12,550 research outputs found

    CoRe-Sleep: A Multimodal Fusion Framework for Time Series Robust to Imperfect Modalities

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    Sleep abnormalities can have severe health consequences. Automated sleep staging, i.e. labelling the sequence of sleep stages from the patient's physiological recordings, could simplify the diagnostic process. Previous work on automated sleep staging has achieved great results, mainly relying on the EEG signal. However, often multiple sources of information are available beyond EEG. This can be particularly beneficial when the EEG recordings are noisy or even missing completely. In this paper, we propose CoRe-Sleep, a Coordinated Representation multimodal fusion network that is particularly focused on improving the robustness of signal analysis on imperfect data. We demonstrate how appropriately handling multimodal information can be the key to achieving such robustness. CoRe-Sleep tolerates noisy or missing modalities segments, allowing training on incomplete data. Additionally, it shows state-of-the-art performance when testing on both multimodal and unimodal data using a single model on SHHS-1, the largest publicly available study that includes sleep stage labels. The results indicate that training the model on multimodal data does positively influence performance when tested on unimodal data. This work aims at bridging the gap between automated analysis tools and their clinical utility.Comment: 10 pages, 4 figures, 2 tables, journa

    Pollution-induced community tolerance in freshwater biofilms – from molecular mechanisms to loss of community functions

