def analyse(path,**kwargs):
restore=res.load(path)
##print(restore.files)
##pt=restore['pt']
##if 'ptsim' in restore.keys():
## ptsim=restore['ptsim']
py=restore['py']
x,X=discrprogr(py,**kwargs)
y=[]
Y=[]
if 'pysim' in restore.keys():
pysim=restore['pysim']
y,Y=discrprogr(pysim,**kwargs)
res.save('../../anres/anresults{}{}'.format(kwargs.get('string',''),kwargs.get('mode','')),x=x,X=X,y=y,Y=Y)
res.dump('../../anres/anresults{}{}'.format(kwargs.get('string',''),kwargs.get('mode','')),x=x,X=X,y=y,Y=Y)
def evaluate(path,**kwargs):
restore=res.load(path)
##print(restore.files)
##pt=restore['pt']
##if 'ptsim' in restore.keys():
## ptsim=restore['ptsim']
py=restore['py']
t0=restore['t0']
dy,DY,disc=evaldiscr(py,**kwargs)
y=[]
Y=[]
if 'pysim' in restore.keys():
pysim=restore['pysim']
y,Y,trash=evaldiscr(pysim,**kwargs)
res.save('../../anres/evresults{}{}'.format(kwargs.get('string',''),kwargs.get('mode','limit')),dy=dy,DY=DY,y=y,Y=Y,t0=disc[:,t0])
res.dump('../../anres/evresults{}{}'.format(kwargs.get('string',''),kwargs.get('mode','limit')),dy=dy,DY=DY,y=y,Y=Y,t0=disc[:,t0])
def run(arguments):
# check if result already exists for this run, and if so, quit
if results.check_exists(arguments):
print('Results already exist for arguments ' + str(arguments))
print('Quitting.')
quit()
#######################################
#######################################
## Step 0: Setup
#######################################
#######################################
np.random.seed(arguments.trial)
bc.util.set_verbosity(arguments.verbosity)
if arguments.coreset_size_spacing == 'log':
Ms = np.unique(
np.logspace(0.,
np.log10(arguments.coreset_size_max),
arguments.coreset_num_sizes,
dtype=np.int32))
else:
Ms = np.unique(
np.linspace(1,
arguments.coreset_size_max,
arguments.coreset_num_sizes,
dtype=np.int32))
#make sure the first size to record is 0
if Ms[0] != 0:
Ms = np.hstack((0, Ms))
#######################################
#######################################
## Step 1: Generate a Synthetic Dataset
#######################################
#######################################
#change these to change the prior / likelihood
mu0 = np.zeros(arguments.data_dim)
Sig0 = np.eye(arguments.data_dim)
Sig = np.eye(arguments.data_dim)
#these are computed
Sig0inv = np.linalg.inv(Sig0)
Siginv = np.linalg.inv(Sig)
LSigInv = np.linalg.cholesky(Siginv) #Siginv = LL^T, L Lower tri
USig = sl.solve_triangular(LSigInv,
np.eye(LSigInv.shape[0]),
lower=True,
overwrite_b=True,
check_finite=False).T # Sig = UU^T, U upper tri
th = np.ones(arguments.data_dim)
logdetSig = np.linalg.slogdet(Sig)[1]
#######################################
#######################################
## Step 2: Calculate Likelihoods/Projectors
#######################################
#######################################
print('Computing true posterior')
x = np.random.multivariate_normal(th, Sig, arguments.data_num)
mup, USigp, LSigpInv = gaussian.weighted_post(mu0, Sig0inv, Siginv, x,
np.ones(x.shape[0]))
Sigp = USigp.dot(USigp.T)
SigpInv = LSigpInv.dot(LSigpInv.T)
#create the log_likelihood function
print('Creating log-likelihood function')
log_likelihood = lambda x, th: gaussian.log_likelihood(
x, th, Siginv, logdetSig)
print('Creating gradient log-likelihood function')
grad_log_likelihood = lambda x, th: gaussian.gradx_log_likelihood(
x, th, Siginv)
print('Creating tuned projector for Hilbert coreset construction')
#create the sampler for the "optimally-tuned" Hilbert coreset
sampler_optimal = lambda n, w, pts: mup + np.random.randn(n, mup.shape[0]
).dot(USigp.T)
prj_optimal = bc.BlackBoxProjector(sampler_optimal, arguments.proj_dim,
log_likelihood, grad_log_likelihood)
print('Creating untuned projector for Hilbert coreset construction')
#create the sampler for the "realistically-tuned" Hilbert coreset
xhat = x[np.random.randint(0, x.shape[0], int(np.sqrt(x.shape[0]))), :]
muhat, USigHat, LSigHatInv = gaussian.weighted_post(
mu0, Sig0inv, Siginv, xhat, np.ones(xhat.shape[0]))
sampler_realistic = lambda n, w, pts: muhat + np.random.randn(
n, muhat.shape[0]).dot(USigHat.T)
prj_realistic = bc.BlackBoxProjector(sampler_realistic, arguments.proj_dim,
log_likelihood, grad_log_likelihood)
print('Creating black box projector')
def sampler_w(n, wts, pts):
if wts is None or pts is None or pts.shape[0] == 0:
wts = np.zeros(1)
pts = np.zeros((1, mu0.shape[0]))
muw, USigw, _ = gaussian.weighted_post(mu0, Sig0inv, Siginv, pts, wts)
return muw + np.random.randn(n, muw.shape[0]).dot(USigw.T)
prj_bb = bc.BlackBoxProjector(sampler_w, arguments.proj_dim,
log_likelihood, grad_log_likelihood)
print('Creating exact projectors')
#TODO need to fix all the transposes in this...
