Migrate release files 301-329

results/gigatime_diag_pixels.csv

@@ -0,0 +1,11 @@
+channel,virtual: frac px p<0.05,virtual: frac px p>0.95,"virtual: frac px in (0.05,0.95)"
+Hoechst,0.578,0.0187,0.4033
+CD68,0.8026,0.0,0.1974
+CD4,0.7998,0.0,0.2002
+CD8a,0.9583,0.0,0.0417
+CD20,0.8913,0.0,0.1087
+PD-L1,0.711,0.0,0.289
+CD3e,0.8316,0.0,0.1684
+Ki67,0.9254,0.0,0.0746
+Pan-CK,0.7442,0.0082,0.2477
+SMA,0.8688,0.0,0.1312

results/gigatime_diag_retrieval.csv

@@ -0,0 +1,4 @@
+pair,mixed-slide gallery,single-slide gallery
+real means <-> GigaTIME means,0.0354,0.0409
+real means <-> UNI2-ridge prediction,0.2611,0.1977
+real means <-> shuffled real (chance),0.0085,

results/joint_ens_long.csv

@@ -0,0 +1,211 @@
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results/joint_ens_tests.csv

@@ -0,0 +1,78 @@
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results/medvtok_long.csv

@@ -0,0 +1,256 @@
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results/medvtok_summary.csv

@@ -0,0 +1,54 @@
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results/medvtok_tests.csv

@@ -0,0 +1,72 @@
+config,vs,pair,ref,new,delta,folds_won,p_paired_t
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results/miphei_diag.csv

@@ -0,0 +1,33 @@
+channel,set,MIPHEI pooled,MIPHEI within-slide,GigaTIME pooled,GigaTIME within-slide
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results/miphei_diag_retrieval.csv

@@ -0,0 +1,7 @@
+set,n,pair,R@1_g100
+clean (official test),109,real <-> MIPHEI (16 ch),0.2716
+clean (official test),109,real <-> MIPHEI (10 shared ch),0.2387
+clean (official test),109,real <-> GigaTIME (10 shared ch),0.0167
+seen (official train),2954,real <-> MIPHEI (16 ch),0.5375
+seen (official train),2954,real <-> MIPHEI (10 shared ch),0.4333
+seen (official train),2954,real <-> GigaTIME (10 shared ch),0.0362

results/pairing_summary.csv

@@ -0,0 +1,263 @@
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results/regimes_long.csv

