hjxdl 0.0.1__tar.gz

hjxdl-0.0.1/.github/workflows/python-publish.yml

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+name: Build and Publish to PyPI
+
+on:
+  push:
+    branches:
+      - main # 确保这匹配你的主分支名
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # 确保能够获取全部历史和标签
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel
+          pip install build  # 确保在构建前安装 build 模块
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.4.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

hjxdl-0.0.1/.gitignore

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+# These are some examples of commonly ignored file patterns.
+# You should customize this list as applicable to your project.
+# Learn more about .gitignore:
+#     https://www.atlassian.com/git/tutorials/saving-changes/gitignore
+
+# Node artifact files
+node_modules/
+dist/
+
+# Compiled Java class files
+*.class
+
+# Compiled Python bytecode
+*.py[cod]
+
+# Log files
+*.log
+
+# Package files
+*.jar
+
+# Maven
+target/
+dist/
+
+# JetBrains IDE
+.idea/
+
+# Unit test reports
+TEST*.xml
+
+# Generated by MacOS
+.DS_Store
+
+# Generated by Windows
+Thumbs.db
+
+# Applications
+*.app
+*.exe
+*.war
+
+# Large media files
+*.mp4
+*.tiff
+*.avi
+*.flv
+*.mov
+*.wmv
+
+test.py
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+.vscode

hjxdl-0.0.1/MANIFEST.in

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+include versioneer.py
+include hdl/_version.py

hjxdl-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: hjxdl
+Version: 0.0.1
+Summary: A collection of functions for Jupyter notebooks
+Home-page: https://github.com/huluxiaohuowa/hdl
+Author: Jianxing Hu
+Author-email: j.hu@pku.edu.cn
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+
+# DL framework by Jianxing
+
+```bash
+git clone git@github.com:huluxiaohuowa/hdl.git
+python setup.py install
+```

hjxdl-0.0.1/README.md

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+# DL framework by Jianxing
+
+```bash
+git clone git@github.com:huluxiaohuowa/hdl.git
+python setup.py install
+```

hjxdl-0.0.1/hdl/_version.py

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+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.1'
+__version_tuple__ = version_tuple = (0, 0, 1)

hjxdl-0.0.1/hdl/args/loss_args.py

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+from tap import Tap
+
+
+class LossArgs(Tap):
+    reduction: str = 'mean'

