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diffusion
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Commit
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Archive 4 checkpoints (1-4)

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Files changed (4) hide show
  1. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_cv4_full.log +80 -0
  2. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_fewshot0.log +78 -0
  3. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_fewshot0_full.log +78 -0
  4. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_fewshot1.log +78 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_cv4_full.log ADDED
@@ -0,0 +1,80 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 29 states x 15224 genes; mixture 21 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|Naive B cell B cell|Plasma cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|ASDC
12
+ 1 1
13
+ DC|cDC1 DC|cDC2
14
+ 1 1
15
+ DC|pDC Monocyte|CD14 monocyte
16
+ 1 1
17
+ Monocyte|CD16 monocyte Monocyte|Intermediate monocyte
18
+ 1 1
19
+ NK cell|CD56bright NK cell NK cell|CD56dim NK cell
20
+ 1 1
21
+ NK cell|Proliferating NK cell Other|Erythrocyte
22
+ 1 1
23
+ Other|ILC Other|Platelet
24
+ 1 1
25
+ Other|Progenitor cell T cell|CD8aa
26
+ 1 1
27
+ T cell|DN T cell T cell|gdT
28
+ 1 1
29
+ T cell|MAIT T cell|Memory CD4 T cell
30
+ 1 1
31
+ T cell|Memory CD8 T cell T cell|Naive CD4 T cell
32
+ 1 1
33
+ T cell|Naive CD8 T cell T cell|Proliferating T cell
34
+ 1 1
35
+ T cell|Treg
36
+ 1
37
+ recommend to have sufficient number of cells in each cell state
38
+ No tumor reference is speficied. Reference cell types are treated equally.
39
+ Number of outlier genes filtered from mixture = 1
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-07 05:06:28.3514
44
+ Estimated time to complete: 19mins
45
+ Estimated finishing time: 2026-10-07 05:24:41.7914
46
+ Start run...
47
+ R Version: R version 4.5.2 (2025-10-31)
48
+
49
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
50
+
51
+
52
+ Stopping cluster
53
+
54
+ Update the reference matrix ...
55
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
56
+
57
+
58
+ Stopping cluster
59
+
60
+ Run Gibbs sampling using updated reference ...
61
+ Current time: 2026-10-07 05:14:06.999689
62
+ Estimated time to complete: 9mins
63
+ Estimated finishing time: 2026-10-07 05:22:12.279689
64
+ Start run...
65
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
66
+
67
+
68
+ Stopping cluster
69
+
70
+ Warning messages:
71
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
76
+ Unknown option on commandline: --file
77
+ Z dims: 21 x 15223 x 6
78
+ genes used after the outlier filter: 15223
79
+ elapsed min: 11.11
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/immicro/cv4_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_fewshot0.log ADDED
@@ -0,0 +1,78 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 27 states x 5233 genes; mixture 102 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|minor B cell|Naive B cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|cDC2
12
+ 1 1
13
+ DC|minor DC|pDC
14
+ 1 1
15
+ Monocyte|CD14 monocyte Monocyte|CD16 monocyte
16
+ 1 1
17
+ Monocyte|Intermediate monocyte NK cell|CD56bright NK cell
18
+ 1 1
19
+ NK cell|CD56dim NK cell NK cell|Proliferating NK cell
20
+ 1 1
21
+ Other|Erythrocyte Other|ILC
22
+ 1 1
23
+ Other|minor T cell|CD8aa
24
+ 1 1
25
+ T cell|DN T cell T cell|gdT
26
+ 1 1
27
+ T cell|MAIT T cell|Memory CD4 T cell
28
+ 1 1
29
+ T cell|Memory CD8 T cell T cell|minor
30
+ 1 1
31
+ T cell|Naive CD4 T cell T cell|Naive CD8 T cell
32
+ 1 1
33
+ T cell|Treg
34
+ 1
35
+ recommend to have sufficient number of cells in each cell state
36
+ No tumor reference is speficied. Reference cell types are treated equally.
37
+ Number of outlier genes filtered from mixture = 6
38
+ Aligning reference and mixture...
39
+ Normalizing reference...
40
+ Run Gibbs sampling...
41
+ Current time: 2026-10-06 17:06:57.678769
42
+ Estimated time to complete: 31mins
43
+ Estimated finishing time: 2026-10-06 17:37:51.998769
44
+ Start run...
45
+ R Version: R version 4.5.2 (2025-10-31)
46
+
47
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
48
+
49
+
50
+ Stopping cluster
51
+
52
+ Update the reference matrix ...
53
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
54
+
55
+
56
+ Stopping cluster
57
+
58
+ Run Gibbs sampling using updated reference ...
59
+ Current time: 2026-10-06 17:17:58.963103
60
+ Estimated time to complete: 17mins
61
+ Estimated finishing time: 2026-10-06 17:34:45.683103
62
+ Start run...
