[DGL-LifeSci] Migration and Refactor (#1226)

* First commit

* Update

* Update splitters

* Update

* Update

* Update

* Update

* Update

* Update

* Migrate ACNN

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Finish classification

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Update

* Update

* trigger CI

* Fix CI

* Update

* Update

* Update

* Add default values

* Rename

* Update deprecation message

apps/life_sci/dgllife/model/model_zoo/gat_predictor.py

+"""GAT-based model for regression and classification on graphs."""
+import torch.nn as nn
+import torch.nn.functional as F
+
+from .mlp_predictor import MLPPredictor
+from ..gnn.gat import GAT
+from ..readout.weighted_sum_and_max import WeightedSumAndMax
+
+class GATPredictor(nn.Module):
+    r"""GAT-based model for regression and classification on graphs.
+
+    GAT is introduced in `Graph Attention Networks <https://arxiv.org/abs/1710.10903>`__.
+    This model is based on GAT and can be used for regression and classification on graphs.
+
+    After updating node representations, we perform a weighted sum with learnable
+    weights and max pooling on them and concatenate the output of the two operations,
+    which is then fed into an MLP for final prediction.
+
+    For classification tasks, the output will be logits, i.e.
+    values before sigmoid or softmax.
+
+    Parameters
+    ----------
+    in_feats : int
+        Number of input node features
+    hidden_feats : list of int
+        ``hidden_feats[i]`` gives the output size of an attention head in the i-th GAT layer.
+        ``len(hidden_feats)`` equals the number of GAT layers. By default, we use ``[32, 32]``.
+    num_heads : list of int
+        ``num_heads[i]`` gives the number of attention heads in the i-th GAT layer.
+        ``len(num_heads)`` equals the number of GAT layers. By default, we use 4 attention heads
+        for each GAT layer.
+    feat_drops : list of float
+        ``feat_drops[i]`` gives the dropout applied to the input features in the i-th GAT layer.
+        ``len(feat_drops)`` equals the number of GAT layers. By default, this will be zero for
+        all GAT layers.
+    attn_drops : list of float
+        ``attn_drops[i]`` gives the dropout applied to attention values of edges in the i-th GAT
+        layer. ``len(attn_drops)`` equals the number of GAT layers. By default, this will be zero
+        for all GAT layers.
+    alphas : list of float
+        Hyperparameters in LeakyReLU, which are the slopes for negative values. ``alphas[i]``
+        gives the slope for negative value in the i-th GAT layer. ``len(alphas)`` equals the
+        number of GAT layers. By default, this will be 0.2 for all GAT layers.
+    residuals : list of bool
+        ``residual[i]`` decides if residual connection is to be used for the i-th GAT layer.
+        ``len(residual)`` equals the number of GAT layers. By default, residual connection
+        is performed for each GAT layer.
+    agg_modes : list of str
+        The way to aggregate multi-head attention results for each GAT layer, which can be either
+        'flatten' for concatenating all-head results or 'mean' for averaging all-head results.
+        ``agg_modes[i]`` gives the way to aggregate multi-head attention results for the i-th
+        GAT layer. ``len(agg_modes)`` equals the number of GAT layers. By default, we flatten
+        multi-head results for intermediate GAT layers and compute mean of multi-head results
+        for the last GAT layer.
+    activations : list of activation function or None
+        ``activations[i]`` gives the activation function applied to the aggregated multi-head
+        results for the i-th GAT layer. ``len(activations)`` equals the number of GAT layers.
+        By default, ELU is applied for intermediate GAT layers and no activation is applied
+        for the last GAT layer.
+    classifier_hidden_feats : int
+        Size of hidden graph representations in the classifier. Default to 128.
+    classifier_dropout : float
+        The probability for dropout in the classifier. Default to 0.
+    n_tasks : int
+        Number of tasks, which is also the output size. Default to 1.
+    """
+    def __init__(self, in_feats, hidden_feats=None, num_heads=None, feat_drops=None, attn_drops=None,
+                 alphas=None, residuals=None, agg_modes=None, activations=None,
+                 classifier_hidden_feats=128, classifier_dropout=0., n_tasks=1):
+        super(GATPredictor, self).__init__()
+
+        self.gnn = GAT(in_feats=in_feats,
+                       hidden_feats=hidden_feats,
+                       num_heads=num_heads,
+                       feat_drops=feat_drops,
+                       attn_drops=attn_drops,
+                       alphas=alphas,
+                       residuals=residuals,
+                       agg_modes=agg_modes,
+                       activations=activations)
+
+        if self.gnn.agg_modes[-1] == 'flatten':
+            gnn_out_feats = self.gnn.hidden_feats[-1] * self.gnn.num_heads[-1]
+        else:
+            gnn_out_feats = self.gnn.hidden_feats[-1]
+        self.readout = WeightedSumAndMax(gnn_out_feats)
+        self.predict = MLPPredictor(2 * gnn_out_feats, classifier_hidden_feats,
+                                    n_tasks, classifier_dropout)
+
+    def forward(self, bg, feats):
+        """Graph-level regression/soft classification.
+
+        Parameters
+        ----------
+        bg : DGLGraph
+            DGLGraph for a batch of graphs.
+        feats : FloatTensor of shape (N, M1)
+            * N is the total number of nodes in the batch of graphs
+            * M1 is the input node feature size, which must match
+              in_feats in initialization
+
+        Returns
+        -------
+        FloatTensor of shape (B, n_tasks)
+            * Predictions on graphs
+            * B for the number of graphs in the batch
+        """
+        node_feats = self.gnn(bg, feats)
+        graph_feats = self.readout(bg, node_feats)
+        return self.predict(graph_feats)

apps/life_sci/dgllife/model/model_zoo/gcn_predictor.py

+"""GCN-based model for regression and classification on graphs."""
+import torch.nn as nn
+
+from .mlp_predictor import MLPPredictor
+from ..gnn.gcn import GCN
+from ..readout.weighted_sum_and_max import WeightedSumAndMax
+
+class GCNPredictor(nn.Module):
+    """GCN-based model for regression and classification on graphs.
+
+    GCN is introduced in `Semi-Supervised Classification with Graph Convolutional Networks
+    <https://arxiv.org/abs/1609.02907>`__. This model is based on GCN and can be used
+    for regression and classification on graphs.
+
+    After updating node representations, we perform a weighted sum with learnable
+    weights and max pooling on them and concatenate the output of the two operations,
+    which is then fed into an MLP for final prediction.
+
+    For classification tasks, the output will be logits, i.e.
+    values before sigmoid or softmax.
+
+    Parameters
+    ----------
+    in_feats : int
+        Number of input node features.
+    hidden_feats : list of int
+        ``hidden_feats[i]`` gives the size of node representations after the i-th GCN layer.
+        ``len(hidden_feats)`` equals the number of GCN layers. By default, we use
+        ``[64, 64]``.
+    activation : list of activation functions or None
+        If None, no activation will be applied. If not None, ``activation[i]`` gives the
+        activation function to be used for the i-th GCN layer. ``len(activation)`` equals
+        the number of GCN layers. By default, ReLU is applied for all GCN layers.
+    residual : list of bool
+        ``residual[i]`` decides if residual connection is to be used for the i-th GCN layer.
+        ``len(residual)`` equals the number of GCN layers. By default, residual connection
+        is performed for each GCN layer.
+    batchnorm : list of bool
+        ``batchnorm[i]`` decides if batch normalization is to be applied on the output of
+        the i-th GCN layer. ``len(batchnorm)`` equals the number of GCN layers. By default,
+        batch normalization is applied for all GCN layers.
+    dropout : list of float
+        ``dropout[i]`` decides the dropout probability on the output of the i-th GCN layer.
+        ``len(dropout)`` equals the number of GCN layers. By default, no dropout is
+        performed for all layers.
+    classifier_hidden_feats : int
+        Size of hidden graph representations in the classifier. Default to 128.
+    classifier_dropout : float
+        The probability for dropout in the classifier. Default to 0.
+    n_tasks : int
+        Number of tasks, which is also the output size. Default to 1.
+    """
+    def __init__(self, in_feats, hidden_feats=None, activation=None, residual=None, batchnorm=None,
+                 dropout=None, classifier_hidden_feats=128, classifier_dropout=0., n_tasks=1):
+        super(GCNPredictor, self).__init__()
+
+        self.gnn = GCN(in_feats=in_feats,
+                       hidden_feats=hidden_feats,
+                       activation=activation,
+                       residual=residual,
+                       batchnorm=batchnorm,
+                       dropout=dropout)
+        gnn_out_feats = self.gnn.hidden_feats[-1]
+        self.readout = WeightedSumAndMax(gnn_out_feats)
+        self.predict = MLPPredictor(2 * gnn_out_feats, classifier_hidden_feats,
+                                    n_tasks, classifier_dropout)
+
+    def forward(self, bg, feats):
+        """Graph-level regression/soft classification.
+
+        Parameters
+        ----------
+        bg : DGLGraph
+            DGLGraph for a batch of graphs.
+        feats : FloatTensor of shape (N, M1)
+            * N is the total number of nodes in the batch of graphs
+            * M1 is the input node feature size, which must match
+              in_feats in initialization
+
+        Returns
+        -------
+        FloatTensor of shape (B, n_tasks)
+            * Predictions on graphs
+            * B for the number of graphs in the batch
+        """
+        node_feats = self.gnn(bg, feats)
+        graph_feats = self.readout(bg, node_feats)
+        return self.predict(graph_feats)

