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.
Ost, L., Montesano, S. C. di, & Edelsbrunner, H.
(
2025
).
Banana Trees for the Persistence in Time Series Experimentally.
[To appear in] The 41st International Symposium on Computational Geometry (SoCG 2025)
,
(
).
https://doi.org/10.48550/arXiv.2405.17920Xu, 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.
[To appear in] 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.
[To appear in] 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.
[To appear in] 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_Uhler1Mazaheri, B., Jain, S., Cook, M., & Bruck, J.
(
2025
).
Omitted Labels in Causality: A Study of Paradoxes.
[To appear in] CLeaR (Causal Learning and Reasoning) 2025
,
(
).
https://doi.org/10.48550/arXiv.2311.06840Zhang, H., Fang, L., Wu, Q., & Yu, P. S.
(
2025
).
DiffPuter: An EM-Driven Diffusion Model for Missing Data Imputation.
[To appear in] The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/forum?id=3fl1SENSYOZhang, C. B. C., Hong, Z.-W., Pacchiano, A., & Agrawal, P.
(
2025
).
ORSO: Accelerating Reward Design via Online Reward Selection and Policy Optimization.
[To appear in] The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://arxiv.org/abs/2410.13837Kausik, C., Mutti, M., Pacchiano, A., & Tewari, A.
(
2025
).
A Theoretical Framework for Partially-Observed Reward States in RLHF.
[To appear in] 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.
[To appear in] 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.
[To appear in] The Thirteenth International Conference on Learning Representations (ICLR 2025)
,
(
).
https://openreview.net/forum?id=h6ktwCPYxEFischer, 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.2503.06358Barabási, 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/s41583-025-00910-9Parres-Gold, J., Levine, M., Emert, B., Stuart, A., & Elowitz, M. B.
(
2025
).
Contextual computation by competitive protein dimerization networks.
Cell
,
188
(
).
https://www.cell.com/cell/fulltext/S0092-8674(25)00105-9Chitra, U., Arnold, B., & Raphael, B. J.
(
2025
).
Resolving discrepancies between chimeric and multiplicative measures of higher-order epistasis.
Nature Communications
,
16
(
1
).
https://www.nature.com/articles/s41467-025-56986-5Najia, M. A., Jha, D. K., Zhang, C., Laurent, B., Kubaczka, C., Markel, A., Li, C., Morris, V., Tompkins, A., Hensch, L., Qin, Y., Chapuy, B., Huang, Y.-C., Morse, M., Marunde, M. R., Vaidya, A., Gillespie, Z. B., Howard, S. A., North, T. E., … Daley, G. Q.
(
2025
).
Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers.
bioRxiv [Preprint]
,
(
).
https://www.biorxiv.org/content/10.1101/2025.01.31.635709v1Chitra, U., Dan, S., Krienen, F., & Raphael, B. J.
(
2025
).
GASTON-Mix: A unified model of spatial gradients and domains using spatial mixture-of-experts.
bioRxiv [Preprint]
,
(
).
https://www.biorxiv.org/content/10.1101/2025.01.31.635955v1Schuster, V.
(
2025
).
Can sparse autoencoders make sense of latent representations?
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2410.11468Chitra, U., Arnold, B. J., Sarkar, H., Sanno, K., Ma, C., Lopez-Darwin, S., & Raphael, B. J.
(
2025
).
Mapping the topography of spatial gene expression with interpretable deep learning.
Nature Methods
,
22
(
2
).
https://www.nature.com/articles/s41592-024-02503-3Schlüter, H. M., & Uhler, C.
(
2025
).
Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.
Nature Communications
,
16
(
1
).
https://www.nature.com/articles/s41467-025-56388-7Chitra, U., Arnold, B. J., Sarkar, H., Ma, C., Lopez-Darwin, S., Sanno, K., & Raphael, B. J.
(
2025
).
Mapping the topography of spatial gene expression with interpretable deep learning.
Nature Methods
,
22, 298–309
(
).
https://doi.org/10.1038/s41592-024-02503-3German, 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.
medRxiv [Preprint]
,
(
).
https://doi.org/10.1101/2024.09.11.24313458Charpignon, M.-L., Matos, J., Nakayama, L. F., Gallifant, J., Alfonso, P. G. I., Cobanaj, M., Fiske, A. M., Gates, A. J., Ho, F. D. V., Jain, U., Kashkooli, M., Link, N., McCoy, L. G., Shaffer, J., & Celi, L. A.
