junidude14 commited on
Commit
8ef7ab2
·
verified ·
1 Parent(s): 1dd6a49

Archive 4 checkpoints (1-4)

Browse files
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/source_data/fig1_corpus_aggregates.json ADDED
@@ -0,0 +1,81 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "pbisc.figure1.corpus.v1",
3
+ "denominator": "all 41,395,184 corpus cells; proportions are cell shares, not donor shares",
4
+ "condition_handling_overlap": "healthy and in vitro are overlapping attributes",
5
+ "aggregates": {
6
+ "assay": {
7
+ "10x": 30967465,
8
+ "Parse": 9697974,
9
+ "ScaleBio + Seq-Well": 729745
10
+ },
11
+ "condition": {
12
+ "Healthy": 36639276,
13
+ "Autoimmune": 2927959,
14
+ "Infection": 1396029,
15
+ "Other": 431920
16
+ },
17
+ "cell_type": {
18
+ "T cell": 24772208,
19
+ "Monocyte": 7373579,
20
+ "B cell": 3744614,
21
+ "NK cell": 3369999,
22
+ "Other / unlabeled": 2134784
23
+ }
24
+ },
25
+ "totals": {
26
+ "cells": 41395184,
27
+ "datasets": 22,
28
+ "samples": 6507,
29
+ "donors": 3199,
30
+ "split_cells": {
31
+ "test": 3892772,
32
+ "train": 33141380,
33
+ "val": 4361032
34
+ },
35
+ "family_cells": {
36
+ "Autoimmune": 2927959,
37
+ "Drug reaction": 25272,
38
+ "Healthy": 36639276,
39
+ "Hematologic": 406648,
40
+ "Infection": 1396029
41
+ },
42
+ "handling_cells": {
43
+ "ex vivo": 31621421,
44
+ "in vitro": 9773763
45
+ }
46
+ },
47
+ "sources": [
48
+ {
49
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_summary.json",
50
+ "sha256": "cbccff88a6872bc67dd80c0dfde7d4741733274194f5fd10e002fe0a633a6fa3"
51
+ },
52
+ {
53
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_assay_condition.csv",
54
+ "sha256": "d3adc5349083175d0a9e0f196cdf03b2eb28001b345e6e5b8f8b7149c90586a6"
55
+ },
56
+ {
57
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_celltypes.csv",
58
+ "sha256": "5b29e8373ad2597f02a2a7535405106f1a2ed0c9a966d828e89d43c1c59e89d1"
59
+ },
60
+ {
61
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_datasets.csv",
62
+ "sha256": "f4314d4e43d0ee3fa2d8c6fcabb616a7fb5cc3e06dd6dbe38a00e389190d0cea"
63
+ },
64
+ {
65
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/README.md",
66
+ "sha256": "ae5ec49b2c2d2c16d065a95165142ba7809a6cb70ed399a884d094bb8f81154a"
67
+ },
68
+ {
69
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods_model.tex",
70
+ "sha256": "059a3e627d5fce2333a4e84af7b6b2ecd918bc88711b4d3efd52ef87a5e112a8"
71
+ },
72
+ {
73
+ "path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods_paired.tex",
74
+ "sha256": "d3414e46865e9d5b2b5ac7b19179801808e105b0f91a1c06c445d0cc98249396"
75
+ },
76
+ {
77
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/PROTOCOL.json",
78
+ "sha256": "0ec308ab9867d4421c57db54611b67576f73f66fab6744c40288c74897c15a74"
79
+ }
80
+ ]
81
+ }
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/source_data/fig2_historical_rank_full.csv ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ design,arm,label,precision,coverage,comp_l1,trainable_parameters,source,source_sha256
2
+ historical_real_bulk_5fold_pooled107,real_full__raw,Full FT,0.8895327102803738,0.6953894080996885,0.1572206245036138,54185184,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,6d168fc230f5afe2d0a7395dad811aea615cae1778200694ce740b7cd0765068
3
+ historical_real_bulk_5fold_pooled107,lora_r4__raw,LoRA r=4,0.9333333333333333,0.7123364485981308,0.18577808236758375,324056,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled/summary.json,3d8f7f9b20e147bb92978ca0e638bf03c7834a7c3dec3b88683dc11a99254fc4
4
+ historical_real_bulk_5fold_pooled107,real_lora__raw,LoRA r=16,0.9241121495327103,0.7842990654205607,0.16172890350786212,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,6d168fc230f5afe2d0a7395dad811aea615cae1778200694ce740b7cd0765068
