Synaptic scaling balances learning in a spiking model of neocortex (Rowan & Neymotin 2013)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:147141
Learning in the brain requires complementary mechanisms: potentiation and activity-dependent homeostatic scaling. We introduce synaptic scaling to a biologically-realistic spiking model of neocortex which can learn changes in oscillatory rhythms using STDP, and show that scaling is necessary to balance both positive and negative changes in input from potentiation and atrophy. We discuss some of the issues that arise when considering synaptic scaling in such a model, and show that scaling regulates activity whilst allowing learning to remain unaltered.
Reference:
1 . Rowan MS,Neymotin SA (2013) Synaptic Scaling Balances Learning in a Spiking Model of Neocortex Adaptive and Natural Computing Algorithms, Tomassini M, Antonioni A, Daolio F, Buesser P, ed. pp.20
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron; Abstract integrate-and-fire adaptive exponential (AdEx) neuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python;
Model Concept(s): Synaptic Plasticity; Long-term Synaptic Plasticity; Learning; STDP; Homeostasis;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Rowan, Mark [m.s.rowan at cs.bham.ac.uk];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
/
stdpscalingpaper
batchscripts
mod
README
alz.hoc
autotune.hoc *
basestdp.hoc *
batch.hoc *
batch2.hoc *
batchcommon
checkirreg.hoc *
clusterrun.sh
col.dot *
col.hoc *
comppowspec.hoc *
condisconcellfig.hoc *
condisconpowfig.hoc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
e2hubsdisconpow.hoc *
e2incconpow.hoc *
filtutils.hoc *
geom.hoc *
graphplug.hoc *
grvec.hoc *
init.hoc *
labels.hoc *
load.hoc *
local.hoc *
makepopspikenq.hoc *
matfftpowplug.hoc *
matpmtmplug.hoc *
matpmtmsubpopplug.hoc *
matspecplug.hoc *
network.hoc *
nload.hoc *
nqpplug.hoc *
nqs.hoc *
nqsnet.hoc *
nrnoc.hoc *
params.hoc
plot.py
plotbatch.sh
plotbatchcluster.sh
powchgtest.hoc *
python.hoc *
pywrap.hoc *
redE2.hoc *
run.hoc
runsim.sh
setup.hoc *
shufmua.hoc *
sim.hoc
simctrl.hoc *
spkts.hoc *
stats.hoc *
stdpscaling.hoc
syncode.hoc *
vsampenplug.hoc *
writedata.hoc
xgetargs.hoc *
                            
// $Id: xgetargs.hoc,v 1.20 2008/05/11 17:19:11 billl Exp $

print "Loading xgetargs.hoc..."

