Delete folder RSNA after moving to output/

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/aligner_30.pth

@@ -1,3 +0,0 @@
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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/aligner_out.txt

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-2024-10-29 03:08:47,564 - Train size: classifier [(27258, 2048)], clip [(27258, 512)]
-2024-10-29 03:08:47,564 - Valid size: classifier [(13766, 2048)], clip [(13766, 512)]
-2024-10-29 03:08:47,564 - Training linear aligner ...
-2024-10-29 03:08:47,564 - Linear alignment train: ((27258, 2048)) --> ((27258, 512)).
-2024-10-29 03:08:47,564 - Linear alignment test: ((13766, 2048)) --> ((13766, 512)).
-2024-10-29 03:08:49,301 - Initial MSE, R^2: 6.008, -0.335
-2024-10-29 03:08:50,583 - Epoch number, 0, train loss: 2.330, test MSE: 1.809, test_r2: 0.598, best MSE: 1.809
-2024-10-29 03:08:51,289 - Epoch number, 1, train loss: 1.716, test MSE: 1.567, test_r2: 0.652, best MSE: 1.567
-2024-10-29 03:08:51,997 - Epoch number, 2, train loss: 1.548, test MSE: 1.455, test_r2: 0.677, best MSE: 1.455
-2024-10-29 03:08:52,740 - Epoch number, 3, train loss: 1.460, test MSE: 1.401, test_r2: 0.689, best MSE: 1.401
-2024-10-29 03:08:53,470 - Epoch number, 4, train loss: 1.400, test MSE: 1.339, test_r2: 0.703, best MSE: 1.339
-2024-10-29 03:08:54,203 - Epoch number, 5, train loss: 1.357, test MSE: 1.304, test_r2: 0.710, best MSE: 1.304
-2024-10-29 03:08:54,950 - Epoch number, 6, train loss: 1.319, test MSE: 1.279, test_r2: 0.716, best MSE: 1.279
-2024-10-29 03:08:55,679 - Epoch number, 7, train loss: 1.292, test MSE: 1.265, test_r2: 0.719, best MSE: 1.265
-2024-10-29 03:08:56,415 - Epoch number, 8, train loss: 1.270, test MSE: 1.237, test_r2: 0.725, best MSE: 1.237
-2024-10-29 03:08:57,165 - Epoch number, 9, train loss: 1.252, test MSE: 1.228, test_r2: 0.727, best MSE: 1.228
-2024-10-29 03:08:57,901 - Epoch number, 10, train loss: 1.233, test MSE: 1.204, test_r2: 0.733, best MSE: 1.204
-2024-10-29 03:08:58,656 - Epoch number, 11, train loss: 1.217, test MSE: 1.185, test_r2: 0.737, best MSE: 1.185
-2024-10-29 03:08:59,421 - Epoch number, 12, train loss: 1.203, test MSE: 1.166, test_r2: 0.741, best MSE: 1.166
-2024-10-29 03:09:00,174 - Epoch number, 13, train loss: 1.191, test MSE: 1.179, test_r2: 0.738, best MSE: 1.166
-2024-10-29 03:09:00,910 - Epoch number, 14, train loss: 1.183, test MSE: 1.159, test_r2: 0.743, best MSE: 1.159
-2024-10-29 03:09:01,653 - Epoch number, 15, train loss: 1.170, test MSE: 1.152, test_r2: 0.744, best MSE: 1.152
-2024-10-29 03:09:02,391 - Epoch number, 16, train loss: 1.162, test MSE: 1.138, test_r2: 0.747, best MSE: 1.138
-2024-10-29 03:09:03,118 - Epoch number, 17, train loss: 1.153, test MSE: 1.137, test_r2: 0.747, best MSE: 1.137
-2024-10-29 03:09:03,844 - Epoch number, 18, train loss: 1.147, test MSE: 1.127, test_r2: 0.750, best MSE: 1.127
-2024-10-29 03:09:04,594 - Epoch number, 19, train loss: 1.138, test MSE: 1.133, test_r2: 0.748, best MSE: 1.127
-2024-10-29 03:09:05,341 - Epoch number, 20, train loss: 1.133, test MSE: 1.125, test_r2: 0.750, best MSE: 1.125
-2024-10-29 03:09:06,066 - Epoch number, 21, train loss: 1.124, test MSE: 1.113, test_r2: 0.753, best MSE: 1.113
-2024-10-29 03:09:06,811 - Epoch number, 22, train loss: 1.121, test MSE: 1.098, test_r2: 0.756, best MSE: 1.098
-2024-10-29 03:09:07,546 - Epoch number, 23, train loss: 1.116, test MSE: 1.097, test_r2: 0.756, best MSE: 1.097
-2024-10-29 03:09:08,279 - Epoch number, 24, train loss: 1.111, test MSE: 1.096, test_r2: 0.756, best MSE: 1.096
-2024-10-29 03:09:09,006 - Epoch number, 25, train loss: 1.106, test MSE: 1.085, test_r2: 0.759, best MSE: 1.085
-2024-10-29 03:09:09,751 - Epoch number, 26, train loss: 1.101, test MSE: 1.082, test_r2: 0.760, best MSE: 1.082
-2024-10-29 03:09:10,488 - Epoch number, 27, train loss: 1.097, test MSE: 1.085, test_r2: 0.759, best MSE: 1.082
-2024-10-29 03:09:11,219 - Epoch number, 28, train loss: 1.093, test MSE: 1.085, test_r2: 0.759, best MSE: 1.082
-2024-10-29 03:09:11,951 - Epoch number, 29, train loss: 1.088, test MSE: 1.073, test_r2: 0.762, best MSE: 1.073
-2024-10-29 03:09:11,964 - Aligner weights saved to /restricted/projectnb/batmanlab/shawn24/PhD/Ladder/out/RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/aligner_30.pth
-2024-10-29 03:09:11,964 - Saved aligner to /restricted/projectnb/batmanlab/shawn24/PhD/Ladder/out/RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/all_slices_y_ensemble_yes_H1_vascular calcifications.pth

