【Hackathon 7th PPSCI No.7】No.7 AI-aided geometric design of anti-infection catheters 论文复现 #986

ADream-ki · 2024-09-02T11:15:24Z

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AI-aided geometric design of anti-infection catheters 论文复现

paddle-bot · 2024-09-02T11:15:30Z

Thanks for your contribution!

HydrogenSulfate

感谢提交PR，有一些修改建议如下，另外提交的代码请使用pre-commit格式化（参考文档：https://paddlescience-docs.readthedocs.io/zh-cn/latest/zh/development/#1）

HydrogenSulfate · 2024-09-03T11:34:01Z

docs/zh/examples/catheter.md

+
+=== "模型训练命令"
+
+    ``sh     python laplace2d.py    ``


请使用三个重音符号包裹代码块，下同

HydrogenSulfate · 2024-09-03T11:34:30Z

docs/zh/examples/catheter.md

+
+| 预训练模型                                                                                                                                                   | 指标                                    |
+| :----------------------------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------- |
+| [GeoFno.pdparams](https://paddle-orghttps://aistudio.baidu.com/datasetdetail/291940.bj.bcebos.com/paddlescience/models/laplace2d/laplace2d_pretrained.pdparams) | Test loss(LPLoss): 0.07319313049316406 |


laplace案例模版的内容请删除干净

预训练模型可以放aistudio或者本PR里，我会帮忙上传

HydrogenSulfate · 2024-09-03T11:35:47Z

docs/zh/examples/laplace2d.md

请不要修改无关文件

HydrogenSulfate · 2024-09-03T11:36:16Z

examples/geofno/conf/geofno.yaml

+hydra:
+  run:
+    # dynamic output directory according to running time and override name
+    dir: outputs_geofno/${now:%Y-%m-%d}/${now:%H-%M-%S}/${hydra.job.override_dirname}
+  job:
+    name: ${mode} # name of logfile
+    chdir: false # keep current working directory unchanged
+  callbacks:
+    init_callback:
+      _target_: ppsci.utils.callbacks.InitCallback
+  sweep:
+    # output directory for multirun
+    dir: ${geofno.run.dir}
+    subdir: ./
+


Suggested change

hydra:

run:

# dynamic output directory according to running time and override name

dir: outputs_geofno/${now:%Y-%m-%d}/${now:%H-%M-%S}/${hydra.job.override_dirname}

job:

name: ${mode} # name of logfile

chdir: false # keep current working directory unchanged

callbacks:

init_callback:

_target_: ppsci.utils.callbacks.InitCallback

sweep:

# output directory for multirun

dir: ${geofno.run.dir}

subdir: ./

defaults:

- ppsci_default

- TRAIN: train_default

- TRAIN/ema: ema_default

- TRAIN/swa: swa_default

- EVAL: eval_default

- INFER: infer_default

- hydra/job/config/override_dirname/exclude_keys: exclude_keys_default

- _self_

hydra:

run:

# dynamic output directory according to running time and override name

dir: outputs_geofno/${now:%Y-%m-%d}/${now:%H-%M-%S}/${hydra.job.override_dirname}

job:

name: ${mode} # name of logfile

chdir: false # keep current working directory unchanged

callbacks:

init_callback:

_target_: ppsci.utils.callbacks.InitCallback

sweep:

# output directory for multirun

dir: ${geofno.run.dir}

subdir: ./

HydrogenSulfate · 2024-09-03T11:36:56Z

examples/geofno/conf/geofno.yaml

+  x_path: "examples/geofno/data/training/x_1d_structured_mesh.npy"
+  y_path: "examples/geofno/data/training/y_1d_structured_mesh.npy"
+  para_path: "examples/geofno/data/training/data_info.npy"
+  output_path: "examples/geofno/data/training/density_1d_data.npy"


请删除路径中的"examples/geofno/"前缀，一般默认当前路径在examples/geofno/下

HydrogenSulfate · 2024-09-03T11:41:44Z

examples/geofno/geofno.py

+    # initialize solver OK
+    solver = ppsci.solver.Solver(
+            model,
+            constraint,
+            cfg.output_dir,
+            optimizer,
+            epochs=cfg.TRAIN.epochs,
+            iters_per_epoch=ITERS_PER_EPOCH,
+            eval_during_train=cfg.TRAIN.eval_during_train,
+            validator=l2rel_validator,
+            save_freq=cfg.TRAIN.save_freq,
+            seed=cfg.seed,
+    )