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    Exposure to herbicides poses a threat to aquatic biofilms by affecting their community structure, physiology and function. These changes render biofilms to become more tolerant, but on the downside community tolerance has ecologic costs. A concept that addresses induced community tolerance to a pollutant (PICT) was introduced by Blanck and Wängberg (1988). The basic principle of the concept is that microbial communities undergo pollution-induced succession when exposed to a pollutant over a long period of time, which changes communities structurally and functionally and enhancing tolerance to the pollutant exposure. However, the mechanisms of tolerance and the ecologic consequences were hardly studied up to date. This thesis addresses the structural and functional changes in biofilm communities and applies modern molecular methods to unravel molecular tolerance mechanisms. Two different freshwater biofilm communities were cultivated for a period of five weeks, with one of the communities being contaminated with 4 μg L-1 diuron. Subsequently, the communities were characterized for structural and functional differences, especially focusing on their crucial role of photosynthesis. The community structure of the autotrophs was assessed using HPLC-based pigment analysis and their functional alterations were investigated using Imaging-PAM fluorometry to study photosynthesis and community oxygen profiling to determine net primary production. Then, the molecular fingerprints of the communities were measured with meta-transcriptomics (RNA-Seq) and GC-based community metabolomics approaches and analyzed with respect to changes in their molecular functions. The communities were acute exposed to diuron for one hour in a dose-response design, to reveal a potential PICT and uncover related adaptation to diuron exposure. The combination of apical and molecular methods in a dose-response design enabled the linkage of functional effects of diuron exposure and underlying molecular mechanisms based on a sensitivity analysis. Chronic exposure to diuron impaired freshwater biofilms in their biomass accrual. The contaminated communities particularly lost autotrophic biomass, reflected by the decrease in specific chlorophyll a content. This loss was associated with a change in the molecular fingerprint of the communities, which substantiates structural and physiological changes. The decline in autotrophic biomass could be due to a primary loss of sensitive autotrophic organisms caused by the selection of better adapted species in the course of chronic exposure. Related to this hypothesis, an increase in diuron tolerance has been detected in the contaminated communities and molecular mechanisms facilitating tolerance have been found. It was shown that genes of the photosystem, reductive-pentose phosphate cycle and arginine metabolism were differentially expressed among the communities and that an increased amount of potential antioxidant degradation products was found in the contaminated communities. This led to the hypothesis that contaminated communities may have adapted to oxidative stress, making them less sensitive to diuron exposure. Moreover, the photosynthetic light harvesting complex was altered and the photoprotective xanthophyll cycle was increased in the contaminated communities. Despite these adaptation strategies, the loss of autotrophic biomass has been shown to impair primary production. This impairment persisted even under repeated short-term exposure, so that the tolerance mechanisms cannot safeguard primary production as a key function in aquatic systems.:1. The effect of chemicals on organisms and their functions .............................. 1 1.1 Welcome to the anthropocene .......................................................................... 1 1.2 From cellular stress responses to ecosystem resilience ................................... 3 1.2.1 The individual pursuit for homeostasis ....................................................... 3 1.2.2 Stability from diversity ................................................................................. 5 1.3 Community ecotoxicology - a step forward in monitoring the effects of chemical pollution? ................................................................................................................. 6 1.4 Functional ecotoxicological assessment of microbial communities ................... 9 1.5 Molecular tools – the key to a mechanistic understanding of stressor effects from a functional perspective in microbial communities? ...................................... 12 2. Aims and Hypothesis ......................................................................................... 14 2.1 Research question .......................................................................................... 14 2.2 Hypothesis and outline .................................................................................... 15 2.3 Experimental approach & concept .................................................................. 16 2.3.1 Aquatic freshwater biofilms as model community ..................................... 16 2.3.2 Diuron as model herbicide ........................................................................ 17 2.3.3 Experimental design ................................................................................. 18 3. Structural and physiological changes in microbial communities after chronic exposure - PICT and altered functional capacity ................................................. 21 3.1 Introduction ..................................................................................................... 21 3.2 Methods .......................................................................................................... 23 3.2.1 Biofilm cultivation ...................................................................................... 23 3.2.2 Dry weight and autotrophic index ............................................................. 23 3.2.4 Pigment analysis of periphyton ................................................................. 23 3.2.4.1 In-vivo pigment analysis for community characterization ....................... 24 3.2.4.2 In-vivo pigment analysis based on Imaging-PAM fluorometry ............... 24 3.2.4.3 In-vivo pigment fluorescence for tolerance detection ............................. 26 3.2.4.4 Ex-vivo pigment analysis by high-pressure liquid-chromatography ....... 27 3.2.5 Community oxygen metabolism measurements ....................................... 28 3.3 Results and discussion ................................................................................... 29 3.3.1 Comparison of the structural community parameters ............................... 29 3.3.2 Photosynthetic activity and primary production of the communities after selection phase ................................................................................................. 33 3.3.3 Acquisition of photosynthetic tolerance .................................................... 34 3.3.4 Primary production at exposure conditions ............................................... 36 3.3.5 Tolerance detection in primary production ................................................ 37 3.4 Summary and Conclusion ........................................................................... 40 4. Community gene expression analysis by meta-transcriptomics ................... 41 4.1 Introduction to meta-transcriptomics ............................................................... 41 4.2. Methods ......................................................................................................... 43 4.2.1 Sampling and RNA extraction................................................................... 43 4.2.2 RNA sequencing analysis ......................................................................... 44 4.2.3 Data assembly and processing................................................................. 45 4.2.4 Prioritization of contigs and annotation ..................................................... 47 4.2.5 Sensitivity analysis of biological processes .............................................. 48 4.3 Results and discussion ................................................................................... 48 4.3.1 Characterization of the meta-transcriptomic fingerprints .......................... 49 4.3.2 Insights into community stress response mechanisms using trend analysis (DRomic’s) ......................................................................................................... 51 4.3.3 Response pattern in the isoform PS genes .............................................. 63 4.5 Summary and conclusion ................................................................................ 65 5. Community metabolome analysis ..................................................................... 66 5.1 Introduction to community metabolomics ........................................................ 66 5.2 Methods .......................................................................................................... 68 5.2.1 Sampling, metabolite extraction and derivatisation................................... 68 5.2.2 GC-TOF-MS analysis ............................................................................... 69 5.2.3 Data processing and statistical analysis ................................................... 69 5.3 Results and discussion ................................................................................... 70 5.3.1 Characterization of the metabolic fingerprints .......................................... 70 5.3.2 Difference in the metabolic fingerprints .................................................... 71 5.3.3 Differential metabolic responses of the communities to short-term exposure of diuron ............................................................................................................ 73 5.4 Summary and conclusion ................................................................................ 78 6. Synthesis ............................................................................................................. 79 6.1 Approaches and challenges for linking molecular data to functional measurements ...................................................................................................... 79 6.2 Methods .......................................................................................................... 83 6.2.1 Summary on the data ............................................................................... 83 6.2.2 Aggregation of molecular data to index values (TELI and MELI) .............. 83 6.2.3 Functional annotation of contigs and metabolites using KEGG ................ 83 6.3 Results and discussion ................................................................................... 85 6.3.1 Results of aggregation techniques ........................................................... 85 6.3.2 Sensitivity analysis of the different molecular approaches and endpoints 86 6.3.3 Mechanistic view of the molecular stress responses based on KEGG functions ............................................................................................................ 89 6.4 Consolidation of the results – holistic interpretation and discussion ............... 93 6.4.1 Adaptation to chronic diuron exposure - from molecular changes to community effects.............................................................................................. 93 6.4.2 Assessment of the ecological costs of Pollution-induced community tolerance based on primary production ............................................................. 94 6.5 Outlook ............................................................................................................ 9