hjxdl-0.0.1/hdl/controllers/explain/shapley.py

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+import copy
+import torch
+import numpy as np
+from scipy.special import comb
+from itertools import combinations
+import torch.nn.functional as F
+from torch_geometric.utils import to_networkx
+from torch_geometric.data import Data, Batch, Dataset, DataLoader
+
+
+def GnnNetsGC2valueFunc(gnnNets, target_class):
+    def value_func(batch):
+        with torch.no_grad():
+            logits = gnnNets(data=batch)
+            probs = F.softmax(logits, dim=-1)
+            score = probs[:, target_class]
+        return score
+    return value_func
+
+
+def GnnNetsNC2valueFunc(gnnNets_NC, node_idx, target_class):
+    def value_func(data):
+        with torch.no_grad():
+            logits = gnnNets_NC(data=data)
+            probs = F.softmax(logits, dim=-1)
+            # select the corresponding node prob through the node idx on all the sampling graphs
+            batch_size = data.batch.max() + 1
+            probs = probs.reshape(batch_size, -1, probs.shape[-1])
+            score = probs[:, node_idx, target_class]
+            return score
+    return value_func
+
+
+def get_graph_build_func(build_method):
+    if build_method.lower() == 'zero_filling':
+        return graph_build_zero_filling
+    elif build_method.lower() == 'split':
+        return graph_build_split
+    else:
+        raise NotImplementedError
+
+
+class MarginalSubgraphDataset(Dataset):
+    def __init__(self, data, exclude_mask, include_mask, subgraph_build_func):
+        self.num_nodes = data.num_nodes
+        self.X = data.x
+        self.edge_index = data.edge_index
+        self.device = self.X.device
+
+        self.label = data.y
+        self.exclude_mask = torch.tensor(exclude_mask).type(torch.float32).to(self.device)
+        self.include_mask = torch.tensor(include_mask).type(torch.float32).to(self.device)
+        self.subgraph_build_func = subgraph_build_func
+
+    def __len__(self):
+        return self.exclude_mask.shape[0]
+
+    def __getitem__(self, idx):
+        exclude_graph_X, exclude_graph_edge_index = self.subgraph_build_func(self.X, self.edge_index, self.exclude_mask[idx])
+        include_graph_X, include_graph_edge_index = self.subgraph_build_func(self.X, self.edge_index, self.include_mask[idx])
+        exclude_data = Data(x=exclude_graph_X, edge_index=exclude_graph_edge_index)
+        include_data = Data(x=include_graph_X, edge_index=include_graph_edge_index)
+        return exclude_data, include_data
+
+
+def marginal_contribution(data: Data, exclude_mask: np.array, include_mask: np.array,
+                          value_func, subgraph_build_func):
+    """ Calculate the marginal value for each pair. Here exclude_mask and include_mask are node mask. """
+    marginal_subgraph_dataset = MarginalSubgraphDataset(data, exclude_mask, include_mask, subgraph_build_func)
+    dataloader = DataLoader(marginal_subgraph_dataset, batch_size=256, shuffle=False, num_workers=0)
+
+    marginal_contribution_list = []
+
+    for exclude_data, include_data in dataloader:
+        exclude_values = value_func(exclude_data)
+        include_values = value_func(include_data)
+        margin_values = include_values - exclude_values
+        marginal_contribution_list.append(margin_values)
+
+    marginal_contributions = torch.cat(marginal_contribution_list, dim=0)
+    return marginal_contributions
+
+
+def graph_build_zero_filling(X, edge_index, node_mask: np.array):
+    """ subgraph building through masking the unselected nodes with zero features """
+    ret_X = X * node_mask.unsqueeze(1)
+    return ret_X, edge_index
+
+
+def graph_build_split(X, edge_index, node_mask: np.array):
+    """ subgraph building through spliting the selected nodes from the original graph """
+    ret_X = X
+    row, col = edge_index
+    edge_mask = (node_mask[row] == 1) & (node_mask[col] == 1)
+    ret_edge_index = edge_index[:, edge_mask]
+    return ret_X, ret_edge_index
+
+
+def l_shapley(coalition: list, data: Data, local_radius: int,
+              value_func: str, subgraph_building_method='zero_filling'):
+    """ shapley value where players are local neighbor nodes """
+    graph = to_networkx(data)
+    num_nodes = graph.number_of_nodes()
