Topological and geometrical structures in neurosciences

[Geo-Sci-Info]

Topology and geometry in neuroscience

chairs of the sessions

• Giovani Petri: ISI Foundation link
• Pierre Baudot: Median link

Topics
This session will focus on the advances on Algebraic Topology and Geometrical methods in neurosciences (see [1-105] bellow, among many others). The field is currently knowing an impressive development coming both:

_ from theoretical neuroscience and machine learning fields, like Graph Neural Networks [30-42], Bayesian geometrical inference [27-29], Message Passing, probability and cohomology [92-95], Information Topology [53-54,62-66,96-105] or Networks [83-85,90-91], higher order n-body statistical interactions [67,74,94-95,99,101]

_ from topological data analysis applications to real neural recordings, ranging from subcellular [43,51] genetic or omic expressions [81,101], spiking dynamic and neural coding [1-25,45-47,50-52,79], to cortical areas fMRI, EEG [26,67-72,76-80,84-89], linguistic [54-61] and consciousness [48,53,102].

Bibliographical references: (to be completed)

Carina Curto, Nora Youngs and Vladimir Itskov and colleagues:

[1] C. Curto, N. Youngs. Neural ring homomorphisms and maps between neural codes. Submitted. arXiv.org preprint.
[2] C. Curto, J. Geneson, K. Morrison. Fixed points of competitive threshold-linear networks. Neural Computation, in press, 2019. arXiv.org preprint.
[3] C. Curto, A. Veliz-Cuba, N. Youngs. Analysis of combinatorial neural codes: an algebraic approach. Book chapter in Algebraic and Combinatorial Computational Biology. R. Robeva, M. Macaulay (Eds), 2018.
[4] C. Curto, V. Itskov. Combinatorial neural codes. Handbook of Discrete and Combinatorial Mathematics, Second Edition, edited by Kenneth H. Rosen, CRC Press, 2018. pdf
[5] C. Curto, E. Gross, J. Jeffries, K. Morrison, M. Omar, Z. Rosen, A. Shiu, N. Youngs. What makes a neural code convex? SIAM J. Appl. Algebra Geometry, vol. 1, pp. 222-238, 2017. pdf, SIAGA link, and arXiv.org preprint
[6] C. Curto. What can topology tells us about the neural code? Bulletin of the AMS, vol. 54, no. 1, pp. 63-78, 2017. pdf, Bulletin link.
[7] C. Curto, K. Morrison. Pattern completion in symmetric threshold-linear networks. Neural Computation, Vol 28, pp. 2825-2852, 2016. pdf, arXiv.org preprint.
[8] C. Giusti, E. Pastalkova, C. Curto, V. Itskov. Clique topology reveals intrinsic geometric structure in neural correlations. PNAS, vol. 112, no. 44, pp. 13455-13460, 2015. pdf, PNAS link.
[9] C. Curto, A. Degeratu, V. Itskov. Encoding binary neural codes in networks of threshold-linear neurons. Neural Computation, Vol 25, pp. 2858-2903, 2013. pdf, arXiv.org preprint.
[10] K. Morrison, C. Curto. Predicting neural network dynamics via graphical analysis. Book chapter in Algebraic and Combinatorial Computational Biology. R. Robeva, M. Macaulay (Eds), 2018. arXiv.org preprint,
[11] C. Curto, V. Itskov, A. Veliz-Cuba, N. Youngs. The neural ring: an algebraic tool for analyzing the intrinsic structure of neural codes. Bulletin of Mathematical Biology, Volume 75, Issue 9, pp. 1571-1611, 2013. arXiv.org preprint.
[12] C. Curto, V. Itskov, K. Morrison, Z. Roth, J.L. Walker. Combinatorial neural codes from a mathematical coding theory perspective. Neural Computation, Vol 25(7):1891-1925, 2013. arXiv.org preprint.
[13] C. Curto, A. Degeratu, V. Itskov. Flexible memory networks. Bulletin of Mathematical Biology, Vol 74(3):590-614, 2012. arXiv.org preprint.
[14] V. Itskov, C. Curto, E. Pastalkova, G. Buzsaki. Cell assembly sequences arising from spike threshold adaptation keep track of time in the hippocampus. Journal of Neuroscience, Vol. 31(8):2828-2834, 2011.
[15] K.D. Harris, P. Bartho, et al.. How do neurons work together? Lessons from auditory cortex. Hearing Research, Vol. 271(1-2), 2011, pp. 37-53.
[16] P. Bartho, C. Curto, A. Luczak, S. Marguet, K.D. Harris. Population coding of tone stimuli in auditory cortex: dynamic rate vector analysis. European Journal of Neuroscience, Vol. 30(9), 2009, pp. 1767-1778.
[17] C. Curto, V. Itskov. Cell groups reveal structure of stimulus space. PLoS Computational Biology, Vol. 4(10): e1000205, 2008.
[18] E. Gross , N. K. Obatake , N. Youngs, Neural ideals and stimulus space visualization, Adv. Appl.Math., 95 (2018), pp. 65–95.
[19] C. Giusti, V. Itskov. A no-go theorem for one-layer feedforward networks. Neural Computation, 26 (11):2527-2540, 2014.
[20] V. Itskov, L.F. Abbott. Capacity of a Perceptron for Sparse Discrimination . Phys. Rev. Lett. 101(1), 2008.
[21] V. Itskov, E. Pastalkova, K. Mizuseki, G. Buzsaki, K.D. Harris. Theta-mediated dynamics of spatial information in hippocampus. Journal of Neuroscience, 28(23), 2008.
[22] V. Itskov, C. Curto, K.D. Harris. Valuations for spike train prediction. Neural Computation, 20(3), 644-667, 2008.
[23] E. Pastalkova, V. Itskov , A. Amarasingham , G. Buzsaki. Internally Generated Cell Assembly Sequences in the Rat Hippocampus. Science 321(5894):1322 - 1327, 2008.
[24] V. Itskov, A. Kunin, Z. Rosen. Hyperplane neural codes and the polar complex. To appear in the Abel Symposia proceedings, Vol. 15, 2019.

