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import argparse, json, os
from pathlib import Path
from typing import Dict, List, Tuple, Optional
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from torch_scatter import scatter_add, scatter_mean
from torch_sparse import coalesce, spspmm
from torch_geometric.data import Data
from torch_geometric.loader import DataLoader
from torch_geometric.datasets import Planetoid, TUDataset
from torch_geometric.nn import GCNConv, global_mean_pool
from rich import print
# ---------------------------
# Utilities: edges and seeds
# ---------------------------
def add_scaled_self_loops(edge_index: Tensor,
edge_weight: Optional[Tensor],
num_nodes: int,
scale: float = 1.0) -> Tuple[Tensor, Tensor]:
"""Add self-loops with a chosen weight (scale). If scale=0, return unchanged."""
if scale == 0.0:
if edge_weight is None:
edge_weight = torch.ones(edge_index.size(1), device=edge_index.device)
return edge_index, edge_weight
device = edge_index.device
self_loops = torch.arange(num_nodes, device=device)
self_index = torch.stack([self_loops, self_loops], dim=0)
self_weight = torch.full((num_nodes,), float(scale), device=device)
if edge_weight is None:
base_w = torch.ones(edge_index.size(1), device=device)
else:
base_w = edge_weight
ei = torch.cat([edge_index, self_index], dim=1)
ew = torch.cat([base_w, self_weight], dim=0)
# coalesce to sum possible duplicates
ei, ew = coalesce(ei, ew, num_nodes, num_nodes, op='add')
return ei, ew
def adjacency_power(edge_index: Tensor, num_nodes: int, k: int = 2) -> Tensor:
"""
Compute (binary) k-th power adjacency using sparse matmul (torch_sparse.spspmm).
Returns a coalesced edge_index (no weights, duplicates removed).
"""
# Build A as (row, col) with all weights 1
device = edge_index.device
row, col = edge_index
val = torch.ones(row.numel(), device=device)
Ai, Av = edge_index, val
# Repeatedly multiply: A^2, then chain if k>2
Ri, Rv = spspmm(Ai, Av, Ai, Av, num_nodes, num_nodes, num_nodes)
# Remove diagonal self-loops in pure power (we can add our own later)
mask = Ri[0] != Ri[1]
Ri = Ri[:, mask]
# (Optional) higher powers: (A^k) – here we keep exactly k=2 for simplicity
return coalesce(Ri, torch.ones(Ri.size(1), device=device), num_nodes, num_nodes)[0]
def build_cluster_graph(edge_index: Tensor,
num_nodes: int,
node2cluster: Tensor,
weight_per_edge: Optional[Tensor] = None,
num_clusters: Optional[int] = None
) -> Tuple[Tensor, Tensor, int]:
"""
Build cluster graph A_c = S^T A S.
node2cluster: [N] long tensor with the cluster id for each node (hard assignment).
Returns (edge_index_c, edge_weight_c, K).
"""
if num_clusters is None:
K = int(node2cluster.max().item()) + 1
else:
K = num_clusters
src, dst = edge_index
csrc = node2cluster[src]
cdst = node2cluster[dst]
edge_c = torch.stack([csrc, cdst], dim=0)
if weight_per_edge is None:
w = torch.ones(edge_c.size(1), device=edge_c.device)
else:
w = weight_per_edge
edge_c, w = coalesce(edge_c, w, K, K, op='add') # sum multiplicities
# # set all weights of cluster edges to 1
# w = torch.ones_like(w)
# mask = edge_c[0] != edge_c[1]
# edge_c, w = edge_c[:, mask], w[mask]
return edge_c, w, K
# -----
# Seeds
# -----
def _parse_clusters_single_file(obj: dict, n_nodes: int) -> Tuple[List[List[int]], Tensor]:
"""
Expect the JSON to have top-level "clusters": [{members:[...], score:...}, ...]
Unassigned nodes become singleton clusters.
If a node appears in multiple clusters, we keep the cluster with largest 'score' then by size.
