Publications
- Molina Catricheo, Constanza Andrea, Boeder, Simon, Guo, Ting, May, G., Berthelot, C., Tuia, Devis, Reinhard, Friedrich Fedor, Remondino, Fabio, and Risse, Benjamin. . NEST3D: A High-Resolution Multimodal Dataset of Sociable Weaver Tree Nests arXiv. doi: 10.48550/ARXIV.2606.14562.
- Radas, Jonathan, Risse, Benjamin, and Vogl, Raimund. . “UniGPT Revisited: From a Simple Chatbot to an API-First AI Platform — Two Years of On-Premises LLM Operations.” in Proceedings of EUNIS 2026 Annual Congress, Vol. 109 of EPiC Series in Computing, edited by Laurence Desnos, Carmen Diaz, Janina Mincer-Daszkiewicz, Lazaros Merakos, Raimund Vogl and Stuart Lucke Ulrike McLellan. online: EasyChair. doi: 10.29007/4rq8.
- Fisch, L, Winter, NR, Goltermann, J, Barkhau, C, Emden, D, Ernsting, J, Konowski, M, Leenings, R, Borgers, T, Flinkenflügel, K, Grotegerd, D, Kraus, A, Leehr, EJ, Meinert, S, Stein, F, Teutenberg, L, Thomas-Odenthal, F, Usemann, P, Hermesdorf, M, Jamalabadi, H, Jansen, A, Nenadić, I, Straube, B, Kircher, T, Berger, K, Risse, B, Dannlowski, U, and Hahn, T. . “deepmriprep: voxel-based morphometry preprocessing via deep neural networks.” Preprint. Nature Computational Science: 1–10.
- Lundquist, UPS, Afridi, S, Berthelot, C, Ngoc, Dat N, Hlebowicz, K, Iannino, E, Laporte-Devylder, L, Maalouf, G, May, G, Meier, K, Molina, Catricheo CA, Rolland, EGA, Rondeau, Saint-Jean C, Shukla, V, Burghardt, T, Christensen, AL, Costelloe, BR, Damen, M, Flack, A, Jensen, K, Midtiby, HS, Mirmehdi, M, Remondino, F, Richardson, T, Risse, B, Tuia, D, Wahlberg, M, Cawthorne, D, Bullock, S, Njoroge, W, Mutisya, S, Watson, M, and Pastucha, E. . “WildDrone: autonomous drone technology for monitoring wildlife populations.” Frontiers in Robotics and AI Volume 12 - 2025. doi: 10.3389/frobt.2025.1695319.
- Boeder, S, Gigengack, F, Roesler, S, Caesar, H, and Risse, B. in Kürze. “ShelfOcc: Native 3D Supervision beyond LiDAR for Vision-Based Occupancy Estimation.” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), edited by T. Kanade, Shimon Ullman, Chandra Kambhamettu and Dimitris N. Metaxas. Denver, USA: IEEE/CVF.
- Becker, M, Konrad, J, Rodriguez, LG, and Risse, B. . “Random Label Prediction Heads for Studying Memorization in Deep Neural Networks.” in The Fourteenth International Conference on Learning Representations (ICLR), edited by Carl Vondrick, Bharath Hariharan, Aleksandra Faust, Lerrel Pinto, Diyi Yang, Colin Raffel and Zhenyu Xue. Rio de Janeiro, Brazil: OpenReview.
- Pielage, Leon, Hätscher, Ole, Back, Mitja, Marschall, Bernhard, and Risse, Benjamin. . “Dynamic Personality Adaptation in Large Language Models via State Machines.” Preprint. Lecture notes in computer science 16817: 509–523. doi: 10.1007/978-3-032-31673-8_34.
- Becker, M, Drees, D, Brückerhoff-Plückelmann, F, Schuck, C, Pernice, W, and Risse, B. . “Activation Functions in Non-Negative Neural Networks.” IEEE Access doi: 10.1109/ACCESS.2025.3622408.
- Pielage, Leon, Schmidle, Paul, Marschall, Bernhard, and Risse, Benjamin. . “Interactive High-Quality Skin Lesion Generation using Diffusion Models for VR-based Dermatological Education.” in IUI '25: Proceedings of the 30th International Conference on Intelligent User Interfaces, edited by Association for Computing Machinery. New York, NY, United States: ACM Press. doi: 10.1145/3708359.3712101.
- Junga, Anna, Kockwelp, Pascal, Valkov, Dimitar, Schulze, Henriette, Bozdere, Philipp, Hätscher, Ole, Ahrens, Helmut, Marschall, Bernhard, Risse, Benjamin, and Holling, Markus. . “Teach the unteachable with a virtual reality (VR) brain death scenario - 800 students and 3 years of experience.” Perspectives on Medical Education 14 (1): 45–54. doi: 10.5334/pme.1427.
- Baumberger, M, Haas, B, Tewes, W, Risse, B, Meyer, N, and Meyer, H. . “Gated recurrent units for modelling time series of soil temperature and moisture: An assessment of performance and process reflectivity.” Environmental Modelling and Software 183: 106245–106245. doi: 10.1016/j.envsoft.2024.106245.
