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Moriconi, Stefano; Rodríguez-Núñez, Omar; Gros, Romane; Felger, Leonard A; Maragkou, Theoni; Hewer, Ekkehard; Pierangelo, Angelo; Novikova, Tatiana; Schucht, Philippe; McKinley, Richard (2024). Near-real-time Mueller polarimetric image processing for neurosurgical intervention. (In Press). International journal of computer assisted radiology and surgery Springer 10.1007/s11548-024-03090-6
Felger, Leonard; Rodríguez-Núñez, Omar; Gros, Romain; Maragkou, Theoni; McKinley, Richard; Moriconi, Stefano; Murek, Michael; Zubak, Irena; Novikova, Tatiana; Pierangelo, Angelo; Schucht, Philippe (2023). Robustness of the wide-field imaging Mueller polarimetry for brain tissue differentiation and white matter fiber tract identification in a surgery-like environment: an ex vivo study. Biomedical optics express, 14(5), pp. 2400-2415. Optical Society of America 10.1364/BOE.486438
Gros, Romain; Rodríguez-Núñez, Omar; Felger, Leonard; Moriconi, Stefano; McKinley, Richard; Pierangelo, Angelo; Novikova, Tatiana; Vassella, Erik; Schucht, Philippe; Hewer, Ekkehard; Maragkou, Theoni (2023). Effects of formalin fixation on polarimetric properties of brain tissue: fresh or fixed? Neurophotonics, 10(2), 025009. SPIE 10.1117/1.NPh.10.2.025009
Rebsamen, Michael; McKinley, Richard; Radojewski, Piotr; Pistor, Maximilian; Friedli, Christoph; Hoepner, Robert; Salmen, Anke; Chan, Andrew; Reyes, Mauricio; Wagner, Franca; Wiest, Roland; Rummel, Christian (2023). Reliable brain morphometry from contrast-enhanced T1w-MRI in patients with multiple sclerosis. Human brain mapping, 44(3), pp. 970-979. Wiley-Blackwell 10.1002/hbm.26117
Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; Sheller, Micah; Wang, Shih-Han; Reina, G Anthony; Foley, Patrick; Gruzdev, Alexey; Karkada, Deepthi; Davatzikos, Christos; Sako, Chiharu; Ghodasara, Satyam; Bilello, Michel; Mohan, Suyash; Vollmuth, Philipp; Brugnara, Gianluca; Preetha, Chandrakanth J; Sahm, Felix; Maier-Hein, Klaus; Zenk, Maximilian; ... (2023). Author Correction: Federated learning enables big data for rare cancer boundary detection. Nature communications, 14(1), p. 436. Nature Publishing Group 10.1038/s41467-023-36188-7
Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; Sheller, Micah; Wang, Shih-Han; Reina, G Anthony; Foley, Patrick; Gruzdev, Alexey; Karkada, Deepthi; Davatzikos, Christos; Sako, Chiharu; Ghodasara, Satyam; Bilello, Michel; Mohan, Suyash; Vollmuth, Philipp; Brugnara, Gianluca; Preetha, Chandrakanth J; Sahm, Felix; Maier-Hein, Klaus; Zenk, Maximilian; ... (2022). Federated learning enables big data for rare cancer boundary detection. Nature communications, 13(1), p. 7346. Nature Publishing Group 10.1038/s41467-022-33407-5
Mehta, Raghav; Filos, Angelos; Baid, Ujjwal; Sako, Chiharu; McKinley, Richard; Rebsamen, Michael; Dätwyler, Katrin; Meier, Raphael; Radojewski, Piotr; Murugesan, Gowtham Krishnan; Nalawade, Sahil; Ganesh, Chandan; Wagner, Ben; Yu, Fang F; Fei, Baowei; Madhuranthakam, Ananth J; Maldjian, Joseph A; Daza, Laura; Gómez, Catalina; Arbeláez, Pablo; ... (2022). QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results. The journal of machine learning for biomedical imaging, 2022 MELBA
Rebsamen, Michael; Radojewski, Piotr; McKinley, Richard; Reyes, Mauricio; Wiest, Roland; Rummel, Christian (2022). A Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI. Frontiers in neurology, 13, p. 812432. Frontiers Media S.A. 10.3389/fneur.2022.812432
