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data_load.py
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602 lines (572 loc) · 28.3 KB
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import torch
import numpy as np
from sklearn.preprocessing import StandardScaler
import math
from collections import defaultdict
import dgl
import utils
import random
import pickle
import os
import torch.nn as nn
from scipy import stats
from sklearn.model_selection import train_test_split
from dgl import dataloading
from dgl import sampling, subgraph, distributed
from tqdm import tqdm, trange
import scipy.sparse as sp
import hashlib
from scipy.sparse.linalg import expm
from scipy.sparse import csr_matrix, diags
def make_order(ls):
a = np.array(ls)
argsorted = np.argsort(a)
orders = np.zeros(a.shape)
a = sorted(a)
# adjust
previous = None
order = 1
for i, _a in enumerate(a):
if previous is None:
previous = _a
orders[argsorted[i]] = order
elif previous != _a:
order += 1
orders[argsorted[i]] = order
previous = _a
else:
orders[argsorted[i]] = order
return orders.tolist()
class Hypergraph:
def __init__(self, args, dataset_name):
self.inputdir = args.inputdir
self.dataname = dataset_name
self.exist_hedgename = args.exist_hedgename
self.valid_inputname = args.valid_inputname
self.test_inputname = args.test_inputname
self.use_gpu = args.use_gpu
self.k = args.k
self.hedge2node = []
self.node2hedge = []
self.hedge2nodepos = [] # hyperedge index -> node positions (after binning)
self._hedge2nodepos = [] # hyperedge index -> node positions (before binning)
self.node2hedgePE = []
self.hedge2nodePE = []
self.weight_flag = False
self.hedge2nodeweight = []
self.node2hedgeweight = []
self.numhedges = 0
self.numnodes = 0
self.hedgeindex = {} # papaercode -> index
self.hedgename = {} # index -> papercode
self.e_feat = []
self.node_reindexing = {} # nodeindex -> reindex
self.node_orgindex = {} # reindex -> nodeindex
self.v_feat = [] # (V, 1)
self.load_graph(args)
print("Data is prepared")
def load_graph(self, args):
# construct connection -------------------------------------------------------
hset = []
if args.k > 0:
with open(self.inputdir + self.dataname + "/sampled_hset_" + str(args.k) + ".txt", "r") as f:
for line in f.readlines():
line = line.rstrip()
hset.append(int(line))
self.max_len = 0
with open(self.inputdir + self.dataname + "/hypergraph.txt", "r") as f:
for _hidx, line in enumerate(f.readlines()):
if (args.k == 0) or ((args.k > 0) and (_hidx in hset)):
tmp = line.split("\t")
hidx = self.numhedges
self.numhedges += 1
if self.exist_hedgename:
papercode = tmp[0][1:-1] # without '
papercode = papercode.rstrip()
self.hedgeindex[papercode] = hidx
self.hedgename[hidx] = papercode
tmp = tmp[1:]
else:
self.hedgeindex[_hidx] = hidx
self.hedgename[hidx] = _hidx
self.hedgeindex[_hidx] = hidx
self.hedgename[hidx] = _hidx
self.hedge2node.append([])
self.hedge2nodepos.append([])
self._hedge2nodepos.append([])
self.hedge2nodePE.append([])
self.hedge2nodeweight.append([])
self.e_feat.append([])
if (self.max_len < len(tmp)):
self.max_len = len(tmp)
for node in tmp:
node = int(node.rstrip())
if node not in self.node_reindexing:
node_reindex = self.numnodes
self.numnodes += 1
self.node_reindexing[node] = node_reindex
self.node_orgindex[node_reindex] = node
self.node2hedge.append([])
self.node2hedgePE.append([])
self.node2hedgeweight.append([])
self.v_feat.append([])
nodeindex = self.node_reindexing[node]
self.hedge2node[hidx].append(nodeindex)
self.node2hedge[nodeindex].append(hidx)
self.hedge2nodePE[hidx].append([])
self.node2hedgePE[nodeindex].append([])
print("Max Size = ", self.max_len)
print("Number of Hyperedges : " + str(self.numhedges))
print("Number of Nodes : " + str(self.numnodes))