(
2025
).
Diversity in the medical research ecosystem: A descriptive scientometric analysis of over 49,000 studies and 150,000 authors published in high-impact medical journals between 2007 and 2022.
BMJ Open
,
15
(
1
).
https://bmjopen.bmj.com/content/15/1/e086982Kumar, A., Shiragur, K., & Uhler, C.
(
2024
).
Learning Mixtures of Unknown Causal Interventions.
Advances in Neural Information Processing Systems (NeurIPS 2024)
,
37
(
).
https://proceedings.neurips.cc/paper_files/paper/2024/hash/1dcee1cd6890ab7fcdf173ec10526da9-Abstract-Conference.htmlBarlow, G. L., Schürch, C. M., Bhate, S. S., Phillips, D., Young, A., Dong, S., Martinez, H. A., Kaber, G., Nagy, N., Ramachandran, S., Meng, J., Korpos, E., Bluestone, J. A., Nolan, G. P., & Bollyky, P. L.
(
2024
).
The Extra-Islet Pancreas Supports Autoimmunity in Human Type 1 Diabetes.
medRxiv [Preprint]
,
(
).
https://pubmed.ncbi.nlm.nih.gov/36993739/Welch, R., Zhang, J., & Uhler, C.
(
2024
).
Identifiability Guarantees for Causal Disentanglement from Purely Observational Data.
The Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024)
,
(
).
https://neurips.cc/virtual/2024/poster/95550Baharav, T., Kang, R., Sullivan, C., Tiwari, M., Luxenberg, E., Tse, D., & Pilanci, M.
(
2024
).
Adaptive Sampling for Efficient Softmax Approximation.
Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024)
,
(
).
https://nips.cc/virtual/2024/poster/94739Venkat, A., Leone, S., Youlten, S. E., Fagerberg, E., Attanasio, J., Joshi, N. S., Perlmutter, M., & Krishnaswamy, S.
(
2024
).
Mapping the gene space at single-cell resolution with gene signal pattern analysis.
Nature Computational Science
,
4
(
12
).
https://www.nature.com/articles/s43588-024-00734-0Rahimov, F., Nieminen, P., Kumari, P., Juuri, E., Nikopensius, T., Paraiso, K., German, J., Karvanen, A., Kals, M., Elnahas, A. G., Karjalainen, J., Kurki, M., Palotie, A., Heliövaara, A., Esko, T., Jukarainen, S., Palta, P., Ganna, A., Patni, A. P., … Rice, D. P.
(
2024
).
High incidence and geographic distribution of cleft palate in Finland are associated with the IRF6 gene.
Nature Communications
,
15
(
1
).
https://www.nature.com/articles/s41467-024-53634-2German, J., Yang, Z., Urbut, S., Vartiainen, P., FinnGen, Natarajan, P., Pattorno, E., Kutalik, Z., Philippakis, A., & Ganna, A.
(
2024
).
Integrating genetic data in target trial emulations improves their design and informs the value of polygenic scores for prognostic and predictive enrichment.
medRxiv [Preprint]
,
(
).
https://www.medrxiv.org/content/10.1101/2024.11.05.24316763v1Huang, T., Song, Z., Ying, R., & Jin, W.
(
2024
).
Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer.
arXiv [Preprint]
,
(
).
http://arxiv.org/abs/2406.09586Abedsoltan, A., Radhakrishnan, A., Wu, J., & Belkin, M.
(
2024
).
Context-Scaling versus Task-Scaling in In-Context Learning.
arXiv [Preprint]
,
(
).
http://arxiv.org/abs/2410.12783Matos, J., Gallifant, J., Chowdhury, A., Economou-Zavlanos, N., Charpignon, M.-L., Gichoya, J., Celi, L. A., Nazer, L., King, H., & Wong, A.-K. I.
(
2024
).
A Clinician’s Guide to Understanding Bias in Critical Clinical Prediction Models.
Critical Care Clinics
,
40
(
4
).
https://doi.org/10.1016/j.ccc.2024.05.011Chen, M., Pacchiano, A., & Zhang, X.