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+S4,"separate, frozen, MLP mIF + linear RNA/text",2,mIF<->text(synthetic) (ORION),emergent,0.0683,0.2797,0.4260000000000001,0.183732491336611,0.073,0.38768118619918823,0.08585858345031738,0.09456521272659302
+S4,"separate, frozen, MLP mIF + linear RNA/text",2,text<->RNA(virtual) (TCGA),emergent,0.073,0.26,0.3962,0.17782547437850982,0.0808,0.38768118619918823,0.08585858345031738,0.09456521272659302
+S4,"separate, frozen, MLP mIF + linear RNA/text",2,text<->mIF(MIPHEI) (TCGA),emergent,0.0364,0.14279999999999998,0.2534,0.11033562583257511,0.0358,0.38768118619918823,0.08585858345031738,0.09456521272659302
+J8,two-stage from S4 heads -> joint residual,2,H&E<->mIF (ORION),trained,0.8006,0.9743999999999999,0.996,0.8749340103768779,0.9259999999999998,0.5561594367027283,0.08585858345031738,0.08043477684259415
+J8,two-stage from S4 heads -> joint residual,2,H&E<->RNA (HEST),trained,0.1288,0.331,0.44970000000000004,0.23818795095849143,0.1394,0.5561594367027283,0.08585858345031738,0.08043477684259415
+J8,two-stage from S4 heads -> joint residual,2,H&E<->text (TCGA),trained,0.23129999999999998,0.5730999999999999,0.7032,0.3876979650894243,0.23739999999999994,0.5561594367027283,0.08585858345031738,0.08043477684259415
+J8,two-stage from S4 heads -> joint residual,2,mIF<->RNA(virtual) (ORION),emergent,0.1165,0.34989999999999993,0.5181,0.23964704983983018,0.15600000000000003,0.5561594367027283,0.08585858345031738,0.08043477684259415
+J8,two-stage from S4 heads -> joint residual,2,mIF<->text(synthetic) (ORION),emergent,0.0629,0.2501,0.381,0.1685131200885478,0.0686,0.5561594367027283,0.08585858345031738,0.08043477684259415
+J8,two-stage from S4 heads -> joint residual,2,text<->RNA(virtual) (TCGA),emergent,0.0608,0.2336,0.37270000000000003,0.16102638393591687,0.07200000000000001,0.5561594367027283,0.08585858345031738,0.08043477684259415
+J8,two-stage from S4 heads -> joint residual,2,text<->mIF(MIPHEI) (TCGA),emergent,0.0319,0.12500000000000003,0.21580000000000002,0.09924978452825503,0.03,0.5561594367027283,0.08585858345031738,0.08043477684259415
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,H&E<->mIF (ORION),trained,0.728,0.9666,0.9907999999999998,0.8308227486806894,0.9481999999999999,0.3550724685192108,0.05035128444433212,0.08227847516536713
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,H&E<->RNA (HEST),trained,0.1623,0.4559,0.6103999999999999,0.30247207366995005,0.19039999999999996,0.3550724685192108,0.05035128444433212,0.08227847516536713
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,H&E<->text (TCGA),trained,0.22240000000000001,0.5885,0.7337,0.3874308650147313,0.24779999999999996,0.3550724685192108,0.05035128444433212,0.08227847516536713
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,mIF<->RNA(virtual) (ORION),emergent,0.12869999999999998,0.4108,0.6084999999999999,0.2697415902884286,0.20639999999999997,0.3550724685192108,0.05035128444433212,0.08227847516536713
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,mIF<->text(synthetic) (ORION),emergent,0.08430000000000001,0.29379999999999995,0.45130000000000003,0.1982385492581279,0.085,0.3550724685192108,0.05035128444433212,0.08227847516536713
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,text<->RNA(virtual) (TCGA),emergent,0.07400000000000001,0.259,0.4053,0.1790460193186958,0.0754,0.3550724685192108,0.05035128444433212,0.08227847516536713