"""
clusters = obj.get("clusters", [])
# Collect candidate cluster id per node with priority by cluster score and size:
per_node = {} # node_id -> (priority_tuple, cluster_idx)
out: List[List[int]] = []
# prepare list of (members, score, size, index)
cinfo = []
for idx, c in enumerate(clusters):
members = c.get("members", [])
score = float(c.get("score", 0.0))
cinfo.append((members, score, len(members), idx))
# make a stable cluster list first
for members, score, size, idx in cinfo:
out.append(list(members))
# assign best cluster per node
chosen = torch.full((n_nodes,), -1, dtype=torch.long)
best_key = [(-1e18, -10) for _ in range(n_nodes)]
for c_idx, (members, score, size, _) in enumerate(cinfo):
key = (score, size)
for u in members:
old = best_key[u]
if key > old: # prioritize larger score, then larger cluster
best_key[u] = key
chosen[u] = c_idx
# any unassigned node becomes its own new cluster
next_c = len(out)
for u in range(n_nodes):
if chosen[u] == -1:
out.append([u])
chosen[u] = next_c
next_c += 1
# Build cluster_scores vector aligned with `out` order, then normalize to [0,1]
base_scores = [float(s) for (_, s, _, _) in cinfo]
K = len(out)
scores = torch.zeros(K, dtype=torch.float32)
# Fill provided cluster scores first
for i, sc in enumerate(base_scores):
scores[i] = sc
# Singletons (appended) remain 0 by default
if len(base_scores) > 0:
smin = min(base_scores)
smax = max(base_scores)
if smax > smin:
# Min-max normalize provided cluster scores; keep singletons at 0
norm = (scores[:len(base_scores)] - smin) / (smax - smin)
scores[:len(base_scores)] = norm
else:
# All equal: treat as confident -> set to 1 for provided clusters
scores[:len(base_scores)] = 1.0
# Shape as (K,1)
cluster_scores = scores.view(-1, 1)
# Return clusters and their normalized scores
return out, cluster_scores
def seeds_to_node2cluster(n_nodes: int, clusters: List[List[int]]) -> Tensor:
node2cluster = torch.full((n_nodes,), -1, dtype=torch.long)
for cid, members in enumerate(clusters):
for u in members:
node2cluster[u] = cid
assert int(node2cluster.min()) >= 0, "All nodes must be assigned a cluster."
return node2cluster
def load_lrmc_seeds_single_graph(seeds_json: str, n_nodes: int) -> Tuple[Tensor, Tensor]:
"""Load seeds for a single big graph (Planetoid)."""
with open(seeds_json, "r") as f:
obj = json.load(f)
clusters, cluster_scores = _parse_clusters_single_file(obj, n_nodes)
node2cluster = seeds_to_node2cluster(n_nodes, clusters)
return node2cluster, cluster_scores
# --------------------------
# Bi-level LRMC layer (1x)
# --------------------------
class BiLevelLRMC(nn.Module):
"""
One round:
1) Node GCN: H1 = GCN_node(X, A_node)
2) Up: Z = mean_{i in c} H1[i] (cluster means via scatter)
Cluster graph: A_c = S^T A_node S
3) Cluster GCN: Z2 = GCN_cluster(Z, A_c)
4) Down: H2 = H1 + W (S Z2)
"""
def __init__(self,
in_dim: int,
hidden_dim: int,
node2cluster: Tensor,
cluster_scores: Tensor,
edge_index_node: Tensor,
num_nodes: int,
self_loop_scale: float = 0.0,
use_a2: bool = False):
super().__init__()
self.num_nodes = num_nodes
self.node2cluster = node2cluster.clone().long()
self.register_buffer("node2cluster_buf", self.node2cluster)
# cluster_scores: (K,1) in [0,1]
self.register_buffer("cluster_scores", cluster_scores.clone().float())
