395 research outputs found

    Machine learning in solar physics

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    The application of machine learning in solar physics has the potential to greatly enhance our understanding of the complex processes that take place in the atmosphere of the Sun. By using techniques such as deep learning, we are now in the position to analyze large amounts of data from solar observations and identify patterns and trends that may not have been apparent using traditional methods. This can help us improve our understanding of explosive events like solar flares, which can have a strong effect on the Earth environment. Predicting hazardous events on Earth becomes crucial for our technological society. Machine learning can also improve our understanding of the inner workings of the sun itself by allowing us to go deeper into the data and to propose more complex models to explain them. Additionally, the use of machine learning can help to automate the analysis of solar data, reducing the need for manual labor and increasing the efficiency of research in this field.Comment: 100 pages, 13 figures, 286 references, accepted for publication as a Living Review in Solar Physics (LRSP

    Neural Reflectance Decomposition

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    Die Erstellung von fotorealistischen Modellen von Objekten aus Bildern oder Bildersammlungen ist eine grundlegende Herausforderung in der Computer Vision und Grafik. Dieses Problem wird auch als inverses Rendering bezeichnet. Eine der größten Herausforderungen bei dieser Aufgabe ist die vielfältige Ambiguität. Der Prozess Bilder aus 3D-Objekten zu erzeugen wird Rendering genannt. Allerdings beeinflussen sich mehrere Eigenschaften wie Form, Beleuchtung und die Reflektivität der Oberfläche gegenseitig. Zusätzlich wird eine Integration dieser Einflüsse durchgeführt, um das endgültige Bild zu erzeugen. Die Umkehrung dieser integrierten Abhängigkeiten ist eine äußerst schwierige und mehrdeutige Aufgabenstellung. Die Lösung dieser Aufgabe ist jedoch von entscheidender Bedeutung, da die automatisierte Erstellung solcher wieder beleuchtbaren Objekte verschiedene Anwendungen in den Bereichen Online-Shopping, Augmented Reality (AR), Virtual Reality (VR), Spiele oder Filme hat. In dieser Arbeit werden zwei Ansätze zur Lösung dieser Aufgabe beschrieben. Erstens wird eine Netzwerkarchitektur vorgestellt, die die Erfassung eines Objekts und dessen Materialien von zwei Aufnahmen ermöglicht. Der Grad der Blicksynthese von diesen Objekten ist jedoch begrenzt, da bei der Dekomposition nur eine einzige Perspektive verwendet wird. Daher wird eine zweite Reihe von Ansätzen vorgeschlagen, bei denen eine Sammlung von 360 Grad verteilten Bildern in die Form, Reflektanz und Beleuchtung gespalten werden. Diese Multi-View-Bilder werden pro Objekt optimiert. Das resultierende Objekt kann direkt in handelsüblicher Rendering-Software oder in Spielen verwendet werden. Wir erreichen dies, indem wir die aktuelle Forschung zu neuronalen Feldern erweitern Reflektanz zu speichern. Durch den Einsatz von Volumen-Rendering-Techniken können wir ein Reflektanzfeld aus natürlichen Bildsammlungen ohne jegliche Ground Truth (GT) Überwachung optimieren. Die von uns vorgeschlagenen Methoden erreichen eine erstklassige Qualität der Dekomposition und ermöglichen neuartige Aufnahmesituationen, in denen sich Objekte unter verschiedenen Beleuchtungsbedingungen oder an verschiedenen Orten befinden können, was üblich für Online-Bildsammlungen ist.Creating relightable objects from images or collections is a fundamental challenge in computer vision and graphics. This problem is also known as inverse rendering. One of the main challenges in this task is the high ambiguity. The creation of images from 3D objects is well defined as rendering. However, multiple properties such as shape, illumination, and surface reflectiveness influence each other. Additionally, an integration of these influences is performed to form the final image. Reversing these integrated dependencies is highly ill-posed and ambiguous. However, solving the task is essential, as automated creation of relightable objects has various applications in online shopping, augmented reality (AR), virtual reality (VR), games, or movies. In this thesis, we propose two approaches to solve this task. First, a network architecture is discussed, which generalizes the decomposition of a two-shot capture of an object from large training datasets. The degree of novel view synthesis is limited as only a singular perspective is used in the decomposition. Therefore, the second set of approaches is proposed, which decomposes a set of 360-degree images. These multi-view images are optimized per object, and the result can be directly used in standard rendering software or games. We achieve this by extending recent research on Neural Fields, which can store information in a 3D neural volume. Leveraging volume rendering techniques, we can optimize a reflectance field from in-the-wild image collections without any ground truth (GT) supervision. Our proposed methods achieve state-of-the-art decomposition quality and enable novel capture setups where objects can be under varying illumination or in different locations, which is typical for online image collections

