/10.48550/arXiv.2403.02820 db/journals/corr/corr2403.html#abs-2403-02820

Erik Jansson Jonathan Krook Klas Modin Ozan Öktem Geometric shape matching for recovering protein conformations from single-particle Cryo-EM data. 2024 abs/2410.00833 CoRR https://doi.org/10.48550/arXiv.2410.00833 db/journals/corr/corr2410.html#abs-2410-00833 streams/journals/corr

Friso de Kruiff Erik J. Bekkers Ozan Öktem Carola-Bibiane Schönlieb Willem Diepeveen Pullback Flow Matching on Data Manifolds. 2024 abs/2410.04543 CoRR https://doi.org/10.48550/arXiv.2410.04543 db/journals/corr/corr2410.html#abs-2410-04543 streams/journals/corr

Emilien Valat Andreas Hauptmann Ozan Öktem Self-Supervised Denoiser Framework. 2024 abs/2411.19593 CoRR https://doi.org/10.48550/arXiv.2411.19593 db/journals/corr/corr2411.html#abs-2411-19593 streams/journals/corr

Thomas Buddenkotte Lorena Escudero Sanchez Mireia Crispin-Ortuzar Ramona Woitek Cathal McCague James D. Brenton Ozan Öktem Evis Sala Leonardo Rundo Calibrating ensembles for scalable uncertainty quantification in deep learning-based medical image segmentation. 107096 2023 September 163 Comput. Biol. Medicine https://doi.org/10.1016/j.compbiomed.2023.107096 db/journals/cbm/cbm163.html#BuddenkotteSCWMBOSR23

Willem Diepeveen Jan Lellmann Ozan Öktem Carola-Bibiane Schönlieb Regularizing Orientation Estimation in Cryogenic Electron Microscopy Three-Dimensional Map Refinement through Measure-Based Lifting over Riemannian Manifolds. 1440-1490 2023 September 16 SIAM J. Imaging Sci. 3 https://doi.org/10.1137/22m1520773 db/journals/siamis/siamis16.html#DiepeveenLOS23

Subhadip Mukherjee Andreas Hauptmann Ozan Öktem Marcelo Pereyra Carola-Bibiane Schönlieb Learned Reconstruction Methods With Convergence Guarantees: A survey of concepts and applications. 164-182 2023 40 IEEE Signal Process. Mag. 1 https://doi.org/10.1109/MSP.2022.3207451 db/journals/spm/spm40.html#MukherjeeHOPS23

Paul Häusner Ozan Öktem Jens Sjölund Neural incomplete factorization: learning preconditioners for the conjugate gradient method. 2023 abs/2305.16368 CoRR https://doi.org/10.48550/arXiv.2305.16368 db/journals/corr/corr2305.html#abs-2305-16368

Willem Diepeveen Carlos Esteve Yagüe Jan Lellmann Ozan Öktem Carola-Bibiane Schönlieb Riemannian geometry for efficient analysis of protein dynamics data. 2023 abs/2308.07818 CoRR https://doi.org/10.48550/arXiv.2308.07818 db/journals/corr/corr2308.html#abs-2308-07818

Chong Chen Runqian Wang Chandrajit Bajaj Ozan Öktem An efficient algorithm to compute the X-ray transform. 1325-1343 2022 99 Int. J. Comput. Math. 7 https://doi.org/10.1080/00207160.2021.1969017 db/journals/ijcm/ijcm99.html#ChenWBO22

Jevgenija Rudzusika Thomas Köhler 0003 Ozan Öktem Deep Learning-Based Dictionary Learning and Tomographic Image Reconstruction. 1729-1764 2022 15 SIAM J. Imaging Sci. 4 https://doi.org/10.1137/21m1445697 db/journals/siamis/siamis15.html#RudzusikaKO22

