wjhou/organ

Code for the paper "ORGAN: Observation-Guided Radiology Report Generation via Tree Reasoning" (ACL'23).

organ's Issues

How can I train this model from scratch?

How can I train this model from scratch without pretrained model?
I try to
./script/run_iu_xray.sh debug checkpoint_name plan_model_name_or_path plan_eval_file
without checkpoint_model but bleu-4 accuracy is not increase above 0.06

CE scores

Hi,

are the scores reported in this paper macro, micro or macro-based F1 scores?

Thanks a lot in advance!

About ./data/mention/

When I reproduce the step 0.2, I don't know what to place in ./data/mention/. It's not in the Readme either. Therefore, could you tell what I should place in ./data/mention/? Thanks in advance.

about checkpoint_name: indicating the location for the pre-trained visual model, mainly for IU Xray dataset

Is checkpoint_name in Step 1 resnet101-5d3b4d8f.pth? If not, Could you please provide the pre-trained model which mentioned in yout paper("For IU X-RAY, we further fine-tune ResNet-101 on CheXpert")? Or should i train from scratch?

FileNotFoundError: [Errno 2] No such file or directory: './data/mention/'

I configured the annontation.json file of the data set and CheXbert, and successfully ran step0.1 without an error. However, I could not find the mention directory when running step0.2. I want to know which step I made the mistake in.

What is the content of ./mention/?

During the code reproduction process, when executing python ./src/plan_extraction.py, a mention folder path will be needed. What is the content of this path? Looking forward to your reply.

about chexbert_dir="./CheXbert/src/data/iu_xray/id2tag.csv"

I'm confused about observation tags extraction. Could you provide this csv file?

AssertionError: Prediction Num != Reference Num

I tried to train mimic-cxr and iu_xray with my trained observation planning.
but when I end up training steps and start evaluate, the length of prediction and reference is different
In debug mode, length of prediction is 1, and length of reference is 16
How can I solve it?