Suggested change

# initialize solver OK

solver = ppsci.solver.Solver(

model,

constraint,

cfg.output_dir,

optimizer,

epochs=cfg.TRAIN.epochs,

iters_per_epoch=ITERS_PER_EPOCH,

eval_during_train=cfg.TRAIN.eval_during_train,

validator=l2rel_validator,

save_freq=cfg.TRAIN.save_freq,

seed=cfg.seed,

)

# initialize solver OK

solver = ppsci.solver.Solver(

model,

constraint,

cfg.output_dir,

optimizer,

epochs=cfg.TRAIN.epochs,

iters_per_epoch=ITERS_PER_EPOCH,

eval_during_train=cfg.TRAIN.eval_during_train,

validator=l2rel_validator,

save_freq=cfg.TRAIN.save_freq,

)

HydrogenSulfate · 2024-09-03T11:41:50Z

examples/geofno/geofno.py

+    # set random seed for reproducibility
+    ppsci.utils.misc.set_random_seed(cfg.seed)
+    # initialize logger
+    logger.init_logger("ppsci", osp.join(cfg.output_dir, f"{cfg.mode}.log"), "info")
+


HydrogenSulfate · 2024-09-03T11:42:36Z

examples/geofno/geofno.py

+
+        plt.legend()
+        plt.tight_layout()
+        plt.savefig("Validation."+str(sample_id)+".pdf")


Suggested change

plt.savefig("Validation."+str(sample_id)+".pdf")

plt.savefig(f"Validation.{sample_id}.pdf")

HydrogenSulfate · 2024-09-03T11:42:58Z

examples/geofno/geofno.py

+        raise ValueError(
+            f"cfg.mode should in ['train', 'eval', 'export', 'infer'], but got '{cfg.mode}'"
+        )


麻烦添加模型导出和推理代码

HydrogenSulfate · 2024-09-03T11:43:58Z

examples/geofno/utilities3.py

+def count_params(model):
+    c = 0
+    for p in model.parameters():
+        c += np.prod(p.shape)  # 使用paddle.prod计算参数的总数
+    return c


不重要的调试函数可以删除

HydrogenSulfate · 2024-09-03T11:59:27Z

docs/zh/examples/catheter.md

+
+| 预训练模型                                                                                                                                                   | 指标                                    |
+| :----------------------------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------- |
+| [GeoFno.pdparams](https://paddle-orghttps://aistudio.baidu.com/datasetdetail/291940.bj.bcebos.com/paddlescience/models/laplace2d/laplace2d_pretrained.pdparams) | Test loss(LPLoss): 0.07319313049316406 |


预训练模型已上传：https://paddle-org.bj.bcebos.com/paddlescience/models/GeoFNO/GeoFNO_pretrained.pdparams

刚刚弄完

链接也弄好了

wangguan1995

to fix

wangguan1995 · 2024-09-05T11:56:37Z

examples/geofno/utilities3.py

+
+
+# loss function with rel/abs Lp loss
+class LpLoss(nn.Layer):


删除utilities3.py
复用：ppsci.loss.L2Loss
如果不能复用，新建一个/workspace/wangguan/Hackathon_7/ppsci/loss/Lp.py

wangguan1995 · 2024-09-05T11:57:07Z

docs/zh/examples/laplace2d.md

复原laplace2.md

wangguan1995

这两个好像还没做，注意下
3. catheter_design.ipynb: Real-time design optimization by using Geo-FNO model and BFGS algorithm.

catheter_analysis.ipynb: Compassion with linear regression model; Visualization of the landscape of the loss function around the optimal design.

wangguan1995 · 2024-09-05T12:13:48Z

docs/zh/examples/catheter.md

+
+## 1. 背景简介
+
+[论文](https://www.science.org/doi/pdf/10.1126/sciadv.adj1741)提出了一种基于人工智能的导尿管几何设计方法，可以有效抑制细菌逆流，从而预防 CAUTI。该方法通过流体动力学和粒子动力学模拟研究细菌运动机制，并使用人工智能模型优化导尿管几何形状，使其能够最大程度地抑制细菌逆流。实验结果表明，该设计能够将细菌逆流的程度降低一到两个数量级，具有安全、有效、易于实施和成本低等优点，有望成为未来 CAUTI 预防的重要手段。


