4,693 research outputs found
Representation learning of drug and disease terms for drug repositioning
Drug repositioning (DR) refers to identification of novel indications for the
approved drugs. The requirement of huge investment of time as well as money and
risk of failure in clinical trials have led to surge in interest in drug
repositioning. DR exploits two major aspects associated with drugs and
diseases: existence of similarity among drugs and among diseases due to their
shared involved genes or pathways or common biological effects. Existing
methods of identifying drug-disease association majorly rely on the information
available in the structured databases only. On the other hand, abundant
information available in form of free texts in biomedical research articles are
not being fully exploited. Word-embedding or obtaining vector representation of
words from a large corpora of free texts using neural network methods have been
shown to give significant performance for several natural language processing
tasks. In this work we propose a novel way of representation learning to obtain
features of drugs and diseases by combining complementary information available
in unstructured texts and structured datasets. Next we use matrix completion
approach on these feature vectors to learn projection matrix between drug and
disease vector spaces. The proposed method has shown competitive performance
with state-of-the-art methods. Further, the case studies on Alzheimer's and
Hypertension diseases have shown that the predicted associations are matching
with the existing knowledge.Comment: Accepted to appear in 3rd IEEE International Conference on
Cybernetics (Spl Session: Deep Learning for Prediction and Estimation
DHLP 1&2: Giraph based distributed label propagation algorithms on heterogeneous drug-related networks
Background and Objective: Heterogeneous complex networks are large graphs
consisting of different types of nodes and edges. The knowledge extraction from
these networks is complicated. Moreover, the scale of these networks is
steadily increasing. Thus, scalable methods are required. Methods: In this
paper, two distributed label propagation algorithms for heterogeneous networks,
namely DHLP-1 and DHLP-2 have been introduced. Biological networks are one type
of the heterogeneous complex networks. As a case study, we have measured the
efficiency of our proposed DHLP-1 and DHLP-2 algorithms on a biological network
consisting of drugs, diseases, and targets. The subject we have studied in this
network is drug repositioning but our algorithms can be used as general methods
for heterogeneous networks other than the biological network. Results: We
compared the proposed algorithms with similar non-distributed versions of them
namely MINProp and Heter-LP. The experiments revealed the good performance of
the algorithms in terms of running time and accuracy.Comment: Source code available for Apache Giraph on Hadoo
Computational Models for Transplant Biomarker Discovery.
Translational medicine offers a rich promise for improved diagnostics and drug discovery for biomedical research in the field of transplantation, where continued unmet diagnostic and therapeutic needs persist. Current advent of genomics and proteomics profiling called "omics" provides new resources to develop novel biomarkers for clinical routine. Establishing such a marker system heavily depends on appropriate applications of computational algorithms and software, which are basically based on mathematical theories and models. Understanding these theories would help to apply appropriate algorithms to ensure biomarker systems successful. Here, we review the key advances in theories and mathematical models relevant to transplant biomarker developments. Advantages and limitations inherent inside these models are discussed. The principles of key -computational approaches for selecting efficiently the best subset of biomarkers from high--dimensional omics data are highlighted. Prediction models are also introduced, and the integration of multi-microarray data is also discussed. Appreciating these key advances would help to accelerate the development of clinically reliable biomarker systems
Recent Trends in Computational Research on Diseases
Recent advances in information technology have brought forth a paradigm shift in science, especially in the biology and medical fields. Statistical methodologies based on high-performance computing and big data analysis are now indispensable for the qualitative and quantitative understanding of experimental results. In fact, the last few decades have witnessed drastic improvements in high-throughput experiments in health science, for example, mass spectrometry, DNA microarray, next generation sequencing, etc. Those methods have been providing massive data involving four major branches of omics (genomics, transcriptomics, proteomics, and metabolomics). Information about amino acid sequences, protein structures, and molecular structures are fundamental data for the prediction of bioactivity of chemical compounds when screening drugs. On the other hand, cell imaging, clinical imaging, and personal healthcare devices are also providing important data concerning the human body and disease. In parallel, various methods of mathematical modelling such as machine learning have developed rapidly. All of these types of data can be utilized in computational approaches to understand disease mechanisms, diagnosis, prognosis, drug discovery, drug repositioning, disease biomarkers, driver mutations, copy number variations, disease pathways, and much more. In this Special Issue, we have published 8 excellent papers dedicated to a variety of computational problems in the biomedical field from the genomic level to the whole-person physiological level
Drug repurposing using biological networks
Drug repositioning is a strategy to identify new uses for existing, approved, or research drugs that are outside the scope of its original medical indication. Drug repurposing is based on the fact that one drug can act on multiple targets or that two diseases can have molecular similarities, among others. Currently, thanks to the rapid advancement of high-performance technologies, a massive amount of biological and biomedical data is being generated. This allows the use of computational methods and models based on biological networks to develop new possibilities for drug repurposing. Therefore, here, we provide an in-depth review of the main applications of drug repositioning that have been carried out using biological network models. The goal of this review is to show the usefulness of these computational methods to predict associations and to find candidate drugs for repositioning in new indications of certain diseases
How Can Network-Pharmacology Contribute to Antiepileptic Drug Development?
Network-pharmacology is a field of pharmacology emerging from the observation that most clinical drugs have multiple targets, contrasting with the previously dominant magic bullet paradigm which proposed the search of exquisitely selective drugs. What is more, drug targets are often involved in multiple diseases and frequently present co-expression patterns. Therefore, useful therapeutic information can be drawn from network representations of drug targets. Here, we discuss potential applications of drug-target networks in the field of antiepileptic drug development.Fil: Di Ianni, Mauricio Emiliano. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas. Cátedra de Química Medicinal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Talevi, Alan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas. Cátedra de Química Medicinal; Argentin
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