apps/life_sci/dgllife/model/model_zoo/jtnn/__init__.py

+"""JTNN Module"""
+from .jtnn_vae import DGLJTNNVAE

apps/life_sci/dgllife/model/model_zoo/jtnn/chemutils.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612, W0703, C0200, R1710
+import rdkit.Chem as Chem
+
+from collections import defaultdict
+from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers
+from scipy.sparse import csr_matrix
+from scipy.sparse.csgraph import minimum_spanning_tree
+
+MST_MAX_WEIGHT = 100
+MAX_NCAND = 2000
+
+def set_atommap(mol, num=0):
+    for atom in mol.GetAtoms():
+        atom.SetAtomMapNum(num)
+
+def get_mol(smiles):
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        return None
+    Chem.Kekulize(mol)
+    return mol
+
+def get_smiles(mol):
+    return Chem.MolToSmiles(mol, kekuleSmiles=True)
+
+def decode_stereo(smiles2D):
+    mol = Chem.MolFromSmiles(smiles2D)
+    dec_isomers = list(EnumerateStereoisomers(mol))
+
+    dec_isomers = [Chem.MolFromSmiles(Chem.MolToSmiles(
+        mol, isomericSmiles=True)) for mol in dec_isomers]
+    smiles3D = [Chem.MolToSmiles(mol, isomericSmiles=True)
+                for mol in dec_isomers]
+
+    chiralN = [atom.GetIdx() for atom in dec_isomers[0].GetAtoms() if int(
+        atom.GetChiralTag()) > 0 and atom.GetSymbol() == "N"]
+    if len(chiralN) > 0:
+        for mol in dec_isomers:
+            for idx in chiralN:
+                mol.GetAtomWithIdx(idx).SetChiralTag(
+                    Chem.rdchem.ChiralType.CHI_UNSPECIFIED)
+            smiles3D.append(Chem.MolToSmiles(mol, isomericSmiles=True))
+
+    return smiles3D
+
+def sanitize(mol):
+    try:
+        smiles = get_smiles(mol)
+        mol = get_mol(smiles)
+    except Exception:
+        return None
+    return mol
+
+def copy_atom(atom):
+    new_atom = Chem.Atom(atom.GetSymbol())
+    new_atom.SetFormalCharge(atom.GetFormalCharge())
+    new_atom.SetAtomMapNum(atom.GetAtomMapNum())
+    return new_atom
+
+def copy_edit_mol(mol):
+    new_mol = Chem.RWMol(Chem.MolFromSmiles(''))
+    for atom in mol.GetAtoms():
+        new_atom = copy_atom(atom)
+        new_mol.AddAtom(new_atom)
+    for bond in mol.GetBonds():
+        a1 = bond.GetBeginAtom().GetIdx()
+        a2 = bond.GetEndAtom().GetIdx()
+        bt = bond.GetBondType()
+        new_mol.AddBond(a1, a2, bt)
+    return new_mol
+
+def get_clique_mol(mol, atoms):
+    smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)
+    new_mol = Chem.MolFromSmiles(smiles, sanitize=False)
+    new_mol = copy_edit_mol(new_mol).GetMol()
+    new_mol = sanitize(new_mol)  # We assume this is not None
+    return new_mol
+
+def tree_decomp(mol):
+    n_atoms = mol.GetNumAtoms()
+    if n_atoms == 1:
+        return [[0]], []
+
+    cliques = []
+    for bond in mol.GetBonds():
+        a1 = bond.GetBeginAtom().GetIdx()
+        a2 = bond.GetEndAtom().GetIdx()
+        if not bond.IsInRing():
+            cliques.append([a1, a2])
+
+    ssr = [list(x) for x in Chem.GetSymmSSSR(mol)]
+    cliques.extend(ssr)
+
+    nei_list = [[] for i in range(n_atoms)]
+    for i in range(len(cliques)):
+        for atom in cliques[i]:
+            nei_list[atom].append(i)
+
+    # Merge Rings with intersection > 2 atoms
+    for i in range(len(cliques)):
+        if len(cliques[i]) <= 2:
+            continue
+        for atom in cliques[i]:
+            for j in nei_list[atom]:
+                if i >= j or len(cliques[j]) <= 2:
+                    continue
+                inter = set(cliques[i]) & set(cliques[j])
+                if len(inter) > 2:
+                    cliques[i].extend(cliques[j])
+                    cliques[i] = list(set(cliques[i]))
+                    cliques[j] = []
+
+    cliques = [c for c in cliques if len(c) > 0]
+    nei_list = [[] for i in range(n_atoms)]
+    for i in range(len(cliques)):
+        for atom in cliques[i]:
+            nei_list[atom].append(i)
+
+    # Build edges and add singleton cliques
+    edges = defaultdict(int)
+    for atom in range(n_atoms):
+        if len(nei_list[atom]) <= 1:
+            continue
+        cnei = nei_list[atom]
+        bonds = [c for c in cnei if len(cliques[c]) == 2]
+        rings = [c for c in cnei if len(cliques[c]) > 4]
+        # In general, if len(cnei) >= 3, a singleton should be added, but 1
+        # bond + 2 ring is currently not dealt with.
+        if len(bonds) > 2 or (len(bonds) == 2 and len(cnei) > 2):
+            cliques.append([atom])
+            c2 = len(cliques) - 1
+            for c1 in cnei:
+                edges[(c1, c2)] = 1
+        elif len(rings) > 2:  # Multiple (n>2) complex rings
+            cliques.append([atom])
+            c2 = len(cliques) - 1
+            for c1 in cnei:
+                edges[(c1, c2)] = MST_MAX_WEIGHT - 1
+        else:
+            for i in range(len(cnei)):
+                for j in range(i + 1, len(cnei)):
+                    c1, c2 = cnei[i], cnei[j]
+                    inter = set(cliques[c1]) & set(cliques[c2])
+                    if edges[(c1, c2)] < len(inter):
+                        # cnei[i] < cnei[j] by construction
+                        edges[(c1, c2)] = len(inter)
+
+    edges = [u + (MST_MAX_WEIGHT - v,) for u, v in edges.items()]
+    if len(edges) == 0:
+        return cliques, edges
+
+    # Compute Maximum Spanning Tree
+    row, col, data = list(zip(*edges))
+    n_clique = len(cliques)
+    clique_graph = csr_matrix((data, (row, col)), shape=(n_clique, n_clique))
+    junc_tree = minimum_spanning_tree(clique_graph)
+    row, col = junc_tree.nonzero()
+    edges = [(row[i], col[i]) for i in range(len(row))]
+    return (cliques, edges)
+
+def atom_equal(a1, a2):
+    return a1.GetSymbol() == a2.GetSymbol() and a1.GetFormalCharge() == a2.GetFormalCharge()
+
+# Bond type not considered because all aromatic (so SINGLE matches DOUBLE)
+
+def ring_bond_equal(b1, b2, reverse=False):
+    b1 = (b1.GetBeginAtom(), b1.GetEndAtom())
+    if reverse:
+        b2 = (b2.GetEndAtom(), b2.GetBeginAtom())
+    else:
+        b2 = (b2.GetBeginAtom(), b2.GetEndAtom())
+    return atom_equal(b1[0], b2[0]) and atom_equal(b1[1], b2[1])
+
+def attach_mols_nx(ctr_mol, neighbors, prev_nodes, nei_amap):
+    prev_nids = [node['nid'] for node in prev_nodes]
+    for nei_node in prev_nodes + neighbors:
+        nei_id, nei_mol = nei_node['nid'], nei_node['mol']
+        amap = nei_amap[nei_id]
+        for atom in nei_mol.GetAtoms():
+            if atom.GetIdx() not in amap:
+                new_atom = copy_atom(atom)
+                amap[atom.GetIdx()] = ctr_mol.AddAtom(new_atom)
+
+        if nei_mol.GetNumBonds() == 0:
+            nei_atom = nei_mol.GetAtomWithIdx(0)
+            ctr_atom = ctr_mol.GetAtomWithIdx(amap[0])
+            ctr_atom.SetAtomMapNum(nei_atom.GetAtomMapNum())
+        else:
+            for bond in nei_mol.GetBonds():
+                a1 = amap[bond.GetBeginAtom().GetIdx()]
+                a2 = amap[bond.GetEndAtom().GetIdx()]
+                if ctr_mol.GetBondBetweenAtoms(a1, a2) is None:
+                    ctr_mol.AddBond(a1, a2, bond.GetBondType())
+                elif nei_id in prev_nids:  # father node overrides
+                    ctr_mol.RemoveBond(a1, a2)
+                    ctr_mol.AddBond(a1, a2, bond.GetBondType())
+    return ctr_mol
+