McKinley, Richard; Wepfer, Rik; Aschwanden, Fabian; Grunder, Lorenz; Muri, Raphaela; Rummel, Christian; Verma, Rajeev; Weisstanner, Christian; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wagner, Franca; Wiest, Roland (2021). Simultaneous lesion and brain segmentation in multiple sclerosis using deep neural networks. Scientific reports, 11(1), p. 1087. Springer Nature 10.1038/s41598-020-79925-4
Rebsamen, Michael; Rummel, Christian; Reyes, Mauricio; Wiest, Roland; McKinley, Richard (2020). Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation. Human brain mapping, 41(17), pp. 4804-4814. Wiley-Blackwell 10.1002/hbm.25159
McKinley, Richard; Wepfer, Rik; Grunder, Lorenz; Aschwanden, Fabian; Fischer, Tim; Friedli, Christoph; Muri, Raphaela; Rummel, Christian; Verma, Rajeev Kumar; Weisstanner, Christian; Wiestler, Benedikt; Berger, Christoph; Eichinger, Paul; Muehlau, Mark; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wiest, Roland; Wagner, Franca (2020). Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence. NeuroImage: Clinical, 25, p. 102104. Elsevier 10.1016/j.nicl.2019.102104
McKinley, Richard; Wepfer, Rik; Aschwanden, Fabian; Grunder, Lorenz; Muri, Raphaela; Rummel, Christian; Verma, Rajeev; Weisstanner, Christian; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wagner, Franca; Wiest, Roland (2020). Robustness of Simultaneous Lesion and Neuroanatomy Segmentation in Multiple Sclerosis Using Deep Neural Networks (In Press). SSRN Electronic Journal Elsevier 10.2139/ssrn.3529469
Kuijf, Hugo J; Biesbroek, J Matthijs; de Bresser, Jeroen; Heinen, Rutger; Andermatt, Simon; Bento, Mariana; Berseth, Matt; Belyaev, Mikhail; Cardoso, M Jorge; Casamitjana, Adria; Collins, D Louis; Dadar, Mahsa; Georgiou, Achilleas; Ghafoorian, Mohsen; Jin, Dakai; Khademi, April; Knight, Jesse; Li, Hongwei; Llado, Xavier; Luna, Miguel; ... (2019). Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities; Results of the WMH Segmentation Challenge. IEEE transactions on medical imaging, 38(11), pp. 2556-2568. Institute of Electrical and Electronics Engineers IEEE 10.1109/TMI.2019.2905770
McKinley, Richard; Marshall, Randolph (2019). Advanced MRI in acute stroke: Is the whole penumbra salvageable? Neurology, 92(21), pp. 983-984. American Academy of Neurology 10.1212/WNL.0000000000007535
Meier, Raphael; Lux, Paula; Jung, Simon; Fischer, Urs; Gralla, Jan; Reyes, Mauricio; Wiest, Roland; McKinley, Richard; Kaesmacher, Johannes (2019). Neural network-derived perfusion Maps for the assessment of lesions in patients with acute ischemic stroke (Submitted). Radiology: artificial intelligence Radiological Society of North America 10.1148/ryai.2019190019
Rebsamen, Michael; Knecht, Urspeter; Reyes, Mauricio; Wiest, Roland; Meier, Raphael; McKinley, Richard (2019). Divide and Conquer: Stratifying Training Data by Tumor Grade Improves Deep Learning-Based Brain Tumor Segmentation. Frontiers in neuroscience, 13, p. 1182. Frontiers Research Foundation 10.3389/fnins.2019.01182
Commowick, Olivier; Istace, Audrey; Kain, Michaël; Laurent, Baptiste; Leray, Florent; Simon, Mathieu; Pop, Sorina Camarasu; Girard, Pascal; Améli, Roxana; Ferré, Jean-Christophe; Kerbrat, Anne; Tourdias, Thomas; Cervenansky, Frédéric; Glatard, Tristan; Beaumont, Jérémy; Doyle, Senan; Forbes, Florence; Knight, Jesse; Khademi, April; Mahbod, Amirreza; ... (2018). Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure. Scientific Reports, 8(1), p. 13650. Nature Publishing Group 10.1038/s41598-018-31911-7
