Publications

Let’s be real, this is probably not a complete list. A more complete list can be found on my Google Scholar.

†: corresponding author *: equal contribution

Preprints

Yunyi Shen, Alex Gagliano. "Diffusion Autoencoders with Perceivers for Long, Irregular and Multimodal Astronomical Sequences" arXiv preprint arXiv:2510.20595 (2025). [download]

Renato Berlinghieri*, Yunyi Shen*, Jialong Jiang, Tamara Broderick. "Oh SnapMMD! Forecasting Stochastic Dynamics Beyond the Schrodinger Bridges End" arXiv preprint arXiv:2505.16082 (2025). [download]

Sun, Hao, Yunyi Shen, Jean-Francois Ton, and Mihaela van der Schaar. "Reusing Embeddings: Reproducible Reward Model Research in Large Language Model Alignment without GPUs." arXiv preprint arXiv:2502.04357 (2025). [download]

Zhao, Qing, and Yunyi Shen. "Explicit modeling of density dependence in spatial capture-recapture models." arXiv preprint arXiv:2412.09431 (2024). [download]

Shen, Yunyi, Lorenzo Masoero, Joshua G. Schraiber, and Tamara Broderick. "Double trouble: Predicting new variant counts across two heterogeneous populations." arXiv preprint arXiv:2403.02154 (2024). [download]

Hongliang Bu and Shen, Yunyi† "Identify local limiting factors of species distribution using min-linear logistic regression." arXiv (2023). [download]

Journal and conference Articles

Jenny Huang*, Yunyi Shen*, Dennis Wei, Tamara Broderick. "Dropping Just a Handful of Preferences Can Change Top Large Language Model Rankings." ICLR 2026, arXiv:2508.11847. [download]

Shen, Yunyi, and Solis-Lemus, Claudia. "Bayesian chain graph models to characterize microbe-environment dynamics." Mathematical Biosciences and Engineering 23 (2). [download]

Huang, Jenny Y., David R. Burt, Yunyi Shen, Tin D. Nguyen, and Tamara Broderick. "Approximations to worst-case data dropping: unmasking failure modes." TMLR 2025, arXiv preprint arXiv:2408.09008 (2024). [download]

Shen, Yunyi*, Hao Sun*, and Jean-François Ton. "Reviving The Classics: Active Reward Modeling in Large Language Model Alignment." arXiv preprint arXiv:2502.04354 (2025) to appear in ICML 2025. [download]

Shen, Yunyi*, Renato Berlinghieri*, and Tamara Broderick. "Multi-marginal Schrödinger Bridges with Iterative Reference Refinement." arXiv preprint arXiv:2408.06277 (2024), AISTATS 2025 (oral). [download]

Sun, Hao*, Yunyi Shen*, and Jean-Francois Ton. "Rethinking Bradley-Terry Models in Preference-Based Reward Modeling: Foundations, Theory, and Alternatives." arXiv preprint arXiv:2411.04991 (2024), ICLR 2025 (oral). [download]

Burt, David R., Yunyi Shen, and Tamara Broderick. "Consistent Validation for Predictive Methods in Spatial Settings." arXiv preprint arXiv:2402.03527 (2024), AISTATS 2025. [download]

Olson, Erik R., Yunyi Shen, PARKER J. Matzinger, Evelyn TATIANA Solano Mora, Guido Saborío-R, and Alejandro Azofeifa. "Conservation crisis? Status of jaguars Panthera onca in Corcovado National Park, Costa Rica." Oryx: 1-12. [download]

Esquivel, J. Arturo*, Yunyi Shen*, Vianey Leos-Barajas, Gwendolyn Eadie, Joshua Speagle, Radu V. Craiu, Amber Medina, and James Davenport. "Detecting stellar flares in photometric data using hidden Markov models." The Astrophysical Journal 979, no. 2 (2025): 141. [download]

Shen, Yunyi, and Solis-Lemus, Claudia. "The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models." Journal of Agricultural, Biological and Environmental Statistics (2024): 1-70. [download]

Shen, Yunyi, Solis-Lemus, Claudia and Deshpande, Sameer K. "Estimating Sparse Direct Effects in Multivariate Regression With the Spike-and-Slab LASSO" Bayesian Analysis 1.1 (2024): 1-25. [download]

Mallinger, J., Goodwin, K., Kirschbaum, A., Shen, Y., Gillam, E., Olson E.. (2023). Species-specific responses to white-nose syndrome in the Great Lakes region. Ecology and Evolution, 13:e10267 [download]

Shen, Yunyi, and Deshpande, Sameer K. "Posterior contraction and uncertainty quantification for the multivariate spike-and-slab LASSO." Journal of Multivariate Analysis, 105493 (2025). [download]

Shen, Yunyi†, Olson, Erik, and Van Deelen, Timothy. R. (2021). Spatially Explicit Modeling of Community Occupancy using Markov Random Field Models with Imperfect Observation: Mesocarnivores in Apostle Islands National Lakeshore. Ecological Modelling 459C (2021) 109712. [download]

Shen, Yunyi, Liu, Mingzhang, Shen, Xiaoli and Li, Sheng. "Using an integrative mapping approach to identify the distribution range and conservation needs of a large threatened mammal, the Asiatic black bear, in China." Global Ecology and Conservation 2021. [download]

Yu, J., Shen, Y., Song, X., Chen, X., Li, S., & Shen, X. (2019). Evaluating the effectiveness of functional zones for black muntjac (Muntiacus crinifrons) protection in qianjiangyuan national park pilot site. Biodiversity Science, 27(1). [download]