class GaussianProjector(bc.Projector):
def project(self, pts, grad=False):
nu = (pts - self.muw).dot(LSigInv)
PsiL = LSigInv.T.dot(self.USigw)
Psi = PsiL.dot(PsiL.T)
nu = np.hstack(
(nu.dot(PsiL), np.sqrt(0.5 * np.trace(np.dot(Psi.T, Psi))) *
np.ones(nu.shape[0])[:, np.newaxis]))
nu *= np.sqrt(nu.shape[1])
if not grad:
return nu
else:
gnu = np.hstack(
(SigLInv.dot(PsiL), np.zeros(pts.shape[1])[:,
np.newaxis])).T
gnu = np.tile(gnu, (pts.shape[0], 1, 1))
gnu *= np.sqrt(gnu.shape[1])
return nu, gnu
def update(self, wts=None, pts=None):
if wts is None or pts is None or pts.shape[0] == 0:
wts = np.zeros(1)
pts = np.zeros((1, mu0.shape[0]))
self.muw, self.USigw, self.LSigwInv = gaussian.weighted_post(
mu0, Sig0inv, Siginv, pts, wts)
prj_optimal_exact = GaussianProjector()
prj_optimal_exact.update(np.ones(x.shape[0]), x)
prj_realistic_exact = GaussianProjector()
prj_realistic_exact.update(np.ones(xhat.shape[0]), xhat)
#######################################
#######################################
## Step 3: Construct Coreset
#######################################
#######################################
##############################
print('Creating coreset construction objects')
#create coreset construction objects
sparsevi_exact = bc.SparseVICoreset(x,
GaussianProjector(),
opt_itrs=arguments.opt_itrs,
step_sched=eval(arguments.step_sched))
sparsevi = bc.SparseVICoreset(x,
prj_bb,
opt_itrs=arguments.opt_itrs,
step_sched=eval(arguments.step_sched))
giga_optimal = bc.HilbertCoreset(x, prj_optimal)
giga_optimal_exact = bc.HilbertCoreset(x, prj_optimal_exact)
giga_realistic = bc.HilbertCoreset(x, prj_realistic)
giga_realistic_exact = bc.HilbertCoreset(x, prj_realistic_exact)
unif = bc.UniformSamplingCoreset(x)
algs = {
'SVI-EXACT': sparsevi_exact,
'SVI': sparsevi,
'GIGA-OPT': giga_optimal,
'GIGA-OPT-EXACT': giga_optimal_exact,
'GIGA-REAL': giga_realistic,
'GIGA-REAL-EXACT': giga_realistic_exact,
'US': unif
}
alg = algs[arguments.alg]
print('Building coreset')
w = []
p = []
cputs = np.zeros(Ms.shape[0])
t_build = 0
for m in range(Ms.shape[0]):
print('M = ' + str(Ms[m]) + ': coreset construction, ' +
arguments.alg + ' ' + str(arguments.trial))
t0 = time.process_time()
itrs = (Ms[m] if m == 0 else Ms[m] - Ms[m - 1])
alg.build(itrs)
t_build += time.process_time() - t0
wts, pts, idcs = alg.get()
#store weights/pts/runtime
w.append(wts)
p.append(pts)
cputs[m] = t_build
##############################
##############################
## Step 4: Evaluate coreset
##############################
##############################
# computing kld and saving results
muw = np.zeros((Ms.shape[0], mu0.shape[0]))
Sigw = np.zeros((Ms.shape[0], mu0.shape[0], mu0.shape[0]))
rklw = np.zeros(Ms.shape[0])
fklw = np.zeros(Ms.shape[0])
csizes = np.zeros(Ms.shape[0])
mu_errs = np.zeros(Ms.shape[0])
Sig_errs = np.zeros(Ms.shape[0])
for m in range(Ms.shape[0]):
csizes[m] = (w[m] > 0).sum()
muw[m, :], USigw, LSigwInv = gaussian.weighted_post(
mu0, Sig0inv, Siginv, p[m], w[m])
Sigw[m, :, :] = USigw.dot(USigw.T)
rklw[m] = gaussian.KL(muw[m, :], Sigw[m, :, :], mup, SigpInv)
fklw[m] = gaussian.KL(mup, Sigp, muw[m, :], LSigwInv.dot(LSigwInv.T))
mu_errs[m] = np.sqrt(((mup - muw[m, :])**2).sum()) / np.sqrt(
(mup**2).sum())
Sig_errs[m] = np.sqrt(((Sigp - Sigw[m, :, :])**2).sum()) / np.sqrt(
(Sigp**2).sum())
results.save(arguments,
csizes=csizes,
Ms=Ms,
cputs=cputs,
rklw=rklw,
fklw=fklw,
mu_errs=mu_errs,
Sig_errs=Sig_errs)
#also save muw/Sigw/etc for plotting coreset visualizations
f = open('results/coreset_data.pk', 'wb')
res = (x, mu0, Sig0, Sig, mup, Sigp, w, p, muw, Sigw)
pk.dump(res, f)
f.close()
bombarolo = nemici[random2]
bomba = bombe.append(Bomb(bombarolo.x_n, bombarolo.y_n))
if 0 <= x <= 693:
paintEdo(x, y)
elif x < 0:
paintEdo(0, y)
else:
paintEdo(693, y)
# pygame.display.update() update only a part of the screen
pygame.display.flip() # update the whole screen
# RESULT SAVING AND RECORD CHECKING---------------
if not quitting:
screen.blit(gameoverdisplay, (0, 0))
pygame.display.flip() # update the whole screen
stringarecord = results.save(missili_sparati, bombe_evitate, nemici_sconfitti)
pygame.time.wait(4000)
record = False
if (
int(stringarecord[0]) == bombe_evitate
or int(stringarecord[1]) == missili_sparati
or int(stringarecord[2]) == nemici_sconfitti
):
record = True
# RESULT VISUALIZATION------------------------------------
if fine:
pygame.font.init()
font = pygame.font.Font("freesansbold.ttf", 32)
stringaresult = (
def run(arguments):
# check if result already exists for this run, and if so, quit
if results.check_exists(arguments):
print('Results already exist for arguments ' + str(arguments))
print('Quitting.')
