Upload 8 files
Browse files- stage_1/checkpoint.pth +3 -0
- stage_1/config_log.txt +135 -0
- stage_1_pretrained_stage_2/checkpoint.pth +3 -0
- stage_1_pretrained_stage_2/config_log.txt +135 -0
- stage_2_full_report/checkpoint.pth +3 -0
- stage_2_full_report/config_log.txt +125 -0
- stage_2_he_only/checkpoint.pth +3 -0
- stage_2_he_only/config_log.txt +125 -0
stage_1/checkpoint.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:21814abd04b40fe9c9816e05124570118496928de8c6ab16d91833004f98f07f
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size 2215724853
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stage_1/config_log.txt
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{
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"run": {
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"task": "image_text_pretrain",
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"lr_sched": "linear_warmup_cosine_lr",
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"init_lr": 0.0001,
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"min_lr": 1e-06,
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"warmup_lr": 1e-06,
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"weight_decay": 0.01,
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"max_epoch": 25,
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"batch_size_train": 20,
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"batch_size_eval": 20,
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"num_workers": 1,
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"warmup_steps": 1000,
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"seed": 42,
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"output_dir": "../output/Pathology/Pretrain_stage1_allinfo_true_query_16_lr_1e-4_epoch_25",
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"amp": true,
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"resume_ckpt_path": null,
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"evaluate": false,
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"train_splits": [
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"train"
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],
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"valid_splits": [
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"val"
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],
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"test_splits": [
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"test"
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],
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"device": "cuda",
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"world_size": 1,
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"dist_url": "env://",
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"distributed": true,
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"save_freq": 10,
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"val_freq": 1,
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"rank": 0,
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"gpu": 0,
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"dist_backend": "nccl"
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},
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"model": {
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"arch": "blip2",
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"load_finetuned": false,
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"finetuned": "",
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"model_type": "pretrain",
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"load_pretrained": false,
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"freeze_vit": true,
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"padding_per_batch": true,
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"vit_model": "identity",
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"max_patches": 3730,
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"num_query_token": 16,
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"max_txt_len": 512,
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"all_info_bool": true
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},
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"datasets": {
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"pathology_dataset": {
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"data_type": "features",
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"build_info": {
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"annotations": {
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"test": {
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"url": "/hpc/dlab_skin_ai/tijn/PathBLIP2/data/pathology/test_data.json",
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"storage": "/hpc/dlab_skin_ai/tijn/PathBLIP2/data/pathology/test_data.json"
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},
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"train": {
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"url": "/hpc/dlab_skin_ai/tijn/PathBLIP2/data/pathology/train_data.json",
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"storage": "/hpc/dlab_skin_ai/tijn/PathBLIP2/data/pathology/train_data.json"
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},
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"val": {
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"url": "/hpc/dlab_skin_ai/tijn/PathBLIP2/data/pathology/val_data.json",
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"storage": "/hpc/dlab_skin_ai/tijn/PathBLIP2/data/pathology/val_data.json"
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}
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},
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"features": {
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"storage": "/hpc/dlab_skin_ai/tijn/PathBLIP2/../../features/hipt_last_layer"
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}
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},
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"text_processor": {
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"train": {
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"name": "pathology_caption"
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},
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"eval": {
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"name": "pathology_caption"
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}
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}
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}
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}
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}
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stage_1_pretrained_stage_2/checkpoint.pth
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version https://git-lfs.github.com/spec/v1
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size 2216167221
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stage_1_pretrained_stage_2/config_log.txt
ADDED
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@@ -0,0 +1,135 @@
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 13 |
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|
| 14 |
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|
| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 20 |
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| 23 |
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"val"
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| 24 |
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| 27 |
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| 29 |
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| 31 |
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| 32 |
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| 37 |
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| 55 |
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| 60 |
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| 72 |
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stage_2_full_report/checkpoint.pth
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stage_2_full_report/config_log.txt
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| 1 |
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stage_2_he_only/checkpoint.pth
ADDED
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 10 |
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| 11 |
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| 12 |
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| 13 |
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 20 |
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| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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| 26 |
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| 27 |
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| 28 |
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| 29 |
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| 30 |
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| 31 |
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| 32 |
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| 33 |
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| 34 |
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| 35 |
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| 36 |
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| 37 |
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| 39 |
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| 40 |
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| 41 |
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| 42 |
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| 43 |
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| 44 |
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| 45 |
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| 46 |
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| 47 |
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| 48 |
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| 49 |
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| 50 |
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| 51 |
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| 52 |
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| 57 |
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| 59 |
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| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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| 65 |
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| 66 |
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| 67 |
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| 68 |
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| 69 |
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| 70 |
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| 71 |
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| 72 |
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| 73 |
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| 74 |
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| 75 |
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| 76 |
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},
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| 77 |
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| 78 |
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| 79 |
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| 80 |
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}
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| 81 |
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},
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| 82 |
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| 83 |
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| 84 |
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}
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| 85 |
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},
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| 86 |
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| 87 |
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| 88 |
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"name": "pathology_caption",
|
| 89 |
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"prompt": "You are an AI assistant specializing in pathology. Your task is to write a detailed medical report for a patient based on their H&E stained whole-slide image(s) (WSIs). </s>"
|
| 90 |
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| 91 |
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| 92 |
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| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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|
| 97 |
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| 98 |
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| 99 |
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