+S4,"separate, frozen, MLP mIF + linear RNA/text",3,text<->mIF(MIPHEI) (TCGA),emergent,0.032,0.12090000000000002,0.21960000000000002,0.09920473885036002,0.032600000000000004,0.3550724685192108,0.05035128444433212,0.08227847516536713
+J8,two-stage from S4 heads -> joint residual,3,H&E<->mIF (ORION),trained,0.7431000000000002,0.9721000000000001,0.9925999999999999,0.8416936831750302,0.9594,0.39311593770980835,0.05152224749326706,0.08544303476810455
+J8,two-stage from S4 heads -> joint residual,3,H&E<->RNA (HEST),trained,0.16400000000000003,0.4594,0.6111,0.3047917798233609,0.1898,0.39311593770980835,0.05152224749326706,0.08544303476810455
+J8,two-stage from S4 heads -> joint residual,3,H&E<->text (TCGA),trained,0.2266,0.5933999999999999,0.7411,0.3930771125306123,0.2482,0.39311593770980835,0.05152224749326706,0.08544303476810455
+J8,two-stage from S4 heads -> joint residual,3,mIF<->RNA(virtual) (ORION),emergent,0.11870000000000001,0.39849999999999997,0.6017,0.26039409496061217,0.19499999999999995,0.39311593770980835,0.05152224749326706,0.08544303476810455
+J8,two-stage from S4 heads -> joint residual,3,mIF<->text(synthetic) (ORION),emergent,0.08349999999999999,0.29350000000000004,0.4509,0.19888016367915753,0.0864,0.39311593770980835,0.05152224749326706,0.08544303476810455
+J8,two-stage from S4 heads -> joint residual,3,text<->RNA(virtual) (TCGA),emergent,0.0698,0.25120000000000003,0.39270000000000005,0.17233539104179904,0.07880000000000001,0.39311593770980835,0.05152224749326706,0.08544303476810455
+J8,two-stage from S4 heads -> joint residual,3,text<->mIF(MIPHEI) (TCGA),emergent,0.030699999999999998,0.11599999999999999,0.20709999999999998,0.09532397263850972,0.0304,0.39311593770980835,0.05152224749326706,0.08544303476810455
+S4,"separate, frozen, MLP mIF + linear RNA/text",4,H&E<->mIF (ORION),trained,0.6441,0.9149000000000003,0.9702000000000001,0.7615899243275567,0.8456,0.38224637508392334,0.04603174701333046,0.12222222238779068
+S4,"separate, frozen, MLP mIF + linear RNA/text",4,H&E<->RNA (HEST),trained,0.18850000000000006,0.5394,0.6952999999999999,0.3479711892586057,0.263,0.38224637508392334,0.04603174701333046,0.12222222238779068
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+S4,"separate, frozen, MLP mIF + linear RNA/text",4,mIF<->text(synthetic) (ORION),emergent,0.08509999999999998,0.2968,0.4561,0.19919398199494584,0.0888,0.38224637508392334,0.04603174701333046,0.12222222238779068
+S4,"separate, frozen, MLP mIF + linear RNA/text",4,text<->RNA(virtual) (TCGA),emergent,0.07050000000000001,0.2469,0.3811,0.1710789876403968,0.07919999999999999,0.38224637508392334,0.04603174701333046,0.12222222238779068
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+J8,two-stage from S4 heads -> joint residual,4,H&E<->RNA (HEST),trained,0.20810000000000003,0.5528000000000001,0.7039000000000002,0.36590326414861585,0.28040000000000004,0.5416666865348816,0.0476190485060215,0.12000000476837158
+J8,two-stage from S4 heads -> joint residual,4,H&E<->text (TCGA),trained,0.24,0.5826,0.7212,0.3960322653701917,0.2412,0.5416666865348816,0.0476190485060215,0.12000000476837158
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+J8,two-stage from S4 heads -> joint residual,4,text<->RNA(virtual) (TCGA),emergent,0.0713,0.2465,0.37760000000000005,0.17217879930637675,0.07400000000000001,0.5416666865348816,0.0476190485060215,0.12000000476837158
+J8,two-stage from S4 heads -> joint residual,4,text<->mIF(MIPHEI) (TCGA),emergent,0.03429999999999999,0.13709999999999997,0.22780000000000006,0.10502179113481169,0.038200000000000005,0.5416666865348816,0.0476190485060215,0.12000000476837158

