need to add spinx for doc generation

Author: Ashutosh Tiwari

examples/sbm_sampler.ipynb

@@ -20,11 +20,12 @@ def __init__(
 
     @property
     def X(self):
-        return self.data.loc[:, self.data.columns != self.group_col].values
+        # can potentially be overloaded by child class
+        return self.data.values
 
     @property
     def y(self):
-        return self.data[:, self.group_col].values
+        return self.data[self.group_col].to_numpy()
 
     def _set_data_df(self) -> pd.DataFrame:
         raise NotImplementedError

graph_ml/datasets/dataset.py

@@ -28,4 +28,3 @@ def _set_data_df(self):
 
     def _set_adj(self):
         return nx.adjacency_matrix(self.graph)
-        pass

graph_ml/datasets/polbooks.py

@@ -0,0 +1,50 @@
+import numpy as np
+from scipy import sparse
+from numba import njit
+
+def to_member_matrix(group_ids):
+    """
+    create a member matrix U such that U[i,k] = 1 if i belongs to group k otherwise U[i,k]=0
+    :param group_ids:
+    :return:
+    """
+    Nr = group_ids.shape[0] # equal to number of samples
+    Nc = int(np.max(group_ids) + 1) # number of classes
+    U = sparse.csr_matrix((np.ones_like(group_ids), (np.arange(Nr), group_ids)), shape=(Nr, Nc))
+    U.data = U.data * 0 + 1
+    return U
+
+
+def matrix_sum_power(A, T):
+    """
+    compute the sum of the powers of the matrix A i.e.,
+    sum_{t=1}^{T} A^t
+    :param A:
+    :param T:
+    :return:
+    """
+    At = np.eye(A.shape[0])
+    As = np.zeros((A.shape[0], A.shape[0]))
+    for _ in range(T):
+        At = A @ At
+        As += At
+    return As
+
+
+@njit(nogil=True)
+def csr_row_cumsum(indptr, data):
+    """
+    compute the cumulative sum of the data array using the indptr array
+    :param indptr:
+    :param data:
+    :return:
+    """
+    out = np.zeros_like(data)
+    for i in range(len(indptr) - 1):
+        start = indptr[i]
+        end = indptr[i + 1]
+        out[start:end] = np.cumsum(data[start:end])
+    return out
+
+
+

graph_ml/utils/utils.py

@@ -41,6 +41,7 @@ torch-geometric = "^2.5.0"
 # url = "https://data.pyg.org/whl/torch-2.1.2+cu121.html"
 # priority = "primary"
 gensim = "^4.3.2"
+numba = "^0.59.0"
 
 [build-system]
 requires = ["poetry_core>=1.9.0"]