Our fellows publish foundational advances in machine learning and new computational methods for biology in leading journals — and present their work at conferences around the world.

Our fellows publish foundational advances in machine learning and new computational methods for biology in leading journals — and present their work at conferences around the world.
Cultrera di Montesano, S., D’Ascenzo, D., Raghavan, S. et al.
(
2026
).
Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss
Nature Computational Science
,
(
).
https://www.nature.com/articles/s43588-025-00945-zWelch, R., Zhang, J., & Uhler, C.
(
2025
).
Identifiability Guarantees for Causal Disentanglement from Purely Observational Data
Thirty-Eighth Conference on Neural Information Processing Systems (NeurIPS 2024)
,
(
).
https://proceedings.neurips.cc/paper_files/paper/2024/file/ba2f8120cd723c63e6d72b5a2fd16803-Paper-Conference.pdfAn, S., Cho, J.-W., Cao, K., Xiong, J., Hemberg, M., & Wan, L.
(
2025
).
scCausalVI disentangles single-cell perturbation responses with causality-aware generative model.
Cell Systems
,
16
(
11
).
https://www.sciencedirect.com/science/article/abs/pii/S2405471225002765?via%3DihubSchaffer, L. V., Hu, M., Qian, G., Moon, K.-M., Pal, A., Soni, N., Latham, A. P., Pontano Vaites, L., Tsai, D., Mattson, N. M., Licon, K., Bachelder, R., Cesnik, A., Gaur, I., Le, T., Leineweber, W., Palar, A., Pulido, E., Qin, Y., … Ideker, T.
(
2025
).
Multimodal cell maps as a foundation for structural and functional genomics
Nature
,
64(8066)
(
222-231
).
https://doi.org/10.1038/s41586-025-08878-3Venkat, A., Youlten, S. E., San Juan, B. P., Purcell, C. A., Gupta, S., Amodio, M., Neumann, D. P., Lock, J. G., Westacott, A. E., McCool, C. S., Burkhardt, D. B., Benz, A., Mollbrink, A., Lundeberg, J., van Dijk, D., Holst, J., Goldstein, L. D., Kummerfeld, S., Krishnaswamy, S., & Chaffer, C. L.
(
2025
).
AAnet Resolves a Continuum of Spatially Localized Cell States to Unveil Intratumoral Heterogeneity
Cancer Discovery
,
15(10)
(
21399-2165
).
https://doi.org/10.1158/2159-8290.CD-24-0684Si, Y., Lee, J. S., Jun, G., Kang, H. M., & Lee, J. H.
(
2025
).
Spatial omics enters the microscopic realm: Opportunities and challenges
Trends in Genetics
,
41(9)
(
774-787
).
https://doi.org/10.1016/j.tig.2025.05.002Zhao, G., Cho, C.-S., Liu, H., Hwang, Y., Si, Y., Kim, M., Deng, Y., Zhao, Y., Xue, C., Guo, Y., Chang, L., Mizrak, D., Yang, B., Kang, H. M., Zhang, J., Lee, J. H., & Chen, Y. E.
(
2025
).
Single-cell spatial transcriptomics unravels the cellular landscape of abdominal aortic aneurysm
JCI Insight
,
10(16)
(
).
https://doi.org/10.1172/jci.insight.190534Yin, L., Liu, M., Shi, Y., Zhang, R., Lui, S. S.-Y., & So, H.-C.
(
2025
).
Uncovering the genetic underpinnings for different psychiatric disorder combinations
medRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2024.08.29.24312761Xiao, Y., Tonekaboni, S., Gerych, W., Suriyakumar, V., & Ghassemi, M.
(
2025
).
When Style Breaks Safety: Defending Language Models Against Superficial Style Alignment
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2506.07452Baharav, Tavor Z., Nicol, P. B., Irizarry, R. A., & Ma, R.
(
2025
).
Stacked SVD or SVD stacked? A Random Matrix Theory perspective on data integration
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2507.22170Piazza, B., Barabási, D. L., Castro, A. F., Menichetti, G., & Barabási, A.-L.
(
2025
).
Physical Network Constraints Define the Lognormal Architecture of the Brain’s Connectome
bioRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.02.27.640551Nori, D., Parsan, A., Uhler, C., & Jin, W.
(
2025
).
BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design
ICML 2025 Generative AI and Biology (GenBio) Workshop
,
(
).
https://openreview.net/forum?id=FblzZHPVaDGangrade, A., Pacchiano, A., Scott, C., & Saligrama, V.
(
2025
).
Feasible Action Search for Bandit Linear Programs via Thompson Sampling.
