HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction.

Code ↔ Paper

11 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 11 matches

[1] § Results › Experimental setting ↔ src/main.py, lines 20–74 · score 0.78 · FreeSolv, scaffold splitting, random seeds, stratified, threshold, QM7
[2] § Methods › Molecular hypergraph construction and representation › Hyperedge representation ↔ src/data/dataset.py, lines 627–719 · score 0.67 · substructure matching, SMARTS patterns, alerts, amides, amines, esters
[3] § Methods › Molecular hypergraph construction and representation › Multimodal hypernode representation ↔ src/data/dataset.py, lines 137–199 · score 0.66 · Gasteiger charge, formal charge, electrons, traditional, aromaticity, ChemBERTa
[4] § Methods › Molecular hypergraph construction and representation › Multimodal hypernode representation ↔ src/data/dataset.py, lines 256–316 · score 0.63 · tokens mapped, atom mapping, ChemBERTa model, tokenized, SMILES, mol
[5] § Results › Experimental setting ↔ src/utils/utils.py, lines 20–79 · score 0.62 · Murcko scaffold splitting, class distribution, threshold, subsets, seeds, 10 %
[6] § Results › Outlier analysis ↔ src/data/dataset.py, lines 627–719 · score 0.60 · c1ccc2c, OC, cc1, Cl, halogen, motifs
[7] § Methods › Molecular hypergraph construction and representation › Hyperedge representation ↔ src/data/dataset.py, lines 34–135 · score 0.59 · isolated atoms, ring connections, RDKit, Node features, substructures, hyperedges
[8] § Results › Interpretability analysis ↔ src/data/dataset.py, lines 759–896 · score 0.56 · carbonyl, donor, bridging, hydrophobic, acceptor, amide
[9] § Results › Experimental setting ↔ src/training/trainer.py, lines 275–389 · score 0.56 · squared error, absolute error, MAE, RMSE, regression, metrics
[10] § Results › Comparison experiments ↔ src/main.py, lines 20–74 · score 0.55 · FreeSolv, random seeds, QM7, Lipophilicity, QM8, regression
[11] § Methods ↔ src/data/dataset.py, lines 34–135 · score 0.51 · ring connections, RDKit, matching, substructures, nodes, Atoms

