Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/data/ye2026_sepsis/disease/draw4/train_samples.txt

@@ -0,0 +1,5 @@
+IC23
+Skin-S142
+Res-PS22
+Abd-S102
+Skin-S46

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/ablation_pretrain_composition.csv

@@ -0,0 +1,421 @@
+family,method,donor,comp_l1,n_reference,n_candidate
+architecture_floor1pct,real_R2_independent,GSM4029896_JB17001,0.20000000000000004,100,100
+architecture_floor1pct,real_R2_independent,GSM4029899_JB17004,0.09999999999999999,100,100
+architecture_floor1pct,real_R2_independent,GSM4029900_JB17005,0.17999999999999994,100,100
+architecture_floor1pct,real_R2_independent,GSM4029901_JB17006,0.24,100,100
+architecture_floor1pct,real_R2_independent,GSM4029902_JB17007,0.16000000000000003,100,100
+architecture_floor1pct,real_R2_independent,GSM4029903_JB17008,0.11999999999999994,100,100
+architecture_floor1pct,real_R2_independent,GSM4029904_JB17015,0.14000000000000004,100,100
+architecture_floor1pct,real_R2_independent,GSM4029907_JB17010,0.21999999999999992,100,100
+architecture_floor1pct,real_R2_independent,GSM4029908_JB17019,0.22,100,100
+architecture_floor1pct,real_R2_independent,GSM4029909_JB17020,0.14000000000000004,100,100
+architecture_floor1pct,real_R2_independent,GSM4029910_JB17021,0.23999999999999996,100,100
+architecture_floor1pct,real_R2_independent,GSM4029911_JB17022,0.30000000000000004,100,100
+architecture_floor1pct,real_R2_independent,GSM4029912_JB17023,0.17999999999999994,100,100
+architecture_floor1pct,real_R2_independent,GSM4029913_JB17024,0.28,100,100
+architecture_floor1pct,real_R2_independent,GSM4029914_JB17017,0.10000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029918_JB18065,0.12000000000000004,100,100
+architecture_floor1pct,real_R2_independent,GSM4029919_JB18066,0.18000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029920_JB18067,0.17999999999999994,100,100
+architecture_floor1pct,real_R2_independent,GSM4029921_JB18068,0.3,100,100
+architecture_floor1pct,real_R2_independent,GSM4029922_JB18069,0.25999999999999995,100,100
+architecture_floor1pct,real_R2_independent,GSM4029924_JB18071,0.25999999999999995,100,100
+architecture_floor1pct,real_R2_independent,GSM4029925_JB18072,0.13999999999999996,100,100
+architecture_floor1pct,real_R2_independent,GSM4029926_JB18073,0.14,100,100
+architecture_floor1pct,real_R2_independent,GSM4029927_JB18074,0.04000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029929_JB18076,0.15999999999999995,100,100
+architecture_floor1pct,real_R2_independent,GSM4029930_JB18077,0.10000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029931_JB18078,0.16000000000000003,100,100
+architecture_floor1pct,real_R2_independent,GSM4029932_JB18079,0.22000000000000003,100,100
+architecture_floor1pct,real_R2_independent,GSM4029933_JB18080,0.12000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029934_JB18081,0.28,100,100
+architecture_floor1pct,real_R2_independent,GSM4029937_JB18086,0.36,100,100
+architecture_floor1pct,real_R2_independent,GSM4029938_JB18083,0.10000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029939_JB18084,0.22000000000000003,100,100
+architecture_floor1pct,real_R2_independent,GSM4029940_JB19001,0.13999999999999999,100,100
+architecture_floor1pct,real_R2_independent,GSM4029943_JB19004,0.20000000000000007,100,100
+architecture_floor1pct,real_R2_independent,GSM4029944_JB19006,0.10000000000000003,100,100
