Mapping and Merging Using Sound and Vision : Automatic Calibration and Map Fusion with Statistical Deformations

Over the last couple of years both cameras, audio and radio sensors have become cheaper and more common in our everyday lives. Such sensors can be used to create maps of where the sensors are positioned and the appearance of the surroundings. For sound and radio, the process of estimating the sender and receiver positions from time of arrival (TOA) or time-difference of arrival (TDOA) measurements is referred to as automatic calibration. The corresponding process for images is to estimate the camera positions as well as the positions of the objects captured in the images. This is called structure from motion (SfM) or visual simultaneous localisation and mapping (SLAM). In this thesis we present studies on how to create such maps, divided into three parts: to find accurate measurements; robust mapping; and merging of maps.The first part is treated in Paper I and involves finding precise – on a subsample level – TDOA measurements. These types of subsample refinements give a high precision, but are sensitive to noise. We present an explicit expression for the variance of the TDOA estimate and study the impact that noise in the signals has. Exact measurements is an important foundation for creating accurate maps. The second part of this thesis includes Papers II–V and covers the topic of robust self-calibration using one-dimensional signals, such as sound or radio. We estimate both sender and receiver positions using TOA and TDOA measurements. The estimation process is divided in two parts, where the first is specific for TOA or TDOA and involves solving a relaxed version of the problem. The second step is common for different types of problems and involves an upgrade from the relaxed solution to the sought parameters. In this thesis we present numerically stable minimal solvers for both these steps for some different setups with senders and receivers. We also suggest frameworks for how to use these solvers together with RANSAC to achieve systems that are robust to outliers, noise and missing data. Additionally, in the last paper we focus on extending self-calibration results, especially for the sound source path, which often cannot be fully reconstructed immediately. The third part of the thesis, Papers VI–VIII, is concerned with the merging of already estimated maps. We mainly focus on maps created from image data, but the methods are applicable to sparse 3D maps coming from different sensor modalities. Merging of maps can be advantageous if there are several map representations of the same environment, or if there is a need for adding new information to an already existing map. We suggest a compact map representation with a small memory footprint, which we then use to fuse maps efficiently. We suggest one method for fusion of maps that are pre-aligned, and one where we additionally estimate the coordinate system. The merging utilises a compact approximation of the residuals and allows for deformations in the original maps. Furthermore, we present minimal solvers for 3D point matching with statistical deformations – which increases the number of inliers when the original maps contain errors

\u3cem\u3eC. elegans\u3c/em\u3e Synmuv B Proteins Regulate Spatial and Temporal Chromatin Compaction During Development

Tissue-specific establishment of repressive chromatin through creation of compact chromatin domains during development is necessary to ensure proper gene expression and cell fate. Caenorhabditis elegans synMuv B proteins are important for the soma/germline fate decision and mutants demonstrate ectopic germline gene expression in somatic tissue, especially at high temperature. We show that C. elegans synMuv B proteins regulate developmental chromatin compaction and that the timing of chromatin compaction is temperature sensitive in both wild type and synMuv B mutants. Chromatin compaction in mutants is delayed into developmental time periods when zygotic gene expression is upregulated and demonstrates an anterior-to-posterior pattern. Loss of this patterned compaction coincides with the developmental time period of ectopic germline gene expression, which leads to a developmental arrest in synMuv B mutants. Finally, accelerated cell division rates at elevated temperature may contribute to a lack of coordination between expression of tissue specific transcription programs and chromatin compaction at high temperature. Thus, chromatin organization during development is regulated both spatially and temporally by synMuv B proteins to establish repressive chromatin in a tissue-specific manner to ensure proper gene expression