Pereira, Sérgio; Meier, Raphael; McKinley, Richard; Wiest, Roland; Alves, Victor; Silva, Carlos A; Reyes, Mauricio (2018). Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation. Medical image analysis, 44, pp. 228-244. Elsevier 10.1016/j.media.2017.12.009
Rummel, Christian; Aschwanden, Fabian; McKinley, Richard; Wagner, Franca; Salmen, Anke; Chan, Andrew; Wiest, Roland (2018). A Fully Automated Pipeline for Normative Atrophy in Patients with Neurodegenerative Disease. Frontiers in neurology, 8, p. 727. Frontiers Media S.A. 10.3389/fneur.2017.00727
McKinley, Richard; Hung, Fan; Wiest, Roland; Liebeskind, David S; Scalzo, Fabien (2018). A Machine Learning Approach to Perfusion Imaging With Dynamic Susceptibility Contrast MR. Frontiers in neurology, 9(717), p. 717. Frontiers Media S.A. 10.3389/fneur.2018.00717
Habegger, Simon; Wiest, Roland; Weder, Bruno; Mordasini, Pasquale; Gralla, Jan; Häni, Levin; Jung, Simon; Reyes, Mauricio; McKinley, Richard (2018). Relating Acute Lesion Loads to Chronic Outcome in Ischemic Stroke-An Exploratory Comparison of Mismatch Patterns and Predictive Modeling. Frontiers in neurology, 9(737), p. 737. Frontiers Media S.A. 10.3389/fneur.2018.00737
Winzeck, Stefan; Hakim, Arsany; McKinley, Richard; Pinto, José A A D S R; Alves, Victor; Silva, Carlos; Pisov, Maxim; Krivov, Egor; Belyaev, Mikhail; Monteiro, Miguel; Oliveira, Arlindo; Choi, Youngwon; Paik, Myunghee Cho; Kwon, Yongchan; Lee, Hanbyul; Kim, Beom Joon; Won, Joong-Ho; Islam, Mobarakol; Ren, Hongliang; Robben, David; ... (2018). ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI. Frontiers in neurology, 9(679), p. 679. Frontiers Media S.A. 10.3389/fneur.2018.00679
Pinto, Adriano; McKinley, Richard; Alves, Victor; Wiest, Roland; Silva, Carlos A; Reyes, Mauricio (2018). Stroke Lesion Outcome Prediction Based on MRI Imaging Combined With Clinical Information. Frontiers in neurology, 9(1060), p. 1060. Frontiers Media S.A. 10.3389/fneur.2018.01060
Jung, Simon; Wiest, Roland; Gralla, Jan; McKinley, Richard; Mattle, Heinrich; Liebeskind, David (2017). Relevance of the cerebral collateral circulation in ischaemic stroke: time is brain, but collaterals set the pace. Swiss medical weekly, 147(w14538), w14538. EMH Schweizerischer Ärzteverlag 10.4414/smw.2017.14538
Da Silva Mendes Pedrosa, Nuno Miguel; McKinley, Richard; Wiest, Roland; Slotboom, Johannes (2017). Improving labeling efficiency in automatic quality control of MRSI data. Magnetic resonance in medicine, 78(6), pp. 2399-2405. Wiley-Liss 10.1002/mrm.26618
Maier, Oskar; Menze, Bjoern H; von der Gablentz, Janina; Häni, Levin; Heinrich, Mattias P; Liebrand, Matthias; Winzeck, Stefan; Basit, Abdul; Bentley, Paul; Chen, Liang; Christiaens, Daan; Dutil, Francis; Egger, Karl; Feng, Chaolu; Glocker, Ben; Götz, Michael; Haeck, Tom; Halme, Hanna-Leena; Havaei, Mohammad; Iftekharuddin, Khan M; ... (2016). ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI. Medical image analysis, 35, pp. 250-269. Elsevier 10.1016/j.media.2016.07.009
Da Silva Mendes Pedrosa, Nuno Miguel; McKinley, Richard; Knecht, Urspeter; Wiest, Roland; Slotboom, Johannes (2016). Automatic quality control in clinical (1) H MRSI of brain cancer. NMR in biomedicine, 29(5), pp. 563-575. Wiley Interscience 10.1002/nbm.3470
