junidude14 commited on
Commit
62d1dea
·
verified ·
1 Parent(s): d390bed

Archive 4 checkpoints (1-4)

Browse files
paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/spec.json ADDED
The diff for this file is too large to render. See raw diff
 
paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_generated_coordinates.csv ADDED
The diff for this file is too large to render. See raw diff
 
paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_provenance.json ADDED
@@ -0,0 +1,214 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "pbisc.figure1.recorded-pca-trajectory.v1",
3
+ "created_at_utc": "2026-10-13T06:52:24.105196+00:00",
4
+ "scope": "Existing ctx2048 E12 EMA illustration; one GSE135779 donor pseudobulk; not final-base or paired bulk-sc validation.",
5
+ "public_source": "https://www.virtualhumanlab.com/research/pbisc-diffusion/",
6
+ "caption": "Four recorded noisy-state PCA frames (steps 0, 17, 33 and 50) from an existing ctx2048 E12 EMA run. All 4,096 tracked cells retain their row identities; axes are fitted once on 4,362 observed cells from the conditioning donor. Colours use frozen final predicted PBMC5+Other labels, revealed according to step/50; early states were not classified. This is computational denoising, not biological time, and the same-donor reference is not independent validation.",
7
+ "selected_steps": [
8
+ 0,
9
+ 17,
10
+ 33,
11
+ 50
12
+ ],
13
+ "selection_reason": "Start, approximately one-third, two-thirds and endpoint of the 50-step recorded sequence; no outcome-based frame selection.",
14
+ "state_times": [
15
+ 1.0,
16
+ 0.6600000262260437,
17
+ 0.3400000035762787,
18
+ 0.0
19
+ ],
20
+ "projection": "PCA2 fitted once on canonically encoded observed value/support states over common measured genes. Generated noisy states are selected and projected without clipping, rescaling or library normalization.",
21
+ "axis_limits": {
22
+ "x": [
23
+ -11.447202682495117,
24
+ 25.44376564025879
25
+ ],
26
+ "y": [
27
+ -8.916685104370117,
28
+ 17.416305541992188
29
+ ]
30
+ },
31
+ "coordinate_fit_repeated": false,
32
+ "new_inference": false,
33
+ "new_annotation": false,
34
+ "coordinate_interpolation": false,
35
+ "point_subsampling": false,
36
+ "tracked_rows": 4096,
37
+ "observed_rows": 4362,
38
+ "point_identity": "Stable row index from the existing recorded coordinate tensor, 0 through 4095",
39
+ "color_semantics": {
40
+ "label_source": "final endpoint annotation only",
41
+ "reveal_fraction": [
42
+ 0.0,
43
+ 0.34,
44
+ 0.66,
45
+ 1.0
46
+ ],
47
+ "rule": "RGB = neutral_grey + (step/50) * (endpoint_type_RGB - neutral_grey)",
48
+ "per_timestep_confidence_available": false,
49
+ "endpoint_confidence_used_for_color": false
50
+ },
51
+ "verification": {
52
+ "web_binary_hash_matches_local_manifest": true,
53
+ "website_and_npz_pca_bit_identical": true,
54
+ "website_and_npz_reference_bit_identical": true,
55
+ "tracked_endpoint_labels_equal": true,
56
+ "all_recorded_frames_inside_fixed_bounds": true
57
+ },
58
+ "sources": [
59
+ {
60
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_recorded_points.npz",
61
+ "sha256": "b9a1221a34f383d1fc76d2e0f04399abe317b8f80a768724c29b8b9d44832e20",
62
+ "bytes": 158685,
63
+ "role": "owned recorded-coordinate snapshot"
64
+ },
65
+ {
66
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_source_methods.json",
67
+ "sha256": "ee587fc6eaecc5fab4dd2f9df42942b9e4dcc6446a8b1a8e890eb78adf07e0ea",
68
+ "bytes": 36415,
69
+ "role": "owned recorded-coordinate snapshot"
70
+ },
71
+ {
72
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_source_provenance.json",
73
+ "sha256": "5734273a768ca09b231f8792a8721970e5e3a2aaddede8c206937f13a79fc532",
74
+ "bytes": 3228,
75
+ "role": "owned recorded-coordinate snapshot"
76
+ },
77
+ {
78
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_generated_coordinates.csv",
79
+ "sha256": "f118921a691bfc16276ae8144617fbfdeec7f9bf9c6b24447a6d5f577ac129c7",
80
+ "bytes": 855269,
81
+ "role": "owned recorded-coordinate snapshot"
82
+ },
83
+ {
84
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_reference_coordinates.csv",
85
+ "sha256": "41042eaf3bdb989a276c34849e584b517ae85c592b7cd400a5ed7f97aa056584",
86
+ "bytes": 248304,
87
+ "role": "owned recorded-coordinate snapshot"
88
+ }
89
+ ],
90
+ "external_source_bindings": [
91
+ {
92
+ "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/interactive-v1/manifest.json",
93
+ "sha256": "d3d88ee10c226caf08d05eff5e8af9348984568c90b7ab2a4ca19203cc62238d",
94
+ "bytes": 217501,
95
+ "role": "website interactive export manifest"
96
+ },
97
+ {
98
+ "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/interactive-v1/cells.bin",
