15,724 research outputs found

    ShakingBot: Dynamic Manipulation for Bagging

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    Bag manipulation through robots is complex and challenging due to the deformability of the bag. Based on dynamic manipulation strategy, we propose a new framework, ShakingBot, for the bagging tasks. ShakingBot utilizes a perception module to identify the key region of the plastic bag from arbitrary initial configurations. According to the segmentation, ShakingBot iteratively executes a novel set of actions, including Bag Adjustment, Dual-arm Shaking, and One-arm Holding, to open the bag. The dynamic action, Dual-arm Shaking, can effectively open the bag without the need to account for the crumpled configuration.Then, we insert the items and lift the bag for transport. We perform our method on a dual-arm robot and achieve a success rate of 21/33 for inserting at least one item across various initial bag configurations. In this work, we demonstrate the performance of dynamic shaking actions compared to the quasi-static manipulation in the bagging task. We also show that our method generalizes to variations despite the bag's size, pattern, and color.Comment: Manipulating bag through robots to baggin

    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

    Segment Anything in Medical Images

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    Segment anything model (SAM) has revolutionized natural image segmentation, but its performance on medical images is limited. This work presents MedSAM, the first attempt at extending the success of SAM to medical images, with the goal of creating a universal tool for the segmentation of various medical targets. Specifically, we first curate a large-scale medical image dataset, encompassing over 200,000 masks across 11 different modalities. Then, we develop a simple fine-tuning method to adapt SAM to general medical image segmentation. Comprehensive experiments on 21 3D segmentation tasks and 9 2D segmentation tasks demonstrate that MedSAM outperforms the default SAM model with an average Dice Similarity Coefficient (DSC) of 22.5% and 17.6% on 3D and 2D segmentation tasks, respectively. The code and trained model are publicly available at \url{https://github.com/bowang-lab/MedSAM}

    Augmented classification for electrical coil winding defects

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    A green revolution has accelerated over the recent decades with a look to replace existing transportation power solutions through the adoption of greener electrical alternatives. In parallel the digitisation of manufacturing has enabled progress in the tracking and traceability of processes and improvements in fault detection and classification. This paper explores electrical machine manufacture and the challenges faced in identifying failures modes during this life cycle through the demonstration of state-of-the-art machine vision methods for the classification of electrical coil winding defects. We demonstrate how recent generative adversarial networks can be used to augment training of these models to further improve their accuracy for this challenging task. Our approach utilises pre-processing and dimensionality reduction to boost performance of the model from a standard convolutional neural network (CNN) leading to a significant increase in accuracy

    Um modelo para suporte automatizado ao reconhecimento, extração, personalização e reconstrução de gráficos estáticos

