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‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/config_yamls/params/0_test_acc_params_tuning_config.yaml‎

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---
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type: preprocessor
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tune_mode: params
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pipeline:
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- type: filter.gene
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target: FilterGenesPlaceHolder
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- type: normalize
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target: Log1P
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params_to_tune:
10+
base:
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min: 1.0
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max: 10.0
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- type: filter.gene
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target: HighlyVariableGenesLogarithmizedByMeanAndDisp
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params_to_tune:
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min_disp:
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min: 0.05
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max: 0.5
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max_disp:
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min: 1.0
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max: 100.0
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min_mean:
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min: 0.0
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max: 0.0125
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max_mean:
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min: 3.0
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max: 20.0
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n_bins:
29+
min: 10
30+
max: 30
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flavor:
32+
values: [seurat, cell_ranger]
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- type: feature.cell
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target: CellPCA
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params:
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out: feature.cell
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log_level: INFO
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params_to_tune:
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n_components:
40+
min: 100
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max: 1000
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svd_solver:
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values: [auto, full, arpack, randomized]
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- type: misc
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target: SetConfig
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params:
47+
config_dict:
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feature_channel: feature.cell
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label_channel: cell_type
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wandb:
51+
entity: xzy11632
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project: dance-dev
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method: bayes
54+
metric:
55+
name: acc
56+
goal: maximize

‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/config_yamls/params/1_test_acc_params_tuning_config.yaml‎

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---
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type: preprocessor
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tune_mode: params
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pipeline:
5+
- type: filter.gene
6+
target: FilterGenesPlaceHolder
7+
- type: normalize
8+
target: Log1P
9+
params_to_tune:
10+
base:
11+
min: 1.0
12+
max: 10.0
13+
- type: filter.gene
14+
target: HighlyVariableGenesLogarithmizedByMeanAndDisp
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params_to_tune:
16+
min_disp:
17+
min: 0.05
18+
max: 0.5
19+
max_disp:
20+
min: 1.0
21+
max: 100.0
22+
min_mean:
23+
min: 0.0
24+
max: 0.0125
25+
max_mean:
26+
min: 3.0
27+
max: 20.0
28+
n_bins:
29+
min: 10
30+
max: 30
31+
flavor:
32+
values: [seurat, cell_ranger]
33+
- type: feature.cell
34+
target: CellSVD
35+
params:
36+
out: feature.cell
37+
log_level: INFO
38+
params_to_tune:
39+
n_components:
40+
min: 100
41+
max: 1000
42+
algorithm:
43+
values: [arpack, randomized]
44+
- type: misc
45+
target: SetConfig
46+
params:
47+
config_dict:
48+
feature_channel: feature.cell
49+
label_channel: cell_type
50+
wandb:
51+
entity: xzy11632
52+
project: dance-dev
53+
method: bayes
54+
metric:
55+
name: acc
56+
goal: maximize

‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/config_yamls/params/2_test_acc_params_tuning_config.yaml‎

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---
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type: preprocessor
3+
tune_mode: params
4+
pipeline:
5+
- type: filter.gene
6+
target: FilterGenesPlaceHolder
7+
- type: normalize
8+
target: Log1P
9+
params_to_tune:
10+
base:
11+
min: 1.0
12+
max: 10.0
13+
- type: filter.gene
14+
target: HighlyVariableGenesLogarithmizedByTopGenes
15+
params_to_tune:
16+
n_top_genes:
17+
min: 100
18+
max: 10000
19+
n_bins:
20+
min: 10
21+
max: 30
22+
flavor:
23+
values: [seurat, cell_ranger]
24+
- type: feature.cell
25+
target: CellPCA
26+
params:
27+
out: feature.cell
28+
log_level: INFO
29+
params_to_tune:
30+
n_components:
31+
min: 100
32+
max: 1000
33+
svd_solver:
34+
values: [auto, full, arpack, randomized]
35+
- type: misc
36+
target: SetConfig
37+
params:
38+
config_dict:
39+
feature_channel: feature.cell
40+
label_channel: cell_type
41+
wandb:
42+
entity: xzy11632
43+
project: dance-dev
44+
method: bayes
45+
metric:
46+
name: acc
47+
goal: maximize

‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/pipeline_params_tuning_config.yaml‎

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---
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type: preprocessor
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tune_mode: pipeline_params
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pipeline_tuning_top_k: 3
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parameter_tuning_freq_n: 20
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pipeline:
7+
- type: filter.gene
8+
include:
9+
- FilterGenesPercentile
10+
- FilterGenesScanpyOrder
11+
- FilterGenesPlaceHolder
12+
default_params:
13+
FilterGenesScanpyOrder:
14+
order: [min_counts, min_cells, max_counts, max_cells]
15+
min_counts: 1
16+
max_counts: 18858
17+
min_cells: 1
18+
max_cells: 7292
19+
- type: normalize
20+
include:
21+
- ScaleFeature
22+
- ScTransform
23+
- Log1P
24+
- NormalizeTotal
25+
- NormalizePlaceHolder
26+
default_params:
27+
ScTransform:
28+
processes_num: 8
29+
- type: filter.gene
30+
include:
31+
- HighlyVariableGenesLogarithmizedByMeanAndDisp
32+
- HighlyVariableGenesRawCount
33+
- HighlyVariableGenesLogarithmizedByTopGenes
34+
- FilterGenesTopK
35+
- FilterGenesRegression
36+
- FilterGenesNumberPlaceHolder
37+
default_params:
38+
FilterGenesTopK:
39+
num_genes: 2742
40+
FilterGenesRegression:
41+
num_genes: 2742
42+
HighlyVariableGenesRawCount:
43+
n_top_genes: 2742
44+
HighlyVariableGenesLogarithmizedByTopGenes:
45+
n_top_genes: 2742
46+
- type: feature.cell
47+
include:
48+
- WeightedFeaturePCA
49+
- WeightedFeatureSVD
50+
- CellPCA
51+
- CellSVD
52+
- GaussRandProjFeature # Registered custom preprocessing func
53+
- FeatureCellPlaceHolder
54+
params:
55+
out: feature.cell
56+
log_level: INFO
57+
default_params:
58+
WeightedFeaturePCA:
59+
split_name: train
60+
WeightedFeatureSVD:
61+
split_name: train
62+
- type: misc
63+
target: SetConfig
64+
params:
65+
config_dict:
66+
feature_channel: feature.cell
67+
label_channel: cell_type
68+
wandb:
69+
entity: xzy11632
70+
project: dance-dev
71+
method: grid # try grid to provide a comprehensive search
72+
metric:
73+
name: acc # val/acc
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goal: maximize

‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/results/params/0_best_test_acc.csv‎