(
2024
).
State-free Reinforcement Learning.
Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024)
,
(
).
https://doi.org/10.48550/arXiv.2409.18439Sikdar, S., Venturini, S., Charpignon, M.-L., Kumar, S., Rinaldi, F., Tudisco, F., Fortunato, S., & Majumder, M. S.
(
2024
).
What we should learn from pandemic publishing.
Nature Human Behaviour
,
8
(
9
).
https://www.nature.com/articles/s41562-024-01969-7Anagnostou, E., Kouvli, M., Karagianni, E., Gamvroula, A., Kalamatianos, T., Stranjalis, G., & Skoularidou, M.
(
2024
).
Romberg’s test revisited: Changes in classical and advanced sway metrics in patients with pure sensory neuropathy.
Neurophysiologie Clinique
,
54
(
5
).
https://pubmed.ncbi.nlm.nih.gov/39042993/Rodríguez, A., Adhikari, B., Srivastava, A., Pei, S., Charpignon, M.-L., Wang, K., Chang, S., Vullikanti, A., & Prakash, B. A.
(
2024
).
epiDAMIK 2024: The Seventh International Workshop on Epidemiology meets Data Mining and Knowledge Discovery.
KDD '24: The Thirtieth ACM SIGKDD Conference on Knowledge Discovery and Data Mining
,
(
).
https://dl.acm.org/doi/10.1145/3637528.3671480Hulland, E. N., Charpignon, M.-L., Hayek, G. Y. E., Zhao, L., Desai, A. N., & Majumder, M. S.
(
2024
).
Estimating time-varying transmission and oral cholera vaccine effectiveness in Haiti and Cameroon, 2021-2023.
medRxiv [Preprint]
,
(
).
Montesano, S. C. di, Draganov, O., Edelsbrunner, H., & Saghafian, M.
(
2024
).
The Euclidean MST-ratio for Bi-colored Lattices.
arXiv [Preprint]
,
(
).
https://arxiv.org/abs/2403.10204Kokot, M., Dehghannasiri, R., Baharav, T., Salzman, J., & Deorowicz, S.
(
2024
).
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2.
Nature Biotechnology
,
(
).
https://doi.org/10.1038/s41587-024-02381-2Mallinar, N., Beaglehole, D., Zhu, L., Radhakrishnan, A., Pandit, P., & Belkin, M.
(
2024
).
Emergence in non-neural models: Grokking modular arithmetic via average gradient outer product.
arXiv [Preprint]
,
(
).
https://doi.org/10.48550/arXiv.2407.20199Zhang, X., Tseo, Y., Bai, Y., Chen, F., & Uhler, C.
(
2024
).
Prediction of protein subcellular localization in single cells.
bioRxiv [Preprint]
,
(
).
https://www.biorxiv.org/content/10.1101/2024.07.25.605178v1McGee, E. M., García de Albéniz, X., Eliassen, H., Yim, K., Dickerman, B., Preston, M., & Hernán, M.
(
2024
).
Target trial emulation of dynamic surveillance strategies for cancer survivors: An application to non-muscle invasive bladder cancer.
Society for Epidemiologic Research (SER) Annual Meeting
,
(
).
Charpignon, M.-L., Celi, L. A., Cobanaj, M., Eber, R., Fiske, A., Gallifant, J., Li, C., Lingamallu, G., Petushkov, A., & Pierce, R.
(
2024
).
Diversity and inclusion: A hidden additional benefit of Open Data.
PLOS Digital Health
,
3
(
7
).
https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0000486Zou, B. J., Levine, M. E., Zaharieva, D. P., Johari, R., & Fox, E.
(
2024
).
Hybrid Squared Neural ODE Causal Modeling and an Application to Glycemic Response.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235:62934-62963
(
).
https://proceedings.mlr.press/v235/zou24b.htmlSong, Z., Zhao, Y., Shi, W., Jin, W., Yang, Y., & Li, L.
(
2024
).
Generative enzyme design guided by functionally important sites and small-molecule substrates.