+architecture_floor1pct,real_R2_independent,GSM4029946_JB19008,0.15999999999999995,100,100
+architecture_floor1pct,real_R2_independent,GSM4029947_JB19009,0.18000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029948_JB19010,0.08000000000000006,100,100
+architecture_floor1pct,real_R2_independent,GSM4029949_JB19011,0.08000000000000002,100,100
+architecture_floor1pct,real_R2_independent,GSM4029951_JB19014,0.09999999999999999,100,100
+architecture_floor1pct,real_R2_independent,GSM4029952_JB19015,0.40000000000000013,100,100
+architecture_floor1pct,bern6k,GSM4029896_JB17001,0.14000000000000007,100,100
+architecture_floor1pct,bern6k,GSM4029899_JB17004,0.34,100,100
+architecture_floor1pct,bern6k,GSM4029900_JB17005,0.2400000000000001,100,100
+architecture_floor1pct,bern6k,GSM4029901_JB17006,0.44000000000000006,100,100
+architecture_floor1pct,bern6k,GSM4029902_JB17007,0.33999999999999997,100,100
+architecture_floor1pct,bern6k,GSM4029903_JB17008,0.19999999999999996,100,100
+architecture_floor1pct,bern6k,GSM4029904_JB17015,0.14,100,100
+architecture_floor1pct,bern6k,GSM4029907_JB17010,0.14000000000000004,100,100
+architecture_floor1pct,bern6k,GSM4029908_JB17019,0.62,100,100
+architecture_floor1pct,bern6k,GSM4029909_JB17020,0.23999999999999996,100,100
+architecture_floor1pct,bern6k,GSM4029910_JB17021,0.8400000000000001,100,100
+architecture_floor1pct,bern6k,GSM4029911_JB17022,0.13999999999999993,100,100
+architecture_floor1pct,bern6k,GSM4029912_JB17023,0.28,100,100
+architecture_floor1pct,bern6k,GSM4029913_JB17024,0.26,100,100
+architecture_floor1pct,bern6k,GSM4029914_JB17017,0.29999999999999993,100,100
+architecture_floor1pct,bern6k,GSM4029918_JB18065,0.18000000000000008,100,100
+architecture_floor1pct,bern6k,GSM4029919_JB18066,0.32000000000000006,100,100
+architecture_floor1pct,bern6k,GSM4029920_JB18067,0.2799999999999999,100,100
+architecture_floor1pct,bern6k,GSM4029921_JB18068,0.24000000000000002,100,100
+architecture_floor1pct,bern6k,GSM4029922_JB18069,0.3999999999999999,100,100
+architecture_floor1pct,bern6k,GSM4029924_JB18071,0.31999999999999995,100,100
+architecture_floor1pct,bern6k,GSM4029925_JB18072,0.4,100,100
+architecture_floor1pct,bern6k,GSM4029926_JB18073,0.28,100,100
+architecture_floor1pct,bern6k,GSM4029927_JB18074,0.12000000000000002,100,100
+architecture_floor1pct,bern6k,GSM4029929_JB18076,0.23999999999999996,100,100
+architecture_floor1pct,bern6k,GSM4029930_JB18077,0.1600000000000001,100,100
+architecture_floor1pct,bern6k,GSM4029931_JB18078,0.07999999999999997,100,100
+architecture_floor1pct,bern6k,GSM4029932_JB18079,0.11999999999999998,100,100
+architecture_floor1pct,bern6k,GSM4029933_JB18080,0.10000000000000003,100,100
+architecture_floor1pct,bern6k,GSM4029934_JB18081,0.44000000000000006,100,100
+architecture_floor1pct,bern6k,GSM4029937_JB18086,0.18,100,100
+architecture_floor1pct,bern6k,GSM4029938_JB18083,0.24000000000000002,100,100
+architecture_floor1pct,bern6k,GSM4029939_JB18084,0.10000000000000002,100,100
+architecture_floor1pct,bern6k,GSM4029940_JB19001,0.22000000000000008,100,100
+architecture_floor1pct,bern6k,GSM4029943_JB19004,0.4600000000000001,100,100
+architecture_floor1pct,bern6k,GSM4029944_JB19006,0.6200000000000001,100,100
+architecture_floor1pct,bern6k,GSM4029946_JB19008,0.12000000000000002,100,100
+architecture_floor1pct,bern6k,GSM4029947_JB19009,0.32000000000000006,100,100
+architecture_floor1pct,bern6k,GSM4029948_JB19010,0.16000000000000003,100,100