quit()
#######################################
#######################################
## Step 0: Setup
#######################################
#######################################
np.random.seed(arguments.trial)
bc.util.set_verbosity(arguments.verbosity)
if arguments.coreset_size_spacing == 'log':
Ms = np.unique(
np.logspace(0.,
np.log10(arguments.coreset_size_max),
arguments.coreset_num_sizes,
dtype=np.int32))
else:
Ms = np.unique(
np.linspace(1,
arguments.coreset_size_max,
arguments.coreset_num_sizes,
dtype=np.int32))
#make sure the first size to record is 0
if Ms[0] != 0:
Ms = np.hstack((0, Ms))
#######################################
#######################################
## Step 1: Load and preprocess data
#######################################
#######################################
#load data and compute true posterior
#each row of x is [lat, lon, price]
print('Loading data')
x = np.load('../data/prices2018.npy')
print('dataset size : ', x.shape)
print('Subsampling down to ' + str(arguments.data_num) + ' points')
idcs = np.arange(x.shape[0])
np.random.shuffle(idcs)
x = x[idcs[:arguments.data_num], :]
#log transform the prices
x[:, 2] = np.log10(x[:, 2])
#get empirical mean/std
datastd = x[:, 2].std()
datamn = x[:, 2].mean()
#bases of increasing size; the last one is effectively a constant
basis_unique_scales = np.array([.2, .4, .8, 1.2, 1.6, 2., 100])
basis_unique_counts = np.hstack(
(arguments.n_bases_per_scale * np.ones(6, dtype=np.int64), 1))
#the dimension of the scaling vector for the above bases
d = basis_unique_counts.sum()
print('Basis dimension: ' + str(d))
#model params
mu0 = datamn * np.ones(d)
Sig0 = (datastd**2 + datamn**2) * np.eye(d)
Sig0inv = np.linalg.inv(Sig0)
#generate basis functions by uniformly randomly picking locations in the dataset
print('Trial ' + str(arguments.trial))
print('Creating bases')
basis_scales = np.array([])
basis_locs = np.zeros((0, 2))
for i in range(basis_unique_scales.shape[0]):
basis_scales = np.hstack(
(basis_scales,
basis_unique_scales[i] * np.ones(basis_unique_counts[i])))
idcs = np.random.choice(np.arange(x.shape[0]),
replace=False,
size=basis_unique_counts[i])
basis_locs = np.vstack((basis_locs, x[idcs, :2]))
print('Converting bases and observations into X/Y matrices')
#convert basis functions + observed data locations into a big X matrix
X = np.zeros((x.shape[0], basis_scales.shape[0]))
for i in range(basis_scales.shape[0]):
X[:, i] = np.exp(-((x[:, :2] - basis_locs[i, :])**2).sum(axis=1) /
(2 * basis_scales[i]**2))
Y = x[:, 2]
Z = np.hstack((X, Y[:, np.newaxis]))
_, bV = np.linalg.eigh(X.T.dot(X))
bV = bV[:, -arguments.proj_dim:]
#######################################
#######################################
## Step 2: Calculate Likelihoods/Projectors
#######################################
#######################################
#get true posterior
print('Computing true posterior')
mup, USigp, LSigpInv = model_linreg.weighted_post(mu0, Sig0inv, datastd**2,
Z, np.ones(X.shape[0]))
Sigp = USigp.dot(USigp.T)
SigpInv = LSigpInv.dot(LSigpInv.T)
#create function to output log_likelihood given param samples
print('Creating log-likelihood function')
log_likelihood = lambda z, th: model_linreg.log_likelihood(
z, th, datastd**2)
print('Creating gradient log-likelihood function')
grad_log_likelihood = lambda z, th: model_linreg.grad_x_log_likelihood(
z, th, datastd**2)
#create tangent space for well-tuned Hilbert coreset alg
print('Creating tuned projector for Hilbert coreset construction')
sampler_optimal = lambda n, w, pts: mup + np.random.randn(n, mup.shape[0]
).dot(USigp.T)
prj_optimal = bc.BlackBoxProjector(sampler_optimal, arguments.proj_dim,
log_likelihood, grad_log_likelihood)
#create tangent space for poorly-tuned Hilbert coreset alg
print('Creating untuned projector for Hilbert coreset construction')
Zhat = Z[np.random.randint(0, Z.shape[0], int(np.sqrt(Z.shape[0]))), :]
muhat, USigHat, LSigHatInv = model_linreg.weighted_post(
mu0, Sig0inv, datastd**2, Zhat, np.ones(Zhat.shape[0]))
sampler_realistic = lambda n, w, pts: muhat + np.random.randn(
n, muhat.shape[0]).dot(USigHat.T)
