groceryheist/cdsc_reddit
1
0
Fork 0
Code

add 2 more umap parameters

Browse Source
This commit is contained in:
Nathan TeBlunthuis 2022-06-08 17:27:37 -07:00
parent 5a40465a62
commit c190791364
4 changed files with 32 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
clustering/Makefile
View File

@ -1,10 +1,10 @@
#srun_cdsc='srun -p comdata-int -A comdata --time=300:00:00 --time-min=00:15:00 --mem=100G --ntasks=1 --cpus-per-task=28'
srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
srun_singularity=srun -p compute-bigmem -A comdata --time=48:00:00 --mem=362G -c 40
similarity_data=/gscratch/comdata/output/reddit_similarity
clustering_data=/gscratch/comdata/output/reddit_clustering
kmeans_selection_grid=--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000]
umap_hdbscan_selection_grid=--min_cluster_sizes=[2] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf] --n_neighbors=[5,15,25,50,75,100] --learning_rate=[1] --min_dist=[0,0.1,0.25,0.5,0.75,0.9,0.99] --local_connectivity=[1]
umap_hdbscan_selection_grid=--min_cluster_sizes=[2] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf] --n_neighbors=[5,15,25,50,75,100] --learning_rate=[1] --min_dist=[0,0.1,0.25,0.5,0.75,0.9,0.99] --local_connectivity=[1] --densmap=[True,False] --n_components=[2,5,10]
hdbscan_selection_grid=--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf]
affinity_selection_grid=--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15]

4
clustering/lsi_base.py
View File

@ -29,7 +29,7 @@ class lsi_grid_sweep(grid_sweep):
self.jobs = list(chain(*map(lambda gs: gs.jobs, self.subgrids)))
class twoway_lsi_grid_sweep(twoway_grid_sweep):
def __init__(self, jobtype, subsweep, inpath, lsi_dimensions, outpath, args1, args2, save_step1):
def __init__(self, jobtype, subsweep, inpath, lsi_dimensions, outpath, args1, args2):
self.jobtype = jobtype
self.subsweep = subsweep
inpath = Path(inpath)
@ -40,5 +40,5 @@ class twoway_lsi_grid_sweep(twoway_grid_sweep):
lsi_nums = [int(p.stem) for p in lsi_paths]
self.hasrun = False
self.subgrids = [self.subsweep(lsi_path, outpath, lsi_dim, args1, args2, save_step1) for lsi_dim, lsi_path in zip(lsi_nums, lsi_paths)]
self.subgrids = [self.subsweep(lsi_path, outpath, lsi_dim, args1, args2) for lsi_dim, lsi_path in zip(lsi_nums, lsi_paths)]
self.jobs = list(chain(*map(lambda gs: gs.jobs, self.subgrids)))

23
clustering/umap_hdbscan_clustering.py
View File

@ -63,25 +63,28 @@ class umap_hdbscan_grid_sweep(twoway_grid_sweep):
min_samples,
cluster_selection_epsilon,
cluster_selection_method,
n_components,
n_neighbors,
learning_rate,
min_dist,
local_connectivity
local_connectivity,
densmap
):
return f"mcs-{min_cluster_size}_ms-{min_samples}_cse-{cluster_selection_epsilon}_csm-{cluster_selection_method}_nn-{n_neighbors}_lr-{learning_rate}_md-{min_dist}_lc-{local_connectivity}"
return f"mcs-{min_cluster_size}_ms-{min_samples}_cse-{cluster_selection_epsilon}_csm-{cluster_selection_method}_nc-{n_components}_nn-{n_neighbors}_lr-{learning_rate}_md-{min_dist}_lc-{local_connectivity}_dm-{densmap}"
@dataclass
class umap_hdbscan_clustering_result(hdbscan_clustering_result):
n_components:int
n_neighbors:int
learning_rate:float
min_dist:float
local_connectivity:int
densmap:bool
class umap_hdbscan_job(twoway_clustering_job):
def __init__(self, infile, outpath, name,
umap_args = {"n_neighbors":15, "learning_rate":1, "min_dist":1, "local_connectivity":1},
umap_args = {"n_components":2,"n_neighbors":15, "learning_rate":1, "min_dist":1, "local_connectivity":1,'densmap':False},
hdbscan_args = {"min_cluster_size":2, "min_samples":1, "cluster_selection_epsilon":0, "cluster_selection_method":'eom'},
save_step1 = False,
*args,
**kwargs):
super().__init__(infile,
@ -91,15 +94,16 @@ class umap_hdbscan_job(twoway_clustering_job):
call2=umap_hdbscan_job._hdbscan_clustering,
args1=umap_args,
args2=hdbscan_args,
save_step1=save_step1,
*args,
**kwargs
)
self.n_components = umap_args['n_components']
self.n_neighbors = umap_args['n_neighbors']
self.learning_rate = umap_args['learning_rate']
self.min_dist = umap_args['min_dist']
self.local_connectivity = umap_args['local_connectivity']
self.densmap = umap_args['densmap']
self.min_cluster_size = hdbscan_args['min_cluster_size']
self.min_samples = hdbscan_args['min_samples']
self.cluster_selection_epsilon = hdbscan_args['cluster_selection_epsilon']
@ -139,14 +143,17 @@ class umap_hdbscan_job(twoway_clustering_job):
min_samples=self.min_samples,
cluster_selection_epsilon=self.cluster_selection_epsilon,
cluster_selection_method=self.cluster_selection_method,
n_components = self.n_components,
n_neighbors = self.n_neighbors,
learning_rate = self.learning_rate,
min_dist = self.min_dist,
local_connectivity=self.local_connectivity
local_connectivity=self.local_connectivity,
densmap=self.densmap
)
return self.result
def run_umap_hdbscan_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], learning_rate=[1], min_dist=[1], local_connectivity=[1],
def run_umap_hdbscan_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], n_components=[2], learning_rate=[1], min_dist=[1], local_connectivity=[1],
densmap=[False],
min_cluster_sizes=[2], min_samples=[1], cluster_selection_epsilons=[0], cluster_selection_methods=['eom']):
"""Run umap + hdbscan clustering once or more with different parameters.
@ -171,6 +178,8 @@ def run_umap_hdbscan_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], l
'learning_rate':list(map(float,learning_rate)),
'min_dist':list(map(float,min_dist)),
'local_connectivity':list(map(int,local_connectivity)),
'n_components':list(map(int, n_components)),
'densmap':list(map(bool,densmap))
}
hdbscan_args = {'min_cluster_size':list(map(int,min_cluster_sizes)),