Alexander Ruys de Perez and colleagues:

[25] A. Ruys de Perez, L.F. Matusevich, A. Shiu, Neural codes and the factor complex, Advances in Applied Mathematics 114 (2020).

Sunghyon Kyeong and colleagues:

[26] Sunghyon Kyeong, Seonjeong Park, Keun-Ah Cheon, Jae-Jin Kim, Dong-Ho Song, and Eunjoo Kim, A New Approach to Investigate the Association between Brain Functional Connectivity and Disease Characteristics of Attention-Deficit/Hyperactivity Disorder: Topological Neuroimaging Data Analysis, PLOS ONE, 10 (9): e0137296, DOI: 10.1371/journal.pone.0137296 (2015)

Jonathan Pillow and colleagues:

[27] Aoi MC & Pillow JW (2017). Scalable Bayesian inference for high-dimensional neural receptive fields. bioRxiv 212217; doi: https://doi.org/10.1101/212217
[28] Aoi MC, Mante V, & Pillow JW. (2020). Prefrontal cortex exhibits multi-dimensional dynamic encoding during decision-making. Nat Neurosci.
[29] Calhoun AJ, Pillow JW, & Murthy M. (2019). Unsupervised identification of the internal states that shape natural behavior. Nature Neuroscience 22:2040-20149.
[30] Dong X, Thanou D, Toni L, et al., 2020, Graph Signal Processing for Machine Learning: A Review and New Perspectives, Ieee Signal Processing Magazine, Vol:37, ISSN:1053-5888, Pages:117-127

Michael Bronstein, Federico Monti, Giorgos Bouritsas and colleagues:

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[33] X. Dong, D. Thanou, L. Toni, M. Bronstein, P. Frossard, Graph Signal Processing for Machine Learning: A Review and New Perspectives, IEEE Signal Processing Magazine (2020), Vol: 37, Pages: 117-127, ISSN: 1053-5888
[34] Y. Wang, Y. Sun, Z. Liu, S.E. Sarma, M. Bronstein, J.M. Solomon, Dynamic Graph CNN for Learning on Point Clouds, ACM Transactions on graphics (2020), Vol: 38, ISSN: 0730-0301
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[36] G. Bouritsas, S. Bokhnyak, S. Ploumpis, M. Bronstein, S. Zafeiriou, Neural 3D Morphable Models: Spiral Convolutional Networks for 3D Shape Representation Learning and Generation, (2019) IEEE/CVF ICCV 2019, 7212
[37] O. Litany, A. Bronstein, M. Bronstein, A. Makadia et al., Deformable Shape Completion with Graph Convolutional Autoencoders (2018), Pages: 1886-1895, ISSN: 1063-6919
[38] R. Levie, F. Monti, X. Bresson X, M. Bronstein, CayleyNets: Graph Convolutional Neural Networks with Complex Rational Spectral Filters, IEEE Transactions on Signal Processing (2018), Vol: 67, Pages: 97-109, ISSN: 1053-587X
[39] F. Monti, K. Otness, M. Bronstein, Motifnet: a motif-based graph convolutional network for directed graphs (2018), Pages: 225-228
[40] F. Monti, M. Bronstein, X. Bresson, Geometric matrix completion with recurrent multi-graph neural networks, Neural Information Processing Systems (2017), Pages: 3700-3710, ISSN: 1049-5258
[41] F. Monti F, D. Boscaini, J. Masci, E. Rodola, J. Svoboda, M. Bronstein, Geometric deep learning on graphs and manifolds using mixture model CNNs, (2017) IEEE Conference on Computer Vision and Pattern Recognition, p: 3-3
[42] M. Bronstein, J. Bruna, Y. LeCun, A. Szlam, P. Vandergheynst et al., Geometric Deep Learning Going beyond Euclidean data, IEEE Signal Processing Magazine (2017), Vol: 34, Pages: 18-42, ISSN: 1053-5888