# update by max degree
for vhedges in self.node2hedge:
if self.max_len < len(vhedges):
self.max_len = len(vhedges)
self.v_feat = torch.tensor(self.v_feat).type('torch.FloatTensor')
for h in range(len(self.e_feat)):
self.e_feat[h] = [0 for _ in range(args.dim_edge)]
self.e_feat = torch.tensor(self.e_feat).type('torch.FloatTensor')
# Split Data ------------------------------------------------------------------------
self.test_index = []
self.valid_index = []
self.validsize = 0
self.testsize = 0
self.trainsize = 0
self.hedge2type = torch.zeros(self.numhedges)
assert os.path.isfile(self.inputdir + self.dataname + "/" + self.valid_inputname + "_" + str(self.k) + ".txt")
with open(self.inputdir + self.dataname + "/" + self.valid_inputname + "_" + str(self.k) + ".txt", "r") as f:
for line in f.readlines():
name = line.rstrip()
if self.exist_hedgename is False:
name = int(name)
index = self.hedgeindex[name]
self.valid_index.append(index)
self.hedge2type[self.valid_index] = 1
self.validsize = len(self.valid_index)
if os.path.isfile(self.inputdir + self.dataname + "/" + self.test_inputname + "_" + str(self.k) + ".txt"):
with open(self.inputdir + self.dataname + "/" + self.test_inputname + "_" + str(self.k) + ".txt", "r") as f:
for line in f.readlines():
name = line.rstrip()
if self.exist_hedgename is False:
name = int(name)
index = self.hedgeindex[name]
self.test_index.append(index)
assert len(self.test_index) > 0
self.hedge2type[self.test_index] = 2
self.testsize = len(self.test_index)
self.trainsize = self.numhedges - (self.validsize + self.testsize)
# extract target ---------------------------------------------------------
print("Extract labels")
with open(self.inputdir + self.dataname + "/hypergraph_pos.txt", "r") as f:
for _hidx, line in enumerate(f.readlines()):
tmp = line.split("\t")
if self.exist_hedgename:
papercode = tmp[0][1:-1] # without ''
if (papercode not in self.hedgeindex):
continue
hidx = self.hedgeindex[papercode]
tmp = tmp[1:]
else:
if (_hidx not in self.hedgeindex):
continue
hidx = self.hedgeindex[_hidx]
if args.binning > 0:
positions = [float(i) for i in tmp]
for nodepos in positions:
self._hedge2nodepos[hidx].append(nodepos)
else:
positions = [int(i) for i in tmp]
for nodepos in positions:
self.hedge2nodepos[hidx].append(nodepos)
# labeled by binning
if args.binning > 0:
weights = sorted([w for h in self.get_data(type=0) for w in self._hedge2nodepos[h]])
total_num = len(weights)
cum = 0
self.binindex = []
for w in weights:
cum += 1
if (cum / total_num) >= ((1.0 / args.binning) * (len(self.binindex) + 1)):
self.binindex.append(w)
print("BinIndex", self.binindex)
with open(self.inputdir + self.dataname + "/binindex.txt", "w") as f:
for binvalue in self.binindex:
f.write(str(binvalue) + "\n")
# float -> int
for h in range(self.numhedges):
for i, w in enumerate(self._hedge2nodepos[h]):
for bi, bv in enumerate(self.binindex):
if w <= bv:
self.hedge2nodepos[h][i] = bi
break
elif bi == (args.output_dim - 1) and w > bv:
self.hedge2nodepos[h][i] = bi
break
# check
for h in range(self.numhedges):
for w in self.hedge2nodepos[h]:
assert w in range(args.binning), str(w)
# extract PE ----------------------------------------------------------------------------------------------------
if args.embedder == "whatsnetLSPE":
if len(args.vorder_input) == 0:
fname = "../%s_%d_wv_%d_%s.npy" % (args.dataset_name, args.k, 44, args.walk)
A = np.load(fname)
A = StandardScaler().fit_transform(A)
A = A.astype('float32')
self.v_pos = torch.tensor(A)
self.order_dim = self.v_pos.shape[1]
print(self.order_dim)
else:
self.order_dim = len(args.vorder_input)
self.v_pos = torch.zeros((self.numnodes, self.order_dim), dtype=torch.float32)
for _i, inputpath in enumerate(args.vorder_input):
