def initialized_nnd_search(
data, indptr, indices, initialization, query_points, dist, dist_args
):
for i in numba.prange(query_points.shape[0]):
tried = set(initialization[0, i])
while True:
# Find smallest flagged vertex
vertex = smallest_flagged(initialization, i)
if vertex == -1:
break
candidates = indices[indptr[vertex] : indptr[vertex + 1]]
for j in range(candidates.shape[0]):
if (
candidates[j] == vertex
or candidates[j] == -1
or candidates[j] in tried
):
continue
d = dist(data[candidates[j]], query_points[i], *dist_args)
unchecked_heap_push(initialization, i, d, candidates[j], 1)
tried.add(candidates[j])
return initialization
def initialize_heaps(data,
n_neighbors,
leaf_array,
dist=dist.euclidean,
dist_args=()):
graph_heap = make_heap(data.shape[0], 10)
search_heap = make_heap(data.shape[0], n_neighbors * 2)
tried = set([(-1, -1)])
for n in range(leaf_array.shape[0]):
for i in range(leaf_array.shape[1]):
if leaf_array[n, i] < 0:
break
for j in range(i + 1, leaf_array.shape[1]):
if leaf_array[n, j] < 0:
break
if (leaf_array[n, i], leaf_array[n, j]) in tried:
continue
d = dist(data[leaf_array[n, i]], data[leaf_array[n, j]],
*dist_args)
unchecked_heap_push(graph_heap, leaf_array[n, i], d,
leaf_array[n, j], 1)
unchecked_heap_push(graph_heap, leaf_array[n, j], d,
leaf_array[n, i], 1)
unchecked_heap_push(search_heap, leaf_array[n, i], d,
leaf_array[n, j], 1)
unchecked_heap_push(search_heap, leaf_array[n, j], d,
leaf_array[n, i], 1)
tried.add((leaf_array[n, i], leaf_array[n, j]))
tried.add((leaf_array[n, j], leaf_array[n, i]))
return graph_heap, search_heap
def sparse_initialized_nnd_search(
inds,
indptr,
data,
search_indptr,
search_inds,
initialization,
query_inds,
query_indptr,
query_data,
sparse_dist,
dist_args,
):
for i in numba.prange(query_indptr.shape[0] - 1):
tried = set(initialization[0, i])
to_inds = query_inds[query_indptr[i]:query_indptr[i + 1]]
to_data = query_data[query_indptr[i]:query_indptr[i + 1]]
while True:
# Find smallest flagged vertex
vertex = smallest_flagged(initialization, i)
if vertex == -1:
break
candidates = search_inds[search_indptr[vertex]:search_indptr[vertex
+ 1]]
for j in range(candidates.shape[0]):
if (candidates[j] == vertex or candidates[j] == -1
or candidates[j] in tried):
continue
from_inds = inds[indptr[candidates[j]]:indptr[candidates[j] +
1]]
from_data = data[indptr[candidates[j]]:indptr[candidates[j] +
1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data,
*dist_args)
unchecked_heap_push(initialization, i, d, candidates[j], 1)
tried.add(candidates[j])
return initialization
def nn_descent(
data,
n_neighbors,
rng_state,
max_candidates=50,
dist=dist.euclidean,
dist_args=(),
n_iters=10,
delta=0.001,
rho=0.5,
rp_tree_init=True,
leaf_array=None,
verbose=False,
seed_per_row=False,
):
n_vertices = data.shape[0]
tried = set([(-1, -1)])
current_graph = make_heap(data.shape[0], n_neighbors)
for i in range(data.shape[0]):
if seed_per_row:
seed(rng_state, i)
indices = rejection_sample(n_neighbors, data.shape[0], rng_state)
for j in range(indices.shape[0]):
d = dist(data[i], data[indices[j]], *dist_args)
heap_push(current_graph, i, d, indices[j], 1)
heap_push(current_graph, indices[j], d, i, 1)
tried.add((i, indices[j]))
tried.add((indices[j], i))
if rp_tree_init:
init_rp_tree(data,
dist,
dist_args,
current_graph,
leaf_array,
tried=tried)
for n in range(n_iters):
if verbose:
print("\t", n, " / ", n_iters)
(new_candidate_neighbors,
old_candidate_neighbors) = new_build_candidates(
current_graph,
n_vertices,
n_neighbors,
max_candidates,
rng_state,
rho,
seed_per_row,
)
c = 0
for i in range(n_vertices):
for j in range(max_candidates):
p = int(new_candidate_neighbors[0, i, j])
if p < 0:
continue
for k in range(j, max_candidates):
q = int(new_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
d = dist(data[p], data[q], *dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
for k in range(max_candidates):
q = int(old_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
d = dist(data[p], data[q], *dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
if c <= delta * n_neighbors * data.shape[0]:
break
return deheap_sort(current_graph)
def sparse_nn_descent_internal_high_memory(
current_graph,
inds,
indptr,
data,
n_vertices,
n_neighbors,
rng_state,
tried,
max_candidates=50,
sparse_dist=sparse_euclidean,
dist_args=(),
n_iters=10,
delta=0.001,
rho=0.5,
verbose=False,
):
for n in range(n_iters):