Kathryn Hess and colleagues:

[43] L. Kanari, H. Dictus, W. Van Geit, A. Chalimourda, B. Coste, J. Shillcock, K. Hess, and H. Markram, Computational synthesis of cortical dendritic morphologies, bioRvix (2020) 10.1101/2020.04.15.040410, submitted.
[44] G. Tauzin, U. Lupo, L. Tunstall, J. Burella Prez, M. Caorsi, A. Medina-Mardones, A, Dassatti, and K. Hess, giotto-tda: a topological data analysis toolkit for machine learning and data exploration, arXiv:2004.02551
[45] E. Mullier, J. Vohryzek, A. Griffa, Y. Alemàn-Gómez, C. Hacker, K. Hess, and P. Hagmann, Functional brain dynamics are shaped by connectome n-simplicial organization, (2020) submitted.
[46] M. Fournier, M. Scolamiero, etal., Topology predicts long-term functional outcome in early psychosis, Molecular Psychiatry (2020). https://doi.org/10.1038/s41380-020-0826-1.
[47] K. Hess, Topological adventures in neuroscience, in the Proceedings of the 2018 Abel Symposium: Topological Data Analysis, Springer Verlag, (2020).
[48] A. Doerig, A. Schurger, K. Hess, and M. H. Herzog, The unfolding argument: why IIT and other causal structure theories of consciousness are empirically untestable, Consciousness and Cognition 72 (2019) 49-59.
[49] L. Kanari, S. Ramaswamy, et al., Objective classification of neocortical pyramidal cells, Cerebral Cortex (2019) bhy339, https://doi.org/10.1093/cercor/bhy339.
[50] J.-B. Bardin, G. Spreemann, K. Hess, Topological exploration of artificial neuronal network dynamics, Network Neuroscience (2019) https://doi.org/10.1162/netn_a_00080.
[51] L. Kanari, P. Dłotko, M. Scolamiero, R. Levi, J. C. Shillcock, K. Hess, and H. Markram, A topological representation of branching morphologies, Neuroinformatics (2017) doi: 10.1007/s12021-017-9341-1.
[52] M. W. Reimann, M. Nolte,et al., Cliques of neurons bound into cavities provide a missing link between structure and function, Front. Comput. Neurosci., 12 June (2017), doi: 10.3389/fncom.2017.00048.

Mathilde Marcoli, Yuri Manin, and colleagues:

