fix: fix some bugs in knowledge base (#378)

* fix a bug in dig_recognizer

* fix some bug in rag

* fix a ci error

rdagent/app/kaggle/loop.py

@@ -41,7 +41,7 @@ class KaggleRDLoop(RDLoop):
                 if PROP_SETTING.knowledge_base != ""
                 else None
             )
-            logger.log_object(knowledge_base, tag="knowledge_base")
+            logger.log_object(knowledge_base.__dict__, tag="knowledge_base")
 
             self.hypothesis_gen: HypothesisGen = import_class(PROP_SETTING.hypothesis_gen)(scen)
             logger.log_object(self.hypothesis_gen, tag="hypothesis generator")

rdagent/core/knowledge_base.py

@@ -14,12 +14,12 @@ class KnowledgeBase:
         if self.path is not None and self.path.exists():
             with self.path.open("rb") as f:
                 self.__dict__.update(
-                    pickle.load(f).__dict__,
+                    pickle.load(f),
                 )  # TODO: because we need to align with init function, we need a less hacky way to do this
 
     def dump(self) -> None:
         if self.path is not None:
             self.path.parent.mkdir(parents=True, exist_ok=True)
-            pickle.dump(self, self.path.open("wb"))
+            pickle.dump(self.__dict__, self.path.open("wb"))
         else:
             logger.warning("KnowledgeBase path is not set, dump failed.")

rdagent/scenarios/kaggle/experiment/digit-recognizer_template/fea_share_preprocess.py

@@ -57,11 +57,6 @@ def clean_and_impute_data(X_train, X_valid, X_test):
     then imputes missing values using the mean strategy.
     Also removes duplicate columns.
     """
-    # Replace inf and -inf with NaNa
-    X_train.replace([np.inf, -np.inf], np.nan, inplace=True)
-    X_valid.replace([np.inf, -np.inf], np.nan, inplace=True)
-    X_test.replace([np.inf, -np.inf], np.nan, inplace=True)
-
     # Impute missing values
     imputer = SimpleImputer(strategy="mean")
     X_train = pd.DataFrame(imputer.fit_transform(X_train), columns=X_train.columns)

rdagent/scenarios/kaggle/experiment/digit-recognizer_template/model/model_nn.py

@@ -0,0 +1,86 @@
+import pandas as pd
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import torch.optim as optim
+from torch.utils.data import DataLoader, TensorDataset
+
+
+# Define the neural network model with Batch Normalization
+class NeuralNetwork(nn.Module):
+    def __init__(self, input_channels, num_classes):
+        super(NeuralNetwork, self).__init__()
+        self.conv1 = nn.Conv2d(in_channels=input_channels, out_channels=30, kernel_size=(3, 3), stride=2)
+        self.dropout1 = nn.Dropout(0.5)
+        self.conv2 = nn.Conv2d(in_channels=30, out_channels=30, kernel_size=(3, 3), stride=2)
+        self.dropout2 = nn.Dropout(0.5)
+        self.flatten = nn.Flatten()
+        self.fc1 = nn.Linear(30 * 6 * 6, 128)  # Adjust based on your input size
+        self.fc2 = nn.Linear(128, num_classes)
+
+    def forward(self, x):
+        x = F.relu(self.conv1(x))
+        x = self.dropout1(x)
+        x = F.relu(self.conv2(x))
+        x = self.dropout2(x)
+        x = self.flatten(x)
+        x = F.relu(self.fc1(x))
+        x = F.softmax(self.fc2(x), dim=1)
+        return x
+
+
+def fit(X_train: pd.DataFrame, y_train: pd.DataFrame, X_valid: pd.DataFrame, y_valid: pd.DataFrame):
+    # Convert data to PyTorch tensors and reshape it for convolutional layers
+    X_train_tensor = (
+        torch.tensor(X_train.values, dtype=torch.float32).view(-1, 1, 28, 28).to(device)
+    )  # Reshape and move to GPU
+    y_train_tensor = torch.tensor(y_train.values, dtype=torch.long).to(device)
+    X_valid_tensor = torch.tensor(X_valid.values, dtype=torch.float32).view(-1, 1, 28, 28).to(device)
+    y_valid_tensor = torch.tensor(y_valid.values, dtype=torch.long).to(device)
+
+    # Create datasets and dataloaders
+    train_dataset = TensorDataset(X_train_tensor, y_train_tensor)
+    valid_dataset = TensorDataset(X_valid_tensor, y_valid_tensor)
+    train_loader = DataLoader(train_dataset, batch_size=128, shuffle=True)
+    valid_loader = DataLoader(valid_dataset, batch_size=128, shuffle=False)
+
+    # Initialize the model, loss function and optimizer
+    model = NeuralNetwork(input_channels=1, num_classes=len(set(y_train))).to(device)
+    criterion = nn.CrossEntropyLoss().to(device)
+    optimizer = optim.Adam(model.parameters(), lr=0.0005)
+
+    # Train the model
+    num_epochs = 400
+    for epoch in range(num_epochs):
+        model.train()
+        for X_batch, y_batch in train_loader:
+            optimizer.zero_grad()
+            outputs = model(X_batch)
+            loss = criterion(outputs, y_batch)
+            loss.backward()
+            optimizer.step()
+
+        # Validate the model
+        model.eval()
+        valid_loss = 0
+        correct = 0
+        with torch.no_grad():
+            for X_batch, y_batch in valid_loader:
+                outputs = model(X_batch)
+                valid_loss += criterion(outputs, y_batch).item()
+                _, predicted = torch.max(outputs, 1)
+                correct += (predicted == y_batch).sum().item()
+
+        accuracy = correct / len(valid_loader.dataset)
+        print(f"Epoch {epoch+1}/{num_epochs}, Validation Accuracy: {accuracy:.4f}")
+
+    return model
+
+
+def predict(model, X):
+    X_tensor = torch.tensor(X.values, dtype=torch.float32).view(-1, 1, 28, 28).to(device)
+    model.eval()
+    with torch.no_grad():
+        outputs = model(X_tensor)
+        _, predicted = torch.max(outputs, 1)
+    return predicted.cpu().numpy().reshape(-1, 1)

rdagent/scenarios/kaggle/experiment/digit-recognizer_template/model/select_nn.py

@@ -0,0 +1,12 @@
+import pandas as pd
+
+
+def select(X: pd.DataFrame) -> pd.DataFrame:
+    """
+    Select relevant features. To be used in fit & predict function.
+    """
+    # For now, we assume all features are relevant. This can be expanded to feature selection logic.
+    if X.columns.nlevels == 1:
+        return X
+    X.columns = ["_".join(str(col)).strip() for col in X.columns.values]
+    return X

rdagent/scenarios/kaggle/experiment/digit-recognizer_template/train.py

@@ -83,6 +83,6 @@ ids = range(1, len(X_test) + 1)
 
 # TODO: fix selection
 print(X_valid_selected.columns)
-y_test_pred = model_l[min_index][1](model_l[min_index][0], model_l[min_index][2].select(X_test))
+y_test_pred = model_l[min_index][1](model_l[min_index][0], model_l[min_index][2].select(X_test)).flatten()
 submission_result = pd.DataFrame({"ImageId": ids, "Label": y_test_pred})
 submission_result.to_csv("submission.csv", index=False)