11,564 research outputs found

    Scaling up integrated photonic reservoirs towards low-power high-bandwidth computing

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    Bayesian Reconstruction of Magnetic Resonance Images using Gaussian Processes

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    A central goal of modern magnetic resonance imaging (MRI) is to reduce the time required to produce high-quality images. Efforts have included hardware and software innovations such as parallel imaging, compressed sensing, and deep learning-based reconstruction. Here, we propose and demonstrate a Bayesian method to build statistical libraries of magnetic resonance (MR) images in k-space and use these libraries to identify optimal subsampling paths and reconstruction processes. Specifically, we compute a multivariate normal distribution based upon Gaussian processes using a publicly available library of T1-weighted images of healthy brains. We combine this library with physics-informed envelope functions to only retain meaningful correlations in k-space. This covariance function is then used to select a series of ring-shaped subsampling paths using Bayesian optimization such that they optimally explore space while remaining practically realizable in commercial MRI systems. Combining optimized subsampling paths found for a range of images, we compute a generalized sampling path that, when used for novel images, produces superlative structural similarity and error in comparison to previously reported reconstruction processes (i.e. 96.3% structural similarity and <0.003 normalized mean squared error from sampling only 12.5% of the k-space data). Finally, we use this reconstruction process on pathological data without retraining to show that reconstructed images are clinically useful for stroke identification

    A Decision Support System for Economic Viability and Environmental Impact Assessment of Vertical Farms

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    Vertical farming (VF) is the practice of growing crops or animals using the vertical dimension via multi-tier racks or vertically inclined surfaces. In this thesis, I focus on the emerging industry of plant-specific VF. Vertical plant farming (VPF) is a promising and relatively novel practice that can be conducted in buildings with environmental control and artificial lighting. However, the nascent sector has experienced challenges in economic viability, standardisation, and environmental sustainability. Practitioners and academics call for a comprehensive financial analysis of VPF, but efforts are stifled by a lack of valid and available data. A review of economic estimation and horticultural software identifies a need for a decision support system (DSS) that facilitates risk-empowered business planning for vertical farmers. This thesis proposes an open-source DSS framework to evaluate business sustainability through financial risk and environmental impact assessments. Data from the literature, alongside lessons learned from industry practitioners, would be centralised in the proposed DSS using imprecise data techniques. These techniques have been applied in engineering but are seldom used in financial forecasting. This could benefit complex sectors which only have scarce data to predict business viability. To begin the execution of the DSS framework, VPF practitioners were interviewed using a mixed-methods approach. Learnings from over 19 shuttered and operational VPF projects provide insights into the barriers inhibiting scalability and identifying risks to form a risk taxonomy. Labour was the most commonly reported top challenge. Therefore, research was conducted to explore lean principles to improve productivity. A probabilistic model representing a spectrum of variables and their associated uncertainty was built according to the DSS framework to evaluate the financial risk for VF projects. This enabled flexible computation without precise production or financial data to improve economic estimation accuracy. The model assessed two VPF cases (one in the UK and another in Japan), demonstrating the first risk and uncertainty quantification of VPF business models in the literature. The results highlighted measures to improve economic viability and the viability of the UK and Japan case. The environmental impact assessment model was developed, allowing VPF operators to evaluate their carbon footprint compared to traditional agriculture using life-cycle assessment. I explore strategies for net-zero carbon production through sensitivity analysis. Renewable energies, especially solar, geothermal, and tidal power, show promise for reducing the carbon emissions of indoor VPF. Results show that renewably-powered VPF can reduce carbon emissions compared to field-based agriculture when considering the land-use change. The drivers for DSS adoption have been researched, showing a pathway of compliance and design thinking to overcome the ‘problem of implementation’ and enable commercialisation. Further work is suggested to standardise VF equipment, collect benchmarking data, and characterise risks. This work will reduce risk and uncertainty and accelerate the sector’s emergence

    A direct-laser-written heart-on-a-chip platform for generation and stimulation of engineered heart tissues