[53] Y. Manin, M. Marcolli Homotopy Theoretic and Categorical Models of Neural Information Networks. arXiv (2020) preprint arXiv:2006.15136
[54] M. Marcolli, Lumen Naturae: Visions of the Abstract in Art and Mathematics, MIT Press (2020)
[55] A. Port, T. Karidi, M. Marcolli, Topological Analysis of Syntactic Structures (2019) arXiv preprint arXiv:1903.05181
[56] M. Marcolli, Motivic information, Bollettino dell'Unione Matematica Italiana (2019) 12 (1-2), 19-41
[57] A. Port, I. Gheorghita, D. Guth, J.M. Clark, C. Liang, S. Dasu, M. Marcolli, Persistent topology of syntax, Mathematics in Computer Science (2018) 12 (1), 33-50 20
[58] K. Shu, S. Aziz, VL Huynh, D Warrick, M Marcolli, Syntactic phylogenetic trees, Foundations of Mathematics and Physics One Century After Hilbert (2018), 417-441
[59] K. Shu, A. Ortegaray, R Berwick, M Marcolli Phylogenetics of Indo-European language families via an algebro-geometric analysis of their syntactic structures. arXiv (2018) preprint arXiv:1712.01719
[60] K. Shu, M. Marcolli, Syntactic structures and code parameters Mathematics in Computer Science (2018) 11 (1), 79-90
[61] K Siva, J Tao, M Marcolli. Syntactic Parameters and Spin Glass Models of Language Change Linguist. Anal (2017) 41 (3-4), 559-608
[62] M. Marcolli, N. Tedeschi, Entropy algebras and Birkhoff factorization. Journal of Geometry and Physics (2015) 97, 243-265
[63] M. Marcolli, Information algebras and their applications. International Conference on Geometric Science of Information (2015), 271-276
[64] K. Siva, J. Tao, M. Marcolli Spin glass models of syntax and language evolution, arXiv preprint (2015) arXiv:1508.00504
[65] Y. Manin, M. Marcolli, Kolmogorov complexity and the asymptotic bound for error-correcting codes Journal of Differential Geometry (2014) 97 (1), 91-108
[66] M. Marcolli, R. Thorngren, Thermodynamic semirings, ArXiv preprint (2011) arXiv:1108.2874

Bosa Tadić and colleagues:

[67] M. Andjelkovic, B. Tadic, R. Melnik, The topology of higher-order complexes associated with brain-function hubs in human connectomes , available on arxiv.org/abs/2006.10357, published in Scientific Reports 10:17320 (2020)
[68] B. Tadic, M. Andjelkovic, M. Suvakov, G.J. Rodgers, Magnetisation Processes in Geometrically Frustrated Spin Networks with Self-Assembled Cliques, Entropy 22(3), 336 (2020)
[69] B. Tadic, M. Andjelkovic, R. Melnik, Functional Geometry of Human Connectomes published in ScientificReports Nature:ScientificReports 9:12060 (2019) previous version: Functional Geometry of Human Connectome and Robustness of Gender Differences, arXiv preprint arXiv:1904.03399 April 6, 2019
[70] B. Tadic, M. Andjelkovic, M. Suvakov, Origin of hyperbolicity in brain-to-brain coordination networks, FRONTIERS in PHYSICS vol.6, ARTICLE{10.3389/fphy.2018.00007}, (2018) OA
[71] B. Tadic, M. Andjelkovic, Algebraic topology of multi-brain graphs: Methods to study the social impact and other factors onto functional brain connections, in Proceedings of BELBI (2016)
[72] B. Tadic, M. Andjelkovic, B.M. Boskoska, Z. Levnajic, Algebraic Topology of Multi-Brain Connectivity Networks Reveals Dissimilarity in Functional Patterns during Spoken Communications, PLOS ONE Vol 11(11), e0166787 (2016)
[73] M. Mitrovic and B. Tadic, Search for Weighted Subgraphs on Complex Networks with MLM, Lecture Notes in Computer Science, Vol. 5102 pp. 551-558 (2008)

Giovanni Petri, Francesco Vaccarino and collaborators:

[74] F. Battiston, G. Cencetti, et al., Networks beyond pairwise interactions: structure and dynamics, Physics Reports (2020), arXiv:2006.01764
[75] M. Guerra, A. De Gregorio, U. Fugacci, G. Petri, F. Vaccarino, Homological scaffold via minimal homology bases. arXiv (2020) preprint arXiv:2004.11606
[76] J. Billings, R. Tivadar, M.M. Murray, B. Franceschiello, G. Petri, Topological Features of Electroencephalography are Reference-Invariant, bioRxiv 2020
[77] J. Billings, M. Saggar, S. Keilholz, G. Petri, Topological Segmentation of Time-Varying Functional Connectivity Highlights the Role of Preferred Cortical Circuits, bioRxiv 2020
[78] E. Ibáñez-Marcelo, L. Campioni, et al., Topology highlights mesoscopic functional equivalence between imagery and perception: The case of hypnotizability. NeuroImage (2019) 200, 437-449
[79] P. Expert, L.D. Lord, M.L. Kringelbach, G. Petri. Topological neuroscience. Network Neuroscience (2019) 3 (3), 653-655
[80] C. Geniesse, O. Sporns, G. Petri, M. Saggar, Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. Network Neuroscience (2019) 3 (3), 763-778
[81] A. Patania, P. Selvaggi, M. Veronese, O. Dipasquale, P. Expert, G. Petri, Topological gene expression networks recapitulate brain anatomy and function. Network Neuroscience (2019) 3 (3), 744-762
[82] E. Ibáñez‐Marcelo, L. Campioni, D.et al.. Spectral and topological analyses of the cortical representation of the head position: Does hypnotizability matter? Brain and behavior (2018) 9 (6), e01277
[83] G. Petri, A. Barrat, Simplicial activity driven model, Physical review letters 121 (22), 228301
[84] A. Phinyomark, E. Ibanez-Marcelo, G. Petri. Resting-state fmri functional connectivity: Big data preprocessing pipelines and topological data analysis. IEEE Transactions on Big Data (2017) 3 (4), 415-428
[85] G. Petri, S. Musslick, B. Dey, K. Ozcimder, D. Turner, N.K. Ahmed, T. Willke. Topological limits to parallel processing capability of network architectures. arXiv preprint (2017) arXiv:1708.03263
[86] K. Ozcimder, B. Dey, S. Musslick, G. Petri, N.K. Ahmed, T.L. Willke, J.D. Cohen, A Formal Approach to Modeling the Cost of Cognitive Control, arXiv preprint (2017) arXiv:1706.00085
[87] L.D. Lord, P. Expert, et al. , Insights into brain architectures from the homological scaffolds of functional connectivity networks, Frontiers in systems neuroscience (2016) 10, 85
[88] J. Binchi, E. Merelli, M. Rucco, G. Petri, F. Vaccarino. jHoles: A Tool for Understanding Biological Complex Networks via Clique Weight Rank Persistent Homology. Electron. Notes Theor. Comput. Sci. (2014) 306, 5-18
[89] G. Petri, P. Expert, F. Turkheimer, R. Carhart-Harris, D. Nutt, P.J. Hellyer et al., Homological scaffolds of brain functional networks. Journal of The Royal Society Interface (2014) 11 (101), 20140873
[90] G. Petri, M. Scolamiero, I. Donato, F. Vaccarino, Topological strata of weighted complex networks. PloS one (2013) 8 (6), e66506
[91] G. Petri, M. Scolamiero, I. Donato, ., Networks and cycles: a persistent homology approach to complex networks Proceedings of the european conference on complex systems (2013), 93-99

Daniel Bennequin, Juan-Pablo Vigneaux, Olivier Peltre, Pierre Baudot and colleagues:

[92] D. Bennequin. G. Sergeant-Perthuis, O. Peltre, and J.P. Vigneaux, Extra-fine sheaves and interaction decompositions, (2020) arXiv:2009.12646
[93] O. Peltre, Message-Passing Algorithms and Homology, PhD Thesis (2020), arXiv:2009.11631
[94] G. Sergeant-Perthuis, Interaction decomposition for presheafs, (2020) arXiv:2008.09029
[95] G. Sergeant-Perthuis, Bayesian/Graphoid intersection property for factorisation models, (2019), arXiv:1903.06026
[96] J.P. Vigneaux, Topology of Statistical Systems: A Cohomological Approach to Information Theory, PhD Thesis (2019).
[97] J.P. Vigneaux, Information structures and their cohomology, in Theory and Applications of Categories, Vol. 35, (2020), No. 38, pp 1476-1529.
[98] J.P. Vigneaux, Information theory with finite vector spaces, in IEEE Transactions on Information Theory, vol. 65, no. 9, pp. 5674-5687, Sept. (2019)
[99] Baudot P., Tapia M., Bennequin, D. , Goaillard J.M., Topological Information Data Analysis. (2019), Entropy, 21(9), 869
[100] Baudot P., The Poincaré-Shannon Machine: Statistical Physics and Machine Learning aspects of Information Cohomology. (2019), Entropy , 21(9),
[101] Tapia M., Baudot P., et al. Neurotransmitter identity and electrophysiological phenotype are genetically coupled in midbrain dopaminergic neurons. Scientific Reports. (2018). BioArXiv168740
[102] Baudot P., Elements of qualitative cognition: an Information Topology Perspective. Physics of Life Reviews. (2019) Arxiv. arXiv:1807.04520
[103] Baudot P., Bennequin D., The homological nature of entropy. Entropy, (2015), 17, 1-66; doi:10.3390
[104] D. Bennequin. Remarks on Invariance in the Primary Visual Systems of Mammals, pages 243–333. Neuromathematics of Vision Part of the series Lecture Notes in Morphogenesis Springer, 2014.
[105] Baudot P., Bennequin D., Information Topology I and II. Random models in Neuroscience (2012)