diff --git a/data/phenotypes/pheno.allium.lilljebjorn.csv b/data/phenotypes/pheno.allium.lilljebjorn.csv
deleted file mode 100644
index b7ea232..0000000
--- a/data/phenotypes/pheno.allium.lilljebjorn.csv
+++ /dev/null
@@ -1,196 +0,0 @@
-public_id,Subtype
-Case_001,HeH
-Case_002,t(12;21)
-Case_003,t(12;21)
-Case_004,ph-like
-Case_005,ph-like
-Case_006,t(12;21)
-Case_007,11q23/MLL
-Case_008,B-other
-Case_009,B-other
-Case_010,11q23/MLL
-Case_011,B-other
-Case_012,HeH
-Case_013,t(12;21)
-Case_014,HeH
-Case_015,HeH
-Case_016,HeH
-Case_017,t(1;19)
-Case_018,HeH
-Case_019,HeH
-Case_020,B-other
-Case_021,HeH
-Case_022,11q23/MLL
-Case_023,HeH
-Case_024,t(12;21)
-Case_025,ph-like
-Case_026,HeH
-Case_027,HeH
-Case_028,HeH
-Case_029,HeH
-Case_030,t(12;21)
-Case_031,HeH
-Case_032,t(12;21)
-Case_033,t(12;21)
-Case_034,ph-like
-Case_035,DUX4-r
-Case_036,HeH
-Case_037,t(12;21)
-Case_038,HeH
-Case_039,B-other
-Case_040,ph-like
-Case_041,t(12;21)
-Case_042,HeH
-Case_043,t(9;22)
-Case_044,HeH
-Case_045,ph-like
-Case_046,t(1;19)
-Case_047,DUX4-r
-Case_048,HeH
-Case_049,HeH
-Case_050,t(12;21)
-Case_051,t(9;22)
-Case_052,t(12;21)
-Case_053,DUX4-r
-Case_054,HeH
-Case_055,HeH
-Case_056,HeH
-Case_057,t(12;21)
-Case_058,11q23/MLL
-Case_059,t(1;19)
-Case_060,PAX5alt
-Case_061,t(12;21)
-Case_062,ph-like
-Case_063,t(1;19)
-Case_064,t(12;21)-like
-Case_065,t(12;21)
-Case_066,t(1;19)
-Case_067,DUX4-r
-Case_068,t(12;21)-like
-Case_069,11q23/MLL
-Case_070,ph-like
-Case_071,t(12;21)
-Case_072,B-other
-Case_073,ph-like
-Case_074,Hypo
-Case_075,DUX4-r
-Case_076,PAX5alt
-Case_077,PAX5alt
-Case_078,HeH
-Case_079,t(9;22)
-Case_080,t(12;21)
-Case_081,B-other
-Case_082,HeH
-Case_083,t(1;19)
-Case_084,t(12;21)
-Case_085,t(12;21)-like
-Case_086,HeH
-Case_087,t(12;21)
-Case_088,Hypo
-Case_089,t(12;21)
-Case_090,HeH
-Case_091,t(12;21)
-Case_092,t(12;21)
-Case_093,t(12;21)
-Case_094,B-other
-Case_095,HeH
-Case_096,HeH
-Case_097,B-other
-Case_098,B-other
-Case_099,t(12;21)
-Case_100,B-other
-Case_101,HeH
-Case_102,11q23/MLL
-Case_103,B-other
-Case_104,HeH
-Case_105,t(12;21)-like
-Case_106,HeH
-Case_107,B-other
-Case_108,HeH
-Case_109,B-other
-Case_110,HeH
-Case_111,t(12;21)-like
-Case_112,HeH
-Case_113,HeH
-Case_114,t(12;21)
-Case_115,11q23/MLL
-Case_116,B-other
-Case_117,t(12;21)
-Case_118,t(12;21)
-Case_119,HeH
-Case_120,11q23/MLL
-Case_121,t(12;21)
-Case_122,ph-like
-Case_123,t(12;21)
-Case_124,DUX4-r
-Case_125,HeH
-Case_126,t(12;21)
-Case_127,11q23/MLL
-Case_128,HeH
-Case_129,t(12;21)
-Case_130,HeH
-Case_131,t(12;21)
-Case_132,t(12;21)