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id,_runtime,_step,_timestamp,_wandb_runtime,acc,params.1.Log1P.base,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.flavor,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.max_disp,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.max_mean,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.min_disp,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.min_mean,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.n_bins,params.3.CellPCA.n_components,params.3.CellPCA.svd_solver,test_acc,train_acc
2+
d4utfiuk,47.3118109703064,0.0,1744797756.455463,46,0.8649681806564331,8.170312096633026,seurat,82.41444810944753,19.508467906122597,0.15674827188219836,0.007904146957401966,27,480,full,0.7989917993545532,0.968934178352356
3+
uzbzm8cq,50.14717078208923,0.0,1744797695.4240415,48,0.8547770977020264,8.026924744165644,seurat,96.24203245012592,17.389187541238844,0.17275423844971305,0.006359277045926333,28,331,full,0.7983616590499878,0.9523657560348512
4+
ega30fon,,,,38,,9.77809737135358,cell_ranger,28.138639347936746,7.698524742036461,0.473344525536503,0.0016986441329249495,12,288,randomized,,
5+
vj9ackhs,210.6256091594696,0.0,1744797580.5404322,209,0.8541401028633118,3.201737041585284,seurat,6.711733169328511,11.31029109511032,0.09496541718745788,0.009458026984920116,16,544,arpack,0.8087586760520935,0.9972916841506958
6+
ud29gykf,,,,34,,7.702925698294669,cell_ranger,79.07171132509728,11.79874918703463,0.1830007037292351,0.00936857338095867,24,240,randomized,,
7+
7d46iqod,46.37393498420715,0.0,1744797308.83708,45,0.856050968170166,6.971421682560361,seurat,24.834464800923303,5.982209438098152,0.4865076619203216,0.000767924607145247,23,279,auto,0.8018273711204529,0.9335669875144958
8+
0652uqa7,,,,35,,7.133680816634382,cell_ranger,38.854705522436085,14.238988415475363,0.07534683075818738,0.007253033618954164,29,701,randomized,,
9+
obsslohb,,,,36,,4.239402130333324,cell_ranger,57.85267561266242,5.926419862012746,0.13006079649756636,0.0008976397546024098,25,308,randomized,,
10+
hjksnfhe,,,,36,,4.508216984887995,cell_ranger,19.28544037301136,12.182102828731876,0.0858847375501296,0.003846875090792693,30,207,auto,,
11+
9jpq0r5q,,,,33,,5.816954129849268,cell_ranger,12.590412142574914,11.79230777612669,0.330954254367392,0.005865432601948485,22,527,arpack,,
12+
xyu05yw0,45.111223459243774,0.0,1744797041.7199795,44,0.8566879034042358,3.545501244838172,seurat,75.15730468808745,18.493525243413437,0.2762884935566321,0.004979399732329079,22,627,full,0.7996219396591187,0.9956985712051392
13+
ojb7ai0p,98.65373682975768,0.0,1744796983.7937517,97,0.8464968204498291,5.071562305578048,seurat,8.252332214116631,8.50390998993355,0.2583983625417949,0.004177940062326447,19,222,arpack,0.8119092583656311,0.9483829736709596
14+
iui5rgl8,,,,34,,5.85574615391398,cell_ranger,18.704718253296015,9.103038978617452,0.4638113365768466,0.01193449244527345,23,153,arpack,,
15+
a93q0yvg,,,,36,,5.320035926901653,cell_ranger,70.41471625336163,10.203703663162605,0.06585847836080559,0.008580026818529015,29,325,auto,,
16+
bgq07ft0,,,,35,,2.4424381715934,cell_ranger,6.841730506936659,10.410057840353431,0.16821840406261368,0.004580239921316741,14,825,full,,
17+
p7z8rbp9,,,,35,,9.234085162094267,cell_ranger,61.70594265376648,18.781364148952235,0.4650482497443296,0.0019668506819838284,14,485,arpack,,
18+
a6xg0cam,47.98486065864563,0.0,1744796621.405269,46,0.856050968170166,6.791697898324696,seurat,46.956628595431965,11.0346538859281,0.06997732671507823,0.008073834912509063,27,140,auto,0.796471357345581,0.9187510013580322
19+
3x7fdx8r,,,,36,,9.71623705510902,cell_ranger,30.48720569207445,6.959203919187857,0.4033112729626156,0.007669735817477955,21,114,auto,,
20+
mtwnn5fs,,,,36,,1.918442129918864,cell_ranger,86.38651924681147,13.751335159950784,0.11603267280560792,0.0024327863088438833,12,867,full,,
21+
kbkuj4h2,218.39594912528992,0.0,1744796451.532273,217,0.8452229499816895,1.6700428855373253,seurat,48.8621375130435,9.302644160080936,0.4333341426212777,0.010074590864898944,26,480,arpack,0.7986767292022705,1.0

‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/results/params/1_best_test_acc.csv‎