Paper

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The authors' code

Python · 1,787 lines · 72 KB · no license · 7 matches

# src/data/dataset.py
import os
import warnings
import numpy as np
import pandas as pd
import torch
from .. import config
from torch_geometric.data import Data, Dataset
from tqdm import tqdm
from rdkit import Chem
from rdkit.Chem import Draw, AllChem, rdMolDescriptors, Descriptors, Crippen, MolSurf
from rdkit.Chem.Scaffolds import MurckoScaffold
from transformers import AutoTokenizer, AutoModel
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
class MoleculeHypergraph:
def __init__(self, feature_type):
self.feature_type = feature_type
self.node_features = []
self.hyperedge_index = None
self.mol = None
self.hyperedges = []
self.hyperedge_labels = []
if self.feature_type != "traditional_only":
self.tokenizer = AutoTokenizer.from_pretrained(config.CHEMBERTA_MODEL_NAME)
self.chemberta_model = AutoModel.from_pretrained(config.CHEMBERTA_MODEL_NAME).to('cpu')
else:
self.tokenizer = None
self.chemberta_model = None
def build_from_mol(self, mol):
self.mol = mol
num_atoms = mol.GetNumAtoms()
functional_groups, fg_labels = self.get_functional_groups(mol)
rings, ring_labels = self.get_ring_structures(mol)
special_structures, special_labels = self.get_special_structures(mol)
hyperedges = []
hyperedge_labels = []
def add_valid_hyperedge(edge, label):
valid_nodes = [node_id for node_id in edge if 0 <= node_id < num_atoms]
if valid_nodes:
is_duplicate = False
sorted_valid_nodes_tuple = tuple(sorted(valid_nodes))
for existing_edge_tuple, existing_label in zip(map(lambda e: tuple(sorted(e)), hyperedges),
hyperedge_labels):
if existing_edge_tuple == sorted_valid_nodes_tuple and existing_label == label:
is_duplicate = True
break
if not is_duplicate:
hyperedges.append(valid_nodes)
hyperedge_labels.append(label)
for edge, label in zip(functional_groups, fg_labels):
add_valid_hyperedge(edge, label)
for edge, label in zip(rings, ring_labels):
add_valid_hyperedge(edge, label)
for edge, label in zip(special_structures, special_labels):
add_valid_hyperedge(edge, label)
ring_atoms = set()
atom_to_ring = {}
for ring_id, ring_node_indices in enumerate(rings):
ring_atoms.update(ring_node_indices)
for atom_idx in ring_node_indices:
atom_to_ring.setdefault(atom_idx, set()).add(ring_id)
for bond in mol.GetBonds():
begin_idx = bond.GetBeginAtom().GetIdx()
end_idx = bond.GetEndAtom().GetIdx()
if begin_idx >= num_atoms or end_idx >= num_atoms:
continue
begin_in_ring = begin_idx in ring_atoms
end_in_ring = end_idx in ring_atoms
if begin_in_ring and end_in_ring:
common_rings = atom_to_ring.get(begin_idx, set()) & atom_to_ring.get(end_idx, set())
if not common_rings:
add_valid_hyperedge([begin_idx, end_idx], 'RingConnector')
elif begin_in_ring != end_in_ring:
add_valid_hyperedge([begin_idx, end_idx], 'RingSubstituent')
all_atoms_in_hyperedges = set()
for he in hyperedges:
all_atoms_in_hyperedges.update(he)
excluded_atoms = set(range(num_atoms)) - all_atoms_in_hyperedges
for atom_idx in list(excluded_atoms):
atom = mol.GetAtomWithIdx(atom_idx)
neighbor_indices = [n.GetIdx() for n in atom.GetNeighbors() if n.GetIdx() < num_atoms]
if neighbor_indices:
current_group = sorted([atom_idx] + neighbor_indices)
is_new_group = True
for existing_edge, existing_label in zip(hyperedges, hyperedge_labels):
if existing_label == 'IsolatedAtomGroup' and sorted(existing_edge) == current_group:
is_new_group = False
break
if is_new_group:
add_valid_hyperedge(current_group, 'IsolatedAtomGroup')
else:
add_valid_hyperedge([atom_idx], 'SingleAtom')
try:
murcko_mol_full = MurckoScaffold.GetScaffoldForMol(mol)
if murcko_mol_full.GetNumAtoms() > 0:
match_indices_full = mol.GetSubstructMatch(murcko_mol_full)
if match_indices_full:
add_valid_hyperedge(list(match_indices_full), 'MurckoScaffoldFull')
if murcko_mol_full.GetNumAtoms() > 0:
murcko_mol_generic = MurckoScaffold.MakeScaffoldGeneric(murcko_mol_full)
if murcko_mol_generic.GetNumAtoms() > 0:
match_indices_generic = mol.GetSubstructMatch(murcko_mol_generic)
if match_indices_generic:
add_valid_hyperedge(list(match_indices_generic), 'MurckoScaffoldCore')
except ImportError:
print(
"Warning: RDKit MurckoScaffold module not available. Skipping Murcko scaffold hyperedges.")
except Exception as e:
print(f"Warning: Error processing Murcko scaffold for molecule {Chem.MolToSmiles(mol)}: {e}")
self.build_node_features(mol)
self.build_hyperedge_index(hyperedges, hyperedge_labels)
return self
def build_node_features(self, mol):
num_atoms = mol.GetNumAtoms()
model_max_length = 512
if hasattr(self.chemberta_model, 'config') and hasattr(self.chemberta_model.config, 'max_position_embeddings'):
model_max_length = self.chemberta_model.config.max_position_embeddings
mol_id = Chem.MolToSmiles(mol)
cache_key = f"{self.feature_type}_{mol_id}"
if hasattr(self, 'feature_cache') and cache_key in self.feature_cache:
self.node_features = self.feature_cache[cache_key]
return self.node_features
if not hasattr(self, 'feature_cache'):
self.feature_cache = {}
if self.feature_type == "traditional_only":
additional_features = []
mol_weight = Descriptors.MolWt(mol) / 500.0 if hasattr(Descriptors, 'MolWt') else 0.0
logp = Crippen.MolLogP(mol) / 10.0 if hasattr(Crippen, 'MolLogP') else 0.0
tpsa = MolSurf.TPSA(mol) / 100.0 if hasattr(MolSurf, 'TPSA') else 0.0
num_rings = len(mol.GetRingInfo().AtomRings()) / 10.0 if hasattr(mol, 'GetRingInfo') else 0.0
charges = [0.0] * num_atoms
try:
AllChem.ComputeGasteigerCharges(mol)
charges = [atom.GetDoubleProp('_GasteigerCharge')
if atom.HasProp('_GasteigerCharge') else 0.0
for atom in mol.GetAtoms()]
charges = [0.0 if (c is None or np.isnan(c) or np.isinf(c)) else c for c in charges]
except:
pass
ring_info = mol.GetRingInfo()
for atom_idx in range(num_atoms):
atom = mol.GetAtomWithIdx(atom_idx)
neighbors = [n.GetIdx() for n in atom.GetNeighbors()]
base_features = [
atom.GetAtomicNum() / 100.0,
atom.GetDegree() / 4.0,
int(atom.GetIsAromatic()),
atom.GetFormalCharge() / 8.0,
atom.GetNumRadicalElectrons() / 8.0,
atom.GetChiralTag() / 10.0,
atom.GetHybridization() / 6.0,
atom.GetImplicitValence() / 8.0,
atom.IsInRing() * 1.0,
len(neighbors) / 8.0,
]
hybridization_features = [
int(str(atom.GetHybridization()) == "SP"),
int(str(atom.GetHybridization()) == "SP2"),
int(str(atom.GetHybridization()) == "SP3"),
]
atom_type_features = [
int(atom.GetAtomicNum() == 1), # H
int(atom.GetAtomicNum() == 6), # C
int(atom.GetAtomicNum() == 7), # N
int(atom.GetAtomicNum() == 8), # O
int(atom.GetAtomicNum() == 9), # F
int(atom.GetAtomicNum() == 15), # P
int(atom.GetAtomicNum() == 16), # S
int(atom.GetAtomicNum() == 17), # Cl
int(atom.GetAtomicNum() == 35), # Br
int(atom.GetAtomicNum() == 53), # I
]
bond_types = [0, 0, 0, 0]
for neighbor in neighbors:
bond = mol.GetBondBetweenAtoms(atom_idx, neighbor)
if bond.GetBondType() == Chem.rdchem.BondType.SINGLE:
bond_types[0] += 1
elif bond.GetBondType() == Chem.rdchem.BondType.DOUBLE:
bond_types[1] += 1
elif bond.GetBondType() == Chem.rdchem.BondType.TRIPLE:
bond_types[2] += 1
elif bond.GetBondType() == Chem.rdchem.BondType.AROMATIC:
bond_types[3] += 1
if sum(bond_types) > 0:
bond_types = [b / sum(bond_types) for b in bond_types]
neighbor_features = []
if neighbors:
neighbor_atomic_nums = [mol.GetAtomWithIdx(n).GetAtomicNum() for n in neighbors]
neighbor_features = [
sum(1 for n in neighbor_atomic_nums if n == 6) / len(neighbors),
sum(1 for n in neighbor_atomic_nums if n == 7) / len(neighbors),
sum(1 for n in neighbor_atomic_nums if n == 8) / len(neighbors),
sum(1 for n in neighbor_atomic_nums if n == 9 or n == 17 or n == 35 or n == 53) / len(neighbors)
]
else:
neighbor_features = [0.0] * 4
additional_chemical_features = [
charges[atom_idx],
atom.GetTotalNumHs() / 4.0,
int(ring_info.IsAtomInRingOfSize(atom_idx, 3)),
int(ring_info.IsAtomInRingOfSize(atom_idx, 5)),
int(ring_info.IsAtomInRingOfSize(atom_idx, 6)),
]
global_mol_features = [mol_weight, logp, tpsa, num_rings]
atom_features = (
base_features +
hybridization_features +
atom_type_features +
bond_types +
neighbor_features +
additional_chemical_features +
global_mol_features
)
additional_features.append(atom_features)
self.node_features = np.array(additional_features, dtype=np.float32)
elif self.feature_type == "chemberta_only":
original_smiles = Chem.MolToSmiles(mol)
atom_mapped_mol = Chem.AddHs(mol)
for atom in atom_mapped_mol.GetAtoms():
atom.SetAtomMapNum(atom.GetIdx() + 1)
inputs = self.tokenizer(
original_smiles,
return_tensors="pt",
truncation=True,
max_length=model_max_length,
padding="max_length"
)
inputs = {k: v.to('cpu') for k, v in inputs.items()}
with torch.no_grad():
outputs = self.chemberta_model(**inputs)
hidden_states = outputs.last_hidden_state.squeeze(0)
tokens = self.tokenizer.convert_ids_to_tokens(inputs['input_ids'][0])
