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In this paper, we present Super-OT, a novel approach to computational lineage tracing that combines a supervised learning framework with optimal transport based on Generative Adversarial Networks (GANs).
Scikit-learn: Machine learning in Python
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M., and Duchesnay, E · 2011
Earlier work this paper cites.
Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development
Bendall, S. C., Davis, K. L., Amir, E.-a. D., Tadmor, M. D., Simonds, E. F., Chen, T. J., Shenfeld, D. K., Nolan, G. P., and Pe’er, D · 2014
Earlier work this paper cites.
Adam: A method for stochastic optimization
Kingma, D. P. and Ba, J · 2014
Earlier work this paper cites.
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
Marco, E., Karp, R. L., Guo, G., Robson, P., Hart, A. H., Trippa, L., and Yuan, G.-C · 2014
Earlier work this paper cites.
Conditional generative adversarial nets, 2014
Mirza, M. and Osindero, S · 2014
Earlier work this paper cites.
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., and Rinn, J. L · 2014
Earlier work this paper cites.
Single-cell RNA-seq with waterfall reveals molecular cascades underlying adult neurogenesis
Shin, J., Berg, D. A., Zhu, Y., Shin, J. Y., Song, J., Bonaguidi, M. A., Enikolopov, G., Nauen, D. W., Christian, K. M., Ming, G.-l., et al · 2015
Earlier work this paper cites.
Tscan: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
Ji, Z. and Ji, H · 2016
Cited alongside, same era.
Wishbone identifies bifurcating developmental trajectories from single-cell data
Setty, M., Tadmor, M. D., Reich-Zeliger, S., Angel, O., Salame, T. M., Kathail, P., Choi, K., Bendall, S., Friedman, N., and Pe’er, D · 2016
Cited alongside, same era.
Improved training of Wasserstein GANs, 2017
Gulrajani, I., Ahmed, F., Arjovsky, M., Dumoulin, V., and Courville, A · 2017
Cited alongside, same era.
Slice: determining cell differentiation and lineage based on single cell entropy
Guo, M., Bao, E. L., Wagner, M., Whitsett, J. A., and Xu, Y · 2017
Cited alongside, same era.
Reversed graph embedding resolves complex single-cell trajectories
Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., and Trapnell, C · 2017
Cited alongside, same era.
Fundamental limits on dynamic inference from single-cell snapshots
Pytorch: An imperative style, high-performance deep learning library
Paszke, A., Gross, S., Massa, F., Lerer, A., Bradbury, J., Chanan, G., Killeen, T., Lin, Z., Gimelshein, N., Antiga, L., Desmaison, A., Kopf, A., Yang, E., DeVito, Z., Raison, M., Tejani, A., Chilamkurthy, S., Steiner, B., Fang, L., Bai, J., and Chintala, S · 2019
Later among the works it cites.
Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming
Schiebinger, G., Shu, J., Tabaka, M., Cleary, B., Subramanian, V., Solomon, A., Liu, S., Lin, S., Berube, P., Lee, L., et al · 2019
Later among the works it cites.
Paga: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Wolf, F. A., Hamey, F. K., Plass, M., Solana, J., Dahlin, J. S., Göttgens, B., Rajewsky, N., Simon, L., and Theis, F. J · 2019
Later among the works it cites.
Scalable unbalanced optimal transport using generative adversarial networks
Yang, K. D. and Uhler, C · 2019
Later among the works it cites.
Lineage tracing on transcriptional landscapes links state to fate during differentiation
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Weinreb, C., Wolock, S., Tusi, B. K., Socolovsky, M., and Klein, A. M · 2018
Cited alongside, same era.
Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F. D., and Klein, A. M · 2020
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Autoencoder and optimal transport to infer single-cell trajectories of biological processes
Yang, K. D., Damodaran, K., Venkatchalapathy, S., Soylemezoglu, A. C., Shivashankar, G., and Uhler, C · 2020
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