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    In this dissertation, we first develop a versatile microfluidic heart-on-a-chip model to generate 3D-engineered human cardiac microtissues in highly-controlled microenvironments. The platform, which is enabled by direct laser writing (DLW), has tailor-made attachment sites for cardiac microtissues and comes with integrated strain actuators and force sensors. Application of external pressure waves to the platform results in controllable time-dependent forces on the microtissues. Conversely, oscillatory forces generated by the microtissues are transduced into measurable electrical outputs. After characterization of the responsivity of the transducers, we demonstrate the capabilities of this platform by studying the response of cardiac microtissues to prescribed mechanical loading and pacing. Next, we tune the geometry and mechanical properties of the platform to enable parametric studies on engineered heart tissues. We explore two geometries: a rectangular seeding well with two attachment sites, and a stadium-like seeding well with six attachment sites. The attachment sites are placed symmetrically in the longitudinal direction. The former geometry promotes uniaxial contraction of the tissues; the latter additionally induces diagonal fiber alignment. We systematically increase the length for both configurations and observe a positive correlation between fiber alignment at the center of the microtissues and tissue length. However, progressive thinning and “necking” is also observed, leading to the failure of longer tissues over time. We use the DLW technique to improve the platform, softening the mechanical environment and optimizing the attachment sites for generation of stable microtissues at each length and geometry. Furthermore, electrical pacing is incorporated into the platform to evaluate the functional dynamics of stable microtissues over the entire range of physiological heart rates. Here, we typically observe a decrease in active force and contraction duration as a function of frequency. Lastly, we use a more traditional ?TUG platform to demonstrate the effects of subthreshold electrical pacing on the rhythm of the spontaneously contracting cardiac microtissues. Here, we observe periodic M:N patterns, in which there are ? cycles of stimulation for every ? tissue contractions. Using electric field amplitude, pacing frequency, and homeostatic beating frequencies of the tissues, we provide an empirical map for predicting the emergence of these rhythms

    Robustness against adversarial attacks on deep neural networks

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    While deep neural networks have been successfully applied in several different domains, they exhibit vulnerabilities to artificially-crafted perturbations in data. Moreover, these perturbations have been shown to be transferable across different networks where the same perturbations can be transferred between different models. In response to this problem, many robust learning approaches have emerged. Adversarial training is regarded as a mainstream approach to enhance the robustness of deep neural networks with respect to norm-constrained perturbations. However, adversarial training requires a large number of perturbed examples (e.g., over 100,000 examples are required for MNIST dataset) trained on the deep neural networks before robustness can be considerably enhanced. This is problematic due to the large computational cost of obtaining attacks. Developing computationally effective approaches while retaining robustness against norm-constrained perturbations remains a challenge in the literature. In this research we present two novel robust training algorithms based on Monte-Carlo Tree Search (MCTS) [1] to enhance robustness under norm-constrained perturbations [2, 3]. The first algorithm searches potential candidates with Scale Invariant Feature Transform method and makes decisions with Monte-Carlo Tree Search method [2]. The second algorithm adopts Decision Tree Search method (DTS) to accelerate the search process while maintaining efficiency [3]. Our overarching objective is to provide computationally effective approaches that can be deployed to train deep neural networks robust against perturbations in data. We illustrate the robustness with these algorithms by studying the resistances to adversarial examples obtained in the context of the MNIST and CIFAR10 datasets. For MNIST, the results showed an average training efforts saving of 21.1\% when compared to Projected Gradient Descent (PGD) and 28.3\% when compared to Fast Gradient Sign Methods (FGSM). For CIFAR10, we obtained an average improvement of efficiency of 9.8\% compared to PGD and 13.8\% compared to FGSM. The results suggest that these two methods here introduced are not only robust to norm-constrained perturbations but also efficient during training. In regards to transferability of defences, our experiments [4] reveal that across different network architectures, across a variety of attack methods from white-box to black-box and across various datasets including MNIST and CIFAR10, our algorithms outperform other state-of-the-art methods, e.g., PGD and FGSM. Furthermore, the derived attacks and robust models obtained on our framework are reusable in the sense that the same norm-constrained perturbations can facilitate robust training across different networks. Lastly, we investigate the robustness of intra-technique and cross-technique transferability and the relations with different impact factors from adversarial strength to network capacity. The results suggest that known attacks on the resulting models are less transferable than those models trained by other state-of-the-art attack algorithms. Our results suggest that exploiting these tree search frameworks can result in significant improvements in the robustness of deep neural networks while saving computational cost on robust training. This paves the way for several future directions, both algorithmic and theoretical, as well as numerous applications to establish the robustness of deep neural networks with increasing trust and safety.Open Acces

