Systematic exploration of unsupervised methods for mapping behavior

Physical Biology

Volumn 14, Issue 1, 2017, Pages

  Todd, Jeremy G ^a,b   Kain, Jamey S ^b   De Bivort, Benjamin L ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

behavioral space; clustering; Drosophila melanogaster; Gaussian mixture model; proprioception; t SNE; unsupervised

Indexed keywords

ALGORITHM; ANIMAL; ANIMAL BEHAVIOR; CLUSTER ANALYSIS; DROSOPHILA; ENTROPY; FEMALE; LIMB; MARKOV CHAIN; NORMAL DISTRIBUTION; PHYSIOLOGY;

ALGORITHMS; ANIMALS; BEHAVIOR, ANIMAL; CLUSTER ANALYSIS; DROSOPHILA; ENTROPY; EXTREMITIES; FEMALE; MARKOV CHAINS; NORMAL DISTRIBUTION;

EID: 85016252371     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/14/1/015002     Document Type: Article

References (62)

1. Baden T, Berens P, Franke K, Roson M R, Bethge M and Euler T 2016 The functional diversity of retinal ganglion cells in the mouse Nature 529 345-50
2. Banfield J D and Raftery A E 1993 Model-based Gaussian and non-Gaussian clustering Biometrics 49 803-21
3. Berman G J, Choi D M, Bialek W and Shaevitz J W 2014 Mapping the stereotyped behaviour of freely moving fruit flies J. R. Soc. Interface. 11 20140672
4. Branson K, Robie A, Bender J, Perona P and Dickinson M 2009 High-throughput ethomics in large groups of Drosophila Nat. Methods 6 451-7
5. Brown A E, Yemini E, Grundy L J, Jucikas T and Schafer W R 2013 A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion Proc. Natl Acad. Sci. 110 791-6
6. Buchanan S M, Kain J S and de Bivort B L 2015 Neuronal control of locomotor handedness in Drosophila Proc. Natl Acad. Sci. 112 6700-5
7. Chandrasekaran S, Ament S A, Eddy J A, Rodriguez-Zas S L, Schatz B R, Price N D and Robinson G E 2011 Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states Proc. Natl Acad. Sci. 108 18020-5
8. Chen S, Lee A Y, Bowens N M, Huber R and Kravitz E A 2002 Fighting fruit flies: a model system for the study of aggression Proc. Natl Acad. Sci. 99 5664-8
9. Cohn R, Morantte I and Ruta V 2015 Coordinated and compartmentalized neuromodulation shapes sensory processing in Drosophila Cell 163 1742-55
10. Costa M, Ostrovsky A D, Manton J D, Prohaska S and Jefferis G S 2014 NBLAST: rapid, sensitive comparison of neuronal structure and construction of neuron family databases
11. Crall J, Souffrant A, Akandwanaho D, Hescock S, Callan S, Coronado W M, Baldwin M and de Bivort B L 2016 Social context modulates idiosyncrasy of behaviour in the gregarious cockroach Blaberus discoidalis Animal Behav. 111 297-305
12. Dankert H, Wang L, Hoopfer E D, Anderson D J and Perona P 2009 Automated monitoring and analysis of social behavior in Drosophila Nat. Methods 6 297-303
13. Dunn T W, Mu Y, Narayan S, Randlett O, Naumann E A, Yang C T, Schier A F, Freeman J, Engert F and Ahrens M B 2016 Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion eLife 5 e12741
14. Garcia V, Nielsen F and Nock R 2010 Hierarchical Gaussian Mixture Models ICASSP 2010
15. Geurten B R, Kern R, Braun E and Egelhaaf M 2010 A syntax of hoverfly flight prototypes J. Exp. Biol. 213 2461-75
16. Gong Z et al 2004 Two interdependent TRPV channel subunits, inactive and Nanchung, mediate hearing in Drosophila J. Neurosci. 24 9059-66
17. Handl J, Knowles J and Kell D B 2005 Computational cluster validation in post-genomic data analysis Bioinformatics 21 3201-12
18. Harris D T, Kallman B R, Mullaney B C and Scott K 2015 Representations of taste modality in the Drosophila brain Neuron 86 1449-60
19. Hennig C 2010 Methods for merging Gaussian mixture components Adv. Data Anal. Class. 4 3-34
20. Hirsch J and Erlenmeyer-Kimling L 1961 Sign of taxis as a property of the genotype Science 134 835-6
21. Isakov A, Buchanan S M, Sullivan B, Ramachandran A, Chapman J K, Lu E S, Mahadevan L and de Bivort B 2016 Recovery of locomotion after injury in Drosophila depends on proprioception J. Exp. Biol. 219 1760-71
22. Jain A K, Murty M N and Flynn P J 1999 Data clustering: a review J. ACM Comput. Surv. 31 264-323
23. Kabra M, Robie A A, Rivera-Alba M, Branson S and Branson K 2013 JAABA: interactive machine learning for automatic annotation of animal behavior Nat. Methods 10 64-7
24. Kain J, Stokes C, Gaudry Q, Song X, Foley J, Wilson R and de Bivort B L 2013 Leg-tracking and automated behavioural classification in Drosophila Nat. Commun. 4 1910
25. Kain J S, Stokes C and de Bivort B L 2012 Phototactic personality in fruit flies and its suppression by serotonin and white Proc. Natl Acad. Sci. 109 19834-9
26. Kain J S, Zhang S, Akhund-Zade J, Samuel A D, Klein M and de Bivort B L 2015 Variability in thermal and phototactic preferences in Drosophila may reflect an adaptive bet-hedging strategy Evolution 69 3171-85
27. Kleinberg J 2002 An impossibility theorem for clustering Adv. Neural Inf. Process. Sys. 15 446-53