Forty-Second International Conference on Machine Learning (ICML 2025)
,
(
).
https://icml.cc/virtual/2025/poster/45807Al-Ghattas, O., Chen, J., & Sanz-Alonso, D.
(
2025
).
On the Estimation of Gaussian Moment Tensors
arXiv [Preprint]
,
(
).
https://arxiv.org/abs/2507.06166Varilly, P., Schifferli, M., Yang, K., Burcham, T., Cronan, P., Glennon, O., Jacks, O., Laning, E., Marrs, L., Oba, K., Yeung, S., Parker, E., Omah, I., Pekar, J. E., Luebbert, L., Andersen, K. G., Park, D. J., Schaffner, S. F., MacInnis, B. L., … Sabeti, P. C.
(
2025
).
Delphy: Scalable, near-real-time Bayesian phylogenetics for outbreaks
bioRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.03.25.645253Uhler, C.
(
2025
).
Causality—Exploiting Multi-Modal Data
KDD '25
,
3-4
(
).
https://doi.org/10.1145/3711896.3736799Baharav, Tavor Z, Dragazis, S., & Pacchiano, A.
(
2025
).
No-Regret Safety: Balancing Tests and Misclassification in Logistic Bandits
ICML 2025 Workshop EXAIT
,
(
).
https://openreview.net/pdf?id=mkwVgBrsALLi, Y., Ma, J., Yang, Y., Wu, Q., Zha, H., & Yan, J.
(
2025
).
Generative Modeling Reinvents Supervised Learning: Label Repurposing with Predictive Consistency Learning
Forty-Second International Conference on Machine Learning (ICML 2025)
,
(
).
https://openreview.net/pdf?id=FO2fu3daSLZhang, H., Fang, L., Wu, Q., & Yu, P. S. 1
(
2025
).
TabNAT: A Continuous-Discrete Joint Generative Framework for Tabular Data
Forty-Second International Conference on Machine Learning (ICML 2025)
,
(
).
https://openreview.net/pdf?id=WbfbT2BH6FWu, Q., Yang, C., 2 Zeng, K., & Bronstein, M.
(
2025
).
Supercharging Graph Transformers with Advective Diffusion
Forty-Second International Conference on Machine Learning (ICML 2025)
,
(
).
https://openreview.net/pdf?id=MaOYl3P84ERusso, A., & Pacchiano, A.
(
2025
).
Adaptive Exploration for Multi-Reward Multi-Policy Evaluation.
Forty-Second International Conference on Machine Learning (ICML 2025)
,
(
).
https://doi.org/10.48550/arXiv.2502.02516German, J., Yang, Z., Urbut, S., Vartiainen, P., FinnGen, Natarajan, P., Pattorno, E., Kutalik, Z., Philippakis, A., & Ganna, A.
(
2025
).
Incorporating genetic data improves target trial emulations and informs the use of polygenic scores in randomized controlled trial design
Nature Genetics
,
(
).
https://www.nature.com/articles/s41588-025-02229-8Sunog, M., Magdamo, C., Charpignon, M.-L., & Albers, M.
(
2025
).
nvestigating Primary Care Indications to Improve the Quality of Electronic Health Record Data in Target Trial Emulation for Dementia
medRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.04.08.25325485Zhou, H., Cao, K., & Lu, Y. Y.
(
2025
).
Securing diagonal integration of multimodal single-cell data against ambiguous mapping
Bioinformatics
,
41(6)
(
).
https://doi.org/10.1093/bioinformatics/btaf345Tonekaboni, S., Behrouzi, T., Weatherhead, A., Fox, E., Blei, D., & Goldenberg, A.
(
2025
).
HDP-Flow: Generalizable Bayesian Nonparametric Model for Time Series State Discovery.
The 41st Conference on Uncertainty in Artificial Intelligence.
,
(
).
https://openreview.net/forum?id=Ti1TMJiprQ&referrer=%5Bthe%20profile%20of%20Emily%20Fox%5D(%2Fprofile%3Fid%3D~Emily_Fox2)Hu, X., & Pacchiano, A.
(
2025
).
Meet Me at the Arm: The Cooperative Multi-Armed Bandits Problem with Shareable Arms.
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2506.10127Shyamal, D., Zhang, J., & Uhler, C.
(
2025
).
Probabilistic Factorial Experimental Design for Combinatorial Interventions.
Forty-second International Conference on Machine Learning (ICML 2025)
,
(
).
https://openreview.net/forum?id=RL6d53a5jjHulland, E. N., Charpignon, M.-L., Berkane, T., & Majumder, M. S.
(
2025
).
