We introduce MELEP, which stands for Muti-label Expected Log of Empirical Predictions, a novel measure to estimate how effective it is to transfer knowledge from a pre-trained model to a downstream task in a multi-label settings. The measure is generic to work with new target data having a different label set from source data. It is also computationally efficient, only requires forward passing the downstream dataset through the pre-trained model once. To the best of our knowledge, we are the first to develop such a transferability metric for multi-label ECG classification problems. Our experiments show that MELEP can predict the performance of pre-trained convolutional and recurrent deep neural networks, on small and imbalanced ECG data. Specifically, strong correlation coefficients, with absolute values exceeding 0.6 in most cases, were observed between MELEP and the actual average F1 scores of the fine-tuned models.