6,906 research outputs found
Deep generative models for network data synthesis and monitoring
Measurement and monitoring are fundamental tasks in all networks, enabling the down-stream management and optimization of the network.
Although networks inherently
have abundant amounts of monitoring data, its access and effective measurement is
another story. The challenges exist in many aspects. First, the inaccessibility of network monitoring data for external users, and it is hard to provide a high-fidelity dataset
without leaking commercial sensitive information. Second, it could be very expensive
to carry out effective data collection to cover a large-scale network system, considering the size of network growing, i.e., cell number of radio network and the number of
flows in the Internet Service Provider (ISP) network. Third, it is difficult to ensure fidelity and efficiency simultaneously in network monitoring, as the available resources
in the network element that can be applied to support the measurement function are
too limited to implement sophisticated mechanisms. Finally, understanding and explaining the behavior of the network becomes challenging due to its size and complex
structure. Various emerging optimization-based solutions (e.g., compressive sensing)
or data-driven solutions (e.g. deep learning) have been proposed for the aforementioned challenges. However, the fidelity and efficiency of existing methods cannot yet
meet the current network requirements.
The contributions made in this thesis significantly advance the state of the art in
the domain of network measurement and monitoring techniques. Overall, we leverage
cutting-edge machine learning technology, deep generative modeling, throughout the
entire thesis. First, we design and realize APPSHOT , an efficient city-scale network
traffic sharing with a conditional generative model, which only requires open-source
contextual data during inference (e.g., land use information and population distribution). Second, we develop an efficient drive testing system â GENDT, based on generative model, which combines graph neural networks, conditional generation, and quantified model uncertainty to enhance the efficiency of mobile drive testing. Third, we
design and implement DISTILGAN, a high-fidelity, efficient, versatile, and real-time
network telemetry system with latent GANs and spectral-temporal networks. Finally,
we propose SPOTLIGHT , an accurate, explainable, and efficient anomaly detection system of the Open RAN (Radio Access Network) system. The lessons learned through
this research are summarized, and interesting topics are discussed for future work in
this domain. All proposed solutions have been evaluated with real-world datasets and
applied to support different applications in real systems
The development of bioinformatics workflows to explore single-cell multi-omics data from T and B lymphocytes
The adaptive immune response is responsible for recognising, containing and eliminating viral infection, and protecting from further reinfection. This antigen-specific response is driven by T and B cells, which recognise antigenic epitopes via highly specific heterodimeric surface receptors, termed T-cell receptors (TCRs) and B cell receptors (BCRs). The theoretical diversity of the receptor repertoire that can be generated via homologous recombination of V, D and J genes is large enough (>1015 unique sequences) that virtually any antigen can be recognised. However, only a subset of these are generated within the human body, and how they succeed in specifically recognising any pathogen(s) and distinguishing these from self-proteins remains largely unresolved.
The recent advances in applying single-cell genomics technologies to simultaneously measure the clonality, surface phenotype and transcriptomic signature of pathogen- specific immune cells have significantly improved understanding of these questions. Single-cell multi-omics permits the accurate identification of clonally expanded populations, their differentiation trajectories, the level of immune receptor repertoire diversity involved in the response and the phenotypic and molecular heterogeneity.
This thesis aims to develop a bioinformatic workflow utilising single-cell multi-omics data to explore, quantify and predict the clonal and transcriptomic signatures of the human T-cell response during and following viral infection. In the first aim, a web application, VDJView, was developed to facilitate the simultaneous analysis and visualisation of clonal, transcriptomic and clinical metadata of T and B cell multi-omics data. The application permits non-bioinformaticians to perform quality control and common analyses of single-cell genomics data integrated with other metadata, thus permitting the identification of biologically and clinically relevant parameters. The second aim pertains to analysing the functional, molecular and immune receptor profiles of CD8+ T cells in the acute phase of primary hepatitis C virus (HCV) infection. This analysis identified a novel population of progenitors of exhausted T cells, and lineage tracing revealed distinct trajectories with multiple fates and evolutionary plasticity. Furthermore, it was observed that high-magnitude IFN-Îł CD8+ T-cell response is associated with the increased probability of viral escape and chronic infection. Finally, in the third aim, a novel analysis is presented based on the topological characteristics of a network generated on pathogen-specific, paired-chain, CD8+ TCRs. This analysis revealed how some cross-reactivity between TCRs can be explained via the sequence similarity between TCRs and that this property is not uniformly distributed across all pathogen-specific TCR repertoires. Strong correlations between the topological properties of the network and the biological properties of the TCR sequences were identified and highlighted.
