Cost-Based Metrics

Cost-Based Metrics for Spike Trains

introduction
cost-based metrics
Dcount, Dspike[q], Dinterval[q]
generalizations and related
dynamic programming algorithm and links to code
applications and references
unsolved problems
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Introduction

Spike trains are considered to be points in an abstract topological space. A spike train metric is a rule which assigns a non-negative number D(Sa,Sb) to pairs of spike trains Sa and Sb which expresses how dissimilar they are.

A metric D is essentially an abstract distance. By definition, metrics have the following properties:

The metrics may be used in a variety of ways -- for example, one can construct a
neural response space via multidimensional scaling of the pairwise distances, and one can assess coding characteristics via comparison of stimulus-dependent clustering across a range of metrics.
top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code applications and references

Cost-based metrics

Cost-based metrics fulfill the above general definition of a metric, and are constructed with the following ingredients:

For any such set of choices, one can define a metric D(Sa,Sb) as the least total cost of any allowed transformation from to Sb via any sequence of spike trains Sa, S1, S2,..., Sn, Sb.
top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code applications and references

Trivial example: the spike count distance Dcount

This is a cost-based metric in which the elementary steps and associated costs are:

The distance between two spike trains is the difference in the number of spikes, independent of when they occur. That is, this metric formalizes the notion that the only significant aspect of a spike train is the number of spikes it contains.
top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code applications and references

The spike time distance Dspike[q]

This is a family of cost-based metrics, parametrized by a "cost per unit time" q (units of 1/sec). The elementary steps and associated costs are:

See diagram.

If q is very small, this becomes the spike count distance. If q is very large, all spike trains are far apart from each other, unless they are nearly identical. For intermediate values of q, the distance between two spike trains is small if they have a similar number of spikes, occurring at similar times.

The motivation for this construction is that neurons which act like coincidence detectors should care about this metric. The value of q corresponds to the temporal precision 1/q of the coincidence detector.

This distance can be calculated efficiently by a dynamic programming algorithm.


An example of a sequence of elementary steps for Dspike which transforms the spike train Sa into Sb.

top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code applications and references

The spike interval distance Dinterval[q]

This is a family of cost-based metrics, parametrized by a "cost per unit time" q (units of 1/sec). The elementary steps and associated costs are:

If q is very small, this becomes the spike count distance. If q is very large, all spike trains are far apart from each other, unless they are nearly identical. For intermediate values of q, the distance between two spike trains is small if they have a similar number of spikes, occurring with similar intervals.

Neurons which show post-tetanic potentiation and similar mechanisms might care about this distance. The optimal value of q corresponds to the temporal precision 1/q of the discrimination between bursts of different carrier frequencies (or interspike intervals).
top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code applications and references


Some generalizations, extensions, and related metrics

Our algorithm can be applied to these generalizations and extensions of the metrics:


Our dynamic programming algorithm cannot readily be applied to the following extensions, but they are nevertheless interesting. See unsolved problems page:

Spike time metrics (one kind of cost-based metrics) are a continuous version of edit-length distances, also known as Levenshtein distances. Spike time metrics reduce to the "earth mover distance" (used in image processing and classification) when the number of spikes is identical, and the cost to move a spike is small.

Euclidean distances that are closely related to the spike time metric but are much easier to compute have been introduced by van Rossum (2001). Houghton and Sen (2007) have generalized the von Rossum distance to the multineuronal context. See van Rossum, M.C.W. (2001) A novel spike distance. Neural Computation 13, 751-763 (download) and Houghton, C., and Sen, K. (2007) A new multi-neuron spike-train metric. Neural Computation, in press. (download).

top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code applications and references


Dynamic programming algorithm for Dspike and Dinterval

This is an adaptation of Sellers' highly efficient dynamic programming algorithm [Sellers, P. H. (1974) On the theory and computation of evolutionary distances. SIAM J. Appl. Math. 26, 787-793] for comparing genetic sequences, which is identical to the Needleman-Wunsch algorithm [Needleman, S., and Wunsch, C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453].

Hint: it is doubly recursive, and reduces the calculation of the distance between spike trains of length Na and Nb to consideration of spike trains of lengths Na-1 and Nb-1. Think about the constraints on the "world lines" of each spike in the above diagram for Dspike.

Spike Train Analysis Toolkit, a user-friendly implementation from the Laboratory of Neuroinformatics that includes algorithms for information estimation via the direct method, the binless method, and the metric space method.