- Thiele, Sebastian, Kockwelp, Jacqueline, Wistuba, Joachim, Kliesch, Sabine, Gromoll, Jörg, and Risse, Benjamin. . “Investigating Imaging, Annotation and Self-Supervision for the Classification of Continuously Developing Cells in Histological Whole Slide Images.” contribution to the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), Tucson, Arizona
- Kockwelp, Jacqueline, Beckmann, Daniel, and Risse, Benjamin. . “Human Gaze Improves Vision Transformers by Token Masking.” contribution to the Gaze Meets Computer Vision @ Winter Conference on Applications of Computer Vision (WACV) Workshops , Tucson, Arizona
- Radas, J, Risse, B, and Vogl, R. . “Building UniGPT: A Customizable On-Premise LLM-Solution for Universities.” in Proceedings of EUNIS 2024 annual congress in Athens, EPiC Series in Computing, edited by R Vogl, L Desnos, J Desnos, S Bolis, L Merakos, G Ferrell, E Tsili and M Roumeliotis. EPiC Series in Computing: EasyChair. doi: 10.29007/jv1l.
- Porschen, Christian and Ernsting, Jan and Brauckmann, Paul and Weiss, Raphael and Würdemann, Till and Booke, Hendrik and Amini, Wida and Maidowski, Ludwig and Risse, Benjamin and Hahn, and Tim and von Groote, Thilo. . “pyAKI—An open source solution to automated acute kidney injury classification.” PloS one 20 (1) e0315325.
- Garcia Rodriguez, Luis, Konrad, Jonas, Drees, Dominik, and Risse, Benjamin. . “S-ROPE: Spectral Frame Representation of Periodic Events.” in Computer Vision – ECCV 2024 Workshops, Vol. 15646 of Lecture Notes in Computer Science, edited by Alessio Del Bue, Cristian Canton, Jordi Pont-Tuset and Tatiana Tommasi. Cham: Springer Nature. doi: 10.1007/978-3-031-92460-6.
- Boeder, S, and Risse, B. . “OccFlowNet: Occupancy Estimation via Differentiable Rendering and Occupancy Flow.” in 2025 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), edited by IEEE. published: Wiley-IEEE Computer Society Press.
- Boeder, S, Gigengack, F, and Risse, B. . “LangOcc: Open Vocabulary Occupancy Estimation via Volume Rendering.” in International Conference on 3D Vision 2025, edited by CVF.
- Boeder, S, Gigengack, F, and Risse, B. . “GaussianFlowOcc: Sparse and Weakly Supervised Occupancy Estimation using Gaussian Splatting and Temporal Flow.” Preprint. arXiv
- Junga, A., Bozdere, P., Hätscher, O., Scherzer, S., Schmidle, P., Schulze, H., Pielage, L., Kockwelp, P., Meyerheim, M., Mergen, M., Risse, B., Marschall, B., Glückselig, T., and Ungru, K. . “Rethinking interaction design: Special implications for interaction concepts in medical education using virtual reality.” Virtual Reality 29 (98). doi: 10.1007/s10055-025-01180-7.
- Ernsting, J, Beeken, PN, Ogoniak, L, Kockwelp, J, Roll, W, Hahn, T, Busch, AS, and Risse, B. . “Towards population scale testis volume segmentation in DIXON MRI.” Computers in Biology and Medicine 198: 111139–111139. doi: 10.1016/j.compbiomed.2025.111139.
- Hüffer, P, Degbelo, A, and Risse, B. . “Geovicla: Automated Classification of Interactive Web-Based Geovisualizations.” in Leibniz International Proceedings in Informatics (LIPIcs), Vol. 12 of Proceedings of the 13th International Conference on Geographic Information Science (GIScience 2025), edited by Katarzyna and Moore Sila-Nowicka, David and Adams Antoni and O'Sullivan and Mark Benjamin and Gahegan. dagstuhl.de: Dagstuhl Publishing. doi: 10.4230/LIPIcs.GIScience.2025.10.
- Bigge, J, Ogueta, M, Garcia, L, and Risse, B. . “Hatching-Box: Automated in situ monitoring of Drosophila melanogaster development in standard rearing vials.” PloS one 20 (9): e0331556–e0331556.
- Wu, J, Beckmann, D, Miller, S, Altmayer, S, Chang, K, Dashevsky, B, Risse, B, Gruhl, D, and Davidzon, G. . “Gaze-assisted agent for safer integration of [18F] FDG-PET/CT AI lesion prediction into clinical workflow.” Journal of Nuclear Medicine 66 (supplement 1): 251398–251398.
- Homberg, Samuel K.R., Modlich, Malte L., Becker, Marlon, Menke, Janosch, Morris, Garrett M., Risse, Benjamin, and Koch, Oliver. . “Interpreting Graph Neural Networks with Myerson Values for Cheminformatics Approaches.” in Artificial Neural Networks and Machine Learning. ICANN 2025 International Workshops and Special Sessions, Vol. 5 of Artificial Neural Networks and Machine Learning - ICANN 2025 International Workshops and Special Sessions, edited by Senn Walter, Sanguineti Marcello, Saudargiene Ausra, V.Tetko Igor, E.P. Villa Alessandro, Jirsa Viktor and Bengio Yoshua. LNCS 16072: Springer Nature. doi: 10.1007/978-3-032-04552-2.