The suite of workflows and methods presented in this thesis are designed to be adaptable to various T and B cell multi-omic datasets. The associated analyses contribute to understanding the role of T and B cells in the adaptive immune response to viral-infection and cancer
Subgrid scale modeling for large eddy simulation of supercritical mixing and combustion
Large eddy simulation (LES) is a widely used modeling and simulation technique in turbulent flow research. While the LES methodology and accompanying subgrid scale (SGS) modeling have been developed and applied over decades, primarily in the context of ideal gas conditions, their extension to complex multi-physics flows encountered in aerospace propulsion requires further refinement. In particular, the application of LES to turbulent flows at supercritical conditions presents several new modeling challenges and uncertainties. The scope of this dissertation is to investigate the theoretical LES formalism and SGS modeling framework for multi-species turbulent mixing and combustion at supercritical pressures. The goal is to identify the deficiencies with the current methodology and to establish a refined and consistent framework that accurately accounts for all the necessary physics.
In this dissertation, a consistent theoretical formulation of the filtered governing equations for LES is derived. Direct numerical simulations (DNS) are performed for spatially evolving non-reacting and reacting mixing layers at supercritical pressures. The complete set of terms in the filtered equations are quantified and analyzed using the DNS datasets. Based on the analyses, two new groups of subgrid terms are identified as important quantities to account in the LES framework. Parametric analyses are performed as a function of the filter resolution to derive resolution considerations for practical LES applications.
The performance and accuracies of two state-of-the-art subgrid modeling approaches for the traditional subgrid fluxes are assessed. The study demonstrates the better performance of scale-similarity based models over the eddy-viscosity based approaches. The study also reveals the deficiencies of conventional subgrid modeling approaches for LES of supercritical combustion. To address the additional modeling requirement for the filtered equation of state, novel subgrid modeling approaches are proposed. The performance of these models are tested and good improvements are demonstrated.Ph.D
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
Investigation of the metabolism of rare nucleotides in plants
Nucleotides are metabolites involved in primary metabolism, and specialized
metabolism and have a regulatory role in various biochemical reactions in all forms of life. While in other organisms, the nucleotide metabolome was characterized
extensively, comparatively little is known about the cellular concentrations of
nucleotides in plants. The aim of this dissertation was to investigate the nucleotide metabolome and enzymes influencing the composition and quantities of nucleotides in plants. For this purpose, a method for the analysis of nucleotides and nucleosides in plants and algae was developed (Chapter 2.1), which comprises efficient quenching of enzymatic
activity, liquid-liquid extraction and solid phase extraction employing a weak-anionexchange resin. This method allowed the analysis of the nucleotide metabolome of plants in great depth including the quantification of low abundant deoxyribonucleotides and deoxyribonucleosides. The details of the method were summarized in an article, serving as a laboratory protocol (Chapter 2.2).
Furthermore, we contributed a review article (Chapter 2.3) that summarizes the
literature about nucleotide analysis and recent technological advances with a focus on plants and factors influencing and hindering the analysis of nucleotides in plants, i.e., a complex metabolic matrix, highly stable phosphatases and physicochemical
properties of nucleotides. To analyze the sub-cellular concentrations of metabolites, a protocol for the rapid isolation of highly pure mitochondria utilizing affinity chromatography was developed (Chapter 2.4).
The method for the purification of nucleotides furthermore contributed to the
comprehensive analysis of the nucleotide metabolome in germinating seeds and in
establishing seedlings of A. thaliana, with a focus on genes involved in the synthesis of thymidilates (Chapter 2.5) and the characterization of a novel enzyme of purine nucleotide degradation, the XANTHOSINE MONOPHOSPHATE PHOSPHATASE (Chapter 2.6). Protein homology analysis comparing A. thaliana, S. cerevisiae, and H. sapiens led to the identification and characterization of an enzyme involved in the metabolite damage repair system of plants, the INOSINE TRIPHOSPHATE PYROPHOSPHATASE (Chapter 2.7). It was shown that this enzyme dephosphorylates deaminated purine nucleotide triphosphates and thus prevents their incorporation into nucleic acids. Lossof-function mutants senesce early and have a constitutively increased content of salicylic acid. Also, the source of deaminated purine nucleotides in plants was investigated and it was shown that abiotic factors contribute to nucleotide damage.Nukleotide sind Metaboliten, die am PrimÀrstoffwechsel und an spezialisierten
StoffwechselvorgÀngen beteiligt sind und eine regulierende Rolle bei verschiedenen
biochemischen Reaktionen in allen Lebensformen spielen. WĂ€hrend bei anderen
Organismen das Nukleotidmetabolom umfassend charakterisiert wurde, ist in Pflanzen
vergleichsweise wenig ĂŒber die zellulĂ€ren Konzentrationen von Nukleotiden bekannt.