    Long Range Gene Regulation in Human Health and Disease

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    The human genome is capable of producing a vast number of phenotypically diverse cells, with incredibly unique roles that contribute to tissue- and developmental-specificity. As such, precise transcriptional control during biological processes such as differentiation, development, and response to environmental stimuli is required. A complex variety of regulatory elements are responsible for this regulation, many of which are still being characterized within the non-coding regions of the genome.In this work, I first investigate the function of the transcription factor Activator Protein 1 (AP-1) in loop-based gene regulation in a model of monocyte-to-macrophage differentiation. I utilized genome editing techniques to interrogate the role of AP-1 binding at Interleukin 1 beta (IL1) enhancers, and preliminary results suggest a mechanism in which a DNA loop connects enhancer-bound AP-1 to IL1, influencing gene expression. These data provide new insights into the mechanisms behind transcriptional control and 3D chromatin structure.I next assay the impact of genetic risk variants on target genes in an ex vivo model of osteoarthritis (OA), in which human chondrocytes are treated with fibronectin fragment (FN-f). This model allows for the study of disease-associated variants in the correct cellular and biological context. We integrated hits from OA genome-wide association studies (GWAS), maps of 3D chromatin structure and enhancer activity in chondrocytes, and previously collected RNA-seq data from our OA model. This work revealed a set of putative causal OA variants and their potential target genes, including suppressor of cytokine signaling 2 (SOCS2). These results provide unique putative OA risk genes for further research and therapeutic development.Finally, I describe my generation of high quality transcriptional and genotype data for use in expression quantitative trait locus (eQTL) analyses in an OA phenotype. These data will serve as the basis for QTL studies that assess both gene expression and chromatin accessibility. The overlap with OA GWAS hits will contribute to the identification of novel putative target genes, risk variants, and their mechanisms.Doctor of Philosoph

    Discontinuous Galerkin methods for Liouville’s equation of geometrical optics

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    Coherent and Holographic Imaging Methods for Immersive Near-Eye Displays

