scholarly journals Learning from low-rank multimodal representations for predicting disease-drug associations

2021 ◽  
Vol 21 (S1) ◽  
Author(s):  
Pengwei Hu ◽  
Yu-an Huang ◽  
Jing Mei ◽  
Henry Leung ◽  
Zhan-heng Chen ◽  
...  
Keyword(s):  
Domain Knowledge ◽  
Computational Models ◽  
Drug Repositioning ◽  
Prediction Method ◽  
Substantial Improvement ◽  
Multimodal Fusion ◽  
Low Rank ◽  
Essential Information ◽  
Similarity Network ◽  
Disease Similarity

Abstract Background Disease-drug associations provide essential information for drug discovery and disease treatment. Many disease-drug associations remain unobserved or unknown, and trials to confirm these associations are time-consuming and expensive. To better understand and explore these valuable associations, it would be useful to develop computational methods for predicting unobserved disease-drug associations. With the advent of various datasets describing diseases and drugs, it has become more feasible to build a model describing the potential correlation between disease and drugs. Results In this work, we propose a new prediction method, called LMFDA, which works in several stages. First, it studies the drug chemical structure, disease MeSH descriptors, disease-related phenotypic terms, and drug-drug interactions. On this basis, similarity networks of different sources are constructed to enrich the representation of drugs and diseases. Based on the fused disease similarity network and drug similarity network, LMFDA calculated the association score of each pair of diseases and drugs in the database. This method achieves good performance on Fdataset and Cdataset, AUROCs were 91.6% and 92.1% respectively, higher than many of the existing computational models. Conclusions The novelty of LMFDA lies in the introduction of multimodal fusion using low-rank tensors to fuse multiple similar networks and combine matrix complement technology to predict potential association. We have demonstrated that LMFDA can display excellent network integration ability for accurate disease-drug association inferring and achieve substantial improvement over the advanced approach. Overall, experimental results on two real-world networks dataset demonstrate that LMFDA able to delivers an excellent detecting performance. Results also suggest that perfecting similar networks with as much domain knowledge as possible is a promising direction for drug repositioning.

scholarly journals Predicting Drug-Disease Association Based on Ensemble Strategy

2021 ◽  
Vol 12 ◽  
Author(s):  
Jianlin Wang ◽  
Wenxiu Wang ◽  
Chaokun Yan ◽  
Junwei Luo ◽  
Ge Zhang
Keyword(s):  
Prediction Models ◽  
Drug Repositioning ◽  
Predictive Ability ◽  
Disease Association ◽  
New Drugs ◽  
Similarity Network ◽  
Disease Similarity ◽  
Ensemble Strategy ◽  
Disease Associations ◽  
Reducing Costs

Drug repositioning is used to find new uses for existing drugs, effectively shortening the drug research and development cycle and reducing costs and risks. A new model of drug repositioning based on ensemble learning is proposed. This work develops a novel computational drug repositioning approach called CMAF to discover potential drug-disease associations. First, for new drugs and diseases or unknown drug-disease pairs, based on their known neighbor information, an association probability can be obtained by implementing the weighted K nearest known neighbors (WKNKN) method and improving the drug-disease association information. Then, a new drug similarity network and new disease similarity network can be constructed. Three prediction models are applied and ensembled to enable the final association of drug-disease pairs based on improved drug-disease association information and the constructed similarity network. The experimental results demonstrate that the developed approach outperforms recent state-of-the-art prediction models. Case studies further confirm the predictive ability of the proposed method. Our proposed method can effectively improve the prediction results.

MDAPlatform: a Component-based Platform for Constructing and Assessing miRNA-disease association Prediction Methods

2021 ◽  
Vol 16 ◽  
Author(s):  
Yayan Zhang ◽  
Guihua Duan ◽  
Cheng Yan ◽  
Haolun Yi ◽  
Fang-Xiang Wu ◽  
...  
Keyword(s):  
Computational Models ◽  
Critical Role ◽  
Prediction Method ◽  
Disease Association ◽  
Prediction Methods ◽  
Comparison Results ◽  
Disease Associations ◽  
Pros And Cons ◽  
Clinical Drugs ◽  
Validation Experiments

Background: Increasing evidence has indicated that miRNA-disease association prediction plays a critical role in the study of clinical drugs. Researchers have proposed many computational models for miRNA-disease prediction. However, there is no unified platform to compare and analyze the pros and cons or share the code and data of these models. Objective: In this study, we develop an easy-to-use platform (MDAPlatform) to construct and assess miRNA-disease association prediction method. Methods: MDAPlatform integrates the relevant data of miRNA, disease and miRNA-disease associations that are used in previous miRNA-disease association prediction studies. Based on the componentized model, it develops differet components of previous computational methods. Results: Users can conduct cross validation experiments and compare their methods with other methods, and the visualized comparison results are also provided. Conclusion: Based on the componentized model, MDAPlatform provides easy-to-operate interfaces to construct the miRNA-disease association method, which is beneficial to develop new miRNA-disease association prediction methods in the future.