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/all_slices_y_ensemble_yes_H2_scattered calcifications.pth

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/all_slices_y_ensemble_yes_H3_benign appearing calcifications.pth

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/all_slices_y_ensemble_yes_H4_bilateral findings.pth

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/all_slices_y_ensemble_yes_H5_small masses.pth

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/attr_embs_report.pth

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/cancer_error_top_100_sent_diff_emb.txt

@@ -1,100 +0,0 @@
-1. multiple densities and calcifications again seen bilaterally
-2. scattered linear type secretory calcifications are noted bilaterally
-3. multiple scattered masses , densities , and calcifications again seen bilaterally
-4. a few scattered densities and multiple scattered calcifications again seen bilaterally
-5. benign - appearing punctate and round calcifications are scattered through the breasts bilaterally
-6. multiple bilateral scattered round calcifications are again seen
-7. a few bilateral scattered benign appearing round and punctate calcifications are again seen in both breasts
-8. multiple scattered densities and calcifications again seen bilaterally
-9. multiple bilateral scattered punctate calcifications are again seen
-10. multiple skin moles are present bilaterally
-11. multiple bilateral scattered round calcifications again seen are considered benign
-12. multiple scattered calcifications and a few scattered densities are again seen bilaterally
-13. numerous moles were marked bilaterally
-14. multiple scattered small masses , densities , and calcifications again seen bilaterally
-15. multiple scattered masses and densities and a few scattered calcifications again seen bilaterally
-16. multiple bilateral scattered punctate and round calcifications again seen appear benign
-17. numerous scattered punctate calcifications are seen again in both breasts
-18. numerous scattered calcifications and a few densities again seen bilaterally
-19. multiple scattered calcifications and densities again seen bilaterally
-20. benign calcifications are identified along with bilateral asymmetries
-21. multiple scattered calcifications and a few densities again seen bilaterally
-22. several bilateral scattered punctate calcifications seen are considered benign
-23. multiple scattered densities and a few calcifications again seen bilaterally
-24. multiple scattered calcifications and densities again seen
-25. a few scattered masses , densities , and calcifications again seen bilaterally
-26. multiple scattered densities and a few calcifications are again seen bilaterally
-27. the scattered calcifications and densities again seen bilaterally
-28. a few scattered small masses and densities and multiple scattered calcifications are again seen bilaterally
-29. multiple scattered calcifications and densities again seen in the right breast
-30. multiple scattered small densities and calcifications again seen bilaterally
-31. multiple scattered small densities and calcifications again seen
-32. bilateral diffusely scattered punctate calcifications are again seen
-33. multiple scattered calcifications and a few scattered densities again seen bilaterally
-34. bilateral diffusely scattered benign appearing round calcifications are again seen
-35. [ date ] and [ date ] bilateral vascular calcifications are noted
-36. a few scattered densities and tiny calcifications again seen bilaterally
-37. vascular calcifications and a few scattered calcifications and densities are again seen
-38. multiple small scattered densities and calcifications again seen bilaterally
-39. several bilateral benign appearing scattered punctate calcifications are again seen in both breasts
-40. vascular calcifications and multiple scattered calcifications and densities again seen bilaterally
-41. bilateral scattered stable round calcifications seen in both breasts are considered benign
-42. a group of subcutaneous and cutaneous calcifications is located in between the two masses
-43. multiple scattered calcifications and small densities again seen
-44. multiple bilateral scattered calcified oil cysts are again seen
-45. bilateral scattered secretory calcifications are stable
-46. vascular calcifications and multiple scattered calcifications and a few scattered densities again seen bilaterally
-47. multiple scattered calcifications and a few masses and densities again seen bilaterally
-48. several bilateral scattered calcified oil cysts are again seen
-49. bilateral vascular calcifications are evident
-50. vascular calcifications and multiple scattered calcifications again seen bilaterally
-51. multiple bilateral scattered calcified oil cysts are also again seen
-52. vascular calcifications and a few scattered calcifications , densities , and small masses again seen bilaterally
-53. vascular calcifications and a few scattered calcifications and densities again seen
-54. vascular calcifications and scattered calcifications again seen bilaterally
-55. vascular calcifications and multiple scattered calcifications and small densities again seen bilaterally
-56. numerous scattered calcifications again seen bilaterally
-57. benign - appearing large rodlike calcifications are also seen within both breasts
-58. multiple small masses and densities and a few scattered calcifications again seen bilaterally
-59. multiple scattered calcifications and a few density is again seen bilaterally
-60. multiple scattered calcifications and a few scattered small densities are again seen bilaterally
-61. extensive calcifications including vascular calcification can be appreciated bilaterally
-62. bilateral nodule vascular calcifications in the right breast are noted
-63. a few scattered densities and calcifications again seen bilaterally
-64. benign calcifications to include vascular calcifications are seen in both breasts
-65. a left postsurgical scar is marked by 2 cutaneous bbs
-66. multiple scattered calcifications and a few scattered small densities again seen bilaterally
-67. vascular calcifications and a few scattered calcifications , small masses and densities again seen bilaterally
-68. the patient is 77 years old
-69. vascular calcifications and multiple scattered calcifications are again seen bilaterally
-70. calcifications are arranged in multiple clusters and are variable in size
-71. vascular calcifications and multiple scattered calcifications and a few scattered small masses and densities again seen bilaterally
-72. bilateral diffusely scattered stable benign appearing round calcifications are again seen
-73. benign secretory calcifications can be identified bilaterally
-74. multiple scattered calcifications and small densities again seen bilaterally
-75. multiple scattered calcifications , masses , and small densities again seen bilaterally
-76. vascular calcifications and a few scattered calcifications and small densities again seen
-77. multiple scattered calcifications and a few densities again seen in both breasts
-78. a right postsurgical scar is marked by 2 cutaneous bbs
-79. multiple bilateral scattered punctate calcifications again seen are considered benign
-80. vascular calcifications and multiple scattered calcifications and a few densities again seen bilaterally
-81. multiple scattered calcifications and a few scattered densities and small masses again seen bilaterally
-82. bilateral scattered stable subcentimeter masses and bilateral scattered round calcifications are considered benign
-83. vascular calcifications and a few scattered calcifications and densities again seen bilaterally
-84. a few typically benign calcifications are noted bilaterally as are vascular calcifications
-85. vascular calcifications and multiple scattered calcifications , small masses , and densities again seen bilaterally
-86. multiple scattered calcifications and a few scattered small densities again seen
-87. multiple bilateral diffusely scattered benign appearing round calcifications are again seen
-88. multiple scattered calcifications again seen bilaterally
-89. multiple scattered calcifications and a few small densities again seen bilaterally
-90. scattered coarse calcifications and vascular calcifications are again seen in both breasts
-91. vascular calcifications and a few scattered calcifications , small masses , and densities again seen bilaterally
-92. vascular calcifications and multiple scattered calcifications are present bilaterally , progressive , but with a benign appearance
-93. the overlying surgical scar is marked by 2 cutaneous bbs
-94. the patient is 78 years old
-95. vascular calcifications and multiple scattered calcifications again seen
-96. vascular calcifications and a few scattered calcifications and densities again seen in both breasts
-97. multiple calcifications again seen bilaterally
-98. vascular calcifications and a few scattered calcifications and small masses and densities again seen bilaterally
-99. multiple stable and benign calcifications and vascular calcifications are again seen in both breasts
-100. few benign calcified patient present bilaterally