McKinley, Richard; Häni, Levin; Gralla, Jan; El-Koussy, Marwan; Bauer, S; Arnold, Marcel; Fischer, Urs; Jung, Simon; Mattmann, Kaspar; Reyes, Mauricio; Wiest, Roland (2016). Fully automated stroke tissue estimation using random forest classifiers (FASTER). Journal of cerebral blood flow and metabolism, 37(8), pp. 2728-2741. Nature Publishing Group 10.1177/0271678X16674221
McKinley, Richard (2013). Canonical proof nets for classical logic. Annals of pure and applied logic, 164(6), pp. 702-732. Elsevier 10.1016/j.apal.2012.05.007
McKinley, Richard (2013). Proof Nets for Herbrand’s Theorem. ACM transactions on computational logic, 14(1), pp. 1-31. New York: ACM 10.1145/2422085.2422090
McKinley, Richard (2008). Soft linear set theory. Journal of logic and algebraic programming, 76(2), pp. 226-245. New York, N.Y.: North-Holland 10.1016/j.jlap.2008.02.010
Rebsamen, Michael; Rummel, Christian; Mürner-Lavanchy, Ines; Reyes, M; Wiest, Roland; McKinley, Richard (2019). Surface-Based Brain Morphometry for the Prediction of Fluid Intelligence in the Neurocognitive Prediction Challenge 2019. In: Pohl, Kilian M.; Thompson, Wesley K.; Adeli, Ehsan; Linguraru, Marius George (eds.) Adolescent Brain Cognitive Development Neurocognitive Prediction. ABCD-NP 2019. Lecture notes in computer science: Vol. 11791 (pp. 26-34). Cham, Switzerland: Springer
McKinley, Richard (2010). Expansion nets: Proof nets for propositional classical logic. In: Fermüller, Christian; Voronkov, Andrei (eds.) Logic for Programming, Artificial Intelligence, and Reasoning. 17th International Conference, LPAR-17, Yogyakarta, Indonesia, October 10-15, 2010. Proceedings 6397 (pp. 535-549). Heidelberg: Springer Verlag 10.1007/978-3-642-16242-8
Brünnler, Kai; McKinley, Richard (2008). An Algorithmic Interpretation of a Deep Inference System. In: Cervesato, Iliano; Veith, Helmut; Voronkov, Andrei (eds.) Logic for Programming, Artificial Intelligence, and Reasoning. 15th International Conference, LPAR 2008, Doha, Qatar, November 22-27, 2008. Proceedings. Lecture Notes in Computer Science: Vol. 5330 (pp. 482-496). Heidelberg: Springer Verlag 10.1007/978-3-540-89439-1_34
McKinley, Richard; Felger, Leonard A.; Hewer, Ekkehard; Maragkou, Theoni; Murek, Michael; Novikova, Tatiana; Rodríguez-Núñez, Omar; Pierangelo, Angelo; Schucht, Philippe (20 May 2022). Machine learning for white matter fibre tract visualization in the human brain via Mueller matrix polarimetric data. In: Unconventional Optical Imaging III 12136 (p. 35). SPIE 10.1117/12.2624465
Jungo, Alain; McKinley, Richard; Meier, Raphael; Knecht, Urspeter; Vera, Luis; Pérez-Beteta, Julián; Molina-García, David; Pérez-García, Víctor M.; Wiest, Roland; Reyes, Mauricio (2018). Towards uncertainty-assisted brain tumor segmentation and survival prediction. In: International Conference On Medical Image Computing & Computer Assisted Intervention. 10.1007/978-3-319-75238-9_40
McKinley, Richard (2009). The alpha-epsilon calculus. In: Proceedings of Workshop on Structures and Deduction.
McKinley, Richard; Grunder, Lorenz; Wepfer, Rik; Aschwanden, Fabian; Fischer, Tim; Friedli, Christoph; Muri, Raphaela; Rummel, Christian; Verma, Rajeev; Weisstanner, Christian; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wiest, Roland; Wagner, Franca (2019). Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence (arXiv). Cornell University