41st International Conference on Machine Learning (ICML 2024)
,
PMLR 235
(
).
https://openreview.net/pdf/b349f5504ef1e6143231064979e2e96feaf5a6a9.pdfZhang, X., Venkatachalapathy, S., Paysan, D., Schaerer, P., Tripodo, C., Uhler, C., & Shivashankar, G. V.
(
2024
).
Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCIS.
Nature Communications
,
15
(
1
).
https://www.nature.com/articles/s41467-024-50285-1Chitra, U., Arnold, B. J., & Raphael, B. J.
(
2024
).
Quantifying higher-order epistasis: Beware the chimera.
bioRxiv [Preprint]
,
(
).
https://www.biorxiv.org/content/10.1101/2024.07.17.603976v1Song, Z., Huang, T., Li, L., & Jin, W.
(
2024
).
SurfPro: Functional Protein Design Based on Continuous Surface.
arXiv [Preprint]
,
(
).
https://arxiv.org/abs/2405.08205Shiragur, K., Zhang, J., & Uhler, C.
(
2024
).
Causal Discovery with Fewer Conditional Independence Tests.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235:45060-45078
(
).
https://proceedings.mlr.press/v235/shiragur24a.htmlPapamarkou, T., Skoularidou, M., Palla, K., Aitchison, L., Arbel, J., Dunson, D., Filippone, M., Fortuin, V., Hennig, P., Hernández-Lobato, J. M., Hubin, A., Immer, A., Karaletsos, T., Khan, M. E., Kristiadi, A., Li, Y., Mandt, S., Nemeth, C., Osborne, M. A., … Zhang, R.
(
2024
).
Position: Bayesian Deep Learning is Needed in the Age of Large-Scale AI.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235:39556-39586
(
).
https://proceedings.mlr.press/v235/papamarkou24b.htmlNazaret, A., Hong, J., Azizi, E., & Blei, D.
(
2024
).
Stable Differentiable Causal Discovery.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235:37413-37445
(
).
https://proceedings.mlr.press/v235/nazaret24a.htmlMisra, D., Pacchiano, A., & Schapire, R. E.
(
2024
).
Provable Interactive Learning with Hindsight Instruction Feedback.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235:35829-35850
(
).
https://proceedings.mlr.press/v235/misra24a.htmlMikhael, P., Chinn, I., & Barzilay, R.
(
2024
).
CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235:35647-35663
(
).
https://proceedings.mlr.press/v235/mikhael24a.htmlDemirel, I., Alaa, A., Philippakis, A., & Sontag, D.
(
2024
).
Prediction-powered Generalization of Causal Inferences.
Proceedings of the Forty-First International Conference on Machine Learning
,
PMLR 235: 10385–10408
(
).
https://proceedings.mlr.press/v235/demirel24a.htmlLalchand, V., Lines, D., & Lawrence, N. D.
(
2024
).
Recurrent VAE with Gaussian Process Decoders for De novo Molecular Generation.
Next Generation of Sequence Modelling Architectures Workshop in the Forty-First International Conference on Machine Learning
,
(
).
https://icml.cc/virtual/2024/36131Hulland, E. N., Charpignon, M.-L., Hayek, G. Y. E., Desai, A. N., & Majumder, M. S.
(
2024
).
“What’s in a name?”: Using mpox as a case study to understand the importance of communication, advocacy, and information accuracy in disease nomenclature.
medRxiv [Preprint].
,
(
).
https://doi.org/10.1101/2024.06.24.24309420Chewi, S., Pont, J., Li, J., Lu, C., & Narayanan, S.
(
2024
).
Query Lower Bounds for Log-concave Sampling.
Journal of the ACM
,
71
(
).
https://dl.acm.org/doi/10.1145/3673651Zhang, C. B. C., Hong, Z.-W., Pacchiano, A., & Agrawal, P.
(
2024
).
ORSO: Accelerating Reward Design via Online Reward Selection and Policy Optimization.
Aligning Reinforcement Learning Experimentalists and Theorists Workshop in the Forty-Second International Conference on Machine Learning
,
(
).
https://openreview.net/forum?id=gL8DMNsvJ3Calvello, E., Kovachki, N. B., Levine, M. E., & Stuart, A. M.
(
2024
).
Continuum Attention for Neural Operators.
arXiv [Preprint]
,
(
).
http://arxiv.org/abs/2406.06486Nori, D., & Jin, W.
