import torch
from torch.nn import functional as F
from torch_scatter import scatter_add, scatter_mean, scatter_max
import networkx as nx
from rdkit import Chem
from rdkit.Chem import Descriptors
from torchdrug import utils
from torchdrug.layers import functional
from torchdrug.core import Registry as R
from torchdrug.metrics.rdkit import sascorer
[docs]@R.register("metrics.auroc")
def area_under_roc(pred, target):
"""
Area under receiver operating characteristic curve (ROC).
Parameters:
pred (Tensor): predictions of shape :math:`(n,)`
target (Tensor): binary targets of shape :math:`(n,)`
"""
order = pred.argsort(descending=True)
target = target[order]
hit = target.cumsum(0)
all = (target == 0).sum() * (target == 1).sum()
auroc = hit[target == 0].sum() / (all + 1e-10)
return auroc
[docs]@R.register("metrics.auprc")
def area_under_prc(pred, target):
"""
Area under precision-recall curve (PRC).
Parameters:
pred (Tensor): predictions of shape :math:`(n,)`
target (Tensor): binary targets of shape :math:`(n,)`
"""
order = pred.argsort(descending=True)
target = target[order]
precision = target.cumsum(0) / torch.arange(1, len(target) + 1, device=target.device)
auprc = precision[target == 1].sum() / ((target == 1).sum() + 1e-10)
return auprc
[docs]@R.register("metrics.r2")
def r2(pred, target):
"""
:math:`R^2` regression score.
Parameters:
pred (Tensor): predictions of shape :math:`(n,)`
target (Tensor): targets of shape :math:`(n,)`
"""
total = torch.var(target, unbiased=False)
residual = F.mse_loss(pred, target)
return 1 - residual / total
[docs]@R.register("metrics.logp")
def logP(pred):
"""
Logarithm of partition coefficient between octanol and water for a compound.
Parameters:
pred (PackedMolecule): molecules to evaluate
"""
logp = []
for mol in pred:
mol = mol.to_molecule()
try:
with utils.no_rdkit_log():
mol.UpdatePropertyCache()
score = Descriptors.MolLogP(mol)
except Chem.AtomValenceException:
score = 0
logp.append(score)
return torch.tensor(logp, dtype=torch.float, device=pred.device)
[docs]@R.register("metrics.plogp")
def penalized_logP(pred):
"""
Logarithm of partition coefficient, penalized by cycle length and synthetic accessibility.
Parameters:
pred (PackedMolecule): molecules to evaluate
"""
# statistics from ZINC250k
logp_mean = 2.4570953396190123
logp_std = 1.434324401111988
sa_mean = 3.0525811293166134
sa_std = 0.8335207024513095
cycle_mean = 0.0485696876403053
cycle_std = 0.2860212110245455
plogp = []
for mol in pred:
cycles = nx.cycle_basis(nx.Graph(mol.edge_list[:, :2].tolist()))
if cycles:
max_cycle = max([len(cycle) for cycle in cycles])
cycle = max(0, max_cycle - 6)
else:
cycle = 0
mol = mol.to_molecule()
try:
with utils.no_rdkit_log():
mol.UpdatePropertyCache()
Chem.GetSymmSSSR(mol)
logp = Descriptors.MolLogP(mol)
sa = sascorer.calculateScore(mol)
logp = (logp - logp_mean) / logp_std
sa = (sa - sa_mean) / sa_std
cycle = (cycle - cycle_mean) / cycle_std
score = logp - sa - cycle
except Chem.AtomValenceException:
score = -30
plogp.append(score)
return torch.tensor(plogp, dtype=torch.float, device=pred.device)
[docs]@R.register("metrics.SA")
def SA(pred):
"""
Synthetic accesibility score.
Parameters:
pred (PackedMolecule): molecules to evaluate
"""
sa = []
for mol in pred:
with utils.no_rdkit_log():
score = sascorer.calculateScore(mol.to_molecule())
sa.append(score)
return torch.tensor(sa, dtype=torch.float, device=pred.device)
[docs]@R.register("metrics.qed")
def QED(pred):
"""
Quantitative estimation of drug-likeness.
Parameters:
pred (PackedMolecule): molecules to evaluate
"""
qed = []
for mol in pred:
try:
with utils.no_rdkit_log():
score = Descriptors.qed(mol.to_molecule())
except Chem.AtomValenceException:
score = -1
qed.append(score)
return torch.tensor(qed, dtype=torch.float, device=pred.device)
[docs]@R.register("metrics.validity")
def chemical_validity(pred):
"""
Chemical validity of molecules.