    Optimizing transcriptomics to study the evolutionary effect of FOXP2

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    The field of genomics was established with the sequencing of the human genome, a pivotal achievement that has allowed us to address various questions in biology from a unique perspective. One question in particular, that of the evolution of human speech, has gripped philosophers, evolutionary biologists, and now genomicists. However, little is known of the genetic basis that allowed humans to evolve the ability to speak. Of the few genes implicated in human speech, one of the most studied is FOXP2, which encodes for the transcription factor Forkhead box protein P2 (FOXP2). FOXP2 is essential for proper speech development and two mutations in the human lineage are believed to have contributed to the evolution of human speech. To address the effect of FOXP2 and investigate its evolutionary contribution to human speech, one can utilize the power of genomics, more specifically gene expression analysis via ribonucleic acid sequencing (RNA-seq). To this end, I first contributed in developing mcSCRB-seq, a highly sensitive, powerful, and efficient single cell RNA-seq (scRNA-seq) protocol. Previously having emerged as a central method for studying cellular heterogeneity and identifying cellular processes, scRNA-seq was a powerful genomic tool but lacked the sensitivity and cost-efficiency of more established protocols. By systematically evaluating each step of the process, I helped find that the addition of polyethylene glycol increased sensitivity by enhancing the cDNA synthesis reaction. This, along with other optimizations resulted in developing a sensitive and flexible protocol that is cost-efficient and ideal in many research settings. A primary motivation driving the extensive optimizations surrounding single cell transcriptomics has been the generation of cellular atlases, which aim to identify and characterize all of the cells in an organism. As such efforts are carried out in a variety of research groups using a number of different RNA-seq protocols, I contributed in an effort to benchmark and standardize scRNA-seq methods. This not only identified methods which may be ideal for the purpose of cell atlas creation, but also highlighted optimizations that could be integrated into existing protocols. Using mcSCRB-seq as a foundation as well as the findings from the scRNA-seq benchmarking, I helped develop prime-seq, a sensitive, robust, and most importantly, affordable bulk RNA-seq protocol. Bulk RNA-seq was frequently overlooked during the efforts to optimize and establish single-cell techniques, even though the method is still extensively used in analyzing gene expression. Introducing early barcoding and reducing library generation costs kept prime-seq cost-efficient, but basing it off of single-cell methods ensured that it would be a sensitive and powerful technique. I helped verify this by benchmarking it against TruSeq generated data and then helped test the robustness by generating prime-seq libraries from over seventeen species. These optimizations resulted in a final protocol that is well suited for investigating gene expression in comprehensive and high-throughput studies. Finally, I utilized prime-seq in order to develop a comprehensive gene expression atlas to study the function of FOXP2 and its role in speech evolution. I used previously generated mouse models: a knockout model containing one non-functional Foxp2 allele and a humanized model, which has a variant Foxp2 allele with two human-specific mutations. To study the effect globally across the mouse, I helped harvest eighteen tissues which were previously identified to express FOXP2. By then comparing the mouse models to wild-type mice, I helped highlight the importance of FOXP2 within lung development and the importance of the human variant allele in the brain. Both mcSCRB-seq and prime-seq have already been used and published in numerous studies to address a variety of biological and biomedical questions. Additionally, my work on FOXP2 not only provides a thorough expression atlas, but also provides a detailed and cost-efficient plan for undertaking a similar study on other genes of interest. Lastly, the studies on FOXP2 done within this work, lay the foundation for future studies investigating the role of FOXP2 in modulating learning behavior, and thereby affecting human speech

