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  1. paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/secA_scsemi_readout.csv +301 -0
  2. paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/secA_scsemi_readout_slide_text.json +45 -0
  3. paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/secA_scsemi_readout.pdf +0 -0
  4. paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/secA_scsemi_readout.png +3 -0
paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/secA_scsemi_readout.csv ADDED
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155
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156
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157
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161
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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200
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201
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203
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204
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205
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215
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216
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219
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226
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227
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paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/secA_scsemi_readout_slide_text.json ADDED
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+ {
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+ "section": "A-scsemi-readout",
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+ "scripts": [
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+ ],
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+ "generated_from": "tools/secA_scsemi_readout.py (rerun to refresh; do not edit by hand)",
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+ "slides": [
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+ {
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+ "title": "Appendix: scSemiProfiler without output threshold",
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+ "layout": "full",
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+ "figures": [
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+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secA_scsemi_readout.png"
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+ ],
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+ "keywords": [
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+ "Official output zeroes values ≤ 10 (fixed)",
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+ "Removed: scSemi coverage up in 5/5 cohorts",
17
+ "No LoRA-5 comparison flips (23/23 same)"
18
+ ],
19
+ "footnote_short": "Modified read-out, not scSemiProfiler's official output. Main slides use the official one.",
20
+ "footnote": "Appendix, sensitivity only. scSemiProfiler's official output (upstream commit c2aea02) is the decoder's ZINB mean with every value <= 10 normalized units set to 0; the cut is fixed in the code (vaegan.myVAE.sample, bound = 10, and fast_semi: xsemi * (xsemi > 10)), not an option. At our cohorts' depth (about 1,000-2,000 UMI per cell on the panel) it removes most low- and mid-expressed genes. Here the same trained per-target models were read out again without that cut (CPU, no retraining, target seeds as in the run), exported and scored exactly as the official arm (same 25 five-donor draws, donors, reference; Giroux disease metrics without sex-linked genes). A control re-read with the cut reproduces the official output: pseudobulk r >= 0.996 over 1790 targets, coverage within 0.015. Because this changes the method's official read-out, the main slides keep the official output. Bars = mean of 5 draws, dots = draws. Source: plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/ (README section 'Read-out sensitivity').",
21
+ "numbers": [
22
+ {
23
+ "value": "ImMicro: coverage LoRA-5 0.79, official 0.04, no threshold 0.23; precision 0.95 / 0.52 / 0.74; L1 0.176 / 0.233 / 0.199",
24
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/per_draw.csv"
25
+ },
26
+ {
27
+ "value": "Sepsis: coverage LoRA-5 0.69, official 0.08, no threshold 0.18; precision 0.91 / 0.73 / 0.77; L1 0.466 / 0.612 / 0.591; logFC r 0.35 / 0.40 / 0.46; top-50 DEG 16.4 / 5.2 / 14.0",
28
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/per_draw.csv"
29
+ },
30
+ {
31
+ "value": "Imperial: coverage LoRA-5 0.74, official 0.06, no threshold 0.42; precision 0.85 / 0.33 / 0.72; L1 0.503 / 0.602 / 0.603; logFC r 0.75 / 0.56 / 0.66; top-50 DEG 113.6 / 46.8 / 94.6",
32
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/per_draw.csv"
33
+ },
34
+ {
35
+ "value": "Giroux: coverage LoRA-5 0.96, official 0.61, no threshold 0.83; precision 1.00 / 0.99 / 1.00; L1 0.256 / 0.270 / 0.273; logFC r 0.30 / 0.40 / 0.45; top-50 DEG 0.2 / 0.0 / 0.0",
36
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/per_draw.csv"
37
+ },
38
+ {
39
+ "value": "Ji: coverage LoRA-5 0.71, official 0.15, no threshold 0.53; precision 0.98 / 0.84 / 0.92; L1 0.513 / 0.592 / 0.575; logFC r 0.33 / 0.15 / 0.19; top-50 DEG 0.2 / 0.0 / 0.0",
40
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/per_draw.csv"
41
+ }
42
+ ]
43
+ }
44
+ ]
45
+ }
paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/secA_scsemi_readout.pdf ADDED
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paper-releases/pbisc-diffusion/updates/20261003T224927Z-deck-appendix-scsemi-readout/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/secA_scsemi_readout.png ADDED

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