+architecture_floor1pct,bern6k,GSM4029949_JB19011,0.13999999999999996,100,100
+architecture_floor1pct,bern6k,GSM4029951_JB19014,0.3000000000000001,100,100
+architecture_floor1pct,bern6k,GSM4029952_JB19015,0.33999999999999997,100,100
+architecture_floor1pct,bernctx2048,GSM4029896_JB17001,0.22,100,100
+architecture_floor1pct,bernctx2048,GSM4029899_JB17004,0.07999999999999996,100,100
+architecture_floor1pct,bernctx2048,GSM4029900_JB17005,0.19999999999999996,100,100
+architecture_floor1pct,bernctx2048,GSM4029901_JB17006,0.17999999999999997,100,100
+architecture_floor1pct,bernctx2048,GSM4029902_JB17007,0.22000000000000008,100,100
+architecture_floor1pct,bernctx2048,GSM4029903_JB17008,0.12,100,100
+architecture_floor1pct,bernctx2048,GSM4029904_JB17015,0.16000000000000003,100,100
+architecture_floor1pct,bernctx2048,GSM4029907_JB17010,0.12000000000000001,100,100
+architecture_floor1pct,bernctx2048,GSM4029908_JB17019,0.7,100,100
+architecture_floor1pct,bernctx2048,GSM4029909_JB17020,0.17999999999999997,100,100
+architecture_floor1pct,bernctx2048,GSM4029910_JB17021,0.24,100,100
+architecture_floor1pct,bernctx2048,GSM4029911_JB17022,0.14,100,100
+architecture_floor1pct,bernctx2048,GSM4029912_JB17023,0.12,100,100
+architecture_floor1pct,bernctx2048,GSM4029913_JB17024,0.26000000000000006,100,100
+architecture_floor1pct,bernctx2048,GSM4029914_JB17017,0.11999999999999994,100,100
+architecture_floor1pct,bernctx2048,GSM4029918_JB18065,0.2000000000000001,100,100
+architecture_floor1pct,bernctx2048,GSM4029919_JB18066,0.23999999999999996,100,100
+architecture_floor1pct,bernctx2048,GSM4029920_JB18067,0.14000000000000004,100,100
+architecture_floor1pct,bernctx2048,GSM4029921_JB18068,0.16,100,100
+architecture_floor1pct,bernctx2048,GSM4029922_JB18069,0.44,100,100
+architecture_floor1pct,bernctx2048,GSM4029924_JB18071,0.2599999999999999,100,100
+architecture_floor1pct,bernctx2048,GSM4029925_JB18072,0.28,100,100
+architecture_floor1pct,bernctx2048,GSM4029926_JB18073,0.16000000000000003,100,100
+architecture_floor1pct,bernctx2048,GSM4029927_JB18074,0.19999999999999998,100,100
+architecture_floor1pct,bernctx2048,GSM4029929_JB18076,0.16000000000000006,100,100
+architecture_floor1pct,bernctx2048,GSM4029930_JB18077,0.08000000000000003,100,100
+architecture_floor1pct,bernctx2048,GSM4029931_JB18078,0.28,100,100
+architecture_floor1pct,bernctx2048,GSM4029932_JB18079,0.22000000000000008,100,100
+architecture_floor1pct,bernctx2048,GSM4029933_JB18080,0.18000000000000002,100,100
+architecture_floor1pct,bernctx2048,GSM4029934_JB18081,0.18000000000000005,100,100
+architecture_floor1pct,bernctx2048,GSM4029937_JB18086,0.14,100,100
+architecture_floor1pct,bernctx2048,GSM4029938_JB18083,0.32,100,100
+architecture_floor1pct,bernctx2048,GSM4029939_JB18084,0.32,100,100
+architecture_floor1pct,bernctx2048,GSM4029940_JB19001,0.16,100,100
+architecture_floor1pct,bernctx2048,GSM4029943_JB19004,0.18000000000000002,100,100
+architecture_floor1pct,bernctx2048,GSM4029944_JB19006,0.4,100,100
+architecture_floor1pct,bernctx2048,GSM4029946_JB19008,0.3599999999999999,100,100
+architecture_floor1pct,bernctx2048,GSM4029947_JB19009,0.30000000000000004,100,100
+architecture_floor1pct,bernctx2048,GSM4029948_JB19010,0.23999999999999994,100,100
+architecture_floor1pct,bernctx2048,GSM4029949_JB19011,0.08,100,100
+architecture_floor1pct,bernctx2048,GSM4029951_JB19014,0.27999999999999997,100,100
+architecture_floor1pct,bernctx2048,GSM4029952_JB19015,0.2800000000000001,100,100
