def go(t=10, m=Uniform(30, 30), i=Uniform(0, 0), seed=0, dt=0.001, f=DoubleExp(1e-3, 1e-1), fS=DoubleExp(1e-3, 1e-1), d1=None, f1=None, e1=None, l1=False, stim=lambda t: np.sin(t)):
if not f1: f1=f
with nengo.Network(seed=seed) as model:
# Stimulus and Nodes
inpt = nengo.Node(stim)
tar = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
pre = nengo.Ensemble(100, 1, max_rates=m, seed=seed, neuron_type=LIF())
lif = nengo.Ensemble(1, 1, max_rates=m, intercepts=i, encoders=Choice([[1]]), neuron_type=LIF(), seed=seed)
wilson = nengo.Ensemble(1, 1, max_rates=m, intercepts=i, encoders=Choice([[1]]), neuron_type=Wilson(), seed=seed)
bio = nengo.Ensemble(1, 1, max_rates=m, intercepts=i, encoders=Choice([[1]]), neuron_type=Bio("Pyramidal"), seed=seed)
nengo.Connection(inpt, pre, synapse=None, seed=seed)
cLif = nengo.Connection(pre, lif, synapse=f1, seed=seed, solver=NoSolver(d1))
cWilson = nengo.Connection(pre, wilson, synapse=f1, seed=seed, solver=NoSolver(d1))
cBio = nengo.Connection(pre, bio, synapse=f1, seed=seed, solver=NoSolver(d1))
pInpt = nengo.Probe(inpt, synapse=None)
pPre = nengo.Probe(pre.neurons, synapse=None)
pLif = nengo.Probe(lif.neurons, synapse=None)
pWilson = nengo.Probe(wilson.neurons, synapse=None)
pBio = nengo.Probe(bio.neurons, synapse=None)
if l1: learnEncoders(cBio, lif, fS, alpha=3e-7) # Encoder Learning (Bio)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
setWeights(cBio, d1, e1)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
e1 = cBio.e if l1 else e1
return dict(
times=sim.trange(),
inpt=sim.data[pInpt],
pre=sim.data[pPre],
lif=sim.data[pLif],
wilson=sim.data[pWilson],
bio=sim.data[pBio],
e1=e1,
)
def go(NPre=100,
N=100,
N2=30,
t=10,
m=Uniform(30, 30),
i=Uniform(-0.8, 0.8),
seed=0,
dt=0.001,
f=DoubleExp(1e-3, 1e-1),
fS=DoubleExp(1e-3, 1e-1),
neuron_type=LIF(),
d1=None,
d2=None,
f1=None,
f2=None,
e1=None,
e2=None,
l1=False,
l2=False,
stim=lambda t: [0, 0]):
if not f1: f1 = f
if not f2: f2 = f
if not np.any(d2): d2 = np.zeros((N, 1))
with nengo.Network(seed=seed) as model:
# Stimulus and Nodes
inpt = nengo.Node(stim)
tar = nengo.Ensemble(1, 2, neuron_type=nengo.Direct())
tar2 = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
pre = nengo.Ensemble(NPre,
2,
radius=2,
max_rates=m,
seed=seed,
neuron_type=LIF())
ens = nengo.Ensemble(N,
2,
radius=2,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed)
ens2 = nengo.Ensemble(N2,
1,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed + 1)
nengo.Connection(inpt, pre, synapse=None, seed=seed)
nengo.Connection(inpt, tar, synapse=f, seed=seed)
nengo.Connection(tar,
tar2,
synapse=f,
function=multiply,
seed=seed + 1)
c1 = nengo.Connection(pre,
ens,
synapse=f1,
seed=seed,
solver=NoSolver(d1))
if isinstance(neuron_type, Bio):
c2 = nengo.Connection(ens,
ens2,
synapse=f2,
seed=seed + 1,
function=multiply)
else:
c2 = nengo.Connection(ens.neurons,
ens2,
synapse=f2,
seed=seed + 1,
transform=d2.T)
pInpt = nengo.Probe(inpt, synapse=None)
pPre = nengo.Probe(pre.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
pEns2 = nengo.Probe(ens2.neurons, synapse=None)
pTar = nengo.Probe(tar, synapse=None)
pTar2 = nengo.Probe(tar2, synapse=None)
# Encoder Learning (Bio)
if l1:
tarEns = nengo.Ensemble(N,
2,
radius=2,
max_rates=m,
intercepts=i,
neuron_type=nengo.LIF(),
seed=seed)
nengo.Connection(tar, tarEns, synapse=None, seed=seed)
learnEncoders(c1, tarEns, fS, alpha=3e-8)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
if l2:
tarEns2 = nengo.Ensemble(N2,
1,
max_rates=m,
intercepts=i,
neuron_type=nengo.LIF(),
seed=seed + 1)
nengo.Connection(tar2, tarEns2, synapse=None)
# nengo.Connection(ens.neurons, tarEns2, synapse=f2, transform=d2.T, seed=seed+1)
learnEncoders(c2, tarEns2, fS, alpha=1e-7)
pTarEns2 = nengo.Probe(tarEns2.neurons, synapse=None)
pTarState = nengo.Probe(tarEns2, synapse=f)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if isinstance(neuron_type, Bio):
setWeights(c1, d1, e1)
setWeights(c2, d2, e2)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
else:
sim.run(t, progress_bar=True)
e1 = c1.e if l1 else e1
e2 = c2.e if l2 else e2
return dict(
times=sim.trange(),
inpt=sim.data[pInpt],
pre=sim.data[pPre],
ens=sim.data[pEns],
ens2=sim.data[pEns2],
tar=sim.data[pTar],
tar2=sim.data[pTar2],
tarEns=sim.data[pTarEns] if l1 else None,
tarEns2=sim.data[pTarEns2] if l2 else None,
tarState=sim.data[pTarState] if l2 else None,
e1=e1,
e2=e2,
)
def go(NPre=100, N=30, t=10, m=Uniform(30, 30), i=Uniform(-0.8, 0.8), seed=0, dt=0.001, f=DoubleExp(1e-3, 1e-1), fS=DoubleExp(1e-3, 1e-1), neuron_type=LIF(), d1=None, d2=None, f1=None, f2=None, e1=None, e2=None, l1=False, l2=False, test=False, freq=1, phase=0, tDrive=0.2):
A = [[1, 1e-1*2*np.pi*freq], [-1e-1*2*np.pi*freq, 1]] # tau*A + I
if isinstance(neuron_type, Bio) and not f1: f1=DoubleExp(1e-3, 1e-1)
if isinstance(neuron_type, Bio) and not f2: f2=DoubleExp(1e-3, 1e-1)
stim = lambda t: [np.sin(2*np.pi*freq*t+phase), np.cos(2*np.pi*freq*t+phase)]
with nengo.Network(seed=seed) as model:
inpt = nengo.Node(stim)
tar = nengo.Ensemble(1, 2, neuron_type=nengo.Direct())
pre = nengo.Ensemble(NPre, 2, max_rates=m, neuron_type=nengo.SpikingRectifiedLinear(), radius=2, seed=seed)
ens = nengo.Ensemble(N, 2, max_rates=m, intercepts=i, neuron_type=neuron_type, radius=2, seed=seed)
nengo.Connection(inpt, tar, synapse=None, transform=A, seed=seed)
nengo.Connection(inpt, pre, synapse=None, seed=seed)
c1 = nengo.Connection(pre, ens, synapse=f1, seed=seed, solver=NoSolver(d1))
pInpt = nengo.Probe(inpt, synapse=None)
pTar = nengo.Probe(tar, synapse=None)
pPre = nengo.Probe(pre.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
# Encoder Learning (Bio)
if l1:
tarEns = nengo.Ensemble(N, 2, max_rates=m, intercepts=i, neuron_type=nengo.LIF(), seed=seed)
nengo.Connection(inpt, tarEns, synapse=None, seed=seed)
learnEncoders(c1, tarEns, fS)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
if l2:
pre2 = nengo.Ensemble(NPre, 2, max_rates=m, neuron_type=nengo.LIF(), seed=seed, radius=2)
tarEns2 = nengo.Ensemble(N, 2, max_rates=m, intercepts=i, neuron_type=nengo.LIF(), seed=seed)
ens2 = nengo.Ensemble(N, 2, max_rates=m, intercepts=i, neuron_type=neuron_type, seed=seed, radius=2)
# ens3 = nengo.Ensemble(N, 2, max_rates=m, intercepts=i, neuron_type=neuron_type, seed=seed, radius=2)
# nengo.Connection(tar, pre2, synapse=f)
# c3 = nengo.Connection(ens, ens2, synapse=f2, seed=seed)
# c4 = nengo.Connection(pre2, ens3, synapse=f1, seed=seed)
# learnEncoders(c3, ens3, fS)
# pTarEns2 = nengo.Probe(ens3.neurons, synapse=None)
# pEns2 = nengo.Probe(ens2.neurons, synapse=None)
nengo.Connection(inpt, pre2, synapse=f)
nengo.Connection(pre2, tarEns2, synapse=f, seed=seed)
c3 = nengo.Connection(ens, ens2, synapse=f2, seed=seed)
learnEncoders(c3, tarEns2, fS, alpha=3e-7)
pTarEns2 = nengo.Probe(tarEns2.neurons, synapse=None)
pEns2 = nengo.Probe(ens2.neurons, synapse=None)
if test:
c2 = nengo.Connection(ens, ens, synapse=f2, seed=seed, solver=NoSolver(d2))
off = nengo.Node(lambda t: 1 if t>tDrive else 0)
nengo.Connection(off, pre.neurons, synapse=None, transform=-1e4*np.ones((NPre, 1)))
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if isinstance(neuron_type, Bio):
setWeights(c1, d1, e1)
if l2: setWeights(c3, d2, e2)
# if l2: setWeights(c4, d1, e1)
if test: setWeights(c2, d2, e2)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
else:
sim.run(t, progress_bar=True)
e1 = c1.e if l1 else e1
e2 = c3.e if l2 else e2
return dict(
times=sim.trange(),
inpt=sim.data[pInpt],
tar=sim.data[pTar],
pre=sim.data[pPre],
ens=sim.data[pEns],
tarEns=sim.data[pTarEns] if l1 else None,
tarEns2=sim.data[pTarEns2] if l2 else None,
ens2=sim.data[pEns2] if l2 else None,
e1=e1,
e2=e2,
)
def go(NPre=100,
N=100,
t=10,
m=Uniform(30, 30),
i=Uniform(-0.8, 0.8),
neuron_type=LIF(),
seed=0,
dt=0.001,
fPre=None,
fEns=None,
fS=DoubleExp(2e-2, 2e-1),
dPreA=None,
dPreB=None,
dEns=None,
ePreA=None,
ePreB=None,
eBio=None,
stage=None,
alpha=1e-6,
eMax=1e0,
stimA=lambda t: np.sin(t),
stimB=lambda t: 0):
with nengo.Network(seed=seed) as model:
inptA = nengo.Node(stimA)
inptB = nengo.Node(stimB)
preInptA = nengo.Ensemble(NPre, 1, radius=3, max_rates=m, seed=seed)
preInptB = nengo.Ensemble(NPre, 1, max_rates=m, seed=seed)
ens = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed)
tarEns = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=nengo.LIF(),
seed=seed)
cpa = nengo.Connection(inptA, preInptA, synapse=None, seed=seed)
cpb = nengo.Connection(inptB, preInptB, synapse=None, seed=seed)
pInptA = nengo.Probe(inptA, synapse=None)
pInptB = nengo.Probe(inptB, synapse=None)
pPreInptA = nengo.Probe(preInptA.neurons, synapse=None)
pPreInptB = nengo.Probe(preInptB.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
if stage == 1:
c0b = nengo.Connection(preInptB,
tarEns,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed + 1)
c1b = nengo.Connection(preInptB,
ens,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed + 1)
learnEncoders(c1b, tarEns, fS, alpha=alpha, eMax=eMax)
if stage == 2:
c0a = nengo.Connection(preInptA,
tarEns,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c0b = nengo.Connection(preInptB,
tarEns,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed + 1)
c1a = nengo.Connection(preInptA,
ens,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c1b = nengo.Connection(preInptB,
ens,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed + 1)
learnEncoders(c1a, tarEns, fS, alpha=alpha, eMax=eMax)
if stage == 3:
c1a = nengo.Connection(preInptA,
ens,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c1b = nengo.Connection(preInptB,
ens,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed + 1)
if stage == 4:
preInptC = nengo.Ensemble(NPre, 1, max_rates=m, seed=seed)
ens2 = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed)
ens3 = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed)
nengo.Connection(inptB, preInptC, synapse=fEns, seed=seed)
c1a = nengo.Connection(preInptA,
ens,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2b = nengo.Connection(preInptB,
