A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data

Machine Learning-Enabled Drug-Induced Toxicity Prediction

Unexpected toxicity has become a significant obstacle to drug candidate development, accounting for 30% of drug discovery failures. Traditional toxicity assessment through animal testing is costly and time-consuming. Big data and artificial intelligence (AI), especially machine learning (ML), are robustly contributing to innovation and progress in toxicology research. However, the optimal AI model for different types of toxicity usually varies, making it essential to conduct comparative analyses of AI methods across toxicity domains. The diverse data sources also pose challenges for researchers focusing on specific toxicity studies. In this review, 10 categories of drug-induced toxicity is examined, summarizing the characteristics and applicable ML models, including both predictive and interpretable algorithms, striking a balance between breadth and depth. Key databases and tools used in toxicity prediction are also highlighted, including toxicology, chemical, multi-omics, and benchmark databases, organized by their focus and function to clarify their roles in drug-induced toxicity prediction. Finally, strategies to turn challenges into opportunities are analyzed and discussed. This review may provide researchers with a valuable reference for understanding and utilizing the available resources to bridge prediction and mechanistic insights, and further advance the application of ML in drugs-induced toxicity prediction.

A mechanistic neural network model predicts both potency and toxicity of antimicrobial combination therapies

Antimicrobial resistance poses a major global threat due to the diminishing efficacy of current treatments and limited new therapies. Combination therapy with existing drugs offers a promising solution, yet current empirical methods often lead to suboptimal efficacy and inadvertent toxicity. The high cost of experimentally testing numerous combinations underscores the need for data-driven methods to streamline treatment design. We introduce CALMA, an approach that predicts the potency and toxicity of multi-drug combinations in Escherichia coli and Mycobacterium tuberculosis. CALMA identified synergistic antimicrobial combinations involving vancomycin and isoniazid that were antagonistic for toxicity, which were validated using in vitro cell viability assays in human cell lines and through mining of patient health records that showed reduced side effects in patients taking combinations identified by CALMA. By combining mechanistic modelling with deep learning, CALMA improves the interpretability of neural networks, identifies key pathways influencing drug interactions, and prioritizes combinations with enhanced potency and reduced toxicity.

MFA-DTI: Drug-target interaction prediction based on multi-feature fusion adopted framework

The identification of drug-target interactions (DTI) is a valuable step in the drug discovery and repositioning process. However, traditional laboratory experiments are time-consuming and expensive. Computational methods have streamlined research to determine DTIs. The application of deep learning methods has significantly improved the prediction performance for DTIs. Modern deep learning methods can leverage multiple sources of information, including sequence data that contains biological structural information, and interaction data. While useful, these methods cannot be effectively applied to each type of information individually (e.g., chemical structure and interaction network) and do not take into account the specificity of DTI data such as low- or zero-interaction biological entities. To overcome these limitations, we propose a method called MFA-DTI (Multi-feature Fusion Adopted framework for DTI). MFA-DTI consists of three modules: an interaction graph learning module that processes the interaction network to generate interaction vectors, a chemical structure learning module that extracts features from the chemical structure, and a fusion module that combines these features for the final prediction. To validate the performance of MFA-DTI, we conducted experiments on six public datasets under different settings. The results indicate that the proposed method is highly effective in various settings and outperforms state-of-the-art methods.

The Convergence of Radiology and Genomics: Advancing Breast Cancer Diagnosis with Radiogenomics

Despite significant progress in the prevention, screening, diagnosis, prognosis, and therapy of breast cancer (BC), it remains a highly prevalent and life-threatening disease affecting millions worldwide. Molecular subtyping of BC is crucial for predictive and prognostic purposes due to the diverse clinical behaviors observed across various types. The molecular heterogeneity of BC poses uncertainties in its impact on diagnosis, prognosis, and treatment. Numerous studies have highlighted genetic and environmental differences between patients from different geographic regions, emphasizing the need for localized research. International studies have revealed that patients with African heritage are often diagnosed at a more advanced stage and exhibit poorer responses to treatment and lower survival rates. Despite these global findings, there is a dearth of in-depth studies focusing on communities in the African region. Early diagnosis and timely treatment are paramount to improving survival rates. In this context, radiogenomics emerges as a promising field within precision medicine. By associating genetic patterns with image attributes or features, radiogenomics has the potential to significantly improve early detection, prognosis, and diagnosis. It can provide valuable insights into potential treatment options and predict the likelihood of survival, progression, and relapse. Radiogenomics allows for visual features and genetic marker linkage that promises to eliminate the need for biopsy and sequencing. The application of radiogenomics not only contributes to advancing precision oncology and individualized patient treatment but also streamlines clinical workflows. This review aims to delve into the theoretical underpinnings of radiogenomics and explore its practical applications in the diagnosis, management, and treatment of BC and to put radiogenomics on a path towards fully integrated diagnostics.