+architecture_floor1pct,bern4xctx512,GSM4029896_JB17001,0.1399999999999999,100,100
+architecture_floor1pct,bern4xctx512,GSM4029899_JB17004,0.19999999999999996,100,100
+architecture_floor1pct,bern4xctx512,GSM4029900_JB17005,0.12000000000000001,100,100
+architecture_floor1pct,bern4xctx512,GSM4029901_JB17006,0.15999999999999998,100,100
+architecture_floor1pct,bern4xctx512,GSM4029902_JB17007,0.20000000000000004,100,100
+architecture_floor1pct,bern4xctx512,GSM4029903_JB17008,0.16000000000000006,100,100
+architecture_floor1pct,bern4xctx512,GSM4029904_JB17015,0.2800000000000001,100,100
+architecture_floor1pct,bern4xctx512,GSM4029907_JB17010,0.18,100,100
+architecture_floor1pct,bern4xctx512,GSM4029908_JB17019,0.6400000000000001,100,100
+architecture_floor1pct,bern4xctx512,GSM4029909_JB17020,0.20000000000000007,100,100
+architecture_floor1pct,bern4xctx512,GSM4029910_JB17021,0.12000000000000001,100,100
+architecture_floor1pct,bern4xctx512,GSM4029911_JB17022,0.22,100,100
+architecture_floor1pct,bern4xctx512,GSM4029912_JB17023,0.08,100,100
+architecture_floor1pct,bern4xctx512,GSM4029913_JB17024,0.17999999999999997,100,100
+architecture_floor1pct,bern4xctx512,GSM4029914_JB17017,0.16000000000000003,100,100
+architecture_floor1pct,bern4xctx512,GSM4029918_JB18065,0.16000000000000003,100,100
+architecture_floor1pct,bern4xctx512,GSM4029919_JB18066,0.2799999999999999,100,100
+architecture_floor1pct,bern4xctx512,GSM4029920_JB18067,0.09999999999999992,100,100
+architecture_floor1pct,bern4xctx512,GSM4029921_JB18068,0.13999999999999996,100,100
+architecture_floor1pct,bern4xctx512,GSM4029922_JB18069,0.5,100,100
+architecture_floor1pct,bern4xctx512,GSM4029924_JB18071,0.18,100,100
+architecture_floor1pct,bern4xctx512,GSM4029925_JB18072,0.13999999999999999,100,100
+architecture_floor1pct,bern4xctx512,GSM4029926_JB18073,0.20000000000000007,100,100
+architecture_floor1pct,bern4xctx512,GSM4029927_JB18074,0.11999999999999988,100,100
+architecture_floor1pct,bern4xctx512,GSM4029929_JB18076,0.22000000000000006,100,100
+architecture_floor1pct,bern4xctx512,GSM4029930_JB18077,0.11999999999999988,100,100
+architecture_floor1pct,bern4xctx512,GSM4029931_JB18078,0.22,100,100
+architecture_floor1pct,bern4xctx512,GSM4029932_JB18079,0.28,100,100
+architecture_floor1pct,bern4xctx512,GSM4029933_JB18080,0.24000000000000007,100,100
+architecture_floor1pct,bern4xctx512,GSM4029934_JB18081,0.21999999999999997,100,100
+architecture_floor1pct,bern4xctx512,GSM4029937_JB18086,0.06000000000000001,100,100
+architecture_floor1pct,bern4xctx512,GSM4029938_JB18083,0.36,100,100
+architecture_floor1pct,bern4xctx512,GSM4029939_JB18084,0.38000000000000006,100,100
+architecture_floor1pct,bern4xctx512,GSM4029940_JB19001,0.10000000000000002,100,100
+architecture_floor1pct,bern4xctx512,GSM4029943_JB19004,0.20000000000000004,100,100
+architecture_floor1pct,bern4xctx512,GSM4029944_JB19006,0.26,100,100
+architecture_floor1pct,bern4xctx512,GSM4029946_JB19008,0.2999999999999999,100,100
+architecture_floor1pct,bern4xctx512,GSM4029947_JB19009,0.4599999999999999,100,100
+architecture_floor1pct,bern4xctx512,GSM4029948_JB19010,0.21999999999999997,100,100
+architecture_floor1pct,bern4xctx512,GSM4029949_JB19011,0.12000000000000004,100,100
+architecture_floor1pct,bern4xctx512,GSM4029951_JB19014,0.28,100,100
+architecture_floor1pct,bern4xctx512,GSM4029952_JB19015,0.24000000000000007,100,100
+architecture_floor1pct,bern4x,GSM4029896_JB17001,0.10000000000000002,100,100