Emanuel Ström Mats Persson Alma Eguizabal Ozan Öktem Photon-Counting CT Reconstruction With a Learned Forward Operator. 536-550 2022 8 IEEE Trans. Computational Imaging https://doi.org/10.1109/TCI.2022.3183405 db/journals/tci/tci8.html#StromPEO22

Buda Bajic Ozan Öktem Jevgenija Rudzusika 3D helical CT reconstruction with memory efficient invertible Learned Primal-Dual method. 2022 abs/2205.11952 CoRR https://doi.org/10.48550/arXiv.2205.11952 db/journals/corr/corr2205.html#abs-2205-11952

Subhadip Mukherjee Andreas Hauptmann Ozan Öktem Marcelo Pereyra Carola-Bibiane Schönlieb Learned reconstruction with convergence guarantees. 2022 abs/2206.05431 CoRR https://doi.org/10.48550/arXiv.2206.05431 db/journals/corr/corr2206.html#abs-2206-05431

Alma Eguizabal Ozan Öktem Mats U. Persson Deep Learning for Material Decomposition in Photon-Counting CT. 2022 abs/2208.03360 CoRR https://doi.org/10.48550/arXiv.2208.03360 db/journals/corr/corr2208.html#abs-2208-03360

Thomas Buddenkotte Lorena Escudero Sanchez Mireia Crispin-Ortuzar Ramona Woitek Cathal McCague James D. Brenton Ozan Öktem Evis Sala Leonardo Rundo Calibrating Ensembles for Scalable Uncertainty Quantification in Deep Learning-based Medical Segmentation. 2022 abs/2209.09563 CoRR https://doi.org/10.48550/arXiv.2209.09563 db/journals/corr/corr2209.html#abs-2209-09563

Subhadip Mukherjee Marcello Carioni Ozan Öktem Carola-Bibiane Schönlieb End-to-end reconstruction meets data-driven regularization for inverse problems. 21413-21425 2021 NeurIPS https://proceedings.neurips.cc/paper/2021/hash/b2df0a0d4116c55f81fd5aa1ef876510-Abstract.html conf/nips/2021 db/conf/nips/neurips2021.html#MukherjeeCOS21 Subhadip Mukherjee Ozan Öktem Carola-Bibiane Schönlieb Adversarially Learned Iterative Reconstruction for Imaging Inverse Problems. 540-552 2021 SSVM https://doi.org/10.1007/978-3-030-75549-2_43 conf/scalespace/2021 db/conf/scalespace/ssvm2021.html#MukherjeeOS21

Subhadip Mukherjee Ozan Öktem Carola-Bibiane Schönlieb Adversarially learned iterative reconstruction for imaging inverse problems. 2021 abs/2103.16151 CoRR https://arxiv.org/abs/2103.16151 db/journals/corr/corr2103.html#abs-2103-16151

Subhadip Mukherjee Marcello Carioni Ozan Öktem Carola-Bibiane Schönlieb End-to-end reconstruction meets data-driven regularization for inverse problems. 2021 abs/2106.03538 CoRR https://arxiv.org/abs/2106.03538 db/journals/corr/corr2106.html#abs-2106-03538

Héctor Andrade-Loarca Gitta Kutyniok Ozan Öktem Philipp Petersen Deep Microlocal Reconstruction for Limited-Angle Tomography. 2021 abs/2108.05732 CoRR https://arxiv.org/abs/2108.05732 db/journals/corr/corr2108.html#abs-2108-05732

Jevgenija Rudzusika Thomas Koehler 0003 Ozan Öktem Deep learning based dictionary learning and tomographic image reconstruction. 2021 abs/2108.11730 CoRR https://arxiv.org/abs/2108.11730 db/journals/corr/corr2108.html#abs-2108-11730

Sebastian Banert Axel Ringh Jonas Adler Johan Karlsson Ozan Öktem Data-Driven Nonsmooth Optimization. 102-131 2020 30 SIAM J. Optim. 1 https://doi.org/10.1137/18M1207685 https://www.wikidata.org/entity/Q126402908 db/journals/siamjo/siamjo30.html#BanertRAKO20