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/cancer_error_top_50_sent_diff_emb.txt

@@ -1,50 +0,0 @@
-1. multiple densities and calcifications again seen bilaterally
-2. scattered linear type secretory calcifications are noted bilaterally
-3. multiple scattered masses , densities , and calcifications again seen bilaterally
-4. a few scattered densities and multiple scattered calcifications again seen bilaterally
-5. benign - appearing punctate and round calcifications are scattered through the breasts bilaterally
-6. multiple bilateral scattered round calcifications are again seen
-7. a few bilateral scattered benign appearing round and punctate calcifications are again seen in both breasts
-8. multiple scattered densities and calcifications again seen bilaterally
-9. multiple bilateral scattered punctate calcifications are again seen
-10. multiple skin moles are present bilaterally
-11. multiple bilateral scattered round calcifications again seen are considered benign
-12. multiple scattered calcifications and a few scattered densities are again seen bilaterally
-13. numerous moles were marked bilaterally
-14. multiple scattered small masses , densities , and calcifications again seen bilaterally
-15. multiple scattered masses and densities and a few scattered calcifications again seen bilaterally
-16. multiple bilateral scattered punctate and round calcifications again seen appear benign
-17. numerous scattered punctate calcifications are seen again in both breasts
-18. numerous scattered calcifications and a few densities again seen bilaterally
-19. multiple scattered calcifications and densities again seen bilaterally
-20. benign calcifications are identified along with bilateral asymmetries
-21. multiple scattered calcifications and a few densities again seen bilaterally
-22. several bilateral scattered punctate calcifications seen are considered benign
-23. multiple scattered densities and a few calcifications again seen bilaterally
-24. multiple scattered calcifications and densities again seen
-25. a few scattered masses , densities , and calcifications again seen bilaterally
-26. multiple scattered densities and a few calcifications are again seen bilaterally
-27. the scattered calcifications and densities again seen bilaterally
-28. a few scattered small masses and densities and multiple scattered calcifications are again seen bilaterally
-29. multiple scattered calcifications and densities again seen in the right breast
-30. multiple scattered small densities and calcifications again seen bilaterally
-31. multiple scattered small densities and calcifications again seen
-32. bilateral diffusely scattered punctate calcifications are again seen
-33. multiple scattered calcifications and a few scattered densities again seen bilaterally
-34. bilateral diffusely scattered benign appearing round calcifications are again seen
-35. [ date ] and [ date ] bilateral vascular calcifications are noted
-36. a few scattered densities and tiny calcifications again seen bilaterally
-37. vascular calcifications and a few scattered calcifications and densities are again seen
-38. multiple small scattered densities and calcifications again seen bilaterally
-39. several bilateral benign appearing scattered punctate calcifications are again seen in both breasts
-40. vascular calcifications and multiple scattered calcifications and densities again seen bilaterally
-41. bilateral scattered stable round calcifications seen in both breasts are considered benign
-42. a group of subcutaneous and cutaneous calcifications is located in between the two masses
-43. multiple scattered calcifications and small densities again seen
-44. multiple bilateral scattered calcified oil cysts are again seen
-45. bilateral scattered secretory calcifications are stable
-46. vascular calcifications and multiple scattered calcifications and a few scattered densities again seen bilaterally
-47. multiple scattered calcifications and a few masses and densities again seen bilaterally
-48. several bilateral scattered calcified oil cysts are again seen
-49. bilateral vascular calcifications are evident
-50. vascular calcifications and multiple scattered calcifications again seen bilaterally

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/cancer_hypothesis_dict.pkl

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/cancer_prompt_dict.pkl

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RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/ladder_discover_slices.txt

