Source code for torch_geometric.nn.models.dimenet

import os
import os.path as osp
from math import sqrt, pi as PI

import numpy as np
import torch
from torch.nn import Linear, Embedding
from torch_scatter import scatter
from torch_sparse import SparseTensor
from torch_geometric.nn import radius_graph
from import download_url
from import makedirs

from ..acts import swish
from ..inits import glorot_orthogonal
from .dimenet_utils import bessel_basis, real_sph_harm

    import sympy as sym
except ImportError:
    sym = None

    os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
    import tensorflow as tf
except ImportError:
    tf = None

qm9_target_dict = {
    0: 'mu',
    1: 'alpha',
    2: 'homo',
    3: 'lumo',
    5: 'r2',
    6: 'zpve',
    7: 'U0',
    8: 'U',
    9: 'H',
    10: 'G',
    11: 'Cv',

class Envelope(torch.nn.Module):
    def __init__(self, exponent):
        super(Envelope, self).__init__()
        self.p = exponent + 1
        self.a = -(self.p + 1) * (self.p + 2) / 2
        self.b = self.p * (self.p + 2)
        self.c = -self.p * (self.p + 1) / 2

    def forward(self, x):
        p, a, b, c = self.p, self.a, self.b, self.c
        x_pow_p0 = x.pow(p - 1)
        x_pow_p1 = x_pow_p0 * x
        x_pow_p2 = x_pow_p1 * x
        return 1. / x + a * x_pow_p0 + b * x_pow_p1 + c * x_pow_p2

class BesselBasisLayer(torch.nn.Module):
    def __init__(self, num_radial, cutoff=5.0, envelope_exponent=5):
        super(BesselBasisLayer, self).__init__()
        self.cutoff = cutoff
        self.envelope = Envelope(envelope_exponent)

        self.freq = torch.nn.Parameter(torch.Tensor(num_radial))


    def reset_parameters(self):
        torch.arange(1, self.freq.numel() + 1, out=self.freq).mul_(PI)

    def forward(self, dist):
        dist = dist.unsqueeze(-1) / self.cutoff
        return self.envelope(dist) * (self.freq * dist).sin()

class SphericalBasisLayer(torch.nn.Module):
    def __init__(self, num_spherical, num_radial, cutoff=5.0,
        super(SphericalBasisLayer, self).__init__()
        assert num_radial <= 64
        self.num_spherical = num_spherical
        self.num_radial = num_radial
        self.cutoff = cutoff
        self.envelope = Envelope(envelope_exponent)

        bessel_forms = bessel_basis(num_spherical, num_radial)
        sph_harm_forms = real_sph_harm(num_spherical)
        self.sph_funcs = []
        self.bessel_funcs = []

        x, theta = sym.symbols('x theta')
        modules = {'sin': torch.sin, 'cos': torch.cos}
        for i in range(num_spherical):
            if i == 0:
                sph1 = sym.lambdify([theta], sph_harm_forms[i][0], modules)(0)
                self.sph_funcs.append(lambda x: torch.zeros_like(x) + sph1)
                sph = sym.lambdify([theta], sph_harm_forms[i][0], modules)
            for j in range(num_radial):
                bessel = sym.lambdify([x], bessel_forms[i][j], modules)

    def forward(self, dist, angle, idx_kj):
        dist = dist / self.cutoff
        rbf = torch.stack([f(dist) for f in self.bessel_funcs], dim=1)
        rbf = self.envelope(dist).unsqueeze(-1) * rbf

        cbf = torch.stack([f(angle) for f in self.sph_funcs], dim=1)

        n, k = self.num_spherical, self.num_radial
        out = (rbf[idx_kj].view(-1, n, k) * cbf.view(-1, n, 1)).view(-1, n * k)
        return out

class EmbeddingBlock(torch.nn.Module):
    def __init__(self, num_radial, hidden_channels, act=swish):
        super(EmbeddingBlock, self).__init__()
        self.act = act

        self.emb = Embedding(95, hidden_channels)
        self.lin_rbf = Linear(num_radial, hidden_channels)
        self.lin = Linear(3 * hidden_channels, hidden_channels)


    def reset_parameters(self):, sqrt(3))

    def forward(self, x, rbf, i, j):
        x = self.emb(x)
        rbf = self.act(self.lin_rbf(rbf))
        return self.act(self.lin([x[i], x[j], rbf], dim=-1)))