ML-FGAT: Identification of multi-label protein subcellular localization by interpretable graph attention networks and feature-generative adversarial networks

The prediction of multi-label protein subcellular localization (SCL) is a pivotal area in bioinformatics research. Recent advancements in protein structure research have facilitated the application of graph neural networks. This paper introduces a novel approach termed ML-FGAT. The approach begins by extracting node information of proteins from sequence data, physical-chemical properties, evolutionary insights, and structural details. Subsequently, various evolutionary techniques are integrated to consolidate multi-view information. A linear discriminant analysis framework, grounded on entropy weight, is then employed to reduce the dimensionality of the merged features. To enhance the robustness of the model, the training dataset is augmented using feature-generative adversarial networks. For the primary prediction step, graph attention networks are employed to determine multi-label protein SCL, leveraging both node and neighboring information. The interpretability is enhanced by analyzing the attention weight parameters. The training is based on the Gram-positive bacteria dataset, while validation employs newly constructed datasets: human, virus, Gram-negative bacteria, plant, and SARS-CoV-2. Following a leave-one-out cross-validation procedure, ML-FGAT demonstrates noteworthy superiority in this domain.

An effective framework for predicting drug-drug interactions based on molecular substructures and knowledge graph neural network

Drug-drug interactions (DDIs) play a central role in drug research, as the simultaneous administration of multiple drugs can have harmful or beneficial effects. Harmful interactions lead to adverse reactions, some of which can be life-threatening, while beneficial interactions can promote efficacy. Therefore, it is crucial for physicians, patients, and the research community to identify potential DDIs. Although many AI-based techniques have been proposed for predicting DDIs, most existing computational models primarily focus on integrating multiple data sources or combining popular embedding methods. Researchers often overlook the valuable information within the molecular structure of drugs or only consider the structural information of drugs, neglecting the relationship or topological information between drugs and other biological objects. In this study, we propose MSKG-DDI - a two-component framework that incorporates the Drug Chemical Structure Graph-based component and the Drug Knowledge Graph-based component to capture multimodal characteristics of drugs. Subsequently, a multimodal fusion neural layer is utilized to explore the complementarity between multimodal representations of drugs. Extensive experiments were conducted using two real-world datasets, and the results demonstrate that MSKG-DDI outperforms other state-of-the-art models in binary-class, multi-class, and multi-label prediction tasks under both transductive and inductive settings. Furthermore, the ablation analysis further confirms the practical usefulness of MSKG-DDI.

MolFPG: Multi-level fingerprint-based Graph Transformer for accurate and robust drug toxicity prediction

Drug toxicity prediction is essential to drug development, which can help screen compounds with potential toxicity and reduce the cost and risk of animal experiments and clinical trials. However, traditional handcrafted feature-based and molecular-graph-based approaches are insufficient for molecular representation learning. To address the problem, we developed an innovative molecular fingerprint Graph Transformer framework (MolFPG) with a global-aware module for interpretable toxicity prediction. Our approach encodes compounds using multiple molecular fingerprinting techniques and integrates Graph Transformer-based molecular representation for feature learning and toxic prediction. Experimental results show that our proposed approach has high accuracy and reliability in predicting drug toxicity. In addition, we explored the relationship between drug features and toxicity through an interpretive analysis approach, which improved the interpretability of the approach. Our results highlight the potential of Graph Transformers and multi-level fingerprints for accelerating the drug discovery process by reliably, effectively alarming drug safety. We believe that our study will provide vital support and reference for further development in the field of drug development and toxicity assessment.