ens2,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed + 1)
c3 = nengo.Connection(ens2,
ens,
synapse=fEns,
solver=NoSolver(dEns),
seed=seed)
c4a = nengo.Connection(preInptA,
ens3,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c4b = nengo.Connection(preInptC,
ens3,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed)
learnEncoders(c3, ens3, fS, alpha=alpha / 10, eMax=eMax)
pTarEns = nengo.Probe(ens3.neurons, synapse=None)
if stage == 5:
c1a = nengo.Connection(preInptA,
ens,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c5 = nengo.Connection(ens,
ens,
synapse=fEns,
solver=NoSolver(dEns),
seed=seed)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if isinstance(neuron_type, Bio):
if stage == 1:
setWeights(c1b, dPreB, ePreB)
if stage == 2:
setWeights(c1a, dPreA, ePreA)
setWeights(c1b, dPreB, ePreB)
if stage == 3:
setWeights(c1a, dPreA, ePreA)
setWeights(c1b, dPreB, ePreB)
if stage == 4:
setWeights(c1a, dPreA, ePreA)
setWeights(c2b, dPreB, ePreB)
setWeights(c4a, dPreA, ePreA)
setWeights(c4b, dPreB, ePreB)
setWeights(c3, dEns, eBio)
if stage == 5:
setWeights(c1a, dPreA, ePreA)
setWeights(c5, dEns, eBio)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
else:
sim.run(t, progress_bar=True)
ePreB = c1b.e if stage == 1 else ePreB
ePreA = c1a.e if stage == 2 else ePreA
eBio = c3.e if stage == 4 else eBio
return dict(
times=sim.trange(),
inptA=sim.data[pInptA],
inptB=sim.data[pInptB],
preInptA=sim.data[pPreInptA],
preInptB=sim.data[pPreInptB],
ens=sim.data[pEns],
tarEns=sim.data[pTarEns],
ePreA=ePreA,
ePreB=ePreB,
eBio=eBio,
)
def go(NPre=100,
N=100,
t=10,
c=None,
seed=1,
dt=0.001,
tTrans=0.01,
stage=None,
alpha=3e-7,
eMax=1e-1,
Tff=0.3,
fPre=DoubleExp(1e-3, 1e-1),
fNMDA=DoubleExp(10.6e-3, 285e-3),
fGABA=DoubleExp(0.5e-3, 1.5e-3),
fS=DoubleExp(1e-3, 1e-1),
dPreA=None,
dPreB=None,
dPreC=None,
dPreD=None,
dFdfw=None,
dEns=None,
dOff=None,
ePreAFdfw=None,
ePreBEns=None,
ePreCOff=None,
eFdfwEns=None,
eEnsEns=None,
ePreDEns=None,
eOffFdfw=None,
stimA=lambda t: 0,
stimB=lambda t: 0,
stimC=lambda t: 0,
stimD=lambda t: 0,
DA=lambda t: 0):
if not c: c = t
with nengo.Network(seed=seed) as model:
inptA = nengo.Node(stimA)
inptB = nengo.Node(stimB)
inptC = nengo.Node(stimC)
inptD = nengo.Node(stimD)
preA = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preB = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preC = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preD = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
fdfw = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed)
ens = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed + 1)
off = nengo.Ensemble(N,
1,
neuron_type=Bio("Interneuron", DA=DA),
seed=seed + 3)
tarFdfw = nengo.Ensemble(N,
1,
max_rates=Uniform(30, 30),
intercepts=Uniform(-0.8, 0.8),
seed=seed)
tarEns = nengo.Ensemble(N,
1,
max_rates=Uniform(30, 30),
intercepts=Uniform(-0.8, 0.8),
seed=seed + 1)
tarOff = nengo.Ensemble(N,
1,
max_rates=Uniform(30, 30),
intercepts=Uniform(0.2, 0.8),
encoders=Choice([[1]]),
seed=seed + 3)
cA = nengo.Connection(inptA, preA, synapse=None, seed=seed)
cB = nengo.Connection(inptB, preB, synapse=None, seed=seed)
cC = nengo.Connection(inptC, preC, synapse=None, seed=seed)
cD = nengo.Connection(inptD, preD, synapse=None, seed=seed)
pInptA = nengo.Probe(inptA, synapse=None)
pInptB = nengo.Probe(inptB, synapse=None)
pInptC = nengo.Probe(inptC, synapse=None)
pInptD = nengo.Probe(inptD, synapse=None)
pPreA = nengo.Probe(preA.neurons, synapse=None)
pPreB = nengo.Probe(preB.neurons, synapse=None)
pPreC = nengo.Probe(preC.neurons, synapse=None)
pPreD = nengo.Probe(preD.neurons, synapse=None)
pFdfw = nengo.Probe(fdfw.neurons, synapse=None)
pTarFdfw = nengo.Probe(tarFdfw.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
pOff = nengo.Probe(off.neurons, synapse=None)
pTarOff = nengo.Probe(tarOff.neurons, synapse=None)
if stage == 0:
nengo.Connection(preD, tarEns, synapse=fPre, seed=seed)
c0 = nengo.Connection(preD,
ens,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
learnEncoders(c0,
tarEns,
fS,
alpha=10 * alpha,
eMax=10 * eMax,
tTrans=tTrans)
if stage == 1:
nengo.Connection(inptA, tarFdfw, synapse=fPre, seed=seed)
nengo.Connection(inptB, tarEns, synapse=fPre, seed=seed)
nengo.Connection(inptC, tarOff, synapse=fPre, seed=seed)
c0 = nengo.Connection(preD,
ens,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2 = nengo.Connection(preB,
ens,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed)
c3 = nengo.Connection(preC,
off,
synapse=fPre,
solver=NoSolver(dPreC),
seed=seed)
learnEncoders(c1,
tarFdfw,
fS,
alpha=3 * alpha,
eMax=3 * eMax,
tTrans=tTrans)
learnEncoders(c2,
tarEns,
fS,
alpha=10 * alpha,
eMax=10 * eMax,
tTrans=tTrans)
learnEncoders(c3,
tarOff,
fS,
alpha=3 * alpha,
eMax=3 * eMax,
tTrans=tTrans)
if stage == 2:
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2 = nengo.Connection(preC,
off,
synapse=fPre,
solver=NoSolver(dPreC),
seed=seed)
if stage == 3:
cB.synapse = fNMDA