token_to_char = {}
smiles_tokens = self.tokenizer.tokenize(original_smiles)
current_pos = 0
for i, token in enumerate(smiles_tokens):
token_to_char[i] = current_pos
clean_token = token.replace('#', '').replace('Ġ', '')
current_pos += len(clean_token)
token_to_atom_map = {}
current_atom_idx = 0
atom_to_token_map = {}
for token_idx, token in enumerate(tokens):
if token == self.tokenizer.cls_token or \
token == self.tokenizer.sep_token or \
token == self.tokenizer.pad_token:
continue
if token.startswith('##'):
if token_idx > 0 and token_idx - 1 in token_to_atom_map:
token_to_atom_map[token_idx] = token_to_atom_map[token_idx - 1]
continue
atom_tokens = ['C', 'c', 'N', 'n', 'O', 'o', 'S', 's', 'P', 'p', 'F', 'Cl', 'Br', 'I',
'[cH]', '[nH]', '[oH]', '[sH]', '[CH]', '[CH2]', '[CH3]', '[NH]', '[NH2]',
'[OH]', '[SH]', '[PH]']
if any(token == t or token.startswith(t) for t in atom_tokens):
if current_atom_idx < num_atoms:
token_to_atom_map[token_idx] = current_atom_idx
if current_atom_idx not in atom_to_token_map:
atom_to_token_map[current_atom_idx] = []
atom_to_token_map[current_atom_idx].append(token_idx)
current_atom_idx += 1
else:
break
feature_dim = hidden_states.shape[1]
atom_features = torch.zeros((num_atoms, feature_dim), device='cpu')
mapped_atom_indices = set()
for atom_idx, token_indices in atom_to_token_map.items():
if atom_idx < num_atoms:
valid_tokens = [ti for ti in token_indices if ti < hidden_states.shape[0]]
if valid_tokens:
weights = torch.ones(len(valid_tokens))
for i, ti in enumerate(valid_tokens):
if not tokens[ti].startswith('##'):
weights[i] = 2.0
weights = weights / weights.sum()
for i, ti in enumerate(valid_tokens):
atom_features[atom_idx] += weights[i] * hidden_states[ti]
mapped_atom_indices.add(atom_idx)
else:
print(f"Warning: No valid token indices for atom {atom_idx}")
for atom_idx in range(num_atoms):
if atom_idx not in mapped_atom_indices:
atom = mol.GetAtomWithIdx(atom_idx)
neighbors = [n.GetIdx() for n in atom.GetNeighbors() if n.GetIdx() in mapped_atom_indices]
if neighbors:
neighbor_features = atom_features[neighbors]
atom_features[atom_idx] = torch.mean(neighbor_features, dim=0)
mapped_atom_indices.add(atom_idx)
unmapped_atoms = [i for i in range(num_atoms) if i not in mapped_atom_indices]
if unmapped_atoms:
valid_token_indices = [
idx for idx, t in enumerate(tokens)
if t != self.tokenizer.cls_token and \
t != self.tokenizer.sep_token and \
t != self.tokenizer.pad_token and \
idx < hidden_states.shape[0]
]
if valid_token_indices:
global_features = torch.mean(hidden_states[valid_token_indices], dim=0)
for atom_idx in unmapped_atoms:
atom_features[atom_idx] = global_features
else:
print(f"Warning: No valid token features for global average in SMILES: {original_smiles[:50]}...")
self.node_features = atom_features.cpu().numpy()
else:
original_smiles = Chem.MolToSmiles(mol)
atom_mapped_mol = Chem.AddHs(mol)
for atom in atom_mapped_mol.GetAtoms():
atom.SetAtomMapNum(atom.GetIdx() + 1)
inputs = self.tokenizer(
original_smiles,
return_tensors="pt",
truncation=True,
max_length=model_max_length,
padding="max_length"
)
inputs = {k: v.to('cpu') for k, v in inputs.items()}
with torch.no_grad():
outputs = self.chemberta_model(**inputs)
hidden_states = outputs.last_hidden_state.squeeze(0)
tokens = self.tokenizer.convert_ids_to_tokens(inputs['input_ids'][0])
token_to_atom_map = {}
atom_to_token_map = {}
current_atom_idx = 0
for token_idx, token in enumerate(tokens):
if token == self.tokenizer.cls_token or \
token == self.tokenizer.sep_token or \
token == self.tokenizer.pad_token:
continue
if token.startswith('##'):
if token_idx > 0 and token_idx - 1 in token_to_atom_map:
token_to_atom_map[token_idx] = token_to_atom_map[token_idx - 1]
continue
atom_tokens = ['C', 'c', 'N', 'n', 'O', 'o', 'S', 's', 'P', 'p', 'F', 'Cl', 'Br', 'I',
'[cH]', '[nH]', '[oH]', '[sH]']
if any(token == t or token.startswith(t) for t in atom_tokens):
if current_atom_idx < num_atoms:
token_to_atom_map[token_idx] = current_atom_idx
if current_atom_idx not in atom_to_token_map:
atom_to_token_map[current_atom_idx] = []
atom_to_token_map[current_atom_idx].append(token_idx)
current_atom_idx += 1
else:
break
feature_dim = hidden_states.shape[1]
atom_features_tensor = torch.zeros((num_atoms, feature_dim), device='cpu')
mapped_atom_indices = set()
for atom_idx, token_indices in atom_to_token_map.items():
if atom_idx < num_atoms:
valid_tokens = [ti for ti in token_indices if ti < hidden_states.shape[0]]
if valid_tokens:
for ti in valid_tokens:
atom_features_tensor[atom_idx] += hidden_states[ti]
atom_features_tensor[atom_idx] /= len(valid_tokens)
mapped_atom_indices.add(atom_idx)
for atom_idx in range(num_atoms):
if atom_idx not in mapped_atom_indices:
atom = mol.GetAtomWithIdx(atom_idx)
neighbors = [n.GetIdx() for n in atom.GetNeighbors() if n.GetIdx() in mapped_atom_indices]
if neighbors:
neighbor_features = atom_features_tensor[neighbors]
atom_features_tensor[atom_idx] = torch.mean(neighbor_features, dim=0)
mapped_atom_indices.add(atom_idx)
else:
valid_token_indices = [
idx for idx, t in enumerate(tokens)
if t != self.tokenizer.cls_token and \
t != self.tokenizer.sep_token and \
t != self.tokenizer.pad_token and \
idx < hidden_states.shape[0]
]
if valid_token_indices:
atom_features_tensor[atom_idx] = torch.mean(hidden_states[valid_token_indices], dim=0)
else:
print(
f"Warning: No valid token features to average for fallback on atom {atom_idx} in SMILES: {original_smiles[:50]}...")
mol_weight = Descriptors.MolWt(mol) / 500.0 if hasattr(Descriptors, 'MolWt') else 0.0
logp = Crippen.MolLogP(mol) / 10.0 if hasattr(Crippen, 'MolLogP') else 0.0
tpsa = MolSurf.TPSA(mol) / 100.0 if hasattr(MolSurf, 'TPSA') else 0.0
charges = [0.0] * num_atoms
try:
AllChem.ComputeGasteigerCharges(mol)
charges = [atom.GetDoubleProp('_GasteigerCharge')
if atom.HasProp('_GasteigerCharge') else 0.0
for atom in mol.GetAtoms()]
charges = [0.0 if (c is None or np.isnan(c) or np.isinf(c)) else c for c in charges]
except:
pass
additional_features_list = []
for atom_idx in range(num_atoms):
atom = mol.GetAtomWithIdx(atom_idx)
neighbors = [n.GetIdx() for n in atom.GetNeighbors()]
base_features = [
atom.GetAtomicNum() / 100.0,
atom.GetDegree() / 4.0,
int(atom.GetIsAromatic()),
atom.GetFormalCharge() / 8.0,
atom.GetNumRadicalElectrons() / 8.0
]
enhanced_features = [
charges[atom_idx],
int(atom.IsInRing()),
atom.GetTotalNumHs() / 4.0,
mol_weight,
logp,
tpsa
]
atom_additional_features = base_features + enhanced_features
additional_features_list.append(atom_additional_features)
additional_features_tensor = torch.tensor(additional_features_list, dtype=torch.float, device='cpu')
bert_weight = 0.6
trad_weight = 0.4
bert_mean = torch.mean(atom_features_tensor, dim=0, keepdim=True)
bert_std = torch.std(atom_features_tensor, dim=0, keepdim=True) + 1e-8
atom_features_tensor = (atom_features_tensor - bert_mean) / bert_std
trad_mean = torch.mean(additional_features_tensor, dim=0, keepdim=True)
trad_std = torch.std(additional_features_tensor, dim=0, keepdim=True) + 1e-8
additional_features_tensor = (additional_features_tensor - trad_mean) / trad_std
atom_features_tensor = bert_weight * atom_features_tensor
additional_features_tensor = trad_weight * additional_features_tensor
final_features = torch.cat([atom_features_tensor, additional_features_tensor], dim=1)
self.node_features = final_features.cpu().numpy()
if hasattr(self, 'use_nonlinear_features') and self.use_nonlinear_features:
self.node_features = self._add_nonlinear_interactions(self.node_features)
self.feature_cache[cache_key] = self.node_features
assert self.node_features.shape[0] == num_atoms, \
f"Feature matrix shape {self.node_features.shape} does not match number of atoms {num_atoms}"
return self.node_features
def _add_nonlinear_interactions(self, features):
if features.shape[1] > 30:
main_features = features[:, :10]
else:
main_features = features
num_samples, num_features = main_features.shape
interactions = []
for i in range(min(5, num_features)):
interactions.append(np.square(main_features[:, i]).reshape(-1, 1))
count = 0
for i in range(min(5, num_features)):
for j in range(i + 1, min(5, num_features)):
if count < 10:
interactions.append((main_features[:, i] * main_features[:, j]).reshape(-1, 1))
count += 1
if interactions:
interaction_features = np.hstack(interactions)
return np.hstack([features, interaction_features])
else:
return features
def build_hyperedge_index(self, hyperedges, hyperedge_labels):
node_idx = []
edge_idx = []
num_nodes = self.mol.GetNumAtoms()
valid_edges = []
valid_labels = []
for edge_id, (hyperedge, label) in enumerate(zip(hyperedges, hyperedge_labels)):
valid_nodes = [node_id for node_id in hyperedge if 0 <= node_id < num_nodes]
if len(valid_nodes) > 0:
if len(valid_nodes) != len(hyperedge):
print(
