Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't
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DOI: 10.1371/journal.pcbi.1000380
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- S. Nirenberg & S. M. Carcieri & A. L. Jacobs & P. E. Latham, 2001. "Retinal ganglion cells act largely as independent encoders," Nature, Nature, vol. 411(6838), pages 698-701, June.
- Michael Socolich & Steve W. Lockless & William P. Russ & Heather Lee & Kevin H. Gardner & Rama Ranganathan, 2005. "Evolutionary information for specifying a protein fold," Nature, Nature, vol. 437(7058), pages 512-518, September.
- Elad Schneidman & Michael J. Berry & Ronen Segev & William Bialek, 2006. "Weak pairwise correlations imply strongly correlated network states in a neural population," Nature, Nature, vol. 440(7087), pages 1007-1012, April.
- William P. Russ & Drew M. Lowery & Prashant Mishra & Michael B. Yaffe & Rama Ranganathan, 2005. "Natural-like function in artificial WW domains," Nature, Nature, vol. 437(7058), pages 579-583, September.
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- Montani, Fernando & Phoka, Elena & Portesi, Mariela & Schultz, Simon R., 2013. "Statistical modelling of higher-order correlations in pools of neural activity," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(14), pages 3066-3086.
- Benjamin Dunn & Maria Mørreaunet & Yasser Roudi, 2015. "Correlations and Functional Connections in a Population of Grid Cells," PLOS Computational Biology, Public Library of Science, vol. 11(2), pages 1-21, February.
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- Arno Onken & Valentin Dragoi & Klaus Obermayer, 2012. "A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts," PLOS Computational Biology, Public Library of Science, vol. 8(6), pages 1-12, June.
- Xi, Ning & Muneepeerakul, Rachata & Azaele, Sandro & Wang, Yougui, 2014. "Maximum entropy model for business cycle synchronization," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 413(C), pages 189-194.
- Gašper Tkačik & Olivier Marre & Dario Amodei & Elad Schneidman & William Bialek & Michael J Berry II, 2014. "Searching for Collective Behavior in a Large Network of Sensory Neurons," PLOS Computational Biology, Public Library of Science, vol. 10(1), pages 1-23, January.
- Montangie, Lisandro & Montani, Fernando, 2015. "Quantifying higher-order correlations in a neuronal pool," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 421(C), pages 388-400.
- Hideaki Shimazaki & Shun-ichi Amari & Emery N Brown & Sonja Grün, 2012. "State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data," PLOS Computational Biology, Public Library of Science, vol. 8(3), pages 1-27, March.
- Porta Mana, PierGianLuca & Rostami, Vahid & Torre, Emiliano & Roudi, Yasser, 2018. "Maximum-entropy and representative samples of neuronal activity: a dilemma," OSF Preprints uz29n, Center for Open Science.
- Christian Donner & Klaus Obermayer & Hideaki Shimazaki, 2017. "Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-27, January.
- Montangie, Lisandro & Montani, Fernando, 2017. "Higher-order correlations in common input shapes the output spiking activity of a neural population," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 471(C), pages 845-861.
- Einat Granot-Atedgi & Gašper Tkačik & Ronen Segev & Elad Schneidman, 2013. "Stimulus-dependent Maximum Entropy Models of Neural Population Codes," PLOS Computational Biology, Public Library of Science, vol. 9(3), pages 1-14, March.
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