1,347 research outputs found

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Design of new algorithms for gene network reconstruction applied to in silico modeling of biomedical data

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    Programa de Doctorado en Biotecnología, Ingeniería y Tecnología QuímicaLínea de Investigación: Ingeniería, Ciencia de Datos y BioinformáticaClave Programa: DBICódigo Línea: 111The root causes of disease are still poorly understood. The success of current therapies is limited because persistent diseases are frequently treated based on their symptoms rather than the underlying cause of the disease. Therefore, biomedical research is experiencing a technology-driven shift to data-driven holistic approaches to better characterize the molecular mechanisms causing disease. Using omics data as an input, emerging disciplines like network biology attempt to model the relationships between biomolecules. To this effect, gene co- expression networks arise as a promising tool for deciphering the relationships between genes in large transcriptomic datasets. However, because of their low specificity and high false positive rate, they demonstrate a limited capacity to retrieve the disrupted mechanisms that lead to disease onset, progression, and maintenance. Within the context of statistical modeling, we dove deeper into the reconstruction of gene co-expression networks with the specific goal of discovering disease-specific features directly from expression data. Using ensemble techniques, which combine the results of various metrics, we were able to more precisely capture biologically significant relationships between genes. We were able to find de novo potential disease-specific features with the help of prior biological knowledge and the development of new network inference techniques. Through our different approaches, we analyzed large gene sets across multiple samples and used gene expression as a surrogate marker for the inherent biological processes, reconstructing robust gene co-expression networks that are simple to explore. By mining disease-specific gene co-expression networks we come up with a useful framework for identifying new omics-phenotype associations from conditional expression datasets.In this sense, understanding diseases from the perspective of biological network perturbations will improve personalized medicine, impacting rational biomarker discovery, patient stratification and drug design, and ultimately leading to more targeted therapies.Universidad Pablo de Olavide de Sevilla. Departamento de Deporte e Informátic

    20th SC@RUG 2023 proceedings 2022-2023

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    Technology for Low Resolution Space Based RSO Detection and Characterisation

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    Space Situational Awareness (SSA) refers to all activities to detect, identify and track objects in Earth orbit. SSA is critical to all current and future space activities and protect space assets by providing access control, conjunction warnings, and monitoring status of active satellites. Currently SSA methods and infrastructure are not sufficient to account for the proliferations of space debris. In response to the need for better SSA there has been many different areas of research looking to improve SSA most of the requiring dedicated ground or space-based infrastructure. In this thesis, a novel approach for the characterisation of RSO’s (Resident Space Objects) from passive low-resolution space-based sensors is presented with all the background work performed to enable this novel method. Low resolution space-based sensors are common on current satellites, with many of these sensors being in space using them passively to detect RSO’s can greatly augment SSA with out expensive infrastructure or long lead times. One of the largest hurtles to overcome with research in the area has to do with the lack of publicly available labelled data to test and confirm results with. To overcome this hurtle a simulation software, ORBITALS, was created. To verify and validate the ORBITALS simulator it was compared with the Fast Auroral Imager images, which is one of the only publicly available low-resolution space-based images found with auxiliary data. During the development of the ORBITALS simulator it was found that the generation of these simulated images are computationally intensive when propagating the entire space catalog. To overcome this an upgrade of the currently used propagation method, Specialised General Perturbation Method 4th order (SGP4), was performed to allow the algorithm to run in parallel reducing the computational time required to propagate entire catalogs of RSO’s. From the results it was found that the standard facet model with a particle swarm optimisation performed the best estimating an RSO’s attitude with a 0.66 degree RMSE accuracy across a sequence, and ~1% MAPE accuracy for the optical properties. This accomplished this thesis goal of demonstrating the feasibility of low-resolution passive RSO characterisation from space-based platforms in a simulated environment

    A Methodology to Enable Concurrent Trade Space Exploration of Space Campaigns and Transportation Systems