results/regimes_summary.csv

@@ -0,0 +1,94 @@
+,,,,R@1,R@1,R@10,R@10,pair_acc,pair_acc
+,,,,mean,std,mean,std,mean,std
+regime,name,kind,pair,,,,,,
+S1,"separate, frozen anchor",trained,H&E<->mIF (ORION),0.6798,0.0341,0.9833,0.0081,0.8965,0.0391
+S1,"separate, frozen anchor",trained,H&E<->RNA (HEST),0.1483,0.0228,0.5492,0.0937,0.1718,0.0274
+S1,"separate, frozen anchor",trained,H&E<->text (TCGA),0.2339,0.0067,0.7281,0.0081,0.2424,0.0077
+S1,"separate, frozen anchor",emergent,mIF<->RNA(virtual) (ORION),0.1083,0.0174,0.5364,0.0317,0.1579,0.0218
+S1,"separate, frozen anchor",emergent,mIF<->text(synthetic) (ORION),0.0764,0.0124,0.445,0.0249,0.0807,0.0138
+S1,"separate, frozen anchor",emergent,text<->RNA(virtual) (TCGA),0.06,0.0028,0.3288,0.0121,0.0627,0.0042
+S1,"separate, frozen anchor",emergent,text<->mIF(MIPHEI) (TCGA),0.0379,0.0048,0.2426,0.0222,0.0394,0.0056
+S2,"separate, two-tower",trained,H&E<->mIF (ORION),0.7937,0.0413,0.9808,0.0146,0.9134,0.0425
+S2,"separate, two-tower",trained,H&E<->RNA (HEST),0.13,0.0309,0.4927,0.0807,0.1317,0.0343
+S2,"separate, two-tower",trained,H&E<->text (TCGA),0.1947,0.0199,0.6679,0.0714,0.1943,0.0237
+S2,"separate, two-tower",emergent,mIF<->RNA(virtual) (ORION),0.0193,0.0054,0.1448,0.0196,0.0155,0.004
+S2,"separate, two-tower",emergent,mIF<->text(synthetic) (ORION),0.0218,0.0025,0.1765,0.0106,0.0205,0.0025
+S2,"separate, two-tower",emergent,text<->RNA(virtual) (TCGA),0.014,0.0025,0.1262,0.0093,0.0171,0.0013
+S2,"separate, two-tower",emergent,text<->mIF(MIPHEI) (TCGA),0.0134,0.0024,0.1242,0.0089,0.0133,0.0031
+J1,"joint, frozen anchor",trained,H&E<->mIF (ORION),0.7057,0.044,0.9828,0.0061,0.9009,0.0387
+J1,"joint, frozen anchor",trained,H&E<->RNA (HEST),0.1484,0.0293,0.5384,0.0973,0.1687,0.0377
+J1,"joint, frozen anchor",trained,H&E<->text (TCGA),0.2365,0.0083,0.7219,0.0103,0.243,0.0126
+J1,"joint, frozen anchor",emergent,mIF<->RNA(virtual) (ORION),0.0939,0.0216,0.4704,0.051,0.1223,0.0343
+J1,"joint, frozen anchor",emergent,mIF<->text(synthetic) (ORION),0.0652,0.0109,0.387,0.0236,0.0646,0.0115
+J1,"joint, frozen anchor",emergent,text<->RNA(virtual) (TCGA),0.0561,0.0074,0.3048,0.024,0.0546,0.0048
+J1,"joint, frozen anchor",emergent,text<->mIF(MIPHEI) (TCGA),0.031,0.0049,0.2122,0.0132,0.0326,0.0053
+J2,"joint, shared H&E head",trained,H&E<->mIF (ORION),0.7609,0.0343,0.9826,0.0151,0.9107,0.0392
+J2,"joint, shared H&E head",trained,H&E<->RNA (HEST),0.1467,0.0328,0.5499,0.1021,0.1574,0.0463