class ResidualLayer(torch.nn.Module):
    def __init__(self, hidden_channels, act=swish):
        super(ResidualLayer, self).__init__()
        self.act = act
        self.lin1 = Linear(hidden_channels, hidden_channels)
        self.lin2 = Linear(hidden_channels, hidden_channels)


    def reset_parameters(self):
        glorot_orthogonal(self.lin1.weight, scale=2.0)
        glorot_orthogonal(self.lin2.weight, scale=2.0)

    def forward(self, x):
        return x + self.act(self.lin2(self.act(self.lin1(x))))

class InteractionBlock(torch.nn.Module):
    def __init__(self, hidden_channels, num_bilinear, num_spherical,
                 num_radial, num_before_skip, num_after_skip, act=swish):
        super(InteractionBlock, self).__init__()
        self.act = act

        self.lin_rbf = Linear(num_radial, hidden_channels, bias=False)
        self.lin_sbf = Linear(num_spherical * num_radial, num_bilinear,

        # Dense transformations of input messages.
        self.lin_kj = Linear(hidden_channels, hidden_channels)
        self.lin_ji = Linear(hidden_channels, hidden_channels)

        self.W = torch.nn.Parameter(
            torch.Tensor(hidden_channels, num_bilinear, hidden_channels))

        self.layers_before_skip = torch.nn.ModuleList([
            ResidualLayer(hidden_channels, act) for _ in range(num_before_skip)
        self.lin = Linear(hidden_channels, hidden_channels)
        self.layers_after_skip = torch.nn.ModuleList([
            ResidualLayer(hidden_channels, act) for _ in range(num_after_skip)


    def reset_parameters(self):
        glorot_orthogonal(self.lin_rbf.weight, scale=2.0)
        glorot_orthogonal(self.lin_sbf.weight, scale=2.0)
        glorot_orthogonal(self.lin_kj.weight, scale=2.0)
        glorot_orthogonal(self.lin_ji.weight, scale=2.0), std=2 / self.W.size(0))
        for res_layer in self.layers_before_skip:
        glorot_orthogonal(self.lin.weight, scale=2.0)
        for res_layer in self.layers_after_skip:

    def forward(self, x, rbf, sbf, idx_kj, idx_ji):
        rbf = self.lin_rbf(rbf)
        sbf = self.lin_sbf(sbf)

        x_ji = self.act(self.lin_ji(x))
        x_kj = self.act(self.lin_kj(x))
        x_kj = x_kj * rbf
        x_kj = torch.einsum('wj,wl,ijl->wi', sbf, x_kj[idx_kj], self.W)
        x_kj = scatter(x_kj, idx_ji, dim=0, dim_size=x.size(0))

        h = x_ji + x_kj
        for layer in self.layers_before_skip:
            h = layer(h)
        h = self.act(self.lin(h)) + x
        for layer in self.layers_after_skip:
            h = layer(h)

        return h

class OutputBlock(torch.nn.Module):
    def __init__(self, num_radial, hidden_channels, out_channels, num_layers,
        super(OutputBlock, self).__init__()
        self.act = act

        self.lin_rbf = Linear(num_radial, hidden_channels, bias=False)
        self.lins = torch.nn.ModuleList()
        for _ in range(num_layers):
            self.lins.append(Linear(hidden_channels, hidden_channels))
        self.lin = Linear(hidden_channels, out_channels, bias=False)


    def reset_parameters(self):
        glorot_orthogonal(self.lin_rbf.weight, scale=2.0)
        for lin in self.lins:
            glorot_orthogonal(lin.weight, scale=2.0)

    def forward(self, x, rbf, i, num_nodes=None):
        x = self.lin_rbf(rbf) * x
        x = scatter(x, i, dim=0, dim_size=num_nodes)
        for lin in self.lins:
            x = self.act(lin(x))
        return self.lin(x)