xgahfl=0
{load_file("decvec.hoc")}
strdef mesg
objref xgabxl,xgabxo

//* xgetargs()
// xgetargs(panel_name,command,arg1[,arg2,...],defaults) // existing or new params -- flag 2
//   may have no named params in this case since just set with call to command
//   eg xgetargs("New","redo","do this","do that","1,2")
// xgetargs(panel_name,command,"a1,a2,..") // existing params -- flag 1
// xgetargs(panel_name,command,strlist)
// xgetargs(1,...) // dismiss after setting
// xgetargs(list,...) // list of helper functions returned by xgetclrfunc()
// eg xgetargs("Random session","newrand","# of patts","patt size  ","overlap   ","5,33,7")
// optional 1st arg flag=1 means to remove panel after command is called
// Union contains: o[0]=VBox, o[1]=argv, [o[2]=param name list] o[3]=orig update
//                 o[4]=helper functions
//                 x[0]=#args, x[1]=flag, x[2]=dismiss x[3-5] reserved for future use
//                 s=panel/button name,t=quit call,u=varlable,v=scratch
obfunc xgetargs () { local i,j,args,flag,dismiss,na localobj o,argv,vb,l,st,xo
  if (!isassigned(xgabxl)) xgabxl=new List()
  st=new String2()
  na=numarg()  
  dismiss=0 i=1 
  xgabxl.append(o=new Union())
  if (argtype(i)==0) { dismiss=$1 i+=1 }
  if (argtype(i)==1) {xo=$oi i+=1} else xo=xgetclrfunc()
  o.os(4,"funcs",xo) // list of helper functions
  o.xs(2,"dismiss",dismiss) // dismiss=1 means dismiss at end
  o.os(1,"argv",argv=new Vector(na))
  argv.resize(0)
  o.os(0,"vb",vb=new VBox())
  sprint(o.t,"xgaqt(%s)",o)
  vb.dismiss_action(o.t)
  o.s=$si i+=1 o.t=$si i+=1
  vb.intercept(1)
  xpanel(o.s)
  xvarlabel(o.u)
  sprint(o.v,"xgetexec(%s)",o)
  xbutton(o.s,o.v)
  excu("xgetbuttn",o.o[4],o)
  if (i==na) { // this should be a list of existing params
    o.xs(1,"flag",flag=1) // flag -- variables have names
    o.os(2,"plist",l=new List()) // list of param names
    if (argtype(i)==2) {
      split_interp=1
      split($si,l) // list of strings
      split($si,argv) // list of values
    } else if (argtype(i)==1) {
      for ltr(xo,$oi) {
        l.append(xo)
        argv.append(str2num(xo.s))
      }
    } else { printf("xgetargs ERRA\n") xpanel() return o=nil}
    args=argv.size
    if (args==0) { // create them
      for ltr(xo,l) {
        sprint(st.s,"%s=1",xo.s) execute(st.s)
        args=l.count argv.resize(args) argv.fill(1)
      }
    } else if (args!=l.count) {printf("xgetargs ERRB %d %d\n",args,l.count) xpanel() return o=nil}
    o.os(3,"orig",argv.c)   // save original values
    o.xs(0,"nargs",args)
    excu("xgetlabl",o.o[4],o)
    for j=0,args-1 {
      sprint(o.v,"%s.x[%d]",argv,j)
      sprint(st.s,"xgetchg(%s,%d)",o,j)
      xvalue(l.o(j).t, o.v, 1, st.s, 1)
    }
  } else {
    j=i i=na
    if (strm($si,"^[a-z]")) { // a named variable; should all be name vars
      o.xs(1,"flag",flag=3) // flag -- variables have names and routine is called with args
      split_interp=1
      split($si,argv)
      o.os(2,"plist",l=new List()) // list of param names
      split($si,l) // list of strings
    } else {
      split_interp=0
      split($si,argv)
      o.xs(1,"flag",flag=2) // flag -- variables may have no names; are just args to a function
    }
    i=j // restore i
    o.xs(0,"nargs",args=argv.size)
    if (args!=na-i) { printf("xgetargs ERRC: mismatch %d %d\n",args,na-i) xpanel() return o=nil }
    o.os(3,"orig",argv.c)   // save original values
    for j=0,args-1 {
      sprint(o.v,"%s.x[%d]",argv,j)
      sprint(st.s,"xgetchg(%s,%d)",o,j)
      xvalue($si,o.v,1,st.s,1)
      if (flag==3) l.o(j).t=$si
      i+=1
    }
  }
  o.u=o.s // start with this label
  // xbutton("Help (2 clicks)","xgah()")
  xpanel()
  vb.intercept(0)
  vb.full_request(1)
  vb.map(o.s)
  xgabxo=o // global for current xgab object
  return o
}

//* xgah() should provide help -- doesn't
proc xgah () { 
  if (xgahfl==1) {
    continue_dialog("Press help button first, then elsewhere for button-specific help")
    xgahfl=0
  } else xgahfl=1
}