- Kockwelp, Jacqueline, Kliesch, Sabine, Gromoll, Jörg, Wistuba, Joachim, and Risse, Benjamin. . “MARTHA - Combining gaze into deep learning for fully quantitative human testicular histology analysis.” Computers in Biology and Medicine 199: 111270. doi: 10.1016/j.compbiomed.2025.111270.
- Becker, Marlon, Altrock, Frederick, and Risse, Benjamin. . “Momentum-SAM: Sharpness Aware Minimization without Computational Overhead.” in Advances in Neural Information Processing Systems 39 (NeurIPS 2025), edited by Danielle Belgrave, Cheng Zhang, Laura Montoya, Hsuan-Tien Lin, Razvan Pascanu, Piotr Koniusz, Marzyeh Ghassemi and Nancy Chen. San Diego: Neural Information Processing Systems Foundation, Inc. (NeurIPS). doi: https://doi.org/10.52202/085713-1850.
- Schilling, M, and Risse, B. . “Cognition in motion: Functional internal models as an evolutionary scaffold in cognitive control.” Behavioral and Brain Sciences 48: e95–e95.
- Boeder, Simon, Gigengack, Fabian, and Risse, Benjamin. . “Gaussianflowocc: Sparse and weakly supervised occupancy estimation using gaussian splatting and temporal flow.” in Proceedings of the IEEE/CVF International Conference on Computer Vision, edited by Hilde Kuehne, Gerard Medioni, Dimitris Samaras, Jingyi Yu and Ramin Zabih. Honolulu, Hawaii: Wiley-IEEE Computer Society Press.
- Becker, Marlon, Butz, Marco, Lemli, David, Schuck, Carsten, and Risse, Benjamin. . “Learning Proposal Distributions in Simulated Annealing via Template Networks: A Case Study in Nanophotonic Inverse Design.” in Pattern Recognition, Vol. 27 of 27th International Conference ICPR 2024, edited by Antonacopoulos Apostolos, Chaudhuri Subhasis, Chellappa Rama, Liu Cheng-Lin, Bhattacharya Saumik and Pal Umapada. Kolkata, India: Springer. doi: 10.1007/978-3-031-78186-5_13.
- Kockwelp, Pascal, Meyerheim, Marcel, Valkov, Dimitar, Mergen, Marvin, Junga, Anna, Krüger, Antonio, Marschall, Bernhard, Holling, Markus, and Risse, Benjamin. . “VR-based Competence Training at Scale: Teaching Clinical Skills in the Context of Virtual Brain Death Examination.” Proceedings of the ACM on Human-Computer Interaction 8 261. doi: 10.1145/3664635.
- Schulte, L, Butz, M, Becker, M, Risse, B, and Schuck, C. . “Accelerating Finite-Difference Frequency-Domain Simulations for Inverse Design Problems in Nanophotonics using Deep Learning.” Journal of the Optical Society of America B 41 (4): 1039–1046. doi: 10.1364/JOSAB.506159.
- Junga, Anna, Schulze, Henriette, Scherzer, Sönke, Hätscher, Ole, Bozdere, Philipp, Schmidle, Paul, Risse, Benjamin, and Marschall, Bernhard. . “Immersive learning in medical education: analyzing behavioral insights to shape the future of VR-based courses.” BMC Medical Education 2024 (24) 1413. doi: 10.1186/s12909-024-06337-7.
- Kockwelp, Jacqueline, Thiele, Sebastian, Bartsch, Jannis, Haalck, Lars, Gromoll, Jörg, Schlatt, Stefan, Exeler, Rita, Bleckmann, Annalen, Lenz, Georg, Wolf, Sebastian, Steffen, Björn, Berdel, Wolfgang Eduard, Schliemann, Christoph, Risse, Benjamin, and Angenendt, Linus. . “Deep learning predicts therapy-relevant genetics in acute myeloid leukemia from Pappenheim-stained bone marrow smears.” Blood Advances 8 (1): 70–79. doi: 10.1182/bloodadvances.2023011076.
- Beckmann, Daniel, Kockwelp, Jacqueline, Gromoll, Joerg, Kiefer, Friedemann, and Risse, Benjamin. . “SAM meets Gaze: Passive Eye Tracking for Prompt-based Instance Segmentation.” Proceedings of Machine Learning Research 2023.
- Haalck, Lars, and Risse, Benjamin. . “Solving the Plane-Sphere Ambiguity in Top-Down Structure-from-Motion.” contribution to the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), Waikoloa, Hawaii doi: 10.1109/WACV57701.2024.00345.
- Gebauer, Eike, Thiele, Sebastian, Ouvrard, Pierre, Sicard, Adrien, and Risse, Benjamin. . “Towards a Dynamic Vision Sensor-based Insect Camera Trap.” contribution to the Winter Conference on Applications of Computer Vision 2024, Waikoloa, Hawaii
- Porschen, C, Ernsting, J, Brauckmann, P, Weiss, R, Würdemann, T, Booke, H, Amini, W, Maidowski, L, Risse, B, Hahn, T, and Groote, T. . “pyAKI - An Open Source Solution to Automated KDIGO classification.” Preprint. arXiv doi: 10.48550/arXiv.2401.12930.
