Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw2/summary.json +1288 -0
- paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3/contrast.csv +27 -0
- paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3/per_donor.csv +0 -0
- paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3/summary.json +1300 -0
paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw2/summary.json
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "imperial_eskd",
|
| 4 |
+
"written_utc": "2026-10-06T02:23:01.012304+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"imperial_eskd",
|
| 9 |
+
"--out",
|
| 10 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw2",
|
| 11 |
+
"--threads",
|
| 12 |
+
"6",
|
| 13 |
+
"--donors",
|
| 14 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fewshot_n5/draw2/test_samples.txt",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"covid_positive",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"covid_negative",
|
| 19 |
+
"--arm",
|
| 20 |
+
"lora5=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/ref_k1000/imperial_eskd/draw2/lora__raw.npz",
|
| 21 |
+
"--arm",
|
| 22 |
+
"lora5_k4000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/generated/imperial_eskd/draw2/paired_test_K4000.npz"
|
| 23 |
+
],
|
| 24 |
+
"arms": [
|
| 25 |
+
"lora5",
|
| 26 |
+
"lora5_k4000"
|
| 27 |
+
],
|
| 28 |
+
"donors": [
|
| 29 |
+
"C20_1004",
|
| 30 |
+
"C20_1404",
|
| 31 |
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"C21_1004",
|
| 32 |
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"C21_1704",
|
| 33 |
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"C21_2504",
|
| 34 |
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"C23_2204",
|
| 35 |
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"C31_1304",
|
| 36 |
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"C31_2004",
|
| 37 |
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"C31_2704",
|
| 38 |
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"C33_1401",
|
| 39 |
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"C33_1601",
|
| 40 |
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"C33_1901",
|
| 41 |
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"C34_1404",
|
| 42 |
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| 43 |
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| 44 |
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|
| 45 |
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|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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| 53 |
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|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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| 59 |
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| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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| 65 |
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| 74 |
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| 77 |
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| 155 |
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| 169 |
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| 170 |
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| 171 |
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],
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| 172 |
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"n_donors": 142,
|
| 173 |
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"reference": {
|
| 174 |
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"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd",
|
| 175 |
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"reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
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| 176 |