人工智能辅助的抗感染导管几何创新设计

在狭窄管道内的流体环境中，细菌能借助流体动力学作用逆流迁移，对使用植入性导管的患者构成泌尿道感染的严重威胁。尽管已有提议采用涂层与结构化表面来抑制导管内的细菌滋生，但遗憾的是，至今尚无一种表面结构或涂层技术能从根本上解决污染难题。鉴于此，我们依据逆流游动的物理原理，创新性地提出了一种几何设计方案，并通过人工智能模型对细菌流入动力学进行预测与优化。相较于传统模拟方法，所采用的傅立叶神经算子人工智能技术实现了显著的速度提升。

在准二维微流体实验中，我们以大肠杆菌为对象，验证了该设计的抗感染机制，并在临床相关流速下，通过3D打印的导管原型对其有效性进行了评估。实验结果显示，我们的导管设计在抑制导管上游端细菌污染方面，实现了1-2个数量级的提升，有望大幅延长导管的安全留置时间，并整体降低导管相关性尿路感染的风险。

wangguan1995 · 2024-09-05T12:15:53Z

docs/zh/examples/catheter.md

+   ![1725428017615](image/catheter/1725428017615.png)
+
+可以看到模型预测结果与真实结果基本一致，模型泛化效果良好。
+


Training Test Loss 也放一下

已经加了

…to H7No7

ADream-ki · 2024-09-09T15:09:09Z

这两个好像还没做，注意下 3. catheter_design.ipynb: Real-time design optimization by using Geo-FNO model and BFGS algorithm.

catheter_analysis.ipynb: Compassion with linear regression model; Visualization of the landscape of the loss function around the optimal design.

加在aistudio那里了

wangguan1995 · 2024-09-23T03:33:54Z

docs/zh/examples/catheter.md

@@ -0,0 +1,195 @@
+# Catheter
+
+<a href="https://aistudio.baidu.com/aistudio/projectdetail/6169897?sUid=455441&shared=1&ts=1684122038217" class="md-button md-button--primary" style>AI Studio 快速体验</a>


这个链接不太对啊....

wangguan1995 · 2024-09-23T03:37:33Z

examples/geofno/catheter.py

+################################################################
+# fourier layer
+################################################################
+class SpectralConv1d(nn.Layer):


神经网络的代码，应归类到：ppsci/arch
调用方式如图：

这样方便网络算法直接，快速的横向对比，对用户友好，别的数据集也可以用这种网络~

wangguan1995 · 2024-09-23T03:39:56Z

examples/geofno/geofno.py

建议把这个案例文件，以及文件夹，命名为catheter
当前的catheter.py，因为其包含了geofno网络架构，建议命名为geofno

抱歉，我马上改掉，最近在写论文

你好，已经按照要求修改了

CLAassistant · 2024-09-25T06:28:29Z

All committers have signed the CLA.

…to H7No7

wangguan1995 · 2024-10-08T08:11:26Z

数据集没有公开，另外需要【挂载】到aistudio项目上

ADream-ki · 2024-10-09T06:43:52Z

抱歉抱歉，忘了公开数据集了，现在已经可以了，请review @wangguan1995

wangguan1995 · 2024-10-10T05:23:03Z

AIStudio需要修复以下内容，最终做到用户【一键跑通训练推理】:

补充数据解压脚本，到3个ipynb文件内

!unzip ./data/data291940/data.zip -d .
!mkdir MyData
!mv ./data/test/ MyData
!mv ./data/training/ MyData

修复 geofno_analysis.ipynb bug：
修复 main.ipynb bug：

ADream-ki · 2024-11-01T13:18:03Z

已经修改了，但是有个问题，这个是怎么回事吗

 @wangguan1995

HydrogenSulfate

这里不用改，固定是hydra

examples/catheter/conf/catheter.yaml

Co-authored-by: HydrogenSulfate <[email protected]>

ADream-ki · 2024-11-01T13:34:06Z

好的好的，我现在试试

ADream-ki · 2024-11-02T14:33:26Z

已经好了，请您review一下

ADream-ki · 2024-11-02T14:50:08Z

@HydrogenSulfate

HydrogenSulfate

感谢提交PR，辛苦按照review修改一下。

修改完毕之后，提交代码之前，请按照文档安装pre-commit：
文档中的图片已经上传至云端，请将文档里的图片地址替换成如下地址：

https://paddle-org.bj.bcebos.com/paddlescience/docs/catheter/1725427977357.png
https://paddle-org.bj.bcebos.com/paddlescience/docs/catheter/1725428017615.png
https://paddle-org.bj.bcebos.com/paddlescience/docs/catheter/1725894134717.png