# # Node graph (optionally with A^2 and/or scaled self-loops)
# ei = edge_index_node
# if use_a2:
# ei = adjacency_power(ei, num_nodes, k=2)
# ei, ew = add_scaled_self_loops(ei, None, num_nodes, scale=self_loop_scale)
# self.register_buffer("edge_index_node", ei)
# self.register_buffer("edge_weight_node", ew)
# 1) Node graph: keep raw A (no A^2), but use A+2I by default
ei_node = edge_index_node
ei_node, ew_node = add_scaled_self_loops(ei_node, None, num_nodes, scale=self_loop_scale)
self.register_buffer("edge_index_node", ei_node)
self.register_buffer("edge_weight_node", ew_node)
# 2) Cluster graph: build from A^2 to keep coarsened graph well connected
ei_base_for_clusters = edge_index_node
if use_a2:
ei_base_for_clusters = adjacency_power(edge_index_node, num_nodes, k=2)
edge_index_c, edge_weight_c, K = build_cluster_graph(
ei_base_for_clusters, num_nodes, self.node2cluster
)
self.register_buffer("edge_index_c", edge_index_c)
self.register_buffer("edge_weight_c", edge_weight_c)
self.num_clusters = K
# GCNs
self.gcn_node = GCNConv(in_dim, hidden_dim, add_self_loops=False, normalize=True)
# self.gcn_cluster = GCNConv(hidden_dim, hidden_dim, add_self_loops=True, normalize=True)
# self.down = nn.Linear(hidden_dim, hidden_dim)
# self.gate = nn.Sequential(
# nn.Linear(2 * hidden_dim, hidden_dim // 2),
# nn.ReLU(),
# nn.Linear(hidden_dim // 2, 1)
# )
# self.lambda_logit = nn.Parameter(torch.tensor(0.0))
def forward(self, x: Tensor) -> Tensor:
# Node GCN
h1 = self.gcn_node(x, self.edge_index_node, self.edge_weight_node)
h1 = F.relu(h1)
# # Up: cluster means
# counts = torch.bincount(self.node2cluster_buf, minlength=self.num_clusters).clamp(min=1).unsqueeze(-1)
# z = scatter_add(h1, self.node2cluster_buf, dim=0, dim_size=self.num_clusters) / counts
# # Cluster GCN
# z2 = self.gcn_cluster(z, self.edge_index_c, self.edge_weight_c)
# z2 = F.relu(z2)
# # Down: broadcast to nodes + residual, scaled by cluster_scores
# z2_nodes = z2[self.node2cluster_buf]
# inj = self.down(z2_nodes)
# gate_in = torch.cat([h1, inj], dim=-1)
# gate_dyn = torch.sigmoid(self.gate(gate_in))
# alpha_seed = 0.25 + 0.75 * self.cluster_scores[self.node2cluster_buf]
# # print(alpha_seed)
# lam = torch.sigmoid(self.lambda_logit)
# # print(lam)
# alpha = lam * alpha_seed + (1 - lam) * gate_dyn
# h2 = h1 + alpha * inj
return h1
# -----------------------------------
# Node classification model (Planetoid)
# -----------------------------------
class NodeLRMCGCN(nn.Module):
def __init__(self, in_dim: int, hidden: int, num_classes: int,
node2cluster: Tensor, cluster_scores: Tensor, edge_index: Tensor, num_nodes: int,
layers: int = 1, self_loop_scale: float = 0.0, use_a2: bool = False, dropout: float = 0.5):
super().__init__()
self.layer = BiLevelLRMC(in_dim, hidden, node2cluster, cluster_scores, edge_index, num_nodes, self_loop_scale, use_a2))
self.cls = nn.Linear(hidden, num_classes)
self.dropout = dropout
def forward(self, x: Tensor) -> Tensor:
h = x
h = layer(h)
h = F.dropout(h, p=self.dropout, training=self.training)
out = self.cls(h)
return out
# ---------------------------------------
# Graph classification with batching (TU)
# ---------------------------------------
class GraphLRMCProvider:
"""
Holds per-graph LRMC assignments and cluster graphs.
Expects a directory with one JSON per graph OR a single JSON with {"graphs":[{"graph_id":int,"clusters":[...]},...]}.
Node indices are local per-graph [0..n_i-1].
