glam4cm 0.1.0__py3-none-any.whl

glam4cm/trainers/metrics.py

@@ -0,0 +1,55 @@
+from sklearn.metrics import (
+    accuracy_score, 
+    balanced_accuracy_score,
+    f1_score,
+    precision_score,
+    recall_score
+)
+
+import torch
+import numpy as np
+
+
+def compute_metrics(p):
+    preds = np.argmax(p.predictions, axis=1)
+    acc = accuracy_score(p.label_ids, preds)
+    balanced_acc = balanced_accuracy_score(p.label_ids, preds)
+    return {
+        'accuracy': acc,
+        'balanced_accuracy': balanced_acc,
+    }
+
+
+def compute_classification_metrics(preds, labels):
+    """
+    Compute F1-score, balanced accuracy, precision, and recall for multi-class classification.
+    
+    Args:
+        preds (torch.Tensor): Predictions from the model (logits or probabilities). Shape: [num_samples, num_classes]
+        labels (torch.Tensor): Ground truth labels. Shape: [num_samples]
+    
+    Returns:
+        dict: Dictionary containing metrics (F1-score, balanced accuracy, precision, recall).
+    """
+    # Convert predictions to class labels
+    preds = torch.argmax(preds, dim=1).cpu().numpy()
+    labels = labels.cpu().numpy()
+
+    metrics = {}
+
+    # F1-score (macro and weighted)
+    metrics['f1_macro'] = f1_score(labels, preds, average='macro')
+    metrics['f1_weighted'] = f1_score(labels, preds, average='weighted')
+
+    # Balanced Accuracy
+    metrics['balanced_accuracy'] = balanced_accuracy_score(labels, preds)
+
+    # Precision (macro and weighted)
+    metrics['precision_macro'] = precision_score(labels, preds, average='macro', zero_division=0)
+    metrics['precision_weighted'] = precision_score(labels, preds, average='weighted', zero_division=0)
+
+    # Recall (macro and weighted)
+    metrics['recall_macro'] = recall_score(labels, preds, average='macro', zero_division=0)
+    metrics['recall_weighted'] = recall_score(labels, preds, average='weighted', zero_division=0)
+
+    return metrics