Parameters:
pred (PackedMolecule): molecules to evaluate
"""
validity = []
for i, mol in enumerate(pred):
with utils.no_rdkit_log():
smiles = mol.to_smiles()
mol = Chem.MolFromSmiles(smiles)
validity.append(1 if mol else 0)
return torch.tensor(validity, dtype=torch.float, device=pred.device)
[docs]@R.register("metrics.variadic_auroc")
def variadic_area_under_roc(pred, target, size):
"""
Area under receiver operating characteristic curve (ROC) for sets with variadic sizes.
Suppose there are :math:`N` sets, and the sizes of all sets are summed to :math:`B`.
Parameters:
pred (Tensor): prediction of shape :math:`(B,)`
target (Tensor): target of shape :math:`(B,)`.
size (Tensor): size of sets of shape :math:`(N,)`
"""
index2graph = functional._size_to_index(size)
_, order = functional.variadic_sort(pred, size, descending=True)
cum_size = (size.cumsum(0) - size)[index2graph]
target = target[order + cum_size]
total_hit = functional.variadic_sum(target, size)
total_hit = total_hit.cumsum(0) - total_hit
hit = target.cumsum(0) - total_hit[index2graph]
hit = torch.where(target == 0, hit, torch.zeros_like(hit))
all = functional.variadic_sum((target == 0).float(), size) * \
functional.variadic_sum((target == 1).float(), size)
auroc = functional.variadic_sum(hit, size) / (all + 1e-10)
return auroc
[docs]@R.register("metrics.variadic_auprc")
def variadic_area_under_prc(pred, target, size):
"""
Area under precision-recall curve (PRC) for sets with variadic sizes.
Suppose there are :math:`N` sets, and the sizes of all sets are summed to :math:`B`.
Parameters:
pred (Tensor): prediction of shape :math:`(B,)`
target (Tensor): target of shape :math:`(B,)`.
size (Tensor): size of sets of shape :math:`(N,)`
"""
index2graph = functional._size_to_index(size)
_, order = functional.variadic_sort(pred, size, descending=True)
cum_size = (size.cumsum(0) - size)[index2graph]
target = target[order + cum_size]
total_hit = functional.variadic_sum(target, size)
total_hit = total_hit.cumsum(0) - total_hit
hit = target.cumsum(0) - total_hit[index2graph]
total = torch.ones_like(target).cumsum(0) - (size.cumsum(0) - size)[index2graph]
precision = hit / total
precision = torch.where(target == 1, precision, torch.zeros_like(precision))
auprc = functional.variadic_sum(precision, size) / \
(functional.variadic_sum((target == 1).float(), size) + 1e-10)
return auprc
[docs]@R.register("metrics.f1_max")
def f1_max(pred, target):
"""
F1 score with the optimal threshold.
This function first enumerates all possible thresholds for deciding positive and negative
samples, and then pick the threshold with the maximal F1 score.
Parameters:
pred (Tensor): predictions of shape :math:`(B, N)`
target (Tensor): binary targets of shape :math:`(B, N)`
"""
order = pred.argsort(descending=True, dim=1)
target = target.gather(1, order)
precision = target.cumsum(1) / torch.ones_like(target).cumsum(1)
recall = target.cumsum(1) / (target.sum(1, keepdim=True) + 1e-10)
is_start = torch.zeros_like(target).bool()
is_start[:, 0] = 1
is_start = torch.scatter(is_start, 1, order, is_start)
all_order = pred.flatten().argsort(descending=True)
order = order + torch.arange(order.shape[0], device=order.device).unsqueeze(1) * order.shape[1]
order = order.flatten()
inv_order = torch.zeros_like(order)
inv_order[order] = torch.arange(order.shape[0], device=order.device)
is_start = is_start.flatten()[all_order]
all_order = inv_order[all_order]
precision = precision.flatten()
recall = recall.flatten()
all_precision = precision[all_order] - \
torch.where(is_start, torch.zeros_like(precision), precision[all_order - 1])
all_precision = all_precision.cumsum(0) / is_start.cumsum(0)
all_recall = recall[all_order] - \
torch.where(is_start, torch.zeros_like(recall), recall[all_order - 1])
all_recall = all_recall.cumsum(0) / pred.shape[0]
all_f1 = 2 * all_precision * all_recall / (all_precision + all_recall + 1e-10)
return all_f1.max()
[docs]@R.register("metrics.accuracy")
def accuracy(pred, target):
"""
Classification accuracy.