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"features_sha256": "e46e5bb1a24eae045efe75125d20e3accaa8f68a1006eb2f60d24159013d4aa7",
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| 177 |
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"n_r1_cells": 21232,
|
| 178 |
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"pca": {
|
| 179 |
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"n_components": 50,
|
| 180 |
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"explained_variance_ratio_sum": 0.25841519236564636,
|
| 181 |
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"n_fit_cells": 21232
|
| 182 |
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},
|
| 183 |
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"r2_control": {
|
| 184 |
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"precision": 0.9693858327053504,
|
| 185 |
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"coverage": 0.9998116051243406,
|
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"density": 1.2866569329314241,
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"n_query": 21232,
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"depth_matched": {
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|
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"density": 1.28150433308214
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}
|
| 193 |
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},
|
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paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3/contrast.csv
ADDED
|
@@ -0,0 +1,27 @@
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
| 1 |
+
arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
|
| 2 |
+
lora5,T cell,mean_cp10k,3031,0.8225328866121204,0.6363131785460265,0.7286072455952531,0.5620620128024106,104,31,104,31,241386,103089,,,,,,,,,,,
|
| 3 |
+
lora5,T cell,pseudobulk_log1p_cpm,3031,0.6446985442954168,0.6151584600190607,0.4371981079348407,0.5995870174366118,104,31,104,31,241386,103089,,,,,,,,,,,
|
| 4 |
+
lora5,B cell,mean_cp10k,3186,0.62274235935065,0.6181604529907424,0.48247067152860684,0.46391790965893787,104,31,104,31,46374,13883,,,,,,,,,,,
|
| 5 |
+
lora5,B cell,pseudobulk_log1p_cpm,3186,0.350809903279728,0.4479445109520174,0.22885480102155475,0.3563683383164116,104,31,104,31,46374,13883,,,,,,,,,,,
|
| 6 |
+
lora5,Monocyte,mean_cp10k,2879,0.7427423371607562,0.7038117222497147,0.5217632499431325,0.6593851386287463,103,31,104,31,74900,42571,,,,,,,,,,,
|
| 7 |
+
lora5,Monocyte,pseudobulk_log1p_cpm,2879,0.6568848948029294,0.6894081488945825,0.412194855512953,0.6094527878457299,103,31,104,31,74900,42571,,,,,,,,,,,
|
| 8 |
+
lora5,NK cell,mean_cp10k,2964,0.7943448114261757,0.6572983397395356,0.6701191189597228,0.5858046433793623,104,31,104,31,67818,37334,,,,,,,,,,,
|
| 9 |
+
lora5,NK cell,pseudobulk_log1p_cpm,2964,0.5417757689640134,0.5733589034230205,0.3524381149755503,0.5124498790617447,104,31,104,31,67818,37334,,,,,,,,,,,
|
| 10 |
+
lora5,T cell,welch_top50_deg,5927,,,,,104,31,104,31,241386,103089,True,35,0.5384615384615384,50,50,873,421,16,0.19047619047619047,50,2000
|
| 11 |
+
lora5,B cell,welch_top50_deg,5927,,,,,104,31,104,31,46374,13883,True,11,0.12359550561797752,50,50,215,669,13,0.14942528735632185,50,2000
|
| 12 |
+
lora5,Monocyte,welch_top50_deg,5927,,,,,103,31,104,31,74900,42571,True,28,0.3888888888888889,50,50,270,383,20,0.25,50,2000
|
| 13 |
+
lora5,NK cell,welch_top50_deg,5927,,,,,104,31,104,31,67818,37334,True,27,0.3698630136986301,50,50,321,305,15,0.17647058823529413,50,2000
|
| 14 |
+
lora5,DC,welch_top50_deg,5927,,,,,104,31,104,31,12959,3693,True,16,0.19047619047619047,50,50,272,111,12,0.13636363636363635,50,2000
|
| 15 |
+
lora5_k4000,T cell,mean_cp10k,3031,0.830477983815028,0.6363131785460265,0.7353825687005642,0.5769530747377981,104,31,104,31,241386,101647,,,,,,,,,,,
|
| 16 |
+