99
+ "sha256": "f69fa11064f759446202fe0ad86260e53378a916eb6bbce4718d81cbb5adec60",
100
+ "bytes": 3412128,
101
+ "role": "website exact recorded coordinates"
102
+ },
103
+ {
104
+ "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/v3/methods.json",
105
+ "sha256": "1d374c2367201d29c54161cbc424fa96194d3764cf1690102085e96c781eba19",
106
+ "bytes": 36423,
107
+ "role": "trajectory/annotation definitions"
108
+ },
109
+ {
110
+ "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/v3/coordinates.npz",
111
+ "sha256": "859a8a9ce86c8a09d1313f2f98b4d4f3bf0f5dadf3501dcb38be5fe5aefad467",
112
+ "bytes": 3021357,
113
+ "role": "bit-identical stored coordinate cross-check"
114
+ }
115
+ ],
116
+ "outputs": [
117
+ {
118
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_four_pca_frames.png",
119
+ "sha256": "e4e812692fa830a4f67e57c7dd6098705c4d91687a4515e38b10945d7fb26688",
120
+ "bytes": 611540,
121
+ "role": "trajectory figure"
122
+ },
123
+ {
124
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_four_pca_frames.pdf",
125
+ "sha256": "3c6bad4a4f2cd480da7d83c77e3d81c28bc6ed441377cd2553dc76b332909a02",
126
+ "bytes": 565568,
127
+ "role": "trajectory figure"
128
+ },
129
+ {
130
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_four_pca_frames.svg",
131
+ "sha256": "cf70ade01fa76bfba093d7b956995313747eb3e884dcb2ce5ce2a6e8c39abb09",
132
+ "bytes": 5454302,
133
+ "role": "trajectory figure"
134
+ },
135
+ {
136
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_00.png",
137
+ "sha256": "83ba7190faf91fe07456afad85aa3c1c91836623e328d6b426e918e599299bfa",
138
+ "bytes": 145906,
139
+ "role": "trajectory figure"
140
+ },
141
+ {
142
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_00.pdf",
143
+ "sha256": "2370796051b106de49f4cd8107e6368c22364d3612e4d4efbd96d2df33d7f5e3",
144
+ "bytes": 144425,
145
+ "role": "trajectory figure"
146
+ },
147
+ {
148
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_00.svg",
149
+ "sha256": "140c82a702d97f131b63b8840178c0d0f148e6bd6d354b5d0ac7bc7573760f4e",
150
+ "bytes": 1362921,
151
+ "role": "trajectory figure"
152
+ },
153
+ {
154
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_17.png",
155
+ "sha256": "7c5eda1479e658ff59dd94c7410ef3d14b4587386fcdbcf23bbd8606f05f2eae",
156
+ "bytes": 224974,
157
+ "role": "trajectory figure"
158
+ },
159
+ {
160
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_17.pdf",
161
+ "sha256": "5e1dda16e7fa73435ffb15176e9d970d168ad88a1d54d0a3085d2f5c924c5a46",
162
+ "bytes": 155196,
163
+ "role": "trajectory figure"
164
+ },
165
+ {
166
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_17.svg",
167
+ "sha256": "2a828a481b552e4766a0f51db0c00e7d0833094430a6d8ff3e608f22f77eaaef",
168
+ "bytes": 1362889,
169
+ "role": "trajectory figure"
170
+ },
171
+ {
172
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_33.png",
173
+ "sha256": "44144bbb2a422236a58637345e0a62f0c035b7cc3940fb2e6e75a2bad10441e7",
174
+ "bytes": 232577,
175
+ "role": "trajectory figure"
176
+ },
177
+ {
178
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_33.pdf",
179
+ "sha256": "ebe90b8e8bc192fc4b78da4fd780024eeb2ac9f300a0919c7373a06398be244c",
180
+ "bytes": 155629,
181
+ "role": "trajectory figure"
182
+ },
183
+ {
184
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_33.svg",
185
+ "sha256": "49ca5d76931d199654da8a143556ff5e00d26827dc961a260eb59c3d1140ed62",
186
+ "bytes": 1361453,
187
+ "role": "trajectory figure"
188
+ },
189
+ {
190
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_50.png",
191
+ "sha256": "e75187507a8bac4fa44b5c316d8c4049800d2b4b368771d355da79366d67fa48",
192
+ "bytes": 242566,
193
+ "role": "trajectory figure"
194
+ },
195
+ {
196
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_50.pdf",
197
+ "sha256": "e9f076e476b056d07714e0c093a1a186a13fef20aad407d5c23de60288dd0241",
198
+ "bytes": 155303,
199
+ "role": "trajectory figure"
200
+ },
201
+ {
202
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/trajectory_step_50.svg",
203
+ "sha256": "4f61d7c6f9dd0484f70505cab221a8221af330685e199a24443a76673afc5e3e",
204
+ "bytes": 1360371,
205
+ "role": "trajectory figure"
206
+ }
207
+ ],
208
+ "renderer": {
209
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/enrich_trajectory_20261013.py",
210
+ "sha256": "8c5dee69b73ab4ca5926fbe15619b395325fd2ce8f0b2dc7ba2975e46f2bc6d4",
211
+ "bytes": 16098,
212
+ "role": "CPU-only saved-coordinate renderer"
213
+ }
214
+ }
paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_recorded_points.npz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b9a1221a34f383d1fc76d2e0f04399abe317b8f80a768724c29b8b9d44832e20
3
+ size 158685