with open(self.inputdir + self.dataname + "/" + inputpath + "_" + str(args.k) + ".txt", "r") as f:
columns = f.readline()
columns = columns[:-1].split("\t")
for line in f.readlines():
line = line.rstrip()
tmp = line.split("\t")
nodeindex = int(tmp[0])
if nodeindex not in self.node_reindexing:
# not include in incidence matrix
continue
node_reindex = self.node_reindexing[nodeindex]
self.v_pos[node_reindex][_i] = float(tmp[1])
self.e_pos = torch.zeros((self.numhedges, self.order_dim), dtype=torch.float32)
self.weight_flag = False
# hedge2nodePE
elif len(args.vorder_input) > 0: # centrality -> PE ------------------------------------------------------------------
self.order_dim = len(args.vorder_input)
for inputpath in args.vorder_input:
vfeat = {} # node -> vfeat
with open(self.inputdir + self.dataname + "/" + inputpath + "_" + str(args.k) + ".txt", "r") as f:
columns = f.readline()
columns = columns[:-1].split("\t")
for line in f.readlines():
line = line.rstrip()
tmp = line.split("\t")
nodeindex = int(tmp[0])
if nodeindex not in self.node_reindexing:
# not include in incidence matrix
continue
node_reindex = self.node_reindexing[nodeindex]
for i, col in enumerate(columns):
vfeat[node_reindex] = float(tmp[i])
if args.whole_order: # in entire nodeset
feats = []
for vidx in range(self.numnodes):
feats.append(vfeat[vidx])
orders = make_order(feats)
for hidx, hedge in enumerate(self.hedge2node):
for vorder, v in enumerate(hedge):
self.hedge2nodePE[hidx][vorder].append((orders[v]) / self.numnodes)
else: # in each hyperedge
for hidx, hedge in enumerate(self.hedge2node):
feats = []
for v in hedge:
feats.append(vfeat[v])
orders = make_order(feats)
for vorder, v in enumerate(hedge):
self.hedge2nodePE[hidx][vorder].append((orders[vorder]) / len(feats))
# check
assert len(self.hedge2nodePE) == self.numhedges
for hidx in range(self.numhedges):
assert len(self.hedge2nodePE[hidx]) == len(self.hedge2node[hidx])
for vorder in self.hedge2nodePE[hidx]:
assert len(vorder) == len(args.vorder_input)
if len(args.eorder_input) == 0:
# node2hedgePE
for vidx, node in enumerate(self.node2hedge):
orders = []
for hidx in node:
for vorder,_v in enumerate(self.hedge2node[hidx]):
if _v == vidx:
orders.append(self.hedge2nodePE[hidx][vorder])
break
self.node2hedgePE[vidx] = orders
else:
for inputpath in args.eorder_input:
efeat = {} # node -> vfeat
with open(self.inputdir + self.dataname + "/" + inputpath + "_" + str(args.k) + ".txt", "r") as f:
for hidx, line in enumerate(f.readlines()):
line = line.rstrip()
centrality = str(line)
efeat[hidx] = centrality
if args.whole_order: # in entire nodeset
feats = []
for hidx in range(self.numhedgds):
feats.append(efeat[hidx])
orders = make_order(feats)
for vidx, hedges in enumerate(self.node2hedge):
for horder, h in enumerate(hedges):
self.node2hedgePE[vidx][horder].append((orders[h]) / self.numhedges)
else: # in each hyperedge
for vidx, hedges in enumerate(self.node2hedge):
feats = []
for h in hedges:
feats.append(efeat[h])
orders = make_order(feats)
for horder, h in enumerate(hedges):
self.node2hedgePE[vidx][horder].append((orders[horder]) / len(feats))
for v in range(self.numnodes):
for horder in range(len(self.node2hedgePE[v])):
diff = self.order_dim - len(self.node2hedgePE[v][horder])
for _ in range(diff):
self.node2hedgePE[v][horder].append(0.0)
# check
assert len(self.node2hedgePE) == self.numnodes
for vidx in range(self.numnodes):
assert len(self.node2hedgePE[vidx]) == len(self.node2hedge[vidx])
for horder in self.node2hedgePE[vidx]:
assert len(horder) == len(args.vorder_input)
self.weight_flag = True
elif len(args.pe) > 0: # ---------------------------------------------------------------------------------------------
