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2022 0630 update #3

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2022 0630 update #3

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69a5cb9
Removed unused self assignments and class variable assignments
sarvo-madhavan Dec 17, 2021
77579b2
Removed additional variables from memory for GC
sarvo-madhavan Dec 17, 2021
bd8d899
Reduced Float Size
sarvo-madhavan Dec 18, 2021
1df1245
fixed clustering issue
bethanne-card Aug 2, 2022
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6 changes: 4 additions & 2 deletions src/python/grinch/agglom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,23 +90,24 @@ def build_dendrogram_hac(self):
"""Run HAC inference."""
st_sims = time.time()
sims = self.csim_multi_feature_knn_batched(np.arange(self.num_points), np.arange(self.num_points))
self.sims = sims
en_sims = time.time()
logging.info('Time to compute sims: %s', en_sims - st_sims)
logging.info('Finished batched similarities!')
st_prep = time.time()
pos_sim = np.maximum(sims, self.min_allowable_sim) - np.minimum(0.0, self.min_allowable_sim)
del sims
dists = 1 / (1 + pos_sim)
del pos_sim
dists = (dists + dists.T) / 2.0
np.fill_diagonal(dists, 0.0)
dists = squareform(dists)
self.dists = dists
en_prep = time.time()
logging.info('Time to compute sims: %s', en_prep - st_prep)
logging.info('Finished preparing distances!')
logging.info('Running hac')
st_linkage = time.time()
Z = linkage(dists, method='average')
del dists
self.Z = Z
en_linkage = time.time()
logging.info('Time to run HAC: %s', en_linkage - st_linkage)
Expand Down Expand Up @@ -311,3 +312,4 @@ def c_dot_feature_sparse(self, idx, c_i, c_j):
def c_dot_feature_sparse_knn(self, idx, c_i, c_j):
res = (c_i @ c_j.T).todense().A
return torch.from_numpy(res.astype(np.float32))