ff = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
fb = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
nengo.Connection(inptA, ff, synapse=fPre, seed=seed)
nengo.Connection(inptB, fb, synapse=fNMDA, seed=seed)
nengo.Connection(fb, tarEns, synapse=fPre, seed=seed)
nengo.Connection(ff,
tarEns,
synapse=fNMDA,
transform=Tff,
seed=seed)
c0 = nengo.Connection(preD,
ens,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2 = nengo.Connection(preB,
ens,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed)
c3 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
learnEncoders(c3,
tarEns,
fS,
alpha=3 * alpha,
eMax=3 * eMax,
tTrans=tTrans)
if stage == 4:
cB.synapse = fNMDA
c0 = nengo.Connection(preD,
ens,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2 = nengo.Connection(preB,
ens,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed)
c3 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
if stage == 5:
preB2 = nengo.Ensemble(NPre,
1,
max_rates=Uniform(30, 30),
seed=seed)
ens2 = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed + 1)
ens3 = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed + 1)
nengo.Connection(inptB, preB2, synapse=fNMDA, seed=seed)
c0a = nengo.Connection(preD,
ens,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c0b = nengo.Connection(preD,
ens2,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c0c = nengo.Connection(preD,
ens3,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c3 = nengo.Connection(preB,
ens2,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed)
c4 = nengo.Connection(ens2,
ens,
synapse=NMDA(),
solver=NoSolver(dEns),
seed=seed)
c5 = nengo.Connection(fdfw,
ens3,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c6 = nengo.Connection(preB2,
ens3,
synapse=fPre,
solver=NoSolver(dPreB),
seed=seed)
learnEncoders(c4, ens3, fS, alpha=alpha, eMax=eMax, tTrans=tTrans)
pTarEns = nengo.Probe(ens3.neurons, synapse=None)
if stage == 9:
c0 = nengo.Connection(preD,
ens,
synapse=fPre,
solver=NoSolver(dPreD),
seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPreA),
seed=seed)
c2 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c3 = nengo.Connection(ens,
ens,
synapse=NMDA(),
solver=NoSolver(dEns),
seed=seed)
c6 = nengo.Connection(preC,
off,
synapse=fPre,
solver=NoSolver(dPreC),
seed=seed)
c7 = nengo.Connection(off,
fdfw,
synapse=GABA(),
solver=NoSolver(dOff),
seed=seed)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if stage == 0:
setWeights(c0, dPreD, ePreDEns)
if stage == 1:
setWeights(c0, dPreD, ePreDEns)
setWeights(c1, dPreA, ePreAFdfw)
setWeights(c2, dPreB, ePreBEns)
setWeights(c3, dPreC, ePreCOff)
if stage == 2:
setWeights(c1, dPreA, ePreAFdfw)
setWeights(c2, dPreC, ePreCOff)
if stage == 3:
setWeights(c0, dPreD, ePreDEns)
setWeights(c1, dPreA, ePreAFdfw)
setWeights(c2, dPreB, ePreBEns)
setWeights(c3, dFdfw, eFdfwEns)
if stage == 4:
setWeights(c0, dPreD, ePreDEns)
setWeights(c1, dPreA, ePreAFdfw)
setWeights(c2, dPreB, ePreBEns)
setWeights(c3, dFdfw, eFdfwEns)
if stage == 5:
setWeights(c0a, dPreD, ePreDEns)
setWeights(c0b, dPreD, ePreDEns)
setWeights(c0c, dPreD, ePreDEns)
setWeights(c1, dPreA, ePreAFdfw)
setWeights(c2, dFdfw, eFdfwEns)
setWeights(c3, dPreB, ePreBEns)
setWeights(c4, dEns, eEnsEns)
setWeights(c5, dFdfw, eFdfwEns)
setWeights(c6, dPreB, ePreBEns)
if stage == 9:
setWeights(c0, dPreD, ePreDEns)
setWeights(c1, dPreA, ePreAFdfw)
setWeights(c2, dFdfw, eFdfwEns)
setWeights(c3, dEns, eEnsEns)
setWeights(c6, dPreC, ePreCOff)
setWeights(c7, dOff, eOffFdfw)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
ePreDEns = c0.e if stage == 0 else ePreDEns
ePreAFdfw = c1.e if stage == 1 else ePreAFdfw
ePreBEns = c2.e if stage == 1 else ePreBEns
ePreCOff = c3.e if stage == 1 else ePreCOff
eFdfwEns = c3.e if stage == 3 else eFdfwEns
eEnsEns = c4.e if stage == 5 else eEnsEns
return dict(
times=sim.trange(),
inptA=sim.data[pInptA],
inptB=sim.data[pInptB],
inptC=sim.data[pInptC],
inptD=sim.data[pInptD],
preA=sim.data[pPreA],
preB=sim.data[pPreB],
preC=sim.data[pPreC],
preD=sim.data[pPreD],
fdfw=sim.data[pFdfw],
ens=sim.data[pEns],
off=sim.data[pOff],
tarFdfw=sim.data[pTarFdfw],
tarEns=sim.data[pTarEns],
tarOff=sim.data[pTarOff],
ePreAFdfw=ePreAFdfw,
ePreBEns=ePreBEns,
ePreCOff=ePreCOff,
ePreDEns=ePreDEns,
eFdfwEns=eFdfwEns,
eEnsEns=eEnsEns,
eOffFdfw=eOffFdfw,
)
def go(NPre=100, N=100, t=10, c=None, seed=0, dt=0.001, Tff=0.3, tTrans=0.01,
stage=None, alpha=3e-7, eMax=1e-1,
fPre=DoubleExp(1e-3, 1e-1), fNMDA=DoubleExp(10.6e-3, 285e-3), fS=DoubleExp(1e-3, 1e-1),
dPreA=None, dPreB=None, dPreC=None, dFdfw=None, dBio=None, dNeg=None, dInh=None,
ePreA=None, ePreB=None, ePreC=None, eFdfw=None, eBio=None, eNeg=None, eInh=None,
stimA=lambda t: 0, stimB=lambda t: 0, stimC=lambda t: 0, DA=lambda t: 0):
if not c: c = t
with nengo.Network(seed=seed) as model:
inptA = nengo.Node(stimA)
inptB = nengo.Node(stimB)
inptC = nengo.Node(stimC)
preA = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preB = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preC = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