+    subgraph_build_func = get_graph_build_func(subgraph_building_method)
+
+    local_region = copy.copy(coalition)
+    for k in range(local_radius - 1):
+        k_neiborhoood = []
+        for node in local_region:
+            k_neiborhoood += list(graph.neighbors(node))
+        local_region += k_neiborhoood
+        local_region = list(set(local_region))
+
+    set_exclude_masks = []
+    set_include_masks = []
+    nodes_around = [node for node in local_region if node not in coalition]
+    num_nodes_around = len(nodes_around)
+
+    for subset_len in range(0, num_nodes_around + 1):
+        node_exclude_subsets = combinations(nodes_around, subset_len)
+        for node_exclude_subset in node_exclude_subsets:
+            set_exclude_mask = np.ones(num_nodes)
+            set_exclude_mask[local_region] = 0.0
+            if node_exclude_subset:
+                set_exclude_mask[list(node_exclude_subset)] = 1.0
+            set_include_mask = set_exclude_mask.copy()
+            set_include_mask[coalition] = 1.0
+
+            set_exclude_masks.append(set_exclude_mask)
+            set_include_masks.append(set_include_mask)
+
+    exclude_mask = np.stack(set_exclude_masks, axis=0)
+    include_mask = np.stack(set_include_masks, axis=0)
+    num_players = len(nodes_around) + 1
+    num_player_in_set = num_players - 1 + len(coalition) - (1 - exclude_mask).sum(axis=1)
+    p = num_players
+    S = num_player_in_set
+    coeffs = torch.tensor(1.0 / comb(p, S) / (p - S + 1e-6))
+
+    marginal_contributions = \
+        marginal_contribution(data, exclude_mask, include_mask, value_func, subgraph_build_func)
+
+    l_shapley_value = (marginal_contributions.squeeze().cpu() * coeffs).sum().item()
+    return l_shapley_value
+
+
+def mc_shapley(coalition: list, data: Data,
+               value_func: str, subgraph_building_method='zero_filling',
+               sample_num=1000) -> float:
+    """ monte carlo sampling approximation of the shapley value """
+    subset_build_func = get_graph_build_func(subgraph_building_method)
+
+    num_nodes = data.num_nodes
+    node_indices = np.arange(num_nodes)
+    coalition_placeholder = num_nodes
+    set_exclude_masks = []
+    set_include_masks = []
+
+    for example_idx in range(sample_num):
+        subset_nodes_from = [node for node in node_indices if node not in coalition]
+        random_nodes_permutation = np.array(subset_nodes_from + [coalition_placeholder])
+        random_nodes_permutation = np.random.permutation(random_nodes_permutation)
+        split_idx = np.where(random_nodes_permutation == coalition_placeholder)[0][0]
+        selected_nodes = random_nodes_permutation[:split_idx]
+        set_exclude_mask = np.zeros(num_nodes)
+        set_exclude_mask[selected_nodes] = 1.0
+        set_include_mask = set_exclude_mask.copy()
+        set_include_mask[coalition] = 1.0
+
+        set_exclude_masks.append(set_exclude_mask)
+        set_include_masks.append(set_include_mask)
+
+    exclude_mask = np.stack(set_exclude_masks, axis=0)
+    include_mask = np.stack(set_include_masks, axis=0)
+    marginal_contributions = marginal_contribution(data, exclude_mask, include_mask, value_func, subset_build_func)
+    mc_shapley_value = marginal_contributions.mean().item()
+
+    return mc_shapley_value
+
+
+def mc_l_shapley(coalition: list, data: Data, local_radius: int,
+                 value_func: str, subgraph_building_method='zero_filling',
+                 sample_num=1000) -> float:
+    """ monte carlo sampling approximation of the l_shapley value """
+    graph = to_networkx(data)
+    num_nodes = graph.number_of_nodes()
+    subgraph_build_func = get_graph_build_func(subgraph_building_method)
+
+    local_region = copy.copy(coalition)
+    for k in range(local_radius - 1):
+        k_neiborhoood = []
+        for node in local_region:
+            k_neiborhoood += list(graph.neighbors(node))
+        local_region += k_neiborhoood
+        local_region = list(set(local_region))
+
+    coalition_placeholder = num_nodes
+    set_exclude_masks = []
+    set_include_masks = []
+    for example_idx in range(sample_num):
+        subset_nodes_from = [node for node in local_region if node not in coalition]