f"Warning: Hyperedge {edge_id} contains invalid nodes, keeping only valid ones: {valid_nodes}")
valid_edges.append(valid_nodes)
valid_labels.append(label)
else:
print(f"Warning: Hyperedge {edge_id} has no valid nodes, discarding")
if not valid_edges:
print("Warning: No valid hyperedges found! Creating a default edge.")
if num_nodes > 0:
valid_edges = [[0]]
valid_labels = ["Default"]
else:
raise ValueError("No valid hyperedges could be created for molecule with no atoms")
self.hyperedges = valid_edges
self.hyperedge_labels = valid_labels
for edge_id, hyperedge in enumerate(valid_edges):
for node_id in hyperedge:
if 0 <= node_id < num_nodes:
node_idx.append(node_id)
edge_idx.append(edge_id)
if not node_idx or not edge_idx:
print("Warning: Empty hyperedge index after processing. Creating fallback index.")
if num_nodes > 0:
node_idx = [0]
edge_idx = [0]
else:
raise ValueError("Cannot create valid hyperedge index for empty molecule")
self.hyperedge_index = np.array([node_idx, edge_idx])
def get_functional_groups(self, mol):
fg_smarts = {
'Amine': '[NX3;H2,H1,H0;!$(NC=O)]',
'QuaternaryAmmonium': '[NX4+]',
'Alcohol': '[OX2H]',
'Phenol': 'c[OH]',
'CarboxylicAcid': 'C(=O)[OX1H0-,OX2H1]',
'Ester': 'C(=O)O[C;!$(C=O)]',
'Ketone': 'C(=O)[C;!$(C=O)]',
'Aldehyde': '[CX3H1](=O)[#6]',
'Ether': '[OD2]([#6])[#6]',
'Amide': 'C(=O)N',
'Halogen': '[F,Cl,Br,I]',
'Sulfonamide': 'S(=O)(=O)N',
'Thiol': '[#16X2H]',
'Disulfide': '[#16X2]-[#16X2]',
'Nitrate': '[N+](=O)[O-]',
'Cyano': '[C]#N',
'Azide': '[N]=[N+]=[N-]',
'Alkyne': '[CX2]#C',
'Alkene': 'C=C',
'Phosphate': '[#15](=O)(O)(O)O',
'Phosphonate': 'P(=O)(O)(O)[C]',
'Sulfate': 'S(=O)(=O)(O)(O)',
'Sulfonate': 'S(=O)(=O)O[C]',
'Sulfoxide': '[#16X3+1][#6]',
'SulfonicAcid': 'S(=O)(=O)[OH]',
'Isocyanate': 'N=C=O',
'Urea': 'N-C(=O)-N',
'Carbamate': 'O=C(O)N',
'Imine': '[CX2]=[NX2]',
'Thioether': '[#16X2][#6]',
'Epoxide': '[C@H1]1O[C@H1]1',
'Peroxide': '[OX2][OX2]',
'BoronicAcid': 'B(O)O',
'Anhydride': 'C(=O)OC(=O)',
'Thiocyanate': '[N-]=C=S',
'Isothiocyanate': 'N=C=S',
'Oxime': '[CX3](=NO)',
'Hydrazone': '[CX3](=NN)',
'Guanidine': 'N=C(N)N',
'Pyridine': 'n1ccccc1',
'Pyrazine': 'n1cnccn1',
'Pyrrole': 'n1cccc1',
'Imidazole': 'n1c[nH]cc1',
'Thiazole': 'c1ncsc1',
'NitroAromatic': '[N](=O)=O[c]',
'Quinone': 'O=C1C=CC(=O)C=C1',
'Piperidine': 'N1CCCCC1',
'Pyrrolidine': 'N1CCCC1',
'Morpholine': 'O1CCNCC1',
'TertiaryButylEster': 'C(=O)OC(C)(C)C',
'IsopropylEster': 'C(=O)O[CH](C)C',
'MethylEster': 'C(=O)OC',
'EthylEster': 'C(=O)OCC',
'PropylEster': 'C(=O)OCCC',
'HexylEster': 'C(=O)OCCCCCC',
'OctylEster': 'C(=O)OCCCCCCCC',
'Fluorine': '[F]',
'Trifluoromethyl': 'C(F)(F)F',
'Adamantane': 'C1C2CC3CC(C1)CC(C2)C3',
'Cyclohexyl': 'C1CCCCC1',
'Sulfone': 'S(=O)(=O)[C,N,O]',
'PhosphineOxide': 'P(=O)[C,N,O]',
'Benzene': 'c1ccccc1',
'Naphthalene': 'c1cccc2ccccc12',
'NitroAromatic': '[$(c-[N+](=O)[O-]),$(c-[N+]-[O-])]',
'Aniline': 'c-[NX3H2]',
'MichaelAcceptor_Enone': '[CX3]=[CX3]-[CX3](=[O,S,N])',
'Epoxide_Alert': '[OD1r3]1[#6r3][#6r3]1',
'Tetrahydroisoquinoline_Core_Alert': 'c1ccc2c(c1)CCNCC2',
'4_Phenylpiperidine_Motif': 'c1ccccc1-C1CCNCC1',
}
functional_groups = []
fg_labels = []
for fg_name, smarts in fg_smarts.items():
try:
pattern = Chem.MolFromSmarts(smarts)
if pattern is None:
warnings.warn(f"Invalid SMARTS pattern: {fg_name} -> {smarts}")
continue
matches = mol.GetSubstructMatches(pattern)
for match in matches:
fg_atoms = set(match)
functional_groups.append(list(fg_atoms))
fg_labels.append(fg_name)
except Exception as e:
warnings.warn(f"Error in matching SMARTS pattern: {fg_name} -> {smarts}: {e}")
continue
return functional_groups, fg_labels
def get_ring_structures(self, mol):
rings = []
labels = []
ring_info = mol.GetRingInfo()
for idxs in ring_info.AtomRings():
is_aromatic = all([mol.GetAtomWithIdx(idx).GetIsAromatic() for idx in idxs])
ring_size = len(idxs)
ring_label = f"AromaticRing_{ring_size}" if is_aromatic else f"Ring_{ring_size}"
rings.append(list(idxs))
labels.append(ring_label)
fused_rings = rdMolDescriptors.CalcNumSpiroAtoms(mol)
if fused_rings > 0:
labels.append("FusedRings")
rings.append([atom.GetIdx() for atom in mol.GetAtoms() if atom.IsInRing()])
return rings, labels
def get_special_structures(self, mol):
special_structures = []
special_labels = []
metal_atomic_numbers = [13, 12, 20, 26, 30, 29, 25, 24, 27, 28, 33, 80, 82, 50]
metal_atoms = [atom.GetIdx() for atom in mol.GetAtoms() if atom.GetAtomicNum() in metal_atomic_numbers]
if metal_atoms:
special_structures.append(metal_atoms)
special_labels.append("MetalAtoms")
ssr = Chem.GetSymmSSSR(mol)
atom_rings = [set(ring) for ring in ssr]
spiro_atoms = set()
for i in range(len(atom_rings)):
for j in range(i + 1, len(atom_rings)):
shared_atoms = atom_rings[i] & atom_rings[j]
if len(shared_atoms) == 1:
spiro_atoms.update(shared_atoms)
if spiro_atoms:
special_structures.append(list(spiro_atoms))
special_labels.append("SpiroAtoms")
return special_structures, special_labels
def generate_enhanced_hyperedge_attributes(self):
num_hyperedges = len(self.hyperedges)
hyperedge_features = np.zeros((num_hyperedges, 5), dtype=np.float32)
if num_hyperedges == 0:
print(f"Warning: No hyperedges found for molecule. Creating default attribute matrix with shape [1, 5].")
return np.zeros((1, 5), dtype=np.float32)
for i, (edge, label) in enumerate(zip(self.hyperedges, self.hyperedge_labels)):
if i >= hyperedge_features.shape[0]:
print(
f"Warning: Hyperedge index {i} exceeds feature matrix dimension {hyperedge_features.shape[0]}. Expanding matrix.")
expanded_features = np.zeros((i + 1, 5), dtype=np.float32)
expanded_features[:hyperedge_features.shape[0]] = hyperedge_features
hyperedge_features = expanded_features
current_label_handled = False
if 'MurckoScaffoldCore' in label:
hyperedge_features[i, 0] = 0.95
current_label_handled = True
elif 'MurckoScaffoldFull' in label:
hyperedge_features[i, 0] = 0.90
current_label_handled = True
if not current_label_handled:
if 'Ring' in label:
if 'Aromatic' in label:
hyperedge_features[i, 0] = 0.85
else:
hyperedge_features[i, 0] = 0.75
elif any(fg in label for fg in ['Amine', 'Alcohol', 'Acid', 'Amide', 'Carbonyl', 'Ester', 'Ketone', 'Aldehyde']):
hyperedge_features[i, 0] = 0.80
elif any(fg in label for fg in ['Halogen', 'Cyano', 'Nitro', 'Sulfonamide', 'Thiol', 'Sulfone']):
hyperedge_features[i, 0] = 0.70
elif 'Connector' in label or 'Bridge' in label or 'Substituent' in label:
hyperedge_features[i, 0] = 0.60
elif 'IsolatedAtomGroup' in label or 'SingleAtom' in label:
hyperedge_features[i, 0] = 0.30
else:
hyperedge_features[i, 0] = 0.50
if 'Ring' in label:
if 'Aromatic' in label:
hyperedge_features[i, 0] = 0.9
else:
hyperedge_features[i, 0] = 0.7
elif any(fg in label for fg in ['Amine', 'Alcohol', 'Acid', 'Amide', 'Carbonyl']):
hyperedge_features[i, 0] = 0.8
elif any(fg in label for fg in ['Halogen', 'Cyano', 'Nitro']):
hyperedge_features[i, 0] = 0.75
elif 'Connector' in label or 'Bridge' in label:
hyperedge_features[i, 0] = 0.6
else:
hyperedge_features[i, 0] = 0.5
hyperedge_size = len(edge)
normalized_size = min(1.0, hyperedge_size / 10.0)
hyperedge_features[i, 1] = normalized_size
electron_feature = 0.0
atom_count = 0
for atom_idx in edge:
if atom_idx < self.mol.GetNumAtoms():
atom = self.mol.GetAtomWithIdx(atom_idx)
atomic_num = atom.GetAtomicNum()
if atomic_num in [7, 8, 9, 17, 35, 53]: # N, O, F, Cl, Br, I
electron_feature += 0.8
elif atomic_num == 6 and atom.GetIsAromatic():
electron_feature += 0.6
elif atomic_num == 6:
electron_feature += 0.4
elif atomic_num == 1:
electron_feature += 0.2
else:
electron_feature += 0.5
atom_count += 1
hyperedge_features[i, 2] = electron_feature / max(1, atom_count)
connectivity = 0.0
for other_idx, other_edge in enumerate(self.hyperedges):
if i != other_idx:
if set(edge).intersection(set(other_edge)):
connectivity += 1.0
hyperedge_features[i, 3] = min(1.0, connectivity / max(1, len(self.hyperedges) / 2))
pharmacophore_patterns = {
'HBondDonor': ['[OH]', '[NH]', '[NH2]'],
'HBondAcceptor': ['[O]', '[N;!$(N-*=O)]'],
'Hydrophobic': ['[C;!$(C=O);!$(C#N)]', '[c]'],
'Aromatic': ['c1ccccc1', 'c1ccncc1'],
'Charged': ['[+]', '[-]', '[N+]', '[O-]']
}
is_pharmacophore = False
for pattern_list in pharmacophore_patterns.values():
for pattern in pattern_list:
patt = Chem.MolFromSmarts(pattern)
if patt and self.mol.HasSubstructMatch(patt):
matches = self.mol.GetSubstructMatches(patt)
for match in matches:
if any(atom_idx in edge for atom_idx in match):
is_pharmacophore = True
break
if is_pharmacophore:
break
if is_pharmacophore:
break
hyperedge_features[i, 4] = 0.9 if is_pharmacophore else 0.4
if hyperedge_features.shape[0] != num_hyperedges:
print(
f"Warning: Final hyperedge feature matrix shape {hyperedge_features.shape} doesn't match expected size {num_hyperedges}. Fixing.")
corrected_features = np.zeros((num_hyperedges, 5), dtype=np.float32)
