Application of deep metric learning to molecular graph similarity

CaMeL-Net: Centroid-aware metric learning for efficient multi-class cancer classification in pathology images

BACKGROUND AND OBJECTIVE

Cancer grading in pathology image analysis is a major task due to its importance in patient care, treatment, and management. The recent developments in artificial neural networks for computational pathology have demonstrated great potential to improve the accuracy and quality of cancer diagnosis. These improvements are generally ascribable to the advance in the architecture of the networks, often leading to increase in the computation and resources. In this work, we propose an efficient convolutional neural network that is designed to conduct multi-class cancer classification in an accurate and robust manner via metric learning.

METHODS

We propose a centroid-aware metric learning network for an improved cancer grading in pathology images. The proposed network utilizes centroids of different classes within the feature embedding space to optimize the relative distances between pathology images, which manifest the innate similarities/dissimilarities between them. For improved optimization, we introduce a new loss function and a training strategy that are tailored to the proposed network and metric learning.

RESULTS

We evaluated the proposed approach on multiple datasets of colorectal and gastric cancers. For the colorectal cancer, two different datasets were employed that were collected from different acquisition settings. the proposed method achieved an accuracy, F1-score, quadratic weighted kappa of 88.7%, 0.849, and 0.946 for the first dataset and 83.3%, 0.764, and 0.907 for the second dataset, respectively. For the gastric cancer, the proposed method obtained an accuracy of 85.9%, F1-score of 0.793, and quadratic weighted kappa of 0.939. We also found that the proposed method outperforms other competing models and is computationally efficient.

CONCLUSIONS

The experimental results demonstrate that the prediction results by the proposed network are both accurate and reliable. The proposed network not only outperformed other related methods in cancer classification but also achieved superior computational efficiency during training and inference. The future study will entail further development of the proposed method and the application of the method to other problems and domains.

Metric Learning for Kernel Ridge Regression: Assessment of Molecular Similarity

Supervised and unsupervised kernel-based algorithms broadly used in physical sciences rely upon the notion of similarity. Their reliance on pre-defined distance metrics - e.g., the Euclidean or Manhattan distance - are problematic especially when used in combination with high-dimensional feature vectors for which the similarity measure does not well-reflect the differences in the target property. Metric learning is an elegant approach to surmount this shortcoming and find a property-informed transformation of the feature space. We propose a new algorithm for metric learning specifically adapted for Kernel Ridge Regression (Metric Learning for Kernel Ridge Regression or MLKRR), with applications in the physical sciences in mind. The MLKRR algorithm is built upon the Metric Learning for Kernel Regression (MLKR) framework based on the Nadaraya-Watson estimator, which we show to be inferior to the KRR estimator for typical physics-based machine learning tasks. Our MLKRR algorithm shows superior predictive performance on the benchmark regression task of atomisation energies of QM9 molecules, as well as generating more meaningful low-dimensional projections of the modified feature space.