11 research outputs found
A local adaptive method for the numerical approximation in seismic wave modelling
No full textWe propose a new numerical approach for the solution of the 2D acoustic wave equation to model the predicted data in the field of active-source seismic inverse problems. This method consists in using an explicit finite difference technique with an adaptive order of approximation of the spatial derivatives that takes into account the local velocity at the grid nodes. Testing our method to simulate the recorded seismograms in a marine seismic acquisition, we found that the low computational time and the low approximation error of the proposed approach make it suitable in the context of seismic inversion problems
Domain Specific Instruction Set Extensions
No full textOver the past years, a considerable amount of effort has been devoted to the definition and implementation of techniques for the optimization and acceleration of applications on various computing platforms. Among these techniques, the extension of a given instruction-set architecture with custom instructions has become a common approach. Custom instructions effectively reduce the dynamic instruction count, which, in turn, leads to increase in performance and reduction in power consumption. Traditionally, existing techniques address Instruction-Set Extension (ISE) on a per-application basis. Anyhow, when many applications have to be considered at the same time, ISE on a per-application basis is, clearly, less effective, as the custom instructions have often limited re-utilization across applications. To overcome this problem, we propose a new framework for the automatic generation of domain-specific ISEs. Experimental results show that, the proposed framework, evaluated on a number of applications from various domains, can effectively generate domain-specific instructions with high utilization factor across the targeted applications. At the same time, the generated instructions reduce the instruction count, 45% on average and upto 80% in special cases. This, in turn, can lead to considerable improvements in performance and reduction of power consumption.Parallel and Distributed SystemsComputer EngineeringElectrical Engineering, Mathematics and Computer Scienc
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells
No full textBACKGROUND: Sophisticated methods to properly pre-process and analyze the increasing collection of single-cell RNA sequencing (scRNA-seq) data are increasingly being developed. On the contrary, the best practices to integrate these data into metabolic networks, aiming at describing metabolic phenotypes within a heterogeneous cell population, have been poorly investigated. In this regard, a critical factor is the presence of false zero values in reactions essential for a fundamental metabolic function, such as biomass or energy production. Here, we investigate the role of denoising strategies in mitigating this problem. METHODS: We applied state-of-the-art denoising strategies - namely MAGIC, ENHANCE, and SAVER - on three public scRNA-seq datasets. We then associated a metabolic flux distribution with every single cell by embedding its noise-free transcriptomics profile in the constraints of the optimization of a core metabolic model. Finally, we used the obtained single-cell optimal metabolic fluxes as features for cluster analysis. We compared the results obtained with different techniques, and with or without the use of denoising. We also investigated the possibility of applying denoising directly on the Reaction Activity Scores, which are metabolic features extracted from the read counts, rather than on the read counts. RESULTS: We show that denoising of transcriptomics data improves the clustering of single cells. We also illustrate that denoising restores important metabolic properties, such as the correlation between cell cycle phase and biomass accumulation, and between the RAS scores of reactions belonging to the same metabolic pathway. We show that MAGIC performs better than ENHANCE and SAVER, and that, denoising applied directly on the RAS matrix could be an effective alternative in removing false zero values from essential metabolic reactions. CONCLUSIONS: Our results indicate that including denoising as a pre-processing operation represents a milestone to integrate scRNA-seq data into Flux Balance Analysis simulations and to perform single-cell cluster analysis with a focus on metabolic phenotypes
Seismic coupling for the Aegean - Anatolian region
No full textSeismic coupling helps define how large the earthquake potential of a region is, as well as the presence of asperities along plate zones. This work seeks to provide an improved picture of the seismic coupling for the Aegean-Anatolian region by taking advantage of extensive seismic and geodetic datasets. To estimate coupling, we compiled a series of by-products that are specific ingredients also for seismic hazard studies. With these by-products, we found that the seismogenic thickness is thinner (10–15 km) or thicker (20 to 30 km) to the east and to the west, respectively and even deeper along the Hellenic subduction zone. The b-value ranges between 0.9 and 1.1 for the entire area with high values concentrated at locations of Late Miocene to -recent volcanism whereas low b-values (<0.8) concentrate along most of the Northern Anatolian fault zone that may suggests stress accumulation. Seismic coupling is low (<35%) or intermediate (35% - 70%) in most of the area, while the Karliova triple junction, on a N-S-oriented belt along the boundary between western and central Anatolia, and the southeastern Peloponnese are fully coupled, suggesting a full seismic release of the entire deformation budget. An intermediate value of seismic coupling is observed for the eastern and central segments of the Northern and Eastern Anatolian Fault zones, for part of the Hellenic volcanic arc, the Kefalonia Transform Fault and the Corinth gulf active faults. Considering historical earthquake data, these intermediate coupling values indicate either aseismic deformation or catalog incompleteness. Furthermore, the time period since large magnitude earthquakes clearly raises the possibility of impending earthquakes on the Northern and Eastern Anatolian Fault zones. A broad seismic gap is evidenced along the Hellenic subduction zone, because of the reduced coupling and the absence of ~M8 earthquakes in the last 700 years, at least. We conclude that in most of the central Aegean Sea aseismic deformation prevails as suggested by the small value of coupling and the modest seismic release over the last millennium
Vulnerability of public transportation networks against directed attacks and cascading failures
No full textThis paper presents some results devoted to providing network analysis functionalities for vulnerability assessment in public transportation networks with respect to disruptive events and/or targeted attacks to stations. The results have been obtained on two public transportation networks: the bus network in Florence, Italy, and the transportation network in the Attika region, Greece. The analysis implements a topological approach, based on graph theory, using a multi-graph to model public transportation networks and analyse vulnerabilities with respect to the removal of one or more of their components. Both directed attacks and cascading failures are considered. While the first type of disruptive events is related to a static analysis, where nodes are removed according to a rank related to some centrality measures, the second type is related to a dynamic analysis, where a failure cascade is simulated making unavailable the node with the highest betweenness value. Vulnerability measures are computed as loss of connectivity and efficiency, with respect to both the two different types of disruptive events considered. This study allows to evidence potential vulnerabilities of the urban networks, that must be considered to support the planning process into the creation of resilient structures
Additional file 1 of Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells
No full textAdditional file 1. Cell-cycle effect on flux cluster analysis
