Publications

Empirical Inference Article Real-time inference for binary neutron star mergers using machine learning Dax, M., Green, S. R., Gair, J., Gupte, N., Pürrer, M., Raymond, V., Wildberger, J., Macke, J. H., Buonanno, A., Schölkopf, B. Nature, 639(8053):49-53, March 2025 (Published) DOI URL BibTeX

Empirical Inference Article Flow Matching for Atmospheric Retrieval of Exoplanets: Where Reliability meets Adaptive Noise Levels Gebhard, T. D., Wildberger, J., Dax, M., Kofler, A., Angerhausen, D., Quanz, S., Schölkopf, B. Astronomy \& Astrophysics, 693, January 2025 (Published) DOI URL BibTeX

Empirical Inference Article Artificial intelligence for modelling infectious disease epidemics Kraemer, M. U. G., Tsui, J. L., Chang, S. Y., Lytras, S., Khurana, M. P., Vanderslott, S., Bajaj, S., Scheidwasser, N., Curran-Sebastian, J. L., Semenova, E., et al. Nature, 638(8051):623-635, February 2025 (Published) DOI URL BibTeX

Empirical Inference Article Early warning of complex climate risk with integrated artificial intelligence Reichstein, M., Benson, V., Blunk, J., Camps-Valls, G., Creutzig, F., Fearnley, C. J., Han, B., Kornhuber, K., Rahaman, N., Schölkopf, B., et al. Nature Communications, 16(1), March 2025 (Published) DOI BibTeX

Empirical Inference Article The Fiction Machine Bottou, L., Schölkopf, B. SIAM News, 58(3), April 2025 (Published) URL BibTeX

Empirical Inference Article A Randomized Controlled Trial on Anonymizing Reviewers to Each Other in Peer Review Discussions Rastogi, C., Song, X., Jin, Z., Stelmakh, I., Daumé III, H., Zhang, K., Shah, N. B. PLOS ONE, 19(12), Public Library of Science, December 2024 (Published) DOI URL BibTeX

Empirical Inference Article A Probabilistic Model behind Self-Supervised Learning Bizeul, A., Schölkopf, B., Allen, C. Transactions on Machine Learning Research, October 2024 (Published) PDF URL BibTeX

Haptic Intelligence Empirical Inference Optics and Sensing Laboratory Software Workshop Article Fiber-Optic Shape Sensing Using Neural Networks Operating on Multispecklegrams Cao, C. G. L., Javot, B., Bhattarai, S., Bierig, K., Oreshnikov, I., Volchkov, V. V. IEEE Sensors Journal, 24(17):27532-27540, September 2024 (Published) DOI BibTeX

Empirical Inference Article Leveraging Task Structures for Improved Identifiability in Neural Network Representations Chen*, W., Horwood*, J., Heo, J., Hernández-Lobato, J. M. Transactions on Machine Learning Research, August 2024, *equal contribution (Published) URL BibTeX

Learning and Dynamical Systems Empirical Inference Article Deep Backtracking Counterfactuals for Causally Compliant Explanations Kladny, K., Kügelgen, J. V., Schölkopf, B., Muehlebach, M. Transactions on Machine Learning Research, July 2024 (Published) arXiv URL BibTeX

Empirical Inference Article Probabilistic pathway-based multimodal factor analysis Immer, A., Stark, S. G., Jacob, F., Bonilla, X., Thomas, T., Kahles, A., Goetze, S., Milani, E. S., Wollscheid, B., Consortium, T. T. P., et al. Bioinformatics, 40(Supplement 1):i189-i198, July 2024 (Published) DOI URL BibTeX

Empirical Inference Article Grundfragen der künstlichen Intelligenz Schölkopf, B. astronomie - Das Magazin, 42, May 2024 (Published) URL BibTeX

Empirical Inference Article SimReadUntil for benchmarking selective sequencing algorithms on ONT devices Mordig, M., Ratsch, G., Kahles, A. Bioinformatics, 40(5):btae199, April 2024 (Published) DOI URL BibTeX