5
+ historical_real_bulk_5fold_pooled107,lora_r64__raw,LoRA r=64,0.9044236760124611,0.8158878504672897,0.1609507558094419,5184896,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled/summary.json,3d8f7f9b20e147bb92978ca0e638bf03c7834a7c3dec3b88683dc11a99254fc4
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/source_data/fig2_historical_rank_full_provenance.json ADDED
@@ -0,0 +1,186 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "pbisc.fig2.rank-realbulk.v1",
3
+ "selection": "quality-size balance; not best on every metric",
4
+ "arms": [
5
+ {
6
+ "arm": "real_full__raw",
7
+ "folds": [
8
+ {
9
+ "fold": 0,
10
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/real_full/RUN.json",
11
+ "sha256": "3a24013d5cccb3f5e27b6eaeccb352b2037c7bd816d45121cf65452bef8741c3",
12
+ "train_samples": 78,
13
+ "validation_samples": 7,
14
+ "test_samples": 22
15
+ },
16
+ {
17
+ "fold": 1,
18
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/real_full/RUN.json",
19
+ "sha256": "9b785b5b007c98a529b794939c9d76a1b3314370049a57a82a2d54f5e2257417",
20
+ "train_samples": 78,
21
+ "validation_samples": 7,
22
+ "test_samples": 22
23
+ },
24
+ {
25
+ "fold": 2,
26
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/real_full/RUN.json",
27
+ "sha256": "cbe286d62b9f88ce6e2ed948ccfb79c66a0f470a0e9665a09b96f8b3dcba9882",
28
+ "train_samples": 79,
29
+ "validation_samples": 7,
30
+ "test_samples": 21
31
+ },
32
+ {
33
+ "fold": 3,
34
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/real_full/RUN.json",
35
+ "sha256": "9b97af2eb93f06bb0bc1e196dce4a5bf1c8f1183b83b9aface44ed066b2b4a55",
36
+ "train_samples": 79,
37
+ "validation_samples": 7,
38
+ "test_samples": 21
39
+ },
40
+ {
41
+ "fold": 4,
42
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/real_full/RUN.json",
43
+ "sha256": "cc6b00dfb5eb58c12d0fe59d53a48931aa041fc01292ca5519d904edeebf7ece",
44
+ "train_samples": 79,
45
+ "validation_samples": 7,
46
+ "test_samples": 21
47
+ }
48
+ ]
49
+ },
50
+ {
51
+ "arm": "lora_r4__raw",
52
+ "folds": [
53
+ {
54
+ "fold": 0,
55
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/lora_r4/RUN.json",
56
+ "sha256": "48d4d0504750e0a3c2ee755834e5a438340088e28f55455a4bec32d86d2a09f3",
57
+ "train_samples": 78,
58
+ "validation_samples": 7,
59
+ "test_samples": 22
60
+ },
61
+ {
62
+ "fold": 1,
63
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/lora_r4/RUN.json",
64
+ "sha256": "0e6a1225f5216be5bed567a5fb62d2537b7b8def82f5b35ff5b853e547e6823d",
65
+ "train_samples": 78,
66
+ "validation_samples": 7,
67
+ "test_samples": 22
68
+ },
69
+ {
70
+ "fold": 2,
71
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/lora_r4/RUN.json",
72
+ "sha256": "63dc7fe0a513d7073de412c32595ddfdc843f826a7ba6e22125b027fb05ec8b0",
73
+ "train_samples": 79,
74
+ "validation_samples": 7,
75
+ "test_samples": 21
76
+ },
77
+ {
78
+ "fold": 3,
79
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/lora_r4/RUN.json",
80
+ "sha256": "0c2dbc1d3d75ad4f86fe06c706723778a160dc4680dd811ef8227cfd33fbe8db",
81
+ "train_samples": 79,
82
+ "validation_samples": 7,
83
+ "test_samples": 21
84
+ },
85
+ {
86
+ "fold": 4,
87
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r4/RUN.json",
88
+ "sha256": "28d094481afaf0db962de97aa5616ffb0ccf5a1f67538c0b93dcf60e7a73a1c4",
89
+ "train_samples": 79,
90
+ "validation_samples": 7,
91
+ "test_samples": 21
92
+ }
93
+ ]
94
+ },
95
+ {
96
+ "arm": "real_lora__raw",
97
+ "folds": [
98
+ {
99
+ "fold": 0,
100
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/real_lora/RUN.json",
101
+ "sha256": "39da59ddb8bcb74600cb8f37729a559552c562e0043e4885e553cca909ade7d2",