- Young, S, Schiffer, C, Wagner, A, Patz, J, Potapenko, A, Herrmann, L, Nordhoff, V, Pock, T, Krallmann, C, Stallmeyer, B, Röpke, A, Kierzek, M, Biagioni, C, Wang, T, Haalck, L, Deuster, D, Hansen, JN, Wachten, D, Risse, B, Behre, HM, Schlatt, S, Kliesch, S, Tüttelmann, F, Brenker, C, and Strünker, T. . “Human fertilization in vivo and in vitro requires the CatSper channel to initiate sperm hyperactivation.” Journal of Clinical Investigation 134 (1). doi: 10.1172/JCI173564.
- Winter, NR, Blanke, J, Leenings, R, Ernsting, J, Fisch, L, Sarink, K, Barkhau, C, Emden, D, Thiel, K, Flinkenflügel, K, Winter, A, Goltermann, J, Meinert, S, Dohm, K, Repple, J, Gruber, M, Leehr, EJ, Opel, N, Grotegerd, D, Redlich, R, Nitsch, R, Bauer, J, Heindel, W, Gross, J, Risse, B, Andlauer, TFM, Forstner, AJ, Nöthen, MM, Rietschel, M, Hofmann, SG, Pfarr, JK, Teutenberg, L, Usemann, P, Thomas-Odenthal, F, Wroblewski, A, Brosch, K, Stein, F, Jansen, A, Jamalabadi, H, Alexander, N, Straube, B, Nenadic, I, Kircher, T, Dannlowski, U, and Hahn, T. . “A Systematic Evaluation of Machine Learning--Based Biomarkers for Major Depressive Disorder.” JAMA Psychiatry 81 (4): 386–395. doi: 10.1001/jamapsychiatry.2023.5083.
- Bauer, N, Beckmann, D, Reinhardt, D, Frost, N, Bobe, S, Erapaneedi, R, Risse, B, and Kiefer, F. . “Therapy-induced modulation of tumor vasculature and oxygenation in a murine glioblastoma model quantified by deep learning-based feature extraction.” Scientific Reports 14 (1): 2034–2034. doi: 10.1038/s41598-024-52268-0.
- Fisch, L., Zumdick, S., Barkhau, C., Emden, D., Ernsting, J., Leenings, R., Sarink, K., Winter, N.R., Risse, B., Dannlowski, U., and Hahn, T. . “deepbet: Fast brain extraction of T1-weighted MRI using Convolutional Neural Networks.” Computers in Biology and Medicine 179. doi: 10.1016/j.compbiomed.2024.108845.
- Shukla, Vandita, Morelli, Luca, Remondino, Fabio, Micheli, Andrea, Tuia, Devis, and Risse, Benjamin. . “Towards Estimation of 3D Poses and Shapes of Animals from Oblique Drone Imagery.” contribution to the ISPRS Technical Commission II Symposium 2024, Las Vegas
- Schwarz, S, Clement, L, Haalck, L, Risse, B, and Wystrach, A. . “Compensation to visual impairments and behavioral plasticity in navigating ants.” Proceedings of the National Academy of Sciences of the United States of America 121 (48): e2410908121.. doi: 10.1073/pnas.2410908121.
- Brückerhoff-Plückelmann, F, Borras, H, Klein, B, Varri, A, Becker, M, Dijkstra, J, Brückerhoff, M, Wright, CD, Salinga, M, Bhaskaran, H, Risse, B, Fröning, H, and Pernice, W. . “Probabilistic photonic computing with chaotic light.” Nature Communications 15 (1): 10445–10445. doi: 10.1038/s41467-024-54931-6.
- Becker, Marlon, and Risse, Benjamin. . “Learned Random Label Predictions as a Neural Network Complexity Metric.” contribution to the Workshop on Scientific Methods for Understanding Deep Learning @NeurIPS , Vancouver
- Boeder, S, Gigengack, F, and Risse, B. . “Occflownet: Towards self-supervised occupancy estimation via differentiable rendering and occupancy flow.” Preprint. arXiv
- Boeder, S, Gigengack, F, and Risse, B. . “Langocc: Self-supervised open vocabulary occupancy estimation via volume rendering.” Preprint. arXiv
- Hätscher, Ole, Junga, Anna, Schulze, Henriette, Kockwelp, Pascal, Risse, Benjamin, Back, Mitja, and Marschall, Bernhard. . “Integration of VR into Medical Education (Workshop).” in Würtual Reality, edited by 2023 University of Würzburg, Department of Psychology I (Marcusstr. 9-11, 97070 Würzburg). Würzburg: University of Würzburg, Department of Psychology. doi: 10.25972/OPUS-31720.
- Barrie, Robert, Haalck, Lars, Risse, Benjamin, Nowotny, Thomas, Graham, Paul, and Buehlman, Cornelia. . “Trail using ants follow idiosyncratic routes in complex landscapes.” Learning and Behavior s13420-023-00615. doi: 10.3758/s13420-023-00615-y.
- Schulze, Henriette, Junga, Anna, Hätscher, Ole, Kockwelp, Pascal, Risse, Benjamin, Holling, Markus, and Marschall, Bernhard. . “Hirntoddiagnostik in Virtual Reality – was denken Studierende darüber?” contributed to the Jahrestagung der Gesellschaft für Medizinische Ausbildung (GMA) 2023, Osnabrück. doi: 10.3205/23GMA227.
