[Example] Add Chem Suzuki-Miyaura 交叉偶联反应产率预测 #1175

YfB1125 · 2025-06-25T08:40:39Z

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Describe

Suzuki-Miyaura 交叉偶联反应是在零价钯配合物催化下，芳基或烯基硼酸或硼酸酯与氯、溴、碘代芳烃或烯烃发生交叉偶联。该反应具有反应条件温和、转化率高的优点，在材料合成、药物研发等领域具有重要作用，但存在开发周期长，试错成本高的问题。本研究通过使用高通量实验数据分析反应底物（包括亲电试剂和亲核试剂），催化配体，碱基，溶剂对偶联反应产率的影响，从而建立预测模型。

paddle-bot · 2025-06-25T08:40:44Z

Thanks for your contribution!

HydrogenSulfate · 2025-06-27T02:26:16Z

jointContribution/XPINNs/XPINN_2D_PoissonsEqn.py

无关内容请不要修改

已恢复权限

HydrogenSulfate · 2025-06-27T02:36:35Z

ppsci/externals/paddle_sparse

无关改动请删除

paddle_sparse已经试着加回来了，不知道这样处理是否合适？不行的话我就重新clone一份然后把现在这个分支全部覆盖掉

HydrogenSulfate · 2025-06-27T05:07:20Z

examples/chem/Chem.py

文件名建议用全小写的 chem.py或者main.py

HydrogenSulfate · 2025-06-27T05:08:04Z

examples/chem/Chem.py

+    global x_train, y_train
+    x_train, y_train = data_processed(x_train, y_train)
+
+    # 构建约束


中文注释建议改为英文

已按照建议修改

HydrogenSulfate · 2025-06-27T05:08:34Z

examples/chem/Chem.py

+            "batch_size": cfg.TRAIN.batch_size,
+        },
+        loss=ppsci.loss.MSELoss("mean"),
+        name="bc_sup",


这个名字可以直接用"sup"，"bc_sup"有一些歧义，你这个案例里应该不会涉及 boundary condition之类的概念吧

不会用到。已按照建议修改

HydrogenSulfate · 2025-06-27T05:10:43Z

examples/chem/config/chem.yaml

+defaults: #
+  - ppsci_default #
+  - TRAIN: train_default #
+  - EVAL: eval_default #
+#  - INFER: infer_default #
+  - _self_ #


建议改成如下内容

Suggested change

defaults: #

- ppsci_default #

- TRAIN: train_default #

- EVAL: eval_default #

# - INFER: infer_default #

- _self_ #

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_

HydrogenSulfate · 2025-06-27T05:12:59Z

examples/chem/config/chem.yaml

+
+

连续空行保留一行即可

HydrogenSulfate · 2025-06-27T05:14:56Z

ppsci/arch/chem.py

+    def __init__(
+        self, input_dim, hidden_dim, hidden_dim2, hidden_dim3, hidden_dim4, output_dim
+    ):
+        super(ChemMultimodalMLP, self).__init__()


Suggested change

super(ChemMultimodalMLP, self).__init__()

super().__init__()

HydrogenSulfate · 2025-06-27T05:16:48Z

ppsci/arch/chem.py

+
+        # 确保权重与特征的维度一致
+        weights = weights.clone().detach()
+
+        # 计算加权和
+        weighted_sum = sum(f * w for f, w in zip(features, weights))
+
+        # 计算权重和
+        total_weight = weights.sum()
+
+        # 返回加权平均


这里的注释可以删掉

[ppsci/arch/chem.py]的内容已按照建议修改

HydrogenSulfate · 2025-06-27T05:17:01Z

ppsci/arch/chem.py

本文件中的注释可以删除，多余空行也请删除

…ence into dev_model_chem

YfB1125 · 2025-06-30T08:06:02Z

请协助上传实验结果示意图，以供文档引用

YfB1125 · 2025-06-30T08:18:46Z

还需要上传与实验结果对应的模型参数，请问怎么操作？

HydrogenSulfate · 2025-07-03T11:04:55Z

@leeleolay 看下

HydrogenSulfate

几处小问题还麻烦修改下
@leeleolay 帮忙上传下数据

HydrogenSulfate · 2025-07-03T11:12:53Z

docs/zh/examples/chem.md

+    ``` sh
+    # 训练:  
+    python chem.py mode=train
+    ```


Suggested change

``` sh

# 训练:

python chem.py mode=train

```

``` sh

python chem.py

```

HydrogenSulfate · 2025-07-03T11:13:01Z

docs/zh/examples/chem.md

+    ``` sh
+    # 评估：
+    python chem.py mode=eval
+    ```


Suggested change

``` sh

# 评估：

python chem.py mode=eval

```

``` sh

python chem.py mode=eval

```

HydrogenSulfate · 2025-07-03T11:14:16Z

examples/chem/chem.py

+    solver.train()
+
+
+def eval(cfg: DictConfig):