//* xgetclrfunc() -- set up the callbacks as empty functions
obfunc xgetclrfunc () { local flag localobj st,xo,o
  flag=0
  if (numarg()==1) if (isobj($o1,"List")) flag=1
  if (flag) { // just clear the functions
    for ltr(xo,$o1) xo.t="" // clear
    return $o1
  } else { // create
    st=new String() o=new List()
    for scase(st,"xgetchg2","xgetexec2","xgaqt2","xgetlabl","xgetbuttn") {
      o.append(new String2(st.s)) }
    if (numarg()==1) $o1=o
    return o
  }
}

//* xgetchg() done after a value is changed
proc xgetchg () { local i localobj o
  o=$o1 i=$2
print "A",o,i,o.o[4]
  if (excu("xgetchg2",o.o[4],o,i)) return
  sprint(o.u,"Press '%s' button for effect",o.s)
}

//* xgetexec() done when the 'make changes' button is pressed
proc xgetexec () { local i,args,dismiss,flag localobj o,l,av,vb,xo
  o=$o1
  if (excu("xgetexec2",o.o[4],o)) return
  args=o.x flag=o.x[1] dismiss=o.x[2] av=o.o[1] vb=o.o
  if (flag==1 || flag==3) {
    l=o.o[2]
    if (args!=l.count || args!=av.size) {
      printf("xgetexec() ERRA %d,%d,%d\n",args,l.count,av.size) return
    }
    for ltr(xo,l,&i) {
      sprint(o.v,"%s=%g",xo.s,av.x[i])
      execute(o.v)
    }
    if (flag==1) { // call the routine -- else will call below
      if (strm(o.t,"[(]")) o.v=o.t else sprint(o.v,"%s(%s)",o.t,o) // no args passed to function
    }
  }
  if (flag==2 || flag==3) {
    sprint(o.v,"%s(",o.t)
    for i=0,args-2 sprint(o.v,"%s%g,",o.v,av.x[i])
    sprint(o.v,"%s%g)",o.v,av.x[i]) 
  }
  execute(o.v)
  o.u="Changes submitted"
  if (dismiss) { xgaqt(o) // get rid of the box
  } else { o.o[3].copy(o.o[1]) } // new set of origs
}
  
//* xgaqt() called when the panel is dismissed
proc xgaqt () { local x localobj av,vb,o
  o=$o1 
  if (excu("xgaqt2",o.o[4],o)) return
  av=o.o[1] vb=o.o
  vb.unmap()
  if ((x=xgabxl.index(o))!=-1) xgabxl.remove(x)
  if (xgabxo==o) xgabxo=nil
}

Rowan MS,Neymotin SA (2013) Synaptic Scaling Balances Learning in a Spiking Model of Neocortex Adaptive and Natural Computing Algorithms, Tomassini M, Antonioni A, Daolio F, Buesser P, ed. pp.20

References and models cited by this paper

References and models that cite this paper

Binzegger T, Douglas RJ, Martin KA (2004) A quantitative map of the circuit of cat primary visual cortex. J Neurosci 24:8441-53 [PubMed]

Busche MA, Eichhoff G, Adelsberger H, Abramowski D, Wiederhold KH, Haass C, Staufenbiel M, Ko (2008) Clusters of hyperactive neurons near amyloid plaques in a mouse model of Alzheimer's disease. Science 321:1686-9

Carnevale NT, Hines ML (2006) The NEURON Book

Chandler B, Grossberg S (2012) Joining distributed pattern processing and homeostatic plasticity in recurrent on-center off-surround shunting networks: noise, saturation, short-term memory, synaptic scaling, and BDNF. Neural Netw 25:21-9

Dan Y, Poo MM (2004) Spike timing-dependent plasticity of neural circuits. Neuron 44:23-30 [PubMed]

Frohlich F, Bazhenov M, Sejnowski TJ (2008) Pathological effect of homeostatic synaptic scaling on network dynamics in diseases of the cortex. J Neurosci 28:1709-20 [PubMed]

Lamsa KP, Kullmann DM, Woodin MA (2010) Spike-timing dependent plasticity in inhibitory circuits. Front Synaptic Neurosci 2:8