28. Kobourov S G 2012 Spring embedders and force directed graph drawing algorithms arXiv:1201.3011
29. Lemon W C, Pulver S R, Höckendorf B, McDole K, Branson K, Freeman J and Keller P J 2015 Whole-central nervous system functional imaging in larval Drosophila Nat. Commun. 6 1-16
30. Li Y and Ngom A 2013 The non-negative matrix factorization toolbox for biological data mining Source Code Biol. Med. 8:10
31. Lloyd S 1982 Least squares quantization in PCM IEEE Trans. Inf. Theory 28 129-37
32. Luo L, Gershow M, Rosenzweig M, Kang K, Fang-Yen C, Garrity P A and Samuel A D 2010 Navigational decision-making in Drosophila thermotaxis J. Neurosci. 30 4261-72
33. Macosko E Z et al 2015 Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets Cell 161 1202-14
34. Marc R E and Jones B W 2002 Molecular phenotyping of retinal ganglion cells J. Neurosci. 22 413-27
35. McLachlan G and Peel D 2000 Finite Mixture Models (Hoboken, NJ: Wiley)
36. Mendes C S, Bartos I, Akay T, Márka S and Mann R S 2013 Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster Elife 2 e00231
37. Meyer F 1994 Topographic distance and watershed lines Signal Process. 38 113-25
38. Murphy K E, Carter C M and Brown S O 2002 The exponential distribution: the good, the bad and the ugly. A practical guide to its implementation IEEE 2002 RAMS Conf.
39. Nguyen J P, Shipley F B, Linder A N, Plummer G S, Liu M, Setru S U, Shaevitz J W and Leifer A M 2016 Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans Proc. Natl Acad. Sci. 113 E1074-81
40. Pearson K 1901 On lines and planes of closest fit to systems of points in space Phil. Mag. 2 559-72
41. Quiroga R Q, Nadasdy Z and Ben-Shaul Y 2004 Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering Neural Comput. 16 1661-87
42. Saeedi A, Hoffman M, Johnson M and Adams R 2016 The segmented iHMM: a simple, efficient hierarchical infinite HMM arXiv:1602.06349v1
43. Salvador S and Chan P 2004 Determining the number of clusters/segments in hierarchical clustering/segmentation algorithms ICTAI 2004 pp 576-84
44. Schwarz G E 1978 Estimating the dimension of a model Ann. Stat. 6 461-4
45. Schwarz R F, Branicky R, Grundy L J, Schafer W R and Brown A E 2015 Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion Plos Compu. Biol. 11 e1004322
46. Seelig J D and Jayaraman V 2015 Neural dynamics for landmark orientation and angular path integration Nature 521 186-91
47. Snyman J 2005 Practical Mathematical Optimization: An Introduction to Basic Optimization Theory and Classical and New Gradient-Based Algorithms (Berlin: Springer) ISBN: 0-387-24348-8 ISBN
48. Stephens G J, Bueno de Mesquita M B, Ryu W S and Bialek W 2011 The emergence of long timescales and stereotyped behavior in C. elegans Proc. Natl Acad. Sci. 108 7286-9
49. Stephens G J, Johnson-Kerner B, Bialek W and Ryu W S 2008 Dimensionality and dynamics in the behavior of C. elegans PLoS Comput. Biol. 4 e1000028
50. Szigeti B, Deogade A and Webb B 2015 Searching for motifs in the behaviour of larval Drosophila melanogaster and Caenorhabditis elegans reveals continuity between behavioural states J. R. Soc. Interface 12 20150899
51. Takemura S Y et al 2013 A visual motion detection circuit suggested by Drosophila connectomics Nature 500 175-81
52. Tasic B et al 2016 Adult mouse cortical cell taxonomy revealed by single cell transcriptomics Nat. Neurosci. 19 335-46
53. Tenenbaum J B, de Silva V and Langford J C 2000 A global geometric framework for nonlinear dimensionality reduction Science 290 2319-23
54. Torgerson W S 1952 Multidimensional scaling: I. Theory and method Psychometrika 17 401-19
55. van der Maaten L and Hinton G 2008 Visualizing data using t-SNE J. Mach. Learn. Res. 9 2579-605
56. van der Maaten L, Postma E and van den Herik H 2009 Dimensionality reduction: a comparative review Tilburg University Technical Report TiCC-TR 2009-005
57. Venkatachalam V et al 2016 Pan-neuronal imaging in roaming Caenorhabditis elegans Proc. Natl Acad. Sci. 113 E1082-8
58. Vogelstein J T, Park Y, Ohyama T, Kerr R A, Truman J W, Priebe C E and Zlatic M 2014 Discovery of brainwide neural-behavioral maps via multiscale unsupervised structure learning Science 344 386-92
59. Waddington C, Woolf B and Perry M M 1954 Environment selection by Drosophila mutants Evolution 8 89-96
60. White J G, Southgate E, Thomson J N and Brenner S 1986 The structure of the nervous system of the nematode Caenorhabditis elegans Phil. Trans. R. Soc. B 314 1-340
61. Wiltschko A B, Johnson M J, Iurilli G, Peterson R E, Katon J M, Pashkovski S L, Abraira V E, Adams R P and Datta S 2015 Mapping sub-second structure in mouse behavior Neuron 88 1121-35
62. Yemini E, Jucikas T, Grundy L J, Brown A E and Schafer W R 2013 A database of Caenorhabditis elegans behavioral phenotypes Nat. Methods 10 877-9