Suggested change

def eval(cfg: DictConfig):

def evaluate(cfg: DictConfig):

HydrogenSulfate · 2025-07-03T11:14:24Z

examples/chem/chem.py

+    if cfg.mode == "train":
+        train(cfg)
+    elif cfg.mode == "eval":
+        eval(cfg)


Suggested change

eval(cfg)

evaluate(cfg)

函数名已修改

leeleolay · 2025-07-04T02:37:41Z

案例名字建议修改为SMCReac或其他有辨识度的名字，Chem的范围太大了

leeleolay · 2025-07-04T02:40:08Z

https://paddle-org.bj.bcebos.com/paddlescience/datasets/SMCReac/data_set.xlsx 数据可参考这个链接，代码里可删除数据文件

leeleolay · 2025-07-04T02:43:04Z

请协助上传实验结果示意图，以供文档引用

https://paddle-org.bj.bcebos.com/paddlescience/docs/SMCReac/chem.png 图片可参考这个链接原始文件可删除

…ence into dev_model_chem

YfB1125 · 2025-07-04T09:04:11Z

案例名字建议修改为SMCReac或其他有辨识度的名字，Chem的范围太大了

案例文件夹重命名为smc_reac，模型重命名为SuzukiMiyauraModel

YfB1125 · 2025-07-09T05:25:13Z

https://paddle-org.bj.bcebos.com/paddlescience/datasets/SMCReac/data_set.xlsx 数据可参考这个链接，代码里可删除数据文件

在smc_reac.md文档中已经新增数据集链接，并删除样例文件夹中的数据文件

leeleolay · 2025-07-10T02:11:16Z

https://paddle-org.bj.bcebos.com/paddlescience/models/smc_reac/smc_reac_model.pdparams 模型权重链接可参考这个

…ence into dev_model_chem

Dubhe-Chang added 5 commits June 25, 2025 13:43

establish example chem

edc3512

make the code consistent with the upstream

e2ab6ec

make the code consistent with the upstream

6356c91

make the code consistent with the upstream

e8ab68c

delete unnecessary file

6ee370c

paddle-bot bot added the contributor label Jun 25, 2025

fix: code format via pre-commit hooks

66c0957

HydrogenSulfate reviewed Jun 27, 2025

View reviewed changes

Dubhe-Chang added 14 commits June 27, 2025 17:36

reset gitmodule

fa853a2

fix: restore accidentally deleted paddle_sparse submodule

9a36d81

fix: update XPINN_2D_PoissonsEqn.py file permissions to 755

865689a

renamed:examples/chem/Chem.py -> examples/chem/chem.py

eaf1054

update examples/chem/chem.py

9b67577

update chem.py

d33f8bf

Merge branch 'dev_model_chem' of https://github.com/YfB1125/PaddleSci…

62d18cf

…ence into dev_model_chem

update chem.yaml

a4f882a

update chem.yaml

41e9f8b

Merge branch 'dev_model_chem' of https://github.com/YfB1125/PaddleSci…

7f8ddce

…ence into dev_model_chem

update ./ppsci/arch/chem.py

aa7d727

update ./ppsci/arch/chem.py

0f3d15c

Merge branch 'dev_model_chem' of https://github.com/YfB1125/PaddleSci…

6c098d9

…ence into dev_model_chem

update chem.md

e53498f

HydrogenSulfate reviewed Jul 3, 2025

View reviewed changes

Dubhe-Chang added 3 commits July 4, 2025 16:44

Merge branch 'dev_model_chem' of https://github.com/YfB1125/PaddleSci…

2b0e527

…ence into dev_model_chem

rename files of the example

13af56a

rename files in ppsci

38b1a8b

Dubhe-Chang added 6 commits July 4, 2025 17:19

chem.md -> smc_reac.md

74da604

update mkdocs.yml

1e2555e

rename eval -> evaluate in smc_reac.py

cf45ac5

add dataset download links in smc_reac.md

d30b1d8

update smc_reac

06b4c44

delete data_set.xlsx

0482f70

Dubhe-Chang added 6 commits July 13, 2025 20:09

Merge branch 'upstream_develop' into dev_model_chem

04ae02d

update smc_reac.md

0759af8

update smc_reac.md

a0a3995

update smc_reac.yaml

3b16af5

Merge branch 'dev_model_chem' of https://github.com/YfB1125/PaddleSci…

2743241

…ence into dev_model_chem

fix(smc_reac): correct evaluate unpacking logic

8126b2a

[Example] Add Chem Suzuki-Miyaura 交叉偶联反应产率预测 #1175

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[Example] Add Chem Suzuki-Miyaura 交叉偶联反应产率预测 #1175

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YfB1125 commented Jun 25, 2025

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YfB1125 commented Jun 30, 2025

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HydrogenSulfate commented Jul 3, 2025

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leeleolay commented Jul 4, 2025 •

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