Andreas Hauptmann Jonas Adler Simon R. Arridge Ozan Öktem Multi-Scale Learned Iterative Reconstruction. 843-856 2020 6 IEEE Trans. Computational Imaging https://doi.org/10.1109/TCI.2020.2990299 db/journals/tci/tci6.html#HauptmannAAO20

Andreas Hauptmann Ozan Öktem Carola Schönlieb Image reconstruction in dynamic inverse problems with temporal models. 2020 abs/2007.10238 CoRR https://arxiv.org/abs/2007.10238 db/journals/corr/corr2007.html#abs-2007-10238

Subhadip Mukherjee Sören Dittmer Zakhar Shumaylov Sebastian Lunz Ozan Öktem Carola-Bibiane Schönlieb Learned convex regularizers for inverse problems. 2020 abs/2008.02839 CoRR https://arxiv.org/abs/2008.02839 db/journals/corr/corr2008.html#abs-2008-02839

Simon R. Arridge Peter Maass Ozan Öktem Carola-Bibiane Schönlieb Solving inverse problems using data-driven models. 1-174 2019 28 Acta Numer. https://doi.org/10.1017/S0962492919000059 db/journals/actanum/actanum28.html#ArridgeMOS19

Chong Chen Barbara Gris Ozan Öktem A New Variational Model for Joint Image Reconstruction and Motion Estimation in Spatiotemporal Imaging. 1686-1719 2019 12 SIAM J. Imaging Sci. 4 https://doi.org/10.1137/18M1234047 https://www.wikidata.org/entity/Q127013371 db/journals/siamis/siamis12.html#ChenGO19

Héctor Andrade-Loarca Gitta Kutyniok Ozan Öktem Philipp Petersen Extraction of Digital Wavefront Sets Using Applied Harmonic Analysis and Deep Neural Networks. 1936-1966 2019 12 SIAM J. Imaging Sci. 4 https://doi.org/10.1137/19M1237594 https://www.wikidata.org/entity/Q126809614 db/journals/siamis/siamis12.html#Andrade-LoarcaK19

Medya Siadat Nasser Aghazadeh Farideh Akbarifard Hjalmar Brismar Ozan Öktem Joint Image Deconvolution and Separation Using Mixed Dictionaries. 3936-3945 2019 28 IEEE Trans. Image Process. 8 https://doi.org/10.1109/TIP.2019.2903316 https://www.wikidata.org/entity/Q92188043 db/journals/tip/tip28.html#SiadatAABO19

Ozan Öktem Camille Pouchol Olivier Verdier Spatiotemporal PET Reconstruction Using ML-EM with Learned Diffeomorphic Deformation. 151-162 2019 MLMIR@MICCAI https://doi.org/10.1007/978-3-030-33843-5_14 conf/miccai/2019mlmir db/conf/miccai/mlmir2019.html#OktemPV19

Héctor Andrade-Loarca Gitta Kutyniok Ozan Öktem Philipp Petersen Extraction of digital wavefront sets using applied harmonic analysis and deep neural networks. 2019 abs/1901.01388 CoRR http://arxiv.org/abs/1901.01388 db/journals/corr/corr1901.html#abs-1901-01388

Andreas Hauptmann Jonas Adler Simon R. Arridge Ozan Öktem Multi-Scale Learned Iterative Reconstruction. 2019 abs/1908.00936 CoRR http://arxiv.org/abs/1908.00936 db/journals/corr/corr1908.html#abs-1908-00936

Ozan Öktem Camille Pouchol Olivier Verdier Spatiotemporal PET reconstruction using ML-EM with learned diffeomorphic deformation. 2019 abs/1908.09515 CoRR http://arxiv.org/abs/1908.09515 db/journals/corr/corr1908.html#abs-1908-09515

