Cost-Sensitive back-propagation neural networks with binarization techniques in addressing multi-class problems and non-competent classifiers

Integrating multi-task and cost-sensitive learning for predicting mortality risk of chronic diseases in the elderly using real-world data

BACKGROUND AND OBJECTIVE

Real-world data encompass population diversity, enabling insights into chronic disease mortality risk among the elderly. Deep learning excels on large datasets, offering promise for real-world data. However, current models focus on single diseases, neglecting comorbidities prevalent in patients. Moreover, mortality is infrequent compared to illness, causing extreme class imbalance that impedes reliable prediction. We aim to develop a deep learning framework that accurately forecasts mortality risk from real-world data by addressing comorbidities and class imbalance.

METHODS

We integrated multi-task and cost-sensitive learning, developing an enhanced deep neural network architecture that extends multi-task learning to predict mortality risk across multiple chronic diseases. Each patient cohort with a chronic disease was assigned to a separate task, with shared lower-level parameters capturing inter-disease complexities through distinct top-level networks. Cost-sensitive functions were incorporated to ensure learning of positive class characteristics for each task and achieve accurate prediction of the risk of death from multiple chronic diseases.

RESULTS

Our study covers 15 prevalent chronic diseases and is experimented with real-world data from 482,145 patients (including 9,516 deaths) in Shenzhen, China. The proposed model is compared with six models including three machine learning models: logistic regression, XGBoost, and CatBoost, and three state-of-the-art deep learning models: 1D-CNN, TabNet, and Saint. The experimental results show that, compared with the other compared algorithms, MTL-CSDNN has better prediction results on the test set (ACC=0.99, REC=0.99, PRAUC=0.97, MCC=0.98, G-means = 0.98).

CONCLUSIONS

Our method provides valuable insights into leveraging real-world data for precise multi-disease mortality risk prediction, offering potential applications in optimizing chronic disease management, enhancing well-being, and reducing healthcare costs for the elderly population.

Learning the protein language of proteome-wide protein-protein binding sites via explainable ensemble deep learning

Protein-protein interactions (PPIs) govern cellular pathways and processes, by significantly influencing the functional expression of proteins. Therefore, accurate identification of protein-protein interaction binding sites has become a key step in the functional analysis of proteins. However, since most computational methods are designed based on biological features, there are no available protein language models to directly encode amino acid sequences into distributed vector representations to model their characteristics for protein-protein binding events. Moreover, the number of experimentally detected protein interaction sites is much smaller than that of protein-protein interactions or protein sites in protein complexes, resulting in unbalanced data sets that leave room for improvement in their performance. To address these problems, we develop an ensemble deep learning model (EDLM)-based protein-protein interaction (PPI) site identification method (EDLMPPI). Evaluation results show that EDLMPPI outperforms state-of-the-art techniques including several PPI site prediction models on three widely-used benchmark datasets including Dset_448, Dset_72, and Dset_164, which demonstrated that EDLMPPI is superior to those PPI site prediction models by nearly 10% in terms of average precision. In addition, the biological and interpretable analyses provide new insights into protein binding site identification and characterization mechanisms from different perspectives. The EDLMPPI webserver is available at http://www.edlmppi.top:5002/ .

Cost-Sensitive Variational Autoencoding Classifier for Imbalanced Data Classification

Classification is among the core tasks in machine learning. Existing classification algorithms are typically based on the assumption of at least roughly balanced data classes. When performing tasks involving imbalanced data, such classifiers ignore the minority data in consideration of the overall accuracy. The performance of traditional classification algorithms based on the assumption of balanced data distribution is insufficient because the minority-class samples are often more important than others, such as positive samples, in disease diagnosis. In this study, we propose a cost-sensitive variational autoencoding classifier that combines data-level and algorithm-level methods to solve the problem of imbalanced data classification. Cost-sensitive factors are introduced to assign a high cost to the misclassification of minority data, which biases the classifier toward minority data. We also designed misclassification costs closely related to tasks by embedding domain knowledge. Experimental results show that the proposed method performed the classification of bulk amorphous materials well.

Globalized Multiple Balanced Subsets With Collaborative Learning for Imbalanced Data

The skewed distribution of data brings difficulties to classify minority and majority samples in the imbalanced problem. The balanced bagging randomly undersampes majority samples several times and combines the selected majority samples with minority samples to form several balanced subsets, in which the numbers of minority and majority samples are roughly equal. However, the balanced bagging is the lack of a unified learning framework. Moreover, it fails to concern the connection of all subsets and the global information of the entire data distribution. To this end, this article puts several balanced subsets into an effective learning framework with a criterion function. In the learning framework, one regularization term called R_S establishes the connection and realizes the collaborative learning of all subsets by requiring the consistent outputs of the minority samples in different subsets. Besides, another regularization term called R_W provides the global information to each basic classifier by reducing the difference between the direction of the solution vector in each subset and that in the entire dataset. The proposed learning framework is called globalized multiple balanced subsets with collaborative learning (GMBSCL). The experimental results validate the effectiveness of the proposed GMBSCL.

Research on Imbalanced Data Classification Based on Classroom-Like Generative Adversarial Networks

Most of the research on machine learning classification methods is based on balanced data; the research on imbalanced data classification needs improvement. Generative adversarial networks (GANs) are able to learn high-dimensional complex data distribution without relying on a prior hypothesis, which has become a hot technology in artificial intelligence. In this letter, we propose a new structure, classroom-like generative adversarial networks (CLGANs), to construct a model with multiple generators. Taking inspiration from the fact that teachers arrange teaching activities according to students' learning situation, we propose a weight allocation function to adaptively adjust the influence weight of generator loss function on discriminator loss function. All the generators work together to improve the degree of discriminator and training sample space, so that a discriminator with excellent performance is trained and applied to the tasks of imbalanced data classification. Experimental results on the Case Western Reserve University data set and 2.4 GHz Indoor Channel Measurements data set show that the data classification ability of the discriminator trained by CLGANs with multiple generators is superior to that of other imbalanced data classification models, and the optimal discriminator can be obtained by selecting the right matching scheme of the generator models.

Interclass Interference Suppression in Multi-Class Problems

Multi-classifiers are widely applied in many practical problems. But the features that can significantly discriminate a certain class from others are often deleted in the feature selection process of multi-classifiers, which seriously decreases the generalization ability. This paper refers to this phenomenon as interclass interference in multi-class problems and analyzes its reason in detail. Then, this paper summarizes three interclass interference suppression methods including the method based on all-features, one-class classifiers and binary classifiers and compares their effects on interclass interference via the 10-fold cross-validation experiments in 14 UCI datasets. Experiments show that the method based on binary classifiers can suppress the interclass interference efficiently and obtain the best classification accuracy among the three methods. Further experiments were done to compare the suppression effect of two methods based on binary classifiers including the one-versus-one method and one-versus-all method. Results show that the one-versus-one method can obtain a better suppression effect on interclass interference and obtain better classification accuracy. By proposing the concept of interclass inference and studying its suppression methods, this paper significantly improves the generalization ability of multi-classifiers.