+def local_attach_nx(ctr_mol, neighbors, prev_nodes, amap_list):
+    ctr_mol = copy_edit_mol(ctr_mol)
+    nei_amap = {nei['nid']: {} for nei in prev_nodes + neighbors}
+
+    for nei_id, ctr_atom, nei_atom in amap_list:
+        nei_amap[nei_id][nei_atom] = ctr_atom
+
+    ctr_mol = attach_mols_nx(ctr_mol, neighbors, prev_nodes, nei_amap)
+    return ctr_mol.GetMol()
+
+# This version records idx mapping between ctr_mol and nei_mol
+
+def enum_attach_nx(ctr_mol, nei_node, amap, singletons):
+    nei_mol, nei_idx = nei_node['mol'], nei_node['nid']
+    att_confs = []
+    black_list = [atom_idx for nei_id, atom_idx,
+                  _ in amap if nei_id in singletons]
+    ctr_atoms = [atom for atom in ctr_mol.GetAtoms() if atom.GetIdx()
+                 not in black_list]
+    ctr_bonds = [bond for bond in ctr_mol.GetBonds()]
+
+    if nei_mol.GetNumBonds() == 0:  # neighbor singleton
+        nei_atom = nei_mol.GetAtomWithIdx(0)
+        used_list = [atom_idx for _, atom_idx, _ in amap]
+        for atom in ctr_atoms:
+            if atom_equal(atom, nei_atom) and atom.GetIdx() not in used_list:
+                new_amap = amap + [(nei_idx, atom.GetIdx(), 0)]
+                att_confs.append(new_amap)
+
+    elif nei_mol.GetNumBonds() == 1:  # neighbor is a bond
+        bond = nei_mol.GetBondWithIdx(0)
+        bond_val = int(bond.GetBondTypeAsDouble())
+        b1, b2 = bond.GetBeginAtom(), bond.GetEndAtom()
+
+        for atom in ctr_atoms:
+            # Optimize if atom is carbon (other atoms may change valence)
+            if atom.GetAtomicNum() == 6 and atom.GetTotalNumHs() < bond_val:
+                continue
+            if atom_equal(atom, b1):
+                new_amap = amap + [(nei_idx, atom.GetIdx(), b1.GetIdx())]
+                att_confs.append(new_amap)
+            elif atom_equal(atom, b2):
+                new_amap = amap + [(nei_idx, atom.GetIdx(), b2.GetIdx())]
+                att_confs.append(new_amap)
+    else:
+        # intersection is an atom
+        for a1 in ctr_atoms:
+            for a2 in nei_mol.GetAtoms():
+                if atom_equal(a1, a2):
+                    # Optimize if atom is carbon (other atoms may change
+                    # valence)
+                    if a1.GetAtomicNum() == 6 and a1.GetTotalNumHs() + a2.GetTotalNumHs() < 4:
+                        continue
+                    new_amap = amap + [(nei_idx, a1.GetIdx(), a2.GetIdx())]
+                    att_confs.append(new_amap)
+
+        # intersection is an bond
+        if ctr_mol.GetNumBonds() > 1:
+            for b1 in ctr_bonds:
+                for b2 in nei_mol.GetBonds():
+                    if ring_bond_equal(b1, b2):
+                        new_amap = amap + [(nei_idx,
+                                            b1.GetBeginAtom().GetIdx(),
+                                            b2.GetBeginAtom().GetIdx()),
+                                           (nei_idx,
+                                            b1.GetEndAtom().GetIdx(),
+                                            b2.GetEndAtom().GetIdx())]
+                        att_confs.append(new_amap)
+
+                    if ring_bond_equal(b1, b2, reverse=True):
+                        new_amap = amap + [(nei_idx,
+                                            b1.GetBeginAtom().GetIdx(),
+                                            b2.GetEndAtom().GetIdx()),
+                                           (nei_idx,
+                                            b1.GetEndAtom().GetIdx(),
+                                            b2.GetBeginAtom().GetIdx())]
+                        att_confs.append(new_amap)
+    return att_confs
+
+# Try rings first: Speed-Up
+
+def enum_assemble_nx(node, neighbors, prev_nodes=None, prev_amap=None):
+    if prev_nodes is None:
+        prev_nodes = []
+    if prev_amap is None:
+        prev_amap = []
+    all_attach_confs = []
+    singletons = [nei_node['nid'] for nei_node in neighbors +
+                  prev_nodes if nei_node['mol'].GetNumAtoms() == 1]
+
+    def search(cur_amap, depth):
+        if len(all_attach_confs) > MAX_NCAND:
+            return None
+        if depth == len(neighbors):
+            all_attach_confs.append(cur_amap)
+            return None
+
+        nei_node = neighbors[depth]
+        cand_amap = enum_attach_nx(node['mol'], nei_node, cur_amap, singletons)
+        cand_smiles = set()
+        candidates = []
+        for amap in cand_amap:
+            cand_mol = local_attach_nx(
+                node['mol'], neighbors[:depth + 1], prev_nodes, amap)
+            cand_mol = sanitize(cand_mol)
+            if cand_mol is None:
+                continue
+            smiles = get_smiles(cand_mol)
+            if smiles in cand_smiles:
+                continue
+            cand_smiles.add(smiles)
+            candidates.append(amap)
+
+        if len(candidates) == 0:
+            return []
+
+        for new_amap in candidates:
+            search(new_amap, depth + 1)
+
+    search(prev_amap, 0)
+    cand_smiles = set()
+    candidates = []
+    for amap in all_attach_confs:
+        cand_mol = local_attach_nx(node['mol'], neighbors, prev_nodes, amap)
+        cand_mol = Chem.MolFromSmiles(Chem.MolToSmiles(cand_mol))
+        smiles = Chem.MolToSmiles(cand_mol)
+        if smiles in cand_smiles:
+            continue
+        cand_smiles.add(smiles)
+        Chem.Kekulize(cand_mol)
+        candidates.append((smiles, cand_mol, amap))
+
+    return candidates
+
+# Only used for debugging purpose
+
+def dfs_assemble_nx(
+        graph,
+        cur_mol,
+        global_amap,
+        fa_amap,
+        cur_node_id,
+        fa_node_id):
+    cur_node = graph.nodes_dict[cur_node_id]
+    fa_node = graph.nodes_dict[fa_node_id] if fa_node_id is not None else None
+
+    fa_nid = fa_node['nid'] if fa_node is not None else -1
+    prev_nodes = [fa_node] if fa_node is not None else []
+
+    children_id = [nei for nei in graph[cur_node_id]
+                   if graph.nodes_dict[nei]['nid'] != fa_nid]
+    children = [graph.nodes_dict[nei] for nei in children_id]
+    neighbors = [nei for nei in children if nei['mol'].GetNumAtoms() > 1]
+    neighbors = sorted(
+        neighbors, key=lambda x: x['mol'].GetNumAtoms(), reverse=True)
+    singletons = [nei for nei in children if nei['mol'].GetNumAtoms() == 1]
+    neighbors = singletons + neighbors
+
+    cur_amap = [(fa_nid, a2, a1)
+                for nid, a1, a2 in fa_amap if nid == cur_node['nid']]
+    cands = enum_assemble_nx(
+        graph.nodes_dict[cur_node_id], neighbors, prev_nodes, cur_amap)
+    if len(cands) == 0:
+        return
+
+    cand_smiles, _, cand_amap = zip(*cands)
+    label_idx = cand_smiles.index(cur_node['label'])
+    label_amap = cand_amap[label_idx]
+
+    for nei_id, ctr_atom, nei_atom in label_amap:
+        if nei_id == fa_nid:
+            continue
+        global_amap[nei_id][nei_atom] = global_amap[cur_node['nid']][ctr_atom]
+
+    # father is already attached
+    cur_mol = attach_mols_nx(cur_mol, children, [], global_amap)
+    for nei_node_id, nei_node in zip(children_id, children):
+        if not nei_node['is_leaf']:
+            dfs_assemble_nx(graph, cur_mol, global_amap,
+                            label_amap, nei_node_id, cur_node_id)