Underimmunisation during the 2025 Texas measles outbreak.
The Lancet Infectious Diseases
,
25
(
6
).
D'Ascenzo, D., & Cultrera di Montesano, S.
(
2025
).
scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics
arXiv [Preprint]
,
(
).
https://arxiv.org/abs/2506.01883Samarah, L. Z., Zheng, C., Xing, X., Lee, W. D., Afriat, A., Chitra, U., MacArthur, M., Lu, W., Jankowski, C. S. R., Ma, C., Hunter, C. J., Raphael, B. J., & Rabinowitz, J. D.
(
2025
).
Spatial metabolic gradients in the liver and small intestine.
bioRxiv [Preprint]
,
(
).
https://www.biorxiv.org/content/10.1101/2025.06.02.657306v1Russo, A., Welch, R., & Pacchiano, A.
(
2025
).
Learning to Explore: An In-Context Learning Approach for Pure Exploration.
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2506.01876Riley, A. R., Kim, Y. J., Flores Morales, J., Charpignon, M.-L., DeVost, M. A., & Chen, Y.-H.
(
2025
).
Inequities in Excess Pandemic Mortality Among Documented and Undocumented Immigrants in California, 2020–2023
American Journal of Public Health
,
(
).
https://doi.org/10.2105/AJPH.2025.308150Wu, Q., Wipf, D., & Yan, J.
(
2025
).
Transformers from Diffusion: A Unified Framework for Neural Message Passing
Journal of Machine Learning Research (JMLR) 2025
,
(
).
https://arxiv.org/abs/2409.09111Turura, Y., Friedman, S. F., Cremer, A., Maddah, M., & Tonekaboni, S.
(
2025
).
The Latentverse: An Open-Source Benchmarking Toolkit for Evaluating Latent Representations.
Conference on Health, Inference, and Learning (CHIL 2025)
,
(
).
https://doi.org/10.1101/2025.04.25.650676Brukhim, N., Pacchiano, A., Dudik, M., & Schapire, R.
(
2025
).
On the Hardness of Bandit Learning.
Conference on Learning Theory (COLT 2025)
,
(
).
https://doi.org/10.48550/arXiv.2506.14746Ost, L., Montesano, S. C. di, & Edelsbrunner, H.
(
2025
).
Banana Trees for the Persistence in Time Series Experimentally.
The 41st International Symposium on Computational Geometry (SoCG 2025)
,
(
).
https://doi.org/10.48550/arXiv.2405.17920Yin, L., Lin, Y., Qiu, J., Xiang, Y., Li, M., Xiao, X., Lui, S. S.-Y., & So, H.-C.
(
2025
).
Integrating brain imaging features and genomic profiles for the subtyping of major depression.
Psychological Medicine
,
55
(
e158
).
https://doi.org/10.1017/S0033291725001096McGee, E. E., Hernán, M. A., Giovannucci, E., Mucci, L. A., Chiu, Y.-H., Eliassen, A. H., & Dickerman, B. A.
(
2025
).
Estimating the Effects of Lifestyle Interventions on Mortality Among Cancer Survivors: A Methodologic Framework
Epidemiology (Cambridge, Mass.)
,
36(5)
(
705-718
).
https://doi.org/10.1097/EDE.0000000000001889Zhang, X., Tseo, Y., Bai, Y., Chen, F., & Uhler, C.
(
2025
).
Prediction of protein subcellular localization in single cells.
Nature Methods
,
22
(
6
).
https://www.nature.com/articles/s41592-025-02696-1McCradden, M. D., Thai, K., Assadi, A., Tonekaboni, S., Stedman, I., Joshi, S., Zhang, M., Chevalier, F., & Goldenberg, A.
(
2025
).
What makes a ‘good’ decision with artificial intelligence? A grounded theory study in paediatric care
BMJ Evidence-Based Medicine
,
30(3)
(
183-193
).
https://doi.org/10.1136/bmjebm-2024-112919Mazaheri, B., Zhang, J., & Uhler, C.
(
2025
).
Meta-Dependence in Conditional Independence Testing
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2504.12594Luebbert, L., Sullivan, D. K., Carilli, M., Eldjárn Hjörleifsson, K., Viloria Winnett, A., Chari, T., & Pachter, L.
(
2025
).
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes
Nature Biotechnology
,
1-10
(
).
https://doi.org/10.1038/s41587-025-02614-yMazaheri, B., Jain, S., Cook, M., & Bruck, J.
(
2025
).
Omitted Labels in Causality: A Study of Paradoxes.