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    Space exploration campaigns detail the ways and means to achieve goals for our human spaceflight programs. Significant strategic, financial, and programmatic investments over long timescales are required to execute them, and therefore must be justified to decision makers. To make an informed down-selection, many alternative campaign designs are presented at the conceptual-level, as a set and sequence of individual missions to perform that meets the goals and constraints of the campaign, either technical or programmatic. Each mission is executed by in-space transportation systems, which deliver either crew or cargo payloads to various destinations. Design of each of these transportation systems is highly dependent on campaign goals and even small changes in subsystem design parameters can prompt significant changes in the overall campaign strategy. However, the current state of the art describes campaign and vehicle design processes that are generally performed independently, which limits the ability to assess these sensitive impacts. The objective of this research is to establish a methodology for space exploration campaign design that represents transportation systems as a collection of subsystems and integrates its design process to enable concurrent trade space exploration. More specifically, the goal is to identify existing campaign and vehicle design processes to use as a foundation for improvement and eventual integration. In the past two decades, researchers have adopted terrestrial logistics and supply chain optimization processes to the space campaign design problem by accounting for the challenges that accompany space travel. Fundamentally, a space campaign is formulated as a network design problem where destinations, such as orbits or surfaces of planetary bodies, are represented as nodes with the routes between them as arcs. The objective of this design problem is to optimize the flow of commodities within network using available transport systems. Given the dynamic nature and the number of commodities involved, each campaign can be modeled as a time-expanded, generalized multi-commodity network flow and solved using a mixed integer programming algorithm. To address the challenge of modeling complex concept of operations (ConOps), this formulation was extended to include paths as a set of arcs, further enabling the inclusion of vehicle stacks and payload transfers in the campaign optimization process. Further, with the focus of transportation system within this research, the typical fixed orbital nodes in the logistics network are modified to represent ranges of orbits, categorized by their characteristic energy. This enables the vehicle design process to vary each orbit in the mission as it desires to find the best one per vehicle. By extension, once integrated, arc costs of dV and dT are updated each iteration. Once campaign goals and external constraints are included, the formulated campaign design process generates alternatives at the conceptual level, where each one identifies the optimal set and sequence of missions to perform. Representing transportation systems as a collection of subsystems introduces challenges in the design of each vehicle, with a high degree of coupling between each subsystem as well as the driving mission. Additionally, sizing of each subsystem can have many inputs and outputs linked across the system, resulting in a complex, multi-disciplinary analysis, and optimization problem. By leveraging the ontology within the Dynamic Rocket Equation Tool, DYREQT, this problem can be solved rapidly by defining each system as a hierarchy of elements and subelements, the latter corresponding to external subsystem-level sizing models. DYREQT also enables the construction of individual missions as a series of events, which can be directly driven and generated by the mission set found by the campaign optimization process. This process produces sized vehicles iteratively by using the mission input, subsystem level sizing models, and the ideal rocket equation. By conducting a literature review of campaign and vehicle design processes, the different pieces of the overall methodology are identified, but not the structure. The specific iterative solver, the corresponding convergence criteria, and initialization scheme are the primary areas for experimentation of this thesis. Using NASA’s reference 3-element Human Landing System campaign, the results of these experiments show that the methodology performs best with the vehicle sizing and synthesis process initializing and a path guess that minimizes dV. Further, a converged solution is found faster using non-linear Gauss Seidel fixed point iteration over Jacobi and set of convergence criteria that covers vehicle masses and mission data. To show improvement over the state of the art, and how it enables concurrent trade studies, this methodology is used at scale in a demonstration using NASA’s Design Reference Architecture 5.0. The LH2 Nuclear Thermal Propulsion (NTP) option is traded with NH3and H2O at the vehicle-level as a way to show the impacts of alternative propellants on the vehicle sizing and campaign strategy. Martian surface stay duration is traded at the campaign-level through two options: long-stay and short-stay. The methodology was able to produce four alternative campaigns over the course of two weeks, which provided data about the launch and aggregation strategy, mission profiles, high-level figures of merit, and subsystem-level vehicle sizes for each alternative. Expectedly, with their lower specific impulses, alternative NTP propellants showed significant growth in the overall mass required to execute each campaign, subsequently represented the number of drop tanks and launches. Further, the short-stay campaign option showed a similar overall mass required compared to its long-stay counterpart, but higher overall costs even given the fewer elements required. Both trade studies supported the overall hypothesis and that integrating the campaign and vehicle design processes addresses the coupling between then and directly shows the impacts of their sensitivities on each other. As a result, the research objective was fulfilled by producing a methodology that was able to address the key gaps identified in the current state of the art.Ph.D

    20th SC@RUG 2023 proceedings 2022-2023

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    On linear, fractional, and submodular optimization

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    In this thesis, we study four fundamental problems in the theory of optimization. 1. In fractional optimization, we are interested in minimizing a ratio of two functions over some domain. A well-known technique for solving this problem is the Newton– Dinkelbach method. We propose an accelerated version of this classical method and give a new analysis using the Bregman divergence. We show how it leads to improved or simplified results in three application areas. 2. The diameter of a polyhedron is the maximum length of a shortest path between any two vertices. The circuit diameter is a relaxation of this notion, whereby shortest paths are not restricted to edges of the polyhedron. For a polyhedron in standard equality form with constraint matrix A, we prove an upper bound on the circuit diameter that is quadratic in the rank of A and logarithmic in the circuit imbalance measure of A. We also give circuit augmentation algorithms for linear programming with similar iteration complexity. 3. The correlation gap of a set function is the ratio between its multilinear and concave extensions. We present improved lower bounds on the correlation gap of a matroid rank function, parametrized by the rank and girth of the matroid. We also prove that for a weighted matroid rank function, the worst correlation gap is achieved with uniform weights. Such improved lower bounds have direct applications in submodular maximization and mechanism design. 4. The last part of this thesis concerns parity games, a problem intimately related to linear programming. A parity game is an infinite-duration game between two players on a graph. The problem of deciding the winner lies in NP and co-NP, with no known polynomial algorithm to date. Many of the fastest (quasi-polynomial) algorithms have been unified via the concept of a universal tree. We propose a strategy iteration framework which can be applied on any universal tree

    (b2023 to 2014) The UNBELIEVABLE similarities between the ideas of some people (2006-2016) and my ideas (2002-2008) in physics (quantum mechanics, cosmology), cognitive neuroscience, philosophy of mind, and philosophy (this manuscript would require a REVOLUTION in international academy environment!)

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    (b2023 to 2014) The UNBELIEVABLE similarities between the ideas of some people (2006-2016) and my ideas (2002-2008) in physics (quantum mechanics, cosmology), cognitive neuroscience, philosophy of mind, and philosophy (this manuscript would require a REVOLUTION in international academy environment!
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