prj_realistic = bc.BlackBoxProjector(sampler_realistic, arguments.proj_dim,
log_likelihood, grad_log_likelihood)
print('Creating black box projector')
def sampler_w(n, wts, pts):
if wts is None or pts is None or pts.shape[0] == 0:
muw = mu0
USigw = np.linalg.cholesky(
Sig0
) #Note: USigw is lower triangular here, below is upper tri. Doesn't matter, just need Sigw = MM^T
else:
muw, USigw, _ = model_linreg.weighted_post(mu0, Sig0inv,
datastd**2, pts, wts)
return muw + np.random.randn(n, muw.shape[0]).dot(USigw.T)
prj_bb = bc.BlackBoxProjector(sampler_w, arguments.proj_dim,
log_likelihood, grad_log_likelihood)
print('Creating exact projectors')
##############################
###Exact projection in SparseVI for gradient computation
#for this model we can do the tangent space projection exactly
class LinRegProjector(bc.Projector):
def __init__(self, bV):
self.bV = bV
def project(self, pts, grad=False):
X = pts[:, :-1]
Y = pts[:, -1]
#beta = X.dot(self.V*np.sqrt(np.maximum(self.lmb, 0.)))
beta = X.dot(self.USigw)
nu = Y - X.dot(self.muw)
#approximation to avoid high memory cost: project the matrix term down to bV.shape[1]**2 dimensions
beta_proj = beta.dot(self.bV)
#lmb2, V2 = np.linalg.eigh(beta.T.dot(beta))
#beta_proj = beta.dot(V2[:, -arguments.proj_dim:])
return np.hstack(
(nu[:, np.newaxis] * beta, 1. / np.sqrt(2.) *
(beta_proj[:, :, np.newaxis] * beta_proj[:, np.newaxis, :]).
reshape(beta.shape[0], arguments.proj_dim**2))) / datastd**2
def update(self, wts, pts):
if wts is None or pts is None or pts.shape[0] == 0:
self.muw = mu0
self.USigw = np.linalg.cholesky(
Sig0
) #Note: USigw here is lower triangular, but keeping naming convention for below stuff. Doesn't matter, just need Sigw = MM^T
else:
self.muw, self.USigw, _ = model_linreg.weighted_post(
mu0, Sig0inv, datastd**2, pts, wts)
#if pts.shape[0] == 0:
# self.muw = mu0
# self.Sigw = Sig0
#else:
# self.muw, self.Sigw = model_linreg.weighted_post(mu0, Sig0inv, datastd**2, pts, wts)
#self.lmb, self.V = np.linalg.eigh(self.LSigw.dot(self.LSigw.T))
prj_optimal_exact = LinRegProjector(bV)
prj_optimal_exact.update(np.ones(Z.shape[0]), Z)
prj_realistic_exact = LinRegProjector(bV)
prj_realistic_exact.update(np.ones(Zhat.shape[0]), Zhat)
#######################################
#######################################
## Step 3: Construct Coreset
#######################################
#######################################
##############################
print('Creating coreset construction objects')
#create coreset construction objects
sparsevi_exact = bc.SparseVICoreset(Z,
LinRegProjector(bV),
opt_itrs=arguments.opt_itrs,
step_sched=eval(arguments.step_sched))
sparsevi = bc.SparseVICoreset(Z,
prj_bb,
opt_itrs=arguments.opt_itrs,
step_sched=eval(arguments.step_sched))
giga_optimal = bc.HilbertCoreset(Z, prj_optimal)
giga_optimal_exact = bc.HilbertCoreset(Z, prj_optimal_exact)
giga_realistic = bc.HilbertCoreset(Z, prj_realistic)
giga_realistic_exact = bc.HilbertCoreset(Z, prj_realistic_exact)
unif = bc.UniformSamplingCoreset(Z)
algs = {
'SVI-EXACT': sparsevi_exact,
'SVI': sparsevi,
'GIGA-OPT': giga_optimal,
'GIGA-OPT-EXACT': giga_optimal_exact,
'GIGA-REAL': giga_realistic,
'GIGA-REAL-EXACT': giga_realistic_exact,
'US': unif
}
alg = algs[arguments.alg]
print('Building coreset')
w = []
p = []
cputs = np.zeros(Ms.shape[0])
t_build = 0
for m in range(Ms.shape[0]):
print('M = ' + str(Ms[m]) + ': coreset construction, ' +
arguments.alg + ' ' + str(arguments.trial))
t0 = time.process_time()
itrs = (Ms[m] if m == 0 else Ms[m] - Ms[m - 1])
alg.build(itrs)
t_build += time.process_time() - t0
wts, pts, idcs = alg.get()
#store weights/pts/runtime
w.append(wts)
p.append(pts)
cputs[m] = t_build
##############################
##############################
## Step 4: Evaluate coreset
##############################
##############################
# computing kld and saving results
muw = np.zeros((Ms.shape[0], mu0.shape[0]))
Sigw = np.zeros((Ms.shape[0], mu0.shape[0], mu0.shape[0]))
rklw = np.zeros(Ms.shape[0])
fklw = np.zeros(Ms.shape[0])
mu_errs = np.zeros(Ms.shape[0])
Sig_errs = np.zeros(Ms.shape[0])
csizes = np.zeros(Ms.shape[0])
for m in range(Ms.shape[0]):
