def initialize(self, X0=None, title='',**kwargs):
"""\
Set initial embedding.
Parameters:
X0 : numpy array or None
Initial embedding. If set to None, the initial embedding is produced
randomly using misc.initial_embedding().
"""
if self.verbose > 0:
print('- MDS.initialize('+title+'):')
if X0 is None:
X0 = misc.initial_embedding(self.N,dim=self.dim,
radius=self.D_rms,**kwargs)
if self.verbose > 0:
print(' method : random')
else:
assert isinstance(X0,np.ndarray)
assert X0.shape == (self.N,self.dim)
if self.verbose > 0:
print(' method : initialization given')
self.X = X0
self.update()
self.X0 = self.X.copy()
if self.verbose > 0:
print(f' initial stress : {self.cost:0.2e}[{self.ncost:0.2e}]')
def initialize(self, X0=None, **kwargs):
"""\
Set initial embedding.
"""
if self.verbose > 0:
print(self.indent + ' TSNE.initialize():')
if X0 is None:
X0 = misc.initial_embedding(self.N,
dim=self.dim,
radius=1,
**kwargs)
#radius=self.D['rms'],**kwargs)
if self.verbose > 0:
print(self.indent + ' method : random')
else:
assert isinstance(X0, np.ndarray)
assert X0.shape == (self.N, self.dim)
if self.verbose > 0:
print(self.indent + ' method : initialization given')
self.update(X0)
self.embedding0 = self.embedding.copy()
if self.verbose > 0:
print(self.indent + f' initial cost : {self.cost:0.2e}')
def initialize_X(self, X0=None, method='random', max_iters=50, **kwargs):
"""\
Set initial embedding using misc.initial function.
Parameters:
Y0 : numpy array
Initial embedding (optional)
number : int > 0
Number of initial embeddings to be generated and saved. When looking for
a minimizer of the stress function, the optimization algorithm is run
using the different initial embeddings and the best solution is
retained.
"""
if self.verbose > 0:
print('- Multiview.initialize_X():')
if X0 is not None:
if self.verbose > 0:
print(' method : X0 given')
assert isinstance(X0, np.ndarray)
assert X0.shape == (self.N, self.persp.dimX)
self.X = X0
else:
if self.verbose > 0:
print(' method : ', method)
if method == 'random':
self.X = misc.initial_embedding(self.N,
dim=self.persp.dimX,
radius=1)
#radius=self.D_rms,**kwargs)
elif method == 'mds':
D = np.average(self.D, axis=0)
vis = mds.MDS(D, dim=self.persp.dimX)
vis.initialize()
vis.optimize(max_iters=max_iters, **kwargs)
self.X = vis.X
self.update()
self.X0 = self.X.copy()
def __init__(self, data, weights=None, data_args=None,
fixed_embedding=None, fixed_projections=None,
initial_embedding=None, initial_projections=None,
visualization_method='mds', visualization_args={},
total_cost_function='rms',
embedding_dimension=3, image_dimension=2,
projection_family='linear',projection_constraint='orthogonal',
hidden_samples=None,
sample_labels=None, perspective_labels=None,
sample_colors=None, image_colors=None,
verbose=0, indent='',
**kwargs):
"""\
Initializes MPSE object.
Parameters
----------
data : list, length (n_perspectives)
List containing distance/dissimilarity/feature data for each
perspective. Each array can be of the following forms:
1) A 1D condensed distance array
2) A square distance matrix
3) An array containing features
***4) A dictionary describing a graph
weights : None or string or array or list
If visualization allows for it, weights to be used in computation of
cost/gradiant of each perspective.
IF a list is given, then the list must have length equal to the number
of perspectives. Otherwise, it is assumed that the given weights are the
same for all perspectives.
The possible weights are described in setup.setup_weights. These are:
1) None : no weights are used
2) string : method to compute weights based on distances
3) function : function to compute weights based on distances
4) array : array containing pairwise weights or node weights, depending
on size (must be of length of distances or of samples).
data_args : dictionary (optional) or list
Optional arguments to pass to distances.setup().
