SVM ensemble based transfer learning for large-scale membrane proteins discrimination

Multi-Source Transfer Learning via Ensemble Approach for Initial Diagnosis of Alzheimer's Disease

Alzheimer’s disease (AD) is one of the most common progressive neurodegenerative diseases, and the number of AD patients has increased year after year with the global aging trend. The onset of AD has a long preclinical stage. If doctors can make an initial diagnosis in the mild cognitive impairment (MCI) stage, it is possible to identify and screen those at a high-risk of developing full-blown AD, and thus the number of new AD patients can be reduced. However, there are problems with the medical datasets including AD data, such as insufficient number of samples and different data distributions. Transfer learning, which can effectively solve the problem of distribution discrepancy between training and test data and an insufficient number of target samples, has attracted increasing attention over recent years. In this paper, we propose a multi-source ensemble transfer learning (METL) approach by introducing ensemble learning and our tri-transfer model that uses Tri-Training, which ensures the transferability of source data by the tri-transfer model and high performance through ensemble learning. The experimental results on the benchmark and AD datasets demonstrate that our proposed approach has effective transferability, robustness, and feasibility, and is superior to existing algorithms. Based on METL, we propose an auxiliary diagnosis system for the initial diagnosis of AD, which helps doctors identify patients in the MCI stage as quickly as possible and with high accuracy so that measures can be taken to prevent or delay the occurrence of AD.

Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways

BACKGROUND

Signaling pathways play important roles in the life processes of cell growth, cell apoptosis and organism development. At present the signal transduction networks are far from complete. As an effective complement to experimental methods, computational modeling is suited to rapidly reconstruct the signaling pathways at low cost. To our knowledge, the existing computational methods seldom simultaneously exploit more than three signaling pathways into one predictive model for the discovery of novel signaling components and the cross-talk modeling between signaling pathways.

RESULTS

In this work, we propose a multi-label multi-instance transfer learning method to simultaneously reconstruct 27 human signaling pathways and model their cross-talks. Computational results show that the proposed method demonstrates satisfactory multi-label learning performance and rational proteome-wide predictions. Some predicted signaling components or pathway targeted proteins have been validated by recent literature. The predicted signaling components are further linked to pathways using the experimentally derived PPIs (protein-protein interactions) to reconstruct the human signaling pathways. Thus the map of the cross-talks via common signaling components and common signaling PPIs is conveniently inferred to provide valuable insights into the regulatory and cooperative relationships between signaling pathways. Lastly, gene ontology enrichment analysis is conducted to gain statistical knowledge about the reconstructed human signaling pathways.

CONCLUSIONS

Multi-label learning framework has been demonstrated effective in this work to model the phenomena that a signaling protein belongs to more than one signaling pathway. As results, novel signaling components and pathways targeted proteins are predicted to simultaneously reconstruct multiple human signaling pathways and the static map of their cross-talks for further biomedical research.

AdaBoost based multi-instance transfer learning for predicting proteome-wide interactions between Salmonella and human proteins

Pathogen-host protein-protein interaction (PPI) plays an important role in revealing the underlying pathogenesis of viruses and bacteria. The need of rapidly mapping proteome-wide pathogen-host interactome opens avenues for and imposes burdens on computational modeling. For Salmonella typhimurium, only 62 interactions with human proteins are reported to date, and the computational modeling based on such a small training data is prone to yield model overfitting. In this work, we propose a multi-instance transfer learning method to reconstruct the proteome-wide Salmonella-human PPI networks, wherein the training data is augmented by homolog knowledge transfer in the form of independent homolog instances. We use AdaBoost instance reweighting to counteract the noise from homolog instances, and deliberately design three experimental settings to validate the assumption that the homolog instances are effective to address the problems of data scarcity and data unavailability. The experimental results show that the proposed method outperforms the existing models and some predictions are validated by the findings from recent literature. Lastly, we conduct gene ontology based clustering analysis of the predicted networks to provide insights into the pathogenesis of Salmonella.