Dataset Information

Computational Intelligence for Studying Sustainability Challenges: Tools and Methods for Dealing With Deep Uncertainty and Complexity.

ABSTRACT: The study of sustainability challenges requires the consideration of multiple coupled systems that are often complex and deeply uncertain. As a result, traditional analytical methods offer limited insights with respect to how to best address such challenges. By analyzing the case of global climate change mitigation, this paper shows that the combination of high-performance computing, mathematical modeling, and computational intelligence tools, such as optimization and clustering algorithms, leads to richer analytical insights. The paper concludes by proposing an analytical hierarchy of computational tools that can be applied to other sustainability challenges.

SUBMITTER: Molina-Perez E

PROVIDER: S-EPMC7805846 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Computational Intelligence for Studying Sustainability Challenges: Tools and Methods for Dealing With Deep Uncertainty and Complexity.

Molina-Perez Edmundo E Esquivel-Flores Oscar A OA Zamora-Maldonado Hilda H

Frontiers in robotics and AI 20200917

The study of sustainability challenges requires the consideration of multiple coupled systems that are often complex and deeply uncertain. As a result, traditional analytical methods offer limited insights with respect to how to best address such challenges. By analyzing the case of global climate change mitigation, this paper shows that the combination of high-performance computing, mathematical modeling, and computational intelligence tools, such as optimization and clustering algorithms, lead ...[more]

PMID: 33501278

Similar Datasets

Project description:The identification of interactions between drugs/compounds and their targets is crucial for the development of new drugs. In vitro screening experiments (i.e. bioassays) are frequently used for this purpose; however, experimental approaches are insufficient to explore novel drug-target interactions, mainly because of feasibility problems, as they are labour intensive, costly and time consuming. A computational field known as 'virtual screening' (VS) has emerged in the past decades to aid experimental drug discovery studies by statistically estimating unknown bio-interactions between compounds and biological targets. These methods use the physico-chemical and structural properties of compounds and/or target proteins along with the experimentally verified bio-interaction information to generate predictive models. Lately, sophisticated machine learning techniques are applied in VS to elevate the predictive performance.The objective of this study is to examine and discuss the recent applications of machine learning techniques in VS, including deep learning, which became highly popular after giving rise to epochal developments in the fields of computer vision and natural language processing. The past 3 years have witnessed an unprecedented amount of research studies considering the application of deep learning in biomedicine, including computational drug discovery. In this review, we first describe the main instruments of VS methods, including compound and protein features (i.e. representations and descriptors), frequently used libraries and toolkits for VS, bioactivity databases and gold-standard data sets for system training and benchmarking. We subsequently review recent VS studies with a strong emphasis on deep learning applications. Finally, we discuss the present state of the field, including the current challenges and suggest future directions. We believe that this survey will provide insight to the researchers working in the field of computational drug discovery in terms of comprehending and developing novel bio-prediction methods.

Project description:Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported phosphopeptide identification and phosphosite localization results, underscoring a critical need for benchmarking. While efforts have been made to compare performance of computational pipelines using data from synthetic phosphopeptides, evaluations involving real application data have been largely limited to comparing the numbers of phosphopeptide identifications due to the lack of appropriate evaluation metrics. We investigated three deep-learning-derived features as potential evaluation metrics: phosphosite probability, Delta RT, and spectral similarity. Predicted phosphosite probability is computed by MusiteDeep, which provides high accuracy as previously reported; Delta RT is defined as the absolute retention time (RT) difference between RTs observed and predicted by AutoRT; and spectral similarity is defined as the Pearson's correlation coefficient between spectra observed and predicted by pDeep2. Using a synthetic peptide dataset, we found that both Delta RT and spectral similarity provided excellent discrimination between correct and incorrect peptide-spectrum matches (PSMs) both when incorrect PSMs involved wrong peptide sequences and even when incorrect PSMs were caused by only incorrect phosphosite localization. Based on these results, we used all the three deep-learning-derived features as evaluation metrics to compare different computational pipelines on diverse set of phosphoproteomic datasets and showed their utility in benchmarking performance of the pipelines. The benchmark metrics demonstrated in this study will enable users to select computational pipelines and parameters for routine analysis of phosphoproteomics data and will offer guidance for developers to improve computational methods.

Dataset Information

Computational Intelligence for Studying Sustainability Challenges: Tools and Methods for Dealing With Deep Uncertainty and Complexity.

Publications

Computational Intelligence for Studying Sustainability Challenges: Tools and Methods for Dealing With Deep Uncertainty and Complexity.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure