def __init__(
self,
profile: sps.csr_matrix,
embedding: np.ndarray,
search_config: Optional[MLPSearchConfig] = None,
):
(
profile_train,
profile_test,
embedding_train,
embedding_test,
) = train_test_split(
profile.astype(np.float32),
embedding.astype(np.float32),
random_state=42,
)
self.profile_train = profile_train
self.profile_test = profile_test
self.embedding_train = jnp.asarray(embedding_train, dtype=jnp.float32)
self.embedding_test = jnp.asarray(embedding_test, dtype=jnp.float32)
if search_config is None:
self.search_config = MLPSearchConfig()
else:
self.search_config = search_config
def saveSparseMatrix(file: str,
matrix: csr_matrix,
colnames: Union[List[str], None] = None) -> None:
""" Save sparse matrix to json file
Args:
ile: file name to store results, full or relative path
matrix (M,N): sparse matrix of size (M,N)
colnames, optional (1,N): column names
Returns:
None
"""
json_content = dict()
if colnames is not None:
json_content["features"] = colnames
json_content["size"] = matrix.shape
matrix = matrix.astype(float)
keys = matrix.todok().keys()
keys = [tuple(map(int, key)) for key in keys]
vals = matrix.todok().values()
vals = list(map(float, vals))
json_content["positions"] = keys
json_content["counts"] = vals
with open(file, "w") as f:
json.dump(json_content, f, indent=4)
def precompute_best_item_indices(self, URM: sps.csr_matrix):
URM = URM.copy()
if self.feature_weighting == "BM25":
URM = URM.astype(np.float32)
URM = okapi_BM_25(URM)
URM = check_matrix(URM, 'csr')
elif self.feature_weighting == "TF-IDF":
URM = URM.astype(np.float32)
URM = TF_IDF(URM)
URM = check_matrix(URM, 'csr')
similarity = Compute_Similarity(URM,
shrink=self.shrink,
topK=self.topK,
normalize=self.normalize,
similarity="cosine")
similarity_matrix = similarity.compute_similarity()
self.sorted_indices = np.array(
np.argsort(-similarity_matrix.todense(), axis=1))
def calculate_diffusion_map(
W: csr_matrix, n_components: int, solver: str, max_t: int, n_jobs: int, random_state: int,
) -> Tuple[np.array, np.array, np.array]:
assert issparse(W)
nc, labels = connected_components(W, directed=True, connection="strong")
logger.info("Calculating connected components is done.")
assert nc == 1
W_norm, diag, diag_half = calculate_normalized_affinity(W.astype(np.float64)) # use double precision to guarantee reproducibility
logger.info("Calculating normalized affinity matrix is done.")
n_jobs = eff_n_jobs(n_jobs)
with threadpool_limits(limits = n_jobs):
if solver == "eigsh":
np.random.seed(random_state)
v0 = np.random.uniform(-1.0, 1.0, W_norm.shape[0])
Lambda, U = eigsh(W_norm, k=n_components, v0=v0)
Lambda = Lambda[::-1]
U = U[:, ::-1]
else:
assert solver == "randomized"
U, S, VT = randomized_svd(
W_norm, n_components=n_components, random_state=random_state
)
signs = np.sign((U * VT.transpose()).sum(axis=0)) # get eigenvalue signs
Lambda = signs * S # get eigenvalues
# remove the first eigen value and vector
Lambda = Lambda[1:]
U = U[:, 1:]
Phi = U / diag_half[:, np.newaxis]
if max_t == -1:
Lambda_new = Lambda / (1.0 - Lambda)
else:
# Find the knee point
x = np.array(range(1, max_t + 1), dtype = float)
y = np.array([calc_von_neumann_entropy(Lambda, t) for t in x])
t = x[find_knee_point(x, y)]
logger.info("Detected knee point at t = {:.0f}.".format(t))
# U_df = U * Lambda #symmetric diffusion component
Lambda_new = Lambda * ((1.0 - Lambda ** t) / (1.0 - Lambda))
Phi_pt = Phi * Lambda_new # asym pseudo component
return Phi_pt, Lambda, Phi # , U_df, W_norm
def _secondary_outputs(self, input_matrix: sparse.csr_matrix):
"""Compute different variables from labels_."""