+J2,"joint, shared H&E head",trained,H&E<->text (TCGA),0.2044,0.0127,0.6759,0.0306,0.2016,0.0181
+J2,"joint, shared H&E head",emergent,mIF<->RNA(virtual) (ORION),0.0609,0.0087,0.3605,0.0342,0.0882,0.0186
+J2,"joint, shared H&E head",emergent,mIF<->text(synthetic) (ORION),0.0598,0.0049,0.3782,0.0198,0.0624,0.0124
+J2,"joint, shared H&E head",emergent,text<->RNA(virtual) (TCGA),0.0442,0.0063,0.2758,0.0229,0.0516,0.0068
+J2,"joint, shared H&E head",emergent,text<->mIF(MIPHEI) (TCGA),0.0306,0.0046,0.2196,0.0177,0.033,0.0081
+J3,"joint, shared H&E head, size-prop.",trained,H&E<->mIF (ORION),0.7397,0.035,0.9826,0.0139,0.8955,0.0401
+J3,"joint, shared H&E head, size-prop.",trained,H&E<->RNA (HEST),0.1384,0.0319,0.5223,0.0799,0.1436,0.0403
+J3,"joint, shared H&E head, size-prop.",trained,H&E<->text (TCGA),0.1871,0.0215,0.6313,0.0434,0.1759,0.0244
+J3,"joint, shared H&E head, size-prop.",emergent,mIF<->RNA(virtual) (ORION),0.0632,0.0157,0.3701,0.0613,0.0872,0.027
+J3,"joint, shared H&E head, size-prop.",emergent,mIF<->text(synthetic) (ORION),0.0598,0.006,0.3649,0.0276,0.0593,0.0094
+J3,"joint, shared H&E head, size-prop.",emergent,text<->RNA(virtual) (TCGA),0.0387,0.0015,0.2491,0.0153,0.0445,0.002
+J3,"joint, shared H&E head, size-prop.",emergent,text<->mIF(MIPHEI) (TCGA),0.0305,0.004,0.213,0.0196,0.0312,0.0057
+J4,"joint, shared H&E head + distill",trained,H&E<->mIF (ORION),0.7646,0.0269,0.9829,0.0158,0.9123,0.0421
+J4,"joint, shared H&E head + distill",trained,H&E<->RNA (HEST),0.1437,0.0241,0.5492,0.0812,0.1508,0.0309
+J4,"joint, shared H&E head + distill",trained,H&E<->text (TCGA),0.2025,0.017,0.6587,0.0373,0.1953,0.0183
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+J5,"joint, residual adapter",trained,H&E<->mIF (ORION),0.7621,0.0464,0.9807,0.0105,0.9054,0.0372
+J5,"joint, residual adapter",trained,H&E<->RNA (HEST),0.142,0.0275,0.5348,0.0885,0.1519,0.0355
+J5,"joint, residual adapter",trained,H&E<->text (TCGA),0.2011,0.0152,0.6598,0.0413,0.1951,0.0188
+J5,"joint, residual adapter",emergent,mIF<->RNA(virtual) (ORION),0.0575,0.0134,0.3535,0.0363,0.0812,0.0247
+J5,"joint, residual adapter",emergent,mIF<->text(synthetic) (ORION),0.0593,0.0134,0.3835,0.0471,0.0627,0.0153
+J5,"joint, residual adapter",emergent,text<->RNA(virtual) (TCGA),0.0442,0.0041,0.2706,0.0234,0.0456,0.0051
+J5,"joint, residual adapter",emergent,text<->mIF(MIPHEI) (TCGA),0.0294,0.0042,0.2108,0.015,0.0297,0.0072
+S3,"separate, frozen anchor, linear head",trained,H&E<->mIF (ORION),0.6419,0.0356,0.9795,0.0108,0.8825,0.0523