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id,_runtime,_step,_timestamp,_wandb_runtime,acc,params.1.Log1P.base,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.flavor,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.max_disp,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.max_mean,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.min_disp,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.min_mean,params.2.HighlyVariableGenesLogarithmizedByMeanAndDisp.n_bins,params.3.CellSVD.algorithm,params.3.CellSVD.n_components,test_acc,train_acc
2+
uizfn4oi,,,,35,,9.592283708680668,cell_ranger,17.361716488166657,3.2648508328153705,0.36397887952879954,0.001865255652119764,25,arpack,951,,
3+
89wrovo2,,,,34,,4.527325222473058,cell_ranger,19.76591380469975,13.589558838383754,0.1150528454197042,0.0005123303251151304,22,randomized,381,,
4+
oybhkskh,,,,34,,9.81228973538792,cell_ranger,18.628831355730867,10.121717633474365,0.4243369972662479,0.003280931002637895,12,arpack,311,,
5+
myn6ezmm,115.25017404556274,0.0,1744799708.898143,114,0.8522292971611023,3.591205392657274,seurat,92.35725929050868,15.419611215321252,0.2234202488924546,0.006474472680324323,20,arpack,249,0.8292375802993774,0.9428070783615112
6+
er9p60gd,43.85332369804382,0.0,1744799579.116253,42,0.849681556224823,9.40178481233523,seurat,81.52011369120419,19.086757023114053,0.2581683872247046,0.001903548704156888,30,arpack,119,0.8235664963722229,0.8884817361831665
7+
34i4jlua,,,,36,,7.83978964878135,cell_ranger,56.1160647910205,4.39256823850017,0.3176606384690982,0.0071110000617185185,26,randomized,702,,
8+
oqd6iw8d,166.6362066268921,0.0,1744799463.8585637,165,0.8535031676292419,8.122586129997938,seurat,38.02688906400246,19.877359007697937,0.3424408196229093,0.0086122201152807,19,arpack,678,0.8355387449264526,0.958897590637207
9+
h20qwqv2,46.77150893211365,0.0,1744799285.668179,45,0.856050968170166,4.5163765809112775,seurat,22.648632707752142,16.107190415780515,0.2246378882077304,0.003489989220409746,26,randomized,107,0.8279772996902466,0.8983590602874756
10+
bmbt664z,202.04082441329956,0.0,1744799223.1073003,200,0.8458598852157593,8.37443607742037,seurat,27.517850441170353,10.660887438165208,0.3284364381582557,0.005120083839608127,23,arpack,957,0.8267170786857605,0.967500388622284
11+
ur80qitt,149.20452332496643,0.0,1744799006.3053153,148,0.8605095744132996,8.991936076989152,seurat,85.11398329946987,19.73670573758769,0.16101097118576949,0.009026780215016732,13,arpack,330,0.8251417875289917,0.9279910922050476
12+
ju4f0t77,49.75007939338684,0.0,1744798842.5818465,48,0.8541401028633118,5.77165806649632,seurat,59.96804063804631,5.002451633259845,0.3418238330036461,0.00920842574450757,26,randomized,826,0.824826717376709,0.9761032462120056
13+
11x29lpw,,,,36,,3.995760875788982,cell_ranger,3.919658564572138,7.738140633153003,0.07597290437608226,0.008925536308894004,24,arpack,718,,
14+
3n20srr3,200.97634530067444,0.0,1744798718.9792843,199,0.8503184914588928,8.056557711146661,seurat,39.99496565360822,4.726841033713995,0.3312401475140898,0.003388175117901775,18,arpack,687,0.8367989659309387,0.9573044180870056
15+
by0iy4nr,267.0848693847656,0.0,1744798505.3573985,265,0.8579617738723755,6.964699645080819,seurat,17.09057425512445,3.3438178264128187,0.07590250023770714,0.009417155576161592,19,arpack,669,0.8333333134651184,0.9738728404045104
16+
r5vx7bv5,180.4981667995453,0.0,1744798226.479205,179,0.8484076261520386,8.981153631936621,seurat,96.43739912690664,5.298399460385278,0.4630681115735784,0.002013331215279249,24,arpack,896,0.8235664963722229,0.9528437256813048
17+
fhb5mb2g,,,,37,,3.2262273969247257,cell_ranger,62.86768127575311,14.601025244083129,0.315510628092163,0.010340419118441788,10,arpack,120,,
18+
6qhrh6j1,,,,34,,3.725783509385733,cell_ranger,63.176145973811664,16.18034841124389,0.18612082039550243,0.0029014028801440193,25,randomized,863,,
19+
zb09ic4b,46.42019510269165,0.0,1744797927.495191,45,0.8490445613861084,3.0925117399738022,seurat,51.60420371361744,16.75267506253798,0.4689906075374886,0.011388480180643557,30,randomized,553,0.8241965770721436,0.9823163747787476
20+
3ytqmkis,,,,34,,9.49714420034261,cell_ranger,49.01357034812099,8.79828220639482,0.1115160089642686,0.0016701915932350612,13,randomized,362,,
21+
bq9b0kzp,50.802841901779175,0.0,1744797820.21883,49,0.8509554266929626,9.429400173341948,seurat,4.177076470152514,15.94412563516979,0.24823760550596985,0.003289231730104975,27,randomized,938,0.8201008439064026,0.9654293656349182