csizes[m] = (w[m] > 0).sum()
muw[m, :], USigw, LSigwInv = model_linreg.weighted_post(
mu0, Sig0inv, datastd**2, p[m], w[m])
Sigw[m, :, :] = USigw.dot(USigw.T)
rklw[m] = model_linreg.KL(muw[m, :], Sigw[m, :, :], mup, SigpInv)
fklw[m] = model_linreg.KL(mup, Sigp, muw[m, :],
LSigwInv.dot(LSigwInv.T))
mu_errs[m] = np.sqrt(((mup - muw[m, :])**2).sum()) / np.sqrt(
(mup**2).sum())
Sig_errs[m] = np.sqrt(((Sigp - Sigw[m, :, :])**2).sum()) / np.sqrt(
(Sigp**2).sum())
results.save(arguments,
csizes=csizes,
Ms=Ms,
cputs=cputs,
rklw=rklw,
fklw=fklw,
mu_errs=mu_errs,
Sig_errs=Sig_errs)
#also save muw/Sigw/etc for plotting coreset visualizations
f = open('results/coreset_data.pk', 'wb')
res = (x, mu0, Sig0, datastd, mup, Sigp, w, p, muw, Sigw)
pk.dump(res, f)
f.close()
''' main file which takes argument from encrypt.py and executes further functions as documented in the file ''' import imgpros import sys import utilities import model import results '''Initializes the inputs taken from encrypt.py and stores them for furthur use''' utilities.intializer(sys.argv) '''Displays a preview of initial 50 frames to help cropping of rotating cell by the user''' utilities.preview() '''Allows user to select a free-size rectangular portion of the first frame consisting of a cell for furthur analysis''' imgpros.crop() '''Performs Linear Regression Analysis the cropped portion of all the frames and outputs the centre of mass(COM) data for and a plot of COM for furthur use''' model.analyze() '''Calculates frequency, change in angle per frame, total clockwise/counter-clockwise time interval and no of frames and all else necessary outputs. Also outputs the finally analyzed data in the form of CSV files and graphs''' model.compute() '''Saves the graphs and CSV files obtained after analysis in the required folder''' results.save()
def run(arguments):
# check if result already exists for this run, and if so, quit
if results.check_exists(arguments):
print('Results already exist for arguments ' + str(arguments))
print('Quitting.')
quit()
#######################################
#######################################
########### Step 0: Setup #############
#######################################
#######################################
np.random.seed(arguments.trial)
bc.util.set_verbosity(arguments.verbosity)
algs = {
'FW': bc.snnls.FrankWolfe,
'GIGA': bc.snnls.GIGA,
'OMP': bc.snnls.OrthoPursuit,
'US': bc.snnls.UniformSampling
}
if arguments.coreset_size_spacing == 'log':
Ms = np.unique(
np.logspace(0.,
np.log10(arguments.coreset_size_max),
arguments.coreset_num_sizes,
dtype=np.int32))
else:
Ms = np.unique(
np.linspace(1,
arguments.coreset_size_max,
arguments.coreset_num_sizes,
dtype=np.int32))
#######################################
#######################################
## Step 1: Generate a Synthetic Dataset
#######################################
#######################################
if arguments.data_type == 'normal':
X = np.random.randn(arguments.data_num, arguments.data_dim)
else:
X = np.eye(arguments.data_num)
############################
############################
## Step 1: Build/Evaluate the Coreset
############################
############################
data_type = arguments.data_type
fldr = arguments.results_folder
err = np.zeros(Ms.shape[0])
csize = np.zeros(Ms.shape[0])
cput = np.zeros(Ms.shape[0])
print('data: ' + arguments.data_type + ', trial ' + str(arguments.trial) +
', alg: ' + arguments.alg)
class IDProjector(bc.Projector):
def update(self, wts, pts):
pass
def project(self, pts, grad=False):
return pts
alg = bc.HilbertCoreset(X, IDProjector(), snnls=algs[arguments.alg])
for m, M in enumerate(Ms):
t0 = time.process_time()
itrs = (Ms[m] if m == 0 else Ms[m] - Ms[m - 1])
alg.build(itrs)
tf = time.process_time()
cput[m] = tf - t0 + cput[m - 1] if m > 0 else tf - t0
wts, pts, idcs = alg.get()
csize[m] = (wts > 0).sum()
err[m] = alg.error()
############################
############################
## Step 2: Save Results
############################
############################
results.save(arguments, err=err, csize=csize, Ms=Ms, cput=cput)
def run(region, N=1000):
"""Run model simulation.