fdfw = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed)
ens = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed+1)
inh = nengo.Ensemble(N, 1, neuron_type=Bio("Interneuron", DA=DA), seed=seed+2)
tarFdfw = nengo.Ensemble(N, 1, max_rates=Uniform(30, 30), intercepts=Uniform(-0.8, 0.8), neuron_type=nengo.LIF(), seed=seed)
tarEns = nengo.Ensemble(N, 1, max_rates=Uniform(30, 30), intercepts=Uniform(-0.8, 0.8), neuron_type=nengo.LIF(), seed=seed+1)
tarInh = nengo.Ensemble(N, 1, max_rates=Uniform(30, 30), intercepts=Uniform(0.2, 0.8), encoders=Choice([[1]]), neuron_type=nengo.LIF(), seed=seed+2)
cA = nengo.Connection(inptA, preA, synapse=None, seed=seed)
cB = nengo.Connection(inptB, preB, synapse=None, seed=seed)
cC = nengo.Connection(inptC, preC, synapse=None, seed=seed)
pInptA = nengo.Probe(inptA, synapse=None)
pInptB = nengo.Probe(inptB, synapse=None)
pInptC = nengo.Probe(inptC, synapse=None)
pPreA = nengo.Probe(preA.neurons, synapse=None)
pPreB = nengo.Probe(preB.neurons, synapse=None)
pPreC = nengo.Probe(preC.neurons, synapse=None)
pFdfw = nengo.Probe(fdfw.neurons, synapse=None)
pTarFdfw = nengo.Probe(tarFdfw.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
pInh = nengo.Probe(inh.neurons, synapse=None)
pTarInh = nengo.Probe(tarInh.neurons, synapse=None)
if stage==1:
nengo.Connection(inptA, tarFdfw, synapse=fPre, seed=seed)
nengo.Connection(inptB, tarEns, synapse=fPre, seed=seed)
nengo.Connection(inptC, tarInh, synapse=fPre, seed=seed)
c1 = nengo.Connection(preA, fdfw, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c2 = nengo.Connection(preB, ens, synapse=fPre, solver=NoSolver(dPreB), seed=seed)
c3 = nengo.Connection(preC, inh, synapse=fPre, solver=NoSolver(dPreC), seed=seed)
learnEncoders(c1, tarFdfw, fS, alpha=alpha, eMax=eMax, tTrans=tTrans)
learnEncoders(c2, tarEns, fS, alpha=3*alpha, eMax=10*eMax, tTrans=tTrans)
learnEncoders(c3, tarInh, fS, alpha=alpha/3, eMax=eMax, tTrans=tTrans)
if stage==2:
c1 = nengo.Connection(preA, fdfw, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c2 = nengo.Connection(preC, inh, synapse=fPre, solver=NoSolver(dPreC), seed=seed)
if stage==3:
cB.synapse = fNMDA
nengo.Connection(inptA, tarFdfw, synapse=fPre, seed=seed)
nengo.Connection(inptB, tarEns, synapse=fPre, seed=seed)
nengo.Connection(tarFdfw, tarEns, synapse=fNMDA, transform=Tff, seed=seed)
c1 = nengo.Connection(preA, fdfw, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c2 = nengo.Connection(preB, ens, synapse=fPre, solver=NoSolver(dPreB), seed=seed)
c3 = nengo.Connection(fdfw, ens, synapse=NMDA(), solver=NoSolver(dFdfw), seed=seed)
learnEncoders(c3, tarEns, fS, alpha=alpha, eMax=eMax, tTrans=tTrans)
if stage==4:
cB.synapse = fNMDA
c1 = nengo.Connection(preA, fdfw, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c2 = nengo.Connection(preB, ens, synapse=fPre, solver=NoSolver(dPreB), seed=seed)
c3 = nengo.Connection(fdfw, ens, synapse=NMDA(), solver=NoSolver(dFdfw), seed=seed)
if stage==5:
preB2 = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
ens2 = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed+1)
ens3 = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed+1)
nengo.Connection(inptB, preB2, synapse=fNMDA, seed=seed)
c1 = nengo.Connection(preA, fdfw, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c2 = nengo.Connection(fdfw, ens, synapse=NMDA(), solver=NoSolver(dFdfw), seed=seed)
c3 = nengo.Connection(preB, ens2, synapse=fPre, solver=NoSolver(dPreB), seed=seed)
c4 = nengo.Connection(ens2, ens, synapse=NMDA(), solver=NoSolver(dBio), seed=seed)
c5 = nengo.Connection(fdfw, ens3, synapse=NMDA(), solver=NoSolver(dFdfw), seed=seed)
c6 = nengo.Connection(preB2, ens3, synapse=fPre, solver=NoSolver(dPreB), seed=seed)
learnEncoders(c4, ens3, fS, alpha=alpha, eMax=eMax, tTrans=tTrans)
pTarEns = nengo.Probe(ens3.neurons, synapse=None)
if stage==6:
preA2 = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
fdfw2 = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed)
fdfw3 = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed)
fdfw4 = nengo.Ensemble(N, 1, neuron_type=Bio("Pyramidal", DA=DA), seed=seed)
tarFdfw4 = nengo.Ensemble(N, 1, max_rates=Uniform(30, 30), intercepts=Uniform(-0.8, 0.8), neuron_type=nengo.LIF(), seed=seed)
nengo.Connection(inptA, tarFdfw4, synapse=fPre, seed=seed)
nengo.Connection(inptB, preA2, synapse=fNMDA, seed=seed)
nengo.Connection(inptC, tarInh, synapse=fPre, seed=seed)
nengo.Connection(tarInh, tarFdfw4.neurons, synapse=None, transform=-1e2*np.ones((N, 1)), seed=seed)
c1 = nengo.Connection(preB, ens, synapse=fPre, solver=NoSolver(dPreB), seed=seed)
c2 = nengo.Connection(ens, fdfw2, synapse=NMDA(), solver=NoSolver(dNeg), seed=seed)
c3 = nengo.Connection(preA2, fdfw3, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c4 = nengo.Connection(preA, fdfw4, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c5 = nengo.Connection(preC, inh, synapse=fPre, solver=NoSolver(dPreC), seed=seed)