- Hätscher, Ole, Junga, Anna, Schulze, Henriette, Kockwelp, Pascal, Risse, Benjamin, Back, D.Mitja, and Marschall, Bernhard. . “Zusammenhang von Persönlichkeitsvariablen und Leistung in der virtuellen medizinischen Ausbildung.” contributed to the Jahrestagung der Gesellschaft für medizinische Ausbildung (GMA) 2023, Osnabrück. doi: 10.3205/23GMA273.
- Butz, Marco, Abazi, Adrian S., Ross, Rene, Risse, Benjamin, and Schuck, Carsten. . “Inverse Design of Nanophotonic Devices using Dynamic Binarization.” Optics Express 31 (10): 15747–15756. doi: 10.1364/OE.484484.
- Wendland, D, Becker, M, Brückerhoff-Plückelmann, F, Bente, I, Busch, K, Risse, B, and Pernice, WH. . “Coherent dimension reduction with integrated photonic circuits exploiting tailored disorder.” Journal of the Optical Society of America B 40 (3): B35–B40.
- Haalck, L, Mangan, M, Wystrach, A, Clement, L, Webb, B, and Risse, B. . “CATER: Combined Animal Tracking & Environment Reconstruction.” Science advances 9 (16): eadg2094–eadg2094.
- Rösler, W, Altenbuchinger, M, Bae{ß}ler, B, Beissbarth, T, Beutel, G, Bock, R, Bubnoff, N, Eckardt, J, Foersch, S, Loeffler, CM, and others. . “An overview and a roadmap for artificial intelligence in hematology and oncology.” Journal of Cancer Research and Clinical Oncology 15: 1–10.
- Butz, M, Leifhelm, A, Becker, M, Risse, B, and Schuck, C. . “A Universal Approach to Nanophotonic Inverse Design through Reinforcement Learning.” in CLEO 2023, paper STh4G.3, edited by Publishing Group Optica. San Jose: Optica. doi: 10.1364/CLEO_SI.2023.STh4G.3.
- Butz, Marco, Leifhelm, Alexander, Becker, Marlon, Risse, Benjamin, and Schuck, Carsten. . “A Novel Approach to Nanophotonic Black-Box Optimization Through Reinforcement Learning.” in Q 30 Nano-optics, edited by DPG. Hannover: Deutsche Physikalische Gesellschaft.
- Kockwelp, Jacqueline, Gromoll, Jörg, Wistuba, Joachim, and Risse, Benjamin. . “EyeGuide - From Gaze Data to Instance Segmentation.” contribution to the The British Machine Vision Conference (BMVC), Aberdeen
- Haalck, Lars, Thiele, Sebastian, and Risse, Benjamin. . “Tracking Tiny Insects in Cluttered Natural Environments using Refinable Recurrent Neural Networks.” contribution to the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), Waikoloa, Hawaii doi: 10.1109/WACV57701.2024.00697.
- Brückerhoff-Plückelmann, Frank, Bente, Ivonne, Becker, Marlon, Vollmar, Niklas, Farmakidis, Nikolaos, Lomonte, Emma, Lenzini, Francesco, Wright, CDavid, Bhaskaran, Harish, Salinga, Martin, Risse, Benjamin, and Pernice, Wolfram HP. . “Event-driven adaptive optical neural network.” Science advances 9 (42): eadi9127. doi: 10.1126/sciadv.adi9127.
- Becker, Marlon, Drees, Dominik, Brückerhoff-Plückelmann, Frank, Schuck, Carsten, Pernice, Wolfram, and Risse, Benjamin. . “Activation Functions in Non-Negative Neural Networks.” contributed to the Machine Learning and the Physical Sciences Workshop, NeurIPS, New Orleans.
- Pielage, Leon, Schmidle, Paul, Marschall, Bernhard, and Risse, Benjamin. . “Diffusion Models in Dermatological Education: Flexible High Quality Image Generation for VR-based Clinical Simulations.” contributed to the NeurIPS'23 Workshop: Generative AI for Education (GAIED), New Orleans, Louisiana.
- Döll, Petra, Sester, Monika, Feuerhake, Udo, Frahm, Holger, Fritzsch, Bernadette, Hezel, Dominik C, Kaus, Boris, Kolditz, Olaf, Linxweiler, Jan, Müller Schmied, Hannes, Nyenah, Emmanuel, Risse, Benjamin, Schielein, Ulrich, Schlauch, Tobias, Streck, Thilo, and van den Oord, Gijs. . “Sustainable research software for high-quality computational research in the Earth System Sciences: Recommendations for universities, funders and the scientific community in Germany.” Preprint. FIG GEO-LEO e-docs doi: 10.23689/fidgeo-5805.
- Becker, Marlon, Riegelmeyer, Jan, Seyfried, Maximilian David, Ravoo, Bart Jan, Schuck, Carsten, and Risse, Benjamin. . “Adaptive Photochemical Nonlinearities for Optical Neural Networks.” Advanced Intelligent Systems 5 (12). doi: 10.1002/aisy.202300229.
- Becker, Marlon, Butz, Marco, Lemli, David, Schuck, Carsten, and Risse, Benjamin. . “Combinatorial Optimization via Memory Metropolis: Template Networks for Proposal Distributions in Simulated Annealing applied to Nanophotonic Inverse Design.” contributed to the Neural Information Processing Systems (NeurIPS) Workshop on AI for Accelerated Materials Design (AI4Mat-2023), New Orleans.