    Machine learning for managing structured and semi-structured data

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    As the digitalization of private, commercial, and public sectors advances rapidly, an increasing amount of data is becoming available. In order to gain insights or knowledge from these enormous amounts of raw data, a deep analysis is essential. The immense volume requires highly automated processes with minimal manual interaction. In recent years, machine learning methods have taken on a central role in this task. In addition to the individual data points, their interrelationships often play a decisive role, e.g. whether two patients are related to each other or whether they are treated by the same physician. Hence, relational learning is an important branch of research, which studies how to harness this explicitly available structural information between different data points. Recently, graph neural networks have gained importance. These can be considered an extension of convolutional neural networks from regular grids to general (irregular) graphs. Knowledge graphs play an essential role in representing facts about entities in a machine-readable way. While great efforts are made to store as many facts as possible in these graphs, they often remain incomplete, i.e., true facts are missing. Manual verification and expansion of the graphs is becoming increasingly difficult due to the large volume of data and must therefore be assisted or substituted by automated procedures which predict missing facts. The field of knowledge graph completion can be roughly divided into two categories: Link Prediction and Entity Alignment. In Link Prediction, machine learning models are trained to predict unknown facts between entities based on the known facts. Entity Alignment aims at identifying shared entities between graphs in order to link several such knowledge graphs based on some provided seed alignment pairs. In this thesis, we present important advances in the field of knowledge graph completion. For Entity Alignment, we show how to reduce the number of required seed alignments while maintaining performance by novel active learning techniques. We also discuss the power of textual features and show that graph-neural-network-based methods have difficulties with noisy alignment data. For Link Prediction, we demonstrate how to improve the prediction for unknown entities at training time by exploiting additional metadata on individual statements, often available in modern graphs. Supported with results from a large-scale experimental study, we present an analysis of the effect of individual components of machine learning models, e.g., the interaction function or loss criterion, on the task of link prediction. We also introduce a software library that simplifies the implementation and study of such components and makes them accessible to a wide research community, ranging from relational learning researchers to applied fields, such as life sciences. Finally, we propose a novel metric for evaluating ranking results, as used for both completion tasks. It allows for easier interpretation and comparison, especially in cases with different numbers of ranking candidates, as encountered in the de-facto standard evaluation protocols for both tasks.Mit der rasant fortschreitenden Digitalisierung des privaten, kommerziellen und öffentlichen Sektors werden immer grĂ¶ĂŸere Datenmengen verfĂŒgbar. Um aus diesen enormen Mengen an Rohdaten Erkenntnisse oder Wissen zu gewinnen, ist eine tiefgehende Analyse unerlĂ€sslich. Das immense Volumen erfordert hochautomatisierte Prozesse mit minimaler manueller Interaktion. In den letzten Jahren haben Methoden des maschinellen Lernens eine zentrale Rolle bei dieser Aufgabe eingenommen. Neben den einzelnen Datenpunkten spielen oft auch deren ZusammenhĂ€nge eine entscheidende Rolle, z.B. ob zwei Patienten miteinander verwandt sind oder ob sie vom selben Arzt behandelt werden. Daher ist das relationale Lernen ein wichtiger Forschungszweig, der untersucht, wie diese explizit verfĂŒgbaren strukturellen Informationen zwischen verschiedenen Datenpunkten nutzbar gemacht werden können. In letzter Zeit haben Graph Neural Networks an Bedeutung gewonnen. Diese können als eine Erweiterung von CNNs von regelmĂ€ĂŸigen Gittern auf allgemeine (unregelmĂ€ĂŸige) Graphen betrachtet werden. Wissensgraphen spielen eine wesentliche Rolle bei der Darstellung von Fakten ĂŒber EntitĂ€ten in maschinenlesbaren Form. Obwohl große Anstrengungen unternommen werden, so viele Fakten wie möglich in diesen Graphen zu speichern, bleiben sie oft unvollstĂ€ndig, d. h. es fehlen Fakten. Die manuelle ÜberprĂŒfung und Erweiterung der Graphen wird aufgrund der großen Datenmengen immer schwieriger und muss daher durch automatisierte Verfahren unterstĂŒtzt oder ersetzt werden, die fehlende Fakten vorhersagen. Das Gebiet der WissensgraphenvervollstĂ€ndigung lĂ€sst sich grob in zwei Kategorien einteilen: Link Prediction und Entity Alignment. Bei der Link Prediction werden maschinelle Lernmodelle trainiert, um unbekannte Fakten zwischen EntitĂ€ten auf der Grundlage der bekannten Fakten vorherzusagen. Entity Alignment zielt darauf ab, gemeinsame EntitĂ€ten zwischen Graphen zu identifizieren, um mehrere solcher Wissensgraphen auf der Grundlage einiger vorgegebener Paare zu verknĂŒpfen. In dieser Arbeit stellen wir wichtige Fortschritte auf dem Gebiet der VervollstĂ€ndigung von Wissensgraphen vor. FĂŒr das Entity Alignment zeigen wir, wie die Anzahl der benötigten Paare reduziert werden kann, wĂ€hrend die Leistung durch neuartige aktive Lerntechniken erhalten bleibt. Wir erörtern auch die LeistungsfĂ€higkeit von Textmerkmalen und zeigen, dass auf Graph-Neural-Networks basierende Methoden Schwierigkeiten mit verrauschten Paar-Daten haben. FĂŒr die Link Prediction demonstrieren wir, wie die Vorhersage fĂŒr unbekannte EntitĂ€ten zur Trainingszeit verbessert werden kann, indem zusĂ€tzliche Metadaten zu einzelnen Aussagen genutzt werden, die oft in modernen Graphen verfĂŒgbar sind. GestĂŒtzt auf Ergebnisse einer groß angelegten experimentellen Studie prĂ€sentieren wir eine Analyse der Auswirkungen einzelner Komponenten von Modellen des maschinellen Lernens, z. B. der Interaktionsfunktion oder des Verlustkriteriums, auf die Aufgabe der Link Prediction. Außerdem stellen wir eine Softwarebibliothek vor, die die Implementierung und Untersuchung solcher Komponenten vereinfacht und sie einer breiten Forschungsgemeinschaft zugĂ€nglich macht, die von Forschern im Bereich des relationalen Lernens bis hin zu angewandten Bereichen wie den Biowissenschaften reicht. Schließlich schlagen wir eine neuartige Metrik fĂŒr die Bewertung von Ranking-Ergebnissen vor, wie sie fĂŒr beide Aufgaben verwendet wird. Sie ermöglicht eine einfachere Interpretation und einen leichteren Vergleich, insbesondere in FĂ€llen mit einer unterschiedlichen Anzahl von Kandidaten, wie sie in den de-facto Standardbewertungsprotokollen fĂŒr beide Aufgaben vorkommen
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