[docs]class DimeNet(torch.nn.Module): r"""The directional message passing neural network (DimeNet) from the `"Directional Message Passing for Molecular Graphs" <>`_ paper. DimeNet transforms messages based on the angle between them in a rotation-equivariant fashion. .. note:: For an example of using a pretrained DimeNet variant, see `examples/ <>`_. Args: hidden_channels (int): Hidden embedding size. out_channels (int): Size of each output sample. num_blocks (int): Number of building blocks. num_bilinear (int): Size of the bilinear layer tensor. num_spherical (int): Number of spherical harmonics. num_radial (int): Number of radial basis functions. cutoff: (float, optional): Cutoff distance for interatomic interactions. (default: :obj:`5.0`) envelope_exponent (int, optional): Shape of the smooth cutoff. (default: :obj:`5`) num_before_skip: (int, optional): Number of residual layers in the interaction blocks before the skip connection. (default: :obj:`1`) num_after_skip: (int, optional): Number of residual layers in the interaction blocks after the skip connection. (default: :obj:`2`) num_output_layers: (int, optional): Number of linear layers for the output blocks. (default: :obj:`3`) act: (function, optional): The activation funtion. (default: :obj:`swish`) """ url = ('' 'dimenet') def __init__(self, hidden_channels, out_channels, num_blocks, num_bilinear, num_spherical, num_radial, cutoff=5.0, envelope_exponent=5, num_before_skip=1, num_after_skip=2, num_output_layers=3, act=swish): super(DimeNet, self).__init__() self.cutoff = cutoff if sym is None: raise ImportError('Package `sympy` could not be found.') self.num_blocks = num_blocks self.rbf = BesselBasisLayer(num_radial, cutoff, envelope_exponent) self.sbf = SphericalBasisLayer(num_spherical, num_radial, cutoff, envelope_exponent) self.emb = EmbeddingBlock(num_radial, hidden_channels, act) self.output_blocks = torch.nn.ModuleList([ OutputBlock(num_radial, hidden_channels, out_channels, num_output_layers, act) for _ in range(num_blocks + 1) ]) self.interaction_blocks = torch.nn.ModuleList([ InteractionBlock(hidden_channels, num_bilinear, num_spherical, num_radial, num_before_skip, num_after_skip, act) for _ in range(num_blocks) ]) self.reset_parameters()
[docs] def reset_parameters(self): self.rbf.reset_parameters() self.emb.reset_parameters() for out in self.output_blocks: out.reset_parameters() for interaction in self.interaction_blocks: interaction.reset_parameters()
[docs] @staticmethod def from_qm9_pretrained(root, dataset, target): if tf is None: raise ImportError( '`DimeNet.from_qm9_pretrained` requires `tensorflow`.') assert target >= 0 and target <= 12 and not target == 4 root = osp.expanduser(osp.normpath(root)) path = osp.join(root, 'pretrained_dimenet', qm9_target_dict[target]) makedirs(path) url = f'{DimeNet.url}/{qm9_target_dict[target]}' if not osp.exists(osp.join(path, 'checkpoint')): download_url(f'{url}/checkpoint', path) download_url(f'{url}/', path) download_url(f'{url}/', path) download_url(f'{url}/ckpt.index', path) path = osp.join(path, 'ckpt') reader = tf.train.load_checkpoint(path) model = DimeNet(hidden_channels=128, out_channels=1, num_blocks=6, num_bilinear=8, num_spherical=7, num_radial=6, cutoff=5.0, envelope_exponent=5, num_before_skip=1, num_after_skip=2, num_output_layers=3) def copy_(src, name, transpose=False): init = reader.get_tensor(f'{name}/.ATTRIBUTES/VARIABLE_VALUE') init = torch.from_numpy(init) if name[-6:] == 'kernel': init = init.t() copy_(model.rbf.freq, 'rbf_layer/frequencies') copy_(model.emb.emb.weight, 'emb_block/embeddings') copy_(model.emb.lin_rbf.weight, 'emb_block/dense_rbf/kernel') copy_(model.emb.lin_rbf.bias, 