min_size = min(hyperedge_features.shape[0], num_hyperedges)
corrected_features[:min_size] = hyperedge_features[:min_size]
hyperedge_features = corrected_features
return hyperedge_features
def get_adjacency_matrix(self):
num_nodes = self.mol.GetNumAtoms()
num_hyperedges = len(self.hyperedges)
adjacency_matrix = np.zeros((num_nodes, num_hyperedges), dtype=int)
for hyperedge_idx, hyperedge in enumerate(self.hyperedges):
for node in hyperedge:
adjacency_matrix[node][hyperedge_idx] = 1
return adjacency_matrix
class MoleculeData(Data):
def __init__(self, x=None, edge_index=None, y=None, hyperedge_attr=None, smiles=None, **kwargs):
super(MoleculeData, self).__init__(**kwargs)
self.hyperedge_attr = None
self.smiles = None
if x is not None:
if not isinstance(x, torch.Tensor):
x = torch.FloatTensor(x)
if x.size(0) == 0:
print("Warning: Empty feature matrix provided")
self.x = x
if edge_index is not None:
if not isinstance(edge_index, torch.Tensor):
edge_index = torch.LongTensor(edge_index)
if edge_index.dim() != 2 or edge_index.size(0) != 2:
print(f"Warning: Unusual edge_index shape: {edge_index.shape}")
self.edge_index = edge_index
if y is not None:
if not isinstance(y, torch.Tensor):
y = torch.FloatTensor(y)
self.y = y
if hyperedge_attr is not None:
if not isinstance(hyperedge_attr, torch.Tensor):
hyperedge_attr = torch.FloatTensor(hyperedge_attr)
self.hyperedge_attr = hyperedge_attr
if smiles is not None:
self.smiles = smiles
@classmethod
def from_cache(cls, filepath):
data = torch.load(filepath)
if not cls.verify_data(data):
raise ValueError("Invalid cached data")
return data
@staticmethod
def verify_data(data):
if not isinstance(data, Data):
print("Invalid data type")
return False
if not hasattr(data, 'x') or not hasattr(data, 'edge_index') or not hasattr(data, 'y'):
print("Missing required attributes in data")
return False
if data.x is None:
print("Data contains None x attribute")
return False
if data.edge_index is None:
print("Data contains None edge_index attribute")
return False
if data.y is None:
print("Data contains None y attribute")
return False
if data.x.size(0) == 0:
print("Empty x in data")
return False
if data.edge_index.numel() == 0:
print("Empty edge_index in data")
return False
if not torch.isfinite(data.x).all():
print("Non-finite values in data.x")
return False
if not torch.isfinite(data.y).all():
print("Non-finite values in data.y")
return False
if hasattr(data, 'hyperedge_attr') and data.hyperedge_attr is not None:
if not torch.isfinite(data.hyperedge_attr).all():
print("Non-finite values in data.hyperedge_attr")
return False
num_nodes = data.x.size(0)
if data.edge_index.numel() > 0:
if data.edge_index.size(0) != 2:
print(f"Invalid edge_index shape: expected (2, N), got {data.edge_index.shape}")
return False
node_indices = data.edge_index[0]
edge_indices = data.edge_index[1]
if node_indices.min().item() < 0 or node_indices.max().item() >= num_nodes:
print(
f"Invalid node indices in edge_index: range [{node_indices.min().item()}, {node_indices.max().item()}], num_nodes={num_nodes}")
return False
if edge_indices.min().item() < 0:
print(f"Invalid edge indices in edge_index: min={edge_indices.min().item()} is negative")
return False
if hasattr(data, 'hyperedge_attr') and data.hyperedge_attr is not None:
num_hyperedges = data.hyperedge_attr.size(0)
if edge_indices.max().item() >= num_hyperedges:
print(
f"Invalid edge indices in edge_index: max={edge_indices.max().item()}, num_hyperedges={num_hyperedges}")
return False
return True
def get_hyperedge_attr(self):
return self.hyperedge_attr
class MoleculeDataset(Dataset):
def __init__(self, data_path, dataset_name, task_type='classification',
max_samples=None, feature_type='combined'):
super(MoleculeDataset, self).__init__()
self.feature_type = feature_type
self.dataset_name = dataset_name.lower()
self.task_type = task_type
self.cache_dir = f"./processed_data/{dataset_name}/"
self.metadata_file = os.path.join(self.cache_dir, "metadata.pt")
self.is_multi_label = False
os.makedirs(self.cache_dir, exist_ok=True)
self.label_encoding = {
'positive': 1,
'negative': -1,
'missing': 0,
'original_to_encoded': {},
'encoded_to_original': {}
}
if self._try_load_cache():
print("\nLoaded processed data from cache")
return
print(f"\nLoading dataset from {data_path}")
df = pd.read_csv(data_path)
print(f"Total records in CSV: {len(df)}")
df.columns = df.columns.str.strip().str.lower()
dataset_handler = getattr(self, f"_process_{self.dataset_name}", None)
if dataset_handler:
dataset_handler(df)
else:
raise ValueError(f"Unsupported dataset: {dataset_name}")
if max_samples is not None:
print(f"\nUsing only the first {max_samples} samples for testing.")
self.smiles_list = self.smiles_list[:max_samples]
self.labels = self.labels[:max_samples]
self.valid_smiles = []
self.valid_indices = []
self.processed_data = []
self.hyperedge_attrs = {}
print("\nProcessing molecules...")
success_count = 0
error_count = 0
empty_count = 0
for i, smiles in enumerate(tqdm(self.smiles_list)):
if pd.isna(smiles):
empty_count += 1
continue
try:
mol = self._robust_smiles_to_mol(smiles)
if mol is None:
error_count += 1
continue
hypergraph = MoleculeHypergraph(feature_type=self.feature_type)
try:
hypergraph.build_from_mol(mol)
except Exception as e:
error_count += 1
print(f"\nError building hypergraph for molecule {i} with SMILES {smiles}: {str(e)}")
continue
if hypergraph.node_features is None or hypergraph.hyperedge_index is None:
error_count += 1
print(f"\nInvalid hypergraph for molecule {i} with SMILES {smiles}")
continue
x = torch.FloatTensor(hypergraph.node_features)
edge_index = torch.LongTensor(hypergraph.hyperedge_index)
num_nodes = x.size(0)
if edge_index.shape[0] != 2:
error_count += 1
print(
f"\nInvalid edge_index shape for molecule {i} with SMILES {smiles}: expected (2, N), got {edge_index.shape}")
continue
node_indices = edge_index[0]
edge_indices = edge_index[1]
if node_indices.max() >= num_nodes or node_indices.min() < 0:
error_count += 1
print(
f"\nInvalid node indices in edge_index for molecule {i} with SMILES {smiles}: range [{node_indices.min()}, {node_indices.max()}], num_nodes={num_nodes}")
continue
num_hyperedges = len(hypergraph.hyperedges)
if edge_indices.max() >= num_hyperedges or edge_indices.min() < 0:
error_count += 1
print(
f"\nInvalid edge indices in edge_index for molecule {i} with SMILES {smiles}: range [{edge_indices.min()}, {edge_indices.max()}], num_hyperedges={num_hyperedges}")
continue
y = self.process_label(i)
if not (torch.isfinite(x).all() and torch.isfinite(y).all()):
error_count += 1
print(f"\nNon-finite values in molecule {i}")
continue
hyperedge_attr = hypergraph.generate_enhanced_hyperedge_attributes()
if hyperedge_attr is None:
print(f"Warning: No hyperedges found for molecule {i}. Creating default attribute.")
hyperedge_attr = np.zeros((1, 5), dtype=np.float32)
if isinstance(hyperedge_attr, torch.Tensor):
self.hyperedge_attrs[smiles] = hyperedge_attr.cpu().numpy()
else:
self.hyperedge_attrs[smiles] = hyperedge_attr
hyperedge_attr_tensor = torch.FloatTensor(hyperedge_attr)
data = MoleculeData(
x=x,
edge_index=edge_index,
y=y,
hyperedge_attr=hyperedge_attr_tensor,
smiles=smiles
)
data.smiles = smiles
self.processed_data.append(data)
self.valid_smiles.append(smiles)
self.valid_indices.append(i)
success_count += 1
except Exception as e:
error_count += 1
print(f"\nError processing molecule {i}: {str(e)}")
continue
if len(self.processed_data) == 0:
raise ValueError("No valid molecules processed!")
self._check_data_validity()
self._save_cache()
print("\nProcessing Summary:")
print(f"Total molecules: {len(self.smiles_list)}")
print(f"Successfully processed: {success_count}")
print(f"Failed to process: {error_count}")
print(f"Empty SMILES: {empty_count}")
self._print_label_statistics()
def _robust_smiles_to_mol(self, smiles):
mol = Chem.MolFromSmiles(smiles)
if mol is not None:
return mol
mol = Chem.MolFromSmiles(smiles, sanitize=False)
if mol is None:
return None
try:
mol.UpdatePropertyCache(strict=False)
for atom in mol.GetAtoms():
if atom.GetSymbol() == 'N':
if atom.GetExplicitValence() >= 4 and atom.GetFormalCharge() == 0:
atom.SetFormalCharge(1)
Chem.SanitizeMol(mol)
return mol
except Exception:
try:
Chem.SanitizeMol(mol, sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL ^ Chem.SanitizeFlags.SANITIZE_PROPERTIES)
return mol
except:
return None
def _process_bace(self, df):
"""处理 BACE 数据集（单标签分类）"""
required_cols = ['mol', 'class']
if not all(col in df.columns for col in required_cols):
raise ValueError(f"bace dataset must contain columns: {required_cols}")
self.smiles_list = df['mol'].values
self.labels = df['class'].values
self.labels = np.where(self.labels == 0, -1, self.labels)
self.label_cols = ['class']
self.is_multi_label = False