glam4cm/utils.py

@@ -0,0 +1,194 @@
+from argparse import ArgumentParser
+import random
+import numpy as np
+import torch
+import os
+import fnmatch
+import json
+from typing import List
+import xmltodict
+from torch_geometric.data import Data
+import hashlib
+import networkx as nx
+from collections import deque
+
+
+
+def find_files_with_extension(root_dir, extension):
+    matching_files: List[str] = list()
+
+    # Recursively search for files with the specified extension
+    for root, _, files in os.walk(root_dir):
+        for filename in fnmatch.filter(files, f'*.{extension}'):
+            matching_files.append(os.path.join(root, filename))
+
+    return matching_files
+
+
+def xml_to_json(xml_string):
+    xml_dict = xmltodict.parse(xml_string)
+    json_data = json.dumps(xml_dict, indent=4)
+    return json_data
+
+
+def set_seed(seed):
+    random.seed(seed)
+    np.random.seed(seed)
+    torch.manual_seed(seed)
+    torch.cuda.manual_seed(seed)
+
+
+def create_dummy_graph(num_nodes, num_edges):
+    # Node and edge attribute types
+    node_types = ['nt1', 'nt2', 'nt3', 'nt4', 'nt5', 'nt6', 'nt7']
+    edge_types = ['et1', 'et2', 'et3', 'et4']
+
+    # Create a graph
+    G = nx.Graph()
+
+    # Add nodes with attributes
+    for i in range(1, num_nodes + 1):
+        G.add_node(i, name=f'node_{i}', type=random.choice(node_types))
+
+    # Add edges with attributes
+    edges_added = 0
+    while edges_added < num_edges:
+        u = random.randint(1, num_nodes)
+        v = random.randint(1, num_nodes)
+        if u != v and not G.has_edge(u, v):  # Ensure no self-loops and no duplicate edges
+            G.add_edge(u, v, name=f'edge_{edges_added + 1}', type=random.choice(edge_types))
+            edges_added += 1
+
+    return G
+
+
+def bfs(graph: nx.Graph, start_node, d, exclude_edges: List[str] = None):
+        """Perform BFS to get all paths up to a given depth."""
+        if exclude_edges is None:
+            exclude_edges = []
+            
+        queue = deque([(start_node, [start_node])])
+        paths = []
+
+        while queue:
+            current_node, path = queue.popleft()
+
+            # Stop if the path length exceeds the maximum depth
+            if len(path) - 1 > d:
+                continue
+
+            # Store the path
+            if len(path) >= 1:  # Exclude single-node paths
+                paths.append(path)
+
+            # Add neighbors to the queue
+            for neighbor in graph.neighbors(current_node):
+                edge = (current_node, neighbor)
+                if neighbor not in path and edge not in exclude_edges:
+                    queue.append((neighbor, path + [neighbor]))
+        
+        return paths
+
+
+def remove_subsets(list_of_lists):
+        sorted_lists = sorted(list_of_lists, key=len, reverse=True)
+        unique_lists = []
+        for lst in sorted_lists:
+            current_set = set(lst)
+            if not any(current_set <= set(ul) for ul in unique_lists):
+                unique_lists.append(lst)
+        
+        return unique_lists
+
+
+def get_size_format(sz):
+	for x in ['bytes', 'KB', 'MB', 'GB', 'TB']:
+		if sz < 1024.0:
+			return "%3.1f %s" % (sz, x)
+		sz /= 1024.0
+	
+
+def get_file_size(file_path):
+	sz = os.path.getsize(file_path)
+	return get_size_format(sz)
+
+def get_directory_size(directory):
+    total_size = 0
+    for dirpath, _, filenames in os.walk(directory):
+        for f in filenames:
+            fp = os.path.join(dirpath, f)
+            total_size += os.path.getsize(fp)
+    return get_size_format(total_size)
+
+def get_tensor_size(tensor: torch.Tensor):
+	return get_size_format(tensor.element_size() * tensor.nelement())
+
+def get_size_of_data(data: Data):
+	size = 0
+	for _, value in data:
+		if isinstance(value, torch.Tensor):
+			size += value.element_size() * value.nelement()
+		elif isinstance(value, int):
+			size += value.bit_length() // 8
+						
+	return get_size_format(size)
+
+
+def md5_hash(input_string):
+    md5_hash = hashlib.md5()
+    md5_hash.update(input_string.encode('utf-8'))
+    return md5_hash.hexdigest()
+
+def randomize_features(dataset: List[Data], num_feats, mode):
+    for data in dataset:
+        num_nodes = data.num_nodes
+        num_edges = data.overall_edge_index.shape[1] if hasattr(data, 'overall_edge_index') else data.edge_index.shape[1]
+        if mode == 'node':
+            data.x = torch.randn((num_nodes, num_feats))
+        elif mode == 'edge':
+            data.edge_attr = torch.randn((num_edges, num_feats))
+        else:
+            raise ValueError("Invalid mode. Choose 'node' or 'edge'.")
+        
+
+def merge_argument_parsers(p1: ArgumentParser, p2: ArgumentParser):
+    merged_parser = ArgumentParser(description="Merged Parser")
+
+    # Combine arguments from parser1
+    for action in p1._actions:
+        if action.dest != "help":  # Skip the help action
+            merged_parser._add_action(action)
+
+    # Combine arguments from parser2
+    for action in p2._actions:
+        if action.dest != "help":  # Skip the help action
+            merged_parser._add_action(action)
+
+    return merged_parser
+
+
+def is_meaningful_line(line: str):
+    stripped_line: str = line.strip()
+    # Ignore empty lines, comments, and docstrings
+    if stripped_line == "" or stripped_line.startswith("#") or stripped_line.startswith('"""') or stripped_line.startswith("'''"):
+        return False
+    return True
+
+def count_lines_of_code_in_file(file_path):
+    with open(file_path, 'r', encoding='utf-8') as file:
+        lines = file.readlines()
+        meaningful_lines = [line for line in lines if is_meaningful_line(line)]
+    return len(meaningful_lines)
+
+def count_total_lines_of_code(directory):
+    total_lines = 0
+    for root, _, files in os.walk(directory):
+        for file in files:
+            if file.endswith('.py'):
+                file_path = os.path.join(root, file)
+                total_lines += count_lines_of_code_in_file(file_path)
+    return total_lines
+
+
+def snake_to_title(snake_str: str):
+    return snake_str.replace("_", " ").title()

