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PyTorch Binary Classification: Fixing the Loss vs. Metric Gap

A developer describes a common pitfall in PyTorch binary classification where high accuracy (92%) on imbalanced datasets masks poor precision-recall performance, recommending tracking metrics like F1-score and AUC-ROC via torchmetrics instead of relying solely on loss. The post advises using class weights in BCEWithLogitsLoss to address class imbalance and provides code for computing validation F1-score correctly.

read2 min views1 publishedJul 24, 2026
PyTorch Binary Classification: Fixing the Loss vs. Metric Gap
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Accuracy is a lie when you're dealing with imbalanced datasets in binary classification. I hit a wall recently where my model showed 92% accuracy during training, but the precision-recall curve looked like a disaster. The core issue is the fundamental difference between the objective function (what the optimizer minimizes) and the evaluation metrics (what we actually care about).

For anyone building a custom training loop, don't rely on the raw loss. I use

In PyTorch, we typically use BCEWithLogitsLoss

for binary tasks. This is a smooth, differentiable function necessary for backpropagation. However, you can't use accuracy as a loss function because it's non-differentiable.

To properly diagnose model performance, I've moved to a setup that tracks these specific metrics per epoch:

Log Loss (Cross-Entropy): The actual value the optimizer is attacking. If this drops but accuracy doesn't move, you're likely dealing with a severe class imbalance.Precision & Recall: Essential for understanding the trade-off between false positives and false negatives.F1-Score: The harmonic mean of the two, which is the only number I trust for "overall" performance on skewed data.AUC-ROC: Measures the model's ability to distinguish between classes regardless of the decision threshold.

For anyone building a custom training loop, don't rely on the raw loss. I use

torchmetrics

to handle the accumulation across batches to avoid the "average of averages" mistake. Here is the basic logic for calculating the F1-score correctly within a validation loop:

import torch
from torchmetrics.classification import BinaryF1Score

f1_metric = BinaryF1Score().to(device)

model.eval()
with torch.no_grad():
    for inputs, targets in val_:
        inputs, targets = inputs.to(device), targets.to(device)
        logits = model(inputs)
        preds = (torch.sigmoid(logits) > 0.5).float()
        f1_metric.update(preds, targets)

final_f1 = f1_metric.compute()
print(f"Validation F1 Score: {final_f1}")

If you see your loss decreasing while your F1-score plateaus or drops, check your class weights in the loss function. Adding pos_weight

to BCEWithLogitsLoss

usually fixes the bias toward the majority class.

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All Replies (3) #

R

Happened to me with fraud detection; high accuracy but it missed every single actual case.

0

S

Did you try adjusting the class weights in BCE loss, or just pray it worked?

0

P

Using an F1-score usually clears things up for me when the classes are skewed.

0

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