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    Lähinäytöt on suunniteltu tarjoamaan realistisia kolmiulotteisia katselukokemuksia, joille on merkittävää tarvetta esimerkiksi työkoneiden etäkäytössä ja 3D-suunnittelussa. Nykyaikaiset lähinäytöt tuottavat kuitenkin edelleen ristiriitaisia visuaalisia vihjeitä, jotka heikentävät immersiivistä kokemusta ja haittaavat niiden miellyttävää käyttöä. Merkittävänä ratkaisuvaihtoehtona pidetään koherentin valon, kuten laservalon, käyttöä näytön valaistukseen, millä voidaan korjata nykyisten lähinäyttöjen puutteita. Erityisesti koherentti valaistus mahdollistaa holografisen kuvantamisen, jota käyttävät holografiset näytöt voivat tarkasti jäljitellä kolmiulotteisten mallien todellisia valoaaltoja. Koherentin valon käyttäminen näyttöjen valaisemiseen aiheuttaa kuitenkin huomiota vaativaa korkean kontrastin häiriötä pilkkukuvioiden muodossa. Lisäksi holografisten näyttöjen laskentamenetelmät ovat laskennallisesti vaativia ja asettavat uusia haasteita analyysin, pilkkuhäiriön ja valon mallintamisen suhteen. Tässä väitöskirjassa tutkitaan laskennallisia menetelmiä lähinäytöille koherentissa kuvantamisjärjestelmässä käyttäen signaalinkäsittelyä, koneoppimista sekä geometrista (säde) ja fysikaalista (aalto) optiikan mallintamista. Työn ensimmäisessä osassa keskitytään holografisten kuvantamismuotojen analysointiin sekä kehitetään hologrammien laskennallisia menetelmiä. Holografian korkeiden laskentavaatimusten ratkaisemiseksi otamme käyttöön holografiset stereogrammit holografisen datan likimääräisenä esitysmuotona. Tarkastelemme kyseisen esitysmuodon visuaalista oikeellisuutta kehittämällä analyysikehyksen holografisen stereogrammin tarjoamien visuaalisten vihjeiden tarkkuudelle akkommodaatiota varten suhteessa sen suunnitteluparametreihin. Lisäksi ehdotamme signaalinkäsittelyratkaisua pilkkuhäiriön vähentämiseksi, ratkaistaksemme nykyisten menetelmien valon mallintamiseen liittyvät visuaalisia artefakteja aiheuttavat ongelmat. Kehitämme myös uudenlaisen holografisen kuvantamismenetelmän, jolla voidaan mallintaa tarkasti valon käyttäytymistä haastavissa olosuhteissa, kuten peiliheijastuksissa. Väitöskirjan toisessa osassa lähestytään koherentin näyttökuvantamisen laskennallista taakkaa koneoppimisen avulla. Kehitämme koherentin akkommodaatioinvariantin lähinäytön suunnittelukehyksen, jossa optimoidaan yhtäaikaisesti näytön staattista optiikka ja näytön kuvan esikäsittelyverkkoa. Lopuksi nopeutamme ehdottamaamme uutta holografista kuvantamismenetelmää koneoppimisen avulla reaaliaikaisia sovelluksia varten. Kyseiseen ratkaisuun sisältyy myös tehokkaan menettelyn kehittäminen funktionaalisten satunnais-3D-ympäristöjen tuottamiseksi. Kehittämämme menetelmä mahdollistaa suurten synteettisten moninäkökulmaisten kuvien datasettien tuottamisen, joilla voidaan kouluttaa sopivia neuroverkkoja mallintamaan holografista kuvantamismenetelmäämme reaaliajassa. Kaiken kaikkiaan tässä työssä kehitettyjen menetelmien osoitetaan olevan erittäin kilpailukykyisiä uusimpien koherentin valon lähinäyttöjen laskentamenetelmien kanssa. Työn tuloksena nähdään kaksi vaihtoehtoista lähestymistapaa ristiriitaisten visuaalisten vihjeiden aiheuttamien nykyisten lähinäyttöongelmien ratkaisemiseksi joko staattisella tai dynaamisella optiikalla ja reaaliaikaiseen käyttöön soveltuvilla laskentamenetelmillä. Esitetyt tulokset ovat näin ollen tärkeitä seuraavan sukupolven immersiivisille lähinäytöille.Near-eye displays have been designed to provide realistic 3D viewing experience, strongly demanded in applications, such as remote machine operation, entertainment, and 3D design. However, contemporary near-eye displays still generate conflicting visual cues which degrade the immersive experience and hinders their comfortable use. Approaches using coherent, e.g., laser light for display illumination have been considered prominent for tackling the current near-eye display deficiencies. Coherent illumination enables holographic imaging whereas holographic displays are expected to accurately recreate the true light waves of a desired 3D scene. However, the use of coherent light for driving displays introduces additional high contrast noise in the form of speckle patterns, which has to be taken care of. Furthermore, imaging methods for holographic displays are computationally demanding and impose new challenges in analysis, speckle noise and light modelling. This thesis examines computational methods for near-eye displays in the coherent imaging regime using signal processing, machine learning, and geometrical (ray) and physical (wave) optics modeling. In the first part of the thesis, we concentrate on analysis of holographic imaging modalities and develop corresponding computational methods. To tackle the high computational demands of holography, we adopt holographic stereograms as an approximative holographic data representation. We address the visual correctness of such representation by developing a framework for analyzing the accuracy of accommodation visual cues provided by a holographic stereogram in relation to its design parameters. Additionally, we propose a signal processing solution for speckle noise reduction to overcome existing issues in light modelling causing visual artefacts. We also develop a novel holographic imaging method to accurately model lighting effects in challenging conditions, such as mirror reflections. In the second part of the thesis, we approach the computational complexity aspects of coherent display imaging through deep learning. We develop a coherent accommodation-invariant near-eye display framework to jointly optimize static display optics and a display image pre-processing network. Finally, we accelerate the corresponding novel holographic imaging method via deep learning aimed at real-time applications. This includes developing an efficient procedure for generating functional random 3D scenes for forming a large synthetic data set of multiperspective images, and training a neural network to approximate the holographic imaging method under the real-time processing constraints. Altogether, the methods developed in this thesis are shown to be highly competitive with the state-of-the-art computational methods for coherent-light near-eye displays. The results of the work demonstrate two alternative approaches for resolving the existing near-eye display problems of conflicting visual cues using either static or dynamic optics and computational methods suitable for real-time use. The presented results are therefore instrumental for the next-generation immersive near-eye displays

    Neural function approximation on graphs: shape modelling, graph discrimination & compression