if self.return_membership or self.return_aggregate:
if np.issubdtype(input_matrix.data.dtype, np.bool_):
input_matrix = input_matrix.astype(float)
if not self.bipartite:
membership = membership_matrix(self.labels_)
if self.return_membership:
self.membership_ = normalize(input_matrix.dot(membership))
if self.return_aggregate:
self.aggregate_ = sparse.csr_matrix(
membership.T.dot(input_matrix.dot(membership)))
else:
if self.labels_col_ is None:
n_labels = max(self.labels_) + 1
membership_row = membership_matrix(self.labels_,
n_labels=n_labels)
membership_col = normalize(
input_matrix.T.dot(membership_row))
else:
n_labels = max(max(self.labels_row_), max(
self.labels_col_)) + 1
membership_row = membership_matrix(self.labels_row_,
n_labels=n_labels)
membership_col = membership_matrix(self.labels_col_,
n_labels=n_labels)
if self.return_membership:
self.membership_row_ = normalize(
input_matrix.dot(membership_col))
self.membership_col_ = normalize(
input_matrix.T.dot(membership_row))
self.membership_ = self.membership_row_
if self.return_aggregate:
aggregate_ = sparse.csr_matrix(
membership_row.T.dot(input_matrix))
aggregate_ = aggregate_.dot(membership_col)
self.aggregate_ = aggregate_
return self
def tree_sampling_divergence(adjacency: sparse.csr_matrix,
dendrogram: np.ndarray,
weights: str = 'degree',
normalized: bool = True) -> float:
"""Tree sampling divergence of a hierarchy (quality metric).
* Graphs
* Digraphs
Parameters
----------
adjacency :
Adjacency matrix of the graph.
dendrogram :
Dendrogram.
weights :
Weights of nodes.
``'degree'`` (default) or ``'uniform'``.
normalized :
If ``True``, normalized score (between 0 and 1).
Returns
-------
score : float
Score.
Example
-------
>>> from sknetwork.hierarchy import tree_sampling_divergence, Paris
>>> from sknetwork.data import house
>>> paris = Paris()
>>> adjacency = house()
>>> dendrogram = paris.fit_transform(adjacency)
>>> score = tree_sampling_divergence(adjacency, dendrogram)
>>> np.round(score, 2)
0.52
References
----------
Charpentier, B. & Bonald, T. (2019).
`Tree Sampling Divergence: An Information-Theoretic Metric for
Hierarchical Graph Clustering.
<https://hal.telecom-paristech.fr/hal-02144394/document>`_
Proceedings of IJCAI.