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-2024-08-06 05:53:35,529 - 
-
-2024-08-06 05:53:35,529 - /restricted/projectnb/batmanlab/shawn24/PhD/Multimodal-mistakes-debug/out/RSNA/Neurips_valid/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect
-2024-08-06 05:53:35,552 - Prediction columns: ('out_put_predict', 'out_put_predict')
-2024-08-06 05:53:35,567 - Avg. accuracy worst group: 0.5844155844155844
-2024-08-06 05:53:35,567 - 
-
-2024-08-06 05:53:35,567 - ##################################################################################################################################
-2024-08-06 05:53:35,567 - ####################################### Cancer error slices #######################################
-2024-08-06 05:53:35,809 - 
-Correct: 0, InCorrect: 0
-2024-08-06 05:53:35,809 - Clf Shapes:
-2024-08-06 05:53:35,809 - img_emb_clf: (13766, 2048)
-2024-08-06 05:53:35,809 - img_emb_clf_corr: (0, 2048), img_emb_clf_incorr: (0, 2048)
-2024-08-06 05:53:35,809 - ==============> Aligner weights and biases <================
-2024-08-06 05:53:35,809 - /restricted/projectnb/batmanlab/shawn24/PhD/Multimodal-mistakes-debug/out/RSNA/Neurips_valid/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/aligner_30.pth
-2024-08-06 05:53:35,867 - 
-W: tensor([ 0.0035,  0.0068, -0.0077, -0.0038, -0.0024,  0.0035, -0.0010,  0.0033,
-         0.0017,  0.0031]), b: tensor([ 0.0017, -0.0026,  0.0014, -0.0008, -0.0024, -0.0022, -0.0019,  0.0024,
-        -0.0044,  0.0014])
-2024-08-06 05:53:35,867 - Shapes after projecting to clip:
-2024-08-06 05:53:35,867 - 
-Correct: (0, 512), InCorrect: (0, 512)
-2024-08-06 05:53:35,867 - 
-Mean Correct: torch.Size([512]), Mean InCorrect: torch.Size([512])
-2024-08-06 05:53:35,867 - ######################################################################
-2024-08-06 05:53:35,867 - Top sentences using the difference of correct and incorrect embeddings:
-2024-08-06 05:53:35,868 - torch.Size([512])
-2024-08-06 05:53:35,868 - /restricted/projectnb/batmanlab/shawn24/PhD/Multimodal-mistakes-debug/out/RSNA/Neurips_valid/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/sent_emb_word_ge_3.npy
-2024-08-06 05:53:35,930 - torch.Size([10018, 512])
-2024-08-06 05:53:35,935 - torch.Size([10018])
-2024-08-06 05:53:35,955 - Length of report sentences: 10018
-2024-08-06 05:53:35,955 - Length of report sentences: 10018
-2024-08-06 05:53:35,955 - 
- 
-2024-08-06 05:53:35,955 - 1. due to patient ' s physical limitations , the axillary tail portions of both breasts could not be included , decreasing the sensitivity of this examination
-2024-08-06 05:53:35,955 - 2. stable benign - appearing calcifications are noted in the left breast
-2024-08-06 05:53:35,955 - 3. benign - appearing calcifications are present throughout the right breasts
-2024-08-06 05:53:35,955 - 4. graph the parenchyma consists of heterogeneous fibroglandular tissue
-2024-08-06 05:53:35,955 - 5. 9 . 6 mm well - rounded mass is seen amongst heterogeneous fibroglandular tissue in the upper outer quadrant of the right breast
-2024-08-06 05:53:35,955 - 6. other benign calcifications are seen in the left breast
-2024-08-06 05:53:35,955 - 7. postsurgical changes from benign excisional biopsy are present in the posterior upper outer left breast
-2024-08-06 05:53:35,955 - 8. ultrasound of the left breast is recommended of the mass in the 12 : 00 position of the middle one third of the left breast
-2024-08-06 05:53:35,955 - 9. multiple scattered calcifications and densities again seen in the right breast
-2024-08-06 05:53:35,955 - 10. a stable low - density nodule is present in the upper outer right breast middle third depth
-2024-08-06 05:53:35,955 - 11. a few small masses and densities again seen
-2024-08-06 05:53:35,955 - 12. the left breast is unremarkable
-2024-08-06 05:53:35,955 - 13. no mammographic evidence of malignancy is identified in the left breast
-2024-08-06 05:53:35,955 - 14. recommend right diagnostic mammogram with right breast ultrasound if indicated
-2024-08-06 05:53:35,955 - 15. two stable nodules in the posterior upper outer left breast which likely represents an intramammary lymph nodes
-2024-08-06 05:53:35,955 - 16. a fibrocystic cluster at 1 : 00 - 2 : 00 at 6 cm from the nipple measures 0 . 5 x 0 . 8 x 0 . 2 cm
-2024-08-06 05:53:35,955 - 17. several scattered punctate calcifications again seen in both breasts appear benign
-2024-08-06 05:53:35,955 - 18. nodular densities are seen in the bilateral breast
-2024-08-06 05:53:35,955 - 19. no other asymmetry left breast : there is a circumscribed nodule in the anterior medial breast , 8 mm in diameter
-2024-08-06 05:53:35,955 - 20. stable postsurgical changes in the right breast with no mammographic evidence of malignancy in either breast
-2024-08-06 05:53:35,955 - 21. spot compression views of the asymmetric nodular densities are recommended in both breasts
-2024-08-06 05:53:35,955 - 22. no significant change from previous exams
-2024-08-06 05:53:35,955 - 23. there is a stable small mass upper outer quadrant right breast
-2024-08-06 05:53:35,955 - 24. please note this cannot correspond to the medial mass seen on mammography as this is in a different quadrant
-2024-08-06 05:53:35,955 - 25. no suspicious mass or asymmetry is seen on the left
-2024-08-06 05:53:35,955 - 26. small scattered nodular densities are noted posterior medially and bilaterally
-2024-08-06 05:53:35,955 - 27. there is a small asymmetry central upper left breast middle depth on the mlo view