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    Graphs serve as a versatile mathematical abstraction of real-world phenomena in numerous scientific disciplines. This thesis is part of the Geometric Deep Learning subject area, a family of learning paradigms, that capitalise on the increasing volume of non-Euclidean data so as to solve real-world tasks in a data-driven manner. In particular, we focus on the topic of graph function approximation using neural networks, which lies at the heart of many relevant methods. In the first part of the thesis, we contribute to the understanding and design of Graph Neural Networks (GNNs). Initially, we investigate the problem of learning on signals supported on a fixed graph. We show that treating graph signals as general graph spaces is restrictive and conventional GNNs have limited expressivity. Instead, we expose a more enlightening perspective by drawing parallels between graph signals and signals on Euclidean grids, such as images and audio. Accordingly, we propose a permutation-sensitive GNN based on an operator analogous to shifts in grids and instantiate it on 3D meshes for shape modelling (Spiral Convolutions). Following, we focus on learning on general graph spaces and in particular on functions that are invariant to graph isomorphism. We identify a fundamental trade-off between invariance, expressivity and computational complexity, which we address with a symmetry-breaking mechanism based on substructure encodings (Graph Substructure Networks). Substructures are shown to be a powerful tool that provably improves expressivity while controlling computational complexity, and a useful inductive bias in network science and chemistry. In the second part of the thesis, we discuss the problem of graph compression, where we analyse the information-theoretic principles and the connections with graph generative models. We show that another inevitable trade-off surfaces, now between computational complexity and compression quality, due to graph isomorphism. We propose a substructure-based dictionary coder - Partition and Code (PnC) - with theoretical guarantees that can be adapted to different graph distributions by estimating its parameters from observations. Additionally, contrary to the majority of neural compressors, PnC is parameter and sample efficient and is therefore of wide practical relevance. Finally, within this framework, substructures are further illustrated as a decisive archetype for learning problems on graph spaces.Open Acces

    3D simulations of oxygenated rocky planetary climates and observational predictions

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    There are now hundreds of known terrestrial exoplanets (rocky planets orbiting other stars), with ~60 considered potentially habitable worlds. In the next two decades, several state-of-the art observatories will observe these exoplanets with unprecedented sensitivity, requiring the parallel use of computational models to constrain their climates. Using Earth’s inhabited paleoclimates as templates may elucidate which exoplanets could host life. I use WACCM6, a three-dimensional (3D) Earth System Model, to simulate Earth’s oxygenated paleoclimates, as well as the climates of Earth-like terrestrial exoplanets. I use these simulations as input to the Planetary Spectrum Generator, a radiative transfer suite, to predict spectroscopic telescope transmission spectra and direct imaging spectra observations of exoplanets. Earth's atmosphere has been oxygenated for the past 2.4 billion years. I find that different amounts of O2 alters the 3D distribution of temperature, clouds, dynamics, and composition, with reduced ozone (O3) concentrations between 0.1 - 50% the present atmospheric level of O2 compared to previous 1D and 3D modelling. Considering these scenarios as Earth-analogue exoplanets, I predict their transmission and direct imaging spectra with next generation telescopes, finding that annual variability in reflected light, which depends on both clouds and composition, could be observable through state-of-the-art high-contrast imaging. I perform simulations of TRAPPIST-1e and Proxima Centauri b, two potentially tidally locked habitable zone exoplanets. Three distinct layers of atmospheric super rotation are resolved in the data. Furthermore, uncertainty in the incident ultraviolet (UV) radiation may lead to ambiguities when interpreting observations and inferring atmospheric oxygenation scenarios. This can be partially resolved with a dedicated, sensitive UV observatory. This thesis demonstrates the requirement for model development to better estimate the O2-O3 relationship across a variety of (exo)planets. Such advances are important for reconstructing Earth's paleoclimates, and are crucial for efforts to determine if any exoplanets host Earth-like biospheres

    Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

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    Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science

    Deploying and processing neural representations of signals

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    Neural representations (NR) have emerged in the last few years as a powerful tool to represent signals from several domains, such as images, 3D shapes, or audio. Indeed, deep neural networks have been shown capable of approximating continuous functions that describe a given signal with theoretical infinite resolution. This finding allows obtaining representations whose memory footprint is fixed and decoupled from the resolution at which the underlying signal can be sampled, something that is not possible with traditional discrete representations, e.g., grids of pixels for images or voxels for 3D shapes. During the last two years, many techniques have been proposed to improve the capability of NR to approximate high-frequency details and to make the optimization procedures required to obtain NR less demanding both in terms of time and data requirements, motivating many researchers to deploy NR as the main form of data representation for complex pipelines. Following this line of research, we first show that NR can approximate precisely Unsigned Distance Functions, providing an effective way to represent garments that feature open 3D surfaces and unknown topology. Then, we present a pipeline to obtain in a few minutes a compact Neural Twin® for a given object, by exploiting the recent advances in modeling neural radiance fields. Furthermore, we move a step in the direction of adopting NR as a standalone representation, by considering the possibility of performing downstream tasks by processing directly the NR weights. We first show that deep neural networks can be compressed into compact latent codes. Then, we show how this technique can be exploited to perform deep learning on implicit neural representations (INR) of 3D shapes, by only looking at the weights of the networks
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