Args:
region (str): Region to run the simulation for.
N (int, optional): Number of samples.
"""
region = region.upper().strip()
print(region)
# load config
with open("model/regions.json") as fp:
_config = json.load(fp)
config = _config[region]
config = {
'dates': ('2020-08-01', '2021-03-13'),
'window': 7,
'weekly': False,
'attributes': 'IRD',
'initial': {
'E': .1,
'I': .1,
'R': 0,
'D': 0
},
'emission': {
'I': (1, 1),
'R': (1, 1),
'D': (1, 1)
},
**config
}
POP = population.get_population(region)
# parse
dates = [datetime.strptime(d, "%Y-%m-%d") for d in config['dates']]
window = config['window']
weekly = config.get('weekly', False)
attributes = config['attributes'].upper()
initial = [
1 - sum(config['initial'].values()), # S
config['initial'].get('E', 0), # E
config['initial'].get('I', 0), # I
config['initial'].get('R', 0), # R
config['initial'].get('D', 0)
] # D
emission = [
config['emission'].get('I',
(1, 1)), config['emission'].get('R', (1, 1)),
config['emission'].get('D', (1, 1))
]
# optimize
params = optimize_spline(region,
dates,
initial=initial,
attributes=attributes,
emission=emission,
window=window,
weekly=weekly)
# simulate result
(sim_lat,
sim_obs), last_values = posterior.simulate_posterior(region=region,
params=params,
dates=dates,
N=N,
initial=initial,
parI=emission[0],
parR=emission[1],
parD=emission[2])
# save result
_results.save((sim_lat, sim_obs), dates, region, params)
def fit(cell,
method,
search_transformation='a',
sample_transformation='a',
start_from_m1=False,
method_1b=False,
repeats=50,
cap=None):
"""
Performs a fit to data from cell ``cell``, using method ``method`` and the
given configuration.
If ``start_from_m1`` is set to ``True``, a single repeat will be run. Else,
the number of repeats will be set by ``repeats`` and ``cap``.
"""
# Check cell and method (better checking happens below)
cell = int(cell)
method = int(method)
# Check compatibility of arguments, is handled in detail later via
# results.reserve_base_name()
if method == 1 and not method_1b:
raise ValueError('Only Method 1b is supported by fit(), not method 1.')
if method != 1 and method_1b:
raise ValueError('Method 1b can only be used if method 1 is chosen.')
# Set method name for screen output
method_name = str(method)
if start_from_m1:
method_name += 'b'
# Create transformation objects
search_transformation = transformations.create(search_transformation)
sample_transformation = transformations.create(sample_transformation)
# Define boundaries
bounds = boundaries.Boundaries(
search_transformation,
sample_transformation,
None if method == 1 else cells.lower_conductance(cell),
)
# Define error function
if method == 1:
g_fixed = results.load_parameters(cell, 1)[-1]
f = errors.E1(cell, search_transformation, fixed_conductance=g_fixed)
elif method == 2:
f = errors.E2(cell, search_transformation)
elif method == 3:
f = errors.E3(cell, search_transformation)
elif method == 4:
f = errors.E4(cell, search_transformation)
elif method == 5:
f = errors.EAP(cell, search_transformation)
else:
raise ValueError('Method not supported: ' + str(method))
# Check number of repeats
if start_from_m1:
repeats = 1
else:
repeats = int(repeats)
if repeats < 1:
raise ValueError('Number of repeats must be at least 1.')
if debug:
repeats = min(3, repeats)
# Check cap on total number of runs
if start_from_m1:
cap = None
elif cap is not None:
cap = int(cap)
if cap < 1:
raise ValueError(
'Cap on total number of runs must be at least 1 (or None).')
# Run
scores = []
for i in range(repeats):
# Cap max runs
cap_info = ''
if cap:
n = results.count(cell, method, search_transformation.code(),
sample_transformation.code(), start_from_m1,
method_1b, False)
if n >= cap:
print()
print('Maximum number of runs reached: terminating.')
print()
return
cap_info = ' (run ' + str(n + 1) + ', capped at ' + str(cap) + ')'
# Show configuration
print()
print('Cell ' + str(cell))
print('Method ' + method_name)
print('Search ' + search_transformation.name())
print('Sample ' + sample_transformation.name())
print('Repeat ' + str(1 + i) + ' of ' + str(repeats) + cap_info)
print()
if start_from_m1:
print('Starting from Method 1 result.')
else:
print('Starting point sampled from boundaries.')