Empirical Inference Article VIPurPCA: Visualizing and Propagating Uncertainty in Principal Component Analysis Zabel, S., Hennig, P., Nieselt, K. IEEE Transactions on Visualization and Computer Graphics, 30(4):2011-2022, April 2024 (Published) DOI BibTeX

Empirical Inference Article Learning Graph Embeddings for Open World Compositional Zero-Shot Learning Mancini, M., Naeem, M. F., Xian, Y., Akata, Z. IEEE Transactions on Pattern Analysis and Machine Intelligence, 46(3):1545-1560, IEEE, New York, NY, March 2024 (Published) DOI BibTeX

Empirical Inference Article Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery Visonà, G., Bouzigon, E., Demenais, F., Schweikert, G. Briefings in Bioinformatics, 25(2), January 2024 (Published) DOI BibTeX

Empirical Inference Article Trained recurrent neural networks develop phase-locked limit cycles in a working memory task Pals, M., Macke, J. H., Barak, O. PLOS Computational Biology, 20(2), February 2024 (Published) DOI BibTeX

Empirical Inference Article Pre-treatment 18F-FDG-PET/CT parameters as biomarkers for progression free survival, best overall response and overall survival in metastatic melanoma patients undergoing first-line immunotherapy Peisen, F., Gerken, A., Dahm, I., Nikolaou, K., Eigentler, T., Amaral, T., Moltz, J. H., Othman, A. E., Gatidis, S. PLOS ONE, 19(1), January 2024 (Published) DOI BibTeX

Empirical Inference Article Towards fully covariant machine learning Villar, S., Hogg, D. W., Yao, W., Kevrekidis, G. A., Schölkopf, B. Transactions on Machine Learning Research, January 2024 (Published) URL BibTeX

Empirical Inference Article Optimal Decision Making Under Strategic Behavior Tsirtsis, S., Tabibian, B., Khajehnejad, M., Singla, A., Schölkopf, B., Gomez-Rodriguez, M. Management Science, 2024, Published Online, In press (In press) DOI BibTeX

Empirical Inference Article Parameterizing pressure-temperature profiles of exoplanet atmospheres with neural networks Gebhard, T. D., Angerhausen, D., Konrad, B. S., Alei, E., Quanz, S. P., Schölkopf, B. Astronomy & Astrophysics, 681, 2024 (Published) DOI BibTeX

Empirical Inference Article Use the 4S (Signal-Safe Speckle Subtraction): Explainable Machine Learning reveals the Giant Exoplanet AF Lep b in High-Contrast Imaging Data from 2011 Bonse, M. J., Gebhard, T. D., Dannert, F. A., Absil, O., Cantalloube, F., Christiaens, V., Cugno, G., Garvin, E. O., Hayoz, J., Kasper, M., et al. The Astronomical Journal, 2024, Accepted (Accepted) arXiv BibTeX

Empirical Inference Article A phenomenological account for causality in terms of elementary actions Janzing, D., Garrido Mejia, S. Journal of Causal Inference, 12(1), 2024 (Published) DOI URL BibTeX

Empirical Inference Article A temperate super-Jupiter imaged with JWST in the mid-infrared Matthews, E. C., Carter, A. L., Pathak, P., Morley, C. V., Phillips, M. W., S. Krishanth, P. M., Feng, F., Bonse, M. J., Boogaard, L. A., Burt, J. A., et al. Nature, 633:789–792, 2024 (Published) DOI URL BibTeX

Empirical Inference Article Connectome-constrained networks predict neural activity across the fly\nvisual system Lappalainen, J. K., Tschopp, F. D., Prakhya, S., McGill, M., Nern, A., Shinomiya, K., Takemura, S., Gruntman, E., Macke, J. H., Turaga, S. C. Nature, 634:1132–1140, 2024 (Published) DOI URL BibTeX

Empirical Inference Article How developments in natural language processing help us in understanding human behaviour Mihalcea, R., Biester, L., Boyd, R. L., Jin, Z., Perez-Rosas, V., Wilson, S., Pennebaker, J. W. Nature Human Behaviour, 8(10):1877-1889, Nature Publishing Group UK London, October 2024 (Published) DOI URL BibTeX