-2024-08-06 05:53:35,955 - 28. suspicious spiculated mass in the retroareolar right breast in approximately the 12 : 00 position associated with pleomorphism and ductal calcifications present over a much broader area
-2024-08-06 05:53:35,955 - 29. there are a few scattered calcifications , mildly progressive , but with a benign appearance
-2024-08-06 05:53:35,955 - 30. a stable nodule is present in the 12 : 00 left breast middle third depth
-2024-08-06 05:53:35,955 - 31. the left breast focal asymmetry needs additional imaging
-2024-08-06 05:53:35,955 - 32. however this does demonstrate modest central vascularity
-2024-08-06 05:53:35,955 - 33. there is a possible developing asymmetry in the medial right breast
-2024-08-06 05:53:35,955 - 34. no suspicious findings or significant changes are present as compared to the prior examination ( s ), the most recent dated [ date ] except that several small benign appearing calcifications are noted on the right new since the previous study
-2024-08-06 05:53:35,955 - 35. stable density upper outer quadrant left breast
-2024-08-06 05:53:35,955 - 36. there is a small asymmetry central lateral right breast on the cc view
-2024-08-06 05:53:35,955 - 37. there is no evidence of new mass , suspicious microcalcifications or nonsurgical distortion
-2024-08-06 05:53:35,955 - 38. a benign nodule in the medial right breast is stable
-2024-08-06 05:53:35,955 - 39. overall pattern appears stable when compared with the 2 previous sonograms dating back to .
-2024-08-06 05:53:35,955 - 40. stable small benign - appearing nodules in both breasts are noted
-2024-08-06 05:53:35,956 - 41. an additional cyst at 4 : 00 and 8 : 00 are identified
-2024-08-06 05:53:35,956 - 42. ultrasound evaluation of the entire right and left breastwas performed by the ultrasonographer
-2024-08-06 05:53:35,956 - 43. an oval focal asymmetry / nodule that is stable over multiple prior mammograms is seen in the lower inner left breast at anterior depth
-2024-08-06 05:53:35,956 - 44. the left breast shows no suspicious findings as compared to the prior examination ( s ), the most recent of which is dated [ date ]
-2024-08-06 05:53:35,956 - 45. there are 8 a few bilateral benign - appearing calcifications
-2024-08-06 05:53:35,956 - 46. this is present in the lower midline of the right breast
-2024-08-06 05:53:35,956 - 47. benign bilateral nodular fibroglandular tissue is seen
-2024-08-06 05:53:35,956 - 48. bilateral nodular asymmetry for which spot compression and true lateral views are recommended for further evaluation
-2024-08-06 05:53:35,956 - 49. there is a new mass in the posterior left breast seen centrally on the cc view , likely inferiorly on the mlo view
-2024-08-06 05:53:35,956 - 50. multiple radiopaque markers denote skin lesions
-2024-08-06 15:12:14,032 - 
-
-2024-08-06 15:12:14,032 - /restricted/projectnb/batmanlab/shawn24/PhD/Multimodal-mistakes-debug/out/RSNA/Neurips_valid/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect
-2024-08-06 15:12:14,041 - Prediction columns: ('out_put_predict', 'out_put_predict')
-2024-08-06 15:12:14,057 - Avg. accuracy worst group: 0.5844155844155844
-2024-08-06 15:12:14,057 - 
-
-2024-08-06 15:12:14,057 - ##################################################################################################################################
-2024-08-06 15:12:14,057 - ####################################### Cancer error slices #######################################
-2024-08-06 15:12:14,082 - 
-Correct: 0, InCorrect: 0
-2024-08-06 15:12:14,082 - Clf Shapes:
-2024-08-06 15:12:14,082 - img_emb_clf: (13766, 2048)
-2024-08-06 15:12:14,082 - img_emb_clf_corr: (0, 2048), img_emb_clf_incorr: (0, 2048)
-2024-08-06 15:12:14,082 - ==============> Aligner weights and biases <================
-2024-08-06 15:12:14,082 - /restricted/projectnb/batmanlab/shawn24/PhD/Multimodal-mistakes-debug/out/RSNA/Neurips_valid/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/aligner_30.pth
-2024-08-06 15:12:14,099 - 
-W: tensor([ 0.0035,  0.0068, -0.0077, -0.0038, -0.0024,  0.0035, -0.0010,  0.0033,
-         0.0017,  0.0031]), b: tensor([ 0.0017, -0.0026,  0.0014, -0.0008, -0.0024, -0.0022, -0.0019,  0.0024,
-        -0.0044,  0.0014])
-2024-08-06 15:12:14,099 - Shapes after projecting to clip:
-2024-08-06 15:12:14,099 - 
-Correct: (0, 512), InCorrect: (0, 512)
-2024-08-06 15:12:14,100 - 
-Mean Correct: torch.Size([512]), Mean InCorrect: torch.Size([512])
-2024-08-06 15:12:14,100 - ######################################################################
-2024-08-06 15:12:14,100 - Top sentences using the difference of correct and incorrect embeddings:
-2024-08-06 15:12:14,100 - torch.Size([512])
-2024-08-06 15:12:14,100 - /restricted/projectnb/batmanlab/shawn24/PhD/Multimodal-mistakes-debug/out/RSNA/Neurips_valid/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/sent_emb_word_ge_3.npy
-2024-08-06 15:12:14,109 - torch.Size([10018, 512])
-2024-08-06 15:12:14,114 - torch.Size([10018])
-2024-08-06 15:12:14,117 - Length of report sentences: 10018
-2024-08-06 15:12:14,117 - Length of report sentences: 10018
-2024-08-06 15:12:14,117 - 
- 
-2024-08-06 15:12:14,117 - 1. due to patient ' s physical limitations , the axillary tail portions of both breasts could not be included , decreasing the sensitivity of this examination
-2024-08-06 15:12:14,117 - 2. stable benign - appearing calcifications are noted in the left breast
-2024-08-06 15:12:14,117 - 3. benign - appearing calcifications are present throughout the right breasts