# Use other positional encoding!
rows, cols = [], [] # construct adjacency matrix
for v in range(self.numnodes):
hedges = self.node2hedge[v]
check = np.zeros(self.numnodes)
for h in hedges:
neighbors = self.hedge2node[h]
for nv in neighbors:
if v < nv and check[nv] == 0:
check[nv] = 1
rows.append(v)
cols.append(nv)
rows.append(nv)
cols.append(v)
A = sp.coo_matrix((np.ones(len(rows)), (np.array(rows), np.array(cols))), shape=(self.numnodes, self.numnodes))
_deg = A.sum(axis=1).squeeze(1)
deg = list(_deg.flat)
deg = np.array(deg)
print("Adj is prepared")
if args.pe in ["DK", "PRWK"]:
# sorting hedge2node, hedge2nodepos
for hidx in range(self.numhedges):
sorted_idx = np.argsort(np.array(self.hedge2node[hidx]))
self.hedge2node[hidx] = np.array(self.hedge2node[hidx])[sorted_idx].tolist()
self.hedge2nodepos[hidx] = np.array(self.hedge2nodepos[hidx])[sorted_idx].tolist()
if args.pe == "DK":
L = sp.diags(deg, dtype=float) - A # No Normalize
beta = 1.0
L = -beta * L
v2v = L
for hidx in trange(self.numhedges, desc="making KD per hedge"):
hedge = self.hedge2node[hidx]
_v2v_e = []
for vidx in range(len(hedge)):
vi = hedge[vidx]
_row = v2v.getrow(vi).toarray()[0]
efeat = []
for nvidx in range(len(hedge)):
nv = hedge[nvidx]
if (_row[nv] < 0 and vidx != nvidx):
assert vi == nv
efeat.append(1.0)
else:
efeat.append(_row[nv])
_v2v_e.append(efeat)
_v2v_e = np.array(_v2v_e)
v2v_e = expm(_v2v_e)
for vorder in range(len(hedge)):
self.hedge2nodePE[hidx][vorder] = v2v_e[vidx].tolist()
for _pe in self.hedge2nodePE[hidx][vorder]:
if _pe < 0:
print(_v2v_e[vidx])
print(v2v_e[vidx])
print(self.hedge2nodePE[hidx][vorder])
assert _pe >= 0
elif args.pe == "PRWK":
L = sp.diags(deg, dtype=float) - A # No Normalize
print("L is prepared")
gamma, p = 0.5, 2
r = sp.eye(self.numnodes) - gamma * L
print("R is prepared")
v2v = r.power(p) # |V|x|V|
for hidx in range(self.numhedges):
hedge = self.hedge2node[hidx]
for vidx in range(len(hedge)):
vi = hedge[vidx]
efeat = []
for nvidx in range(len(hedge)):
nv = hedge[nvidx]
_row = v2v.getrow(vi).toarray()[0]
efeat.append(_row[nv])
self.hedge2nodePE[hidx][vidx] = efeat
for _pe in self.hedge2nodePE[hidx][vidx]:
assert _pe >= 0
self.weight_flag = True
# For HNN ----------------------------------------------------------------------------------
if args.embedder == "hnn":
print("Extract matrices for HNN")
nodedeg = []
hedgedeg = []
for hedges in self.node2hedge:
nodedeg.append(len(hedges))
for nodes in self.hedge2node:
hedgedeg.append(len(nodes))
self.invDV = torch.pow(torch.FloatTensor(nodedeg), -1)
self.invDE = torch.pow(torch.FloatTensor(hedgedeg),-1)
# calculating PE DE^{-1} := emat, P D^{-1} := vmat
# P = H DE^{-1} H^{T} D^{-T}, PE = H^{T} D^{-T} H DE^{-1}
DE = sp.diags([d**(-1) for d in hedgedeg], dtype=np.float32)
D = sp.diags([d**(-1) for d in nodedeg], dtype=np.float32)
rows, cols, datas = [], [], []
for h in range(self.numhedges):
for vi, w in enumerate(self.hedge2node[h]):