lora5_k4000,T cell,pseudobulk_log1p_cpm,3031,0.6279967376765133,0.6151584600190607,0.4115070037733797,0.59826740528313,104,31,104,31,241386,101647,,,,,,,,,,,
|
| 17 |
+
lora5_k4000,B cell,mean_cp10k,3186,0.587514380089862,0.6181604529907424,0.4335623029192398,0.461259007213601,104,31,104,31,46374,14225,,,,,,,,,,,
|
| 18 |
+
lora5_k4000,B cell,pseudobulk_log1p_cpm,3186,0.3617575502892512,0.4479445109520174,0.24060258609221438,0.3594710096821059,104,31,104,31,46374,14225,,,,,,,,,,,
|
| 19 |
+
lora5_k4000,Monocyte,mean_cp10k,2879,0.730815978339781,0.7038117222497147,0.511476834457113,0.6429759875201022,103,31,104,31,74900,45588,,,,,,,,,,,
|
| 20 |
+
lora5_k4000,Monocyte,pseudobulk_log1p_cpm,2879,0.6472074249551689,0.6894081488945825,0.4092046018149294,0.5923906996928807,103,31,104,31,74900,45588,,,,,,,,,,,
|
| 21 |
+
lora5_k4000,NK cell,mean_cp10k,2964,0.8061523421790995,0.6572983397395356,0.687228130527874,0.5906434435011937,104,31,104,31,67818,35080,,,,,,,,,,,
|
| 22 |
+
lora5_k4000,NK cell,pseudobulk_log1p_cpm,2964,0.5367507205975839,0.5733589034230205,0.3515180142938813,0.5016122862147755,104,31,104,31,67818,35080,,,,,,,,,,,
|
| 23 |
+
lora5_k4000,T cell,welch_top50_deg,5927,,,,,104,31,104,31,241386,101647,True,37,0.5873015873015873,50,50,873,348,16,0.19047619047619047,50,2000
|
| 24 |
+
lora5_k4000,B cell,welch_top50_deg,5927,,,,,104,31,104,31,46374,14225,True,11,0.12359550561797752,50,50,215,562,13,0.14942528735632185,50,2000
|
| 25 |
+
lora5_k4000,Monocyte,welch_top50_deg,5927,,,,,103,31,104,31,74900,45588,True,26,0.35135135135135137,50,50,270,373,20,0.25,50,2000
|
| 26 |
+
lora5_k4000,NK cell,welch_top50_deg,5927,,,,,104,31,104,31,67818,35080,True,29,0.4084507042253521,50,50,321,241,15,0.17647058823529413,50,2000
|
| 27 |
+
lora5_k4000,DC,welch_top50_deg,5927,,,,,104,31,103,30,12959,4154,True,16,0.19047619047619047,50,50,272,113,12,0.13636363636363635,50,2000
|
paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3/per_donor.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3/summary.json
ADDED
|
@@ -0,0 +1,1300 @@
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "imperial_eskd",
|
| 4 |
+
"written_utc": "2026-10-06T02:29:22.787526+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"imperial_eskd",
|
| 9 |
+
"--out",
|
| 10 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw3",
|
| 11 |
+
"--threads",
|
| 12 |
+
"6",
|
| 13 |
+
"--donors",
|
| 14 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fewshot_n5/draw3/test_samples.txt",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"covid_positive",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"covid_negative",
|
| 19 |
+
"--arm",
|
| 20 |
+
"lora5=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/ref_k1000/imperial_eskd/draw3/lora__raw.npz",
|
| 21 |
+
"--arm",
|
| 22 |
+
"lora5_k4000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/generated/imperial_eskd/draw3/paired_test_K4000.npz"
|
| 23 |
+
],
|
| 24 |
+
"arms": [
|
| 25 |
+
"lora5",
|
| 26 |
+
"lora5_k4000"
|
| 27 |
+
],
|
| 28 |
+
"donors": [
|
| 29 |
+
"C20_1004",
|
| 30 |
+
"C20_1404",
|
| 31 |
+
"C21_1004",
|
| 32 |
+
"C21_1704",
|
| 33 |
+
"C21_2504",
|
| 34 |
+
"C23_2204",
|
| 35 |
+
"C33_1401",
|
| 36 |
+
"C33_1601",
|
| 37 |
+
"C33_1901",
|
| 38 |
+
"C34_1404",
|
| 39 |
+
"C34_2104",
|
| 40 |
+
"C34_2504",
|
| 41 |
+
"C36_1504",
|
| 42 |
+
"C36_1704",
|
| 43 |
+
"C36_2104",
|
| 44 |
+
"C42_1504",
|
| 45 |
+
"C42_2204",
|
| 46 |
+
"C42_2704",
|
| 47 |
+
"C58_1604",
|
| 48 |
+
"C58_2501",
|
| 49 |
+
"C58_2901",
|
| 50 |
+
"C58_0102",
|
| 51 |
+
"C58_0402",
|
| 52 |
+
"C58_1003",
|
| 53 |
+
"C60_2504",
|
| 54 |
+
"C63_1704",
|
| 55 |
+
"C63_2404",
|
| 56 |
+
"C63_2904",
|
| 57 |
+
"C65_1704",
|
| 58 |
+
"C65_2104",
|
| 59 |
+
"C65_2504",
|
| 60 |
+
"C69_1804",
|
| 61 |
+
"C82_2504",
|
| 62 |
+
"C85_2004",
|
| 63 |
+
"C93_2104",
|
| 64 |
+
"C93_2704",
|
| 65 |
+
"C93_0405",
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