apps/life_sci/dgllife/model/model_zoo/jtnn/jtmpn.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612, W1508
+# pylint: disable=redefined-outer-name
+import os
+import rdkit.Chem as Chem
+import torch
+import torch.nn as nn
+
+import dgl.function as DGLF
+from dgl import DGLGraph, mean_nodes
+
+from .nnutils import cuda
+
+ELEM_LIST = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na',
+             'Ca', 'Fe', 'Al', 'I', 'B', 'K', 'Se', 'Zn', 'H', 'Cu', 'Mn', 'unknown']
+
+ATOM_FDIM = len(ELEM_LIST) + 6 + 5 + 1
+BOND_FDIM = 5
+MAX_NB = 10
+
+PAPER = os.getenv('PAPER', False)
+
+def onek_encoding_unk(x, allowable_set):
+    if x not in allowable_set:
+        x = allowable_set[-1]
+    return [x == s for s in allowable_set]
+
+# Note that during graph decoding they don't predict stereochemistry-related
+# characteristics (i.e. Chiral Atoms, E-Z, Cis-Trans).  Instead, they decode
+# the 2-D graph first, then enumerate all possible 3-D forms and find the
+# one with highest score.
+
+def atom_features(atom):
+    return (torch.Tensor(onek_encoding_unk(atom.GetSymbol(), ELEM_LIST)
+                         + onek_encoding_unk(atom.GetDegree(),
+                                             [0, 1, 2, 3, 4, 5])
+                         + onek_encoding_unk(atom.GetFormalCharge(),
+                                             [-1, -2, 1, 2, 0])
+                         + [atom.GetIsAromatic()]))
+
+def bond_features(bond):
+    bt = bond.GetBondType()
+    return torch.Tensor([bt == Chem.rdchem.BondType.SINGLE,
+                         bt == Chem.rdchem.BondType.DOUBLE,
+                         bt == Chem.rdchem.BondType.TRIPLE,
+                         bt == Chem.rdchem.BondType.AROMATIC,
+                         bond.IsInRing()])
+
+def mol2dgl_single(cand_batch):
+    cand_graphs = []
+    tree_mess_source_edges = []  # map these edges from trees to...
+    tree_mess_target_edges = []  # these edges on candidate graphs
+    tree_mess_target_nodes = []
+    n_nodes = 0
+    atom_x = []
+    bond_x = []
+
+    for mol, mol_tree, ctr_node_id in cand_batch:
+        n_atoms = mol.GetNumAtoms()
+
+        g = DGLGraph()
+
+        for i, atom in enumerate(mol.GetAtoms()):
+            assert i == atom.GetIdx()
+            atom_x.append(atom_features(atom))
+        g.add_nodes(n_atoms)
+
+        bond_src = []
+        bond_dst = []
+        for i, bond in enumerate(mol.GetBonds()):
+            a1 = bond.GetBeginAtom()
+            a2 = bond.GetEndAtom()
+            begin_idx = a1.GetIdx()
+            end_idx = a2.GetIdx()
+            features = bond_features(bond)
+
+            bond_src.append(begin_idx)
+            bond_dst.append(end_idx)
+            bond_x.append(features)
+            bond_src.append(end_idx)
+            bond_dst.append(begin_idx)
+            bond_x.append(features)
+
+            x_nid, y_nid = a1.GetAtomMapNum(), a2.GetAtomMapNum()
+            # Tree node ID in the batch
+            x_bid = mol_tree.nodes_dict[x_nid - 1]['idx'] if x_nid > 0 else -1
+            y_bid = mol_tree.nodes_dict[y_nid - 1]['idx'] if y_nid > 0 else -1
+            if x_bid >= 0 and y_bid >= 0 and x_bid != y_bid:
+                if mol_tree.has_edge_between(x_bid, y_bid):
+                    tree_mess_target_edges.append(
+                        (begin_idx + n_nodes, end_idx + n_nodes))
+                    tree_mess_source_edges.append((x_bid, y_bid))
+                    tree_mess_target_nodes.append(end_idx + n_nodes)
+                if mol_tree.has_edge_between(y_bid, x_bid):
+                    tree_mess_target_edges.append(
+                        (end_idx + n_nodes, begin_idx + n_nodes))
+                    tree_mess_source_edges.append((y_bid, x_bid))
+                    tree_mess_target_nodes.append(begin_idx + n_nodes)
+
+        n_nodes += n_atoms
+        g.add_edges(bond_src, bond_dst)
+        cand_graphs.append(g)
+
+    return cand_graphs, torch.stack(atom_x), \
+        torch.stack(bond_x) if len(bond_x) > 0 else torch.zeros(0), \
+        torch.LongTensor(tree_mess_source_edges), \
+        torch.LongTensor(tree_mess_target_edges), \
+        torch.LongTensor(tree_mess_target_nodes)
+
+mpn_loopy_bp_msg = DGLF.copy_src(src='msg', out='msg')
+mpn_loopy_bp_reduce = DGLF.sum(msg='msg', out='accum_msg')
+
+class LoopyBPUpdate(nn.Module):
+    def __init__(self, hidden_size):
+        super(LoopyBPUpdate, self).__init__()
+        self.hidden_size = hidden_size
+
+        self.W_h = nn.Linear(hidden_size, hidden_size, bias=False)
+
+    def forward(self, node):
+        msg_input = node.data['msg_input']
+        msg_delta = self.W_h(node.data['accum_msg'] + node.data['alpha'])
+        msg = torch.relu(msg_input + msg_delta)
+        return {'msg': msg}
+
+if PAPER:
+    mpn_gather_msg = [
+        DGLF.copy_edge(edge='msg', out='msg'),
+        DGLF.copy_edge(edge='alpha', out='alpha')
+    ]
+else:
+    mpn_gather_msg = DGLF.copy_edge(edge='msg', out='msg')
+
+if PAPER:
+    mpn_gather_reduce = [
+        DGLF.sum(msg='msg', out='m'),
+        DGLF.sum(msg='alpha', out='accum_alpha'),
+    ]
+else:
+    mpn_gather_reduce = DGLF.sum(msg='msg', out='m')
+
+class GatherUpdate(nn.Module):
+    def __init__(self, hidden_size):
+        super(GatherUpdate, self).__init__()
+        self.hidden_size = hidden_size
+
+        self.W_o = nn.Linear(ATOM_FDIM + hidden_size, hidden_size)
+
+    def forward(self, node):
+        if PAPER:
+            #m = node['m']
+            m = node.data['m'] + node.data['accum_alpha']
+        else:
+            m = node.data['m'] + node.data['alpha']
+        return {
+            'h': torch.relu(self.W_o(torch.cat([node.data['x'], m], 1))),
+        }
+
+class DGLJTMPN(nn.Module):
+    def __init__(self, hidden_size, depth):
+        nn.Module.__init__(self)
+
+        self.depth = depth
+
+        self.W_i = nn.Linear(ATOM_FDIM + BOND_FDIM, hidden_size, bias=False)
+
+        self.loopy_bp_updater = LoopyBPUpdate(hidden_size)
+        self.gather_updater = GatherUpdate(hidden_size)
+        self.hidden_size = hidden_size
+
+        self.n_samples_total = 0
+        self.n_nodes_total = 0
+        self.n_edges_total = 0
+        self.n_passes = 0
+
+    def forward(self, cand_batch, mol_tree_batch):
+        cand_graphs, tree_mess_src_edges, tree_mess_tgt_edges, tree_mess_tgt_nodes = cand_batch
+
+        n_samples = len(cand_graphs)
+
+        cand_line_graph = cand_graphs.line_graph(
+            backtracking=False, shared=True)
+
+        n_nodes = cand_graphs.number_of_nodes()
+        n_edges = cand_graphs.number_of_edges()
+
+        cand_graphs = self.run(
+            cand_graphs, cand_line_graph, tree_mess_src_edges, tree_mess_tgt_edges,
+            tree_mess_tgt_nodes, mol_tree_batch)
+
+        g_repr = mean_nodes(cand_graphs, 'h')
+
+        self.n_samples_total += n_samples
+        self.n_nodes_total += n_nodes
+        self.n_edges_total += n_edges
+        self.n_passes += 1
+
+        return g_repr
+
+    def run(self, cand_graphs, cand_line_graph, tree_mess_src_edges, tree_mess_tgt_edges,
+            tree_mess_tgt_nodes, mol_tree_batch):
+        n_nodes = cand_graphs.number_of_nodes()
+
+        cand_graphs.apply_edges(
+            func=lambda edges: {'src_x': edges.src['x']},
+        )
+
+        bond_features = cand_line_graph.ndata['x']
+        source_features = cand_line_graph.ndata['src_x']
+        features = torch.cat([source_features, bond_features], 1)
+        msg_input = self.W_i(features)
+        cand_line_graph.ndata.update({
+            'msg_input': msg_input,
+            'msg': torch.relu(msg_input),
+            'accum_msg': torch.zeros_like(msg_input),
+        })
+        zero_node_state = bond_features.new(n_nodes, self.hidden_size).zero_()
+        cand_graphs.ndata.update({
+            'm': zero_node_state.clone(),
+            'h': zero_node_state.clone(),
+        })
+
+        cand_graphs.edata['alpha'] = \
+            cuda(torch.zeros(cand_graphs.number_of_edges(), self.hidden_size))
+        cand_graphs.ndata['alpha'] = zero_node_state
+        if tree_mess_src_edges.shape[0] > 0:
+            if PAPER:
+                src_u, src_v = tree_mess_src_edges.unbind(1)
+                tgt_u, tgt_v = tree_mess_tgt_edges.unbind(1)
+                alpha = mol_tree_batch.edges[src_u, src_v].data['m']
+                cand_graphs.edges[tgt_u, tgt_v].data['alpha'] = alpha
+            else:
+                src_u, src_v = tree_mess_src_edges.unbind(1)
+                alpha = mol_tree_batch.edges[src_u, src_v].data['m']
+                node_idx = (tree_mess_tgt_nodes
+                            .to(device=zero_node_state.device)[:, None]
+                            .expand_as(alpha))
+                node_alpha = zero_node_state.clone().scatter_add(0, node_idx, alpha)
+                cand_graphs.ndata['alpha'] = node_alpha
+                cand_graphs.apply_edges(
+                    func=lambda edges: {'alpha': edges.src['alpha']},
+                )
+
+        for i in range(self.depth - 1):
+            cand_line_graph.update_all(
+                mpn_loopy_bp_msg,
+                mpn_loopy_bp_reduce,
+                self.loopy_bp_updater,
+            )
+
+        cand_graphs.update_all(
+            mpn_gather_msg,
+            mpn_gather_reduce,
+            self.gather_updater,
+        )
+
+        return cand_graphs

