Publications by Taha Emre
2024
- Emre T., Chakravarty A., Lachinov D., Rivail A., Schmidt-Erfurth U., Bogunović H.
Learning Temporally Equivariance for Degenerative Disease Progression in OCT by Predicting Future Representations.
In Linguraru M.G., Dou Q., Feragen A., Giannarou S., Glocker B., Lekadir K., Schnabel J.A. (Eds.) Medical Image Computing and Computer Assisted Intervention – MICCAI 2024. 27th International Conference, Marrakesh, Morocco, 6–10 October 2024, Proceedings, Part XII, Lecture Notes in Computer Science 15012, Springer, Cham, 196–206, (2024) [bib]
@INCOLLECTION{emre2024ltef196206, author = {Emre, T.~ and Chakravarty, A.~ and Lachinov, D.~ and Rivail, A.~ and Schmidt-Erfurth, U.~ and Bogunović, H.~}, title = {Learning Temporally Equivariance for Degenerative Disease Progression in OCT by Predicting Future Representations.}, booktitle = {Medical Image Computing and Computer Assisted Intervention – MICCAI 2024. 27th International Conference, Marrakesh, Morocco, 6–10 October 2024, Proceedings, Part XII}, publisher = {Springer}, year = {2024}, editor = {Linguraru,M.G.;Dou,Q.;Feragen,A.;Giannarou,S.;Glocker,B.;Lekadir,K.;Schnabel,J.A.}, number = {15012}, series = {Lecture Notes in Computer Science}, pages = {196--206}, address = {Cham}, month = {oct}, url = {https://doi.org/10.1007/978-3-031-72390-2_19} } - Chakravarty A., Emre T., Lachinov D., Rivail A., Scholl H., Fritsche L., Sivaprasad S., Rueckert D., Lotery A., Schmidt-Erfurth U., Bogunović H.
Forecasting Disease Progression with Parallel Hyperplanes in Longitudinal Retinal OCT.
In Linguraru M.G., Dou Q., Feragen A., Giannarou S., Glocker B., Lekadir K., Schnabel J.A. (Eds.) Medical Image Computing and Computer Assisted Intervention – MICCAI 2024 27th International Conference, Marrakesh, Morocco, 6–10 October 2024, Proceedings, Part V, Lecture Notes in Computer Science 15005, Springer, Cham, 273–283, (2024) [bib]
@INCOLLECTION{chakravarty2024fdpw273283, author = {Chakravarty, A.~ and Emre, T.~ and Lachinov, D.~ and Rivail, A.~ and Scholl, H.~ and Fritsche, L.~ and Sivaprasad, S.~ and Rueckert, D.~ and Lotery, A.~ and Schmidt-Erfurth, U.~ and Bogunović, H.~}, title = {Forecasting Disease Progression with Parallel Hyperplanes in Longitudinal Retinal OCT.}, booktitle = {Medical Image Computing and Computer Assisted Intervention – MICCAI 2024 27th International Conference, Marrakesh, Morocco, 6–10 October 2024, Proceedings, Part V}, publisher = {Springer}, year = {2024}, editor = {Linguraru,M.G.;Dou,Q.;Feragen,A.;Giannarou,S.;Glocker,B.;Lekadir,K.;Schnabel,J.A.}, number = {15005}, series = {Lecture Notes in Computer Science}, pages = {273--283}, address = {Cham}, doi = {10.1007/978-3-031-72086-4_26}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85206571158\&doi=10.1007%2f978-3-031-72086-4_26\&partnerID=40\&md5=779eb79b2e5c5c1820ca5fd47d7a1b67} } - Chakravarty A., Emre T., Leingang O., Riedl S., Mai J., Scholl H.P.N., Sivaprasad S., Rueckert D., Lotery A., Schmidt-Erfurth U., Bogunovic H.
Morph-SSL: Self-Supervision with Longitudinal Morphing for Forecasting AMD Progression from OCT Volumes.