A Hypergraph-Based Knowledge Representation Model for Smart Product-Service System Development

2021 ◽  
Author(s):  
Wang Zuoxu ◽  
Li Xinyu ◽  
Chen Chun-Hsien ◽  
Zheng Pai
Keyword(s):  
Knowledge Representation ◽  
Domain Knowledge ◽  
Manufacturing Companies ◽  
Binary Relations ◽  
Fundamental Study ◽  
Essential Information ◽  
Knowledge Reasoning ◽  
Representation Model ◽  
Product Service ◽  
Smart Product

Abstract In the trend of digital servitization, manufacturing companies have been transforming their business paradigms to Smart product-service systems (Smart PSS) by integrating products and associated services as bundles. To support the knowledge-intensive process of Smart PSS development, massive domain knowledge should be well-organized and reused. However, due to the existence of non-binary relations caused by product-service bundles (PSB) and context-awareness concerns in the Smart PSS development activities, conventional graph-based approaches for knowledge representation may lose essential information in transforming non-binary relations into binary ones, and hence cause incorrect results in the subsequent knowledge queries. To mitigate this problem, a hypergraph-based knowledge representation model for Smart PSS was proposed, which represents the non-binary relations among multiple entities with hyperedges. Technically, the knowledge source and the typical hyperedge schema in Smart PSS development are identified in this paper. A detailed case study in the scenarios of 3D printing troubleshooting and PSB recommendation was conducted to showcase the proposed hypergraph-based knowledge representation model and demonstrate its validity. The results show that the hypergraph-based knowledge model significantly relieves the sparsity in the ordinary KG by adding multiple hyperedges. It is anticipated that the proposed hypergraph knowledge representation model can serve as a fundamental study for further knowledge reasoning activities.

scholarly journals NEDD: a network embedding based method for predicting drug-disease associations

2020 ◽  
Vol 21 (S13) ◽  
Author(s):  
Renyi Zhou ◽  
Zhangli Lu ◽  
Huimin Luo ◽  
Ju Xiang ◽  
Min Zeng ◽  
...  
Keyword(s):  
Drug Repositioning ◽  
Computational Method ◽  
Heterogeneous Information ◽  
Gold Standard Dataset ◽  
Disease Similarity ◽  
Disease Associations ◽  
Meta Path ◽  
Approved Drugs ◽  
Low Dimensional ◽  
Novel Associations

Abstract Background Drug discovery is known for the large amount of money and time it consumes and the high risk it takes. Drug repositioning has, therefore, become a popular approach to save time and cost by finding novel indications for approved drugs. In order to distinguish these novel indications accurately in a great many of latent associations between drugs and diseases, it is necessary to exploit abundant heterogeneous information about drugs and diseases. Results In this article, we propose a meta-path-based computational method called NEDD to predict novel associations between drugs and diseases using heterogeneous information. First, we construct a heterogeneous network as an undirected graph by integrating drug-drug similarity, disease-disease similarity, and known drug-disease associations. NEDD uses meta paths of different lengths to explicitly capture the indirect relationships, or high order proximity, within drugs and diseases, by which the low dimensional representation vectors of drugs and diseases are obtained. NEDD then uses a random forest classifier to predict novel associations between drugs and diseases. Conclusions The experiments on a gold standard dataset which contains 1933 validated drug–disease associations show that NEDD produces superior prediction results compared with the state-of-the-art approaches.

scholarly journals DeepCU: Integrating both Common and Unique Latent Information for Multimodal Sentiment Analysis

2019 ◽  
Author(s):  
Sunny Verma ◽  
Chen Wang ◽  
Liming Zhu ◽  
Wei Liu
Keyword(s):  
Sentiment Analysis ◽  
Multimodal Fusion ◽  
Low Rank ◽  
Specific Information ◽  
Common Information ◽  
Unique Information ◽  
The Common ◽  
Multimodal Data Fusion ◽  
Real World Datasets ◽  
Multimodal Sentiment Analysis