+architecture_floor1pct,bern4x,GSM4029899_JB17004,0.13999999999999999,100,100
+architecture_floor1pct,bern4x,GSM4029900_JB17005,0.2,100,100
+architecture_floor1pct,bern4x,GSM4029901_JB17006,0.18,100,100
+architecture_floor1pct,bern4x,GSM4029902_JB17007,0.14000000000000004,100,100
+architecture_floor1pct,bern4x,GSM4029903_JB17008,0.36,100,100
+architecture_floor1pct,bern4x,GSM4029904_JB17015,0.22000000000000003,100,100
+architecture_floor1pct,bern4x,GSM4029907_JB17010,0.21999999999999997,100,100
+architecture_floor1pct,bern4x,GSM4029908_JB17019,0.8800000000000001,100,100
+architecture_floor1pct,bern4x,GSM4029909_JB17020,0.1199999999999999,100,100
+architecture_floor1pct,bern4x,GSM4029910_JB17021,0.30000000000000004,100,100
+architecture_floor1pct,bern4x,GSM4029911_JB17022,0.21999999999999997,100,100
+architecture_floor1pct,bern4x,GSM4029912_JB17023,0.41999999999999993,100,100
+architecture_floor1pct,bern4x,GSM4029913_JB17024,0.42,100,100
+architecture_floor1pct,bern4x,GSM4029914_JB17017,0.34,100,100
+architecture_floor1pct,bern4x,GSM4029918_JB18065,0.1600000000000001,100,100
+architecture_floor1pct,bern4x,GSM4029919_JB18066,0.43999999999999995,100,100
+architecture_floor1pct,bern4x,GSM4029920_JB18067,0.20000000000000007,100,100
+architecture_floor1pct,bern4x,GSM4029921_JB18068,0.28,100,100
+architecture_floor1pct,bern4x,GSM4029922_JB18069,0.39999999999999997,100,100
+architecture_floor1pct,bern4x,GSM4029924_JB18071,0.52,100,100
+architecture_floor1pct,bern4x,GSM4029925_JB18072,0.3,100,100
+architecture_floor1pct,bern4x,GSM4029926_JB18073,0.26000000000000006,100,100
+architecture_floor1pct,bern4x,GSM4029927_JB18074,0.3599999999999999,100,100
+architecture_floor1pct,bern4x,GSM4029929_JB18076,0.2800000000000001,100,100
+architecture_floor1pct,bern4x,GSM4029930_JB18077,0.32,100,100
+architecture_floor1pct,bern4x,GSM4029931_JB18078,0.07999999999999999,100,100
+architecture_floor1pct,bern4x,GSM4029932_JB18079,0.13999999999999999,100,100
+architecture_floor1pct,bern4x,GSM4029933_JB18080,0.40000000000000013,100,100
+architecture_floor1pct,bern4x,GSM4029934_JB18081,0.32000000000000006,100,100
+architecture_floor1pct,bern4x,GSM4029937_JB18086,0.13999999999999996,100,100
+architecture_floor1pct,bern4x,GSM4029938_JB18083,0.38,100,100
+architecture_floor1pct,bern4x,GSM4029939_JB18084,0.23999999999999996,100,100
+architecture_floor1pct,bern4x,GSM4029940_JB19001,0.30000000000000004,100,100
+architecture_floor1pct,bern4x,GSM4029943_JB19004,0.42,100,100
+architecture_floor1pct,bern4x,GSM4029944_JB19006,0.3800000000000001,100,100
+architecture_floor1pct,bern4x,GSM4029946_JB19008,0.28,100,100
+architecture_floor1pct,bern4x,GSM4029947_JB19009,0.36000000000000004,100,100
+architecture_floor1pct,bern4x,GSM4029948_JB19010,0.14,100,100
+architecture_floor1pct,bern4x,GSM4029949_JB19011,0.21999999999999995,100,100
+architecture_floor1pct,bern4x,GSM4029951_JB19014,0.38,100,100
+architecture_floor1pct,bern4x,GSM4029952_JB19015,0.26000000000000006,100,100
+panel_floor0.1pct,real_R2_independent,GSM4029896_JB17001,0.20000000000000004,100,100
+panel_floor0.1pct,real_R2_independent,GSM4029899_JB17004,0.09999999999999999,100,100
+panel_floor0.1pct,real_R2_independent,GSM4029900_JB17005,0.17999999999999994,100,100
+panel_floor0.1pct,real_R2_independent,GSM4029901_JB17006,0.24,100,100
+panel_floor0.1pct,real_R2_independent,GSM4029902_JB17007,0.16000000000000003,100,100