+        random_nodes_permutation = np.array(subset_nodes_from + [coalition_placeholder])
+        random_nodes_permutation = np.random.permutation(random_nodes_permutation)
+        split_idx = np.where(random_nodes_permutation == coalition_placeholder)[0][0]
+        selected_nodes = random_nodes_permutation[:split_idx]
+        set_exclude_mask = np.ones(num_nodes)
+        set_exclude_mask[local_region] = 0.0
+        set_exclude_mask[selected_nodes] = 1.0
+        set_include_mask = set_exclude_mask.copy()
+        set_include_mask[coalition] = 1.0
+
+        set_exclude_masks.append(set_exclude_mask)
+        set_include_masks.append(set_include_mask)
+
+    exclude_mask = np.stack(set_exclude_masks, axis=0)
+    include_mask = np.stack(set_include_masks, axis=0)
+    marginal_contributions = \
+        marginal_contribution(data, exclude_mask, include_mask, value_func, subgraph_build_func)
+
+    mc_l_shapley_value = (marginal_contributions).mean().item()
+    return mc_l_shapley_value
+
+
+def gnn_score(coalition: list, data: Data, value_func: str,
+              subgraph_building_method='zero_filling') -> torch.Tensor:
+    """ the value of subgraph with selected nodes """
+    num_nodes = data.num_nodes
+    subgraph_build_func = get_graph_build_func(subgraph_building_method)
+    mask = torch.zeros(num_nodes).type(torch.float32).to(data.x.device)
+    mask[coalition] = 1.0
+    ret_x, ret_edge_index = subgraph_build_func(data.x, data.edge_index, mask)
+    mask_data = Data(x=ret_x, edge_index=ret_edge_index)
+    mask_data = Batch.from_data_list([mask_data])
+    score = value_func(mask_data)
+    # get the score of predicted class for graph or specific node idx
+    return score.item()
+
+
+def NC_mc_l_shapley(coalition: list, data: Data, local_radius: int,
+                    value_func: str, node_idx: int = -1,
+                    subgraph_building_method='zero_filling', sample_num=1000) -> float:
+    """ monte carlo approximation of l_shapley where the target node is kept in both subgraph """
+    graph = to_networkx(data)
+    num_nodes = graph.number_of_nodes()
+    subgraph_build_func = get_graph_build_func(subgraph_building_method)
+
+    local_region = copy.copy(coalition)
+    for k in range(local_radius - 1):
+        k_neiborhoood = []
+        for node in local_region:
+            k_neiborhoood += list(graph.neighbors(node))
+        local_region += k_neiborhoood
+        local_region = list(set(local_region))
+
+    coalition_placeholder = num_nodes
+    set_exclude_masks = []
+    set_include_masks = []
+    for example_idx in range(sample_num):
+        subset_nodes_from = [node for node in local_region if node not in coalition]
+        random_nodes_permutation = np.array(subset_nodes_from + [coalition_placeholder])
+        random_nodes_permutation = np.random.permutation(random_nodes_permutation)
+        split_idx = np.where(random_nodes_permutation == coalition_placeholder)[0][0]
+        selected_nodes = random_nodes_permutation[:split_idx]
+        set_exclude_mask = np.ones(num_nodes)
+        set_exclude_mask[local_region] = 0.0
+        set_exclude_mask[selected_nodes] = 1.0
+        if node_idx != -1:
+            set_exclude_mask[node_idx] = 1.0
+        set_include_mask = set_exclude_mask.copy()
+        set_include_mask[coalition] = 1.0  # include the node_idx
+
+        set_exclude_masks.append(set_exclude_mask)
+        set_include_masks.append(set_include_mask)
+
+    exclude_mask = np.stack(set_exclude_masks, axis=0)
+    include_mask = np.stack(set_include_masks, axis=0)
+    marginal_contributions = \
+        marginal_contribution(data, exclude_mask, include_mask, value_func, subgraph_build_func)
+
+    mc_l_shapley_value = (marginal_contributions).mean().item()
+    return mc_l_shapley_value
+
+
+def sparsity(coalition: list, data: Data, subgraph_building_method='zero_filling'):
+    if subgraph_building_method == 'zero_filling':
+        return 1.0 - len(coalition) / data.num_nodes
+
+    elif subgraph_building_method == 'split':
+        row, col = data.edge_index
+        node_mask = torch.zeros(data.x.shape[0])
+        node_mask[coalition] = 1.0
+        edge_mask = (node_mask[row] == 1) & (node_mask[col] == 1)
+        return 1.0 - edge_mask.sum() / edge_mask.shape[0]