102
+ "train_samples": 78,
103
+ "validation_samples": 7,
104
+ "test_samples": 22
105
+ },
106
+ {
107
+ "fold": 1,
108
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/real_lora/RUN.json",
109
+ "sha256": "7272ce13c350a719a0d39aa5126a21234def2278cb21489ec80ffcef531b1b95",
110
+ "train_samples": 78,
111
+ "validation_samples": 7,
112
+ "test_samples": 22
113
+ },
114
+ {
115
+ "fold": 2,
116
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/real_lora/RUN.json",
117
+ "sha256": "8bffafdb6045bf89f7dc6c03be6b25a6b181f93a9ff6f3bc11f28de3426e2d0e",
118
+ "train_samples": 79,
119
+ "validation_samples": 7,
120
+ "test_samples": 21
121
+ },
122
+ {
123
+ "fold": 3,
124
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/real_lora/RUN.json",
125
+ "sha256": "ba55c51c487b5a1bf53ab9bc23f502038af352460d3d2f3a0c1e285757ede387",
126
+ "train_samples": 79,
127
+ "validation_samples": 7,
128
+ "test_samples": 21
129
+ },
130
+ {
131
+ "fold": 4,
132
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/real_lora/RUN.json",
133
+ "sha256": "0ccc2f86752cbde21307e110303358dfd75ae9d38d230bcb108b5121921d6fed",
134
+ "train_samples": 79,
135
+ "validation_samples": 7,
136
+ "test_samples": 21
137
+ }
138
+ ]
139
+ },
140
+ {
141
+ "arm": "lora_r64__raw",
142
+ "folds": [
143
+ {
144
+ "fold": 0,
145
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/lora_r64/RUN.json",
146
+ "sha256": "b12a8f3925845c0abc406bb2a4c46589aa3db67a5014003b2e3f7ded20bd3b99",
147
+ "train_samples": 78,
148
+ "validation_samples": 7,
149
+ "test_samples": 22
150
+ },
151
+ {
152
+ "fold": 1,
153
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/lora_r64/RUN.json",
154
+ "sha256": "fcdc09eeeeaa6858e22b17914e443a2d9bcee0dc0e2f4672ed25672a2af5463e",
155
+ "train_samples": 78,
156
+ "validation_samples": 7,
157
+ "test_samples": 22
158
+ },
159
+ {
160
+ "fold": 2,
161
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/lora_r64/RUN.json",
162
+ "sha256": "9f2e00ec01d939e9c7f8899697f94c32c4478e9f678770860e3c1d36aa0820bd",
163
+ "train_samples": 79,
164
+ "validation_samples": 7,
165
+ "test_samples": 21
166
+ },
167
+ {
168
+ "fold": 3,
169
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/lora_r64/RUN.json",
170
+ "sha256": "e4f6db1bd1178570e83668ccedcdb8a50507b9374bb948d5610fbc6c27a11936",
171
+ "train_samples": 79,
172
+ "validation_samples": 7,
173
+ "test_samples": 21
174
+ },
175
+ {
176
+ "fold": 4,
177
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r64/RUN.json",
178
+ "sha256": "9a81cb42ae97c17513200d6ac53de89e6cb5c404640113e64439e145a847e0f6",
179
+ "train_samples": 79,
180
+ "validation_samples": 7,
181
+ "test_samples": 21
182
+ }
183
+ ]
184
+ }
185
+ ]
186
+ }
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/source_data/fig2_strict_curve.csv ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ design,fold,n_pairs,target_pairs_used,arm,precision,coverage,comp_l1,support_sha256,summary,summary_sha256
2
+ strict_exact_n,fold0,5,5,lora,0.9945454545454545,0.9075757575757576,0.18047144313256866,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
3
+ strict_exact_n,fold0,5,5,pairedcal,0.9887878787878788,0.7245454545454545,0.22241275521199746,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
4
+ strict_exact_n,fold0,5,5,scsemi,0.7363636363636363,0.08666666666666667,0.2568256469172848,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
5
+ strict_exact_n,fold0,5,0,raw,0.9103030303030303,0.403030303030303,0.47238641254571206,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
6
+ strict_exact_n,fold0,5,0,refcal,0.8821212121212121,0.16303030303030303,0.15475386729011903,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46