IEEE Transactions on Medical Imaging 43(9), 3224–3239, (2024) [bib]
@ARTICLE{chakravarty2024mswl32243239, author = {Chakravarty, A.~ and Emre, T.~ and Leingang, O.~ and Riedl, S.~ and Mai, J.~ and Scholl, H.P.N.~ and Sivaprasad, S.~ and Rueckert, D.~ and Lotery, A.~ and Schmidt-Erfurth, U.~ and Bogunovic, H.~}, title = {Morph-SSL: Self-Supervision with Longitudinal Morphing for Forecasting AMD Progression from OCT Volumes.}, journal = {IEEE Transactions on Medical Imaging}, year = {2024}, volume = {43}, number = {9}, pages = {3224--3239}, doi = {10.1109/TMI.2024.3390940} } - Emre T., Chakravarty A., Rivail A., Lachinov D., Leingang O., Riedl S., Mai J., Scholl H., Sivaprasad S., Rueckert D., Lotery A., Schmidt-Erfurth U., Bogunovic H., for the PINNACLE Consortium
3DTINC: Time-Equivariant Non-Contrastive Learning for Predicting Disease Progression from Longitudinal OCTs.
IEEE Transactions on Medical Imaging 43(9), 3200–3210, (2024) [bib]
@ARTICLE{emre20243tnl32003210, author = {Emre, T.~ and Chakravarty, A.~ and Rivail, A.~ and Lachinov, D.~ and Leingang, O.~ and Riedl, S.~ and Mai, J.~ and Scholl, H.~ and Sivaprasad, S.~ and Rueckert, D.~ and Lotery, A.~ and Schmidt-Erfurth, U.~ and Bogunovic, H.~ and {for the PINNACLE Consortium}}, title = {3DTINC: Time-Equivariant Non-Contrastive Learning for Predicting Disease Progression from Longitudinal OCTs.}, journal = {IEEE Transactions on Medical Imaging}, year = {2024}, volume = {43}, number = {9}, pages = {3200--3210}, issn = {0278-0062}, doi = {10.1109/TMI.2024.3391215} } - Chakravarty A., Emre T., Lachinov D., Rivail A., Schmidt-Erfurth U., Bogunović H.
Predicting Age-Related Macular Degeneration Progression from Retinal Optical Coherence Tomography with Intra-Subject Temporal Consistency.
In Burgos N., Petitjean C., Vakalopoulou M., Christodoulidis S., Coupe P., Delingette H., Lartizien C., Mateus D. (Eds.) Proceedings of the 7th International Conference on Medical Imaging with Deep Learning, Paris, France, 3-5 July 2024, Proceedings of Machine Learning Research 250, JMLR, Cambridge, MA, 184–198, (2024) [bib]
@INCOLLECTION{chakravarty2024pamd184198, author = {Chakravarty, A.~ and Emre, T.~ and Lachinov, D.~ and Rivail, A.~ and Schmidt-Erfurth, U.~ and Bogunović, H.~}, title = {Predicting Age-Related Macular Degeneration Progression from Retinal Optical Coherence Tomography with Intra-Subject Temporal Consistency.}, booktitle = {Proceedings of the 7th International Conference on Medical Imaging with Deep Learning, Paris, France, 3-5 July 2024}, publisher = {JMLR}, year = {2024}, editor = {Burgos,N.;Petitjean,C.;Vakalopoulou,M.;Christodoulidis,S.;Coupe,P.;Delingette,H.;Lartizien,C.;Mateus,D.}, number = {250}, series = {Proceedings of Machine Learning Research}, pages = {184--198}, address = {Cambridge, MA}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85216617327\&partnerID=40\&md5=79052e7a1c0b0a98bd3b4388f2dd11dc} }
2023
- Emre T., Oghbaie M., Chakravarty A., Rivail A., Riedl S., Mai J., P.N. Scholl H., Sivaprasad S., Rueckert D., Lotery A., Schmidt-Erfurth U., Bogunović H.