apps/life_sci/dgllife/model/model_zoo/jtnn/jtnn_dec.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612
+import numpy as np
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+import dgl.function as DGLF
+from dgl import batch, dfs_labeled_edges_generator
+
+from .chemutils import enum_assemble_nx, get_mol
+from .mol_tree_nx import DGLMolTree
+from .nnutils import GRUUpdate, cuda
+
+MAX_NB = 8
+MAX_DECODE_LEN = 100
+
+def dfs_order(forest, roots):
+    edges = dfs_labeled_edges_generator(forest, roots, has_reverse_edge=True)
+    for e, l in zip(*edges):
+        # I exploited the fact that the reverse edge ID equal to 1 xor forward
+        # edge ID for molecule trees.  Normally, I should locate reverse edges
+        # using find_edges().
+        yield e ^ l, l
+
+dec_tree_node_msg = DGLF.copy_edge(edge='m', out='m')
+dec_tree_node_reduce = DGLF.sum(msg='m', out='h')
+
+def dec_tree_node_update(nodes):
+    return {'new': nodes.data['new'].clone().zero_()}
+
+dec_tree_edge_msg = [DGLF.copy_src(
+    src='m', out='m'), DGLF.copy_src(src='rm', out='rm')]
+dec_tree_edge_reduce = [
+    DGLF.sum(msg='m', out='s'), DGLF.sum(msg='rm', out='accum_rm')]
+
+def have_slots(fa_slots, ch_slots):
+    if len(fa_slots) > 2 and len(ch_slots) > 2:
+        return True
+    matches = []
+    for i, s1 in enumerate(fa_slots):
+        a1, c1, h1 = s1
+        for j, s2 in enumerate(ch_slots):
+            a2, c2, h2 = s2
+            if a1 == a2 and c1 == c2 and (a1 != "C" or h1 + h2 >= 4):
+                matches.append((i, j))
+
+    if len(matches) == 0:
+        return False
+
+    fa_match, ch_match = list(zip(*matches))
+    if len(set(fa_match)) == 1 and 1 < len(fa_slots) <= 2:  # never remove atom from ring
+        fa_slots.pop(fa_match[0])
+    if len(set(ch_match)) == 1 and 1 < len(ch_slots) <= 2:  # never remove atom from ring
+        ch_slots.pop(ch_match[0])
+
+    return True
+
+def can_assemble(mol_tree, u, v_node_dict):
+    u_node_dict = mol_tree.nodes_dict[u]
+    u_neighbors = mol_tree.successors(u)
+    u_neighbors_node_dict = [
+        mol_tree.nodes_dict[_u]
+        for _u in u_neighbors
+        if _u in mol_tree.nodes_dict
+    ]
+    neis = u_neighbors_node_dict + [v_node_dict]
+    for i, nei in enumerate(neis):
+        nei['nid'] = i
+
+    neighbors = [nei for nei in neis if nei['mol'].GetNumAtoms() > 1]
+    neighbors = sorted(
+        neighbors, key=lambda x: x['mol'].GetNumAtoms(), reverse=True)
+    singletons = [nei for nei in neis if nei['mol'].GetNumAtoms() == 1]
+    neighbors = singletons + neighbors
+    cands = enum_assemble_nx(u_node_dict, neighbors)
+    return len(cands) > 0
+
+def create_node_dict(smiles, clique=None):
+    if clique is None:
+        clique = []
+    return dict(
+        smiles=smiles,
+        mol=get_mol(smiles),
+        clique=clique,
+    )
+
+class DGLJTNNDecoder(nn.Module):
+    def __init__(self, vocab, hidden_size, latent_size, embedding=None):
+        nn.Module.__init__(self)
+
+        self.hidden_size = hidden_size
+        self.vocab_size = vocab.size()
+        self.vocab = vocab
+
+        if embedding is None:
+            self.embedding = nn.Embedding(self.vocab_size, hidden_size)
+        else:
+            self.embedding = embedding
+
+        self.dec_tree_edge_update = GRUUpdate(hidden_size)
+
+        self.W = nn.Linear(latent_size + hidden_size, hidden_size)
+        self.U = nn.Linear(latent_size + 2 * hidden_size, hidden_size)
+        self.W_o = nn.Linear(hidden_size, self.vocab_size)
+        self.U_s = nn.Linear(hidden_size, 1)
+
+    def forward(self, mol_trees, tree_vec):
+        '''
+        The training procedure which computes the prediction loss given the
+        ground truth tree
+        '''
+        mol_tree_batch = batch(mol_trees)
+        mol_tree_batch_lg = mol_tree_batch.line_graph(
+            backtracking=False, shared=True)
+        n_trees = len(mol_trees)
+
+        return self.run(mol_tree_batch, mol_tree_batch_lg, n_trees, tree_vec)
+
+    def run(self, mol_tree_batch, mol_tree_batch_lg, n_trees, tree_vec):
+        node_offset = np.cumsum([0] + mol_tree_batch.batch_num_nodes)
+        root_ids = node_offset[:-1]
+        n_nodes = mol_tree_batch.number_of_nodes()
+        n_edges = mol_tree_batch.number_of_edges()
+
+        mol_tree_batch.ndata.update({
+            'x': self.embedding(mol_tree_batch.ndata['wid']),
+            'h': cuda(torch.zeros(n_nodes, self.hidden_size)),
+            # whether it's newly generated node
+            'new': cuda(torch.ones(n_nodes).bool()),
+        })
+
+        mol_tree_batch.edata.update({
+            's': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'm': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'r': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'z': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'src_x': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'dst_x': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'rm': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'accum_rm': cuda(torch.zeros(n_edges, self.hidden_size)),
+        })
+
+        mol_tree_batch.apply_edges(
+            func=lambda edges: {
+                'src_x': edges.src['x'], 'dst_x': edges.dst['x']},
+        )
+
+        # input tensors for stop prediction (p) and label prediction (q)
+        p_inputs = []
+        p_targets = []
+        q_inputs = []
+        q_targets = []
+
+        # Predict root
+        mol_tree_batch.pull(
+            root_ids,
+            dec_tree_node_msg,
+            dec_tree_node_reduce,
+            dec_tree_node_update,
+        )
+        # Extract hidden states and store them for stop/label prediction
+        h = mol_tree_batch.nodes[root_ids].data['h']
+        x = mol_tree_batch.nodes[root_ids].data['x']
+        p_inputs.append(torch.cat([x, h, tree_vec], 1))
+        # If the out degree is 0 we don't generate any edges at all
+        root_out_degrees = mol_tree_batch.out_degrees(root_ids)
+        q_inputs.append(torch.cat([h, tree_vec], 1))
+        q_targets.append(mol_tree_batch.nodes[root_ids].data['wid'])
+
+        # Traverse the tree and predict on children
+        for eid, p in dfs_order(mol_tree_batch, root_ids):
+            u, v = mol_tree_batch.find_edges(eid)
+
+            p_target_list = torch.zeros_like(root_out_degrees)
+            p_target_list[root_out_degrees > 0] = 1 - p
+            p_target_list = p_target_list[root_out_degrees >= 0]
+            p_targets.append(p_target_list.clone().detach())
+
+            root_out_degrees -= (root_out_degrees == 0).long()
+            root_out_degrees -= torch.tensor(np.isin(root_ids,
+                                                     v).astype('int64'))
+
+            mol_tree_batch_lg.pull(
+                eid,
+                dec_tree_edge_msg,
+                dec_tree_edge_reduce,
+                self.dec_tree_edge_update,
+            )
+            is_new = mol_tree_batch.nodes[v].data['new']
+            mol_tree_batch.pull(
+                v,
+                dec_tree_node_msg,
+                dec_tree_node_reduce,
+                dec_tree_node_update,
+            )
+            # Extract
+            n_repr = mol_tree_batch.nodes[v].data
+            h = n_repr['h']
+            x = n_repr['x']
+            tree_vec_set = tree_vec[root_out_degrees >= 0]
+            wid = n_repr['wid']
+            p_inputs.append(torch.cat([x, h, tree_vec_set], 1))
+            # Only newly generated nodes are needed for label prediction
