stanford-ribonanza-rna-folding-public
所属分类：生物医药技术
开发工具：Python
文件大小：0KB
下载次数：0
上传日期：2023-12-08 07:13:12
上 传 者：
sh-1993
说明： 斯坦福核糖核酸折叠公开
(stanford ribonanza rna folding public)
文件列表:
LICENSE.txt (1059, 2023-12-07)
input/ (0, 2023-12-07)
libs/ (0, 2023-12-07)
src/ (0, 2023-12-07)
src/exp064/ (0, 2023-12-07)
src/exp064/apply_filter_pl.py (2495, 2023-12-07)
src/exp064/eval.py (5346, 2023-12-07)
src/exp064/eval_with_err.py (6883, 2023-12-07)
src/exp064/make_oof.py (5274, 2023-12-07)
src/exp064/train.py (28193, 2023-12-07)
src/exp064/train.sh (4656, 2023-12-07)
src/exp064/train_finetune.py (10025, 2023-12-07)
src/exp070/ (0, 2023-12-07)
src/exp070/eval.py (5346, 2023-12-07)
src/exp070/make_oof.py (5274, 2023-12-07)
src/exp070/train.py (30860, 2023-12-07)
src/exp070/train.sh (9410, 2023-12-07)
src/exp070/train_finetune.py (8367, 2023-12-07)
src/exp071/ (0, 2023-12-07)
src/exp071/apply_filter_pl.py (2878, 2023-12-07)
src/exp071/eval.py (5894, 2023-12-07)
src/exp071/eval_with_err.py (7431, 2023-12-07)
src/exp071/make_oof.py (5673, 2023-12-07)
src/exp071/train.py (29873, 2023-12-07)
src/exp071/train.sh (4946, 2023-12-07)
src/exp071/train_finetune.py (10419, 2023-12-07)
src/exp072/ (0, 2023-12-07)
src/exp072/eval.py (5346, 2023-12-07)
src/exp072/make_oof.py (5274, 2023-12-07)
src/exp072/train.py (30660, 2023-12-07)
src/exp072/train.sh (5140, 2023-12-07)
src/exp072/train_finetune.py (8380, 2023-12-07)
src/scripts/ (0, 2023-12-07)
src/scripts/make_structure_feat_test.py (3925, 2023-12-07)
src/scripts/make_structure_feat_train.py (4247, 2023-12-07)
# 4th place solution (tattaka's part)
## Environment
Use [Kaggle Docker](https://console.cloud.google.com/gcr/images/kaggle-gpu-images/GLOBAL/python).
## Usage
0. Place competition data in the `input` directory
1. make bp_matrix
```bash
$ cd src/scripts
$ python make_structure_feat_train.py
$ python make_structure_feat_test.py
```
Place contrafold bpps and unzip in in the `input` directory
* https://www.kaggle.com/code/tattaka/contrafold-test-bpps-1000000
* https://www.kaggle.com/code/tattaka/contrafold-test-bpps-500000-1000000
* https://www.kaggle.com/code/tattaka/contrafold-test-bpps-0-500000
* https://www.kaggle.com/code/tattaka/contrafold-train-bpps-600000
* https://www.kaggle.com/code/tattaka/contrafold-train-bpps-300000-600000
* https://www.kaggle.com/code/tattaka/contrafold-train-bpps-0-300000
2. Training
```bash
$ cd src/exp064 && sh train.sh
$ cd src/exp070 && sh train.sh
$ cd src/exp071 && sh train.sh
$ cd src/exp072 && sh train.sh
```
## License
MIT
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