self.process_label = lambda idx: torch.FloatTensor([[float(self.labels[idx])]])
print("\nLabel distribution in original data:")
print(df['class'].value_counts(normalize=True))
def _process_bbbp(self, df):
"""处理 BBBP 数据集（单标签分类）"""
required_cols = ['smiles', 'p_np']
if not all(col in df.columns for col in required_cols):
raise ValueError(f"BBBP dataset must contain columns: {required_cols}")
self.smiles_list = df['smiles'].values
self.labels = df['p_np'].values
self.labels = np.where(self.labels == 0, -1, self.labels)
self.label_cols = ['p_np']
self.is_multi_label = False
self.process_label = lambda idx: torch.FloatTensor([[float(self.labels[idx])]])
print("\nLabel distribution in original data:")
print(df['p_np'].value_counts(normalize=True))
def _process_sider(self, df):
"""处理 SIDER 数据集（多标签分类）"""
if 'smiles' not in df.columns:
raise ValueError("SIDER dataset must contain a 'smiles' column")
self.smiles_list = df['smiles'].values
label_cols = [col for col in df.columns if col != 'smiles']
self.label_cols = label_cols
self.labels = df[label_cols].values.astype(float)
self.labels = np.where(self.labels == 0, -1, self.labels)
self.is_multi_label = True
self.process_label = lambda idx: torch.FloatTensor(self.labels[idx]).unsqueeze(0)
print("\nLabel distribution in original data:")
print(df[label_cols].apply(lambda x: pd.value_counts(x, normalize=True)))
def _process_clintox(self, df):
"""处理 ClinTox 数据集（单标签分类）"""
if 'smiles' not in df.columns:
raise ValueError("ClinTox dataset must contain a 'smiles' column")
label_cols = ['fda_approved', 'ct_tox']
required_cols = ['smiles'] + label_cols
if not all(col in df.columns for col in required_cols):
raise ValueError(f"ClinTox dataset must contain columns: {required_cols}")
self.smiles_list = df['smiles'].values
self.labels = df[label_cols].values.astype(float)
self.labels = np.where(self.labels == 0, -1, self.labels)
self.labels = np.nan_to_num(self.labels, nan=0)
self.label_cols = label_cols
self.is_multi_label = True
self.process_label = lambda idx: torch.FloatTensor(self.labels[idx]).unsqueeze(0)
def _process_tox21(self, df):
"""处理 Tox21 数据集（多标签分类）"""
if 'smiles' not in df.columns:
raise ValueError("Tox21 dataset must contain a 'smiles' column")
self.smiles_list = df['smiles'].values
label_cols = [col for col in df.columns if col.lower() not in ['smiles', 'mol_id']]
self.label_cols = label_cols
self.labels = df[label_cols].values.astype(float)
self.labels = np.where(self.labels == 0, -1, self.labels)
self.labels = np.nan_to_num(self.labels, nan=0)
self.is_multi_label = True
self.process_label = lambda idx: torch.FloatTensor(self.labels[idx]).unsqueeze(0)
print("\nLabel distribution after processing:")
print(df[label_cols].apply(lambda x: pd.value_counts(x, normalize=True)))
def _process_toxcast(self, df):
"""处理 ToxCast 数据集（多标签分类）"""
if 'smiles' not in df.columns:
raise ValueError("ToxCast dataset must contain a 'smiles' column")
self.smiles_list = df['smiles'].values
label_cols = [col for col in df.columns if col != 'smiles']
self.label_cols = label_cols
self.labels = df[label_cols].values.astype(float)
self.labels = np.where(self.labels == 0, -1, self.labels)
self.labels = np.nan_to_num(self.labels, nan=0)
self.is_multi_label = True
self.process_label = lambda idx: torch.FloatTensor(self.labels[idx]).unsqueeze(0)
print("\nLabel distribution in original data:")
print(df[label_cols].apply(lambda x: pd.value_counts(x, normalize=True)))
def _process_esol(self, df):
"""处理 ESOL 数据集（单目标回归）"""
required_cols = ['smiles', 'measured log solubility in mols per litre']
if not all(col in df.columns for col in required_cols):
raise ValueError(f"ESOL dataset must contain columns: {required_cols}")
self.smiles_list = df['smiles'].values
self.labels = df['measured log solubility in mols per litre'].values.astype(float)
self.label_cols = ['log_solubility']
self.is_multi_label = False
self.task_type = 'regression'
self.process_label = lambda idx: torch.FloatTensor([[float(self.labels[idx])]])
print("\nESOL dataset statistics:")
print(f"Min solubility: {np.min(self.labels):.2f}")
print(f"Max solubility: {np.max(self.labels):.2f}")
print(f"Mean solubility: {np.mean(self.labels):.2f}")
print(f"Std solubility: {np.std(self.labels):.2f}")
def _process_freesolv(self, df):
"""处理 FreeSolv 数据集（单目标回归）"""
required_cols = ['smiles', 'expt']
if not all(col in df.columns for col in required_cols):
raise ValueError(f"FreeSolv dataset must contain columns: {required_cols}")
self.smiles_list = df['smiles'].values
self.labels = df['expt'].values.astype(float)
self.label_cols = ['expt']
self.is_multi_label = False
self.task_type = 'regression'
self.process_label = lambda idx: torch.FloatTensor([[float(self.labels[idx])]])
print("\nFreeSolv dataset statistics:")
print(f"Min expt: {np.min(self.labels):.2f}")
print(f"Max expt: {np.max(self.labels):.2f}")
print(f"Mean expt: {np.mean(self.labels):.2f}")
print(f"Std expt: {np.std(self.labels):.2f}")
def _process_lipophilicity(self, df):
"""处理 Lipophilicity 数据集（单目标回归）"""
required_cols = ['cmpd_chemblid', 'exp', 'smiles']
if not all(col in df.columns for col in required_cols):
raise ValueError(f"Lipophilicity dataset must contain columns: {required_cols}")
self.smiles_list = df['smiles'].values
self.labels = df['exp'].values.astype(float)
self.label_cols = ['exp']
self.is_multi_label = False
self.task_type = 'regression'
self.process_label = lambda idx: torch.FloatTensor([[float(self.labels[idx])]])
print("\nLipophilicity dataset statistics:")
print(f"Min exp: {np.min(self.labels):.2f}")
print(f"Max exp: {np.max(self.labels):.2f}")
print(f"Mean exp: {np.mean(self.labels):.2f}")
print(f"Std exp: {np.std(self.labels):.2f}")
def _process_qm8(self, df):
"""处理 QM8 数据集（多目标回归）"""
required_cols = ['smiles']
if not all(col in df.columns for col in required_cols):
raise ValueError("QM8 dataset must contain a 'smiles' column")
self.smiles_list = df['smiles'].values
label_cols = [col for col in df.columns if col != 'smiles']
self.label_cols = label_cols
self.labels = df[label_cols].values.astype(float)
self.is_multi_label = True
self.task_type = 'regression'
self.process_label = lambda idx: torch.FloatTensor(self.labels[idx]).unsqueeze(0)
print("\nQM8 dataset statistics:")
print(f"Label columns: {label_cols}")
print(f"Min values: {np.min(self.labels, axis=0)}")
print(f"Max values: {np.max(self.labels, axis=0)}")
print(f"Mean values: {np.mean(self.labels, axis=0)}")
print(f"Std values: {np.std(self.labels, axis=0)}")
def _process_qm7(self, df):
"""
处理 QM7 数据集
"""
if 'smiles' not in df.columns:
raise ValueError("QM7 dataset must contain a 'smiles' column")
possible_targets = ['u0_atom', 'u0', 'target', 'eat']
target_col = next((c for c in possible_targets if c in df.columns), None)
if target_col is None:
target_col = [c for c in df.columns if c != 'smiles'][-1]
print(f"Warning: Specific QM7 target column not found. Using '{target_col}' as target.")
self.smiles_list = df['smiles'].values
self.labels = df[target_col].values.astype(float)
self.label_cols = [target_col]
self.is_multi_label = False
self.task_type = 'regression'
self.process_label = lambda idx: torch.FloatTensor([[float(self.labels[idx])]])
print(f"\nQM7 dataset statistics ({target_col}):")
print(f"Total samples: {len(self.labels)}")
print(f"Min: {np.min(self.labels):.4f}")
print(f"Max: {np.max(self.labels):.4f}")
print(f"Mean: {np.mean(self.labels):.4f}")
print(f"Std: {np.std(self.labels):.4f}")
def _check_data_validity(self):
if len(self.processed_data) == 0:
print("Warning: No processed data to check validity.")
return
if self.task_type == 'classification':
invalid_tasks = []
if self.is_multi_label:
if not hasattr(self, 'label_cols') or not self.label_cols:
print("Warning: Cannot check validity, label_cols not defined.")
return
num_tasks = len(self.label_cols)
if num_tasks == 0:
print("Warning: Cannot check validity, num_tasks is zero.")
return
for task_idx in range(num_tasks):
task_labels = []
for data in self.processed_data:
if hasattr(data, 'y') and data.y is not None and data.y.dim() == 2 and data.y.shape[0] == 1 and data.y.shape[1] > task_idx:
try:
label_value = data.y[0, task_idx].item()
task_labels.append(label_value)
except IndexError:
print(f"Warning: IndexError accessing data.y[0, {task_idx}] for data with y shape {data.y.shape}. Skipping.")
except Exception as e:
print(f"Warning: Error accessing label for task {task_idx}: {e}. Skipping.")
if not task_labels:
print(f"Warning: No valid labels found for task {task_idx} ({self.label_cols[task_idx]}).")
invalid_tasks.append((self.label_cols[task_idx], []))
continue
valid_labels = [v for v in task_labels if not np.isnan(v)]
if not valid_labels:
print(f"Warning: All labels are NaN for task {task_idx} ({self.label_cols[task_idx]}) after filtering.")
invalid_tasks.append((self.label_cols[task_idx], []))