Empirical Inference Article Low-power scalable multilayer optoelectronic neural networks enabled with incoherent light Song, A., Kottapalli, S. N. M., Goyal, R., Schoelkopf, B., Fischer, P. Nature Communications, 15:10692, 2024 (Published) DOI URL BibTeX

Empirical Inference Article Neonatal apnea and hypopnea prediction in infants with Robin sequence with neural additive models for time series Vetter, J., Lim, K., Dijkstra, T. M. H., Dargaville, P. A., Kohlbacher, O., Macke, J. H., Poets, C. F. PLOS Health Digital, 3(12):e0000678, 2024, Accepted (Accepted) DOI URL BibTeX

Empirical Inference Article Machine-Learning-Aided Prediction of Brain Metastases Development in Non-Small-Cell Lung Cancers Visonà, G., Spiller, L. M., Hahn, S., Hattingen, E., Vogl, T. J., Schweikert, G., Bankov, K., Demes, M., Reis, H., Wild, P., et al. Clinical lung cancer, 24(8):e311-e322, December 2023 (Published) DOI BibTeX

Empirical Inference Article Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information Visonà, G., Duroux, D., Miranda, L., Sükei, E., Li, Y., Borgwardt, K., Oliver, C. Bioinformatics, 39(12), December 2023 (Published) DOI BibTeX

Empirical Inference Article Data-Efficient Learning via Minimizing Hyperspherical Energy Cao, X., Liu, W., Tsang, I. W. IEEE transactions on pattern analysis and machine intelligence, 45(11):13422-13437, November 2023 (Published) DOI BibTeX

Empirical Inference Article Deep learning-based age estimation from clinical Computed Tomography image data of the thorax and abdomen in the adult population Kerber, B., Hepp, T., Küstner, T., Gatidis, S. PLOS ONE, 18(11), November 2023 (Published) DOI BibTeX

Empirical Inference Article Kernel-Based Independence Tests for Causal Structure Learning on Functional Data Laumann, F., von Kügelgen, J., Park, J., Schölkopf, B., Barahona, M. Entropy, 25(12), November 2023 (Published) DOI BibTeX

Empirical Inference Article Variational Causal Dynamics: Discovering Modular World Models from Interventions Lei, A., Schölkopf, B., Posner, I. Transactions on Machine Learning Research, November 2023 (Published) URL BibTeX

Empirical Inference Article A taxonomy and review of generalization research in NLP Hupkes, D., Giulianelli, M., Dankers, V., Artetxe, M., Elazar, Y., Pimentel, T., Christodoulopoulos, C., Lasri, K., Saphra, N., Sinclair, A., et al. Nature Machine Intelligence, 5(10):1161-1174, October 2023 (Published) DOI BibTeX

Empirical Inference Article Artificial Intelligence in Oncological Hybrid Imaging Feuerecker, B., Heimer, M. M., Geyer, T., Fabritius, M. P., Gu, S., Schachtner, B., Beyer, L., Ricke, J., Gatidis, S., Ingrisch, M., et al. Nuklearmedizin, 62(5):296-305, October 2023 (Published) DOI BibTeX

Empirical Inference Article Can Whole-Body Baseline CT Radiomics Add Information to the Prediction of Best Response, Progression-Free Survival, and Overall Survival of Stage IV Melanoma Patients Receiving First-Line Targeted Therapy: A Retrospective Register Study Peisen, F., Gerken, A., Dahm, I., Nikolaou, K., Eigentler, T., Amaral, T., Moltz, J. H., Othman, A. E., Gatidis, S., Dondi, F. Diagnostics (Basel), 13(20), October 2023 (Published) DOI BibTeX

Empirical Inference Article CROCODILE - Incorporating medium-resolution spectroscopy of close-in directly imaged exoplanets into atmospheric retrievals via cross-correlation Hayoz, J., Cugno, G., Quanz, S. P., Patapis, P., Alei, E., Bonse, M. J., Dannert, F. A., Garvin, E. O., Gebhard, T. D., Konrad, B. S., et al. Astronomy & Astrophysics, 678, October 2023 (Published) DOI BibTeX