glam4cm-0.1.0.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Syed Juned Ali
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

glam4cm-0.1.0.dist-info/METADATA

@@ -0,0 +1,86 @@
+Metadata-Version: 2.2
+Name: glam4cm
+Version: 0.1.0
+Summary: Graph Neural Networks and Language Models Trainer (Separate or combined) for conceptual models
+Author-email: Syed Juned Ali <syed.juned.ali@tuwien.ac.at>
+License: MIT License
+        
+        Copyright (c) 2025 Syed Juned Ali
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/junaidiiith/glam4cm
+Project-URL: Issues, https://github.com/junaidiiith/glam4cm/issues
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: langchain-text-splitters
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: torch
+Requires-Dist: numpy
+Requires-Dist: transformers
+Requires-Dist: sentence-transformers
+Requires-Dist: tqdm
+Requires-Dist: networkx
+Requires-Dist: torch_geometric
+Requires-Dist: pandas
+Requires-Dist: tensorboardX
+Requires-Dist: xmltodict
+Requires-Dist: fasttext
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+
+# glam4cm
+
+The data in this archive is derived from the user-contributed content on the
+Cooking Stack Exchange website (https://cooking.stackexchange.com/), used under
+CC-BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0/).
+
+The original data dump can be downloaded from:
+https://archive.org/download/stackexchange/cooking.stackexchange.com.7z
+and details about the dump obtained from:
+https://archive.org/details/stackexchange
+
+We distribute two files, under CC-BY-SA 3.0:
+
+ - cooking.stackexchange.txt, which contains all question titles and
+   their associated tags (one question per line, tags are prefixed by
+   the string "__label__") ;
+
+ - cooking.stackexchange.id, which contains the corresponding row IDs,
+   from the original data dump.
+
+
+Node classification
+  Language Model
+    Freezing parameters
+    Effect of attributes
+    Effect of edge information
+    Edge of partial node type information
+
+  GNN
+    GCNConv, SAGEConv, GATConv
+    Random Node Embeddings
+    Bert Node Embeddings
+    Finetuned Node Embeddings
+    Random Edge Embeddings
+    Bert Edge Embeddings
+    Finetuned Edge Embeddings

glam4cm-0.1.0.dist-info/RECORD

@@ -0,0 +1,72 @@
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+glam4cm-0.1.0.dist-info/LICENSE,sha256=NzIgfG9Z6TaC4HlY6ownebjdGY0DKUXSgF5sM7bmxZI,1071
+glam4cm-0.1.0.dist-info/METADATA,sha256=OJb9bm54MjDp6aA9gm0C0A7kxz1jndGW1GhAZFJOQeA,3260
+glam4cm-0.1.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+glam4cm-0.1.0.dist-info/entry_points.txt,sha256=sZ-zOIJOyDP-vpTyVTTbdDyNando8uRVQmaFuAo_nuM,45
+glam4cm-0.1.0.dist-info/top_level.txt,sha256=6V4mFMBo1sE2bowD9n2sxYv_ao8IsS8rR1ArAhfpQ4w,8
+glam4cm-0.1.0.dist-info/RECORD,,

glam4cm-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (75.8.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

glam4cm-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+glam4cm = glam4cm.run:main

glam4cm-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+glam4cm