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+    "command": [
+      "/home/sj_server_1/miniforge3/envs/scanvi/bin/python",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py",
+      "--model-dir",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_model",
+      "--query",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/work/ablation_composition_v1/selected_readout.h5ad",
+      "--out-dir",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/work/ablation_composition_v1/annotation",
+      "--method-name",
+      "ablation_pc_selected_readout",
+      "--dataset-id",
+      "004_A_GSE135779_SLE_PBMC",
+      "--split",
+      "primary_kmeans",
+      "--sample-id-col",
+      "sample_id",
+      "--batch-key-col",
+      "batch_key",
+      "--seed",
+      "20260916",
+      "--device",
+      "cpu",
+      "--num-threads",
+      "2",
+      "--eval-batch-size",
+      "2048"
+    ],
+    "device": "cpu",
+    "query_sha256": "6763da3ec3fd21d984654b0af71ad77c632d16f8398a62b32617daf8054c3acf",
+    "labels": {
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+      "bytes": 4772
+    }
+  },
+  "recipe": {
+    "reference": "the same 4200 real R1 cells used to fit P/C geometry",
+    "candidate": "100 cells per donor; exact P/C selected arrays verified by SHA256",
+    "real_control": "independent 4200 real R2 cells; same observed R1 reference",
+    "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+    "classifier_fitting": "external AIFI only; zero query training",
+    "label_space": [
+      "T cell",
+      "B cell",
+      "Monocyte",
+      "NK cell",
+      "DC",
+      "Other"
+    ],
+    "classifier_gene_space": {
+      "join_key": "ensembl_id",
+      "model_genes": 1005,
+      "query_genes": 1006,
+      "model_genes_missing_from_query_zero_padded": 0,
+      "query_genes_outside_model_dropped": 1,
+      "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+    },
+    "readout": "same selected 1006-gene Poisson integer counts as P/C; real counts untouched",
+    "summary": "unweighted mean of donor L1 errors; L1=sum over all six label fractions",
+    "biological_unit": "donor",
+    "sampling_seed": 20261012,
+    "poisson_seed": 20260916,
+    "families_separate": true,
+    "real_label_concordance_with_original_frozen_annotation": 1.0
+  },
+  "limitations": [
+    "Single 100-cell draw per donor; donor sampling noise is shown by the independent real R2 control.",
+    "Architecture 1% and gene-panel 0.1% floors remain separate comparisons.",
+    "Composition describes frozen-annotator categories, not manual ground-truth identities.",
+    "The fixed AIFI annotator consumes 1005 of the 1006 measured P/C genes; no missing genes are fabricated."
+  ],
+  "outputs": {
+    "ablation_pretrain_composition.csv": {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/source_data/ablation_pretrain_composition.csv",
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+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/source_data/ablation_pretrain_composition_proportions.csv",
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+      "bytes": 167132
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+    "ablation_pretrain_composition_summary.csv": {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/source_data/ablation_pretrain_composition_summary.csv",
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+      "bytes": 771
+    }
+  }
+}