Pretrained Deep 2.5D Models for Efficient Predictive Modeling from Retinal OCT: A PINNACLE Study Report.
In Antony B., Chen H., Fang H., Fu H., Li C.S., Zheng Y. (Eds.) Ophthalmic Medical Image Analysis: 10th International Workshop, OMIA 2023, Held in Conjunction with MICCAI 2023, Vancouver, BC, Canada, 12 October 2023, Proceedings, Lecture Notes in Computer Science 14096, Springer, Cham, 132–141, (2023) [bib]
@INCOLLECTION{emre2023pd2m132141, author = {Emre, T.~ and Oghbaie, M.~ and Chakravarty, A.~ and Rivail, A.~ and Riedl, S.~ and Mai, J.~ and P.N. Scholl, H.~ and Sivaprasad, S.~ and Rueckert, D.~ and Lotery, A.~ and Schmidt-Erfurth, U.~ and Bogunović, H.~}, title = {Pretrained Deep 2.5D Models for Efficient Predictive Modeling from Retinal OCT: A PINNACLE Study Report.}, booktitle = {Ophthalmic Medical Image Analysis: 10th International Workshop, OMIA 2023, Held in Conjunction with MICCAI 2023, Vancouver, BC, Canada, 12 October 2023, Proceedings}, publisher = {Springer}, year = {2023}, editor = {Antony,B.;Chen,H.;Fang,H.;Fu,H.;Li,C.S.;Zheng,Y.}, number = {14096}, series = {Lecture Notes in Computer Science}, pages = {132--141}, address = {Cham}, url = {https://www.doi.org/10.1007/978-3-031-44013-7_14} } - Oghbaie M., Araújo T., Emre T., Schmidt-Erfurth U., Bogunović H.
Transformer-Based End-to-End Classification of Variable-Length Volumetric Data.
In Greenspan H., Madabhushi A., Mousavi P., Salcudean S., Duncan J., Syeda-Mahmood T., Taylor R. (Eds.) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2023, 26th International Conference, Vancouver, BC, Canada, October 8–12, 2023, Proceedings, Part VI, Lecture Notes in Computer Science 14225, Springer, Cham, 358–367, (2023) [bib]
@INCOLLECTION{oghbaie2023teco358367, author = {Oghbaie, M.~ and Araújo, T.~ and Emre, T.~ and Schmidt-Erfurth, U.~ and Bogunović, H.~}, title = {Transformer-Based End-to-End Classification of Variable-Length Volumetric Data.}, booktitle = {Medical Image Computing and Computer-Assisted Intervention – MICCAI 2023, 26th International Conference, Vancouver, BC, Canada, October 8–12, 2023, Proceedings, Part VI}, publisher = {Springer}, year = {2023}, editor = {Greenspan,H.;Madabhushi,A.;Mousavi,P.;Salcudean,S.;Duncan,J.;Syeda-Mahmood,T.;Taylor,R.}, number = {14225}, series = {Lecture Notes in Computer Science}, pages = {358--367}, address = {Cham}, url = {https://doi.org/10.1007/978-3-031-43987-2_35} }
2022
- Emre T., Chakravarty A., Rivail A., Riedl S., Schmidt-Erfurth U., Bogunović H.
TINC: Temporally Informed Non-Contrastive Learning for Disease Progression Modeling in Retinal OCT Volumes.
