Domain-adversarial multi-task framework for novel therapeutic property prediction of compounds

MBFusion: Multi-modal balanced fusion and multi-task learning for cancer diagnosis and prognosis

Pathological images and molecular omics are important information for predicting diagnosis and prognosis. The two kinds of heterogeneous modal data contain complementary information, and the effective fusion of the two modals can better reveal the complex mechanisms of cancer. However, due to the different representation learning methods, the expression strength of different modals in different tasks varies greatly, so that many multimodal fusions do not achieve the best results. In this paper, MBFusion is proposed, to achieve multiple tasks such as prediction of diagnosis and prognosis through multi-modal balanced fusion. The MBFusion framework uses two kinds of specially constructed graph convolutional network to extract the features of molecular omics data, and uses ResNet to extract the features of pathological image data and retain important deep features by using attention and clustering, which effectively improves both kinds of the features representation, making their expressive ability balanced and comparable. The features of these two modal data are then fused through cross-attention Transformer, and the fused features are used to learn both tasks of cancer subtype classification and survival analysis by using multi-task learning. In this paper, MBFusion and other state of the art methods are compared on two public cancer datasets, and MBFusion shows an improvement of up to 10.1% by three kinds of evaluation metrics. In the ablation experiment, MBFusion explores the contribution of each modal data and each framework module to the performance. Furthermore, the interpretability of MBFusion is explained in detail to show the value of application.

Drug repositioning based on multi-view learning with matrix completion

Determining drug indications is a critical part of the drug development process. However, traditional drug discovery is expensive and time-consuming. Drug repositioning aims to find potential indications for existing drugs, which is considered as an important alternative to the traditional drug discovery. In this article, we propose a multi-view learning with matrix completion (MLMC) method to predict the potential associations between drugs and diseases. Specifically, MLMC first learns the comprehensive similarity matrices from five drug similarity matrices and two disease similarity matrices based on the multi-view learning (ML) with Laplacian graph regularization, and updates the drug-disease association matrix simultaneously. Then, we introduce matrix completion (MC) to add some positive entries in original association matrix based on low-rank structure, and re-execute the multi-view learning algorithm for association prediction. At last, the prediction results of the above two operations are integrated as the final output. Evaluated by 10-fold cross-validation and de novo tests, MLMC achieves higher prediction accuracy than the current state-of-the-art methods. Moreover, case studies confirm the ability of our method in novel drug-disease association discovery. The codes of MLMC are available at https://github.com/BioinformaticsCSU/MLMC. Contact: jxwang@mail.csu.edu.cn.

In silico drug repositioning based on integrated drug targets and canonical correlation analysis

Background

Besides binding to proteins, the most recent advances in pharmacogenomics indicate drugs can regulate the expression of non-coding RNAs (ncRNAs). The polypharmacological feature in drugs enables us to find new uses for existing drugs (namely drug repositioning). However, current computational methods for drug repositioning mainly consider proteins as drug targets. Meanwhile, these methods identify only statistical relationships between drugs and diseases. They provide little information about how drug-disease associations are formed at the molecular target level.

Methods

Herein, we first comprehensively collect proteins and two categories of ncRNAs as drug targets from public databases to construct drug–target interactions. Experimentally confirmed drug-disease associations are downloaded from an established database. A canonical correlation analysis (CCA) based method is then applied to the two datasets to extract correlated sets of targets and diseases. The correlated sets are regarded as canonical components, and they are used to investigate drug’s mechanism of actions. We finally develop a strategy to predict novel drug-disease associations for drug repositioning by combining all the extracted correlated sets.

Results

We receive 400 canonical components which correlate targets with diseases in our study. We select 4 components for analysis and find some top-ranking diseases in an extracted set might be treated by drugs interfacing with the top-ranking targets in the same set. Experimental results from 10-fold cross-validations show integrating different categories of target information results in better prediction performance than only using proteins or ncRNAs as targets. When compared with 3 state-of-the-art approaches, our method receives the highest AUC value 0.8576. We use our method to predict new indications for 789 drugs and confirm 24 predictions in the top 1 predictions.

Conclusions

To the best of our knowledge, this is the first computational effort which combines both proteins and ncRNAs as drug targets for drug repositioning. Our study provides a biologically relevant interpretation regarding the forming of drug-disease associations, which is useful for guiding future biomedical tests.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01203-1.

Dual Transcriptomic and Molecular Machine Learning Predicts all Major Clinical Forms of Drug Cardiotoxicity

Computational methods can increase productivity of drug discovery pipelines, through overcoming challenges such as cardiotoxicity identification. We demonstrate prediction and preservation of cardiotoxic relationships for six drug-induced cardiotoxicity types using a machine learning approach on a large collected and curated dataset of transcriptional and molecular profiles (1,131 drugs, 35% with known cardiotoxicities, and 9,933 samples). The algorithm generality is demonstrated through validation in an independent drug dataset, in addition to cross-validation. The best prediction attains an average accuracy of 79% in area under the curve (AUC) for safe versus risky drugs, across all six cardiotoxicity types on validation and 66% on the unseen set of drugs. Individual cardiotoxicities for specific drug types are also predicted with high accuracy, including cardiac disorder signs and symptoms for a previously unseen set of anti-inflammatory agents (AUC = 80%) and heart failures for an unseen set of anti-neoplastic agents (AUC = 76%). Besides, independent testing on transcriptional data from the Drug Toxicity Signature Generation Center (DToxS) produces similar results in terms of accuracy and shows an average AUC of 72% for previously seen drugs and 60% for unseen respectively. Given the ubiquitous manifestation of multiple drug adverse effects in every human organ, the methodology is expected to be applicable to additional tissue-specific side effects beyond cardiotoxicity.