"""
adjacency = check_format(adjacency)
check_square(adjacency)
check_min_nnz(adjacency.nnz, 1)
adjacency = adjacency.astype(float)
n = adjacency.shape[0]
check_min_size(n, 2)
adjacency.data /= adjacency.data.sum()
aggregate_graph, height, cluster_weight, edge_sampling, weights_row, weights_col = _instanciate_vars(
adjacency, weights)
node_sampling = np.zeros(n - 1)
for t in range(n - 1):
i = int(dendrogram[t][0])
j = int(dendrogram[t][1])
if i >= n and height[i - n] == dendrogram[t][2]:
edge_sampling[t] = edge_sampling[i - n]
edge_sampling[i - n] = 0
node_sampling[t] = node_sampling[i - n]
elif j >= n and height[j - n] == dendrogram[t][2]:
edge_sampling[t] = edge_sampling[j - n]
edge_sampling[j - n] = 0
node_sampling[t] = node_sampling[j - n]
if j in aggregate_graph.neighbors[i]:
edge_sampling[t] += aggregate_graph.neighbors[i][j]
node_sampling[t] += aggregate_graph.cluster_out_weights[i] * aggregate_graph.cluster_in_weights[j] + \
aggregate_graph.cluster_out_weights[j] * aggregate_graph.cluster_in_weights[i]
height[t] = dendrogram[t][2]
aggregate_graph.merge(i, j)
index = np.where(edge_sampling)[0]
score = edge_sampling[index].dot(
np.log(edge_sampling[index] / node_sampling[index]))
if normalized:
inv_out_weights = sparse.diags(weights_row, shape=(n, n), format='csr')
inv_out_weights.data = 1 / inv_out_weights.data
inv_in_weights = sparse.diags(weights_col, shape=(n, n), format='csr')
inv_in_weights.data = 1 / inv_in_weights.data
sampling_ratio = inv_out_weights.dot(adjacency.dot(inv_in_weights))
inv_out_weights.data = np.ones(len(inv_out_weights.data))
inv_in_weights.data = np.ones(len(inv_in_weights.data))
edge_sampling = inv_out_weights.dot(adjacency.dot(inv_in_weights))
mutual_information = edge_sampling.data.dot(np.log(
sampling_ratio.data))
score /= mutual_information
return score
def get_score(self, profile: sps.csr_matrix) -> DenseScoreArray:
user_embedding: DenseMatrix = self.mlp.predict(
profile.astype(np.float32).toarray())
return self.cf_rec.get_score_from_user_embedding(
user_embedding).astype(np.float64)
def tree_sampling_divergence(adjacency: sparse.csr_matrix,
dendrogram: np.ndarray,
weights: str = 'degree',
normalized: bool = True) -> float:
"""Tree sampling divergence of a hierarchy (quality metric).
Parameters
----------
adjacency :
Adjacency matrix of the graph.
dendrogram :
Dendrogram.
weights :
Weights of nodes.
``'degree'`` (default) or ``'uniform'``.
normalized :
If ``True``, normalized score (between 0 and 1).
Returns
-------
score : float
Score.
Example
-------
>>> from sknetwork.hierarchy import tree_sampling_divergence, Paris
>>> from sknetwork.data import house
>>> paris = Paris()
>>> adjacency = house()
>>> dendrogram = paris.fit_transform(adjacency)
>>> score = tree_sampling_divergence(adjacency, dendrogram)
>>> np.round(score, 2)
0.05
References
----------
Charpentier, B. & Bonald, T. (2019).
`Tree Sampling Divergence: An Information-Theoretic Metric for
Hierarchical Graph Clustering.
<https://hal.telecom-paristech.fr/hal-02144394/document>`_
Proceedings of IJCAI.
"""
adjacency = check_format(adjacency)
check_square(adjacency)
check_min_nnz(adjacency.nnz, 1)
adjacency = adjacency.astype(float)
n = adjacency.shape[0]
check_min_size(n, 2)
adjacency.data /= adjacency.data.sum()
edge_sampling, node_sampling, _ = get_sampling_distributions(
adjacency, dendrogram, weights)
index = np.where(edge_sampling)[0]
score = edge_sampling[index].dot(
np.log(edge_sampling[index] / node_sampling[index]))
if normalized:
weights_row = get_probs(weights, adjacency)
weights_col = get_probs(weights, adjacency.T)
inv_out_weights = sparse.diags(weights_row, shape=(n, n), format='csr')
inv_out_weights.data = 1 / inv_out_weights.data
inv_in_weights = sparse.diags(weights_col, shape=(n, n), format='csr')
inv_in_weights.data = 1 / inv_in_weights.data
sampling_ratio = inv_out_weights.dot(adjacency.dot(inv_in_weights))
inv_out_weights.data = np.ones(len(inv_out_weights.data))
inv_in_weights.data = np.ones(len(inv_in_weights.data))
edge_sampling = inv_out_weights.dot(adjacency.dot(inv_in_weights))
mutual_information = edge_sampling.data.dot(np.log(
sampling_ratio.data))
if mutual_information > 0:
score /= mutual_information
return score