63
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
64
+
65
+
66
+ Stopping cluster
67
+
68
+ Warning messages:
69
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
70
+ Unknown option on commandline: --file
71
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ Z dims: 102 x 5227 x 6
76
+ genes used after the outlier filter: 5227
77
+ elapsed min: 16.27
78
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/immicro/fewshot0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_fewshot0_full.log ADDED
@@ -0,0 +1,78 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 27 states x 14209 genes; mixture 102 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|minor B cell|Naive B cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|cDC2
12
+ 1 1
13
+ DC|minor DC|pDC
14
+ 1 1
15
+ Monocyte|CD14 monocyte Monocyte|CD16 monocyte
16
+ 1 1
17
+ Monocyte|Intermediate monocyte NK cell|CD56bright NK cell
18
+ 1 1
19
+ NK cell|CD56dim NK cell NK cell|Proliferating NK cell
20
+ 1 1
21
+ Other|Erythrocyte Other|ILC
22
+ 1 1
23
+ Other|minor T cell|CD8aa
24
+ 1 1
25
+ T cell|DN T cell T cell|gdT
26
+ 1 1
27
+ T cell|MAIT T cell|Memory CD4 T cell
28
+ 1 1
29
+ T cell|Memory CD8 T cell T cell|minor
30
+ 1 1
31
+ T cell|Naive CD4 T cell T cell|Naive CD8 T cell
32
+ 1 1
33
+ T cell|Treg
34
+ 1
35
+ recommend to have sufficient number of cells in each cell state
36
+ No tumor reference is speficied. Reference cell types are treated equally.
37
+ Number of outlier genes filtered from mixture = 1
38
+ Aligning reference and mixture...
39
+ Normalizing reference...
40
+ Run Gibbs sampling...
41
+ Current time: 2026-10-07 00:22:11.895435
42
+ Estimated time to complete: 1hrs 12mins
43
+ Estimated finishing time: 2026-10-07 01:33:55.415435
44
+ Start run...
45
+ R Version: R version 4.5.2 (2025-10-31)
46
+
47
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
48
+
49
+
50
+ Stopping cluster
51
+
52
+ Update the reference matrix ...
53
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
54
+
55
+
56
+ Stopping cluster
57
+
58
+ Run Gibbs sampling using updated reference ...
59
+ Current time: 2026-10-07 00:54:21.397175
60
+ Estimated time to complete: 36mins
61
+ Estimated finishing time: 2026-10-07 01:29:34.677175
62
+ Start run...
63
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
64
+
65
+
66
+ Stopping cluster
67
+
68
+ Warning messages:
69
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
70
+ Unknown option on commandline: --file
71
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ Z dims: 102 x 14208 x 6
76
+ genes used after the outlier filter: 14208
77
+ elapsed min: 46.43
78
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/immicro/fewshot0_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_immicro_fewshot1.log ADDED
@@ -0,0 +1,78 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 28 states x 5281 genes; mixture 102 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|minor B cell|Naive B cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|cDC1
12
+ 1 1
13
+ DC|cDC2 DC|minor
14
+ 1 1
15
+ DC|pDC Monocyte|CD14 monocyte
16
+ 1 1
17
+ Monocyte|CD16 monocyte Monocyte|Intermediate monocyte
18
+ 1 1
19
+ NK cell|CD56bright NK cell NK cell|CD56dim NK cell
20
+ 1 1
21
+ NK cell|Proliferating NK cell Other|ILC
22
+ 1 1
23
+ Other|minor Other|Progenitor cell
24
+ 1 1
25
+ T cell|CD8aa T cell|DN T cell
26
+ 1 1
27
+ T cell|gdT T cell|MAIT
28
+ 1 1
29
+ T cell|Memory CD4 T cell T cell|Memory CD8 T cell
30
+ 1 1
31
+ T cell|Naive CD4 T cell T cell|Naive CD8 T cell
32
+ 1 1
33
+ T cell|Proliferating T cell T cell|Treg
34
+ 1 1
35
+ recommend to have sufficient number of cells in each cell state
36
+ No tumor reference is speficied. Reference cell types are treated equally.
37
+ Number of outlier genes filtered from mixture = 6
38
+ Aligning reference and mixture...
39
+ Normalizing reference...
40
+ Run Gibbs sampling...
41
+ Current time: 2026-10-06 17:23:19.248059
42
+ Estimated time to complete: 32mins
43
+ Estimated finishing time: 2026-10-06 17:55:07.648059
44
+ Start run...
45
+ R Version: R version 4.5.2 (2025-10-31)
46
+
47
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
48
+
49
+
50
+ Stopping cluster
51
+
52
+ Update the reference matrix ...
53
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
54
+
55
+
56
+ Stopping cluster
57
+
58
+ Run Gibbs sampling using updated reference ...
59
+ Current time: 2026-10-06 17:34:07.362461
60
+ Estimated time to complete: 15mins
61
+ Estimated finishing time: 2026-10-06 17:48:33.682461
62
+ Start run...
63
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
64
+
65
+
66
+ Stopping cluster
67
+
68
+ Warning messages:
69
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
70
+ Unknown option on commandline: --file
71
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ Z dims: 102 x 5275 x 6
76
+ genes used after the outlier filter: 5275
77
+ elapsed min: 15.9
78
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/immicro/fewshot1