-2024-08-06 15:12:14,117 - 4. graph the parenchyma consists of heterogeneous fibroglandular tissue
-2024-08-06 15:12:14,117 - 5. 9 . 6 mm well - rounded mass is seen amongst heterogeneous fibroglandular tissue in the upper outer quadrant of the right breast
-2024-08-06 15:12:14,117 - 6. other benign calcifications are seen in the left breast
-2024-08-06 15:12:14,117 - 7. postsurgical changes from benign excisional biopsy are present in the posterior upper outer left breast
-2024-08-06 15:12:14,117 - 8. ultrasound of the left breast is recommended of the mass in the 12 : 00 position of the middle one third of the left breast
-2024-08-06 15:12:14,117 - 9. multiple scattered calcifications and densities again seen in the right breast
-2024-08-06 15:12:14,117 - 10. a stable low - density nodule is present in the upper outer right breast middle third depth
-2024-08-06 15:12:14,117 - 11. a few small masses and densities again seen
-2024-08-06 15:12:14,117 - 12. the left breast is unremarkable
-2024-08-06 15:12:14,117 - 13. no mammographic evidence of malignancy is identified in the left breast
-2024-08-06 15:12:14,117 - 14. recommend right diagnostic mammogram with right breast ultrasound if indicated
-2024-08-06 15:12:14,117 - 15. two stable nodules in the posterior upper outer left breast which likely represents an intramammary lymph nodes
-2024-08-06 15:12:14,118 - 16. a fibrocystic cluster at 1 : 00 - 2 : 00 at 6 cm from the nipple measures 0 . 5 x 0 . 8 x 0 . 2 cm
-2024-08-06 15:12:14,118 - 17. several scattered punctate calcifications again seen in both breasts appear benign
-2024-08-06 15:12:14,118 - 18. nodular densities are seen in the bilateral breast
-2024-08-06 15:12:14,118 - 19. no other asymmetry left breast : there is a circumscribed nodule in the anterior medial breast , 8 mm in diameter
-2024-08-06 15:12:14,118 - 20. stable postsurgical changes in the right breast with no mammographic evidence of malignancy in either breast
-2024-08-06 15:12:14,118 - 21. spot compression views of the asymmetric nodular densities are recommended in both breasts
-2024-08-06 15:12:14,118 - 22. no significant change from previous exams
-2024-08-06 15:12:14,118 - 23. there is a stable small mass upper outer quadrant right breast
-2024-08-06 15:12:14,118 - 24. please note this cannot correspond to the medial mass seen on mammography as this is in a different quadrant
-2024-08-06 15:12:14,118 - 25. no suspicious mass or asymmetry is seen on the left
-2024-08-06 15:12:14,118 - 26. small scattered nodular densities are noted posterior medially and bilaterally
-2024-08-06 15:12:14,118 - 27. there is a small asymmetry central upper left breast middle depth on the mlo view
-2024-08-06 15:12:14,118 - 28. suspicious spiculated mass in the retroareolar right breast in approximately the 12 : 00 position associated with pleomorphism and ductal calcifications present over a much broader area
-2024-08-06 15:12:14,118 - 29. there are a few scattered calcifications , mildly progressive , but with a benign appearance
-2024-08-06 15:12:14,118 - 30. a stable nodule is present in the 12 : 00 left breast middle third depth
-2024-08-06 15:12:14,118 - 31. the left breast focal asymmetry needs additional imaging
-2024-08-06 15:12:14,118 - 32. however this does demonstrate modest central vascularity
-2024-08-06 15:12:14,118 - 33. there is a possible developing asymmetry in the medial right breast
-2024-08-06 15:12:14,118 - 34. no suspicious findings or significant changes are present as compared to the prior examination ( s ), the most recent dated [ date ] except that several small benign appearing calcifications are noted on the right new since the previous study
-2024-08-06 15:12:14,118 - 35. stable density upper outer quadrant left breast
-2024-08-06 15:12:14,118 - 36. there is a small asymmetry central lateral right breast on the cc view
-2024-08-06 15:12:14,118 - 37. there is no evidence of new mass , suspicious microcalcifications or nonsurgical distortion
-2024-08-06 15:12:14,118 - 38. a benign nodule in the medial right breast is stable
-2024-08-06 15:12:14,118 - 39. overall pattern appears stable when compared with the 2 previous sonograms dating back to .
-2024-08-06 15:12:14,118 - 40. stable small benign - appearing nodules in both breasts are noted
-2024-08-06 15:12:14,118 - 41. an additional cyst at 4 : 00 and 8 : 00 are identified
-2024-08-06 15:12:14,118 - 42. ultrasound evaluation of the entire right and left breastwas performed by the ultrasonographer
-2024-08-06 15:12:14,118 - 43. an oval focal asymmetry / nodule that is stable over multiple prior mammograms is seen in the lower inner left breast at anterior depth
-2024-08-06 15:12:14,118 - 44. the left breast shows no suspicious findings as compared to the prior examination ( s ), the most recent of which is dated [ date ]
-2024-08-06 15:12:14,118 - 45. there are 8 a few bilateral benign - appearing calcifications
-2024-08-06 15:12:14,118 - 46. this is present in the lower midline of the right breast
-2024-08-06 15:12:14,118 - 47. benign bilateral nodular fibroglandular tissue is seen
-2024-08-06 15:12:14,118 - 48. bilateral nodular asymmetry for which spot compression and true lateral views are recommended for further evaluation
-2024-08-06 15:12:14,118 - 49. there is a new mass in the posterior left breast seen centrally on the cc view , likely inferiorly on the mlo view
-2024-08-06 15:12:14,118 - 50. multiple radiopaque markers denote skin lesions