+            # NOTE: The following works since the uncomputed messages are zeros.
+
+            q_input = torch.cat([h, tree_vec_set], 1)[is_new]
+            q_target = wid[is_new]
+            if q_input.shape[0] > 0:
+                q_inputs.append(q_input)
+                q_targets.append(q_target)
+        p_targets.append(torch.zeros((root_out_degrees == 0).sum()).long())
+
+        # Batch compute the stop/label prediction losses
+        p_inputs = torch.cat(p_inputs, 0)
+        p_targets = cuda(torch.cat(p_targets, 0))
+        q_inputs = torch.cat(q_inputs, 0)
+        q_targets = torch.cat(q_targets, 0)
+
+        q = self.W_o(torch.relu(self.W(q_inputs)))
+        p = self.U_s(torch.relu(self.U(p_inputs)))[:, 0]
+
+        p_loss = F.binary_cross_entropy_with_logits(
+            p, p_targets.float(), reduction='sum'
+        ) / n_trees
+        q_loss = F.cross_entropy(q, q_targets, reduction='sum') / n_trees
+        p_acc = ((p > 0).long() == p_targets).sum().float() / \
+            p_targets.shape[0]
+        q_acc = (q.max(1)[1] == q_targets).float().sum() / q_targets.shape[0]
+
+        self.q_inputs = q_inputs
+        self.q_targets = q_targets
+        self.q = q
+        self.p_inputs = p_inputs
+        self.p_targets = p_targets
+        self.p = p
+
+        return q_loss, p_loss, q_acc, p_acc
+
+    def decode(self, mol_vec):
+        assert mol_vec.shape[0] == 1
+
+        mol_tree = DGLMolTree(None)
+
+        init_hidden = cuda(torch.zeros(1, self.hidden_size))
+
+        root_hidden = torch.cat([init_hidden, mol_vec], 1)
+        root_hidden = F.relu(self.W(root_hidden))
+        root_score = self.W_o(root_hidden)
+        _, root_wid = torch.max(root_score, 1)
+        root_wid = root_wid.view(1)
+
+        mol_tree.add_nodes(1)   # root
+        mol_tree.nodes[0].data['wid'] = root_wid
+        mol_tree.nodes[0].data['x'] = self.embedding(root_wid)
+        mol_tree.nodes[0].data['h'] = init_hidden
+        mol_tree.nodes[0].data['fail'] = cuda(torch.tensor([0]))
+        mol_tree.nodes_dict[0] = root_node_dict = create_node_dict(
+            self.vocab.get_smiles(root_wid))
+
+        stack, trace = [], []
+        stack.append((0, self.vocab.get_slots(root_wid)))
+
+        all_nodes = {0: root_node_dict}
+        first = True
+        new_node_id = 0
+        new_edge_id = 0
+
+        for step in range(MAX_DECODE_LEN):
+            u, u_slots = stack[-1]
+            udata = mol_tree.nodes[u].data
+            x = udata['x']
+            h = udata['h']
+
+            # Predict stop
+            p_input = torch.cat([x, h, mol_vec], 1)
+            p_score = torch.sigmoid(self.U_s(torch.relu(self.U(p_input))))
+            backtrack = (p_score.item() < 0.5)
+
+            if not backtrack:
+                # Predict next clique.  Note that the prediction may fail due
+                # to lack of assemblable components
+                mol_tree.add_nodes(1)
+                new_node_id += 1
+                v = new_node_id
+                mol_tree.add_edges(u, v)
+                uv = new_edge_id
+                new_edge_id += 1
+
+                if first:
+                    mol_tree.edata.update({
+                        's': cuda(torch.zeros(1, self.hidden_size)),
+                        'm': cuda(torch.zeros(1, self.hidden_size)),
+                        'r': cuda(torch.zeros(1, self.hidden_size)),
+                        'z': cuda(torch.zeros(1, self.hidden_size)),
+                        'src_x': cuda(torch.zeros(1, self.hidden_size)),
+                        'dst_x': cuda(torch.zeros(1, self.hidden_size)),
+                        'rm': cuda(torch.zeros(1, self.hidden_size)),
+                        'accum_rm': cuda(torch.zeros(1, self.hidden_size)),
+                    })
+                    first = False
+
+                mol_tree.edges[uv].data['src_x'] = mol_tree.nodes[u].data['x']
+                # keeping dst_x 0 is fine as h on new edge doesn't depend on that.
+
+                # DGL doesn't dynamically maintain a line graph.
+                mol_tree_lg = mol_tree.line_graph(
+                    backtracking=False, shared=True)
+
+                mol_tree_lg.pull(
+                    uv,
+                    dec_tree_edge_msg,
+                    dec_tree_edge_reduce,
+                    self.dec_tree_edge_update.update_zm,
+                )
+                mol_tree.pull(
+                    v,
+                    dec_tree_node_msg,
+                    dec_tree_node_reduce,
+                )
+
+                vdata = mol_tree.nodes[v].data
+                h_v = vdata['h']
+                q_input = torch.cat([h_v, mol_vec], 1)
+                q_score = torch.softmax(
+                    self.W_o(torch.relu(self.W(q_input))), -1)
+                _, sort_wid = torch.sort(q_score, 1, descending=True)
+                sort_wid = sort_wid.squeeze()
+
+                next_wid = None
+                for wid in sort_wid.tolist()[:5]:
+                    slots = self.vocab.get_slots(wid)
+                    cand_node_dict = create_node_dict(
+                        self.vocab.get_smiles(wid))
+                    if (have_slots(u_slots, slots) and can_assemble(mol_tree, u, cand_node_dict)):
+                        next_wid = wid
+                        next_slots = slots
+                        next_node_dict = cand_node_dict
+                        break
+
+                if next_wid is None:
+                    # Failed adding an actual children; v is a spurious node
+                    # and we mark it.
+                    vdata['fail'] = cuda(torch.tensor([1]))
+                    backtrack = True
+                else:
+                    next_wid = cuda(torch.tensor([next_wid]))
+                    vdata['wid'] = next_wid
+                    vdata['x'] = self.embedding(next_wid)
+                    mol_tree.nodes_dict[v] = next_node_dict
+                    all_nodes[v] = next_node_dict
+                    stack.append((v, next_slots))
+                    mol_tree.add_edge(v, u)
+                    vu = new_edge_id
+                    new_edge_id += 1
+                    mol_tree.edges[uv].data['dst_x'] = mol_tree.nodes[v].data['x']
+                    mol_tree.edges[vu].data['src_x'] = mol_tree.nodes[v].data['x']
+                    mol_tree.edges[vu].data['dst_x'] = mol_tree.nodes[u].data['x']
+
+                    # DGL doesn't dynamically maintain a line graph.
+                    mol_tree_lg = mol_tree.line_graph(
+                        backtracking=False, shared=True)
+                    mol_tree_lg.apply_nodes(
+                        self.dec_tree_edge_update.update_r,
+                        uv
+                    )
+
+            if backtrack:
+                if len(stack) == 1:
+                    break   # At root, terminate
+
+                pu, _ = stack[-2]
+                u_pu = mol_tree.edge_id(u, pu)
+
+                mol_tree_lg.pull(
+                    u_pu,
+                    dec_tree_edge_msg,
+                    dec_tree_edge_reduce,
+                    self.dec_tree_edge_update,
+                )
+                mol_tree.pull(
+                    pu,
+                    dec_tree_node_msg,
+                    dec_tree_node_reduce,
+                )
+                stack.pop()
+
+        effective_nodes = mol_tree.filter_nodes(
+            lambda nodes: nodes.data['fail'] != 1)
+        effective_nodes, _ = torch.sort(effective_nodes)
+        return mol_tree, all_nodes, effective_nodes