If a list is passed, then the length must be the number of perspectives
and each element must be a dictionary. Then, each set of distances will
be set up using a different set of arguments.
fixed_embedding : array
If an array is given, this is assumed to be the true embedding and
by default optimization is done w.r.t. the projections only.
fixed_projections : list
If a list is given, this is assumed to be the true projections and by
default optimization is done w.r.t. the embedding coordinates only.
initial_embedding : array
If given, this is the initial embedding used.
initial_projections : list
If given, this is the initial projections used.
visualization_method : str
Visualization method. Current options are 'mds' and 'tsne'.
The visualization method can be different for different perspectives,
by passing a list of visualization methods instead.
visualization_args : dict
Dictionary with arguments to pass to each visualization method.
Different arguments can be passed to different visualization methods
by passing a list of dictionaries instead.
embedding_dimension : int
Dimension of embedding.
image_dimension : int
Dimension of image (after projection). Each perspective can have a
different image dimension, by specifying a list instead.
projection_family : str
Projection family. Options are 'linear'.
projection_constraint : str
Constraints on projection family. Options are None, 'orthogonal',
'similar'.
embedding_dimension : int > 0
Dimension of the embedding.
Alternative name: embedding_dimension
projection_dimension : int or array
Dimension of projections. Can be different for each perspective.
persp : Object instance of projections.Persp class or int > 0.
Describes set of allowed projection functions and stores list of
projection parameters. See perspective.py. If instead of a Persp object
a positive integer int is given, then it is assumed that
embedding_dimension=image_dimension=int
and that all projections are the identity.
sample_labels : list (optional)
List containing labels of samples (used in plots).
sample_colors : array (optional)
Array containing color value of samples (used in plots).
image_colors : array-like, shape (n_perspectives, n_samples)
Colors for each image.
"""
self.verbose, self.indent = verbose, indent
if verbose > 0:
print(indent+'mview.MPSE():')
##set up sets of distances from data
self.distances = setup.setup_distances_from_multiple_perspectives(
data, data_args)
self.n_perspectives = len(self.distances)
self.n_samples = scipy.spatial.distance.num_obs_y(self.distances[0])
##set up weights from data
if isinstance(weights,list) or isinstance(weights, np.ndarray):
assert len(weights) == self.n_perspectives
self.weights = weights
else:
self.weights = [weights]*self.n_perspectives
for i in range(self.n_perspectives):
self.weights[i] = setup.setup_weights(self.distances[i], \
self.weights[i], min_weight = 0)
##set up parameters
self.embedding_dimension = embedding_dimension
self.image_dimension = image_dimension
self.projection_family = projection_family
self.projection_constraint = projection_constraint
proj = projections.PROJ(embedding_dimension,image_dimension,
projection_family,projection_constraint)
self.proj = proj
##set up hidden samples
if hidden_samples is not None:
assert isinstance(hidden_samples, list)
assert len(hidden_samples) == self.n_perspectives
self.hidden_samples = hidden_samples
if verbose > 0:
print(indent+' data details:')
print(indent+f' number of perspectives : {self.n_perspectives}')
print(indent+f' number of samples : {self.n_samples}')
print(indent+' visualization details:')
print(indent+' embedding dimension :',self.embedding_dimension)
print(indent+f' image dimension : {self.image_dimension}')
print(indent+f' visualization type : {visualization_method}')
#setup sample labels:
if sample_labels is not None:
assert len(sample_labels) == self.n_samples
self.sample_labels = sample_labels
#setup perspective labels:
if perspective_labels is None:
perspective_labels = range(1,self.n_perspectives+1)
else:
assert len(perspective_labels) == self.n_perspectives
self.perspective_labels = perspective_labels
#setup colors:
self.sample_colors = sample_colors
self.image_colors = image_colors
#setup visualization instances:
self.visualization_instances = []
self.visualization_method = visualization_method
if isinstance(visualization_method,str):
visualization_method = [visualization_method]*self.n_perspectives
if isinstance(visualization_args,dict):
visualization_args = [visualization_args]*self.n_perspectives
for i in range(self.n_perspectives):
assert visualization_method[i] in ['mds','tsne']
if self.verbose > 0:
print(' setup visualization instance for perspective',
self.perspective_labels[i],':')
if visualization_method[i] == 'mds':
vis = mds.MDS(self.distances[i],
weights = self.weights[i],
embedding_dimension=self.image_dimension,
verbose=self.verbose, indent=self.indent+' ',
**visualization_args[i])
elif visualization_method[i] == 'tsne':
vis = tsne.TSNE(self.distances[i],
