Cortical model with reinforcement learning drives realistic virtual arm (Dura-Bernal et al 2015)

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Accession:183014
We developed a 3-layer sensorimotor cortical network of consisting of 704 spiking model-neurons, including excitatory, fast-spiking and low-threshold spiking interneurons. Neurons were interconnected with AMPA/NMDA, and GABAA synapses. We trained our model using spike-timing-dependent reinforcement learning to control a virtual musculoskeletal human arm, with realistic anatomical and biomechanical properties, to reach a target. Virtual arm position was used to simultaneously control a robot arm via a network interface.
References:
1 . Dura-Bernal S, Zhou X, Neymotin SA, Przekwas A, Francis JT, Lytton WW (2015) Cortical Spiking Network Interfaced with Virtual Musculoskeletal Arm and Robotic Arm. Front Neurorobot 9:13 [PubMed]
2 . Dura-Bernal S, Li K, Neymotin SA, Francis JT, Principe JC, Lytton WW (2016) Restoring behavior via inverse neurocontroller in a lesioned cortical spiking model driving a virtual arm. Front. Neurosci. Neuroprosthetics 10:28
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Neocortex M1 pyramidal pyramidal tract L5B cell; Neocortex M1 pyramidal intratelencephalic L2-5 cell; Neocortex M1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neostriatum fast spiking interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python (web link to model);
Model Concept(s): Synaptic Plasticity; Learning; Reinforcement Learning; STDP; Reward-modulated STDP; Sensory processing; Motor control;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu]; Dura, Salvador [ salvadordura at gmail.com];
Search NeuronDB for information about:  Neocortex M1 pyramidal intratelencephalic L2-5 cell; Neocortex M1 pyramidal pyramidal tract L5B cell; Neocortex M1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
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arm2dms_modeldb
mod
msarm
stimdata
README.html
analyse_funcs.py
analysis.py
armGraphs.py
arminterface_pipe.py
basestdp.hoc
bicolormap.py
boxes.hoc *
bpf.h *
col.hoc
colors.hoc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc *
grvec.hoc
hinton.hoc *
hocinterface.py
infot.hoc *
init.hoc
intfsw.hoc *
labels.hoc
load.hoc
load.py
local.hoc *
main.hoc
main_demo.hoc
main_neurostim.hoc
misc.h *
misc.py *
msarm.hoc
network.hoc
neuroplot.py *
neurostim.hoc
nload.hoc
nqs.hoc *
nqsnet.hoc *
nrnoc.hoc
params.hoc
perturb.hoc
python.hoc
pywrap.hoc *
run.hoc
runbatch_neurostim.py
runsim_neurostim
samutils.hoc *
saveoutput.hoc
saveoutput2.hoc
setup.hoc *
sim.hoc
sim.py
sim_demo.py
simctrl.hoc *
stats.hoc *
stim.hoc
syncode.hoc *
units.hoc *
vector.py
xgetargs.hoc *
                            
// $Id: xgetargs.hoc,v 1.20 2008/05/11 17:19:11 billl Exp $

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
  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
}

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