In Wang L., Dou Q., Fletcher P.T., Speidel S., Li S. (Eds.) Medical Image Computing and Computer Assisted Intervention – MICCAI 2022, 25th International Conference, Singapore, 18–22 September 2022, Proceedings, Part II, Lecture Notes in Computer Science 13432, Springer, Cham, 625–634, (2022) [bib]
@INCOLLECTION{emre2022ttin625634, author = {Emre, T.~ and Chakravarty, A.~ and Rivail, A.~ and Riedl, S.~ and Schmidt-Erfurth, U.~ and Bogunović, H.~}, title = {TINC: Temporally Informed Non-Contrastive Learning for Disease Progression Modeling in Retinal OCT Volumes.}, booktitle = {Medical Image Computing and Computer Assisted Intervention – MICCAI 2022, 25th International Conference, Singapore, 18–22 September 2022, Proceedings, Part II}, publisher = {Springer}, year = {2022}, editor = {Wang,L.;Dou,Q.;Fletcher,P.T.;Speidel,S.;Li,S.}, number = {13432}, series = {Lecture Notes in Computer Science}, pages = {625--634}, address = {Cham}, month = {sep}, url = {https://www.doi.org/10.1007/978-3-031-16434-7_60} } - Mascagni P., Vardazaryan A., Alapatt D., Urade T., Emre T., Fiorillo C., Pessaux P., Mutter D., Marescaux J., Costamagna G., Dallemagne B., Padoy N.
Artificial Intelligence for Surgical Safety: Automatic Assessment of the Critical View of Safety in Laparoscopic Cholecystectomy Using Deep Learning.
Annals of Surgery 275(5), 955–961, (2022) [bib]
@ARTICLE{mascagni2022aiss955961, author = {Mascagni, P.~ and Vardazaryan, A.~ and Alapatt, D.~ and Urade, T.~ and Emre, T.~ and Fiorillo, C.~ and Pessaux, P.~ and Mutter, D.~ and Marescaux, J.~ and Costamagna, G.~ and Dallemagne, B.~ and Padoy, N.~}, title = {Artificial Intelligence for Surgical Safety: Automatic Assessment of the Critical View of Safety in Laparoscopic Cholecystectomy Using Deep Learning.}, journal = {Annals of Surgery}, year = {2022}, volume = {275}, number = {5}, pages = {955--961}, issn = {0003-4932}, doi = {10.1097/SLA.0000000000004351}, url = {https://journals.lww.com/annalsofsurgery/fulltext/2022/05000/artificial_intelligence_for_surgical_safety_.20.aspx}, keywords = {artificial intelligence;deep learning;anatomical segmentation;computer vision;critical view of safety;laparoscopic cholecystectomy;surgical data science;surgical safety} }
2020
- Mascagni P., Fiorillo C., Urade T., Emre T., Yu T., Wakabayashi T., Felli E., Perretta S., Swanstrom L., Mutter D., Marescaux J., Pessaux P., Costamagna G., Padoy N., Dallemagne B.
Formalizing Video Documentation of the Critical View of Safety in Laparoscopic Cholecystectomy: A Step Towards Artificial Intelligence Assistance to Improve Surgical Safety.
Surgical Endoscopy 34(6), 2709–2714, (2020) [bib]
@ARTICLE{mascagni2020fvdc27092714, author = {Mascagni, P.~ and Fiorillo, C.~ and Urade, T.~ and Emre, T.~ and Yu, T.~ and Wakabayashi, T.~ and Felli, E.~ and Perretta, S.~ and Swanstrom, L.~ and Mutter, D.~ and Marescaux, J.~ and Pessaux, P.~ and Costamagna, G.~ and Padoy, N.~ and Dallemagne, B.~}, title = {Formalizing Video Documentation of the Critical View of Safety in Laparoscopic Cholecystectomy: A Step Towards Artificial Intelligence Assistance to Improve Surgical Safety.}, journal = {Surgical Endoscopy}, year = {2020}, volume = {34}, number = {6}, pages = {2709--2714}, issn = {1432-2218 0930-2794}, doi = {10.1007/s00464-019-07149-3}, keywords = {Female;Humans;Male;Artificial Intelligence/*standards;Bile duct injury;Cholecystectomy;Laparoscopic/*methods;Critical View of Safety;Laparoscopic cholecystectomy;Objective video reporting;Surgical data science;Surgical safety;Video Recording/*methods} }