embedding_dimension=self.image_dimension,
verbose=self.verbose, indent=self.indent+' ',
**visualization_args[i])
self.visualization_instances.append(vis)
self.visualization = self.visualization_instances
#setup objectives:
if total_cost_function == 'rms':
self.total_cost_function = lambda individual_costs : \
np.sqrt(np.sum(individual_costs**2)/self.n_perspectives)
else:
assert callable(total_cost_function)
self.total_cost_function = total_cost_function
def cost_function(X,Q,Y=None,**kwargs):
if Y is None:
Y = self.proj.project(Q,X)
individual_costs = np.zeros(self.n_perspectives)
for k in range(self.n_perspectives):
individual_costs[k] = \
self.visualization[k].objective(Y[k],**kwargs)
cost = self.total_cost_function(individual_costs)
return cost, individual_costs
self.cost_function = cost_function
#setup gradient function:
if self.projection_family == 'linear':
def gradient(embedding,projections,batch_size=None,indices=None,
return_embedding=True,return_projections=True,
return_cost=True, return_individual_costs=False):
"""\
Returns MPSE gradient(s), along with cost and individual costs
(optional).
Parameters
----------
embedding : numpy array
Current embedding.
projections : numpy array
Current projections (as a single array).
return_embedding : boolean
If True, returns MPSE gradient w.r.t. embedding.
return_projections : boolean
If True, returns MPSE gradient w.r.t. projections.
return_cost : boolean
If True, returns MPSE cost.
return_individual_costs : boolean
If True, returns individual embedding costs.
"""
if return_embedding:
dX = np.zeros(embedding.shape)
if return_projections:
dQ = []
individual_costs = np.empty(self.n_perspectives)
Y = self.proj.project(projections,embedding)
for k in range(self.n_perspectives):
dY_k, cost_k = self.visualization[k].gradient(
Y[k],batch_size=batch_size,indices=indices)
individual_costs[k] = cost_k
if return_embedding:
dX += dY_k @ projections[k][:2, :3]
if return_projections:
dQ.append(dY_k.T @ embedding)
if return_embedding:
dX /= self.n_perspectives
cost = self.total_cost_function(individual_costs)
if return_embedding is False:
grad = np.array(dQ)
elif return_projections is False:
grad = dX
else:
grad = [dX,np.array(dQ)]
if return_individual_costs:
return grad, cost, individual_costs
else:
return grad, cost
self.gradient = gradient
else:
def gradient_X(X,Q,Y=None):
pgradient = self.proj.compute_gradient(X[0],params_list=Q)
if Y is None:
Y = self.proj.project(X,params_list=Q)
gradient = np.zeros((self.n_samples,self.embedding_dimension))
for k in range(self.n_perspectives):
gradient += self.visualization[k].gradient(Y[k]) \
@ pgradient[k]
return gradient
self.gradient_X = gradient_X
#set up initial embedding and projections (fixed optional):
if verbose > 0:
print(indent+' initialize:')
#set fixed and initial embedding:
if fixed_embedding is not None:
if verbose > 0:
print(indent+' fixed embedding : True')
self.embedding = fixed_embedding
self.initial_embedding = fixed_embedding
self.fixed_embedding = True
else:
if verbose > 0:
print(indent+' fixed embedding : False')
if initial_embedding is None:
if verbose > 0:
print(indent+' initial embedding : random')
self.initial_embedding = misc.initial_embedding(
self.n_samples,dim=self.embedding_dimension, radius=1)
else:
assert isinstance(initial_embedding,np.ndarray)
assert initial_embedding.shape == (
self.n_samples, self.embedding_dimension)
if verbose > 0:
print(indent+' initial embedding : given')
self.initial_embedding = initial_embedding
self.embedding = self.initial_embedding
self.fixed_embedding = False
#set fixed and initial projections:
if fixed_projections is not None:
if isinstance(fixed_projections,str):
fixed_projections = self.proj.generate(number= \
self.n_perspectives,method=fixed_projections)
assert(all([isinstance(fp,np.ndarray) for fp in fixed_projections]))
fixed_projections = [f[:2, :3] for f in fixed_projections]
self.projections = fixed_projections
self.initial_projections = fixed_projections
self.fixed_projections = True
if verbose > 0:
print(indent+' fixed projections : True')
else:
if verbose > 0:
print(indent+' fixed projections : False')
if initial_projections is None:
if verbose > 0:
print(indent+' initial projections : random')
self.initial_projections = self.proj.generate(
number=self.n_perspectives, **kwargs)
else:
if verbose > 0:
print(indent+' initial projections : given')
if isinstance(initial_projections,str):
initial_projections = self.proj.generate(number= \
self.n_perspectives,method=initial_projections)
self.initial_projections = initial_projections
self.projections = self.initial_projections
self.fixed_projections = False
print(indent+' Projection is:')
print(self.projections)
self.initial_cost = None
self.initial_individual_cost = None
self.computation_history = []
self.time = 0
self.update(**kwargs)
def __init__(self,
data,
dim=2,
weights=None,
estimate=True,
safety=1e-4,
normalize=True,
initial_embedding='random',
sample_colors=None,
verbose=0,
indent='',
**kwargs):
"""\
Initializes MDS object.
