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grinch's Issues

The python code results on simple clustering example show things have serious bug or do work at all!

Give you a simple example: [1,2, 10,11,12, 54]. Your python code generates a completely wrong clustering tree.
I figured out the starting insert a new data point from 10 becomes completely misleading. It breaks 1 and 2 pairs which should be not!
In fact to get valid nearest neighbor you need search up the whole tree without breaking tighter sibling pairs.
Your introduction example using high dimension random numbers fool yourself and others who try to validate the algorithm.
Without correction I think that your work is not serious at all!

Python example is broken

Hi there,

The python version of the code is currently broken. There seem to be an assertion that fails. See the full error below.

$ python src/python/grinch/run_grinch_example.py
wandb: (1) Create a W&B account
wandb: (2) Use an existing W&B account
wandb: (3) Don't visualize my results
wandb: Enter your choice: 3
wandb: You chose 'Don't visualize my results'
wandb: Offline run mode, not syncing to the cloud.
wandb: W&B syncing is set to `offline` in this directory.  Run `wandb online` to enable cloud syncing.
/Users/istefan/workspace/grinch/src/python/grinch/run_grinch_example.py:9: DeprecationWarning: This function is deprecated. Please call randint(0, 10 + 1) instead
  point_labels = np.random.random_integers(0,10,100)
INFO:absl:[Grinch] points (100, 5)
INFO:absl:Using centroid = l2
INFO:absl:Using csim = dot
grinch_build_dendrogram:   1%|          | 1/100 [00:00<00:00, 597.73it/s]
Traceback (most recent call last):
  File "/Users/istefan/workspace/grinch/src/python/grinch/run_grinch_example.py", line 12, in <module>
    grinch.build_dendrogram()
  File "/Users/istefan/workspace/grinch/src/python/grinch/grinch_alg.py", line 507, in build_dendrogram
    self.insert(i)
  File "/Users/istefan/workspace/grinch/src/python/grinch/grinch_alg.py", line 520, in insert
    parent = self.node_from_nodes(sib, i)
  File "/Users/istefan/workspace/grinch/src/python/grinch/grinch_alg.py", line 487, in node_from_nodes
    assert self.next_node_id >= self.max_num_points
AssertionError

wandb: Waiting for W&B process to finish, PID 51394
wandb: Program failed with code 1.
wandb: Find user logs for this run at: /Users/istefan/workspace/grinch/wandb/offline-run-20210107_185142-15tc99ou/logs/debug.log
wandb: Find internal logs for this run at: /Users/istefan/workspace/grinch/wandb/offline-run-20210107_185142-15tc99ou/logs/debug-internal.log
wandb: Run summary:
wandb:                        time/search_time 0
wandb:                        time/rotate_time 0
wandb:                         time/graft_time 0
wandb:                        time/update_time 0
wandb:              time/graft_score_only_time 0
wandb:                  time/graft_search_time 0
wandb:        time/graft_get_comparison_scores 0
wandb:   time/find_dependent_update_nodes_time 0
wandb:          time/mark_for_lazy_update_time 0
wandb:           time/time_getting_descendants 0
wandb:                           time/lca_time 0
wandb:                      time/centroid_time 0
wandb:                  rotate/total_performed 0
wandb:                 rotate/total_considered 0
wandb:                   rotate/inst_performed 0
wandb:                  rotate/inst_considered 0
wandb:                   graft/total_performed 0
wandb:                  graft/total_considered 0
wandb:                   graft/total_allowable 0
wandb:                 graft/percent_allowable 0.0
wandb:                    graft/inst_performed 0
wandb:                           point_counter 0
wandb:                                   _step 0
wandb:                                _runtime 4
wandb:                              _timestamp 1610045506
wandb: Run history:
wandb:                        time/search_time ▁
wandb:                        time/rotate_time ▁
wandb:                         time/graft_time ▁
wandb:                        time/update_time ▁
wandb:              time/graft_score_only_time ▁
wandb:                  time/graft_search_time ▁
wandb:        time/graft_get_comparison_scores ▁
wandb:   time/find_dependent_update_nodes_time ▁
wandb:          time/mark_for_lazy_update_time ▁
wandb:           time/time_getting_descendants ▁
wandb:                           time/lca_time ▁
wandb:                      time/centroid_time ▁
wandb:                  rotate/total_performed ▁
wandb:                 rotate/total_considered ▁
wandb:                   rotate/inst_performed ▁
wandb:                  rotate/inst_considered ▁
wandb:                   graft/total_performed ▁
wandb:                  graft/total_considered ▁
wandb:                   graft/total_allowable ▁
wandb:                 graft/percent_allowable ▁
wandb:                    graft/inst_performed ▁
wandb:                           point_counter ▁
wandb:                                   _step ▁
wandb:                                _runtime ▁
wandb:                              _timestamp ▁
wandb:
wandb: You can sync this run to the cloud by running:
wandb: wandb sync /Users/istefan/workspace/grinch/wandb/offline-run-20210107_185142-15tc99ou

In case this matters for debugging, these are the packages I have installed in my environment:

$ pip list
Package         Version
--------------- ---------
absl-py         0.11.0
certifi         2020.12.5
chardet         4.0.0
click           7.1.2
configparser    5.0.1
docker-pycreds  0.4.0
gitdb           4.0.5
GitPython       3.1.12
idna            2.10
numpy           1.19.5
pip             20.3.1
promise         2.3
protobuf        3.14.0
psutil          5.8.0
python-dateutil 2.8.1
PyYAML          5.3.1
requests        2.25.1
scipy           1.6.0
sentry-sdk      0.19.5
setuptools      51.0.0
shortuuid       1.0.1
six             1.15.0
smmap           3.0.4
subprocess32    3.5.4
tqdm            4.55.1
urllib3         1.26.2
wandb           0.10.12
watchdog        1.0.2
wheel           0.36.1

Please let me know if you have suggestions how to fix this.

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