    When to be critical? Performance and evolvability in different regimes of neural Ising agents

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    It has long been hypothesized that operating close to the critical state is beneficial for natural, artificial and their evolutionary systems. We put this hypothesis to test in a system of evolving foraging agents controlled by neural networks that can adapt agents' dynamical regime throughout evolution. Surprisingly, we find that all populations that discover solutions, evolve to be subcritical. By a resilience analysis, we find that there are still benefits of starting the evolution in the critical regime. Namely, initially critical agents maintain their fitness level under environmental changes (for example, in the lifespan) and degrade gracefully when their genome is perturbed. At the same time, initially subcritical agents, even when evolved to the same fitness, are often inadequate to withstand the changes in the lifespan and degrade catastrophically with genetic perturbations. Furthermore, we find the optimal distance to criticality depends on the task complexity. To test it we introduce a hard and simple task: for the hard task, agents evolve closer to criticality whereas more subcritical solutions are found for the simple task. We verify that our results are independent of the selected evolutionary mechanisms by testing them on two principally different approaches: a genetic algorithm and an evolutionary strategy. In summary, our study suggests that although optimal behaviour in the simple task is obtained in a subcritical regime, initializing near criticality is important to be efficient at finding optimal solutions for new tasks of unknown complexity.Comment: arXiv admin note: substantial text overlap with arXiv:2103.1218

    Robo3D: Towards Robust and Reliable 3D Perception against Corruptions

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    The robustness of 3D perception systems under natural corruptions from environments and sensors is pivotal for safety-critical applications. Existing large-scale 3D perception datasets often contain data that are meticulously cleaned. Such configurations, however, cannot reflect the reliability of perception models during the deployment stage. In this work, we present Robo3D, the first comprehensive benchmark heading toward probing the robustness of 3D detectors and segmentors under out-of-distribution scenarios against natural corruptions that occur in real-world environments. Specifically, we consider eight corruption types stemming from adversarial weather conditions, external disturbances, and internal sensor failure. We uncover that, although promising results have been progressively achieved on standard benchmarks, state-of-the-art 3D perception models are at risk of being vulnerable to corruptions. We draw key observations on the use of data representations, augmentation schemes, and training strategies, that could severely affect the model's performance. To pursue better robustness, we propose a density-insensitive training framework along with a simple flexible voxelization strategy to enhance the model resiliency. We hope our benchmark and approach could inspire future research in designing more robust and reliable 3D perception models. Our robustness benchmark suite is publicly available.Comment: 33 pages, 26 figures, 26 tables; code at https://github.com/ldkong1205/Robo3D project page at https://ldkong.com/Robo3

    Deep Learning for Scene Flow Estimation on Point Clouds: A Survey and Prospective Trends

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    Aiming at obtaining structural information and 3D motion of dynamic scenes, scene flow estimation has been an interest of research in computer vision and computer graphics for a long time. It is also a fundamental task for various applications such as autonomous driving. Compared to previous methods that utilize image representations, many recent researches build upon the power of deep analysis and focus on point clouds representation to conduct 3D flow estimation. This paper comprehensively reviews the pioneering literature in scene flow estimation based on point clouds. Meanwhile, it delves into detail in learning paradigms and presents insightful comparisons between the state-of-the-art methods using deep learning for scene flow estimation. Furthermore, this paper investigates various higher-level scene understanding tasks, including object tracking, motion segmentation, etc. and concludes with an overview of foreseeable research trends for scene flow estimation

    Deep Transfer Learning Applications in Intrusion Detection Systems: A Comprehensive Review

