The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Inferring single-trial neural population dynamics using sequential auto-encoders
Open accessAbstract
Neuroscience is experiencing a revolution in which simultaneous recording of thousands of neurons is revealing population dynamics that are not apparent from single-neuron responses. This structure is typically extracted from data averaged across many trials, but deeper understanding requires studying phenomena detected in single trials, which is challenging due to incomplete sampling of the neural population, trial-to-trial variability, and fluctuations in action potential timing. We introduce latent factor analysis via dynamical systems, a deep learning method to infer latent dynamics from single-trial neural spiking data. When applied to a variety of macaque and human motor cortical datasets, latent factor analysis via dynamical systems accurately predicts observed behavioral variables, extracts precise firing rate estimates of neural dynamics on single trials, infers perturbations to those dynamics that correlate with behavioral choices, and combines data from non-overlapping recording sessions spanning months to improve inference of underlying dynamics. LFADS, a deep learning method for analyzing neural population activity, can extract neural dynamics from single-trial recordings, stitch separate datasets into a single model, and infer perturbations, for example, from behavioral choices to these dynamics.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
(2008) · Journal of Machine Learning Research · Cited by 33,051
Auto-Encoding Variational Bayes
Kingma, D. P., & Welling, M. (2013) · arXiv · doi:10.48550/arxiv.1312.6114 · Cited by 20,067
Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling
Chung, J., Gulcehre, C., Cho, K., & Bengio, Y. (2014) · arXiv · doi:10.48550/arxiv.1412.3555 · Cited by 11,008
Improving neural networks by preventing co-adaptation of feature detectors
Hinton, G. E., Srivastava, N., Krizhevsky, A., Sutskever, I., & Salakhutdinov, R. R. (2012) · arXiv · doi:10.48550/arxiv.1207.0580 · Cited by 6,382
A mechanism for cognitive dynamics: neuronal communication through neuronal coherence.
Fries, P. (2005) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2005.08.011 · Cited by 4,284
Advances in Neural Information Processing Systems 27 (NIPS 2014)
Zhong, M., Goddard, N., & Sutton, C. A. (2014) · Cited by 2,440
Stochastic Backpropagation and Approximate Inference in Deep Generative Models
Rezende, D. J., Mohamed, S., & Wierstra, D. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1401.4082 · Cited by 2,405
Recurrent Neural Network Regularization
Zaremba, W., Sutskever, I., & Vinyals, O. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1409.2329 · Cited by 2,123
Generating Sentences from a Continuous Space
Bowman, S. R., Vilnis, L., Vinyals, O., Dai, A., Jozefowicz, R., & Bengio, S. (2016) · Proceedings of The 20th SIGNLL Conference on Computational Natural Language Learning · doi:10.18653/v1/k16-1002 · Cited by 2,061
Context-dependent computation by recurrent dynamics in prefrontal cortex
Mante, V., Sussillo, D., Shenoy, K. V., & Newsome, W. T. (2013) · Nature · doi:10.1038/nature12742 · Cited by 1,847
Self-citation
Cited by
Opportunities and obstacles for deep learning in biology and medicine
Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Zietz, M., Hoffman, M. M., et al. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2017.0387 · Cited by 2,310
A guide to machine learning for biologists
Greener, J. G., Kandathil, S. M., Moffat, L., & Jones, D. T. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00407-0 · Cited by 2,127
Computation Through Neural Population Dynamics
Vyas, S., Golub, M. D., Sussillo, D., & Shenoy, K. V. (2020) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-092619-094115 · Cited by 671
Self-citationLearnable latent embeddings for joint behavioural and neural analysis
Schneider, S., Lee, J. H., & Mathis, M. W. (2023) · Nature · doi:10.1038/s41586-023-06031-6 · Cited by 348
Deep reinforcement learning and its neuroscientific implications
Botvinick, M., Wang, J. X., Dabney, W., Miller, K. J., & Kurth-Nelson, Z. (2020) · Neuron · doi:10.1016/j.neuron.2020.06.014 · Cited by 269
Metadata
- Authors
- Pandarinath, C., O’Shea, D. J., Collins, J., Jozefowicz, R., Stavisky, S. D., Kao, J. C., Trautmann, E. M., Kaufman, M. T., Ryu, S. I., Hochberg, L. R., Henderson, J. M., Shenoy, K. V., Abbott, L. F., & Sussillo, D.
- Venue
- Nature Methods
- Published
- 2018-09-17
- Volume
- 15
- Issue
- 10
- Pages
- 805-815
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2951777958
- Cited by
- 686
- References
- 55
- FWCI
- 30.99
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Inferring single-trial neural population dynamics using sequential auto-encoders. https://app.cochat.ai/papers/10.1038/s41592-018-0109-9
- The paper
- Pandarinath, C., O’Shea, D. J., Collins, J., Jozefowicz, R., Stavisky, S. D., Kao, J. C., Trautmann, E. M., Kaufman, M. T., Ryu, S. I., Hochberg, L. R., Henderson, J. M., Shenoy, K. V., Abbott, L. F., & Sussillo, D. (2018). Inferring single-trial neural population dynamics using sequential auto-encoders. Nature Methods. https://doi.org/10.1038/s41592-018-0109-9
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