- Mergen, Marvin*, Junga, Anna*, Risse, Benjamin, Valkov, Dimitar, Graf, Norbert, and Marschall, Bernhard. . “Immersive training of clinical decision making with AI driven virtual patients-a new VR platform called medical tr.AI.ning.” GMS Journal for Medical Education 40 (2). doi: 10.3205/zma001600.
- Junga, Anna, Kockwelp, Pascal, Valkov, Dimitar, Marschall, Bernhard, Hartwig, Sophia, Stummer, Walter, Risse, Benjamin, and Holling, Markus. . “Virtual Reality based teaching – a paradigm shift in education?” contributed to the 73. Jahrestagung Deutsche Gesellschaft für Neurochirurgie, Köln. doi: 10.3205/22DGNC538.
- Bobe, S, Beckmann, D, Klump, DM, Dierkes, C, Kirschnick, N, Redder, E, Bauer, N, Schäfers, M, Erapaneedi, R, Risse, B, van, de Pavert SA, and Kiefer, F. . “Volumetric imaging reveals VEGF-C-dependent formation of hepatic lymph vessels in mice.” Frontiers in cell and developmental biology 10: 949896–949896. doi: 10.3389/fcell.2022.949896.
- Hahn, T, Ernsting, J, Winter, NR, Holstein, V, Leenings, R, Beisemann, M, Fisch, L, Sarink, K, Emden, D, Opel, N, Redlich, R, Repple, J, Grotegerd, D, Meinert, S, Hirsch, JG, Niendorf, T, Endemann, B, Bamberg, F, Kröncke, T, Bülow, R, Völzke, H, von, Stackelberg O, Sowade, RF, Umutlu, L, Schmidt, B, Caspers, S, Kugel, H, Kircher, T, Risse, B, Gaser, C, Cole, JH, Dannlowski, U, and Berger, K. . “An Uncertainty-Aware, Shareable and Transparent Neural Network Architecture for Brain-Age Modeling.” Science advances 8 (1): eabg9471–eabg9471. doi: 10.1126/sciadv.abg9471.
- Tuia, D, Kellenberger, B, Beery, S, Costelloe, BR, Zuffi, S, Risse, B, Mathis, A, Mathis, MW, van, Langevelde F, Burghardt, T, Kays, R, Klinck, H, Wikelski, M, Couzin, ID, van, Horn G, Crofoot, MC, Stewart, CV, and Berger-Wolf, T. . “Perspectives in machine learning for wildlife conservation.” Nature Communications 13 (1): 792–807. doi: 10.1038/s41467-022-27980-y.
- Kockwelp, P, Junga, A, Valkov, D, Marschall, B, Holling, M, and Risse, B. . “Towards VR Simulation-Based Training in Brain Death Determination.” contribution to the 2022 IEEE Conference on Virtual Reality and 3D User Interfaces Abstracts and Workshops (VRW), Christchurch doi: 10.1109/VRW55335.2022.00065.
- Thiele, Sebastian, and Risse, Benjamin. . “Narrowing Attention in Capsule Networks.” in 26th International Conference on Pattern Recognition, edited by IEEE. 26th International Conference on Pattern Recognition (ICPR): Wiley-IEEE Press.
- Kockwelp, Jacqueline, Thiele, Sebastian, Kockwelp, Pascal, Bartsch, Jannis, Schliemann, Christoph, Angenendt, Linus, and Risse, Benjamin. . “Cell Selection-based Data Reduction Pipeline for Whole Slide Image Analysis of Acute Myeloid Leukemia.” in The IEEE / CVF Computer Vision and Pattern Recognition Conference (CVPR), In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, edited by IEEE/CVF. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. doi: 10.1109/CVPRW56347.2022.00199.
- Riegelmeyer, Jan, Eich, Alexander, Becker, Marlon, Risse, Benjamin, and Schuck, Carsten. . “Development of a nanophotonic nonlinear unit for optical artificial neural networks.” contributed to the DPG Springmeeting 2022, Erlangen.
- Butz, Marco, Leifhelm, Alexander, Becker, Marlon, Risse, Benjamin, and Schuck, Carsten. . “Inverse Design of Nanophotonic Devices based on Reinforcement Learning.” in Q 38 Photonics II, edited by DPG. Erlangen: Deutsche Physikalische Gesellschaft.
- Bian, A, Jiang, X, Berh, D, and Risse, B. . “Resolving colliding larvae by fitting ASM to random walker-based pre-segmentations.” IEEE/ACM Transactions on Computational Biology and Bioinformatics 18 (3): 1184–1194.
- Valkov, Dimitar Thiele Sebastian, and Huesmann, Karim Risse Benjamin. . “Touch Recognition on Complex 3D Printed Surfaces using Filter Response Analysis.” in IEEE Conference on Virtual Reality and 3D User Interfaces Abstracts and Workshops (VRW), edited by IEEE. online: Wiley-IEEE Computer Society Press. doi: 10.1109/VRW52623.2021.00043.
- Huesmann, Karim Rodriguez Luis Garcia, and Linsen, Lars Risse Benjamin. . “The Impact of Activation Sparsity on Overfitting in Convolutional Neural Networks.” in The Impact of Activation Sparsity on Overfitting in Convolutional Neural Networks Springer International Publishing.