# Get base filename to store results in
with results.reserve_base_name(cell, method,
search_transformation.code(),
sample_transformation.code(),
start_from_m1, method_1b) as base:
print('Storing results using base ' + base)
# Choose starting point
if start_from_m1:
# Start from method 1 results
p0 = results.load_parameters(cell, 1) # Model space
q0 = search_transformation.transform(p0) # Search space
else:
# Choose random starting point
# Allow resampling, in case error calculation fails
print('Choosing starting point')
q0 = f0 = float('inf')
while not np.isfinite(f0):
q0 = bounds.sample() # Search space
f0 = f(q0) # Initial score
# Create optimiser
opt = pints.OptimisationController(f,
q0,
boundaries=bounds,
method=pints.CMAES)
opt.set_log_to_file(base + '.csv', True)
opt.set_max_iterations(3 if debug else None)
#opt.set_parallel(True)
opt.set_parallel(False)
# Run optimisation
with np.errstate(all='ignore'): # Ignore numpy warnings
q, s = opt.run() # Search space
p = search_transformation.detransform(q) # Model space
if method_1b:
p = np.concatenate((p, [g_fixed]))
# Store results for this run
results.save(base, p, s, opt.time(), opt.evaluations())
scores.append(s)
# Order scores
order = np.argsort(scores)
scores = np.asarray(scores)[order]
# Show results
print('Best scores:')
for score in scores[:10]:
print(score)
print('Mean & std of score:')
print(np.mean(scores))
print(np.std(scores))
print('Worst score:')
print(scores[-1])
def run(arguments):
# check if result already exists for this run, and if so, quit
if results.check_exists(arguments):
print('Results already exist for arguments ' + str(arguments))
print('Quitting.')
quit()
#######################################
#######################################
########### Step 0: Setup #############
#######################################
#######################################
np.random.seed(arguments.trial)
bc.util.set_verbosity(arguments.verbosity)
if arguments.coreset_size_spacing == 'log':
Ms = np.unique(
np.logspace(0.,
np.log10(arguments.coreset_size_max),
arguments.coreset_num_sizes,
dtype=np.int32))
else:
Ms = np.unique(
np.linspace(1,
arguments.coreset_size_max,
arguments.coreset_num_sizes,
dtype=np.int32))
#######################################
#######################################
## Step 1: Define Model
#######################################
#######################################
if arguments.model == "lr":
import model_lr as model
elif arguments.model == "poiss":
import model_poiss as model
#######################################
#######################################
## Step 2: Load Dataset & run full MCMC / Laplace
#######################################
#######################################
print('Loading dataset ' + arguments.dataset)
X, Y, Z, Zt, D = model.load_data('../data/' + arguments.dataset + '.npz')
#NOTE: Sig0 is currently coded as identity in model_lr and model_pr (see log_prior).
#so if you change Sig0 here things might break.
#TODO: fix that...
mu0 = np.zeros(Z.shape[1])
Sig0 = np.eye(Z.shape[1])
LSig0 = np.eye(Z.shape[1])
print('Checking for cached full MCMC samples')
mcmc_cache_filename = 'mcmc_cache/full_samples_' + arguments.model + '_' + arguments.dataset + '.npz'
if os.path.exists(mcmc_cache_filename):
print('Cache exists, loading')
tmp__ = np.load(mcmc_cache_filename)
full_samples = tmp__['samples']
full_mcmc_time_per_itr = tmp__['t']
else:
print('Cache doesnt exist, running MCMC')
#convert Y to Stan LR label format
stanY = np.zeros(Y.shape[0])
stanY[:] = Y
stanY[stanY == -1] = 0
sampler_data = {
'x': X,
'y': stanY.astype(int),
'w': np.ones(X.shape[0]),
'd': X.shape[1],
'n': X.shape[0]
}
full_samples, t_full_mcmc = mcmc.run(sampler_data,
arguments.mcmc_samples_full,
arguments.model,
model.stan_representation,
arguments.trial)
full_samples = full_samples['theta']
#TODO right now *2 to account for burn; but this should all be specified via tunable arguments
full_mcmc_time_per_itr = t_full_mcmc / (arguments.mcmc_samples_full *
2)
if not os.path.exists('mcmc_cache'):
os.mkdir('mcmc_cache')
np.savez(mcmc_cache_filename,
samples=full_samples,
t=full_mcmc_time_per_itr)
#######################################
#######################################
## Step 3: Calculate Likelihoods/Projectors
#######################################
#######################################
#get Gaussian approximation to the true posterior
print('Approximating true posterior')
mup = full_samples.mean(axis=0)
Sigp = np.cov(full_samples, rowvar=False)
LSigp = np.linalg.cholesky(Sigp)
LSigpInv = solve_triangular(LSigp,
np.eye(LSigp.shape[0]),
lower=True,