"""
def __init__(self, dataset, seeds_path: str, use_a2: bool = True):
"""
dataset: any iterable/sequence of torch_geometric.data.Data
"""
self.dataset = dataset
self.root = Path(seeds_path)
self.per_graph: Dict[int, Dict[str, Tensor]] = {}
# Try single JSON with all graphs
single_json = None
if self.root.is_file() and self.root.suffix.lower() == ".json":
single_json = json.loads(Path(self.root).read_text())
for gid, data in enumerate(dataset):
n = data.num_nodes
if single_json is not None and "graphs" in single_json:
# Structure: {"graphs":[{"graph_id":int,"clusters":[...]}]}
entry = None
for g in single_json["graphs"]:
if int(g.get("graph_id", -1)) == gid:
entry = g
break
if entry is None:
# fallback: singleton clusters
node2cluster = torch.arange(n, dtype=torch.long)
cluster_scores = torch.ones(n, 1, dtype=torch.float32) # singletons -> treat as 1
else:
clusters, cluster_scores = _parse_clusters_single_file(entry, n)
node2cluster = seeds_to_node2cluster(n, clusters)
else:
# One JSON per graph e.g. seeds_dir/graph_000123.json
guess = self.root / f"graph_{gid:06d}.json"
if guess.exists():
obj = json.loads(guess.read_text())
clusters, cluster_scores = _parse_clusters_single_file(obj, n)
node2cluster = seeds_to_node2cluster(n, clusters)
else:
node2cluster = torch.arange(n, dtype=torch.long) # singleton fallback
cluster_scores = torch.ones(n, 1, dtype=torch.float32)
ei = data.edge_index
if use_a2:
ei = adjacency_power(ei, n, k=2)
ei_c, ew_c, K = build_cluster_graph(ei, n, node2cluster)
self.per_graph[gid] = {
"node2cluster": node2cluster,
"cluster_scores": cluster_scores,
"edge_index_c": ei_c,
"edge_weight_c": ew_c,
"num_clusters": torch.tensor([K]),
}
def get(self, graph_id: int):
rec = self.per_graph[graph_id]
return (rec["node2cluster"], rec["cluster_scores"], rec["edge_index_c"], rec["edge_weight_c"],
int(rec["num_clusters"][0].item()))
class GraphLRMCGCN(nn.Module):
"""
Batched version:
- Run node-level GCN over batch graph (standard).
- Up: per-graph scatter to cluster means; build a batched cluster-graph by offsetting cluster ids.
- Cluster GCN over the batched cluster graph.
- Down: broadcast cluster features back to nodes and residual.
- Graph head: global mean pooling -> MLP.
"""
def __init__(self, in_dim: int, hidden: int, num_classes: int,
self_loop_scale: float = 0.0, use_a2: bool = False, dropout: float = 0.5):
super().__init__()
self.gcn_node = GCNConv(in_dim, hidden, add_self_loops=False, normalize=True)
self.gcn_cluster = GCNConv(hidden, hidden, add_self_loops=True, normalize=True)
self.down = nn.Linear(hidden, hidden)
# Classifier takes concatenated node and cluster embeddings (2 * hidden)
self.cls = nn.Linear(2 * hidden, num_classes)
self.self_loop_scale = self_loop_scale
self.use_a2 = use_a2
self.dropout = dropout
self.gate = nn.Sequential(
nn.Linear(2 * hidden, hidden // 2),
nn.ReLU(),
nn.Linear(hidden // 2, 1)
)
self.lambda_logit = nn.Parameter(torch.tensor(0.0))
def forward(self, data: Data, provider: GraphLRMCProvider) -> Tensor:
# Single-graph only: no batching.
x, edge_index = data.x, data.edge_index
num_nodes = x.size(0)
# Node graph prep
ei = edge_index
if self.use_a2:
ei = adjacency_power(ei, num_nodes, k=2)
ei, ew = add_scaled_self_loops(ei, None, num_nodes, scale=self.self_loop_scale)
# Node GCN
h1 = self.gcn_node(x, ei, ew)
h1 = F.relu(h1)
# Fetch LRMC seeds/cluster-graph for this graph
assert hasattr(data, 'gid'), "Each graph must carry a 'gid' attribute for provider lookup."