Fortran, matlab, and c code for the metrics

L. Allison's code for edit-length distances

top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related applications and references


Selected Applications and References

Reviews

Victor, J.D. (2015) Spike train distance. In: Encyclopedia of Computational Neuroscience. Ed: D. Jaeger & R. Jung, pp 2808-2814. Springer New York, Heidelberg ,Dordrecht, London, online.
Summary and download

Houghton, C., and Victor, J.D. (2011) Measuring representational distances – the spike metric approach. In Understanding Visual Population Codes – Towards a Common Multivariate Framework for Cell Recording and Functional Imaging. Eds: Nikolaus Kriegeskorte and Gabriel Kreiman. MIT Press, in press.
Abstract and download

Victor, J.D., and Purpura, K.P. (2010) Spike Metrics. In: Analysis of Parallel Spike Trains. Ed. Stefan Rotter and Sonja Gruen. Springer, pp. 129-156.
Abstract and download

Goldberg, D.H., Victor, J.D., Gardner, E.P., and Gardner, D., (2009) Spike Train Analysis Toolkit: Enabling wider application of information-theoretic techniques to neurophysiology. Neuroinformatics 7, 165-178.
Abstract, download, and links to code

Victor, J.D. (2005) Spike train metrics. Current Opinion in Neurobiology 15, 585–592.
Abstract and download

Theory and algorithms

Diez, D.M., Schoenberg, F.P., and Woody, C.D. (2012) Algorithms for computing spike time distance and point process prototypes with application to feline neuronal responses to acoustic stimuli. J. Neurosci. Meth. 203, 186-192 Download
This describes an alternative algorithm for the multineuronal metric, more efficient than the Aronov (2009) algorithm when there are 5 or more neurons

Dubbs, A.J., Seiler, B.A., and Magnasco, M.O. (2009) A fast Lp spike alignment metric. arXiv:0907.3137v2.
Dubbs, A.J., Seiler, B.A., and Magnasco, M.O. (2010) A fast Lp spike alignment metric. Neural Computation 11, 2785-2808.
Download
These describe an alternative algorithm based on bipartitre graphs for calculating Dspike and related metrics, and also discuss some theoretical advantages for the use of an L2 metric, rather than the L1 metric described here.

Kreuz, T., Haas, J.S., Morelli, A., Abarbanel, H.D.I., and Politi, A. (2007) Measuring spike train synchrony. J Neurosci Methods 165, 151.
Download and code
This describes another interval-based metric for comparing spike trains, and compares six different metrics, including Dspike

Victor, J.D., Goldberg, D., and Gardner, D. (2007) Dynamic programming algorithms for comparing multineuronal spike trains via cost-based metrics and alignments. J. Neurosci. Meth. 161, 351-360.
Abstract and download
This describes dynamic programming algorithms for computing generalizations of Dspike, parallel in one or more cost parameters. The algorithm also extends to Lp-metrics

Aronov, D. (2005) A metric-space approach to the study of information coding by neuronal populations. Senior Thesis, Columbia University.
Download

Aronov, D., and Victor, J. (2004) Non-Euclidean properties of spike train metric spaces. Phys. Rev. E69, 61905.
Abstract, download, and related notes

Aronov, D. (2003) Fast algorithm for the metric-space analysis of simultaneous responses of multiple single neurons. J. Neuroscience Methods 124, 175-179.
Abstract, download, and code

Visual neurophysiology

Victor, J.D., and Purpura, K. (1997) Metric-space analysis of spike trains: theory, algorithms, and application. Network 8, 127-164. Abstract and code

More references from our lab

Keat, Reinagel, Reid, and Meister (2001) Predicting every spike: a model for the responses of visual neurons. Neuron 30, 803-817. pdf from Neuron
This describes a generalization to sequences of burst events. The authors also describe a novel approach to pruning the dynamic programming algorithm.

Hitt, Dodge, and Barlow (2003) Information content in responses of Limulus optic nerve fibers. Arvo Abstract 3253. Link to ARVO abstracts

Auditory neurophysiology

Machens, C.K., Prinz, P., Stemmler, M.B., Ronacher, B., and Herz, A.V.M. (2001) Discrimination of behaviorally relevant signals by auditory receptor neurons. Neurocomputing 38, 263-268. pdf from Machens' site pdf from Herz's site

Machens, C.K., Schutze, H., Franz, A., Kolesnikova, O., Stemmler, M.B., Ronacher, B., and Herz, A.V.M. (2001) Single auditory neurons rapidly discriminate conspecific communication signals. Nature Neurosci. 6, 341-342. pdf from Nature Neuroscience pdf from Ronacher's site

Wohlgemuth, S., and Ronacher, B. (2007) Auditory discrimination of amplitude modulations based on metric distances of spike trains. J. Neurophysiol. 97, 3082-3092. pdf from J. Neurophysiol.