Héctor Andrade-Loarca Gitta Kutyniok Ozan Öktem Shearlets as Feature Extractor for Semantic Edge Detection: The Model-Based and Data-Driven Realm. 2019 abs/1911.12159 CoRR http://arxiv.org/abs/1911.12159 db/journals/corr/corr1911.html#abs-1911-12159

Chong Chen Ozan Öktem Indirect Image Registration with Large Diffeomorphic Deformations. 575-617 2018 11 SIAM J. Imaging Sci. 1 https://doi.org/10.1137/17M1134627 https://www.wikidata.org/entity/Q130173767 db/journals/siamis/siamis11.html#ChenO18

Medya Siadat Nasser Aghazadeh Ozan Öktem Reordering for improving global Arnoldi-Tikhonov method in image restoration problems. 497-504 2018 12 Signal Image Video Process. 3 https://doi.org/10.1007/s11760-017-1185-5 https://www.wikidata.org/entity/Q113106051 db/journals/sivp/sivp12.html#SiadatAO18

Jonas Adler Ozan Öktem Learned Primal-Dual Reconstruction. 1322-1332 2018 37 IEEE Trans. Medical Imaging 6 https://doi.org/10.1109/TMI.2018.2799231 https://www.wikidata.org/entity/Q56446294 db/journals/tmi/tmi37.html#AdlerO18

Sebastian Lunz Carola Schönlieb Ozan Öktem Adversarial Regularizers in Inverse Problems. 8516-8525 2018 NeurIPS https://proceedings.neurips.cc/paper/2018/hash/d903e9608cfbf08910611e4346a0ba44-Abstract.html http://papers.nips.cc/paper/8070-adversarial-regularizers-in-inverse-problems conf/nips/2018 db/conf/nips/nips2018.html#LunzSO18

Sebastian Lunz Ozan Öktem Carola-Bibiane Schönlieb Adversarial Regularizers in Inverse Problems. 2018 abs/1805.11572 CoRR http://arxiv.org/abs/1805.11572 db/journals/corr/corr1805.html#abs-1805-11572

Barbara Gris Chong Chen Ozan Öktem Image reconstruction through metamorphosis. 2018 abs/1806.01225 CoRR http://arxiv.org/abs/1806.01225 db/journals/corr/corr1806.html#abs-1806-01225

Jonas Adler Sebastian Lunz Olivier Verdier Carola-Bibiane Schönlieb Ozan Öktem Task adapted reconstruction for inverse problems. 2018 abs/1809.00948 CoRR http://arxiv.org/abs/1809.00948 db/journals/corr/corr1809.html#abs-1809-00948

Jonas Adler Ozan Öktem Deep Bayesian Inversion. 2018 abs/1811.05910 CoRR http://arxiv.org/abs/1811.05910 db/journals/corr/corr1811.html#abs-1811-05910

Chong Chen Barbara Gris Ozan Öktem A New Variational Model for Joint Image Reconstruction and Motion Estimation in Spatiotemporal Imaging. 2018 abs/1812.03446 CoRR http://arxiv.org/abs/1812.03446 db/journals/corr/corr1812.html#abs-1812-03446

Axel Ringh Xiaodong Zhuge Willem Jan Palenstijn Kees Joost Batenburg Ozan Öktem High-Level Algorithm Prototyping: An Example Extending the TVR-DART Algorithm. 109-121 2017 DGCI https://doi.org/10.1007/978-3-319-66272-5_10 conf/dgci/2017 db/conf/dgci/dgci2017.html#RinghZPBO17

Jonas Adler Ozan Öktem Solving ill-posed inverse problems using iterative deep neural networks. 2017 abs/1704.04058 CoRR http://arxiv.org/abs/1704.04058 db/journals/corr/corr1704.html#AdlerO17