overwrite_b=True,
check_finite=False)
#create tangent space for well-tuned Hilbert coreset alg
print('Creating tuned projector for Hilbert coreset construction')
muHat, LSigHat, LSigHatInv = get_laplace(np.ones(Z.shape[0]),
Z,
np.zeros(Z.shape[1]),
model,
diag=False)
sampler_optimal = lambda n, w, pts: muHat + np.random.randn(
n, muHat.shape[0]).dot(LSigHat.T)
prj_optimal = bc.BlackBoxProjector(sampler_optimal, arguments.proj_dim,
model.log_likelihood,
model.grad_z_log_likelihood)
#create tangent space for poorly-tuned Hilbert coreset alg
print('Creating untuned projector for Hilbert coreset construction')
Zhat = Z[np.random.randint(0, Z.shape[0], int(np.sqrt(Z.shape[0]))), :]
muHat2, LSigHat2, LSigHat2Inv = get_laplace(np.ones(Zhat.shape[0]),
Zhat,
np.zeros(Zhat.shape[1]),
model,
diag=False)
sampler_realistic = lambda n, w, pts: muHat2 + np.random.randn(
n, muHat2.shape[0]).dot(LSigHat2.T)
prj_realistic = bc.BlackBoxProjector(sampler_realistic, arguments.proj_dim,
model.log_likelihood,
model.grad_z_log_likelihood)
print('Creating black box projector')
def sampler_w(n, wts, pts):
if wts is None or pts is None or pts.shape[0] == 0:
muw = mu0
LSigw = LSig0
else:
muw, LSigw, _ = get_laplace(wts,
pts,
np.zeros(Z.shape[1]),
model,
diag=False)
return muw + np.random.randn(n, muw.shape[0]).dot(LSigw.T)
prj_bb = bc.BlackBoxProjector(sampler_w, arguments.proj_dim,
model.log_likelihood,
model.grad_z_log_likelihood)
#######################################
#######################################
## Step 4: Construct Coreset
#######################################
#######################################
print('Creating coreset construction objects')
#create coreset construction objects
sparsevi = bc.SparseVICoreset(Z,
prj_bb,
opt_itrs=arguments.opt_itrs,
step_sched=eval(arguments.step_sched))
giga_optimal = bc.HilbertCoreset(Z, prj_optimal)
giga_realistic = bc.HilbertCoreset(Z, prj_realistic)
unif = bc.UniformSamplingCoreset(Z)
algs = {
'SVI': sparsevi,
'GIGA-OPT': giga_optimal,
'GIGA-REAL': giga_realistic,
'US': unif
}
alg = algs[arguments.alg]
cputs = np.zeros(Ms.shape[0])
mcmc_time_per_itr = np.zeros(Ms.shape[0])
csizes = np.zeros(Ms.shape[0])
Fs = np.zeros(Ms.shape[0])
rklw = np.zeros(Ms.shape[0])
fklw = np.zeros(Ms.shape[0])
mu_errs = np.zeros(Ms.shape[0])
Sig_errs = np.zeros(Ms.shape[0])
print('Running coreset construction / MCMC for ' + arguments.dataset +
' ' + arguments.alg + ' ' + str(arguments.trial))
t_alg = 0.
for m in range(Ms.shape[0]):
print('M = ' + str(Ms[m]) + ': coreset construction, ' +
arguments.alg + ' ' + arguments.dataset + ' ' +
str(arguments.trial))
#this runs alg up to a level of M; on the next iteration, it will continue from where it left off
t0 = time.process_time()
itrs = (Ms[m] if m == 0 else Ms[m] - Ms[m - 1])
alg.build(itrs)
t_alg += time.process_time() - t0
wts, pts, idcs = alg.get()
print('M = ' + str(Ms[m]) + ': MCMC')
# Use MCMC on the coreset, measure time taken
stanY = np.zeros(idcs.shape[0])
stanY[:] = Y[idcs]
stanY[stanY == -1] = 0
sampler_data = {
'x': X[idcs, :],
'y': stanY.astype(int),
'w': wts,
'd': X.shape[1],
'n': idcs.shape[0]
}
cst_samples, t_cst_mcmc = mcmc.run(sampler_data,
arguments.mcmc_samples_coreset,
arguments.model,
model.stan_representation,
arguments.trial)
cst_samples = cst_samples['theta']
#TODO see note above re: full mcmc sampling
t_cst_mcmc_per_step = t_cst_mcmc / (arguments.mcmc_samples_coreset * 2)
print('M = ' + str(Ms[m]) + ': Approximating posterior with Gaussian')
muw = cst_samples.mean(axis=0)
Sigw = np.cov(cst_samples, rowvar=False)
LSigw = np.linalg.cholesky(Sigw)
LSigwInv = solve_triangular(LSigw,
np.eye(LSigw.shape[0]),
lower=True,
overwrite_b=True,
check_finite=False)
print('M = ' + str(Ms[m]) + ': Computing metrics')
cputs[m] = t_alg
mcmc_time_per_itr[m] = t_cst_mcmc_per_step
csizes[m] = (wts > 0).sum()
gcs = np.array([
model.grad_th_log_joint(Z[idcs, :], full_samples[i, :], wts)
for i in range(full_samples.shape[0])
])
gfs = np.array([
model.grad_th_log_joint(Z, full_samples[i, :], np.ones(Z.shape[0]))
for i in range(full_samples.shape[0])
])
Fs[m] = (((gcs - gfs)**2).sum(axis=1)).mean()
rklw[m] = KL(muw, Sigw, mup, LSigpInv.T.dot(LSigpInv))
fklw[m] = KL(mup, Sigp, muw, LSigwInv.T.dot(LSigwInv))
mu_errs[m] = np.sqrt(((mup - muw)**2).sum()) / np.sqrt((mup**2).sum())
Sig_errs[m] = np.sqrt(((Sigp - Sigw)**2).sum()) / np.sqrt(
(Sigp**2).sum())
results.save(arguments,
csizes=csizes,
Ms=Ms,
cputs=cputs,
Fs=Fs,
full_mcmc_time_per_itr=full_mcmc_time_per_itr,
mcmc_time_per_itr=mcmc_time_per_itr,
rklw=rklw,
fklw=fklw,
mu_errs=mu_errs,
Sig_errs=Sig_errs)