Olfactory neurophysiology

Bäcker, A., MacLeod, K., Wehr, M., and Laurent, G. (1998) Disruption of neuronal synchronization impairs reliable reconstruction of odors by beta lobe cells but not by projection neurons of the antennal lobe of the locust. Soc. Neurosci. Abstr. 24, 911.

MacLeod, K., Bäcker A., & Laurent, G. (1998) Who reads temporal information contained across synchronized and oscillatory spike trains? Nature 395, 693-698.

Somatosensosry neurophysiology

Saal, H.P., Vijayakumar, S., and Johansson, R.S. (2009) Information about complex fingertip parameters in individual human tactile afferent neurons. The Journal of Neuroscience 29, 8022– 8031.
Download

Brasselet, R., Johansson, R.S., and Arleo, A. (2011) Quantifying neurotransmission reliability through metrics-based information analysis. Neural Computation 23, 852-81·
Download

Weber, A.I., Saal, H.P., Lieber, J.D., Cheng, J.-W., Manfredi, L.R., Dammann, J.F. III, and Bensmaia, S.J. (2013) Spatial and temporal codes mediate the tactile perception of natural textures. Proc. Natl. Acad. Sci. USA 110, 17107-17112.
Download

Gustatory neurophysiology

Di Lorenzo, P., Chen, J.-Y., and Victor, J.D. (2009) Quality time: Representation of a multidimensional sensory domain through temporal coding. J. Neurosci. 29, 9227-9238.
Abstract and download

Di Lorenzo, P.M, and Victor, J.D. (2003) Taste response variability and temporal coding in the nucleus of the solitary tract of the rat. J. Neurophysiol. 90, 1418-1431.
Abstract and download

Electric sense

Kreiman, G., Gabbiani, F., Metzner, W., & Koch, C. (1998) Robustness of amplitude modulation encoding by P-receptor afferent spike trains of weakly electric fish. Soc. Neurosci. Abstr. 196, 911.

Kreiman, G., Krahe, R., Metzner, W., Koch, C., & Gabbiani, F. (2000) Robustness and variability of neuronal coding by amplitude-sensitive afferents in the weakly electric fish Eigenmannia. J. Neurophysiol. 84, 189-204. Abstract

Birdsong

Huetz, C., Lebas, N., Del Negro, C., Lehongre, K., Tarroux, P, and Edeline, J.M. (2004) Do HVc neurons use a temporal code to represent the bird own song (BOS)? Soc. Neurosci. Abstr. 333.2 101.

Huetz, C., Del Negro, C., Lebas, N., Tarroux, P. & Edeline, J.M. (2006) Contribution of spike timing to the information transmitted by HVC neurons. Eur J Neurosci 24, 1091-108. PubMed entry

Le Wang, Narayan, Grana, Shamir, and Sen (2007) Cortical discrimination of complex natural stimuli: Can single neurons match behavior? J. Neurosci. 27,582-589 J. Neurosci. online
The authors use Dspike, Dinterval, and the van Rossum metric.

Neural development

Ciarleglio, C.M., Khakhalin, A.S., Wang, A.F., Constantino, A.C., Yip, S.P., and Aizenman, C.D. (2015) Multivariate analysis of electrophysiological diversity of Xenopus visual neurons during development and plasticity eLife 2015;4:e11351. Download from eLife

Computational studies

Tiesinga, P.H.E. (2004) Chaos-induced modulation of reliability boosts output firing rate in downstream cortical areas. Phys. Rev. E69, 031912. Download from Paul Tiesinga's website

Cost-based metrics ("edit length metrics") in EEG classfication

Wu, L., and Gotman, J. (1998) Segmentation and classification of EEG during epileptic seizures. Electroenceph. Clin. Neurophysiol. 106, 344-356.

Geophysics: earthquake patterns

Schoenberg, F.P., and Tranbarger, K.E. (2004) Description of earthquake aftershock sequences using prototype point patterns. Download from Katherine Tranbarger's website
Comments and questions
top introduction cost-based metrics Dcount Dspike[q] Dinterval[q] generalizations and related dynamic programming algorithm and links to code