Suppose there are :math:`N` sets and :math:`C` categories.
Parameters:
pred (Tensor): prediction of shape :math:`(N, C)`
target (Tensor): target of shape :math:`(N,)`
"""
return (pred.argmax(dim=-1) == target).float().mean()
[docs]@R.register("metrics.variadic_accuracy")
def variadic_accuracy(input, target, size):
"""
Classification accuracy for categories with variadic sizes.
Suppose there are :math:`N` samples, and the number of categories in all samples is summed to :math:`B`.
Parameters:
input (Tensor): prediction of shape :math:`(B,)`
target (Tensor): target of shape :math:`(N,)`. Each target is a relative index in a sample.
size (Tensor): number of categories of shape :math:`(N,)`
"""
index2graph = functional._size_to_index(size)
input_class = scatter_max(input, index2graph)[1]
target_index = target + size.cumsum(0) - size
accuracy = (input_class == target_index).float()
return accuracy
[docs]@R.register("metrics.variadic_top_precision")
def variadic_top_precision(pred, target, size, k):
"""
Top-k precision for sets with variadic sizes.
Suppose there are :math:`N` sets, and the sizes of all sets are summed to :math:`B`.
Parameters:
pred (Tensor): prediction of shape :math:`(B,)`
target (Tensor): target of shape :math:`(B,)`
size (Tensor): size of sets of shape :math:`(N,)`
k (LongTensor): the k in "top-k" for different sets of shape :math:`(N,)`
"""
index = functional.variadic_topk(pred, size, k, largest=True)[1]
index = index + (size.cumsum(0) - size).repeat_interleave(k)
precision = functional.variadic_sum(target[index], k) / k
precision[size < k] = 0
return precision
[docs]@R.register("metrics.mcc")
def matthews_corrcoef(pred, target):
"""
Matthews correlation coefficient between prediction and target.
Definition follows matthews_corrcoef for K classes in sklearn.
For details, see: `https://scikit-learn.org/stable/modules/model_evaluation.html#matthews-corrcoef`
Parameters:
pred (Tensor): prediction of shape :math: `(N, K)`
target (Tensor): target of shape :math: `(N,)`
"""
num_class = pred.size(-1)
pred = pred.argmax(-1)
ones = torch.ones(len(target), device=pred.device)
confusion_matrix = scatter_add(ones, target * num_class + pred, dim=0, dim_size=num_class ** 2)
confusion_matrix = confusion_matrix.view(num_class, num_class)
t = confusion_matrix.sum(dim=1)
p = confusion_matrix.sum(dim=0)
c = confusion_matrix.trace()
s = confusion_matrix.sum()
return (c * s - t @ p) / ((s * s - p @ p) * (s * s - t @ t) + 1e-10).sqrt()
[docs]@R.register("metrics.pearsonr")
def pearsonr(pred, target):
"""
Pearson correlation between prediction and target.
Parameters:
pred (Tensor): prediction of shape :math: `(N,)`
target (Tensor): target of shape :math: `(N,)`
"""
pred_mean = pred.float().mean()
target_mean = target.float().mean()
pred_centered = pred - pred_mean
target_centered = target - target_mean
pred_normalized = pred_centered / pred_centered.norm(2)
target_normalized = target_centered / target_centered.norm(2)
pearsonr = pred_normalized @ target_normalized
return pearsonr
[docs]@R.register("metrics.spearmanr")
def spearmanr(pred, target):
"""
Spearman correlation between prediction and target.
Parameters:
pred (Tensor): prediction of shape :math: `(N,)`
target (Tensor): target of shape :math: `(N,)`
"""
def get_ranking(input):
input_set, input_inverse = input.unique(return_inverse=True)
order = input_inverse.argsort()
ranking = torch.zeros(len(input_inverse), device=input.device)
ranking[order] = torch.arange(1, len(input) + 1, dtype=torch.float, device=input.device)
# for elements that have the same value, replace their rankings with the mean of their rankings
mean_ranking = scatter_mean(ranking, input_inverse, dim=0, dim_size=len(input_set))
ranking = mean_ranking[input_inverse]
return ranking
pred = get_ranking(pred)
target = get_ranking(target)
covariance = (pred * target).mean() - pred.mean() * target.mean()
pred_std = pred.std(unbiased=False)
target_std = target.std(unbiased=False)
spearmanr = covariance / (pred_std * target_std + 1e-10)
return spearmanr