25
clustering/umap_hdbscan_clustering_lsi.py
View File

@ -9,14 +9,13 @@ class umap_hdbscan_clustering_result_lsi(umap_hdbscan_clustering_result, lsi_res
pass
class umap_hdbscan_lsi_job(umap_hdbscan_job, lsi_mixin):
def __init__(self, infile, outpath, name, umap_args, hdbscan_args, lsi_dims, save_step1=False):
def __init__(self, infile, outpath, name, umap_args, hdbscan_args, lsi_dims):
super().__init__(
infile,
outpath,
name,
umap_args,
hdbscan_args,
save_step1
hdbscan_args
)
super().set_lsi_dims(lsi_dims)
@ -32,8 +31,7 @@ class umap_hdbscan_lsi_grid_sweep(twoway_lsi_grid_sweep):
lsi_dims,
outpath,
umap_args,
hdbscan_args,
save_step1
hdbscan_args
):
super().__init__(umap_hdbscan_lsi_job,
@ -42,8 +40,7 @@ class umap_hdbscan_lsi_grid_sweep(twoway_lsi_grid_sweep):
lsi_dims,
outpath,
umap_args,
hdbscan_args,
save_step1
hdbscan_args
)
@ -55,11 +52,11 @@ class _umap_hdbscan_lsi_grid_sweep(twoway_grid_sweep):
lsi_dim,
umap_args,
hdbscan_args,
save_step1):
):
self.lsi_dim = lsi_dim
self.jobtype = umap_hdbscan_lsi_job
super().__init__(self.jobtype, inpath, outpath, self.namer, umap_args, hdbscan_args, save_step1, lsi_dim)
super().__init__(self.jobtype, inpath, outpath, self.namer, umap_args, hdbscan_args, lsi_dim)
def namer(self, *args, **kwargs):
@ -67,8 +64,9 @@ class _umap_hdbscan_lsi_grid_sweep(twoway_grid_sweep):
s += f"_lsi-{self.lsi_dim}"
return s
def run_umap_hdbscan_lsi_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], learning_rate=[1], min_dist=[1], local_connectivity=[1],
min_cluster_sizes=[2], min_samples=[1], cluster_selection_epsilons=[0], cluster_selection_methods=['eom'], lsi_dimensions='all', save_step1 = False):
def run_umap_hdbscan_lsi_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], n_components=[2], learning_rate=[1], min_dist=[1], local_connectivity=[1],
densmap=[False],
min_cluster_sizes=[2], min_samples=[1], cluster_selection_epsilons=[0], cluster_selection_methods=['eom'], lsi_dimensions='all'):
"""Run hdbscan clustering once or more with different parameters.
Usage:
@ -90,6 +88,8 @@ def run_umap_hdbscan_lsi_grid_sweep(savefile, inpath, outpath, n_neighbors = [15
'learning_rate':list(map(float,learning_rate)),
'min_dist':list(map(float,min_dist)),
'local_connectivity':list(map(int,local_connectivity)),
'n_components':list(map(int, n_components)),
'densmap':list(map(bool,densmap))
}
hdbscan_args = {'min_cluster_size':list(map(int,min_cluster_sizes)),
@ -101,8 +101,7 @@ def run_umap_hdbscan_lsi_grid_sweep(savefile, inpath, outpath, n_neighbors = [15
lsi_dimensions,
outpath,
umap_args,
hdbscan_args,
save_step1
hdbscan_args
)