+S3,"separate, frozen anchor, linear head",trained,H&E<->RNA (HEST),0.1562,0.0238,0.5582,0.0887,0.1868,0.0437
+S3,"separate, frozen anchor, linear head",trained,H&E<->text (TCGA),0.2365,0.0061,0.7286,0.008,0.2496,0.0053
+S3,"separate, frozen anchor, linear head",emergent,mIF<->RNA(virtual) (ORION),0.1225,0.0088,0.575,0.0269,0.1774,0.0137
+S3,"separate, frozen anchor, linear head",emergent,mIF<->text(synthetic) (ORION),0.0705,0.0122,0.4284,0.025,0.0738,0.011
+S3,"separate, frozen anchor, linear head",emergent,text<->RNA(virtual) (TCGA),0.0689,0.002,0.3703,0.0106,0.0782,0.0031
+S3,"separate, frozen anchor, linear head",emergent,text<->mIF(MIPHEI) (TCGA),0.0384,0.0014,0.2507,0.0073,0.0429,0.0024
+J4b,"joint, shared H&E head + distill x10",trained,H&E<->mIF (ORION),0.7679,0.0325,0.9847,0.0156,0.916,0.0379
+J4b,"joint, shared H&E head + distill x10",trained,H&E<->RNA (HEST),0.1491,0.0335,0.5569,0.1108,0.1624,0.0517
+J4b,"joint, shared H&E head + distill x10",trained,H&E<->text (TCGA),0.2087,0.0094,0.6737,0.0317,0.2034,0.0139
+J4b,"joint, shared H&E head + distill x10",emergent,mIF<->RNA(virtual) (ORION),0.067,0.0148,0.3747,0.0606,0.0891,0.0204
+J4b,"joint, shared H&E head + distill x10",emergent,mIF<->text(synthetic) (ORION),0.0583,0.005,0.3603,0.0286,0.0581,0.0072
+J4b,"joint, shared H&E head + distill x10",emergent,text<->RNA(virtual) (TCGA),0.0469,0.003,0.2767,0.0185,0.0532,0.006
+J4b,"joint, shared H&E head + distill x10",emergent,text<->mIF(MIPHEI) (TCGA),0.0299,0.0028,0.2091,0.0202,0.0324,0.005
+J6,"joint, shared H&E head, uncertainty wt.",trained,H&E<->mIF (ORION),0.7648,0.034,0.9805,0.0174,0.9084,0.0416
+J6,"joint, shared H&E head, uncertainty wt.",trained,H&E<->RNA (HEST),0.1363,0.0335,0.5198,0.1074,0.1411,0.0407
+J6,"joint, shared H&E head, uncertainty wt.",trained,H&E<->text (TCGA),0.1955,0.0216,0.6422,0.0687,0.1894,0.0267
+J6,"joint, shared H&E head, uncertainty wt.",emergent,mIF<->RNA(virtual) (ORION),0.0571,0.0084,0.3366,0.0441,0.0749,0.0215
+J6,"joint, shared H&E head, uncertainty wt.",emergent,mIF<->text(synthetic) (ORION),0.0546,0.0145,0.3521,0.0553,0.0564,0.0203
+J6,"joint, shared H&E head, uncertainty wt.",emergent,text<->RNA(virtual) (TCGA),0.041,0.0084,0.2576,0.0346,0.0454,0.009
+J6,"joint, shared H&E head, uncertainty wt.",emergent,text<->mIF(MIPHEI) (TCGA),0.0273,0.0072,0.207,0.0359,0.0314,0.0107
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results/rnafm_summary.csv