CLeaR (Causal Learning and Reasoning) 2025
,
(
).
https://doi.org/10.48550/arXiv.2311.06840Xu, W., Wu, Q., Liang, Z., Han, J., Ning, X., Shi, Y., Lin, W., & Zhang, Y.
(
2025
).
SLMRec: Distilling Large Language Models into Small for Sequential Recommendation.
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://doi.org/10.48550/arXiv.2405.17890Russo, A., Song, Y., & Pacchiano, A.
(
2025
).
Pure Exploration with Feedback Graphs.
The 28th International Conference on Artificial Intelligence and Statistics (AISTATS 2025)
,
(
).
https://openreview.net/forum?id=ybpHHnBf7xMazaheri, B., Squires, C., & Uhler, C.
(
2025
).
Synthetic Potential Outcomes and Causal Mixture Identifiability.
The 28th International Conference on Artificial Intelligence and Statistics (AISTATS 2025)
,
(
).
https://openreview.net/forum?id=J1CJaSnmKg&referrer=%5Bthe%20profile%20of%20Caroline%20Uhler%5D(%2Fprofile%3Fid%3D~Caroline_Uhler1Pourmousa, M., Jain, S., Barnaeva, E., Jin, W., Hochuli, J., Itkin, Z., Maxfield, T., Melo-Filho, C., Thieme, A., Wilson, K., Klumpp-Thomas, C., Michael, S., Southall, N., Jaakkola, T., Muratov, E. N., Barzilay, R., Tropsha, A., Ferrer, M., & Zakharov, A. V.
(
2025
).
AI-driven discovery of synergistic drug combinations against pancreatic cancer.
Nature Communications
,
16
(
1
).
https://www.nature.com/articles/s41467-025-56818-6An, S., Cho, J.-W., Cao, K., Xiong, J., Hemberg, M., & Wan, L.
(
2025
).
Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference
Sankararaman, S. (eds) Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science
,
15647
(
).
https://doi.org/10.1007/978-3-031-90252-9_35Luebbert, L., & Pachter, L.
(
2025
).
Agnostic viral detection at single-cell resolution reveals novel viruses
Nature Biotechnology
,
(
).
https://doi.org/10.1038/s41587-025-02638-4German, J., Cordioli, M., Tozzo, V., Urbut, S., Arumäe, K., Smit, R. A. J., Lee, J., Li, J. H., Janucik, A., Ding, Y., Akinkuolie, A., Heyne, H., Eoli, A., Saad, C., Al-Sarraj, Y., Abdel-latif, R., Barry, A., Wang, Z., Team, E. B. research, … Ganna, A.
(
2025
).
Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery: A multi-ancestry study in 10,960 individuals from 9 biobanks.
Nature Medicine
,
(
).
https://pubmed.ncbi.nlm.nih.gov/40251273/Liu, T., Huang, T., Jin, W., Chu, T., Ying, R., & Zhao, H.
(
2025
).
spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model
boRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.04.22.649977Liu, H., Yuan, L., & Shivashankar, G. V.
(
2025
).
Identifying regulators of aged fibroblast activation in 3D tissue models
bioRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.02.10.636275Liu, H., Yuan, L., Baldi, L., Sornapudi, T. R., & Shivashankar, G. V.
(
2025
).
Compressive Forces Induce Epigenetic Activation of Aged Human Dermal Fibroblasts Through ERK Signaling Pathway
Aging Cell
,
24
(
6
).
https://doi.org/10.1111/acel.70035Liu, E., Zhang, J., & Uhler, C.
(
2025
).
Learning Genetic Perturbation Effects with Variational Causal Inference
bioRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.06.05.657988Lenkiewicz, J., Churas, C., Hu, M., Qian, G., Jain, M., Levinson, M. A., Al Manir, S., Qin, Y., Fong, D., Ono, K., Chen, J., Gao, C., Pratt, D., Parker, J. A., Clark, T., Ideker, T., & Schaffer, L. V.
(
2025
).
Cell Mapping Toolkit: An end-to-end pipeline for mapping subcellular organization
Bioinformatics
,
41
(
6
).
https://doi.org/10.1093/bioinformatics/btaf205Labade, A. S., Chiang, Z. D., Comenho, C., Reginato, P. L., Payne, A. C., Earl, A. S., Shrestha, R., Duarte, F. M., Habibi, E., Zhang, R., Church, G. M., Boyden, E. S., Chen, F., & Buenrostro, J. D.
(
2025
).