Lefort S, Tomm C, Floyd Sarria JC, Petersen CC (2009) The excitatory neuronal network of the C2 barrel column in mouse primary somatosensory cortex. Neuron 61:301-16 [PubMed]

Lytton WW, Omurtag A, Neymotin SA, Hines ML (2008) Just in time connectivity for large spiking networks Neural Comput 20(11):2745-56 [Journal] [PubMed]

   JitCon: Just in time connectivity for large spiking networks (Lytton et al. 2008) [Model]

Lytton WW, Stewart M (2006) Rule-based firing for network simulations. Neurocomputing 69:1160-1164

McClelland JL, McNaughton BL, O'Reilly RC (1995) Why there are complementary learning systems in the hippocampus and neocortex: insights from the successes and failures of connectionist models of learning and memory. Psychol Rev 102:419-57 [PubMed]

Neymotin S, Kerr C, Francis J, Lytton W (2011) Training oscillatory dynamics with spike-timing-dependent plasticity in a computer model of neocortex Signal Processing in Medicine and Biology Symposium (SPMB), IEEE :1-6

Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75 [Journal] [PubMed]

   Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) [Model]

Prieto G, Parker R, Vernon_iii F (2009) A Fortran 90 library for multitaper spectrum analysis Computers Geosciences 35:1701-1710

Rowan M (2011) Effects of Compensation, Connectivity and Tau in a Computational Model of Alzheimer's Disease Proc. IJCNN, IEEE :543-550

Rowan M (2012) Information-selectivity of Beta-amyloid pathology in an associative memory model. Front Comput Neurosci 6:2-23 [PubMed]

Rutherford LC, Nelson SB, Turrigiano GG (1998) BDNF has opposite effects on the quantal amplitude of pyramidal neuron and interneuron excitatory synapses. Neuron 21:521-30 [PubMed]

Small DH (2008) Network dysfunction in Alzheimer's disease: does synaptic scaling drive disease progression? Trends Mol Med 14:103-8 [PubMed]

Trasande CA, Ramirez JM (2007) Activity deprivation leads to seizures in hippocampal slice cultures: is epilepsy the consequence of homeostatic plasticity? J Clin Neurophysiol 24:154-64 [PubMed]

Turrigiano G (2011) Too many cooks? Intrinsic and synaptic homeostatic mechanisms in cortical circuit refinement. Annu Rev Neurosci 34:89-103 [PubMed]

Turrigiano GG (2008) The self-tuning neuron: synaptic scaling of excitatory synapses. Cell 135:422-35 [PubMed]

van Rossum MC, Bi GQ, Turrigiano GG (2000) Stable Hebbian learning from spike timing-dependent plasticity. J Neurosci 20:8812-21 [PubMed]

Zhang LI, Tao HW, Holt CE, Harris WA, Poo M (1998) A critical window for cooperation and competition among developing retinotectal synapses. Nature 395:37-44 [PubMed]

Eguchi A, Neymotin SA and Stringer SM (2014) Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity 8:16. doi: Front. Neural Circuits 8:16 [Journal]

   Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014) [Model]

Neymotin SA, Chadderdon GL, Kerr CC, Francis JT, Lytton WW (2013) Reinforcement learning of 2-joint virtual arm reaching in a computer model of sensorimotor cortex Neural Computation 25(12):3263-93 [Journal] [PubMed]

   Sensorimotor cortex reinforcement learning of 2-joint virtual arm reaching (Neymotin et al. 2013) [Model]

Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW (2015) Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model Neural Computation 27(4):898-924 [Journal] [PubMed]

   Neuronal dendrite calcium wave model (Neymotin et al, 2015) [Model]

Rowan MS, Neymotin SA, Lytton WW (2014) Electrostimulation to reduce synaptic scaling driven progression of Alzheimer's disease. Front Comput Neurosci 8:39 [Journal] [PubMed]

   Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014) [Model]

(27 refs)