- Haalck, Lars Risse Benjamin. . “Embedded Dense Camera Trajectories in Multi-Video Image Mosaics by Geodesic Interpolation-based Reintegration.” contribution to the Winter Conference on Applications of Computer Vision, Waikoloa, Hawaii
- Thiele, Sebastian, Haalck, Lars, Struffert, Marvin, Scherber, Christoph, and Risse, Benjamin. . “Towards Visual Insect Camera Traps.” contribution to the International Conference on Pattern Recognition (ICPR) Workshop on Visual observation and analysis of Vertebrate And Insect Behavior (VAIB), Milan
- Leenings, R, Winter, NR, Plagwitz, L, Holstein, V, Ernsting, J, Sarink, K, Fisch, L, Steenweg, J, Kleine-Vennekate, L, Gebker, J, Emden, D, Grotegerd, D, Opel, N, Risse, B, Jiang, X, Dannlowski, U, and Hahn, T. . “PHOTONAI-A Python API for rapid machine learning model development.” PloS one 16. doi: 10.1371/journal.pone.0254062.
- Huesmann, K, Klemm, S, Linsen, L, and Risse, B. . Exploiting the Full Capacity of Deep Neural Networks while Avoiding Overfitting by Targeted Sparsity Regularization arXiv e-print:2002.09237: CoRR.
- Leenings, R, Winter, NR, Plagwitz, L, Holstein, V, Ernsting, J, Steenweg, J, Gebker, J, Sarink, K, Emden, D, Grotegerd, D, and others. . “PHOTON--A Python API for Rapid Machine Learning Model Development.” arXiv preprint arXiv:2002.05426 2020.
- Neuert, H, Deing, P, Krukkert, K, Naffin, E, Steffes, G, Risse, B, Silies, M, and Klämbt, C. . “The Drosophila NCAM homolog Fas2 signals independently of adhesion.” Development 147 (2). doi: 10.1242/dev.181479.
- Haalck, L, Mangan, M, Webb, B, and Risse, B. . “Towards image-based animal tracking in natural environments using a freely moving camera.” Journal of Neuroscience Methods 330: 108455.. doi: 10.1016/j.jneumeth.2019.108455.
- Gkanias, E, Risse, B, Mangan, M, and Webb, B. . “From skylight input to behavioural output: a computational model of the insect polarised light compass.” PLoS Computational Biology 15 (7): e1007123.. doi: 10.1371/journal.pcbi.1007123.
- Berh, D, Scherzinger, A, Otto, N, Jiang, X, Klämbt, C, and Risse, B. . “Automatic non-invasive heartbeat quantification of Drosophila pupae.” Computers in Biology and Medicine 93: 189–199.
- Otto, N, Marelja, Z, Schoofs, A, Kranenburg, H, Bittern, J, Yildirim, K, Berh, D, Bethke, M, Thomas, S, Rode, S, Risse, B, Jiang, X, Pankratz, M, Leimkuehler, S, and Klämbt, C. . “The Sulfite Oxidase Shopper controls neuronal activity by regulating glutamate homeostasis in Drosophila ensheathing glia.” Nature Communications 9 (1): 3514.
- Kiel, M, Berh, D, Daniel, J, Otto, N, Steege, A, Jiang, X, Liebau, E, and Risse, B. . “A Multi-Purpose Worm Tracker Based on FIM.” Preprint. bioRxiv
- Risse, B, Mangan, M, and Webb, B. . “Possibilities, Constraints and Limitations of Image-based Animal Tracking in Natural Environments.” contribution to the Measuring Behavior, Manchester, UK
- Risse, B, Mangan, M, Stürzl, W, and Webb, B. . “Software to convert terrestrial LiDAR scans of natural environments into photorealistic meshes.” Environmental Modelling and Software 99: 88–100. doi: 10.1016/j.envsoft.2017.09.018.
- Klemm, S, Jiang, X, and Risse, B. . “Deep distance transform to segment visually indistinguishable merged objects.” contribution to the Proc. of 40th German Conference on Pattern Recognition (GCPR), Stuttgart
- Almeida-Carvalho MJ, Berh D, ......, Jiang X, ......, Risse B, and ......, Zlatic M. . “The Ol1mpiad: Concordance of behavioural faculties of stage 1 and stage 3 Drosophila larvae.” Journal of Experimental Biology 220: 2452–2475. doi: 10.1242/jeb.156646.
- Risse, B, Berh, D, Otto, N, Klämbt, C, and Jiang, X. . “FIMTrack: An open source tracking and locomotion analysis software for small animals.” PLoS Computational Biology 13 (5): e1005530.. doi: 10.1371/journal.pcbi.1005530.
- Berh, D, Risse, B, Michels, T, Otto, N, Jiang, X, and Klämbt, C. . “A FIM-based long-term in-vial monitoring system for Drosophila larvae.” IEEE Transactions on Biomedical Engineering 64 (8): 1862–1874.
- Risse, B, Mangan, M, Del, Pero L, and Webb, B. . “Visual Tracking of Small Animals in Cluttered Natural Environments Using a Freely Moving Camera.” in Proceedings of the IEEE International Conference on Computer Vision (ICCV), 2017, edited by Vision Foundation Computer. Venice: Wiley-IEEE Computer Society Press. doi: 10.1109/ICCVW.2017.335.