Parameters:
data : array or dictionary
Distance/dissimilarity/feature data, which can have any of the
following formats:
1) a 1D condensed distance array
2) a square distance matrix/array
3) a feature array
4) a dictionary describing a graph
dim : int > 0
Embedding dimension.
weights : None or str or callable or array
Weights to be used in defining MDS stress.
verbose : int >= 0
Print status of methods in MDS object if verbose > 0.
indent : str
When printing, add indent before printing every new line.
"""
self.verbose = verbose
self.indent = indent
if self.verbose > 0:
print(self.indent + 'mview.MDS():')
self.distances = setup.setup_distances(data, **kwargs)
self.n_samples = scipy.spatial.distance.num_obs_y(self.distances)
if safety is None:
self.minimum_distance = None
else:
assert safety > 0 and safety <= 1e-2
self.minimum_distance = np.max(self.distances) * safety
self.distances = np.maximum(self.distances, self.minimum_distance)
self.weights = setup.setup_weights(self.distances, weights=weights)
self.normalize = normalize
if sample_colors is None:
self.sample_colors = self.distances[0:self.n_samples]
else:
self.sample_colors = sample_colors
assert isinstance(dim, int)
assert dim > 0
self.dim = dim
assert isinstance(estimate, bool)
self.estimate = estimate
self.objective = lambda X, **kwargs: stress(
self.distances, X, weights=self.weights, normalize=self.normalize)
def gradient(embedding, batch_size=None, indices=None, **kwargs):
if batch_size is None or batch_size >= self.n_samples:
return full_gradient(self.distances,
embedding,
weights=self.weights,
normalize=self.normalize,
minimum_distance=self.minimum_distance)
else:
return batch_gradient(self.distances,
embedding,
batch_size,
indices,
weights=self.weights,
normalize=self.normalize,
minimum_distance=self.minimum_distance)
self.gradient = gradient
if verbose > 0:
print(indent + ' data details:')
print(indent + f' number of samples : {self.n_samples}')
if self.weights is None:
print(indent + f' weighted : False')
else:
print(indent + f' weighted : True')
print(indent + ' embedding details:')
print(indent + f' embedding dimension : {self.dim}')
#save or compute initial embedding
if isinstance(initial_embedding, np.ndarray):
assert initial_embedding.shape == (self.n_samples, self.dim)
if self.verbose > 0:
print(' initial embedding : given')
self.X0 = initial_embedding
self.X = self.X0
elif initial_embedding == 'random':
self.X0 = misc.initial_embedding(self.n_samples,
dim=self.dim,
radius=1,
**kwargs)
self.X = self.X0
if self.verbose > 0:
print(' initial embedding : random')
else:
assert initial_embedding is None
#save initial costs
if initial_embedding is not None:
self.initial_cost = self.objective(self.X0, **kwargs)
self.cost = self.initial_cost
if self.verbose > 0:
print(f' initial stress : {self.cost:0.2e}')
self.computation_history = []