v = self.hedge2node[h][vi]
rows.append(v)
cols.append(h)
datas.append(1)
H = csr_matrix((datas, (rows, cols)), shape=(self.numnodes, self.numhedges), dtype=np.float32)
print("DE, D, H")
P = H * DE * H.T * D.T
PE = H.T * D.T * H * DE
eMat = PE * DE
vMat = P * D
print("eMat, vMat")
# convert to torch
rows, cols = eMat.nonzero()
datas = eMat.data
self.eMat = torch.sparse_coo_tensor([rows,cols], datas, dtype=torch.float32)
rows, cols = vMat.nonzero()
datas = vMat.data
self.vMat = torch.sparse_coo_tensor([rows,cols], datas, dtype=torch.float32)
print("torch eMat, vMat")
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
self.invDV = self.invDV.to(device)
self.invDE = self.invDE.to(device)
self.eMat = self.eMat.to(device)
self.vMat = self.vMat.to(device)
# For HGNN & HCHA ----------------------------------------------------------------------------------
if args.embedder == "hgnn" or args.embedder == "hcha":
nodedeg = []
hedgedeg = []
for hedges in self.node2hedge:
nodedeg.append(len(hedges))
for nodes in self.hedge2node:
hedgedeg.append(len(nodes))
self.DV2 = torch.pow(torch.FloatTensor(nodedeg), -0.5)
self.invDE = torch.pow(torch.FloatTensor(hedgedeg),-1)
if self.use_gpu or args.embedder == "hcha":
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
self.DV2 = self.DV2.to(device)
self.invDE = self.invDE.to(device)
# applying alpha and beta in HNHN ---------------------------------------------------------
if args.embedder == "hnhn" or args.embedder == "transformerHNHN":
print("weight")
e_weight = []
v_weight = []
for neighbor_hedges in self.node2hedge:
v_weight.append(len(neighbor_hedges))
for hedge in self.hedge2node:
e_weight.append(len(hedge))
use_exp_wt = args.use_exp_wt
e_reg_weight = torch.zeros(self.numhedges)
v_reg_weight = torch.zeros(self.numnodes)
for hidx in range(self.numhedges):
e_wt = e_weight[hidx]
e_reg_wt = torch.exp(args.alpha_e*e_wt) if use_exp_wt else e_wt**args.alpha_e
e_reg_weight[hidx] = e_reg_wt
for vidx in range(self.numnodes):
v_wt = v_weight[vidx]
v_reg_wt = torch.exp(args.alpha_v*v_wt) if use_exp_wt else v_wt**args.alpha_v
v_reg_weight[vidx] = v_reg_wt
v_reg_sum = torch.zeros(self.numnodes) # <- e_reg_weight2v_sum
e_reg_sum = torch.zeros(self.numhedges) # <- v_reg_weight2e_sum
for hidx, hedges in enumerate(self.hedge2node):
for vidx in hedges:
v_reg_sum[vidx] += e_reg_wt
e_reg_sum[hidx] += v_reg_wt
e_reg_sum[e_reg_sum==0] = 1
v_reg_sum[v_reg_sum==0] = 1
self.e_reg_weight = torch.Tensor(e_reg_weight).unsqueeze(-1)
self.v_reg_sum = torch.Tensor(v_reg_sum).unsqueeze(-1)
self.v_reg_weight = torch.Tensor(v_reg_weight).unsqueeze(-1)
self.e_reg_sum = torch.Tensor(e_reg_sum).unsqueeze(-1)
# check
for hidx, hedges in enumerate(self.hedge2node):
e_reg_sum = self.e_reg_sum[hidx]
v_reg_sum = 0
for vidx in hedges:
v_reg_sum += self.v_reg_weight[vidx]
assert abs(e_reg_sum - v_reg_sum) < 1e-4
if self.use_gpu:
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
