paper.bib

@article{Boudreau2023, 
  doi = {10.55458/neurolibre.00014}, 
  year = {2023}, 
  publisher = {NeuroLibre}, 
  author = {Mathieu Boudreau and Agah Karakuzu and Julien Cohen-Adad and Ecem Bozkurt and Madeline Carr and Marco Castellaro and Luis Concha and Mariya Doneva and Seraina Dual and Alex Ensworth and Alexandru Foias and Véronique Fortier and Refaat E. Gabr and Guillaume Gilbert and Carri K. Glide-Hurst and Matthew Grech-Sollars and Siyuan Hu and Oscar Jalnefjord and Jorge Jovicich and Kübra Keskin and Peter Koken and Anastasia Kolokotronis and Simran Kukran and Nam. G. Lee and Ives R. Levesque and Bochao Li and Dan Ma and Burkhard Mädler and Nyasha Maforo and Jamie Near and Erick Pasaye and Alonso Ramirez-Manzanares and Ben Statton and Christian Stehning and Stefano Tambalo and Ye Tian and Chenyang Wang and Kilian Weis and Niloufar Zakariaei and Shuo Zhang and Ziwei Zhao and Nikola Stikov}, 
  title = {Results of the ISMRM 2020 joint Reproducible Research & Quantitative MR study groups reproducibility challenge on phantom and human brain T1 mapping}, 
  journal = {NeuroLibre Reproducible Preprints} 
}

@article{ting2021neurostimulation,
  doi = {10.3389/fnins.2021.649459},      
  title={Neurostimulation for stroke rehabilitation},
  author={Ting, Windsor Kwan-Chun and Fadul, Fa{\"\i}za Abdou-Rahaman and Fecteau, Shirley and Ethier, Christian},
  journal={Frontiers in neuroscience},
  volume={15},
  pages={649459},
  year={2021},
  publisher={Frontiers Media SA}
}

@Article{james2018neuromodulation,
  author    = {James, Nicholas D and McMahon, Stephen B and Field-Fote, Edelle C and Bradbury, Elizabeth J},
  journal   = {The Lancet Neurology},
  title     = {Neuromodulation in the restoration of function after spinal cord injury},
  year      = {2018},
  number    = {10},
  pages     = {905--917},
  volume    = {17},
  doi       = {10.1016/s1474-4422(18)30287-4},
  publisher = {Elsevier},
}

@Article{schupbach2017directional,
  author    = {Sch{\"u}pbach, Michael and Chabardes, St{\'e}phan and Matthies, Cordula and Pollo, Claudio and Steigerwald, Frank and Timmermann, Lars and Visser Vandewalle, Veerle and Volkmann, Jens and Schuurman, P Richard},
  journal   = {Movement disorders},
  title     = {Directional leads for deep brain stimulation: Opportunities and challenges.},
  year      = {2017},
  number    = {10},
  pages     = {1371--1375},
  volume    = {32},
  doi       = {10.1002/mds.27096},
  publisher = {Wiley-Blackwell},
}

@Article{anderson2018optimized,
  author    = {Anderson, Daria Nesterovich and Osting, Braxton and Vorwerk, Johannes and Dorval, Alan D and Butson, Christopher R},
  journal   = {Journal of neural engineering},
  title     = {Optimized programming algorithm for cylindrical and directional deep brain stimulation electrodes},
  year      = {2018},
  number    = {2},
  pages     = {026005},
  volume    = {15},
  doi       = {10.1088/1741-2552/aaa14b},
  publisher = {IOP Publishing},
}

@Article{de2021future,
  author    = {De Ridder, Dirk and Maciaczyk, Jarek and Vanneste, Sven},
  journal   = {Expert Review of Medical Devices},
  title     = {The future of neuromodulation: smart neuromodulation},
  year      = {2021},
  number    = {4},
  pages     = {307--317},
  volume    = {18},
  doi       = {10.1080/17434440.2021.1909470},
  publisher = {Taylor \& Francis},
}

@Article{won2020emerging,
  author    = {Won, Sang Min and Song, Enming and Reeder, Jonathan T and Rogers, John A},
  journal   = {Cell},
  title     = {Emerging modalities and implantable technologies for neuromodulation},
  year      = {2020},
  number    = {1},
  pages     = {115--135},
  volume    = {181},
  doi       = {10.1016/j.cell.2020.02.054},
  publisher = {Elsevier},
}

@Article{jun2017fully,
  author    = {Jun, James J and Steinmetz, Nicholas A and Siegle, Joshua H and Denman, Daniel J and Bauza, Marius and Barbarits, Brian and Lee, Albert K and Anastassiou, Costas A and Andrei, Alexandru and Ayd{\i}n, {\c{C}}a{\u{g}}atay and others},
  journal   = {Nature},
  title     = {Fully integrated silicon probes for high-density recording of neural activity},
  year      = {2017},
  number    = {7679},
  pages     = {232--236},
  volume    = {551},
  doi       = {10.1038/nature24636},
  publisher = {Nature Publishing Group UK London},
}