@@ -0,0 +1,193 @@
+,,,,R@1,R@1,R@10,R@10,pair_acc,pair_acc
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results/text_emergent_probes.csv

@@ -0,0 +1,463 @@
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results/textenc_summary.csv

@@ -0,0 +1,147 @@
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results/virtual_completion.csv

@@ -0,0 +1,661 @@
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results/virtual_validation.csv

@@ -0,0 +1,180 @@
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+ORION,1,text synthetic<->mIF real (10 means),"emergent, real x virtual",False,545,0.0346,0.038200000000000005
+ORION,1,text synthetic<->mIF virtual (10 means),"emergent, virtual x virtual",True,545,0.0301,0.0412
+TCGA,1,H&E<->mIF virtual (10 means),virtual (cross-dataset head),True,2868,0.034300000000000004,0.0302
+TCGA,1,text<->mIF virtual (10 means),"emergent, real x virtual",False,2868,0.0235,0.0194
+TCGA,1,RNA virtual<->mIF virtual (10 means),"emergent, virtual x virtual",True,2868,0.027699999999999995,0.019600000000000003
+ORION,2,H&E<->mIF real (10 means),trained (real),False,547,0.2805,0.3736
+ORION,2,H&E<->mIF virtual (10 means),virtual calibration,True,547,0.051699999999999996,0.06339999999999998
+ORION,2,mIF real<->mIF virtual (10 means),virtual calibration,False,547,0.06810000000000001,0.0702
+ORION,2,mIF real (10 means)<->RNA virtual,"emergent, real x virtual",False,547,0.0788,0.0784
+ORION,2,mIF virtual (10 means)<->RNA virtual,"emergent, virtual x virtual",True,547,0.0325,0.0294
+ORION,2,text synthetic<->mIF real (10 means),"emergent, real x virtual",False,547,0.0481,0.05659999999999999
+ORION,2,text synthetic<->mIF virtual (10 means),"emergent, virtual x virtual",True,547,0.0263,0.0294
+TCGA,2,H&E<->mIF virtual (10 means),virtual (cross-dataset head),True,2868,0.032799999999999996,0.0302
+TCGA,2,text<->mIF virtual (10 means),"emergent, real x virtual",False,2868,0.0225,0.0166
+TCGA,2,RNA virtual<->mIF virtual (10 means),"emergent, virtual x virtual",True,2868,0.0216,0.022799999999999997
+ORION,3,H&E<->mIF real (10 means),trained (real),False,704,0.2975,0.3732000000000001
+ORION,3,H&E<->mIF virtual (10 means),virtual calibration,True,704,0.05279999999999999,0.0556
+ORION,3,mIF real<->mIF virtual (10 means),virtual calibration,False,704,0.053200000000000004,0.05659999999999999
+ORION,3,mIF real (10 means)<->RNA virtual,"emergent, real x virtual",False,704,0.0762,0.09360000000000002
+ORION,3,mIF virtual (10 means)<->RNA virtual,"emergent, virtual x virtual",True,704,0.0226,0.0222
+ORION,3,text synthetic<->mIF real (10 means),"emergent, real x virtual",False,704,0.049400000000000006,0.049600000000000005
+ORION,3,text synthetic<->mIF virtual (10 means),"emergent, virtual x virtual",True,704,0.0295,0.0264
+TCGA,3,H&E<->mIF virtual (10 means),virtual (cross-dataset head),True,2868,0.0315,0.0262
+TCGA,3,text<->mIF virtual (10 means),"emergent, real x virtual",False,2868,0.020399999999999995,0.0154
+TCGA,3,RNA virtual<->mIF virtual (10 means),"emergent, virtual x virtual",True,2868,0.019100000000000002,0.0208
+ORION,4,H&E<->mIF real (10 means),trained (real),False,699,0.26030000000000003,0.3342
+ORION,4,H&E<->mIF virtual (10 means),virtual calibration,True,699,0.04870000000000001,0.04819999999999999
+ORION,4,mIF real<->mIF virtual (10 means),virtual calibration,False,699,0.06509999999999999,0.05040000000000001
+ORION,4,mIF real (10 means)<->RNA virtual,"emergent, real x virtual",False,699,0.0683,0.0708
+ORION,4,mIF virtual (10 means)<->RNA virtual,"emergent, virtual x virtual",True,699,0.027699999999999995,0.023400000000000004
+ORION,4,text synthetic<->mIF real (10 means),"emergent, real x virtual",False,699,0.0536,0.05659999999999999
+ORION,4,text synthetic<->mIF virtual (10 means),"emergent, virtual x virtual",True,699,0.027700000000000006,0.0288
+TCGA,4,H&E<->mIF virtual (10 means),virtual (cross-dataset head),True,2868,0.0323,0.025800000000000003
+TCGA,4,text<->mIF virtual (10 means),"emergent, real x virtual",False,2868,0.021299999999999996,0.017400000000000002
+TCGA,4,RNA virtual<->mIF virtual (10 means),"emergent, virtual x virtual",True,2868,0.0215,0.0188
+TCGA calib,0,H&E<->text real,trained (real),False,1000,0.18429999999999996,0.16500000000000004
+TCGA calib,0,H&E<->text synthetic,virtual calibration,True,1000,0.13419999999999999,0.13979999999999998
+TCGA calib,0,text real<->text synthetic,virtual calibration,False,1000,0.0797,0.07660000000000002
+TCGA calib,0,text real<->RNA virtual,"emergent, real x virtual",False,1000,0.038299999999999994,0.0366
+TCGA calib,0,text synthetic<->RNA virtual,"emergent, virtual x virtual",True,1000,0.039400000000000004,0.041199999999999994
+TCGA calib,1,text real<->RNA virtual,"emergent, real x virtual",False,1000,0.0411,0.039200000000000006
+TCGA calib,1,text synthetic<->RNA virtual,"emergent, virtual x virtual",True,1000,0.050199999999999995,0.061200000000000004
+TCGA calib,2,text real<->RNA virtual,"emergent, real x virtual",False,1000,0.0416,0.04
+TCGA calib,2,text synthetic<->RNA virtual,"emergent, virtual x virtual",True,1000,0.044500000000000005,0.05239999999999998
+TCGA calib,3,text real<->RNA virtual,"emergent, real x virtual",False,1000,0.041100000000000005,0.03900000000000001
+TCGA calib,3,text synthetic<->RNA virtual,"emergent, virtual x virtual",True,1000,0.043800000000000006,0.04819999999999999
+TCGA calib,4,text real<->RNA virtual,"emergent, real x virtual",False,1000,0.033699999999999994,0.0366
+TCGA calib,4,text synthetic<->RNA virtual,"emergent, virtual x virtual",True,1000,0.044,0.0396