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/ladder_discover_slices_performance_ERM.txt

@@ -1,8 +0,0 @@
-Accuracy for Cancer patients with calc: 0.7761194029850746
-Accuracy for Cancer patients without  calc (Worst Group): 0.5844155844155844
-Accuracy for Cancer overall patients: 0.6736111111111112
-
-
-AUROC for overall (Mean): 0.8131673684275611
-AUROC for positive disease with  calc vs all negatives: 0.8595001694303376
-AUROC for positive disease without  calc vs all negatives: 0.7728518143082618

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/ladder_mitigate_slices.txt

@@ -1,8 +0,0 @@
-Accuracy for Cancer patients with calc: 0.9430379746835443
-Accuracy for Cancer patients without  calc (Worst Group): 0.8529411764705882
-Accuracy for Cancer overall patients: 0.9013605442176871
-
-
-AUROC for overall (Mean): 0.895507500879049
-AUROC for positive disease with  calc vs all negatives: 0.915349755874333
-AUROC for positive disease without  calc vs all negatives: 0.8724554693404102

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/ladder_validate_slices_w_LLM-cancer.txt

@@ -1,20 +0,0 @@
-Hypothesis Dictionary:
-{'H1': 'The classifier is making mistake as it is biased toward vascular calcifications', 'H2': 'The classifier is making mistake as it is biased toward scattered calcifications', 'H3': 'The classifier is making mistake as it is biased toward benign appearing calcifications', 'H4': 'The classifier is making mistake as it is biased toward bilateral findings', 'H5': 'The classifier is making mistake as it is biased toward small masses'}
-
-Prompt Dictionary:
-{'H1_vascular calcifications': ['The image shows vascular calcifications.', 'Vascular calcifications are present in the mammogram.', 'This mammogram contains vascular calcifications.', 'Identify the presence of vascular calcifications in the image.', 'Vascular calcifications are evident in this image.'], 'H2_scattered calcifications': ['The image shows scattered calcifications.', 'Scattered calcifications are present in the mammogram.', 'This mammogram contains scattered calcifications.', 'Identify the presence of scattered calcifications in the image.', 'Scattered calcifications are evident in this image.'], 'H3_benign appearing calcifications': ['The image shows benign appearing calcifications.', 'Benign appearing calcifications are present in the mammogram.', 'This mammogram contains benign appearing calcifications.', 'Identify the presence of benign appearing calcifications in the image.', 'Benign appearing calcifications are evident in this image.']}
-==============================================
-0 H1_vascular calcifications
-Accuracy on the error slice (where attribute absent, the hypothesis failed): 0.5614035087719298
-Accuracy on the bias aligned slice (where attribute present, the hypothesis passed): 0.8438818565400844
-==============================================
-==============================================
-1 H2_scattered calcifications
-Accuracy on the error slice (where attribute absent, the hypothesis failed): 0.4583333333333333
-Accuracy on the bias aligned slice (where attribute present, the hypothesis passed): 0.8536585365853658
-==============================================
-==============================================
-2 H3_benign appearing calcifications
-Accuracy on the error slice (where attribute absent, the hypothesis failed): 0.59375
-Accuracy on the bias aligned slice (where attribute present, the hypothesis passed): 0.8434782608695652
-==============================================