(
2024
).
RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching.
arXiv [Preprint]
,
(
).
https://arxiv.org/abs/2405.18768Urbut, S. M., Yeung, M. W., Khurshid, S., Cho, S. M. J., Schuermans, A., German, J., Taraszka, K., Paruchuri, K., Fahed, A. C., Ellinor, P. T., Trinquart, L., Parmigiani, G., Gusev, A., & Natarajan, P.
(
2024
).
MSGene: A multistate model using genetic risk and the electronic health record applied to lifetime risk of coronary artery disease.
Nature Communications
,
15
(
1
).
https://www.nature.com/articles/s41467-024-49296-9Afshar, A., & Pacchiano, A.
(
2024
).
Learning Rate-Free Reinforcement Learning: A Case for Model Selection with Non-Stationary Objectives.
I Can’t Believe It’s Not Better Workshop: Failure Modes of Sequential Decision-Making in Practice (Reinforcement Learning Conference 2024)
,
(
).
https://openreview.net/forum?id=ZPqipusx5gWu, J.-L., Levine, M. E., Schneider, T., & Stuart, A.
(
2024
).
Learning about structural errors in models of complex dynamical systems.
Journal of Computational Physics
,
513
(
113157
).
https://www.sciencedirect.com/science/article/pii/S0021999124004066Nazaret, A., & Blei, D.
(
2024
).
Extremely Greedy Equivalence Search.
The Fortieth Conference on Uncertainty in Artificial Intelligence
,
(
).
https://openreview.net/forum?id=2gIMX9UxRNZhang, J., Jennings, J., Hilmkil, A., Pawlowski, N., Zhang, C., & Ma, C.
(
2024
).
Towards Causal Foundation Model: On Duality between Causal Inference and Attention.
arXiv [Preprint]
,
(
).
https://arxiv.org/abs/2310.00809McGee, E. E., Zeleznik, O. A., Balasubramanian, R., Hu, J., Rosner, B. A., Wactawski-Wende, J., Clish, C. B., Avila-Pacheco, J., Willett, W. C., Rexrode, K. M., Tamimi, R. M., & Eliassen, A. H.
(
2024
).
Differences in metabolomic profiles between Black and White women in the U.S.: Analyses from two prospective cohorts.
European Journal of Epidemiology
,
39
(
6
).
https://pubmed.ncbi.nlm.nih.gov/38703248/Chen, Y., Pacchiano, A., & Paschalidis, I. C.
(
2024
).
Multiple-policy Evaluation via Density Estimation.
arXiv [Preprint]
,
(
).
http://arxiv.org/abs/2404.00195Lopes, E.W., McGee, E. M., Ananthakrishnan, A. N., Burke, K. E., Richter, J.E., Chan, A.T., & Khalili, H.
(
2024
).
Guideline-based Healthy Diet and Lifestyle Interventions for the Prevention of Crohn's Disease: A Target Trial Emulation.
Digestive Disease Week
,
(
).
https://ddw.digitellinc.com/p/s/guideline-based-healthy-diet-and-lifestyle-interventions-for-the-prevention-of-crohns-disease-a-target-trial-emulation-6980Chandra, J., Charpignon, M.-L., Bhaskar, A., Therriault, A., Chen, Y.-H., Mooney, A., Dahleh, M. A., Kiang, M. V., & Dominici, F.
(
2024
).
Excess Fatal Overdoses in the United States During the COVID-19 Pandemic by Geography and Substance.
American Journal of Public Health
,
114
(
6
).
https://ajph.aphapublications.org/doi/10.2105/AJPH.2024.307618Zhang, J., Shiragur, K., & Uhler, C.
(
2024
).
Membership Testing in Markov Equivalence Classes via Independence Queries.
Proceedings of The Twenty-Seventh International Conference on Artificial Intelligence and Statistics
,
PMLR 238:3925-3933
(
).
https://proceedings.mlr.press/v238/zhang24k.htmlNazaret, A.O.R., Shi, C., & Blei, D
(
2024
).
On the Misspecification of Linear Assumptions in Synthetic Controls.
Proceedings of The 27th International Conference on Artificial Intelligence and Statistics
,
PMLR 238:3790-3798
(
).
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