apps/life_sci/dgllife/model/model_zoo/jtnn/jtnn_enc.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612
+import numpy as np
+import torch
+import torch.nn as nn
+
+import dgl.function as DGLF
+from dgl import batch, bfs_edges_generator
+
+from .nnutils import GRUUpdate, cuda
+
+MAX_NB = 8
+
+def level_order(forest, roots):
+    edges = bfs_edges_generator(forest, roots)
+    _, leaves = forest.find_edges(edges[-1])
+    edges_back = bfs_edges_generator(forest, roots, reverse=True)
+    yield from reversed(edges_back)
+    yield from edges
+
+enc_tree_msg = [DGLF.copy_src(src='m', out='m'),
+                DGLF.copy_src(src='rm', out='rm')]
+enc_tree_reduce = [DGLF.sum(msg='m', out='s'),
+                   DGLF.sum(msg='rm', out='accum_rm')]
+enc_tree_gather_msg = DGLF.copy_edge(edge='m', out='m')
+enc_tree_gather_reduce = DGLF.sum(msg='m', out='m')
+
+class EncoderGatherUpdate(nn.Module):
+    def __init__(self, hidden_size):
+        nn.Module.__init__(self)
+        self.hidden_size = hidden_size
+
+        self.W = nn.Linear(2 * hidden_size, hidden_size)
+
+    def forward(self, nodes):
+        x = nodes.data['x']
+        m = nodes.data['m']
+        return {
+            'h': torch.relu(self.W(torch.cat([x, m], 1))),
+        }
+
+class DGLJTNNEncoder(nn.Module):
+    def __init__(self, vocab, hidden_size, embedding=None):
+        nn.Module.__init__(self)
+        self.hidden_size = hidden_size
+        self.vocab_size = vocab.size()
+        self.vocab = vocab
+
+        if embedding is None:
+            self.embedding = nn.Embedding(self.vocab_size, hidden_size)
+        else:
+            self.embedding = embedding
+
+        self.enc_tree_update = GRUUpdate(hidden_size)
+        self.enc_tree_gather_update = EncoderGatherUpdate(hidden_size)
+
+    def forward(self, mol_trees):
+        mol_tree_batch = batch(mol_trees)
+
+        # Build line graph to prepare for belief propagation
+        mol_tree_batch_lg = mol_tree_batch.line_graph(
+            backtracking=False, shared=True)
+
+        return self.run(mol_tree_batch, mol_tree_batch_lg)
+
+    def run(self, mol_tree_batch, mol_tree_batch_lg):
+        # Since tree roots are designated to 0.  In the batched graph we can
+        # simply find the corresponding node ID by looking at node_offset
+        node_offset = np.cumsum([0] + mol_tree_batch.batch_num_nodes)
+        root_ids = node_offset[:-1]
+        n_nodes = mol_tree_batch.number_of_nodes()
+        n_edges = mol_tree_batch.number_of_edges()
+
+        # Assign structure embeddings to tree nodes
+        mol_tree_batch.ndata.update({
+            'x': self.embedding(mol_tree_batch.ndata['wid']),
+            'h': cuda(torch.zeros(n_nodes, self.hidden_size)),
+        })
+
+        # Initialize the intermediate variables according to Eq (4)-(8).
+        # Also initialize the src_x and dst_x fields.
+        # TODO: context?
+        mol_tree_batch.edata.update({
+            's': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'm': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'r': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'z': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'src_x': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'dst_x': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'rm': cuda(torch.zeros(n_edges, self.hidden_size)),
+            'accum_rm': cuda(torch.zeros(n_edges, self.hidden_size)),
+        })
+
+        # Send the source/destination node features to edges
+        mol_tree_batch.apply_edges(
+            func=lambda edges: {
+                'src_x': edges.src['x'], 'dst_x': edges.dst['x']},
+        )
+
+        # Message passing
+        # I exploited the fact that the reduce function is a sum of incoming
+        # messages, and the uncomputed messages are zero vectors.  Essentially,
+        # we can always compute s_ij as the sum of incoming m_ij, no matter
+        # if m_ij is actually computed or not.
+        for eid in level_order(mol_tree_batch, root_ids):
+            #eid = mol_tree_batch.edge_ids(u, v)
+            mol_tree_batch_lg.pull(
+                eid,
+                enc_tree_msg,
+                enc_tree_reduce,
+                self.enc_tree_update,
+            )
+
+        # Readout
+        mol_tree_batch.update_all(
+            enc_tree_gather_msg,
+            enc_tree_gather_reduce,
+            self.enc_tree_gather_update,
+        )
+
+        root_vecs = mol_tree_batch.nodes[root_ids].data['h']
+
+        return mol_tree_batch, root_vecs