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/prompt.txt

@@ -1,141 +0,0 @@
-
-    Context: Breast cancer classification from mammograms using a deep neural network
-    Analysis post training: On a validation set, 
-    a. Get the difference between the image embeddings of correct and incorrectly classified samples to estimate the features present in the correctly classified samples but missing in the misclassified samples.
-    b. Retrive the top 50 sentences from radiology report that matches closely to the embedding difference in step a.
-    c. The sentence list is given below:
-    1. multiple densities and calcifications again seen bilaterally
-2. scattered linear type secretory calcifications are noted bilaterally
-3. multiple scattered masses , densities , and calcifications again seen bilaterally
-4. a few scattered densities and multiple scattered calcifications again seen bilaterally
-5. benign - appearing punctate and round calcifications are scattered through the breasts bilaterally
-6. multiple bilateral scattered round calcifications are again seen
-7. a few bilateral scattered benign appearing round and punctate calcifications are again seen in both breasts
-8. multiple scattered densities and calcifications again seen bilaterally
-9. multiple bilateral scattered punctate calcifications are again seen
-10. multiple skin moles are present bilaterally
-11. multiple bilateral scattered round calcifications again seen are considered benign
-12. multiple scattered calcifications and a few scattered densities are again seen bilaterally
-13. numerous moles were marked bilaterally
-14. multiple scattered small masses , densities , and calcifications again seen bilaterally
-15. multiple scattered masses and densities and a few scattered calcifications again seen bilaterally
-16. multiple bilateral scattered punctate and round calcifications again seen appear benign
-17. numerous scattered punctate calcifications are seen again in both breasts
-18. numerous scattered calcifications and a few densities again seen bilaterally
-19. multiple scattered calcifications and densities again seen bilaterally
-20. benign calcifications are identified along with bilateral asymmetries
-21. multiple scattered calcifications and a few densities again seen bilaterally
-22. several bilateral scattered punctate calcifications seen are considered benign
-23. multiple scattered densities and a few calcifications again seen bilaterally
-24. multiple scattered calcifications and densities again seen
-25. a few scattered masses , densities , and calcifications again seen bilaterally
-26. multiple scattered densities and a few calcifications are again seen bilaterally
-27. the scattered calcifications and densities again seen bilaterally
-28. a few scattered small masses and densities and multiple scattered calcifications are again seen bilaterally
-29. multiple scattered calcifications and densities again seen in the right breast
-30. multiple scattered small densities and calcifications again seen bilaterally
-31. multiple scattered small densities and calcifications again seen
-32. bilateral diffusely scattered punctate calcifications are again seen
-33. multiple scattered calcifications and a few scattered densities again seen bilaterally
-34. bilateral diffusely scattered benign appearing round calcifications are again seen
-35. [ date ] and [ date ] bilateral vascular calcifications are noted
-36. a few scattered densities and tiny calcifications again seen bilaterally
-37. vascular calcifications and a few scattered calcifications and densities are again seen
-38. multiple small scattered densities and calcifications again seen bilaterally
-39. several bilateral benign appearing scattered punctate calcifications are again seen in both breasts
-40. vascular calcifications and multiple scattered calcifications and densities again seen bilaterally
-41. bilateral scattered stable round calcifications seen in both breasts are considered benign
-42. a group of subcutaneous and cutaneous calcifications is located in between the two masses
-43. multiple scattered calcifications and small densities again seen
-44. multiple bilateral scattered calcified oil cysts are again seen
-45. bilateral scattered secretory calcifications are stable
-46. vascular calcifications and multiple scattered calcifications and a few scattered densities again seen bilaterally
-47. multiple scattered calcifications and a few masses and densities again seen bilaterally
-48. several bilateral scattered calcified oil cysts are again seen
-49. bilateral vascular calcifications are evident
-50. vascular calcifications and multiple scattered calcifications again seen bilaterally
-51. multiple bilateral scattered calcified oil cysts are also again seen
-52. vascular calcifications and a few scattered calcifications , densities , and small masses again seen bilaterally
-53. vascular calcifications and a few scattered calcifications and densities again seen
-54. vascular calcifications and scattered calcifications again seen bilaterally
-55. vascular calcifications and multiple scattered calcifications and small densities again seen bilaterally
-56. numerous scattered calcifications again seen bilaterally
-57. benign - appearing large rodlike calcifications are also seen within both breasts
-58. multiple small masses and densities and a few scattered calcifications again seen bilaterally
-59. multiple scattered calcifications and a few density is again seen bilaterally
-60. multiple scattered calcifications and a few scattered small densities are again seen bilaterally
-61. extensive calcifications including vascular calcification can be appreciated bilaterally
-62. bilateral nodule vascular calcifications in the right breast are noted
-63. a few scattered densities and calcifications again seen bilaterally
-64. benign calcifications to include vascular calcifications are seen in both breasts
-65. a left postsurgical scar is marked by 2 cutaneous bbs
-66. multiple scattered calcifications and a few scattered small densities again seen bilaterally
-67. vascular calcifications and a few scattered calcifications , small masses and densities again seen bilaterally
-68. the patient is 77 years old
-69. vascular calcifications and multiple scattered calcifications are again seen bilaterally
-70. calcifications are arranged in multiple clusters and are variable in size
-71. vascular calcifications and multiple scattered calcifications and a few scattered small masses and densities again seen bilaterally
-72. bilateral diffusely scattered stable benign appearing round calcifications are again seen
-73. benign secretory calcifications can be identified bilaterally
-74. multiple scattered calcifications and small densities again seen bilaterally
-75. multiple scattered calcifications , masses , and small densities again seen bilaterally
-76. vascular calcifications and a few scattered calcifications and small densities again seen
-77. multiple scattered calcifications and a few densities again seen in both breasts
-78. a right postsurgical scar is marked by 2 cutaneous bbs
-79. multiple bilateral scattered punctate calcifications again seen are considered benign
-80. vascular calcifications and multiple scattered calcifications and a few densities again seen bilaterally
-81. multiple scattered calcifications and a few scattered densities and small masses again seen bilaterally
-82. bilateral scattered stable subcentimeter masses and bilateral scattered round calcifications are considered benign
-83. vascular calcifications and a few scattered calcifications and densities again seen bilaterally
-84. a few typically benign calcifications are noted bilaterally as are vascular calcifications
-85. vascular calcifications and multiple scattered calcifications , small masses , and densities again seen bilaterally
-86. multiple scattered calcifications and a few scattered small densities again seen
-87. multiple bilateral diffusely scattered benign appearing round calcifications are again seen
-88. multiple scattered calcifications again seen bilaterally
-89. multiple scattered calcifications and a few small densities again seen bilaterally
-90. scattered coarse calcifications and vascular calcifications are again seen in both breasts
-91. vascular calcifications and a few scattered calcifications , small masses , and densities again seen bilaterally
-92. vascular calcifications and multiple scattered calcifications are present bilaterally , progressive , but with a benign appearance
-93. the overlying surgical scar is marked by 2 cutaneous bbs
-94. the patient is 78 years old
-95. vascular calcifications and multiple scattered calcifications again seen
-96. vascular calcifications and a few scattered calcifications and densities again seen in both breasts
-97. multiple calcifications again seen bilaterally
-98. vascular calcifications and a few scattered calcifications and small masses and densities again seen bilaterally
-99. multiple stable and benign calcifications and vascular calcifications are again seen in both breasts
-100. few benign calcified patient present bilaterally
-
-    
-    Task: 
-    Ignore '___' as they are due to anonymization.
-    Consider the consistent attributes present in the descriptions of correctly classified and misclassified samples regarding the positive cancer patients. Formulate hypotheses based on these attributes. Attributes are all the concepts (e.g, explicit or implicit anatomies, observations, any symptom of change related to the disease, demography related information or any concept leading to potential bias) in the sentences other than the class label (Cancer in this case). Assess how these characteristics might be influencing the classifier's performance. Your response should contain only the list of top hypothesis, nothing else. For the response, you should be the following python dictionary template, no extra sentence:
-    
-        hypothesis_dict = {
-        "H1": "The classifier is making mistake  as it is biased toward <attribute>",
-        "H2": "The classifier is making mistake as it is biased toward <attribute>",
-        "H3": "The classifier is making mistake as it is biased toward <attribute>",
-        ...
-        }
-    
-    
-    To effectively test Hypothesis 1 (H1) using the CLIP language encoder, you need to create prompts that explicitly validate H1. These prompts will help to generate text embeddings that capture the essence of the hypothesis, which can be used to compute similarity with the image embeddings from the dataset. The goal is to see if the images where the model makes mistakes are those that aligns with H1 or violates H1. The prompts are python list. Remember, your focus is only the class label "Cancer" (i.e, positive cancer cases)
-    
-    Do this for all the hypothesis. Your final response should follow the following list of dictionaries, nothing else:
-    
-    
-    prompt_dict = {
-        "H1_<attribute>": [List of prompts],
-        "H2_<attribute>": [List of prompts]
-        ...
-    }
-
-    
-    
-    Each attribute hypothesis should contain 5 prompts.
-    
-    So final response should follow the below format strictly (nothing else, no extra sentence): 
-    ```python
-        hypothesis_dict 
-        prompt_dict 
-    ```
-    

RSNA/fold0/aucroc0.89/clip_img_encoder_tf_efficientnet_b5_ns-detect/test_additional_info.pkl

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