'emb_block/dense_rbf/bias') copy_(model.emb.lin.weight, 'emb_block/dense/kernel') copy_(model.emb.lin.bias, 'emb_block/dense/bias') for i, block in enumerate(model.output_blocks): copy_(block.lin_rbf.weight, f'output_blocks/{i}/dense_rbf/kernel') for j, lin in enumerate(block.lins): copy_(lin.weight, f'output_blocks/{i}/dense_layers/{j}/kernel') copy_(lin.bias, f'output_blocks/{i}/dense_layers/{j}/bias') copy_(block.lin.weight, f'output_blocks/{i}/dense_final/kernel') for i, block in enumerate(model.interaction_blocks): copy_(block.lin_rbf.weight, f'int_blocks/{i}/dense_rbf/kernel') copy_(block.lin_sbf.weight, f'int_blocks/{i}/dense_sbf/kernel') copy_(block.lin_kj.weight, f'int_blocks/{i}/dense_kj/kernel') copy_(block.lin_kj.bias, f'int_blocks/{i}/dense_kj/bias') copy_(block.lin_ji.weight, f'int_blocks/{i}/dense_ji/kernel') copy_(block.lin_ji.bias, f'int_blocks/{i}/dense_ji/bias') copy_(block.W, f'int_blocks/{i}/bilinear') for j, layer in enumerate(block.layers_before_skip): copy_(layer.lin1.weight, f'int_blocks/{i}/layers_before_skip/{j}/dense_1/kernel') copy_(layer.lin1.bias, f'int_blocks/{i}/layers_before_skip/{j}/dense_1/bias') copy_(layer.lin2.weight, f'int_blocks/{i}/layers_before_skip/{j}/dense_2/kernel') copy_(layer.lin2.bias, f'int_blocks/{i}/layers_before_skip/{j}/dense_2/bias') copy_(block.lin.weight, f'int_blocks/{i}/final_before_skip/kernel') copy_(block.lin.bias, f'int_blocks/{i}/final_before_skip/bias') for j, layer in enumerate(block.layers_after_skip): copy_(layer.lin1.weight, f'int_blocks/{i}/layers_after_skip/{j}/dense_1/kernel') copy_(layer.lin1.bias, f'int_blocks/{i}/layers_after_skip/{j}/dense_1/bias') copy_(layer.lin2.weight, f'int_blocks/{i}/layers_after_skip/{j}/dense_2/kernel') copy_(layer.lin2.bias, f'int_blocks/{i}/layers_after_skip/{j}/dense_2/bias') # Use the same random seed as the official DimeNet` implementation. random_state = np.random.RandomState(seed=42) perm = torch.from_numpy(random_state.permutation(np.arange(130831))) train_idx = perm[:110000] val_idx = perm[110000:120000] test_idx = perm[120000:] return model, (dataset[train_idx], dataset[val_idx], dataset[test_idx])
[docs] def triplets(self, edge_index, num_nodes): row, col = edge_index # j->i value = torch.arange(row.size(0), device=row.device) adj_t = SparseTensor(row=col, col=row, value=value, sparse_sizes=(num_nodes, num_nodes)) adj_t_row = adj_t[row] num_triplets = adj_t_row.set_value(None).sum(dim=1).to(torch.long) # Node indices (k->j->i) for triplets. idx_i = col.repeat_interleave(num_triplets) idx_j = row.repeat_interleave(num_triplets) idx_k = mask = idx_i != idx_k # Remove i == k triplets. idx_i, idx_j, idx_k = idx_i[mask], idx_j[mask], idx_k[mask] # Edge indices (k-j, j->i) for triplets. idx_kj =[mask] idx_ji =[mask] return col, row, idx_i, idx_j, idx_k, idx_kj, idx_ji
[docs] def forward(self, z, pos, batch=None): """""" edge_index = radius_graph(pos, r=self.cutoff, batch=batch) i, j, idx_i, idx_j, idx_k, idx_kj, idx_ji = self.triplets( edge_index, num_nodes=z.size(0)) # Calculate distances. dist = (pos[i] - pos[j]).pow(2).sum(dim=-1).sqrt() # Calculate angles. pos_i = pos[idx_i] pos_ji, pos_ki = pos[idx_j] - pos_i, pos[idx_k] - pos_i a = (pos_ji * pos_ki).sum(dim=-1) b = torch.cross(pos_ji, pos_ki).norm(dim=-1) angle = torch.atan2(b, a) rbf = self.rbf(dist) sbf = self.sbf(dist, angle, idx_kj) # Embedding block. x = self.emb(z, rbf, i, j) P = self.output_blocks[0](x, rbf, i, num_nodes=pos.size(0)) # Interaction blocks. for interaction_block, output_block in zip(self.interaction_blocks, self.output_blocks[1:]): x = interaction_block(x, rbf, sbf, idx_kj, idx_ji) P += output_block(x, rbf, i) return P.sum(dim=0) if batch is None else scatter(P, batch, dim=0)