continue
unique = np.unique(valid_labels)
if len(unique) < 2:
invalid_tasks.append((self.label_cols[task_idx], unique))
else:
try:
label_values = []
for data in self.processed_data:
if hasattr(data, 'y') and data.y is not None and data.y.dim() == 2 and data.y.shape == (1, 1):
try:
label_value = data.y[0, 0].item()
label_values.append(label_value)
except IndexError:
print(f"Warning: IndexError accessing data.y[0, 0] for data with y shape {data.y.shape}. Skipping.")
except Exception as e:
print(f"Warning: Error accessing single label: {e}. Skipping.")
if not label_values:
print("Warning: No valid labels found for single-label task.")
invalid_tasks.append(('main_label', []))
else:
unique = np.unique(label_values)
if len(unique) < 2:
invalid_tasks.append(('main_label', unique))
except Exception as e:
print(f"Error analyzing single-label distribution: {str(e)}")
if invalid_tasks:
print("\nWARNING: Found tasks with only one class (or no valid labels):")
for task, classes in invalid_tasks:
if classes:
print(f" Task {task}: classes {classes}")
else:
print(f" Task {task}: No valid labels found.")
print("This may cause evaluation metrics like AUC/AUPR to fail or be unreliable!")
def get_original_label_value(self, encoded_value):
if hasattr(self, 'label_encoding') and 'encoded_to_original' in self.label_encoding:
return self.label_encoding['encoded_to_original'].get(encoded_value, encoded_value)
return encoded_value
def is_missing_label(self, encoded_value):
if hasattr(self, 'label_encoding'):
return encoded_value == self.label_encoding['missing']
return False
def _print_label_statistics(self):
try:
if self.is_multi_label and self.dataset_name in ['sider', 'tox21', 'toxcast']:
print("\nLabel distribution in processed data:")
for idx, col in enumerate(self.label_cols):
if idx < self.labels.shape[1]:
label_values = self.labels[:, idx]
unique, counts = np.unique(label_values, return_counts=True)
print(f"{col}:")
for u, c in zip(unique, counts):
print(f" Label {u}: {c} samples ({c / len(label_values) * 100:.2f}%)")
elif self.dataset_name in ['qm8', 'qm9']:
try:
processed_labels_array = []
for data in self.processed_data:
if data.y.numel() > 0:
processed_labels_array.append(data.y.cpu().numpy())
processed_labels_array = np.array(processed_labels_array)
print("\nProcessed label statistics (per dimension):")
for i, col in enumerate(self.label_cols):
if i < processed_labels_array.shape[1]:
col_values = processed_labels_array[:, i]
print(
f"{col}: Min={col_values.min():.4f}, Max={col_values.max():.4f}, Mean={col_values.mean():.4f}, Std={col_values.std():.4f}")
except Exception as e:
print(f"Error computing label statistics: {str(e)}")
else:
try:
processed_labels = []
for data in self.processed_data:
if data.y.numel() >= 1:
processed_labels.append(data.y[0].item())
unique_labels = np.unique(processed_labels)
print("\nLabel distribution in processed data:")
for label in unique_labels:
count = sum(1 for y in processed_labels if y == label)
print(f"Label {label}: {count} samples ({count / len(processed_labels) * 100:.2f}%)")
except Exception as e:
print(f"Error computing label distribution: {str(e)}")
except Exception as e:
print(f"Error in label statistics calculation: {str(e)}")
def _save_hyperedge_attrs(self):
for data in self.processed_data:
if hasattr(data, 'smiles') and data.smiles and hasattr(data,
'hyperedge_attr') and data.hyperedge_attr is not None:
if isinstance(data.hyperedge_attr, torch.Tensor):
self.hyperedge_attrs[data.smiles] = data.hyperedge_attr.cpu().numpy()
else:
self.hyperedge_attrs[data.smiles] = data.hyperedge_attr
hyperedge_attrs_file = os.path.join(self.cache_dir, "hyperedge_attrs.pt")
torch.save(self.hyperedge_attrs, hyperedge_attrs_file)
print(f"Saved hyperedge attributes for {len(self.hyperedge_attrs)} molecules")
def _get_cache_filename(self, idx):
return os.path.join(self.cache_dir, f"mol_{idx}.pt")
def _save_metadata(self):
has_hyperedge_attr = False
if self.processed_data and len(self.processed_data) > 0:
sample_item = self.processed_data[0]
has_hyperedge_attr = hasattr(sample_item, 'hyperedge_attr') and sample_item.hyperedge_attr is not None
metadata = {
'dataset_name': self.dataset_name,
'task_type': self.task_type,
'num_classes': self._get_num_classes(),
'label_cols': self.label_cols,
'is_multi_label': self.is_multi_label,
'valid_indices': self.valid_indices,
'has_hyperedge_attr': has_hyperedge_attr,
'label_encoding': getattr(self, 'label_encoding', {})
}
torch.save(metadata, self.metadata_file)
def _load_metadata(self):
if os.path.exists(self.metadata_file):
try:
metadata = torch.load(self.metadata_file)
if metadata.get('dataset_name') == self.dataset_name:
self.label_cols = metadata.get('label_cols', [])
self.is_multi_label = metadata.get('is_multi_label', False)
self.valid_indices = metadata.get('valid_indices', [])
self.task_type = metadata.get('task_type', self.task_type)
self.has_hyperedge_attr = metadata.get('has_hyperedge_attr', False)
self.label_encoding = metadata.get('label_encoding', {
'positive': 1,
'negative': -1,
'missing': 0,
'original_to_encoded': {},
'encoded_to_original': {}
})
return True
return False
except Exception as e:
print(f"Error loading metadata: {str(e)}")
return False
return False
def _try_load_cache(self):
if not self._load_metadata():
return False
cache_files = [f for f in os.listdir(self.cache_dir) if
f.endswith(".pt") and not f == "metadata.pt" and not f == "hyperedge_attrs.pt"]
if not cache_files:
return False
print("\nChecking cached data...")
self.hyperedge_attrs = {}
hyperedge_attrs_file = os.path.join(self.cache_dir, "hyperedge_attrs.pt")
if os.path.exists(hyperedge_attrs_file):
try:
self.hyperedge_attrs = torch.load(hyperedge_attrs_file)
print(f"Loaded hyperedge attributes dictionary for {len(self.hyperedge_attrs)} molecules")
except Exception as e:
print(f"Error loading hyperedge attributes: {e}")
self.hyperedge_attrs = {}
self.processed_data = []
self.valid_smiles = []
success = 0
failures = 0
max_idx = -1
for f in cache_files:
try:
idx = int(f.split('_')[1].split('.')[0])
max_idx = max(max_idx, idx)
except:
continue
for idx in tqdm(range(max_idx + 1)):
cache_file = self._get_cache_filename(idx)
if os.path.exists(cache_file):
try:
data = torch.load(cache_file)
if not hasattr(data, 'x') or data.x is None or data.x.shape[0] == 0:
print(f"Skipping invalid cache file (bad x): {cache_file}")
failures += 1
continue
if not hasattr(data, 'edge_index') or data.edge_index is None:
print(f"Skipping invalid cache file (bad edge_index): {cache_file}")
failures += 1
continue
if not hasattr(data, 'y') or data.y is None:
print(f"Skipping invalid cache file (bad y): {cache_file}")
failures += 1
continue
smiles = getattr(data, 'smiles', None)
hyperedge_attr = getattr(data, 'hyperedge_attr', None)
if hyperedge_attr is None and smiles is not None and smiles in self.hyperedge_attrs:
hyperedge_attr_np = self.hyperedge_attrs[smiles]
hyperedge_attr = torch.FloatTensor(hyperedge_attr_np)
print(f"Recovered hyperedge attributes for molecule with SMILES {smiles}")
cleaned_data = MoleculeData(
x=data.x.clone(),
edge_index=data.edge_index.clone(),
y=data.y.clone(),
hyperedge_attr=hyperedge_attr.clone() if hyperedge_attr is not None else None,
smiles=smiles
)
self.processed_data.append(cleaned_data)
if smiles is not None:
self.valid_smiles.append(smiles)
success += 1
except Exception as e:
print(f"Error loading cache file {cache_file}: {str(e)}")
failures += 1
print(f"Loaded {success}/{len(cache_files)} valid cached entries ({failures} failures)")
return success > 0
def _save_cache(self):
print("\nSaving processed data to cache...")
os.makedirs(self.cache_dir, exist_ok=True)
for idx, data in enumerate(tqdm(self.processed_data)):
try:
smiles = getattr(data, 'smiles', None)
hyperedge_attr = getattr(data, 'hyperedge_attr', None)
data_cpu = MoleculeData(
x=data.x.cpu(),
edge_index=data.edge_index.cpu(),
y=data.y.cpu(),
hyperedge_attr=hyperedge_attr.cpu() if hyperedge_attr is not None else None,
smiles=smiles
)
torch.save(data_cpu, self._get_cache_filename(idx))
except Exception as e:
print(f"Error saving {idx}: {str(e)}")
self._save_hyperedge_attrs()
self._save_metadata()
print(f"Saved metadata to {self.metadata_file}")
def len(self):
return len(self.processed_data)
def get(self, idx):
return self.processed_data[idx]
@property
def num_node_features(self):
if len(self.processed_data) == 0:
raise ValueError("Dataset is empty!")
return self.processed_data[0].x.size(1)
def _get_num_classes(self):
if self.task_type == 'regression':
if self.is_multi_label:
return len(self.label_cols)
else:
return 1
elif self.is_multi_label:
return len(self.label_cols)
else:
return 1
@property
def num_classes(self):
if len(self.processed_data) == 0:
raise ValueError("Dataset is empty!")
return self._get_num_classes()