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation
Science
,
389
(
6758
).
https://doi.org/10.1126/science.adt2781Krishnan, A., Anahtar, M. N., Valeri, J. A., Jin, W., Donghia, N. M., Sieben, L., Luttens, A., Zhang, Y., Modaresi, S. M., Hennes, A., Fromer, J., Bandyopadhyay, P., Chen, J. C., Rehman, D., Desai, R., Edwards, P., Lach, R. S., Aschtgen, M.-S., Gaborieau, M., … Collins, J. J.
(
2025
).
A generative deep learning approach to de novo antibiotic design
Cell
,
(
).
https://doi.org/10.1016/j.cell.2025.07.033Nagaraj, S., Gerych, W., Tonekaboni, S., Goldenberg, A., Ustun, B., & Hartvigsen, T.
(
2025
).
Learning Under Temporal Label Noise.
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/pdf?id=5o0phqAhsPWang, C., Gupta, S., Zhang, X., Tonekaboni, S., Jegelka, S., Jaakkola, T., & Uhler, C.
(
2025
).
An Information Criterion for Controlled Disentanglement of Multimodal Data
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/pdf?id=3n4RY25UWPZhang, H., Fang, L., Wu, Q., & Yu, P. S.
(
2025
).
DiffPuter: An EM-Driven Diffusion Model for Missing Data Imputation.
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/forum?id=3fl1SENSYOKausik, C., Mutti, M., Pacchiano, A., & Tewari, A.
(
2025
).
A Theoretical Framework for Partially-Observed Reward States in RLHF.
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/forum?id=OjAU0LLDbeChen, Y., Wu, Q., & Yan, J.
(
2025
).
Regularizing Energy among Training Samples for Out-of-Distribution Generalization.
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/forum?id=Lbx9zdURxePacchiano, A.
(
2025
).
Second Order Bounds for Contextual Bandits with Function Approximation.
The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/forum?id=h6ktwCPYxEBerliner Senderey, A., Mushkat, T., Hadass, O., Carmeli, D., Hayek, S., Charpingnon, M.-L., Jacobson, E., & Balicer, R. D.
(
2025
).
Real-world impact of physical activity reward-driven digital app use on cardiometabolic and cardiovascular disease incidence.
Communications Medicine,
,
5
(
1
).
https://doi.org/10.1038/s43856-025-00792-zShankar, P., Liang, H., Chitra, U., & Singh, R.
(
2025
).
Decoding the causal drivers of spatial cellular topology.
bioRxiv [Preprint]
,
(
).
https://www.biorxiv.org/content/10.1101/2025.03.19.644241v2Fischer, D. S., Villanueva, M. A., Winter, P. S., & Shalek, A. K.
(
2025
).
Adapting systems biology to address the complexity of human disease in the single-cell era.
Nature Reviews Genetics
,
(
).
https://www.nature.com/articles/s41576-025-00821-6Shenfeld, I., Faltings, F., Agrawal, P., & Pacchiano, A.
(
2025
).
Language Model Personalization via Reward Factorization.
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2503.06358Huang, Y.-H., Belk, J. A., Zhang, R., Weiser, N. E., Chiang, Z., Jones, M. G., Mischel, P. S., Buenrostro, J. D., & Chang, H. Y.
(
2025
).
Unified molecular approach for spatial epigenome, transcriptome, and cell lineages
Proceedings of the National Academy of Sciences (PNAS)
,
122
(
16
).
https://doi.org/10.1073/pnas.2424070122Huang, T., Liu, T., Babadi, M., Ying, R., & Jin, W.
(
2025
).
STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images
bioRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2025.04.19.649665Huang, T., Liu, T., Babadi, M., Jin, W., & Ying, R.
(
2025
).
Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2506.05361Hu, Y., Horlbeck, M. A., Zhang, R., Ma, S., Shrestha, R., Kartha, V. K., Duarte, F. M., Hock, C., Savage, R. E., Labade, A., Kletzien, H., Meliki, A., Castillo, A., Durand, N. C., Mattei, E., Anderson, L. J., Tay, T., Earl, A. S., Shoresh, N., … Buenrostro, J. D.
(
2025
).
Multiscale footprints reveal the organization of cis-regulatory elements
Nature
,
638
(
8051
).
https://doi.org/10.1038/s41586-024-08443-4Barabási, D. L., Ferreira Castro, A., & Engert, F.
(
2025
).
Three systems of circuit formation: Assembly, updating and tuning.
Nature Reviews Neuroscience
,
26
(
4
).
https://www.nature.com/articles/s41583-025-00910-9Hu, G., Gold, J., Chitra, U., Joshi, S., & Raphael, B. J.
(
2025
).
Anomaly detection in spatial transcriptomics via spatially localized density comparison
Bioinformatics
,
41
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