c6 = nengo.Connection(inh, fdfw4, synapse=GABA(), solver=NoSolver(dInh), seed=seed)
learnEncoders(c2, fdfw3, fS, alpha=alpha, eMax=eMax, tTrans=tTrans)
learnEncoders(c6, tarFdfw4, fS, alpha=1e3*alpha, eMax=1e3*eMax, tTrans=tTrans, inh=True)
pFdfw2 = nengo.Probe(fdfw2.neurons, synapse=None)
pFdfw4 = nengo.Probe(fdfw4.neurons, synapse=None)
pTarFdfw2 = nengo.Probe(fdfw3.neurons, synapse=None)
pTarFdfw4 = nengo.Probe(tarFdfw4.neurons, synapse=None)
if stage==7:
c1 = nengo.Connection(preA, fdfw, synapse=fPre, solver=NoSolver(dPreA), seed=seed)
c2 = nengo.Connection(fdfw, ens, synapse=NMDA(), solver=NoSolver(dFdfw), seed=seed)
c3 = nengo.Connection(ens, ens, synapse=NMDA(), solver=NoSolver(dBio), seed=seed)
c4 = nengo.Connection(ens, fdfw, synapse=NMDA(), solver=NoSolver(dNeg), seed=seed)
c5 = nengo.Connection(preC, inh, synapse=fPre, solver=NoSolver(dPreC), seed=seed)
c6 = nengo.Connection(inh, fdfw, synapse=GABA(), solver=NoSolver(dInh), seed=seed)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if stage==1:
setWeights(c1, dPreA, ePreA)
setWeights(c2, dPreB, ePreB)
setWeights(c3, dPreC, ePreC)
if stage==2:
setWeights(c1, dPreA, ePreA)
setWeights(c2, dPreC, ePreC)
if stage==3:
setWeights(c1, dPreA, ePreA)
setWeights(c2, dPreB, ePreB)
setWeights(c3, dFdfw, eFdfw)
if stage==4:
setWeights(c1, dPreA, ePreA)
setWeights(c2, dPreB, ePreB)
setWeights(c3, dFdfw, eFdfw)
if stage==5:
setWeights(c1, dPreA, ePreA)
setWeights(c2, dFdfw, eFdfw)
setWeights(c3, dPreB, ePreB)
setWeights(c4, dBio, eBio)
setWeights(c5, dFdfw, eFdfw)
setWeights(c6, dPreB, ePreB)
if stage==6:
setWeights(c1, dPreB, ePreB)
setWeights(c2, dNeg, eNeg)
setWeights(c3, dPreA, ePreA)
setWeights(c4, dPreA, ePreA)
setWeights(c5, dPreC, ePreC)
setWeights(c6, dInh, eInh)
if stage==7:
setWeights(c1, dPreA, ePreA)
setWeights(c2, dFdfw, eFdfw)
setWeights(c3, dBio, eBio)
setWeights(c4, dNeg, eNeg)
setWeights(c5, dPreC, ePreC)
setWeights(c6, dInh, eInh)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
ePreA = c1.e if stage==1 else ePreA
ePreB = c2.e if stage==1 else ePreB
ePreC = c3.e if stage==1 else ePreC
eFdfw = c3.e if stage==3 else eFdfw
eBio = c4.e if stage==5 else eBio
eNeg = c2.e if stage==6 else eNeg
eInh = c6.e if stage==6 else eInh
return dict(
times=sim.trange(),
inptA=sim.data[pInptA],
inptB=sim.data[pInptB],
inptC=sim.data[pInptC],
preA=sim.data[pPreA],
preB=sim.data[pPreB],
preC=sim.data[pPreC],
fdfw=sim.data[pFdfw],
ens=sim.data[pEns],
inh=sim.data[pInh],
tarFdfw=sim.data[pTarFdfw],
tarEns=sim.data[pTarEns],
tarInh=sim.data[pTarInh],
fdfw2=sim.data[pFdfw2] if stage==6 else None,
fdfw4=sim.data[pFdfw4] if stage==6 else None,
tarFdfw2=sim.data[pTarFdfw2] if stage==6 else None,
tarFdfw4=sim.data[pTarFdfw4] if stage==6 else None,
ePreA=ePreA,
ePreB=ePreB,
ePreC=ePreC,
eFdfw=eFdfw,
eBio=eBio,
eNeg=eNeg,
eInh=eInh,
)
def go(NPre=100,
N=100,
t=10,
m=Uniform(30, 30),
i=Uniform(-0.8, 0.8),
seed=0,
dt=0.001,
f=DoubleExp(1e-3, 1e-2),
fS=DoubleExp(1e-3, 1e-1),
neuron_type=LIF(),
d1a=None,
d1b=None,
d2=None,
f1a=None,
f1b=None,
f2=None,
e1a=None,
e1b=None,
e2=None,
l1a=False,
l1b=False,
l2=False,
l3=False,
test=False,
stim=lambda t: np.sin(t),
stim2=lambda t: 0):
with nengo.Network(seed=seed) as model:
inpt = nengo.Node(stim)
intg = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
preInpt = nengo.Ensemble(NPre, 1, radius=3, max_rates=m, seed=seed)
preIntg = nengo.Ensemble(NPre, 1, max_rates=m, seed=seed)
ens = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed)
nengo.Connection(inpt, intg, synapse=1 / s, seed=seed)
c0a = nengo.Connection(inpt, preInpt, synapse=None, seed=seed)
c0b = nengo.Connection(intg, preIntg, synapse=None, seed=seed)
c1a = nengo.Connection(preInpt,
ens,
synapse=f1a,
solver=NoSolver(d1a),
seed=seed)
pInpt = nengo.Probe(inpt, synapse=None)
pIntg = nengo.Probe(intg, synapse=None)
pPreInpt = nengo.Probe(preInpt.neurons, synapse=None)
pPreIntg = nengo.Probe(preIntg.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
if l1b: # preIntg-to-ens
tarEns = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=nengo.LIF(),
seed=seed)
nengo.Connection(preIntg,
tarEns,
synapse=f1b,
solver=NoSolver(d1b),
seed=seed + 1)
c1b = nengo.Connection(preIntg,
ens,
synapse=f1b,
solver=NoSolver(d1b),
seed=seed + 1)
learnEncoders(c1b, tarEns, fS)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
if l1a: # preInpt-to-ens, given preIntg-to-ens
inpt2 = nengo.Node(stim2)
tarEns = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=nengo.LIF(),
seed=seed)
nengo.Connection(preInpt,
tarEns,
synapse=f1a,
solver=NoSolver(d1a),
seed=seed)
c0b.transform = 0
nengo.Connection(inpt2, preIntg, synapse=None, seed=seed)
nengo.Connection(preIntg,
tarEns,
synapse=f1b,
solver=NoSolver(d1b),
seed=seed + 1)
c1b = nengo.Connection(preIntg,
ens,
synapse=f1b,
solver=NoSolver(d1b),
seed=seed + 1)
learnEncoders(c1a, tarEns, fS)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
if l2: # ens readout, given preIntg and preInpt
c1b = nengo.Connection(preIntg,
