Fetching the paper…
Reading the bibliography…
It is increasingly common to encounter data from dynamic processes captured by static cross-sectional measurements over time, particularly in biomedical settings.
On the Translocation of Masses
Kantorovich, L. V · 1942
Earlier work this paper cites.
The epigenotype
Waddington, C. H · 1942
Earlier work this paper cites.
A relationship between arbitrary positive matrices and doubly stochastic matrices, 1964
Sinkhorn, R · 1964
Earlier work this paper cites.
The Speed of Mean Glivenko-Cantelli Convergence
Dudley, R. M · 1969
Earlier work this paper cites.
A family of embedded Runge-Kutta formulae
Dormand, J. and Prince, P · 1980
Earlier work this paper cites.
A computational fluid mechanics solution to the Monge-Kantorovich mass transfer problem
Benamou, J.-D. and Brenier, Y · 2000
Earlier work this paper cites.
Broken Limits to Life Expectancy
Oeppen, J. and Vaupel, J. W · 2002
Earlier work this paper cites.
Numerical resolution of an “unbalanced” mass transport problem
Benamou, J.-D · 2003
Earlier work this paper cites.
Optimal Transport, Old and New
Villani, C · 2008
Earlier work this paper cites.
Stacked Denoising Autoencoders: Learning Useful Representations in a Deep Network with a Local Denoising Criterion
Vincent, P., Larochelle, H., Lajoie, I., Bengio, Y., and Manzagol, P.-A · 2010
Earlier work this paper cites.
Contractive Auto-Encoders: Explicit Invariance During Feature Extraction
Rifai, S., Vincent, P., Muller, X., Glorot, X., and Bengio, Y · 2011
Earlier work this paper cites.
Sinkhorn Distances: Lightspeed Computation of Optimal Transport
Cuturi, M · 2013
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.
Optimal Transport with Proximal Splitting
Papadakis, N., Peyré, G., and Oudet, E · 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.
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
Cotney, J., Muhle, R. A., Sanders, S. J., Liu, L., Willsey, A. J., Niu, W., Liu, W., Klei, L., Lei, J., Yin, J., Reilly, S. K., Tebbenkamp, A. T., Bichsel, C., Pletikos, M., Sestan, N., Roeder, K., State, M. W., Devlin, B., and Noonan, J. P · 2015
Earlier work this paper cites.
Adam: A Method for Stochastic Optimization
Kingma, D. P. and Ba, J · 2015
Cited alongside, same era.
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., Trombetta, J. J., Weitz, D. A., Sanes, J. R., Shalek, A. K., Regev, A., and McCarroll, S. A · 2015
Cited alongside, same era.
Variational Inference with Normalizing Flows
Rezende, D. J. and Mohamed, S · 2015
Cited alongside, same era.
Diffusion pseudotime robustly reconstructs lineage branching
Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F., and Theis, F. J · 2016
Cited alongside, same era.
Learning Population-Level Diffusions with Generative Recurrent Networks
Hashimoto, T. B., Gifford, D. K., and Jaakkola, T. S · 2016
Cited alongside, same era.
CHD8 haploinsufficiency results in autistic-like phenotypes in mice
FFJORD: Free-form Continuous Dynamics for Scalable Reversible Generative Models
Grathwohl, W., Chen, R. T. Q., Bettencourt, J., Sutskever, I., and Duvenaud, D · 2019
Later among the works it cites.
A Direct O ~ ( 1 / ϵ CLOSE \tilde{O}(1/\epsilon ) Iteration Parallel Algorithm for Optimal Transport
Jambulapati, A., Sidford, A., and Tian, K · 2019
Later among the works it cites.
Organoid single-cell genomic atlas uncovers human-specific features of brain development
Kanton, S., Boyle, M. J., He, Z., Santel, M., Weigert, A., Sanchís-Calleja, F., Guijarro, P., Sidow, L., Fleck, J. S., Han, D., Qian, Z., Heide, M., Huttner, W. B., Khaitovich, P., Pääbo, S., Treutlein, B., and Camp, J. G · 2019
Later among the works it cites.
Generalized Sliced Wasserstein Distances
Kolouri, S., Nadjahi, K., Simsekli, U., Badeau, R., and Rohde, G · 2019
Later among the works it cites.
Visualizing structure and transitions in high-dimensional biological data
Moon, K. R., van Dijk, D., Wang, Z., Gigante, S., Burkhardt, D. B., Chen, W. S., Yim, K., van den Elzen, A., Hirn, M. J., Coifman, R. R., Ivanova, N. B., Wolf, G., and Krishnaswamy, S · 2019
Later among the works it cites.
alphaXiv searches the wider corpus for related work and actual follow-ups.
alphaXiv is searching for related work…
Katayama, Y., Nishiyama, M., Shoji, H., Ohkawa, Y., Kawamura, A., Sato, T., Suyama, M., Takumi, T., Miyakawa, T., and Nakayama, K. I · 2016
Cited alongside, same era.
Improving Variational Inference with Inverse Autoregressive Flow
Kingma, D. P., Salimans, T., Jozefowicz, R., Chen, X., Sutskever, I., and Welling, M · 2016
Cited alongside, same era.
Masked Autoregressive Flow for Density Estimation
Papamakarios, G., Pavlakou, T., and Murray, I · 2017
Cited alongside, same era.
Unbalanced optimal transport: Dynamic and Kantorovich formulations
Chizat, L., Peyré, G., Schmitzer, B., and Vialard, F.-X · 2018
Cited alongside, same era.
RNA velocity of single cells
La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., Fan, J., Borm, L. E., Liu, Z., van Bruggen, D., Guo, J., He, X., Barker, R., Sundström, E., Castelo-Branco, G., Cramer, P., Adameyko, I., Linnarsson, S., and Kharchenko, P. V · 2018
Cited alongside, same era.
Optimal Entropy-Transport problems and a new Hellinger–Kantorovich distance between positive measures
Liero, M., Mielke, A., and Savaré, G · 2018
Cited alongside, same era.
Geometry Based Data Generation
Lindenbaum, O., Stanley, J., Wolf, G., and Krishnaswamy, S · 2018
Cited alongside, same era.
Subspace Detours: Building Transport Plans that are Optimal on Subspace Projections
Muzellec, B. and Cuturi, M · 2019
Later among the works it cites.
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.
Computational Optimal Transport
Peyré, G. and Cuturi, M · 2019
Later among the works it cites.
A comparison of single-cell trajectory inference methods
Saelens, W., Cannoodt, R., Todorov, H., and Saeys, Y · 2019
Later among the works it cites.
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
Schiebinger, G., Shu, J., Tabaka, M., Cleary, B., Subramanian, V., Solomon, A., Gould, J., Liu, S., Lin, S., Berube, P., Lee, L., Chen, J., Brumbaugh, J., Rigollet, P., Hochedlinger, K., Jaenisch, R., Regev, A., and Lander, E. S · 2019
Later among the works it cites.
Sharp asymptotic and finite-sample rates of convergence of empirical measures in Wasserstein distance
Weed, J. and Bach, F · 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.
The emergence and promise of single-cell temporal-omics approaches
Lederer, A. R. and La Manno, G · 2020
Closest in time.
Scalable Gradients for Stochastic Differential Equations
Li, X., Wong, T.-K. L., Chen, R. T. Q., and Duvenaud, D · 2020
Closest in time.
NASC-seq monitors RNA synthesis in single cells
Hendriks, G.-J., Jung, L. A., Larsson, A. J. M., Lidschreiber, M., Andersson Forsman, O., Lidschreiber, K., Cramer, P., and Sandberg, R · 2041
Closest in time.