-Case_133,B-other
-Case_134,t(12;21)
-Case_135,11q23/MLL
-Case_136,HeH
-Case_137,HeH
-Case_138,t(12;21)
-Case_139,t(9;22)
-Case_140,t(1;19)
-Case_141,B-other
-Case_142,t(12;21)
-Case_143,t(12;21)
-Case_144,ph-like
-Case_145,ph-like
-Case_146,HeH
-Case_147,HeH
-Case_148,HeH
-Case_149,t(12;21)
-Case_150,ph-like
-Case_151,B-other
-Case_152,11q23/MLL
-Case_153,HeH
-Case_154,t(9;22)
-Case_155,t(12;21)
-Case_156,ph-like
-Case_157,t(1;19)
-Case_158,HeH
-Case_159,HeH
-Case_160,t(1;19)
-Case_161,ph-like
-Case_162,HeH
-Case_163,11q23/MLL
-Case_164,HeH
-Case_165,t(1;19)
-Case_166,HeH
-Case_167,11q23/MLL
-Case_168,t(12;21)
-Case_169,t(9;22)
-Case_170,11q23/MLL
-Case_171,t(12;21)
-Case_172,B-other
-Case_173,HeH
-Case_174,DUX4-r
-Case_175,HeH
-Case_176,t(12;21)-like
-Case_177,B-other
-Case_178,t(12;21)
-Case_179,DUX4-r
-Case_180,t(12;21)
-Case_181,iAMP21
-Case_182,HeH
-Case_183,t(1;19)
-Case_184,B-other
-Case_185,HeH
-Case_186,t(12;21)
-Case_187,t(12;21)
-Case_188,HeH
-Case_189,t(12;21)
-Case_190,t(12;21)
-Case_191,HeH
-Case_192,t(1;19)
-Case_193,t(12;21)
-Case_194,HeH
-Case_195,t(1;19)
diff --git a/data/phenotypes/pheno.allium.tran.csv b/data/phenotypes/pheno.allium.tran.csv
deleted file mode 100644
index 7b9b60d..0000000
--- a/data/phenotypes/pheno.allium.tran.csv
+++ /dev/null
@@ -1,174 +0,0 @@
-public_id,Subtype
-16-001,ETV6::RUNX1
-16-002,ETV6::RUNX1
-16-003,ETV6::RUNX1
-16-006,ETV6::RUNX1
-16-008,T-ALL
-16-011,T-ALL
-16-012,ETV6::RUNX1
-16-014,hyperdiploid
-16-015,hyperdiploid
-16-017,PAX5alt
-16-021,TCF3::PBX1
-16-022,B-other
-16-025,hyperdiploid
-16-027,DUX4-r
-16-029,DUX4-r
-16-033,DUX4-r
-16-035,T-ALL
-16-037,B-other
-16-038,KMT2A-r
-16-039,PAX5alt
-16-042,T-ALL
-16-044,BCR::ABL-like
-16-047,BCR::ABL-like
-16-048,hyperdiploid
-16-049,hyperdiploid
-16-050,ETV6::RUNX1
-16-052,T-ALL
-16-053,T-ALL
-16-056,T-ALL
-16-057,T-ALL
-16-059,T-ALL
-16-065,ETV6::RUNX1
-16-068,hypodiploid
-16-070,ETV6::RUNX1
-16-074,ETV6::RUNX1
-16-076,ETV6::RUNX1
-16-077,BCR::ABL-like
-16-082,MEF2D-r
-16-086,B-other
-16-089,ZNF384-r
-16-090,hyperdiploid
-16-092,ETV6::RUNX1
-16-094,ETV6::RUNX1
-16-095,T-ALL
-16-098,T-ALL
-16-099,KMT2A-r
-16-100,ETV6::RUNX1
-16-102,BCR::ABL-like
-16-103,hyperdiploid
-16-104,T-ALL
-16-105,DUX4-r
-16-106,ETV6::RUNX1
-16-108,ETV6::RUNX1-like
-16-114,T-ALL
-16-115,ETV6::RUNX1
-16-116,KMT2A-r
-16-129,hypodiploid
-16-131,hyperdiploid
-16-132,KMT2A-r
-16-138,T-ALL
-16-139,ETV6::RUNX1
-16-140,ETV6::RUNX1
-16-141,hyperdiploid
-16-144,T-ALL
-16-152,ETV6::RUNX1
-16-155,T-ALL
-16-158,hyperdiploid