if verbose:
print("\t", n, " / ", n_iters)
(new_candidate_neighbors,
old_candidate_neighbors) = new_build_candidates(
current_graph,
n_vertices,
n_neighbors,
max_candidates,
rng_state,
rho,
False,
)
c = 0
for i in range(n_vertices):
for j in range(max_candidates):
p = int(new_candidate_neighbors[0, i, j])
if p < 0:
continue
for k in range(j, max_candidates):
q = int(new_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
from_inds = inds[indptr[p]:indptr[p + 1]]
from_data = data[indptr[p]:indptr[p + 1]]
to_inds = inds[indptr[q]:indptr[q + 1]]
to_data = data[indptr[q]:indptr[q + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data,
*dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
for k in range(max_candidates):
q = int(old_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
from_inds = inds[indptr[p]:indptr[p + 1]]
from_data = data[indptr[p]:indptr[p + 1]]
to_inds = inds[indptr[q]:indptr[q + 1]]
to_data = data[indptr[q]:indptr[q + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data,
*dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
if c <= delta * n_neighbors * n_vertices:
return
def nn_descent_internal_high_memory(
current_graph,
data,
n_neighbors,
rng_state,
tried,
max_candidates=50,
dist=dist.euclidean,
dist_args=(),
n_iters=10,
delta=0.001,
rho=0.5,
verbose=False,
seed_per_row=False,
):
n_vertices = data.shape[0]
for n in range(n_iters):
if verbose:
print("\t", n, " / ", n_iters)
(new_candidate_neighbors,
old_candidate_neighbors) = new_build_candidates(
current_graph,
n_vertices,
n_neighbors,
max_candidates,
rng_state,
rho,
seed_per_row,
)
c = 0
for i in range(n_vertices):
for j in range(max_candidates):
p = int(new_candidate_neighbors[0, i, j])
if p < 0:
continue
for k in range(j, max_candidates):
q = int(new_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
d = dist(data[p], data[q], *dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
for k in range(max_candidates):
q = int(old_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
d = dist(data[p], data[q], *dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
if c <= delta * n_neighbors * data.shape[0]:
return
def sparse_nn_descent(
inds,
indptr,
data,
n_vertices,
n_neighbors,
rng_state,
max_candidates=50,
sparse_dist=sparse_euclidean,
dist_args=(),
n_iters=10,
delta=0.001,
rho=0.5,
rp_tree_init=True,
leaf_array=None,
verbose=False,
):
tried = set([(-1, -1)])
current_graph = make_heap(n_vertices, n_neighbors)
for i in range(n_vertices):
indices = rejection_sample(n_neighbors, n_vertices, rng_state)
for j in range(indices.shape[0]):
from_inds = inds[indptr[i]:indptr[i + 1]]
from_data = data[indptr[i]:indptr[i + 1]]
to_inds = inds[indptr[indices[j]]:indptr[indices[j] + 1]]
to_data = data[indptr[indices[j]]:indptr[indices[j] + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data, *dist_args)
heap_push(current_graph, i, d, indices[j], 1)
heap_push(current_graph, indices[j], d, i, 1)
tried.add((i, indices[j]))
tried.add((indices[j], i))
if rp_tree_init:
sparse_init_rp_tree(
inds,
indptr,
data,
sparse_dist,
dist_args,
current_graph,
leaf_array,
tried=tried,
)
for n in range(n_iters):
if verbose:
print("\t", n, " / ", n_iters)
(new_candidate_neighbors,
old_candidate_neighbors) = new_build_candidates(
current_graph,
n_vertices,
n_neighbors,
max_candidates,
rng_state,
rho,
False,
)
c = 0
for i in range(n_vertices):
for j in range(max_candidates):
p = int(new_candidate_neighbors[0, i, j])
if p < 0:
continue
for k in range(j, max_candidates):
q = int(new_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
from_inds = inds[indptr[p]:indptr[p + 1]]
from_data = data[indptr[p]:indptr[p + 1]]
to_inds = inds[indptr[q]:indptr[q + 1]]
to_data = data[indptr[q]:indptr[q + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data,
*dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
for k in range(max_candidates):
q = int(old_candidate_neighbors[0, i, k])
if q < 0 or (p, q) in tried:
continue
from_inds = inds[indptr[p]:indptr[p + 1]]
from_data = data[indptr[p]:indptr[p + 1]]
to_inds = inds[indptr[q]:indptr[q + 1]]
to_data = data[indptr[q]:indptr[q + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data,
*dist_args)
c += unchecked_heap_push(current_graph, p, d, q, 1)
tried.add((p, q))
if p != q:
c += unchecked_heap_push(current_graph, q, d, p, 1)
tried.add((q, p))
if c <= delta * n_neighbors * n_vertices:
break
return deheap_sort(current_graph)