@Article{tsai2017very,
  author    = {Tsai, David and Sawyer, Daniel and Bradd, Adrian and Yuste, Rafael and Shepard, Kenneth L},
  journal   = {Nature Communications},
  title     = {A very large-scale microelectrode array for cellular-resolution electrophysiology},
  year      = {2017},
  number    = {1},
  pages     = {1802},
  volume    = {8},
  doi       = {10.1038/s41467-017-02009-x},
  publisher = {Nature Publishing Group UK London},
}

@Article{pineau2009treating,
  author    = {Pineau, Joelle and Guez, Arthur and Vincent, Robert and Panuccio, Gabriella and Avoli, Massimo},
  journal   = {International journal of neural systems},
  title     = {Treating epilepsy via adaptive neurostimulation: a reinforcement learning approach},
  year      = {2009},
  number    = {04},
  pages     = {227--240},
  volume    = {19},
  doi       = {10.1142/s0129065709001987},
  publisher = {World Scientific},
}

@InProceedings{gao2023offline,
  author    = {Gao, Qitong and Schmidt, Stephen L and Chowdhury, Afsana and Feng, Guangyu and Peters, Jennifer J and Genty, Katherine and Grill, Warren M and Turner, Dennis A and Pajic, Miroslav},
  booktitle = {Proceedings of the ACM/IEEE 14th International Conference on Cyber-Physical Systems (with CPS-IoT Week 2023)},
  title     = {Offline learning of closed-loop deep brain stimulation controllers for parkinson disease treatment},
  year      = {2023},
  pages     = {44--55},
  doi       = {10.1145/3576841.3585925},
}

@Article{gebodh2021novel,
  author    = {Gebodh, Nigel and Bikson, Marom},
  journal   = {Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation},
  title     = {A novel approach to closed-loop neuromodulation with machine learning},
  year      = {2021},
  number    = {6},
  pages     = {1662},
  volume    = {14},
  doi       = {10.1016/j.brs.2021.10.235},
  publisher = {Elsevier},
}

@article{de2021predictive,
  title={Predictive clinical decision support system using machine learning and imaging biomarkers in patients with neurostimulation therapy: a pilot study},
  author={De Andres, Jose and Ten-Esteve, Amadeo and Harutyunyan, Anushik and Romero-Garcia, Carolina S and Fabregat-Cid, Gustavo and Asensio-Samper, Juan Marcos and Alberich-Bayarri, Angel and Marti-Bonmati, Luis and others},
  journal={Pain Physician},
  volume={24},
  number={8},
  pages={E1279},
  year={2021},
  publisher={American Society of Interventional Pain Physician}
}

@InProceedings{shukla2014towards,
  author       = {Shukla, Pitamber and Basu, Ishita and Tuninetti, Daniela},
  booktitle    = {2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society},
  title        = {Towards closed-loop deep brain stimulation: decision tree-based essential tremor patient's state classifier and tremor reappearance predictor},
  year         = {2014},
  organization = {IEEE},
  pages        = {2605--2608},
  doi          = {10.1109/embc.2014.6944156},
}

@InProceedings{shukla2012neural,
  author       = {Shukla, Pitamber and Basu, Ishita and Graupe, Daniel and Tuninetti, Daniela and Slavin, Konstantin V},
  booktitle    = {2012 annual international conference of the IEEE engineering in medicine and biology society},
  title        = {A neural network-based design of an on-off adaptive control for Deep Brain Stimulation in movement disorders},
  year         = {2012},
  organization = {IEEE},
  pages        = {4140--4143},
  doi          = {10.1109/embc.2012.6346878},
}

@Article{medaglia2020personalizing,
  author    = {Medaglia, John D and Erickson, Brian and Zimmerman, Jared and Kelkar, Apoorva},
  journal   = {International Journal of Psychophysiology},
  title     = {Personalizing neuromodulation},
  year      = {2020},
  pages     = {101--110},
  volume    = {154},
  doi       = {10.1016/j.ijpsycho.2019.01.002},
  publisher = {Elsevier},
}

@Article{yu2021reinforcement,
  author    = {Yu, Chao and Liu, Jiming and Nemati, Shamim and Yin, Guosheng},
  journal   = {ACM Computing Surveys (CSUR)},
  title     = {Reinforcement learning in healthcare: A survey},
  year      = {2021},
  number    = {1},
  pages     = {1--36},
  volume    = {55},
  doi       = {10.1145/3477600},
  publisher = {ACM New York, NY},
}