Empirical Inference Article A historical perspective of biomedical explainable AI research Malinverno, L., Barros, V., Ghisoni, F., Visonà, G., Kern, R., Nickel, P. J., Ventura, B. E., Šimić, I., Stryeck, S., Manni, F., et al. Patterns, 4(9), September 2023 (Published) DOI BibTeX

Empirical Inference Article Neural Causal Structure Discovery from Interventions Ke*, N. R., Bilaniuk*, O., Goyal, A., Bauer, S., Larochelle, H., Schölkopf, B., Mozer, M. C., Pal, C., Bengio, Y. Transactions on Machine Learning Research, September 2023, *equal contribution (Published) URL BibTeX

Empirical Inference Article Simulation-based inference for efficient identification of generative models in computational connectomics Boelts, J., Harth, P., Gao, R., Udvary, D., Yáñez, F., Baum, D., Hege, H., Oberlaender, M., Macke, J. H. PLOS Computational Biology, 19(9):1-28, September 2023 (Published) DOI BibTeX

Empirical Inference Article Some Remarks on Identifiability of Independent Component Analysis in Restricted Function Classes Buchholz, S. Transactions on Machine Learning Research, September 2023 (Published) URL BibTeX

Empirical Inference Article Chasing rainbows and ocean glints: Inner working angle constraints for the Habitable Worlds Observatory Vaughan, S. R., Gebhard, T. D., Bott, K., Casewell, S. L., Cowan, N. B., Doelman, D. S., Kenworthy, M., Mazoyer, J., Millar-Blanchaer, M. A., Trees, V. J. H., et al. Monthly Notices of the Royal Astronomical Society, 524(4):5477-5485, August 2023 (Published) DOI BibTeX

Empirical Inference Article Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning Hawkins-Hooker, A., Visonà, G., Narendra, T., Rojas-Carulla, M., Schölkopf, B., Schweikert, G. Nature Communications, 14(1), August 2023 (Published) DOI BibTeX

Haptic Intelligence Autonomous Learning Empirical Inference Article Minsight: A Fingertip-Sized Vision-Based Tactile Sensor for Robotic Manipulation Andrussow, I., Sun, H., Kuchenbecker, K. J., Martius, G. Advanced Intelligent Systems, 5(8):2300042, August 2023, Inside back cover (Published) DOI BibTeX

Empirical Inference Article A network approach to atomic spectra Wellnitz, D., Kekić, A., Heiss, J., Gertz, M., Weidemüller, M., Spitz, A. Journal of Physics: Complexity, 4(3), July 2023 (Published) DOI BibTeX

Empirical Inference Article Catastrophic overfitting can be induced with discriminative non-robust features Ortiz-Jimenez*, G., de Jorge*, P., Sanyal, A., Bibi, A., Dokania, P. K., Frossard, P., Rogez, G., Torr, P. Transactions on Machine Learning Research , July 2023, *equal contribution (Published) PDF Code URL BibTeX

Empirical Inference Article Comparing Apples with Apples: Robust Detection Limits for Exoplanet High-contrast Imaging in the Presence of Non-Gaussian Noise Bonse, M. J., Garvin, E. O., Gebhard, T. D., Dannert, F. A., Cantalloube, F., Cugno, G., Absil, O., Hayoz, J., Milli, J., Kasper, M., et al. The American Astronomical Society, 166(2), July 2023 (Published) DOI BibTeX

Empirical Inference Article Dexterous robotic manipulation using deep reinforcement learning and knowledge transfer for complex sparse reward-based tasks Wang, Q., Sanchez, F. R., McCarthy, R., Bulens, D. C., McGuinness, K., O’Connor, N., Wüthrich, M., Widmaier, F., Bauer, S., Redmond, S. J. Expert Systems, 40(6), July 2023 (Published) DOI URL BibTeX

Empirical Inference Article Classifying the unknown: Insect identification with deep hierarchical Bayesian learning Badirli, S., Picard, C. J., Mohler, G., Richert, F., Akata, Z., Dundar, M. Methods in Ecology and Evolution, 14(6):1515-1530, June 2023 (Published) DOI BibTeX

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