Ziel dieser Dissertation war es, das Nukleotidmetabolom und die Enzyme zu
untersuchen, die die Zusammensetzung und Menge der Nukleotide in Pflanzen
beeinflussen. Zu diesem Zweck wurde eine Methode zur Analyse von Nukleotiden und
Nukleosiden in Pflanzen und Algen entwickelt (Kapitel 2.1), die ein effizientes Stoppen
enzymatischer AktivitĂ€t, eine FlĂŒssig-FlĂŒssig-Extraktion und eine
Festphasenextraktion unter Verwendung eines schwachen Ionenaustauschers
umfasst. Mit dieser Methode konnte das Nukleotidmetabolom von Pflanzen eingehend
analysiert werden, einschlieĂlich der Quantifizierung von Desoxyribonukleotiden und
Desoxyribonukleosiden mit geringer Abundanz. Die Einzelheiten der Methode wurden
in einem Artikel zusammengefasst, der als Laborprotokoll dient (Kapitel 2.2).
DarĂŒber hinaus wurde ein Ăbersichtsartikel (Kapitel 2.3) verfasst, der die Literatur
ĂŒber die Analyse von Nukleotiden und die jĂŒngsten technologischen Fortschritte
zusammenfasst. Der Schwerpunkt lag hierbei auf Pflanzen und Faktoren, die die
Analyse von Nukleotiden in Pflanzen beeinflussen oder behindern, d. h. eine komplexe
Matrix, hochstabile Phosphatasen und physikalisch-chemische Eigenschaften von
Nukleotiden.
Um die subzellulÀren Konzentrationen von Metaboliten zu analysieren, wurde ein
Protokoll fĂŒr die schnelle Isolierung hochreiner Mitochondrien unter Verwendung einer
AffinitÀtschromatographie entwickelt (Kapitel 2.4).
Die Methode zur Analyse von Nukleotiden trug auĂerdem zu einer umfassenden
Analyse des Nukleotidmetaboloms in keimenden Samen und in sich etablierenden
Keimlingen von A. thaliana bei, wobei der Schwerpunkt auf Genen lag, die an der
Synthese von Thymidilaten beteiligt sind (Kapitel 2.5), sowie zu der Charakterisierung
eines neuen Enzyms des Purinnukleotidabbaus, der XANTHOSINE
MONOPHOSPHATE PHOSPHATASE (Kapitel 2.6). Eine Proteinhomologieanalyse, die A. thaliana, S. cerevisiae und H. sapiens
miteinander verglich fĂŒhrte zur Identifizierung und Charakterisierung eines Enzyms,
das an der Reparatur von geschÀdigten Metaboliten in Pflanzen beteiligt ist, der
INOSINE TRIPHOSPHATE PYROPHOSPHATASE (Kapitel 2.7). Es konnte gezeigt
werden, dass dieses Enzym desaminierte Purinnukleotidtriphosphate
dephosphoryliert und so deren Einbau in NukleinsÀuren verhindert.
Funktionsverlustmutanten altern frĂŒh und weisen einen konstitutiv erhöhten Gehalt an SalicylsĂ€ure auf. AuĂerdem wurde die Quelle der desaminierten Purinnukleotide in Pflanzen untersucht, und es wurde gezeigt, dass abiotische Faktoren zur
NukleotidschÀdigung beitragen
Posthuman Creative Styling can a creative writerâs style of writing be described as procedural?
This thesis is about creative styling â the styling a creative writer might use to make their writing
unique. It addresses the question as to whether such styling can be described as procedural. Creative
styling is part of the technique a creative writer uses when writing. It is how they make the text more
âlivelyâ by use of tips and tricks they have either learned or discovered. In essence these are rules, ones
the writer accrues over time by their practice. The thesis argues that the use and invention of these
rules can be set as procedures. and so describe creative styling as procedural.
The thesis follows from questioning why it is that machines or algorithms have, so far, been
incapable of producing creative writing which has value. Machine-written novels do not abound on
the bookshelves and writing styled by computers is, on the whole, dull in comparison to human-crafted
literature. It came about by thinking how it would be possible to reach a point where writing by people
and procedural writing are considered to have equal value. For this reason the thesis is set in a
posthuman context, where the differences between machines and people are erased.
The thesis uses practice to inform an original conceptual space model, based on quality dimensions
and dynamic-inter operation of spaces. This model gives an example of the procedures which a
posthuman creative writer uses when engaged in creative styling. It suggests an original formulation
for the conceptual blending of conceptual spaces, based on the casting of qualities from one space to
another. In support of and informing its arguments are ninety-nine examples of creative writing
practice which show the procedures by which style has been applied, created and assessed. It provides
a route forward for further joint research into both computational and human-coded creative writing
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