gid = int(data.gid.view(-1)[0].item())
node2cluster_g, cluster_scores_g, edge_index_c, edge_weight_c, K = provider.get(gid)
node2cluster_g = node2cluster_g.to(x.device)
edge_index_c = edge_index_c.to(x.device)
edge_weight_c = edge_weight_c.to(x.device)
cluster_scores_g = cluster_scores_g.to(x.device)
# Up: cluster means
counts = torch.bincount(node2cluster_g, minlength=K).clamp(min=1).unsqueeze(-1)
z = scatter_add(h1, node2cluster_g, dim=0, dim_size=K) / counts
# Cluster GCN
z2 = self.gcn_cluster(z, edge_index_c, edge_weight_c)
z2 = F.relu(z2)
# Down: broadcast to nodes and residual
z2_nodes = z2[node2cluster_g]
inj = self.down(z2_nodes)
gate_in = torch.cat([h1, inj], dim=-1) # (N, 2H)
gate_dyn = torch.sigmoid(self.gate(gate_in)) # (N, 1)
# normalize cluster_scores to [0.25,1] so singletons still pass some signal
alpha_seed = 0.25 + 0.75 * cluster_scores_g[node2cluster_g]
lam = torch.sigmoid(self.lambda_logit)
alpha = lam * alpha_seed + (1 - lam) * gate_dyn
print(lam)
h2 = h1 + alpha * inj
# Graph head: simple mean over nodes
h2 = F.dropout(h2, p=self.dropout, training=self.training)
g_nodes = h2.mean(dim=0, keepdim=True)
g_clust = z2.mean(dim=0, keepdim=True)
g = torch.cat([g_nodes, g_clust], dim=-1)
out = self.cls(g)
return out
# -------------
# Training glue
# -------------
def train_node(task_ds: str, seeds_json: str, hidden=64, layers=1, epochs=300,
lr=0.01, weight_decay=5e-4, dropout=0.5, self_loop_scale=0.0, use_a2=False, seed=0):
torch.manual_seed(seed)
ds = Planetoid(root=f"./data/{task_ds}", name=task_ds)
data = ds[0]
n, c_in, n_cls = data.num_nodes, ds.num_node_features, ds.num_classes
node2cluster, cluster_scores = load_lrmc_seeds_single_graph(seeds_json, n)
model = NodeLRMCGCN(c_in, hidden, n_cls, node2cluster, cluster_scores, data.edge_index, n,
layers=layers, self_loop_scale=self_loop_scale, use_a2=use_a2, dropout=dropout).to('cpu')
opt = torch.optim.Adam(model.parameters(), lr=lr, weight_decay=weight_decay)
def step():
# Train step: compute loss with dropout on, then evaluate metrics with dropout off.
model.train()
opt.zero_grad(set_to_none=True)
out_train = model(data.x)
loss = F.cross_entropy(out_train[data.train_mask], data.y[data.train_mask])
loss.backward()
opt.step()
# Evaluation pass in eval mode to report metrics without dropout.
with torch.no_grad():
model.eval()
out_eval = model(data.x)
def acc(mask):
pred = out_eval[mask].argmax(dim=1)
pred_t = torch.as_tensor(pred)
y_t = torch.as_tensor(data.y)
return (pred_t == y_t[mask]).float().mean().item()
return loss.item(), acc(data.train_mask), acc(data.val_mask), acc(data.test_mask)
best_val, best_test = 0.0, 0.0
for ep in range(1, epochs + 1):
loss, tr, va, te = step()
if va > best_val:
best_val, best_test = va, te
if ep % 20 == 0:
print(f"[{ep:04d}] loss={loss:.4f} train={tr:.3f} val={va:.3f} test={te:.3f} best_test={best_test:.3f}")
print(f"Best val={best_val:.3f} test@best={best_test:.3f}")
def train_graph(dataset_name: str, seeds_path: str, hidden=64, epochs=100,
lr=0.001, weight_decay=1e-4, dropout=0.5, self_loop_scale=0.0, use_a2=False, seed=0):
torch.manual_seed(seed)
ds = TUDataset(root=f"./data/{dataset_name}", name=dataset_name)