self.e_reg_weight = self.e_reg_weight.to(device)
self.v_reg_sum = self.v_reg_sum.to(device)
self.v_reg_weight = self.v_reg_weight.to(device)
self.e_reg_sum = self.e_reg_sum.to(device)
# UniGCNII ----------------------------------------------------------------------------------
if args.embedder == "unigcnii":
degV = []
for vidx, hedges in enumerate(self.node2hedge):
degV.append(len(hedges))
degE = []
for eidx, nodes in enumerate(self.hedge2node):
avgdeg = 0
for v in nodes:
avgdeg += (degV[v] / len(nodes))
degE.append(avgdeg)
self.degV = torch.Tensor(degV).pow(-0.5).unsqueeze(-1)
self.degE = torch.Tensor(degE).pow(-0.5).unsqueeze(-1)
if self.use_gpu:
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
self.degV = self.degV.to(device)
self.degE = self.degE.to(device)
def get_data(self, type=0):
hedgelist = ((self.hedge2type == type).nonzero(as_tuple=True)[0])
if self.use_gpu is False:
hedgelist = hedgelist.tolist()
return hedgelist
# Generate DGL Graph ==============================================================================================
def gen_DGLGraph(args, hedge2node, hedge2nodepos, node2hedge, device):
data_dict = defaultdict(list)
in_edge_label = []
con_edge_label = []
for hidx, hedge in enumerate(hedge2node):
for vorder, v in enumerate(hedge):
data_dict[('node', 'in', 'edge')].append((v, hidx))
data_dict[('edge', 'con', 'node')].append((hidx, v))
in_edge_label.append(hedge2nodepos[hidx][vorder])
con_edge_label.append(hedge2nodepos[hidx][vorder])
in_edge_label = torch.Tensor(in_edge_label)
con_edge_label = torch.Tensor(con_edge_label)
g = dgl.heterograph(data_dict)
g['in'].edata['label'] = in_edge_label
g['con'].edata['label'] = con_edge_label
return g
def gen_weighted_DGLGraph(args, hedge2node, hedge2nodePE, hedge2nodepos, node2hedge, node2hedgeorder, device):
edgefeat_dim = 0
for efeat_list in hedge2nodePE:
efeat_dim = len(efeat_list[0])
edgefeat_dim = max(edgefeat_dim, efeat_dim)
print("Edge Feat Dim ", edgefeat_dim)
data_dict = defaultdict(list)
in_edge_weights = []
in_edge_label = []
con_edge_weights = []
con_edge_label = []
for hidx, hedge in enumerate(hedge2node):
for vorder, v in enumerate(hedge):
# connection
data_dict[('node', 'in', 'edge')].append((v, hidx))
data_dict[('edge', 'con', 'node')].append((hidx, v))
# edge feat
efeat = hedge2nodePE[hidx][vorder]
efeat += np.zeros(edgefeat_dim - len(efeat)).tolist()
in_edge_weights.append(efeat)
con_edge_weights.append(efeat)
# label
in_edge_label.append(hedge2nodepos[hidx][vorder])
con_edge_label.append(hedge2nodepos[hidx][vorder])
in_edge_weights = torch.Tensor(in_edge_weights)
con_edge_weights = torch.Tensor(con_edge_weights)
in_edge_label = torch.Tensor(in_edge_label)
con_edge_label = torch.Tensor(con_edge_label)
g = dgl.heterograph(data_dict)
g['in'].edata['weight'] = in_edge_weights
g['con'].edata['weight'] = con_edge_weights
g['in'].edata['label'] = in_edge_label
g['con'].edata['label'] = con_edge_label
return g