HydrogenSulfate · 2024-11-05T10:34:41Z

examples/catheter/conf/catheter.yaml

+    batch_size: 20
+    d: 2
+    p: 2
+  pretrained_model_path: "https://paddle-org.bj.bcebos.com/paddlescience/models/GeoFNO/GeoFNO_pretrained.pdparams"


为什么训练的时候要载入预训练模型呢？

HydrogenSulfate · 2024-11-05T10:36:00Z

docs/zh/examples/catheter.md

+其中
+
+- `dt(q)` 代表细菌方向变化率
+- `ω ⃗ ` 代表流体涡量


此处第二个字符是不是不能正常显示？

确实，他有一个乱码了

HydrogenSulfate · 2024-11-05T10:37:23Z

docs/zh/examples/catheter.md

+
+=== "模型训练命令"
+
+    ``sh     python catheter.py    ``


Suggested change

``sh python catheter.py ``

``` sh

python catheter.py

```

HydrogenSulfate · 2024-11-05T10:38:36Z

examples/catheter/catheter.py

+
+    # set model
+    model = ppsci.arch.FNO1d(**cfg.MODEL)
+    model.set_state_dict(paddle.load(cfg.TRAIN.pretrained_model_path))


训练模型时，为什么要加载预训练模型呢？

因为我发现模型初始化并不稳定

因为我发现模型初始化并不稳定

模型的初始化跟随机种子相关，而模型运行之前，随机种子应该是在callback.py里固定了：

PaddleScience/ppsci/utils/callbacks.py

Lines 86 to 96 in 645e438

# fix random seed for reproducibility

misc.set_random_seed(full_cfg.seed)

# initialze logger while creating output directory

logger.init_logger(

"ppsci",

osp.join(full_cfg.output_dir, f"{full_cfg.mode}.log")

if full_cfg.output_dir and full_cfg.mode not in ["export", "infer"]

else None,

full_cfg.log_level,

)

，你说的初始化不稳定是指随机初始化对训练最终精度影响较大吗？

一般实验可复现性通过固定随机种子来保证，加载固定的参数这种做法不太常见

不知道是不是我电脑问题，我设置了随机数种子，但他有时候就是随机数不一样，我改改再试试

HydrogenSulfate · 2024-11-05T10:40:21Z

examples/catheter/catheter.py

+def evaluate(cfg: DictConfig):
+    # set model
+    model = ppsci.arch.FNO1d(**cfg.MODEL)
+    model.set_state_dict(paddle.load(cfg.TRAIN.model_path))


Suggested change

model.set_state_dict(paddle.load(cfg.TRAIN.model_path))

ppsci.utils.save_load.load_pretrain(

model,

cfg.EVAL.pretrained_model_path,

)

HydrogenSulfate · 2024-11-05T10:49:43Z

examples/catheter/conf/catheter.yaml

+  LOSS:
+    batch_size: 20
+    d: 2
+    p: 2


LOSS:这个字段是不是可以删除？代码里好像没用到这个字段

HydrogenSulfate · 2024-11-05T10:50:15Z

examples/catheter/conf/catheter.yaml

+    epochs: 2001
+    learning_rate: 0.001
+    milestones: [160, 400, 750, 1000, 1300, 1600, 1800]
+    gamma: 0.25
+  epochs: 1001


两处的epochs为什么会不一样呢

HydrogenSulfate · 2024-11-05T10:50:35Z

examples/catheter/conf/catheter.yaml

+
+# inference settings
+INFER:
+  export_path: ./inference/catheter


文件结尾补充一行空行

HydrogenSulfate · 2024-11-05T10:50:47Z

ppsci/arch/__init__.py

在arch.md里也添加一下FNO1d

HydrogenSulfate · 2024-11-05T10:51:13Z

ppsci/arch/geofno.py

+
+        """
+        1D Fourier layer. It does FFT, linear transform, and Inverse FFT.
+        """
+