rna_sets.py

@@ -0,0 +1,55 @@
+"""Shared RNA inputs for the RNA foundation-model extractors (43_*.py).
+
+load(name) -> (X, genes): X = scipy CSR float32 raw(-like) counts (n_spot, n_gene), genes = HGNC symbols (np.array str)
+  hest     : HEST-1k Visium real counts (9484 spots, 14,802 common genes)             -> training / test of H&E<->RNA
+  hest_v   : STPath virtual RNA of the same 9484 HEST spots (calibration only)
+  orion_v  : STPath virtual RNA of the 3187 ORION tiles (test only)
+  tcga_v   : STPath virtual RNA of the 6144 TCGA text patches (test only)
+  dlpfc    : DLPFC external Visium real counts (482 spots, 33,538 genes)            -> external test only
+STPath outputs log1p counts; virtual counts = round(expm1(pred)) so that the zero pattern means "not detected"
+as in real Visium (models that tokenise expressed genes would otherwise see all 14,791 genes as expressed).
+Output convention of every extractor: cache/rnafm/<model>_<set>.npy, float16 (n_spot, D), row order = the set's.
+"""
+import os
+
+import numpy as np
+import pandas as pd
+import scipy.sparse as sp
+
+from common import CACHE
+
+SETS = ["hest", "hest_v", "orion_v", "tcga_v", "dlpfc"]
+OUT = os.path.join(CACHE, "rnafm")
+_STP = {"hest_v": "hest_val", "orion_v": "orion", "tcga_v": "tcga_text"}
+
+
+def load(name):
+    if name == "hest":
+        X = sp.load_npz(os.path.join(CACHE, "hest", "counts.npz")).tocsr().astype(np.float32)
+        g = pd.read_csv(os.path.join(CACHE, "hest", "genes.csv")).gene.values
+    elif name in _STP:
+        p = np.load(os.path.join(CACHE, "stpath", f"{_STP[name]}_pred.npy")).astype(np.float32)
+        X = sp.csr_matrix(np.rint(np.expm1(p).clip(0)).astype(np.float32))
+        g = pd.read_csv(os.path.join(CACHE, "stpath", f"{_STP[name]}_genes.csv")).gene.values
+    elif name == "dlpfc":
+        X = sp.csr_matrix(np.load(os.path.join(CACHE, "external", "dlpfc_counts_full.npy")).astype(np.float32))
+        g = pd.read_csv(os.path.join(CACHE, "external", "dlpfc_genes_full.csv")).gene.values
+    else:
+        raise KeyError(name)
+    X.eliminate_zeros()
+    return X, np.asarray(g, dtype=str)
+
+
+def save(model, name, E):
+    os.makedirs(OUT, exist_ok=True)
+    E = np.asarray(E, dtype=np.float32)
+    assert np.isfinite(E).all(), (model, name)
+    np.save(os.path.join(OUT, f"{model}_{name}.npy"), E.astype(np.float16))
+    print(f"[{model}] {name}: saved {E.shape}", flush=True)
+
+
+if __name__ == "__main__":
+    for s in SETS:
+        X, g = load(s)
+        nnz = np.diff(X.indptr)
+        print(f"{s:8s} {X.shape}  genes/spot median {np.median(nnz):.0f}  UMI/spot median {np.median(np.asarray(X.sum(1)).ravel()):.0f}")

setup_encoders.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+# Fetch the third-party code / weights that embed.py needs for RAW inputs (images, text, counts, mIF tiles).
+# Not needed for the feature-level API (E.*_from_feats), evaluate_saved.py or training (52_final_model.py).
+#
+#   PYTHON=python bash setup_encoders.sh
+#
+# Code is cloned at the exact commits the features were extracted with; nothing is pip-installed. The other frozen
+# encoders (KEEP, BiomedCLIP, Qwen3-Embedding-0.6B, Tahoe-x1, SE-600M, AIDO.Cell, VirTues weights) are downloaded
+# from the Hugging Face Hub on first use at pinned revisions (see the 4x_ / 14_ scripts).
+# UNI2-h is gated (MahmoodLab/UNI2-h, accept the licence on its HF page): either log in with an account that has
+# access, or point $UNI2_PATH at a local pytorch_model.bin.
+set -euo pipefail
+cd "$(dirname "$0")"
+PY=${PYTHON:-python}
+mkdir -p ext/medvtok
+
+clone() {  # url dir commit
+  [ -d "$2/.git" ] || git clone -q "$1" "$2"
+  git -C "$2" checkout -q "$3"
+  echo "$2 @ $(git -C "$2" rev-parse --short HEAD)"
+}
+clone https://github.com/bunnelab/virtues.git ext/virtues 2c9c6cb            # VirTues model code (MIT)
+clone https://github.com/genbio-ai/ModelGenerator.git ext/modelgenerator bda6f2d  # AIDO.Cell gene list
+clone https://github.com/Masaaki-75/medvtok.git ext/medvtok/repo a558c24     # MedVTok model code (MIT)
+
+# MedVTok weights (3.3 GB; MIT)
+"$PY" -I -c "from huggingface_hub import snapshot_download as s; print(s('massaki75/medvtok', revision='9e70a000b1040ce498450a877da91a8fe02dac41', local_dir='ext/medvtok/weights', allow_patterns=['ckpt.pth', 'config.json']))"
+
+# ext/marker_embeddings/ (ESM-2 embeddings of the 16 marker proteins, VirTues input) ships with this repo
+test -d ext/marker_embeddings/esm2_t30_150M_UR50D && echo "marker embeddings ok"
+"$PY" -I -c "import os, sys; sys.path.insert(0, os.getcwd()); import embed; p = os.environ.get('UNI2_PATH', embed.UNI2_LOCAL); print('UNI2-h:', p if os.path.exists(p) else 'will be downloaded from the gated HF repo MahmoodLab/UNI2-h')"