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    Data charts are widely used in our daily lives, being present in regular media, such as newspapers, magazines, web pages, books, and many others. A well constructed data chart leads to an intuitive understanding of its underlying data and in the same way, when data charts have wrong design choices, a redesign of these representations might be needed. However, in most cases, these charts are shown as a static image, which means that the original data are not usually available. Therefore, automatic methods could be applied to extract the underlying data from the chart images to allow these changes. The task of recognizing charts and extracting data from them is complex, largely due to the variety of chart types and their visual characteristics. Computer Vision techniques for image classification and object detection are widely used for the problem of recognizing charts, but only in images without any disturbance. Other features in real-world images that can make this task difficult are not present in most literature works, like photo distortions, noise, alignment, etc. Two computer vision techniques that can assist this task and have been little explored in this context are perspective detection and correction. These methods transform a distorted and noisy chart in a clear chart, with its type ready for data extraction or other uses. The task of reconstructing data is straightforward, as long the data is available the visualization can be reconstructed, but the scenario of reconstructing it on the same context is complex. Using a Visualization Grammar for this scenario is a key component, as these grammars usually have extensions for interaction, chart layers, and multiple views without requiring extra development effort. This work presents a model for automated support for custom recognition, and reconstruction of charts in images. The model automatically performs the process steps, such as reverse engineering, turning a static chart back into its data table for later reconstruction, while allowing the user to make modifications in case of uncertainties. This work also features a model-based architecture along with prototypes for various use cases. Validation is performed step by step, with methods inspired by the literature. This work features three use cases providing proof of concept and validation of the model. The first use case features usage of chart recognition methods focused on documents in the real-world, the second use case focus on vocalization of charts, using a visualization grammar to reconstruct a chart in audio format, and the third use case presents an Augmented Reality application that recognizes and reconstructs charts in the same context (a piece of paper) overlaying the new chart and interaction widgets. The results showed that with slight changes, chart recognition and reconstruction methods are now ready for real-world charts, when taking time, accuracy and precision into consideration.Os gráficos de dados são amplamente utilizados na nossa vida diária, estando presentes nos meios de comunicação regulares, tais como jornais, revistas, páginas web, livros, e muitos outros. Um gráfico bem construído leva a uma compreensão intuitiva dos seus dados inerentes e da mesma forma, quando os gráficos de dados têm escolhas de conceção erradas, poderá ser necessário um redesenho destas representações. Contudo, na maioria dos casos, estes gráficos são mostrados como uma imagem estática, o que significa que os dados originais não estão normalmente disponíveis. Portanto, poderiam ser aplicados métodos automáticos para extrair os dados inerentes das imagens dos gráficos, a fim de permitir estas alterações. A tarefa de reconhecer os gráficos e extrair dados dos mesmos é complexa, em grande parte devido à variedade de tipos de gráficos e às suas características visuais. As técnicas de Visão Computacional para classificação de imagens e deteção de objetos são amplamente utilizadas para o problema de reconhecimento de gráficos, mas apenas em imagens sem qualquer ruído. Outras características das imagens do mundo real que podem dificultar esta tarefa não estão presentes na maioria das obras literárias, como distorções fotográficas, ruído, alinhamento, etc. Duas técnicas de visão computacional que podem ajudar nesta tarefa e que têm sido pouco exploradas neste contexto são a deteção e correção da perspetiva. Estes métodos transformam um gráfico distorcido e ruidoso em um gráfico limpo, com o seu tipo pronto para extração de dados ou outras utilizações. A tarefa de reconstrução de dados é simples, desde que os dados estejam disponíveis a visualização pode ser reconstruída, mas o cenário de reconstrução no mesmo contexto é complexo. A utilização de uma Gramática de Visualização para este cenário é um componente chave, uma vez que estas gramáticas têm normalmente extensões para interação, camadas de gráficos, e visões múltiplas sem exigir um esforço extra de desenvolvimento. Este trabalho apresenta um modelo de suporte automatizado para o reconhecimento personalizado, e reconstrução de gráficos em imagens estáticas. O modelo executa automaticamente as etapas do processo, tais como engenharia inversa, transformando um gráfico estático novamente na sua tabela de dados para posterior reconstrução, ao mesmo tempo que permite ao utilizador fazer modificações em caso de incertezas. Este trabalho também apresenta uma arquitetura baseada em modelos, juntamente com protótipos para vários casos de utilização. A validação é efetuada passo a passo, com métodos inspirados na literatura. Este trabalho apresenta três casos de uso, fornecendo prova de conceito e validação do modelo. O primeiro caso de uso apresenta a utilização de métodos de reconhecimento de gráficos focando em documentos no mundo real, o segundo caso de uso centra-se na vocalização de gráficos, utilizando uma gramática de visualização para reconstruir um gráfico em formato áudio, e o terceiro caso de uso apresenta uma aplicação de Realidade Aumentada que reconhece e reconstrói gráficos no mesmo contexto (um pedaço de papel) sobrepondo os novos gráficos e widgets de interação. Os resultados mostraram que com pequenas alterações, os métodos de reconhecimento e reconstrução dos gráficos estão agora prontos para os gráficos do mundo real, tendo em consideração o tempo, a acurácia e a precisão.Programa Doutoral em Engenharia Informátic

    Foundations for programming and implementing effect handlers

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    First-class control operators provide programmers with an expressive and efficient means for manipulating control through reification of the current control state as a first-class object, enabling programmers to implement their own computational effects and control idioms as shareable libraries. Effect handlers provide a particularly structured approach to programming with first-class control by naming control reifying operations and separating from their handling. This thesis is composed of three strands of work in which I develop operational foundations for programming and implementing effect handlers as well as exploring the expressive power of effect handlers. The first strand develops a fine-grain call-by-value core calculus of a statically typed programming language with a structural notion of effect types, as opposed to the nominal notion of effect types that dominates the literature. With the structural approach, effects need not be declared before use. The usual safety properties of statically typed programming are retained by making crucial use of row polymorphism to build and track effect signatures. The calculus features three forms of handlers: deep, shallow, and parameterised. They each offer a different approach to manipulate the control state of programs. Traditional deep handlers are defined by folds over computation trees, and are the original con-struct proposed by Plotkin and Pretnar. Shallow handlers are defined by case splits (rather than folds) over computation trees. Parameterised handlers are deep handlers extended with a state value that is threaded through the folds over computation trees. To demonstrate the usefulness of effects and handlers as a practical programming abstraction I implement the essence of a small UNIX-style operating system complete with multi-user environment, time-sharing, and file I/O. The second strand studies continuation passing style (CPS) and abstract machine semantics, which are foundational techniques that admit a unified basis for implementing deep, shallow, and parameterised effect handlers in the same environment. The CPS translation is obtained through a series of refinements of a basic first-order CPS translation for a fine-grain call-by-value language into an untyped language. Each refinement moves toward a more intensional representation of continuations eventually arriving at the notion of generalised continuation, which admit simultaneous support for deep, shallow, and parameterised handlers. The initial refinement adds support for deep handlers by representing stacks of continuations and handlers as a curried sequence of arguments. The image of the resulting translation is not properly tail-recursive, meaning some function application terms do not appear in tail position. To rectify this the CPS translation is refined once more to obtain an uncurried representation of stacks of continuations and handlers. Finally, the translation is made higher-order in order to contract administrative redexes at translation time. The generalised continuation representation is used to construct an abstract machine that provide simultaneous support for deep, shallow, and parameterised effect handlers. kinds of effect handlers. The third strand explores the expressiveness of effect handlers. First, I show that deep, shallow, and parameterised notions of handlers are interdefinable by way of typed macro-expressiveness, which provides a syntactic notion of expressiveness that affirms the existence of encodings between handlers, but it provides no information about the computational content of the encodings. Second, using the semantic notion of expressiveness I show that for a class of programs a programming language with first-class control (e.g. effect handlers) admits asymptotically faster implementations than possible in a language without first-class control