__init__的docstring需要移动到类定义，即class SpectralConv1d下方

inference我再改改，其他已经好了

ADream-ki changed the title ~~【Hackathon 7th】No.7 AI-aided geometric design of anti-infection catheters 论文复现~~ 【Hackathon 7th No.7】No.7 AI-aided geometric design of anti-infection catheters 论文复现 Sep 2, 2024

paddle-bot bot added the contributor label Sep 2, 2024

luotao1 mentioned this pull request Sep 3, 2024

【Hackathon 7th】开源贡献个人挑战赛（偷跑版） PaddlePaddle/Paddle#67603

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HydrogenSulfate reviewed Sep 3, 2024

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luotao1 assigned luotao1, HydrogenSulfate and wangguan1995 Sep 4, 2024

luotao1 added the PaddlePaddle Hackathon label Sep 4, 2024

黑客松No.7

ac2f8b7

ADream-ki force-pushed the H7No7 branch from 35cc0c3 to ac2f8b7 Compare September 4, 2024 10:50

Merge branch 'develop' into H7No7

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ADream-ki added 2 commits September 9, 2024 23:03

update

d83e908

Merge branch 'H7No7' of https://github.com/ADream-ki/PaddleScience in…

6e79fcd

…to H7No7

luotao1 changed the title ~~【Hackathon 7th No.7】No.7 AI-aided geometric design of anti-infection catheters 论文复现~~ 【Hackathon 7th PPSCI No.7】No.7 AI-aided geometric design of anti-infection catheters 论文复现 Sep 18, 2024

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Merge branch 'develop' into H7No7

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ADream-ki added 3 commits September 25, 2024 18:34

NO7

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update

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Merge branch 'H7No7' of https://github.com/ADream-ki/PaddleScience in…

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…to H7No7

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fix config

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Update examples/catheter/conf/catheter.yaml

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Co-authored-by: HydrogenSulfate <[email protected]>

update config

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ADream-ki dismissed HydrogenSulfate’s stale review via 3426afd November 6, 2024 14:08

Merge branch 'PaddlePaddle:develop' into H7No7

07392b1

	plt.savefig("Validation."+str(sample_id)+".pdf")
	plt.savefig(f"Validation.{sample_id}.pdf")


		## 1. 背景简介

		[论文](https://www.science.org/doi/pdf/10.1126/sciadv.adj1741)提出了一种基于人工智能的导尿管几何设计方法，可以有效抑制细菌逆流，从而预防 CAUTI。该方法通过流体动力学和粒子动力学模拟研究细菌运动机制，并使用人工智能模型优化导尿管几何形状，使其能够最大程度地抑制细菌逆流。实验结果表明，该设计能够将细菌逆流的程度降低一到两个数量级，具有安全、有效、易于实施和成本低等优点，有望成为未来 CAUTI 预防的重要手段。

		![1725428017615](image/catheter/1725428017615.png)

		可以看到模型预测结果与真实结果基本一致，模型泛化效果良好。

		@@ -0,0 +1,195 @@
		# Catheter

		<a href="https://aistudio.baidu.com/aistudio/projectdetail/6169897?sUid=455441&shared=1&ts=1684122038217" class="md-button md-button--primary" style>AI Studio 快速体验</a>

	# fix random seed for reproducibility
	misc.set_random_seed(full_cfg.seed)

	# initialze logger while creating output directory
	logger.init_logger(
	"ppsci",
	osp.join(full_cfg.output_dir, f"{full_cfg.mode}.log")
	if full_cfg.output_dir and full_cfg.mode not in ["export", "infer"]
	else None,
	full_cfg.log_level,
	)

-    model.set_state_dict(paddle.load(cfg.TRAIN.model_path))
+    ppsci.utils.save_load.load_pretrain(
+        model,
+        cfg.EVAL.pretrained_model_path,
+    )

【Hackathon 7th PPSCI No.7】No.7 AI-aided geometric design of anti-infection catheters 论文复现 #986

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【Hackathon 7th PPSCI No.7】No.7 AI-aided geometric design of anti-infection catheters 论文复现 #986

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ADream-ki commented Sep 2, 2024 • edited Loading

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ADream-ki commented Sep 2, 2024 •

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CLAassistant commented Sep 25, 2024 •

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wangguan1995 commented Oct 8, 2024 •

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