@Article{arlotti2018eight,
  author    = {Arlotti, Mattia and Marceglia, Sara and Foffani, Guglielmo and Volkmann, Jens and Lozano, Andres M and Moro, Elena and Cogiamanian, Filippo and Prenassi, Marco and Bocci, Tommaso and Cortese, Francesca and others},
  journal   = {Neurology},
  title     = {Eight-hours adaptive deep brain stimulation in patients with Parkinson disease},
  year      = {2018},
  number    = {11},
  pages     = {e971--e976},
  volume    = {90},
  doi       = {10.1212/wnl.0000000000005121},
  publisher = {AAN Enterprises},
}

@Article{rosa2015adaptive,
  author    = {Rosa, Manuela and Arlotti, Mattia and Ardolino, Gianluca and Cogiamanian, Filippo and Marceglia, Sara and Di Fonzo, Alessio and Cortese, Francesca and Rampini, Paolo M and Priori, Alberto},
  journal   = {Movement Disorders},
  title     = {Adaptive deep brain stimulation in a freely moving parkinsonian patient},
  year      = {2015},
  number    = {7},
  pages     = {1003},
  volume    = {30},
  doi       = {10.1002/mds.26241},
  publisher = {Wiley},
}

@Article{swann2018adaptive,
  author    = {Swann, Nicole C and De Hemptinne, Coralie and Thompson, Margaret C and Miocinovic, Svjetlana and Miller, Andrew M and Ostrem, Jill L and Chizeck, Howard J and Starr, Philip A and others},
  journal   = {Journal of neural engineering},
  title     = {Adaptive deep brain stimulation for Parkinson’s disease using motor cortex sensing},
  year      = {2018},
  number    = {4},
  pages     = {046006},
  volume    = {15},
  doi       = {10.1088/1741-2552/aabc9b},
  publisher = {IOP Publishing},
}

@Article{bonizzato2023autonomous,
  author    = {Bonizzato, Marco and Hottin, Rose Guay and C{\^o}t{\'e}, Sandrine L and Massai, Elena and Choini{\`e}re, L{\'e}o and Macar, Uzay and Laferri{\`e}re, Samuel and Sirpal, Parikshat and Quessy, Stephan and Lajoie, Guillaume and others},
  journal   = {Cell Reports Medicine},
  title     = {Autonomous optimization of neuroprosthetic stimulation parameters that drive the motor cortex and spinal cord outputs in rats and monkeys},
  year      = {2023},
  number    = {4},
  volume    = {4},
  doi       = {10.1016/j.xcrm.2023.101008},
  publisher = {Elsevier},
}

@Article{choiniere2024gaussian,
  author    = {Choini{\`e}re, L{\'e}o and Guay-Hottin, Rose and Picard, R{\'e}mi and Lajoie, Guillaume and Bonizzato, Marco and Dancause, Numa},
  journal   = {STAR protocols},
  title     = {Gaussian-process-based Bayesian optimization for neurostimulation interventions in rats},
  year      = {2024},
  number    = {1},
  pages     = {102885},
  volume    = {5},
  doi       = {10.1016/j.xpro.2024.102885},
  publisher = {Elsevier},
}

@Article{laferriere2020hierarchical,
  author    = {Laferriere, Samuel and Bonizzato, Marco and C{\^o}t{\'e}, Sandrine L and Dancause, Numa and Lajoie, Guillaume},
  journal   = {IEEE Transactions on Neural Systems and Rehabilitation Engineering},
  title     = {Hierarchical Bayesian optimization of spatiotemporal neurostimulations for targeted motor outputs},
  year      = {2020},
  number    = {6},
  pages     = {1452--1460},
  volume    = {28},
  doi       = {10.1109/tnsre.2020.2987001},
  publisher = {IEEE},
}

@Article{sarikhani2022automated,
  author    = {Sarikhani, Parisa and Ferleger, Benjamin and Mitchell, Kyle and Ostrem, Jill and Herron, Jeffrey and Mahmoudi, Babak and Miocinovic, Svjetlana},
  journal   = {Journal of neural engineering},
  title     = {Automated deep brain stimulation programming with safety constraints for tremor suppression in patients with Parkinson’s disease and essential tremor},
  year      = {2022},
  number    = {4},
  pages     = {046042},
  volume    = {19},
  doi       = {10.1088/1741-2552/ac86a2},
  publisher = {IOP Publishing},
}

@Article{aiello2023recalibration,
  author    = {Aiello, Giovanna and Valle, Giacomo and Raspopovic, Stanisa},
  journal   = {Journal of Neural Engineering},
  title     = {Recalibration of neuromodulation parameters in neural implants with adaptive Bayesian optimization},
  year      = {2023},
  number    = {2},
  pages     = {026037},
  volume    = {20},
  doi       = {10.1088/1741-2552/acc975},
  publisher = {IOP Publishing},
}