dataset.py at commit 171920e, no license · at the source

Overview

Authors: Jiani Ma¹, Qi Yang¹, Lin Zhang¹, Hui Liu¹, Yuanting Zheng^2,3

ORCID iDs: Lin Zhang, Yuanting Zheng

Institutions: China University of Mining and Technology (China); The University of Melbourne (Australia); Huazhong Agricultural University (China)

Journal: Computational and structural biotechnology journal, volume 35, issue 1, article 0036

Dates: received 19 December 2025; accepted 15 March 2026; published online 9 April 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.34133/csbj.0036 · PMID 41971950 · PMCID PMC13062488 · OpenAlex W7137359194

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: cellular / molecular (subfield)

Methods: Preprocessing, Machine learning

Journal subjects: General

Topic: Computational Drug Discovery Methods (Computational Theory and Mathematics, Computer Science), according to OpenAlex

Funding: China Postdoctoral Science Foundation (2024M763546)

Citations: not cited yet (Europe PMC); 42 references in the paper

Abstract

Accurate molecular property prediction is a central task in drug discovery, yet existing methods often struggle to simultaneously capture higher-order molecular structures and chemically grounded semantic information. Graph neural networks are limited to pairwise atomic interactions, while Simplified Molecular Input Line Entry System-based language models lack explicit structural grounding, leading to incomplete structure–property representations. In this work, we propose HYG-mol, an interpretable molecular property prediction framework that integrates hypergraph-based structural modeling with multimodal chemical semantics. Molecules are represented as hypergraphs in which chemically meaningful substructures, such as functional groups and ring systems, are explicitly encoded as hyperedges, enabling direct modeling of higher-order structural dependencies. Chemical semantic information derived from a pretrained language model is fused with physicochemical descriptors at the atomic level. A hypergraph attention network is employed to capture cross-scale interactions and to identify substructures relevant to the prediction task. Extensive evaluations on MoleculeNet benchmark datasets demonstrate that HYG-mol consistently outperforms state-of-the-art baseline methods across both classification and regression tasks. Ablation and interpretability analyses further validate the effectiveness of the proposed representation and reveal strong correspondence between model-identified substructures and chemically meaningful motifs. Overall, HYG-mol provides a unified and interpretable framework for molecular property prediction by explicitly grounding chemical semantics in higher-order structural representations.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.

sutera777/HYG-mol

License: none: the authors keep all their rights

State: the link answers, verified on 29 September 2026

Evidence: files inventoried

Commit: 171920ec65c262afd5beaf00af3eb67f706e60b8, 15 March 2026

Languages: Python (15)

Size: 27 files, 15 scripts

Software Heritage: not archived

Found in: “Data Availability”

Holds: README, environment (requirements.txt)

Not found: license file, CITATION.cff, tests, continuous integration, documentation

Tools: PyTorch (7 files), NumPy (6 files), RDKit (4 files), PyTorch Geometric (3 files), scikit-learn (2 files), Matplotlib (1 file), pandas (1 file), Hugging Face Transformers (1 file)

Availability: 1 check, the latest on 29 September 2026: the link answers

29 September 2026: the link answers

16 files

__init__.py, Python, 1 line
src/__init__.py, Python, 1 line
src/config.py, Python, 46 lines
src/data/__init__.py, Python, 1 line
src/data/dataloader.py, Python, 210 lines
src/data/dataset.py, Python, 1,787 lines, 7 matches
src/explainability/__init__.py, Python, 1 line
src/explainability/analyzer.py, Python, 851 lines
src/main.py, Python, 487 lines, 2 matches
src/models/__init__.py, Python, 1 line
src/models/networks.py, Python, 321 lines
src/training/__init__.py, Python, 1 line
src/training/trainer.py, Python, 389 lines, 1 match
src/utils/__init__.py, Python, 1 line
src/utils/utils.py, Python, 381 lines, 1 match
README.md, Text, 56 lines

At the source: github.com/sutera777/HYG-mol

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
15 scripts, each with its path and the digest of its content;
11 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability

The data used to support the findings of this study are available from the corresponding authors upon reasonable request. The molecular property data were derived from the MoleculeNet benchmark dataset (https://moleculenet.org/), which is publicly accessible. The code for the HYG-mol framework and related experimental scripts are deposited in GitHub (https://github.com/sutera777/HYG-mol).

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 1 funder, 26 references.

Cite

This paper

Ma, J., Yang, Q., Zhang, L., Liu, H., & Zheng, Y. (2026). HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction. Computational and structural biotechnology journal, 35(1), 0036. https://doi.org/10.34133/csbj.0036

BibTeX

@article{ma2026hyg, author = {Ma, Jiani and Yang, Qi and Zhang, Lin and Liu, Hui and Zheng, Yuanting}, title = {{HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction}}, journal = {Computational and structural biotechnology journal}, year = {2026}, month = apr, volume = {35}, number = {1}, pages = {0036}, publisher = {AAAS Science Partner Journal Program}, issn = {2001-0370}, doi = {10.34133/csbj.0036}, url = {https://doi.org/10.34133/csbj.0036}, pmid = {41971950}, pmcid = {PMC13062488} }

RIS

TY - JOUR AU - Ma, Jiani AU - Yang, Qi AU - Zhang, Lin AU - Liu, Hui AU - Zheng, Yuanting TI - HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction T2 - Computational and structural biotechnology journal J2 - Comput Struct Biotechnol J PY - 2026 DA - 2026/04/09 VL - 35 IS - 1 SP - 0036 SN - 2001-0370 PB - AAAS Science Partner Journal Program DO - 10.34133/csbj.0036 UR - https://doi.org/10.34133/csbj.0036 LA - en ER -

CSL-JSON

{ "id": "10.34133/csbj.0036", "type": "article-journal", "title": "HYG-mol: An Interpretable Multimodal Hypergraph Framework for Molecular Property Prediction", "container-title": "Computational and structural biotechnology journal", "author": [ { "family": "Ma", "given": "Jiani" }, { "family": "Yang", "given": "Qi" }, { "family": "Zhang", "given": "Lin" }, { "family": "Liu", "given": "Hui" }, { "family": "Zheng", "given": "Yuanting" } ], "container-title-short": "Comput Struct Biotechnol J", "volume": "35", "issue": "1", "page": "0036", "DOI": "10.34133/csbj.0036", "PMID": "41971950", "PMCID": "PMC13062488", "ISSN": "2001-0370", "publisher": "AAAS Science Partner Journal Program", "URL": "https://doi.org/10.34133/csbj.0036", "language": "en", "issued": { "date-parts": [ [ 2026, 4, 9 ] ] } }

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[6] doi:10.3390/ijms27156614 [code]: Candidalysin Inhibits <i>Porphyromonas gingivalis</i> Lipoprotein-Induced IL-1β Production in BV-2 Microglia via Hydrophobic Microbial Interactions.
Journal: International journal of molecular sciences
In common: RDKit, PyTorch Geometric, PyTorch, 4 other tools, cellular / molecular
[7] doi:10.1038/s41586-026-10670-w [code]: Zero-shot design of drug-binding proteins via neural iterative selection-expansion.
Journal: Nature
In common: RDKit, PyTorch Geometric, PyTorch, 4 other tools, cellular / molecular
[8] doi:10.1038/s41598-026-53415-5 [code]: Computational design and immunoinformatics validation of a T cell multi-epitope vaccine targeting glioblastoma stem cells.
Journal: Scientific reports
In common: RDKit, PyTorch Geometric, PyTorch, 4 other tools, cellular / molecular
[9] doi:10.1038/s41586-026-10391-0 [code]: Cell-type-targeted mitochondrial transplantation rescues cell degeneration.
Journal: Nature
In common: RDKit, PyTorch Geometric, PyTorch, 4 other tools, cellular / molecular
[10] doi:10.1021/acs.biochem.5c00596 [code]: Cargo Recognition of Nesprin-2 by the Dynein Adapter Bicaudal D2 for a Nuclear Positioning Pathway That Is Important for Brain Development.
Journal: Biochemistry
In common: RDKit, PyTorch Geometric, PyTorch, 4 other tools, cellular / molecular

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