-16-161,hyperdiploid
-16-162,hyperdiploid
-16-164,BCR::ABL-like
-16-167,T-ALL
-16-170,B-other
-16-171,T-ALL
-16-174,T-ALL
-16-176,hyperdiploid
-16-177,T-ALL
-16-179,BCR::ABL-like
-16-182,hyperdiploid
-16-186,hyperdiploid
-16-189,DUX4-r
-16-191,T-ALL
-16-192,TCF3::PBX1
-16-194,hyperdiploid
-16-196,T-ALL
-16-199,hyperdiploid
-16-200,TCF3::PBX1
-16-201,T-ALL
-16-202,B-other
-16-204,B-other
-16-205,TCF3::PBX1
-16-207,ZNF384-r
-16-210,hyperdiploid
-16-215,hyperdiploid
-16-217,T-ALL
-16-218,ZNF384-r
-16-220,B-other
-16-221,ETV6::RUNX1
-16-222,B-other
-16-223,T-ALL
-16-225,BCR::ABL-like
-16-226,PAX5alt
-16-227,T-ALL
-16-229,TCF3::PBX1
-16-230,DUX4-r
-16-231,PAX5alt
-16-232,BCR::ABL-like
-16-233,T-ALL
-16-238,ETV6::RUNX1
-16-239,hyperdiploid
-16-240,PAX5 P80R
-16-241,T-ALL
-16-242,hyperdiploid
-16-243,ETV6::RUNX1
-16-244,T-ALL
-16-245,T-ALL
-16-249,hyperdiploid
-16-252,T-ALL
-16-253,BCR::ABL-like
-16-256,T-ALL
-16-257,hyperdiploid
-16-258,TCF3::PBX1
-16-261,PAX5alt
-16-265,B-other
-16-266,iAMP21
-16-267,ETV6::RUNX1
-16-268,DUX4-r
-16-269,PAX5alt
-16-270,ZNF384-r
-16-272,hyperdiploid
-16-273,hyperdiploid
-16-279,hyperdiploid
-16-280,TCF3::PBX1
-16-282,hyperdiploid
-16-284,DUX4-r
-16-286,PAX5alt
-16-287,hyperdiploid
-16-291,"hyperdiploid,PAX5alt"
-16-293,ETV6::RUNX1
-16-294,DUX4-r
-16-295,hyperdiploid
-16-296,T-ALL
-16-302,hyperdiploid
-16-304,ETV6::RUNX1
-16-306,hyperdiploid
-16-312,ETV6::RUNX1
-16-315,hypodiploid
-16-319,KMT2A-r
-16-322,ETV6::RUNX1
-16-326,BCR::ABL-like
-16-328,DUX4-r
-16-335,hyperdiploid
-16-338,hyperdiploid
-16-339,hyperdiploid
-16-340,T-ALL
-16-341,"BCR::ABL1,iAMP21"
-16-342,hyperdiploid
-16-343,BCR::ABL-like
-16-346,NUTM1-r
-16-347,B-other
-16-348,BCR::ABL1
-16-350,ETV6::RUNX1
-16-352,ETV6::RUNX1
-16-354,ETV6::RUNX1
-16-359,B-other
-16-362,T-ALL
-16-363,ETV6::RUNX1-like
-16-364,B-other
-16-367,T-ALL
-16-372,B-other
-16-373,T-ALL
-16-374,hyperdiploid
-16-376,BCR::ABL-like
-16-378,B-other
diff --git a/data/phenotypes/pheno.lilljebjorn.csv b/data/phenotypes/pheno.lilljebjorn.csv
deleted file mode 100644
index c5a350b..0000000
--- a/data/phenotypes/pheno.lilljebjorn.csv
+++ /dev/null
@@ -1,196 +0,0 @@
-ID;Subtype
-1;High hyperdiploidy
-2;ETV6-RUNX1
-3;ETV6-RUNX1
-4;Ph-like
-5;Ph-like
-6;ETV6-RUNX1
-7;MLL
-8;B-other, with fusion
-9;B-other, with fusion
-10;MLL
-11;B-other, with fusion
-12;High hyperdiploidy
-13;ETV6-RUNX1
-14;High hyperdiploidy
-15;High hyperdiploidy
-16;High hyperdiploidy
-17;TCF3-PBX1
-18;High hyperdiploidy
-19;High hyperdiploidy
-20;B-other, with fusion
-21;High hyperdiploidy
