Search results for "Computation"
showing 10 items of 7362 documents
Advancing Deep Learning for Earth Sciences: From Hybrid Modeling to Interpretability
2020
Machine learning and deep learning in particular have made a huge impact in many fields of science and engineering. In the last decade, advanced deep learning methods have been developed and applied to remote sensing and geoscientific data problems extensively. Applications on classification and parameter retrieval are making a difference: methods are very accurate, can handle large amounts of data, and can deal with spatial and temporal data structures efficiently. Nevertheless, several important challenges need still to be addressed. First, current standard deep architectures cannot deal with long-range dependencies so distant driving processes (in space or time) are not captured, and the…
MetNet: A two-level approach to reconstructing and comparing metabolic networks
2021
Metabolic pathway comparison and interaction between different species can detect important information for drug engineering and medical science. In the literature, proposals for reconstructing and comparing metabolic networks present two main problems: network reconstruction requires usually human intervention to integrate information from different sources and, in metabolic comparison, the size of the networks leads to a challenging computational problem. We propose to automatically reconstruct a metabolic network on the basis of KEGG database information. Our proposal relies on a two-level representation of the huge metabolic network: the first level is graph-based and depicts pathways a…
The promise of spintronics for unconventional computing
2021
Novel computational paradigms may provide the blueprint to help solving the time and energy limitations that we face with our modern computers, and provide solutions to complex problems more efficiently (with reduced time, power consumption and/or less device footprint) than is currently possible with standard approaches. Spintronics offers a promising basis for the development of efficient devices and unconventional operations for at least three main reasons: (i) the low-power requirements of spin-based devices, i.e., requiring no standby power for operation and the possibility to write information with small dynamic energy dissipation, (ii) the strong nonlinearity, time nonlocality, and/o…
Non-equilibrium Markov state modeling of periodically driven biomolecules
2019
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external p…
GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation
2020
Atomistic simulations of large biomolecular systems with chemical variability such as constant pH dynamic protonation offer multiple challenges in high performance computing. One of them is the correct treatment of the involved electrostatics in an efficient and highly scalable way. Here we review and assess two of the main building blocks that will permit such simulations: (1) An electrostatics library based on the Fast Multipole Method (FMM) that treats local alternative charge distributions with minimal overhead, and (2) A $λ$-dynamics module working in tandem with the FMM that enables various types of chemical transitions during the simulation. Our $λ$-dynamics and FMM implementations d…
Nonnegative Tensor Train Decompositions for Multi-domain Feature Extraction and Clustering
2016
Tensor train (TT) is one of the modern tensor decomposition models for low-rank approximation of high-order tensors. For nonnegative multiway array data analysis, we propose a nonnegative TT (NTT) decomposition algorithm for the NTT model and a hybrid model called the NTT-Tucker model. By employing the hierarchical alternating least squares approach, each fiber vector of core tensors is optimized efficiently at each iteration. We compared the performances of the proposed method with a standard nonnegative Tucker decomposition (NTD) algorithm by using benchmark data sets including event-related potential data and facial image data in multi-domain feature extraction and clustering tasks. It i…
Computational Intelligence and Citizen Communication in the Smart City
2016
Information and communication are at the core of the intelligent city of tomorrow, and the key components of a smart city cannot prescind from data exchanges and interconnectedness. Citizen communication is an integral part of the smart city’s development plans: freedom of information and involvement in collective decisions, e-democracy and decision-making feedback can be greatly enhanced in an intelligent city, and, among other smart city components, foster a new era of participation and wise decisions. In this contribution we describe the methodologies that can be implemented in order to correctly develop automatic recognition systems for citizen communication, paying special attention to…
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats
2020
© The Author(s) 2020.
AnyOLAP
2021
The volume of data that is processed and produced by modern data-intensive applications is constantly increasing. Of course, along with the volume, the interest in analyzing and interpreting this data increases as well. As a consequence, more and more DBMSs and processing frameworks are specialized towards the efficient execution of long-running, read-only analytical queries. Unfortunately, to enable analysis, the data first has to be moved from the source application to the analytics tool via a lengthy ETL process, which increases the runtime and complexity of the analysis pipeline. In this work, we advocate to simply skip ETL altogether. With AnyOLAP, we can perform online analysis of dat…
Advanced computation in cardiovascular physiology: New challenges and opportunities
2021
Recent developments in computational physiology have successfully exploited advanced signal processing and artificial intelligence tools for predicting or uncovering characteristic features of physiological and pathological states in humans. While these advanced tools have demonstrated excellent diagnostic capabilities, the high complexity of these computational 'black boxes’ may severely limit scientific inference, especially in terms of biological insight about both physiology and pathological aberrations. This theme issue highlights current challenges and opportunities of advanced computational tools for processing dynamical data reflecting autonomic nervous system dynamics, with a speci…