‎examples/tuning/cta_actinn/1027-1357-1641-517-706-777-850-972_245-332-377-398-405-455-470-492/results/params/2_best_test_acc.csv‎

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id,_runtime,_step,_timestamp,_wandb_runtime,acc,params.1.Log1P.base,params.2.HighlyVariableGenesLogarithmizedByTopGenes.flavor,params.2.HighlyVariableGenesLogarithmizedByTopGenes.n_bins,params.2.HighlyVariableGenesLogarithmizedByTopGenes.n_top_genes,params.3.CellPCA.n_components,params.3.CellPCA.svd_solver,test_acc,train_acc
2+
bndry5i6,48.596322774887085,0.0,1744802006.571494,47,0.862420380115509,6.601145487815989,seurat,22,5448,263,randomized,0.8008821606636047,0.9522064924240112
3+
aqomwnag,49.4192955493927,0.0,1744801943.0739815,48,0.8649681806564331,5.76137767612344,seurat,26,6577,349,randomized,0.8081285357475281,0.9716424942016602
4+
csgwpg8d,49.65722894668579,0.0,1744801811.851145,48,0.8630573153495789,5.6657812655789925,seurat,26,5935,315,randomized,0.8046628832817078,0.9649513959884644
5+
ggm3v4nc,203.92976689338684,0.0,1744801749.2551858,202,0.8573248386383057,4.219895824468678,seurat,23,5692,373,arpack,0.8011972308158875,0.9851840138435364
6+
mudj77ko,217.9996726512909,0.0,1744801525.2108097,216,0.8605095744132996,5.8762512507470435,seurat,25,7565,397,arpack,0.7993068695068359,0.9788115620613098
7+
gk33y1k6,185.68456387519836,0.0,1744801292.2712789,184,0.8636942505836487,6.863318582352371,seurat,26,5636,339,arpack,0.7983616590499878,0.9630396962165833
8+
bj2u2pir,161.05736422538757,0.0,1744801093.093444,159,0.862420380115509,3.522422176548102,seurat,21,4351,292,arpack,0.8059231042861938,0.9821571111679076
9+
ofgzn04r,194.49892902374268,0.0,1744800915.402904,193,0.8547770977020264,1.6842532947196174,seurat,22,7192,343,arpack,0.8093887567520142,1.0
10+
fjkmzudp,46.39413905143738,0.0,1744800709.139481,45,0.7585987448692322,4.49053243500606,seurat,23,438,887,randomized,0.6947069764137268,0.8128086924552917
11+
uls7quj5,,,,34,,3.040135167659625,cell_ranger,29,3813,807,auto,,
12+
r16yt8tz,,,,33,,7.606406584486177,cell_ranger,17,9576,522,randomized,,
13+
uy3wk2me,51.99806261062622,0.0,1744800549.5161936,50,0.8573248386383057,1.3665347646755004,seurat,18,5288,428,randomized,0.8046628832817078,1.0
14+
mj86jh5k,,,,34,,1.733756818642966,cell_ranger,21,885,509,arpack,,
15+
4ofywe1m,59.620694398880005,0.0,1744800435.4358015,58,0.8662420511245728,4.448343057213419,seurat,14,4617,114,full,0.8065532445907593,0.9270352125167848
16+
9h2taoxi,,,,34,,4.939959856636423,cell_ranger,12,3024,257,arpack,,
17+
pzzc45pz,,,,34,,9.95391202118814,cell_ranger,30,6752,740,randomized,,
18+
fi78fu4y,237.12256026268005,0.0,1744800268.5563602,236,0.8617834448814392,5.201770130687656,seurat,26,4791,535,arpack,0.8049779534339905,0.9886888861656188
19+
8llvjwon,51.24683618545532,0.0,1744800018.4926002,50,0.862420380115509,9.543642665852456,seurat,29,4993,914,randomized,0.8002520203590393,0.9917157888412476
20+
9h473qpe,,,,36,,3.4109153448039775,cell_ranger,13,1023,883,auto,,
21+
wvk7pimh,,,,33,,3.020901091210584,cell_ranger,21,6309,168,auto,,

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