def singleLocusSigmoid():
x0=0.001;s=0.5;maxGen=100
times_ = T.ivector("times"); x0_ = T.scalar("x0 ")
S__=theano.shared(np.asarray(s, dtype = theano.config.floatX), 'S')
pred_= sig_(0.5*S__*times_ + logit_(x0_))
Feedforward_ = theano.function(inputs=[x0_,times_], outputs=pred_)
pd.Series(Feedforward_(x0,range(maxGen))).plot();
pd.Series(sig(0.5*s*np.arange(maxGen)+logit(x0))).plot()
def singleMultiLocusHafVariableTime():
from popgen.TimeSeries.RNN.Utils import Z
x0=0.001;s=0.5;maxGen=100;numReplicates=3;times=np.tile(np.arange(maxGen+1),(numReplicates,1)).T.astype(np.float32)
initC0 = np.arange(numReplicates,dtype=np.float32)*logit(x0)
c__=theano.shared(initC0, 'c')
# c__=theano.shared(np.asarray(logit(x0), dtype = theano.config.floatX), 'S')
times_ = T.fmatrix();rep_ = T.iscalar();maxGenerations_ = T.ivector()
target_ = (T.matrix(),T.vector())[numReplicates==1]
S__=theano.shared(np.asarray(s, dtype = np.float32), 'S')
loss_= (target_[:maxGenerations_[rep_],rep_] - Z(T.nnet.sigmoid(0.5*S__*times_[:maxGenerations_[rep_],rep_] +c__[rep_]),200,20))**2
reps_=T.ivector()
cost_, _ = theano.scan(lambda rep: (target_[:maxGenerations_[rep],rep] - times_[:maxGenerations_[rep],rep]).sum() , sequences=reps_); cost_=cost_.sum()
Loss_ = theano.function(inputs=[target_, times_, maxGenerations_, reps_], outputs=[results])
times
target=times+1
target[:,1]+=1
target[:,2]+=1
target
lastGenerationIndex=[10,20,30]
reps=range(numReplicates)
Loss_(target,times,lastGenerationIndex,reps)
target
import popgen.TimeSeries.RNN.MultiLocusHAFOptimizingAllVarsVariableTimeOld as RNN
numReplicates=3 ; s=0.02;generationStep=100
sim = Simulation.Simulation(numReplicates=numReplicates, s=s, generationStep=generationStep);
sim.forwardSimulation();
sim.getAverageHAF().plot()
sim.getAverageHAF().diff().plot()
y=sim.getAverageHAF();times=sim.getGenerationTimes()
replicateIndex=range(sim.numReplicates)
reload(RNN)
n=2000;theta=20
lastGenerationIndex=sim.filterTimeSamplesWithHighNegDer()
rnn=RNN.MultiLocusHAFOptimizingAllVarsVariableTimeOld(sim.X0.min(),lastGenerationIndex=lastGenerationIndex, initS=sim.s, initTheta=theta, times=sim.getGenerationTimes(), numReplicates=sim.numReplicates,initSviaLineSearch=False)
rnn.Loss_(y.values,np.tile(times,(3,1)).T.astype(np.float32),n,list(lastGenerationIndex),replicateIndex)
Z(sig(0.5*times*sim.s + logit(sim.X0.min())),n,theta)
i=10
j=0
for j,i in enumerate(lastGenerationIndex):
print ((Z(sig(0.5*times*sim.s + logit(sim.X0.min())),n,theta)[:i] - y.values[:i,j])**2).sum()
print lastGenerationIndex
def hardSweep():
param=pd.read_pickle('/home/arya/out/vineet/param0.1_1.pd')
reload(Simulation)
s=0.01
X0=param['initHaps'].mean(0)
param['siteUnderSelection']=param['initHaps'].mean(0).argmin()
param['s']=s
param['numReplicates']=3
param['maxGeneration']=500
param['generationStep']=100
param['startGeneration']=0
X = Simulation.Simulation.forwardSimulationHardSweep(param)
def sig(x): return 1./(1+np.exp(-x))
if not param['startGeneration']:
x0=X0[param['siteUnderSelection']]
else:
x0=X[param['startGeneration']/param['generationStep'] -1,param['siteUnderSelection'],:].mean()
x0
c=np.log(1-x0)-np.log(x0)
z=sig(s*np.array(range(param['startGeneration'],param['maxGeneration']+1,param['generationStep'])[1:])/2. -c)
pd.DataFrame(np.append(X[:,3,:],z[:,None],axis=1)).plot()
y= np.array([[np.linalg.norm(X[t,:,r])**2 for t in range(X.shape[0])] for r in range(param['numReplicates'])]).T
y0=np.linalg.norm(X0)**2
theta=Estimate.watterson(np.tile(param['initHaps'],(10,1)));n=2000
theta=Estimate.watterson(param['initHaps']);n=200
a=[(y0 ,Z(X0[3], n, theta))]
for t in range(5):
a.append((y[t] ,Z(X[t,3,:], n, theta)))
pd.DataFrame(a)
times=range(param['startGeneration'],param['maxGeneration']+1,param['generationStep'])[1:]
times
x0_ = T.scalar("x0")
n_ = T.scalar("n")
theta_ = T.scalar("theta")
times_ = T.ivector("times")
S__=theano.shared(np.asarray(s, dtype = theano.config.floatX), 'S')
predall_, updatesRecurrence_ = theano.scan(lambda x_prev, s: (s*x_prev*x_prev+s*x_prev +2*x_prev)/(2*s*x_prev+2), outputs_info=x0_,non_sequences=S__,n_steps=times_[-1])
pred_=Z(predall_[times_-1],n_,theta_) #we only have target at some generations e.g. 10,20,...
Feedforward_ = theano.function(inputs=[x0_,times_,n_,theta_], outputs=pred_, updates=updatesRecurrence_)
Feedforward_(x0,times,n,theta)
x0
y
times
Z(X[:,3,:],n,theta)
theta,n
z
Z(z,2000,17)
pd.DataFrame(np.append(X[:,3,:],z[:,None],axis=1))
def Nu0(s,t,nu0,n,theta): return Z(sig(np.array(t)*s/2 +logit(nu0)),n,theta)
initNu0=0.005; final_momentum=0.9; initial_momentum=0.5;momentum_switchover=5;times=range(1,801);S=3;lr=1e-2;maxIter=10000;initS=0.05; initTheta= 20; numReplicates=3;n=2000
def Nu(s,t,nu0): return np.array([sig(t*s/2 +logit(nu)) for nu in nu0]).T def Nu0(s,t,nu0,n,theta): return Z(sig(np.array(t)*s/2 +logit(nu0)),n,theta)