-22;MLL
-23;High hyperdiploidy
-24;ETV6-RUNX1
-25;Ph-like
-26;High hyperdiploidy
-27;High hyperdiploidy
-28;High hyperdiploidy
-29;High hyperdiploidy
-30;ETV6-RUNX1
-31;High hyperdiploidy
-32;ETV6-RUNX1
-33;ETV6-RUNX1
-34;Ph-like
-35;DUX4-rearranged
-36;High hyperdiploidy
-37;ETV6-RUNX1
-38;High hyperdiploidy
-39;B-other, with fusion
-40;Ph-like
-41;ETV6-RUNX1
-42;High hyperdiploidy
-43;BCR-ABL1
-44;High hyperdiploidy
-45;Ph-like
-46;TCF3-PBX1
-47;DUX4-rearranged
-48;High hyperdiploidy
-49;High hyperdiploidy
-50;ETV6-RUNX1
-51;BCR-ABL1
-52;ETV6-RUNX1
-53;DUX4-rearranged
-54;High hyperdiploidy
-55;High hyperdiploidy
-56;High hyperdiploidy
-57;ETV6-RUNX1
-58;MLL
-59;TCF3-PBX1
-60;"dic(9;20)"
-61;ETV6-RUNX1
-62;Ph-like
-63;TCF3-PBX1
-64;ETV6-RUNX1-like
-65;ETV6-RUNX1
-66;TCF3-PBX1
-67;DUX4-rearranged
-68;ETV6-RUNX1-like
-69;MLL
-70;Ph-like
-71;ETV6-RUNX1
-72;B-other, without fusion
-73;Ph-like
-74;Hypodiploid
-75;DUX4-rearranged
-76;"dic(9;20)"
-77;"dic(9;20)"
-78;High hyperdiploidy
-79;BCR-ABL1
-80;ETV6-RUNX1
-81;B-other, with fusion
-82;High hyperdiploidy
-83;TCF3-PBX1
-84;ETV6-RUNX1
-85;ETV6-RUNX1-like
-86;High hyperdiploidy
-87;ETV6-RUNX1
-88;Hypodiploid
-89;ETV6-RUNX1
-90;High hyperdiploidy
-91;ETV6-RUNX1
-92;ETV6-RUNX1
-93;ETV6-RUNX1
-94;B-other, without fusion
-95;High hyperdiploidy
-96;High hyperdiploidy
-97;B-other, with fusion
-98;B-other, without fusion
-99;ETV6-RUNX1
-100;B-other, with fusion
-101;High hyperdiploidy
-102;MLL
-103;B-other, without fusion
-104;High hyperdiploidy
-105;ETV6-RUNX1-like
-106;High hyperdiploidy
-107;B-other, with fusion
-108;High hyperdiploidy
-109;B-other, with fusion
-110;High hyperdiploidy
-111;ETV6-RUNX1-like
-112;High hyperdiploidy
-113;High hyperdiploidy
-114;ETV6-RUNX1
-115;MLL
-116;B-other, with fusion
-117;ETV6-RUNX1
-118;ETV6-RUNX1
-119;High hyperdiploidy
-120;MLL
-121;ETV6-RUNX1
-122;Ph-like
-123;ETV6-RUNX1
-124;DUX4-rearranged
-125;High hyperdiploidy
-126;ETV6-RUNX1
-127;MLL
-128;High hyperdiploidy
-129;ETV6-RUNX1
-130;High hyperdiploidy
-131;ETV6-RUNX1
-132;ETV6-RUNX1
-133;B-other, with fusion
-134;ETV6-RUNX1
-135;MLL
-136;High hyperdiploidy
-137;High hyperdiploidy
-138;ETV6-RUNX1
-139;BCR-ABL1
-140;TCF3-PBX1
-141;B-other, with fusion
-142;ETV6-RUNX1
-143;ETV6-RUNX1
-144;Ph-like
-145;Ph-like
-146;High hyperdiploidy
-147;High hyperdiploidy
-148;High hyperdiploidy
-149;ETV6-RUNX1
-150;Ph-like
-151;B-other, with fusion
-152;MLL
-153;High hyperdiploidy
-154;BCR-ABL1
-155;ETV6-RUNX1
-156;Ph-like
-157;TCF3-PBX1
-158;High hyperdiploidy
-159;High hyperdiploidy