Attention-based cross domain graph neural network for prediction of drug-drug interactions

Drug-drug interactions (DDI) may lead to adverse reactions in human body and accurate prediction of DDI can mitigate the medical risk. Currently, most of computer-aided DDI prediction methods construct models based on drug-associated features or DDI network, ignoring the potential information contained in drug-related biological entities such as targets and genes. Besides, existing DDI network-based models could not make effective predictions for drugs without any known DDI records. To address the above limitations, we propose an attention-based cross domain graph neural network (ACDGNN) for DDI prediction, which considers the drug-related different entities and propagate information through cross domain operation. Different from the existing methods, ACDGNN not only considers rich information contained in drug-related biomedical entities in biological heterogeneous network, but also adopts cross-domain transformation to eliminate heterogeneity between different types of entities. ACDGNN can be used in the prediction of DDIs in both transductive and inductive setting. By conducting experiments on real-world dataset, we compare the performance of ACDGNN with several state-of-the-art methods. The experimental results show that ACDGNN can effectively predict DDIs and outperform the comparison models.

Golgi_DF: Golgi proteins classification with deep forest

Introduction

Golgi is one of the components of the inner membrane system in eukaryotic cells. Its main function is to send the proteins involved in the synthesis of endoplasmic reticulum to specific parts of cells or secrete them outside cells. It can be seen that Golgi is an important organelle for eukaryotic cells to synthesize proteins. Golgi disorders can cause various neurodegenerative and genetic diseases, and the accurate classification of Golgi proteins is helpful to develop corresponding therapeutic drugs.

Methods

This paper proposed a novel Golgi proteins classification method, which is Golgi_DF with the deep forest algorithm. Firstly, the classified proteins method can be converted the vector features containing various information. Secondly, the synthetic minority oversampling technique (SMOTE) is utilized to deal with the classified samples. Next, the Light GBM method is utilized to feature reduction. Meanwhile, the features can be utilized in the penultimate dense layer. Therefore, the reconstructed features can be classified with the deep forest algorithm.

Results

In Golgi_DF, this method can be utilized to select the important features and identify Golgi proteins. Experiments show that the well-performance than the other art-of-the state methods. Golgi_DF as a standalone tools, all its source codes publicly available at https://github.com/baowz12345/golgiDF.

Discussion

Golgi_DF employed reconstructed feature to classify the Golgi proteins. Such method may achieve more available features among the UniRep features.

An omics-to-omics joint knowledge association subtensor model for radiogenomics cross-modal modules from genomics and ultrasonic images of breast cancers

The radiogenomics analysis can provide the connections between genomics and radiomics, which can infer the genomic features of tumors from their radiogenomic associations through the low-cost and non-invasiveness screening ultrasonic images. Although there are a number of pioneer approaches exploring the connections between genomic aberrations and ultrasonic features, these studies mainly focus on the relationship between ultrasonic features and only the most popular cancer genes, confronting two difficulties: missing many-to-many relationships as omics-to-omics view, and confounding group-specific associations with whole sample associations. To overcome the difficulty of omics-to-omics view and the issue of tumor heterogeneity, we propose an omics-to-omics joint knowledge association subtensor model. Specifically, the subtensor factorization framework can successfully discover the joint cross-modal module via an omics-to-omics view, while the sparse weight sample indication strategy can mine sample subgroups from the multi-omic data with tumor heterogeneity. The experimental evaluation result shows the jointness of the discovered modules across omics, their association with tumorigenesis contribution, and their relation for cancer related functions. In summary, our proposed omics-to-omics joint knowledge association subtensor model can serve as an efficient tool for radiogenomic knowledge associations, promoting the cross-modal knowledge graph construction of in explainable artificial intelligence cancer diagnosis.

ToxMVA: An end-to-end multi-view deep autoencoder method for protein toxicity prediction

Effectively predicting protein toxicity plays an essential step in the early stage of protein-based drug discovery, which is of great help to speed up novel drug screening and reduce costs. Recently, several relevant datasets have been designed, and then machine learning-based methods have been proposed to predict the toxicity of the protein and have shown satisfactory performance. However, previous studies generally directly concatenate different protein features, which may introduce irrelevant information and decrease model performance. In this study, we present a novel end-to-end deep learning-based method called ToxMVA, to predict protein toxicity. To be specific, we first build comprehensive feature profiles of proteins based on primary sequences, including sequential, physicochemical, and contextual semantic information. Next, an autoencoder network is introduced to integrate the multi-view information for obtaining a more concise and accurate feature representation. Extensive experimental results on three datasets demonstrate that ToxMVA has superior performance for protein toxicity prediction and shows better robustness among three different datasets.