Chong Chen Ozan Öktem Indirect Image Registration with Large Diffeomorphic Deformations. 2017 abs/1706.04048 CoRR http://arxiv.org/abs/1706.04048 db/journals/corr/corr1706.html#ChenO17

Jonas Adler Ozan Öktem Learned Primal-dual Reconstruction. 2017 abs/1707.06474 CoRR http://arxiv.org/abs/1707.06474 db/journals/corr/corr1707.html#AdlerO17aa

Jonas Adler Axel Ringh Ozan Öktem Johan Karlsson Learning to solve inverse problems using Wasserstein loss. 2017 abs/1710.10898 CoRR http://arxiv.org/abs/1710.10898 db/journals/corr/corr1710.html#abs-1710-10898

Guozhi Dong Aniello Raffaele Patrone Otmar Scherzer Ozan Öktem Infinite Dimensional Optimization Models and PDEs for Dejittering. 678-689 2015 SSVM https://doi.org/10.1007/978-3-319-18461-6_54 conf/scalespace/2015 db/conf/scalespace/ssvm2015.html#DongPSO15 Ozan Öktem Mathematics of Electron Tomography. 937-1031 2015 Handbook of Mathematical Methods in Imaging https://doi.org/10.1007/978-1-4939-0790-8_43 reference/sp/2015mmi db/reference/sp/mmi2015.html#Oktem15

Ajay Gopinath Guoliang Xu David Ress Ozan Öktem Sriram Subramaniam Chandrajit L. Bajaj Shape-Based Regularization of Electron Tomographic Reconstruction. 2241-2252 2012 31 IEEE Trans. Medical Imaging 12 https://doi.org/10.1109/TMI.2012.2214229 https://www.wikidata.org/entity/Q34393723 db/journals/tmi/tmi31.html#GopinathXROSB12

Eric Todd Quinto Ozan Öktem Local Tomography in Electron Microscopy. 1282-1303 2008 68 SIAM J. Appl. Math. 5 https://doi.org/10.1137/07068326X db/journals/siamam/siamam68.html#QuintoO08

Jonas Adler Nasser Aghazadeh Farideh Akbarifard Joakim Andén Héctor Andrade-Loarca Simon R. Arridge Chandrajit L. BajajChandrajit Bajaj Buda Bajic Sebastian Banert Matthieu Barreau Kees Joost Batenburg Erik J. Bekkers James D. Brenton Hjalmar Brismar Thomas Buddenkotte Marcello Carioni Chong Chen Mireia Crispin-Ortuzar Willem Diepeveen Giuseppe Alessio D'Inverno Sören Dittmer Guozhi Dong Alma Eguizabal Carlos EsteveCarlos Esteve Yagüe Ajay Gopinath Barbara Gris Andreas Hauptmann Paul Häusner Johannes A. J. Huber Axel Janson Erik Jansson Johan Karlsson Thomas Köhler 0003Thomas Koehler 0003 Jonathan Krook Friso de Kruiff Gitta Kutyniok Jan Lellmann Sebastian Lunz Peter Maass Cathal McCague Klas Modin Kateryna Morozovska Subhadip Mukherjee Benedikt Neyses Eric Oldgren Linus Olofsson Willem Jan Palenstijn Aniello Raffaele Patrone Marcelo Pereyra Mats PerssonMats U. Persson Philipp Petersen Aurora Poggi Camille Pouchol Eric Todd Quinto David Ress Axel Ringh Jevgenija Rudzusika Leonardo Rundo Evis Sala Knut Salomonsson Lorena Escudero Sanchez Otmar Scherzer Carola-Bibiane SchönliebCarola SchönliebCarola B. Schönlieb Zakhar Shumaylov Medya Siadat Jens Sjölund Emanuel Ström Sriram Subramaniam Anna-Karin Tornberg Emilien Valat Olivier Verdier Runqian Wang Melanie Weber Ramona Woitek Guoliang Xu Xiaodong Zhuge