ens,
synapse=f1b,
solver=NoSolver(d1b),
seed=seed + 1)
if l3: # ens2-to-ens, given preInpt-ens and preIntg-ens2
ens2 = nengo.Ensemble(N,
1,
max_rates=m,
intercepts=i,
neuron_type=neuron_type,
seed=seed)
c0a.synapse = f
c2a = nengo.Connection(preInpt,
ens2,
synapse=f1a,
solver=NoSolver(d1a),
seed=seed)
c2b = nengo.Connection(preIntg,
ens2,
synapse=f1b,
solver=NoSolver(d1b),
seed=seed + 1)
c3 = nengo.Connection(ens2,
ens,
synapse=f2,
solver=NoSolver(d2),
seed=seed)
learnEncoders(c3, ens2, fS)
pTarEns2 = nengo.Probe(ens2.neurons, synapse=None)
if test:
c5 = nengo.Connection(ens,
ens,
synapse=f2,
solver=NoSolver(d2),
seed=seed)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if isinstance(neuron_type, Bio):
if l1b:
setWeights(c1b, d1b, e1b)
if l1a:
setWeights(c1a, d1a, e1a)
setWeights(c1b, d1b, e1b)
if l2:
setWeights(c1a, d1a, e1a)
setWeights(c1b, d1b, e1b)
if l3:
setWeights(c1a, d1a, e1a)
setWeights(c2a, d1a, e1a)
setWeights(c2b, d1b, e1b)
setWeights(c3, d2, e2)
if test:
setWeights(c1a, d1a, e1a)
setWeights(c5, d2, e2)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
else:
sim.run(t, progress_bar=True)
e1a = c1a.e if l1a else e1a
e1b = c1b.e if l1b else e1b
e2 = c3.e if l3 else e2
return dict(
times=sim.trange(),
inpt=sim.data[pInpt],
intg=sim.data[pIntg],
preInpt=sim.data[pPreInpt],
preIntg=sim.data[pPreIntg],
ens=sim.data[pEns],
tarEns=sim.data[pTarEns] if l1a or l1b else None,
tarEns2=sim.data[pTarEns2] if l3 else None,
e1a=e1a,
e1b=e1b,
e2=e2,
)
def go(NPre=300,
NBias=100,
N=30,
t=10,
seed=1,
dt=0.001,
Tff=0.3,
tTrans=0.01,
stage=None,
alpha=3e-7,
eMax=1e-1,
fPre=DoubleExp(1e-3, 1e-1),
fNMDA=DoubleExp(10.6e-3, 285e-3),
fGABA=DoubleExp(0.5e-3, 1.5e-3),
fS=DoubleExp(1e-3, 1e-1),
dPre=None,
dFdfw=None,
dEns=None,
dBias=None,
ePreFdfw=None,
ePreEns=None,
ePreBias=None,
eFdfwEns=None,
eBiasEns=None,
eEnsEns=None,
stimA=lambda t: 0,
stimB=lambda t: 0,
stimC=lambda t: 0.01,
DA=lambda t: 0):
with nengo.Network(seed=seed) as model:
inptA = nengo.Node(stimA)
inptB = nengo.Node(stimB)
inptC = nengo.Node(stimC)
preA = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preB = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
preC = nengo.Ensemble(NPre, 1, max_rates=Uniform(30, 30), seed=seed)
fdfw = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed)
ens = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed + 1)
bias = nengo.Ensemble(NBias,
1,
neuron_type=Bio("Interneuron", DA=DA),
seed=seed + 2)
tarFdfw = nengo.Ensemble(N,
1,
max_rates=Uniform(30, 30),
intercepts=Uniform(-0.8, 0.8),
seed=seed)
tarEns = nengo.Ensemble(N,
1,
max_rates=Uniform(30, 30),
intercepts=Uniform(-0.8, 0.8),
seed=seed + 1)
tarBias = nengo.Ensemble(NBias,
1,
max_rates=Uniform(30, 30),
intercepts=Uniform(-0.8, -0.2),
encoders=Choice([[1]]),
seed=seed + 2)
cA = nengo.Connection(inptA, preA, synapse=None, seed=seed)
cB = nengo.Connection(inptB, preB, synapse=None, seed=seed)
cC = nengo.Connection(inptC, preC, synapse=None, seed=seed)
pInptA = nengo.Probe(inptA, synapse=None)
pInptB = nengo.Probe(inptB, synapse=None)
pInptC = nengo.Probe(inptC, synapse=None)
pPreA = nengo.Probe(preA.neurons, synapse=None)
pPreB = nengo.Probe(preB.neurons, synapse=None)
pPreC = nengo.Probe(preC.neurons, synapse=None)
pFdfw = nengo.Probe(fdfw.neurons, synapse=None)
pTarFdfw = nengo.Probe(tarFdfw.neurons, synapse=None)
pEns = nengo.Probe(ens.neurons, synapse=None)
pTarEns = nengo.Probe(tarEns.neurons, synapse=None)
pBias = nengo.Probe(bias.neurons, synapse=None)
pTarBias = nengo.Probe(tarBias.neurons, synapse=None)
if stage == 0: # readout decoders for [preA, preB, preC]
pass
if stage == 1: # encoders for [preA, preC] to [fdfw, bias]
nengo.Connection(inptA, tarFdfw, synapse=fPre, seed=seed)
nengo.Connection(inptC, tarBias, synapse=fPre, seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
learnEncoders(c1,
tarFdfw,
fS,
alpha=3 * alpha,
eMax=3 * eMax,
tTrans=tTrans)
learnEncoders(c2,
tarBias,
fS,
alpha=alpha,
eMax=eMax,
tTrans=tTrans)
if stage == 2: # readout decoders for fdfw and bias
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
if stage == 3: # encoders for [bias] to ens
# nengo.Connection(inptC, tarBias, synapse=fPre, seed=seed)
nengo.Connection(inptC, tarEns, synapse=fGABA, seed=seed)
c1 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(bias,
ens,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
learnEncoders(c2,
tarEns,
fS,
alpha=1e3 * alpha,
eMax=1e3 * eMax,
tTrans=tTrans)
if stage == 4: # encoders for [preB] to [ens]
# nengo.Connection(inptC, tarBias, synapse=fPre, seed=seed)
nengo.Connection(inptC, tarEns, synapse=fGABA, seed=seed)
nengo.Connection(inptB, tarEns, synapse=fPre, seed=seed)
c1 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(bias,
ens,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
c3 = nengo.Connection(preB,
ens,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
learnEncoders(c3,
tarEns,
fS,
alpha=3 * alpha,
eMax=3 * eMax,
tTrans=tTrans)
if stage == 5: # encoders for [fdfw] to ens