Multimodal sentiment analysis combines information available from visual, textual, and acoustic representations for sentiment prediction. The recent multimodal fusion schemes combine multiple modalities as a tensor and obtain either; the common information by utilizing neural networks, or the unique information by modeling low-rank representation of the tensor. However, both of these information are essential as they render inter-modal and intra-modal relationships of the data. In this research, we first propose a novel deep architecture to extract the common information from the multi-mode representations. Furthermore, we propose unique networks to obtain the modality-specific information that enhances the generalization performance of our multimodal system. Finally, we integrate these two aspects of information via a fusion layer and propose a novel multimodal data fusion architecture, which we call DeepCU (Deep network with both Common and Unique latent information). The proposed DeepCU consolidates the two networks for joint utilization and discovery of all-important latent information. Comprehensive experiments are conducted to demonstrate the effectiveness of utilizing both common and unique information discovered by DeepCU on multiple real-world datasets. The source code of proposed DeepCU is available at https://github.com/sverma88/DeepCU-IJCAI19.

scholarly journals Multimodal phenotypic axes of Parkinson’s disease

2020 ◽  
Author(s):  
Ross D. Markello ◽  
Golia Shafiei ◽  
Christina Tremblay ◽  
Ronald B. Postuma ◽  
Alain Dagher ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Large Scale ◽  
De Novo ◽  
Patient Characteristics ◽  
Multimodal Fusion ◽  
Compact Set ◽  
Similarity Network ◽  
Mri Morphometry ◽  
Low Dimensional

Individuals with Parkinson’s disease present with a complex clinical phenotype, encompassing sleep, motor, cognitive, and affective disturbances. However, characterizations of PD are typically made for the “average” patient, ignoring patient heterogeneity and obscuring important individual differences. Modern large-scale data sharing efforts provide a unique opportunity to precisely investigate individual patient characteristics, but there exists no analytic framework for comprehensively integrating data modalities. Here we apply an unsupervised learning method—similarity network fusion—to objectively integrate MRI morphometry, dopamine active transporter binding, protein assays, and clinical measurements from n = 186 individuals with de novo Parkinson’s disease from the Parkinson’s Progression Markers Initiative. We show that multimodal fusion captures inter-dependencies among data modalities that would otherwise be overlooked by field standard techniques like data concatenation. We then examine how patient subgroups derived from fused data map onto clinical phenotypes, and how neuroimaging data is critical to this delineation. Finally, we identify a compact set of phenotypic axes that span the patient population, demonstrating that this continuous, low-dimensional projection of individual patients presents a more parsimonious representation of heterogeneity in the sample compared to discrete biotypes. Altogether, these findings showcase the potential of similarity network fusion for combining multimodal data in heterogeneous patient populations.

scholarly journals ON THE JOINT EXPLOITATION OF OPTICAL AND SAR SATELLITE IMAGERY FOR GRASSLAND MONITORING

2020 ◽  
Vol XLIII-B3-2020 ◽  
pp. 591-598
Author(s):  
A. Garioud ◽  
S. Valero ◽  
S. Giordano ◽  
C. Mallet
Keyword(s):  
Temporal Dynamics ◽  
Agricultural Practices ◽  
Physical Nature ◽  
Multimodal Fusion ◽  
Contextual Knowledge ◽  
Essential Information ◽  
Object Based ◽  
Frequent Monitoring ◽  
Operational Solution ◽  
Sentinel 2

Abstract. Time series of optical and Synthetic Aperture RADAR (SAR) images provide complementary knowledge about the cover and use of the Earth surface since they exhibit information of distinct physical nature. They have proved to be particularly relevant for monitoring large areas with high temporal dynamics and related to significant ecosystem services. Grasslands are such crucial surfaces, both in terms of economic and environmental issues and the automatic and frequent monitoring of their agricultural practices is required for many purposes. To address this problem, the deep-based SenDVI framework is presented. SenDVI proposes an object-based methodology to estimate NDVI values from Sentinel-1 SAR observations and contextual knowledge (weather, terrain). Values are regressed every 6 days for compliance with monitoring purposes. Very satisfactory results are obtained with this low-level multimodal fusion strategy (R2 = 0.84 on a Sentinel-2 tile). Finer analysis is however required to fully assess the relevance of each modality (Sentinel-1, Sentinel-2, weather, terrain) and feature sets and to propose the simplest conceivable framework. Results show that not all features are necessary and can be discarded while others have a mandatory contribution to the regression task. Moreover, experiments prove that accuracy can be improved by not saturating the network with non-essential information (among contextual knowledge in particular). This allows to move towards more operational solution.

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