- Otto, N, Risse, B, Berh, D, Bittern, J, Jiang, X, and Klämbt, C. . “Interactions among Drosophila larvae before and during collision.” Scientific Reports 11 (6): 31564. doi: 10.1038/srep31564.
- Risse, B, Mangan, M, and Webb, B. . “Tracking, Mapping and Reconstruction. Modelling the Visual Perception of Desert Ants.” contribution to the Animal Movement International Symposium, Lund, Sweden
- Risse, B, Mangan, M, and Webb, B. . “Habitat3D: Recreating the History of Visual Experience of Individual Insects.” contribution to the International Congress of Neuroethology, Montevideo, Uruguay
- Risse, B, Mangan, M, Del, Pero L, and Webb, B. . “HabiTracks: Visual Tracking of Insects in Their Natural Habitat.” contribution to the International Congress of Neuroethology, Montevideo, Uruguay
- Risse, B, Otto, N, Berh, D, Jiang, X, Kiel, M, and Klämbt, C. . “FIM2c : A Multi-Colour, Multi-Purpose Imaging System to Manipulate and Analyse Animal Behaviour.” IEEE Transactions on Biomedical Engineering 64: 1–1..
- Risse, B., Berh, D., Otto, N., Jiang, X., and Klämbt, C. . “Quantifying subtle locomotion phenotypes of Drosophila larvae using internal structures based on FIM images.” Computers in Biology and Medicine 63 (null): 269–276. doi: 10.1016/j.compbiomed.2014.08.026.
- Risse, B, Berh, D, Otto, N, Jiang, X, and Klämbt, C. . “Imaging Modalities for Semi-Translucent Animals and Their Impact on Quantitative Analysis.” in VAIB Workshop, ICPR
- Risse, B., Otto, N., Berh, D., Jiang, X., and Klämbt, C. . “FIM imaging and FIMTrack: Two new tools allowing high-throughput and cost effective locomotion analysis.” Journal of Visualized Experiments 94.
- Lammel, U., Bechtold, M., B, B.Risse, Berh, D., Fleige, A., Bunse, I., Jiang, X., Klämbt, C., and Bogdan, S. . “The Drosophila FHOD1-like formin Knittrig acts through Rok to promote stress fiber formation and directed macrophage migration during the cellular immune response.” Development 141 (6): 1366–1380. doi: 10.1242/dev.101352.
- Tao, J, Risse, B, and Jiang, X. . “Stereo and Motion Based 3D High Density Object Tracking.” Image and Video Technology 2014: 136–148. doi: 10.1007/978-3-642-53842-1_12.
- Risse, B, Berh, D, Otto, N, Jiang, X, and Klämbt, C. . “FIM2C and the Analysis of Collision Behavior.” contribution to the Flies, Worms and Robots: Combining Perspectives on Minibrains and Behavior Conference, Sant Feliu de Guixols, Spain
- Jiang, X, Dawood, M, Gigengack, F, Risse, B, Schmid, S, Tenbrinck, D, and Schäfers, K. . “Biomedical Imaging: a Computer Vision Perspective.” in Computer Analysis of Images and Patterns, edited by Wilson et al.: CAIP 2013 R.. Berlin, Heidelberg: Springer VDI Verlag.
- Risse, B, Jiang, X, and Klämbt, C. . “FIM: Frustrated Total Internal Reflection Based Imaging for Biomedical Applications.” ERCIM News 95 (Image Understanding): 11–12.
- Sander, M., Squarr, A.J., Risse, B., Jiang, X., and Bogdan, S. . “Drosophila pupal macrophages - A versatile tool for combined ex vivo and in vivo imaging of actin dynamics at high resolution.” European Journal of Cell Biology 2013. doi: 10.1016/j.ejcb.2013.09.003.
- Risse, B., Thomas, S., Otto, N., Löpmeier, T., Valkov, D., Jiang, X., and Klämbt, C. . “FIM, a novel FTIR-based imaging method for high throughput locomotion analysis.” PloS one 8 (1): e53963.. doi: 10.1371/journal.pone.0053963.
- Risse, B, Berh, D, Tao, J, Jiang, X, Klette, R, and Klämbt, C. . “Comparison of two 3D tracking paradigms for freely flying insects.” EURASIP J Image Video Process 2013 (1): 57.. doi: 10.1186/1687-5281-2013-57.
- Risse, B, Otto, N, Berh, D, Jiang, X, and Klämbt, C. . “Tracking of Colliding Larvae.” contribution to the Conference on Neurobiology of Drosophila, New York, USA
- Schmidt, I, Thomas, S, Kain, P, Risse, B, Naffin, E, and Klämbt, C. . “Kinesin heavy chain function in Drosophila glial cells controls neuronal activity.” Journal of Neuroscience 32 (22): 7466–7476. doi: 10.1523/JNEUROSCI.0349-12.2012.
- Tao, J, Risse, B, Jiang, X, and Klette, R. . “3D Trajectory Estimation of Simulated Fruit Flies.” In Proc 27th IVCNZ, Dunedin 2012.
- Risse, B, Thomas, S, Jiang, X, and Klämbt, C. . “FIM: FTIR Based Image Acquisition and Tracking.” contribution to the Conference on Behavioral Neurogenetics of Drosophila Larva (Maggot Meeting), Ashburn, USA