cB.synapse = fNMDA
tarPreA = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
tarPreB = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
tarPreC = nengo.Ensemble(1, 1, neuron_type=nengo.Direct())
nengo.Connection(inptA, tarPreA, synapse=fPre, seed=seed)
nengo.Connection(inptB, tarPreB, synapse=fNMDA, seed=seed)
nengo.Connection(inptC, tarPreC, synapse=fPre, seed=seed)
nengo.Connection(tarPreA,
tarEns,
synapse=fNMDA,
transform=Tff,
seed=seed)
nengo.Connection(tarPreB, tarEns, synapse=fPre, seed=seed)
nengo.Connection(tarPreC, tarEns, synapse=fGABA, seed=seed)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(preB,
ens,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c3 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c4 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c5 = nengo.Connection(bias,
ens,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
learnEncoders(c4,
tarEns,
fS,
alpha=3 * alpha,
eMax=3 * eMax,
tTrans=tTrans)
if stage == 6: # readout decoders for ens
cB.synapse = fNMDA
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(preB,
ens,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c3 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c4 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c5 = nengo.Connection(bias,
ens,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
if stage == 7: # encoders from ens to ens
preB2 = nengo.Ensemble(NPre,
1,
max_rates=Uniform(30, 30),
seed=seed)
ens2 = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed + 1) # acts as preB input to ens
ens3 = nengo.Ensemble(N,
1,
neuron_type=Bio("Pyramidal", DA=DA),
seed=seed + 1) # acts as tarEns
nengo.Connection(inptB, preB2, synapse=fNMDA, seed=seed)
pTarEns = nengo.Probe(ens3.neurons, synapse=None)
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(preB,
ens2,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c3 = nengo.Connection(preB2,
ens3,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c4 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c5 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c6 = nengo.Connection(fdfw,
ens3,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c7 = nengo.Connection(bias,
ens,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
c8 = nengo.Connection(bias,
ens2,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
c9 = nengo.Connection(bias,
ens3,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
c10 = nengo.Connection(ens2,
ens,
synapse=NMDA(),
solver=NoSolver(dEns),
seed=seed)
learnEncoders(c10, ens3, fS, alpha=alpha, eMax=eMax, tTrans=tTrans)
if stage == 8: # test
c1 = nengo.Connection(preA,
fdfw,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c2 = nengo.Connection(preC,
bias,
synapse=fPre,
solver=NoSolver(dPre),
seed=seed)
c3 = nengo.Connection(fdfw,
ens,
synapse=NMDA(),
solver=NoSolver(dFdfw),
seed=seed)
c4 = nengo.Connection(bias,
ens,
synapse=GABA(),
solver=NoSolver(dBias),
seed=seed)
c5 = nengo.Connection(ens,
ens,
synapse=NMDA(),
solver=NoSolver(dEns),
seed=seed)
with nengo.Simulator(model, seed=seed, dt=dt, progress_bar=False) as sim:
if stage == 0:
pass
if stage == 1:
setWeights(c1, dPre, ePreFdfw)
setWeights(c2, dPre, ePreBias)
if stage == 2:
setWeights(c1, dPre, ePreFdfw)
setWeights(c2, dPre, ePreBias)
if stage == 3:
setWeights(c1, dPre, ePreBias)
setWeights(c2, dBias, eBiasEns)
if stage == 4:
setWeights(c1, dPre, ePreBias)
setWeights(c2, dBias, eBiasEns)
setWeights(c3, dPre, ePreEns)
if stage == 5:
setWeights(c1, dPre, ePreFdfw)
setWeights(c2, dPre, ePreEns)
setWeights(c3, dPre, ePreBias)
setWeights(c4, dFdfw, eFdfwEns)
setWeights(c5, dBias, eBiasEns)
if stage == 6:
setWeights(c1, dPre, ePreFdfw)
setWeights(c2, dPre, ePreEns)
setWeights(c3, dPre, ePreBias)
setWeights(c4, dFdfw, eFdfwEns)
setWeights(c5, dBias, eBiasEns)
if stage == 7:
setWeights(c1, dPre, ePreFdfw)
setWeights(c2, dPre, ePreEns)
setWeights(c3, dPre, ePreEns)
setWeights(c4, dPre, ePreBias)
setWeights(c5, dFdfw, eFdfwEns)
setWeights(c6, dFdfw, eFdfwEns)
setWeights(c7, dBias, eBiasEns)
setWeights(c8, dBias, eBiasEns)
setWeights(c9, dBias, eBiasEns)
setWeights(c10, dEns, eEnsEns)
if stage == 8:
setWeights(c1, dPre, ePreFdfw)
setWeights(c2, dPre, ePreBias)
setWeights(c3, dFdfw, eFdfwEns)
setWeights(c4, dBias, eBiasEns)
setWeights(c5, dEns, eEnsEns)
neuron.h.init()
sim.run(t, progress_bar=True)
reset_neuron(sim, model)
ePreFdfw = c1.e if stage == 1 else ePreFdfw
ePreBias = c2.e if stage == 1 else ePreBias
eBiasEns = c2.e if stage == 3 else eBiasEns
ePreEns = c3.e if stage == 4 else ePreEns
eFdfwEns = c4.e if stage == 5 else eFdfwEns
eEnsEns = c10.e if stage == 7 else eEnsEns
return dict(
times=sim.trange(),
inptA=sim.data[pInptA],
inptB=sim.data[pInptB],
inptC=sim.data[pInptC],
preA=sim.data[pPreA],
fdfw=sim.data[pFdfw],
ens=sim.data[pEns],
bias=sim.data[pBias],
tarFdfw=sim.data[pTarFdfw],
tarEns=sim.data[pTarEns],
tarBias=sim.data[pTarBias],
ePreFdfw=ePreFdfw,
ePreEns=ePreEns,
ePreBias=ePreBias,
eFdfwEns=eFdfwEns,
eBiasEns=eBiasEns,
eEnsEns=eEnsEns,
)