apps/life_sci/dgllife/model/model_zoo/jtnn/mol_tree.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612
+import copy
+import rdkit.Chem as Chem
+
+def get_slots(smiles):
+    mol = Chem.MolFromSmiles(smiles)
+    return [(atom.GetSymbol(), atom.GetFormalCharge(), atom.GetTotalNumHs())
+            for atom in mol.GetAtoms()]
+
+class Vocab(object):
+    def __init__(self, smiles_list):
+        self.vocab = smiles_list
+        self.vmap = {x: i for i, x in enumerate(self.vocab)}
+        self.slots = [get_slots(smiles) for smiles in self.vocab]
+
+    def get_index(self, smiles):
+        return self.vmap[smiles]
+
+    def get_smiles(self, idx):
+        return self.vocab[idx]
+
+    def get_slots(self, idx):
+        return copy.deepcopy(self.slots[idx])
+
+    def size(self):
+        return len(self.vocab)

apps/life_sci/dgllife/model/model_zoo/jtnn/mol_tree_nx.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612
+import numpy as np
+import rdkit.Chem as Chem
+from dgl import DGLGraph
+
+from .chemutils import (decode_stereo, enum_assemble_nx, get_clique_mol,
+                        get_mol, get_smiles, set_atommap, tree_decomp)
+
+class DGLMolTree(DGLGraph):
+    def __init__(self, smiles):
+        DGLGraph.__init__(self)
+        self.nodes_dict = {}
+
+        if smiles is None:
+            return
+
+        self.smiles = smiles
+        self.mol = get_mol(smiles)
+
+        # Stereo Generation
+        mol = Chem.MolFromSmiles(smiles)
+        self.smiles3D = Chem.MolToSmiles(mol, isomericSmiles=True)
+        self.smiles2D = Chem.MolToSmiles(mol)
+        self.stereo_cands = decode_stereo(self.smiles2D)
+
+        # cliques: a list of list of atom indices
+        cliques, edges = tree_decomp(self.mol)
+        root = 0
+        for i, c in enumerate(cliques):
+            cmol = get_clique_mol(self.mol, c)
+            csmiles = get_smiles(cmol)
+            self.nodes_dict[i] = dict(
+                smiles=csmiles,
+                mol=get_mol(csmiles),
+                clique=c,
+            )
+            if min(c) == 0:
+                root = i
+        self.add_nodes(len(cliques))
+
+        # The clique with atom ID 0 becomes root
+        if root > 0:
+            for attr in self.nodes_dict[0]:
+                self.nodes_dict[0][attr], self.nodes_dict[root][attr] = \
+                    self.nodes_dict[root][attr], self.nodes_dict[0][attr]
+
+        src = np.zeros((len(edges) * 2,), dtype='int')
+        dst = np.zeros((len(edges) * 2,), dtype='int')
+        for i, (_x, _y) in enumerate(edges):
+            x = 0 if _x == root else root if _x == 0 else _x
+            y = 0 if _y == root else root if _y == 0 else _y
+            src[2 * i] = x
+            dst[2 * i] = y
+            src[2 * i + 1] = y
+            dst[2 * i + 1] = x
+        self.add_edges(src, dst)
+
+        for i in self.nodes_dict:
+            self.nodes_dict[i]['nid'] = i + 1
+            if self.out_degree(i) > 1:    # Leaf node mol is not marked
+                set_atommap(self.nodes_dict[i]['mol'],
+                            self.nodes_dict[i]['nid'])
+            self.nodes_dict[i]['is_leaf'] = (self.out_degree(i) == 1)
+
+    def treesize(self):
+        return self.number_of_nodes()
+
+    def _recover_node(self, i, original_mol):
+        node = self.nodes_dict[i]
+
+        clique = []
+        clique.extend(node['clique'])
+        if not node['is_leaf']:
+            for cidx in node['clique']:
+                original_mol.GetAtomWithIdx(cidx).SetAtomMapNum(node['nid'])
+
+        for j in self.successors(i).numpy():
+            nei_node = self.nodes_dict[j]
+            clique.extend(nei_node['clique'])
+            if nei_node['is_leaf']:  # Leaf node, no need to mark
+                continue
+            for cidx in nei_node['clique']:
+                # allow singleton node override the atom mapping
+                if cidx not in node['clique'] or len(nei_node['clique']) == 1:
+                    atom = original_mol.GetAtomWithIdx(cidx)
+                    atom.SetAtomMapNum(nei_node['nid'])
+
+        clique = list(set(clique))
+        label_mol = get_clique_mol(original_mol, clique)
+        node['label'] = Chem.MolToSmiles(
+            Chem.MolFromSmiles(get_smiles(label_mol)))
+        node['label_mol'] = get_mol(node['label'])
+
+        for cidx in clique:
+            original_mol.GetAtomWithIdx(cidx).SetAtomMapNum(0)
+
+        return node['label']
+
+    def _assemble_node(self, i):
+        neighbors = [self.nodes_dict[j] for j in self.successors(i).numpy()
+                     if self.nodes_dict[j]['mol'].GetNumAtoms() > 1]
+        neighbors = sorted(
+            neighbors, key=lambda x: x['mol'].GetNumAtoms(), reverse=True)
+        singletons = [self.nodes_dict[j] for j in self.successors(i).numpy()
+                      if self.nodes_dict[j]['mol'].GetNumAtoms() == 1]
+        neighbors = singletons + neighbors
+
+        cands = enum_assemble_nx(self.nodes_dict[i], neighbors)
+
+        if len(cands) > 0:
+            self.nodes_dict[i]['cands'], self.nodes_dict[i]['cand_mols'], _ = list(
+                zip(*cands))
+            self.nodes_dict[i]['cands'] = list(self.nodes_dict[i]['cands'])
+            self.nodes_dict[i]['cand_mols'] = list(
+                self.nodes_dict[i]['cand_mols'])
+        else:
+            self.nodes_dict[i]['cands'] = []
+            self.nodes_dict[i]['cand_mols'] = []
+
+    def recover(self):
+        for i in self.nodes_dict:
+            self._recover_node(i, self.mol)
+
+    def assemble(self):
+        for i in self.nodes_dict:
+            self._assemble_node(i)

apps/life_sci/dgllife/model/model_zoo/jtnn/nnutils.py

+# pylint: disable=C0111, C0103, E1101, W0611, W0612
+import os
+import torch
+import torch.nn as nn
+
+from torch.autograd import Variable
+
+def create_var(tensor, requires_grad=None):
+    if requires_grad is None:
+        return Variable(tensor)
+    else:
+        return Variable(tensor, requires_grad=requires_grad)
+
+def cuda(tensor):
+    if torch.cuda.is_available() and not os.getenv('NOCUDA', None):
+        return tensor.cuda()
+    else:
+        return tensor
+
+class GRUUpdate(nn.Module):
+    def __init__(self, hidden_size):
+        nn.Module.__init__(self)
+        self.hidden_size = hidden_size
+
+        self.W_z = nn.Linear(2 * hidden_size, hidden_size)
+        self.W_r = nn.Linear(hidden_size, hidden_size, bias=False)
+        self.U_r = nn.Linear(hidden_size, hidden_size)
+        self.W_h = nn.Linear(2 * hidden_size, hidden_size)
+
+    def update_zm(self, node):
+        src_x = node.data['src_x']
+        s = node.data['s']
+        rm = node.data['accum_rm']
+        z = torch.sigmoid(self.W_z(torch.cat([src_x, s], 1)))
+        m = torch.tanh(self.W_h(torch.cat([src_x, rm], 1)))
+        m = (1 - z) * s + z * m
+        return {'m': m, 'z': z}
+
+    def update_r(self, node, zm=None):
+        dst_x = node.data['dst_x']
+        m = node.data['m'] if zm is None else zm['m']
+        r_1 = self.W_r(dst_x)
+        r_2 = self.U_r(m)
+        r = torch.sigmoid(r_1 + r_2)
+        return {'r': r, 'rm': r * m}
+
+    def forward(self, node):
+        dic = self.update_zm(node)
+        dic.update(self.update_r(node, zm=dic))
+        return dic
+
+def move_dgl_to_cuda(g):
+    g.ndata.update({k: cuda(g.ndata[k]) for k in g.ndata})
+    g.edata.update({k: cuda(g.edata[k]) for k in g.edata})

apps/life_sci/dgllife/model/model_zoo/mgcn_predictor.py

+"""MGCN"""
+import torch.nn as nn
+
+from ..gnn import MGCNGNN
+from ..readout import MLPNodeReadout
+
+__all__ = ['MGCNPredictor']
+
+class MGCNPredictor(nn.Module):
+    """MGCN for for regression and classification on graphs.
+
+    MGCN is introduced in `Molecular Property Prediction: A Multilevel Quantum Interactions
+    Modeling Perspective <https://arxiv.org/abs/1906.11081>`__.
+
+    Parameters
+    ----------
+    feats : int
+        Size for the node and edge embeddings to learn. Default to 128.
+    n_layers : int
+        Number of gnn layers to use. Default to 3.
+    classifier_hidden_feats : int
+        Size for hidden representations in the classifier. Default to 64.
+    n_tasks : int
+        Number of tasks, which is also the output size. Default to 1.
+    num_node_types : int
+        Number of node types to embed. Default to 100.
+    num_edge_types : int
+        Number of edge types to embed. Default to 3000.
+    cutoff : float
+        Largest center in RBF expansion. Default to 5.0
+    gap : float
+        Difference between two adjacent centers in RBF expansion. Default to 1.0
+    """
+    def __init__(self, feats=128, n_layers=3, classifier_hidden_feats=64, n_tasks=1,
+                 num_node_types=100, num_edge_types=3000, cutoff=5.0, gap=1.0):
+        super(MGCNPredictor, self).__init__()
+
+        self.gnn = MGCNGNN(feats=feats,
+                           n_layers=n_layers,
+                           num_node_types=num_node_types,
+                           num_edge_types=num_edge_types,
+                           cutoff=cutoff,
+                           gap=gap)
+        self.readout = MLPNodeReadout(node_feats=(n_layers + 1) * feats,
+                                      hidden_feats=classifier_hidden_feats,
+                                      graph_feats=n_tasks,
+                                      activation=nn.Softplus(beta=1, threshold=20))
+
+    def forward(self, g, node_types, edge_dists):
+        """Graph-level regression/soft classification.
+
+        Parameters
+        ----------
+        g : DGLGraph
+            DGLGraph for a batch of graphs.
+        node_types : int64 tensor of shape (V)
+            Node types to embed, V for the number of nodes.
+        edge_dists : float32 tensor of shape (E, 1)
+            Distances between end nodes of edges, E for the number of edges.
+
+        Returns
+        -------
+        float32 tensor of shape (G, n_tasks)
+            Prediction for the graphs in the batch. G for the number of graphs.
+        """
+        node_feats = self.gnn(g, node_types, edge_dists)
+        return self.readout(g, node_feats)

apps/life_sci/dgllife/model/readout/__init__.py

+"""
+Readout functions for computing molecular representations
+out of node and edge representations.
+"""
+from .attentivefp_readout import *
+from .weighted_sum_and_max import *
+from .mlp_readout import *