HVCModelCode

Code for model in Okubo et al.

Emily Mackevicius 7/18/2015, based on Hannah Payne's code which builds off Ila Fiete's model, with help from Michale Fee and Tatsuo Okubo.

To run 1 iteration of the model:

###HVCIter See this file for step-by-step model dynamics and learning.

To get paper figures:

###AlternatingDifferentiation Code to generate Figure 5 a-f, which shows alternating seed neuron differentiation, from subsong through protosyllable stage through splitting.

Relies on:

HVCIter Runs 1 iteration of the model. See this file for step-by-step model dynamics and learning.

plotSubsong Plotting function for subsong network diagram and raster.

plotHVCnet Plots network diagram.

plotAlternating Plots network activity

findLatency Called by plotting functions, tests what neurons participate in each syllable, and at what latencies.

###BoutOnsetDifferentiation Code to generate Extended Data Figure 10 a-d, which shows bout onset differentiation.

Relies on:

HVCIter Runs 1 iteration of the model. See this file for step-by-step model dynamics and learning.

plotHVCnet_boutOnset Plotting function for bout onset network diagram and raster.

findLatency Called by plotting functions, tests what neurons participate in each syllable, and at what latencies.

###HVCModelCode Generates Figure 5 a-d and Extended Data Figure 10 a-d. All in one .m file, including functions it depends on, for posting with the paper.

###sigLatDistOverDev.m Latency distribution over development (Fig 5 e).

###RunHVC_boutOnsetElement.m Bout onset element differentiation (EDF 10 e-h)

###RunHVC_split_intoThree.m Motif learning, (EDF 10 i-k)

##To get movies: ###runHVC_split_movie.m Alternating differentiation movie for supp

###BoutOnsetDifferentiation_movie.m Bout onset movie for supp

###RunHVC_boutOnset_Movies Bout onset movie to visualize (sorted) weight matrix and activity over development, and multi-dimensional scaling of weight matrix