    Neural Natural Language Generation: A Survey on Multilinguality, Multimodality, Controllability and Learning

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    Developing artificial learning systems that can understand and generate natural language has been one of the long-standing goals of artificial intelligence. Recent decades have witnessed an impressive progress on both of these problems, giving rise to a new family of approaches. Especially, the advances in deep learning over the past couple of years have led to neural approaches to natural language generation (NLG). These methods combine generative language learning techniques with neural-networks based frameworks. With a wide range of applications in natural language processing, neural NLG (NNLG) is a new and fast growing field of research. In this state-of-the-art report, we investigate the recent developments and applications of NNLG in its full extent from a multidimensional view, covering critical perspectives such as multimodality, multilinguality, controllability and learning strategies. We summarize the fundamental building blocks of NNLG approaches from these aspects and provide detailed reviews of commonly used preprocessing steps and basic neural architectures. This report also focuses on the seminal applications of these NNLG models such as machine translation, description generation, automatic speech recognition, abstractive summarization, text simplification, question answering and generation, and dialogue generation. Finally, we conclude with a thorough discussion of the described frameworks by pointing out some open research directions.This work has been partially supported by the European Commission ICT COST Action “Multi-task, Multilingual, Multi-modal Language Generation” (CA18231). AE was supported by BAGEP 2021 Award of the Science Academy. EE was supported in part by TUBA GEBIP 2018 Award. BP is in in part funded by Independent Research Fund Denmark (DFF) grant 9063-00077B. IC has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 838188. EL is partly funded by Generalitat Valenciana and the Spanish Government throught projects PROMETEU/2018/089 and RTI2018-094649-B-I00, respectively. SMI is partly funded by UNIRI project uniri-drustv-18-20. GB is partly supported by the Ministry of Innovation and the National Research, Development and Innovation Office within the framework of the Hungarian Artificial Intelligence National Laboratory Programme. COT is partially funded by the Romanian Ministry of European Investments and Projects through the Competitiveness Operational Program (POC) project “HOLOTRAIN” (grant no. 29/221 ap2/07.04.2020, SMIS code: 129077) and by the German Academic Exchange Service (DAAD) through the project “AWAKEN: content-Aware and netWork-Aware faKE News mitigation” (grant no. 91809005). ESA is partially funded by the German Academic Exchange Service (DAAD) through the project “Deep-Learning Anomaly Detection for Human and Automated Users Behavior” (grant no. 91809358)

    BECOMEBECOME - A TRANSDISCIPLINARY METHODOLOGY BASED ON INFORMATION ABOUT THE OBSERVER

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    ABSTRACT Andrea T. R. Traldi BECOMEBECOME A Transdisciplinary Methodology Based on Information about the Observer The present research dissertation has been developed with the intention to provide practical strategies and discover new intellectual operations which can be used to generate Transdisciplinary insight. For this reason, this thesis creates access to new knowledge at different scales. Firstly, as it pertains to the scale of new knowledge generated by those who attend Becomebecome events. The open-source nature of the Becomebecome methodology makes it possible for participants in Becomebecome workshops, training programmes and residencies to generate new insight about the specific project they are working on, which then reinforce and expand the foundational principles of the theoretical background. Secondly, as it pertains to the scale of the Becomebecome framework, which remains independent of location and moment in time. The method proposed to access Transdisciplinary knowledge constitutes new knowledge in itself because the sequence of activities, described as physical and mental procedures and listed as essential criteria, have never been found organised 6 in such a specific order before. It is indeed the order in time, i.e. the sequence of the ideas and activities proposed, which allows one to transform Disciplinary knowledge via a new Transdisciplinary frame of reference. Lastly, new knowledge about Transdisciplinarity as a field of study is created as a consequence of the heretofore listed two processes. The first part of the thesis is designated ‘Becomebecome Theory’ and focuses on the theoretical background and the intellectual operations necessary to support the creation of new Transdisciplinary knowledge. The second part of the thesis is designated ‘Becomebecome Practice’ and provides practical examples of the application of such operations. Crucially, the theoretical model described as the foundation for the Becomebecome methodology (Becomebecome Theory) is process-based and constantly checked against the insight generated through Becomebecome Practice. To this effect, ‘information about the observer’ is proposed as a key notion which binds together Transdisciplinary resources from several studies in the hard sciences and humanities. It is a concept that enables understanding about why and how information that is generated through Becomebecome Practice is considered of paramount importance for establishing the reference parameters necessary to access Transdisciplinary insight which is meaningful to a specific project, a specific person, or a specific moment in time
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