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    Globally, the external Internet is increasingly being connected to the contemporary industrial control system. As a result, there is an immediate need to protect the network from several threats. The key infrastructure of industrial activity may be protected from harm by using an intrusion detection system (IDS), a preventive measure mechanism, to recognize new kinds of dangerous threats and hostile activities. The most recent artificial intelligence (AI) techniques used to create IDS in many kinds of industrial control networks are examined in this study, with a particular emphasis on IDS-based deep transfer learning (DTL). This latter can be seen as a type of information fusion that merge, and/or adapt knowledge from multiple domains to enhance the performance of the target task, particularly when the labeled data in the target domain is scarce. Publications issued after 2015 were taken into account. These selected publications were divided into three categories: DTL-only and IDS-only are involved in the introduction and background, and DTL-based IDS papers are involved in the core papers of this review. Researchers will be able to have a better grasp of the current state of DTL approaches used in IDS in many different types of networks by reading this review paper. Other useful information, such as the datasets used, the sort of DTL employed, the pre-trained network, IDS techniques, the evaluation metrics including accuracy/F-score and false alarm rate (FAR), and the improvement gained, were also covered. The algorithms, and methods used in several studies, or illustrate deeply and clearly the principle in any DTL-based IDS subcategory are presented to the reader

    Self-Supervised Scene Dynamic Recovery from Rolling Shutter Images and Events

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    Scene Dynamic Recovery (SDR) by inverting distorted Rolling Shutter (RS) images to an undistorted high frame-rate Global Shutter (GS) video is a severely ill-posed problem, particularly when prior knowledge about camera/object motions is unavailable. Commonly used artificial assumptions on motion linearity and data-specific characteristics, regarding the temporal dynamics information embedded in the RS scanlines, are prone to producing sub-optimal solutions in real-world scenarios. To address this challenge, we propose an event-based RS2GS framework within a self-supervised learning paradigm that leverages the extremely high temporal resolution of event cameras to provide accurate inter/intra-frame information. % In this paper, we propose to leverage the event camera to provide inter/intra-frame information as the emitted events have an extremely high temporal resolution and learn an event-based RS2GS network within a self-supervised learning framework, where real-world events and RS images can be exploited to alleviate the performance degradation caused by the domain gap between the synthesized and real data. Specifically, an Event-based Inter/intra-frame Compensator (E-IC) is proposed to predict the per-pixel dynamic between arbitrary time intervals, including the temporal transition and spatial translation. Exploring connections in terms of RS-RS, RS-GS, and GS-RS, we explicitly formulate mutual constraints with the proposed E-IC, resulting in supervisions without ground-truth GS images. Extensive evaluations over synthetic and real datasets demonstrate that the proposed method achieves state-of-the-art and shows remarkable performance for event-based RS2GS inversion in real-world scenarios. The dataset and code are available at https://w3un.github.io/selfunroll/

    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

    Learning disentangled speech representations

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    A variety of informational factors are contained within the speech signal and a single short recording of speech reveals much more than the spoken words. The best method to extract and represent informational factors from the speech signal ultimately depends on which informational factors are desired and how they will be used. In addition, sometimes methods will capture more than one informational factor at the same time such as speaker identity, spoken content, and speaker prosody. The goal of this dissertation is to explore different ways to deconstruct the speech signal into abstract representations that can be learned and later reused in various speech technology tasks. This task of deconstructing, also known as disentanglement, is a form of distributed representation learning. As a general approach to disentanglement, there are some guiding principles that elaborate what a learned representation should contain as well as how it should function. In particular, learned representations should contain all of the requisite information in a more compact manner, be interpretable, remove nuisance factors of irrelevant information, be useful in downstream tasks, and independent of the task at hand. The learned representations should also be able to answer counter-factual questions. In some cases, learned speech representations can be re-assembled in different ways according to the requirements of downstream applications. For example, in a voice conversion task, the speech content is retained while the speaker identity is changed. And in a content-privacy task, some targeted content may be concealed without affecting how surrounding words sound. While there is no single-best method to disentangle all types of factors, some end-to-end approaches demonstrate a promising degree of generalization to diverse speech tasks. This thesis explores a variety of use-cases for disentangled representations including phone recognition, speaker diarization, linguistic code-switching, voice conversion, and content-based privacy masking. Speech representations can also be utilised for automatically assessing the quality and authenticity of speech, such as automatic MOS ratings or detecting deep fakes. The meaning of the term "disentanglement" is not well defined in previous work, and it has acquired several meanings depending on the domain (e.g. image vs. speech). Sometimes the term "disentanglement" is used interchangeably with the term "factorization". This thesis proposes that disentanglement of speech is distinct, and offers a viewpoint of disentanglement that can be considered both theoretically and practically
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