-160;TCF3-PBX1
-161;Ph-like
-162;High hyperdiploidy
-163;MLL
-164;High hyperdiploidy
-165;TCF3-PBX1
-166;High hyperdiploidy
-167;MLL
-168;ETV6-RUNX1
-169;BCR-ABL1
-170;MLL
-171;ETV6-RUNX1
-172;B-other, with fusion
-173;High hyperdiploidy
-174;DUX4-rearranged
-175;High hyperdiploidy
-176;ETV6-RUNX1-like
-177;B-other, with fusion
-178;ETV6-RUNX1
-179;DUX4-rearranged
-180;ETV6-RUNX1
-181;iAMP21
-182;High hyperdiploidy
-183;TCF3-PBX1
-184;B-other, with fusion
-185;High hyperdiploidy
-186;ETV6-RUNX1
-187;ETV6-RUNX1
-188;High hyperdiploidy
-189;ETV6-RUNX1
-190;ETV6-RUNX1
-191;High hyperdiploidy
-192;TCF3-PBX1
-193;ETV6-RUNX1
-194;High hyperdiploidy
-195;TCF3-PBX1
\ No newline at end of file
diff --git a/predict.py b/predict.py
index c00d90d..0efb33d 100644
--- a/predict.py
+++ b/predict.py
@@ -2,7 +2,7 @@
 from src.allium.gex_classifier import GEXClassifier
 
 testX = pd.read_csv('/home/mariya/Data/tran/counts.allium.tran.csv', index_col="public_id")
-pheno = pd.read_csv('/home/mariya/Development/allium/data/phenotypes/pheno.allium.tran.csv', index_col = "public_id")
+pheno = pd.read_csv('/home/mariya/Data/tran/pheno.allium.tran.csv', index_col = "public_id")
 
 gc = GEXClassifier('v3')
 
diff --git a/src/experiments/lilljebjorn/standardize_phenotypes.py b/src/experiments/lilljebjorn/standardize_phenotypes.py
index 39982a6..4487bd2 100644
--- a/src/experiments/lilljebjorn/standardize_phenotypes.py
+++ b/src/experiments/lilljebjorn/standardize_phenotypes.py
@@ -3,7 +3,7 @@
 import os
 
 # GEX data from Lilljebjorn et al. 2016
-path_to_data = '/Users/marly389/Data/lilljebjorn/'
+path_to_data = '/home/mariya/Data/lilljebjorn/'
 input_file = f'{path_to_data}/pheno.lilljebjorn.csv'
 output_file = f'{path_to_data}/pheno.allium.lilljebjorn.csv'
 
diff --git a/src/experiments/lilljebjorn/subtypes_to_allium.yml b/src/experiments/lilljebjorn/subtypes_to_allium.yml
index e62c061..9321373 100644
--- a/src/experiments/lilljebjorn/subtypes_to_allium.yml
+++ b/src/experiments/lilljebjorn/subtypes_to_allium.yml
@@ -1,13 +1,13 @@
-High hyperdiploidy: HeH
-ETV6-RUNX1: t(12;21)
-Ph-like: ph-like
-MLL: 11q23/MLL
+High hyperdiploidy: hyperdiploid
+ETV6-RUNX1: ETV6::RUNX1
+Ph-like: BCR::ABL1-like
+MLL: KMT2A-r
 B-other, with fusion: B-other
-TCF3-PBX1: t(1;19)
+TCF3-PBX1: TCF3::PBX1
 DUX4-rearranged: DUX4-r
-BCR-ABL1: t(9;22)
+BCR-ABL1: BCR::ABL1
 dic(9;20): PAX5alt
-ETV6-RUNX1-like: t(12;21)-like
+ETV6-RUNX1-like: ETV6::RUNX1-like
 B-other, without fusion: B-other
-Hypodiploid: Hypo
+Hypodiploid: hypodiploid