num_classes = ds.num_classes
c_in = ds.num_node_features if ds.num_node_features > 0 else 1
# Materialize dataset into a list of Data objects to make mutations persistent.
graphs: List[Data] = []
for i, g in enumerate(ds):
gc = g.clone()
# Attach persistent global id for provider lookup across splits/batches
gc.gid = torch.tensor([i], dtype=torch.long)
graphs.append(gc)
# If dataset has no node features, use degree as a 1-D feature for each graph.
if ds.num_node_features == 0:
for g in graphs:
deg = torch.bincount(g.edge_index[0], minlength=g.num_nodes).float().view(-1, 1)
g.x = deg
provider = GraphLRMCProvider(graphs, seeds_path)
idx = torch.randperm(len(graphs))
ntrain = int(0.8 * len(ds))
nval = int(0.1 * len(ds))
# Build splits from the materialized list
train_ds = [graphs[i] for i in idx[:ntrain]]
val_ds = [graphs[i] for i in idx[ntrain:ntrain + nval]]
test_ds = [graphs[i] for i in idx[ntrain + nval:]]
device = 'cpu'
model = GraphLRMCGCN(c_in, hidden, num_classes,
self_loop_scale=self_loop_scale, use_a2=use_a2, dropout=dropout).to(device)
opt = torch.optim.Adam(model.parameters(), lr=lr, weight_decay=weight_decay)
@torch.no_grad()
def evaluate(graph_list: List[Data]):
model.eval()
tot, correct = 0, 0
for g in graph_list:
g = g.to(device)
logits = model(g, provider)
pred = logits.argmax(dim=1)
pred_t = torch.as_tensor(pred)
y_t = torch.as_tensor(g.y)
correct += (pred_t == y_t).sum().item()
tot += g.y.size(0)
return correct / tot
best_val, best_test = 0.0, 0.0
for ep in range(1, epochs + 1):
model.train()
for g in train_ds:
g = g.to(device)
opt.zero_grad(set_to_none=True)
logits = model(g, provider)
loss = F.cross_entropy(logits, g.y)
loss.backward()
opt.step()
if ep % 5 == 0:
va = evaluate(val_ds)
te = evaluate(test_ds)
if va > best_val:
best_val, best_test = va, te
print(f"[{ep:03d}] val={va:.3f} test={te:.3f} best_test@val={best_test:.3f}")
print(f"Best val={best_val:.3f} test@best={best_test:.3f}")
# -----------
# Entrypoint
# -----------
def main():
p = argparse.ArgumentParser()
p.add_argument("--task", choices=["node", "graph"], required=True)
p.add_argument("--dataset", required=True, help="Cora/Citeseer/Pubmed or DD/PROTEINS/COLLAB/ENZYMES")
p.add_argument("--seeds", required=True, help="Path to seeds JSON (node task) or dir/single JSON (graph task)")
p.add_argument("--hidden", type=int, default=64)
p.add_argument("--layers", type=int, default=1)
p.add_argument("--epochs", type=int, default=300)
p.add_argument("--batch_size", type=int, default=64)
p.add_argument("--lr", type=float, default=0.01)
p.add_argument("--wd", type=float, default=5e-4)
p.add_argument("--dropout", type=float, default=0.5)
p.add_argument("--self_loop_scale", type=float, default=0.0, help="use 2.0 to mimic A+2I")
p.add_argument("--use_a2", action="store_true", help="use A^2 connectivity augmentation")
p.add_argument("--seed", type=int, default=0)
args = p.parse_args()
if args.task == "node":
for i in range(42, 60):
train_node(args.dataset, args.seeds, hidden=args.hidden, layers=args.layers, epochs=args.epochs, lr=args.lr,
weight_decay=args.wd, dropout=args.dropout, self_loop_scale=args.self_loop_scale,
use_a2=args.use_a2, seed=i)
else:
for i in range(42, 60):
train_graph(args.dataset, args.seeds, hidden=args.hidden, epochs=max(100, args.epochs),
lr=min(args.lr, 0.001), weight_decay=args.wd, dropout=args.dropout,
self_loop_scale=args.self_loop_scale, use_a2=args.use_a2, seed=i)
if __name__ == "__main__":
main()
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