Data preprocessing

[komorebino]

What should I do if I want to implement the step of Data preprocessing on the window system? I have downloaded the data set and I have tried set benchmark _ path = c:/users/LGD/Bert-RBP-master/benchmark.gz. set OUTPUT_PATH=./datasets python generate_datasets.py --path_to_benchmark %BENCHMARK_PATH% --path_to_output %OUTPUT_PATH% This command, but my folder is still empty.

[kkyamada]

I am sorry for the delay in response. Firstly, could you verify if all the file paths and related elements have been set up correctly? If everything appears to be configured correctly, could you share any error messages or unusual outputs you've come across while running the code? Alternatively, I would recommend using the code in a Linux environment with enough allocation of GPU memory.

[komorebino]

Thank you for your reply. I have solved this problem, because my memory is not enough. But when I visualized the results, I lacked relevant files. Could you please show me your debugging steps? Thank you very much

[kkyamada]

Thank you for your updates. I am glad to hear that you could solve the original problem! For the next question, could you please specify which visualization and files you are talking about?

[komorebino]

visualization.ipynb

[komorebino]

[komorebino]

i coulde not found the file

[kkyamada]

There are some things I would like to confirm.

• Do you have the regiontype file for the baseline model? Its filename is specified as filename = os.path.join(MASTER_DIR, rbp, SUBDIR_BASELINE, "analyze_regiontype_type0.npy"). The path should be ./sample_dataset/YOUR_RBP/baseline_model/analyze_regiontype/analyze_regiontype_type0.npy if you are using the default parameters and please make sure the path is matching to where you have the regiontype file.
• Do you see the the figure (ones for the finetuned model and ones for the baseline model) appearing on the notebook below the command box? If both are yes, I believe the figure should be saved in the same directory as you have the visulization.ipynb. Hope these help and please let me know if you have any other questions.

[Revel123456]

我是否需要使用自己的数据集将序列中的 T 转换为 U 以进行 RBP 预测？还是没有必要？我们还能获得正确的预测吗？在复制DNA序列时是否需要将DNA序列转换为RNA序列？