@Article{grahn2014restoration,
  author    = {Grahn, Peter J and Mallory, Grant W and Berry, B Michael and Hachmann, Jan T and Lobel, Darlene A and Lujan, J Luis},
  journal   = {Frontiers in neuroscience},
  title     = {Restoration of motor function following spinal cord injury via optimal control of intraspinal microstimulation: toward a next generation closed-loop neural prosthesis},
  year      = {2014},
  pages     = {296},
  volume    = {8},
  doi       = {10.3389/fnins.2014.00296},
  publisher = {Frontiers Media SA},
}

@Article{losanno2021bayesian,
  author    = {Losanno, E and Badi, M and Wurth, S and Borgognon, S and Courtine, G and Capogrosso, M and Rouiller, EM and Micera, S},
  journal   = {Journal of Neural Engineering},
  title     = {Bayesian optimization of peripheral intraneural stimulation protocols to evoke distal limb movements},
  year      = {2021},
  number    = {6},
  pages     = {066046},
  volume    = {18},
  doi       = {10.1088/1741-2552/ac3f6c},
  publisher = {IOP Publishing},
}

@Article{rowald2022activity,
  author    = {Rowald, Andreas and Komi, Salif and Demesmaeker, Robin and Baaklini, Edeny and Hernandez-Charpak, Sergio Daniel and Paoles, Edoardo and Montanaro, Hazael and Cassara, Antonino and Becce, Fabio and Lloyd, Bryn and others},
  journal   = {Nature medicine},
  title     = {Activity-dependent spinal cord neuromodulation rapidly restores trunk and leg motor functions after complete paralysis},
  year      = {2022},
  number    = {2},
  pages     = {260--271},
  volume    = {28},
  doi       = {10.1038/s41591-021-01663-5},
  publisher = {Nature Publishing Group US New York},
}

@Article{wagner2018targeted,
  author    = {Wagner, Fabien B and Mignardot, Jean-Baptiste and Le Goff-Mignardot, Camille G and Demesmaeker, Robin and Komi, Salif and Capogrosso, Marco and Rowald, Andreas and Se{\'a}{\~n}ez, Ismael and Caban, Miroslav and Pirondini, Elvira and others},
  journal   = {Nature},
  title     = {Targeted neurotechnology restores walking in humans with spinal cord injury},
  year      = {2018},
  number    = {7729},
  pages     = {65--71},
  volume    = {563},
  doi       = {10.1038/s41586-018-0649-2},
  publisher = {Nature Publishing Group UK London},
}

@Article{capogrosso2013computational,
  author    = {Capogrosso, Marco and Wenger, Nikolaus and Raspopovic, Stanisa and Musienko, Pavel and Beauparlant, Janine and Luciani, Lorenzo Bassi and Courtine, Gr{\'e}goire and Micera, Silvestro},
  journal   = {Journal of Neuroscience},
  title     = {A computational model for epidural electrical stimulation of spinal sensorimotor circuits},
  year      = {2013},
  number    = {49},
  pages     = {19326--19340},
  volume    = {33},
  doi       = {10.1523/jneurosci.1688-13.2013},
  publisher = {Soc Neuroscience},
}

@Article{wang2023machine,
  author    = {Wang, David X and Ng, Nicole and Seger, Sarah E and Ekstrom, Arne D and Kriegel, Jennifer L and Lega, Bradley C},
  journal   = {Cerebral Cortex},
  title     = {Machine learning classifiers for electrode selection in the design of closed-loop neuromodulation devices for episodic memory improvement},
  year      = {2023},
  number    = {13},
  pages     = {8150--8163},
  volume    = {33},
  doi       = {10.1093/cercor/bhad105},
  publisher = {Oxford University Press},
}

@Article{greenhill2020bayesian,
  author    = {Greenhill, Stewart and Rana, Santu and Gupta, Sunil and Vellanki, Pratibha and Venkatesh, Svetha},
  journal   = {IEEE access},
  title     = {Bayesian optimization for adaptive experimental design: A review},
  year      = {2020},
  pages     = {13937--13948},
  volume    = {8},
  doi       = {10.1109/access.2020.2966228},
  publisher = {IEEE},
}

@Article{guay2025robust,
  author    = {Guay-Hottin, Rose and Kardassevitch, Lison and Pham, Hugo and Lajoie, Guillaume and Bonizzato, Marco},
  journal   = {Knowledge-Based Systems},
  title     = {Robust prior-biased acquisition function for human-in-the-loop Bayesian optimization},
  year      = {2025},
  pages     = {113039},
  doi       = {10.1016/j.knosys.2025.113039},
  publisher = {Elsevier},
}