Resource Sharing for Multi-Tenant Nosql Data Store in Cloud

Thesis (Ph.D.) - Indiana University, Informatics and Computing, 2015Multi-tenancy hosting of users in cloud NoSQL data stores is favored by cloud providers because it enables resource sharing at low operating cost. Multi-tenancy takes several forms depending on whether the back-end file system is a local file system (LFS) or a parallel file system (PFS), and on whether tenants are independent or share data across tenants In this thesis I focus on and propose solutions to two cases: independent data-local file system, and shared data-parallel file system. In the independent data-local file system case, resource contention occurs under certain conditions in Cassandra and HBase, two state-of-the-art NoSQL stores, causing performance degradation for one tenant by another. We investigate the interference and propose two approaches. The first provides a scheduling scheme that can approximate resource consumption, adapt to workload dynamics and work in a distributed fashion. The second introduces a workload-aware resource reservation approach to prevent interference. The approach relies on a performance model obtained offline and plans the reservation according to different workload resource demands. Results show the approaches together can prevent interference and adapt to dynamic workloads under multi-tenancy. In the shared data-parallel file system case, it has been shown that running a distributed NoSQL store over PFS for shared data across tenants is not cost effective. Overheads are introduced due to the unawareness of the NoSQL store of PFS. This dissertation targets the key-value store (KVS), a specific form of NoSQL stores, and proposes a lightweight KVS over a parallel file system to improve efficiency. The solution is built on an embedded KVS for high performance but uses novel data structures to support concurrent writes, giving capability that embedded KVSs are not designed for. Results show the proposed system outperforms Cassandra and Voldemort in several different workloads

Modelos de compressão e ferramentas para dados ómicos

The ever-increasing growth of the development of high-throughput sequencing technologies and as a consequence, generation of a huge volume of data, has revolutionized biological research and discovery. Motivated by that, we investigate in this thesis the methods which are capable of providing an efficient representation of omics data in compressed or encrypted manner, and then, we employ them to analyze omics data. First and foremost, we describe a number of measures for the purpose of quantifying information in and between omics sequences. Then, we present finite-context models (FCMs), substitution-tolerant Markov models (STMMs) and a combination of the two, which are specialized in modeling biological data, in order for data compression and analysis. To ease the storage of the aforementioned data deluge, we design two lossless data compressors for genomic and one for proteomic data. The methods work on the basis of (a) a combination of FCMs and STMMs or (b) the mentioned combination along with repeat models and a competitive prediction model. Tested on various synthetic and real data showed their outperformance over the previously proposed methods in terms of compression ratio. Privacy of genomic data is a topic that has been recently focused by developments in the field of personalized medicine. We propose a tool that is able to represent genomic data in a securely encrypted fashion, and at the same time, is able to compact FASTA and FASTQ sequences by a factor of three. It employs AES encryption accompanied by a shuffling mechanism for improving the data security. The results show it is faster than general-purpose and special-purpose algorithms. Compression techniques can be employed for analysis of omics data. Having this in mind, we investigate the identification of unique regions in a species with respect to close species, that can give us an insight into evolutionary traits. For this purpose, we design two alignment-free tools that can accurately find and visualize distinct regions among two collections of DNA or protein sequences. Tested on modern humans with respect to Neanderthals, we found a number of absent regions in Neanderthals that may express new functionalities associated with evolution of modern humans. Finally, we investigate the identification of genomic rearrangements, that have important roles in genetic disorders and cancer, by employing a compression technique. For this purpose, we design a tool that is able to accurately localize and visualize small- and large-scale rearrangements between two genomic sequences. The results of applying the proposed tool on several synthetic and real data conformed to the results partially reported by wet laboratory approaches, e.g., FISH analysis.O crescente crescimento do desenvolvimento de tecnologias de sequenciamento de alto rendimento e, como consequência, a geração de um enorme volume de dados, revolucionou a pesquisa e descoberta biológica. Motivados por isso, nesta tese investigamos os métodos que fornecem uma representação eficiente de dados ómicros de maneira compactada ou criptografada e, posteriormente, os usamos para análise. Em primeiro lugar, descrevemos uma série de medidas com o objetivo de quantificar informação em e entre sequencias ómicas. Em seguida, apresentamos modelos de contexto finito (FCMs), modelos de Markov tolerantes a substituição (STMMs) e uma combinação dos dois, especializados na modelagem de dados biológicos, para compactação e análise de dados. Para facilitar o armazenamento do dilúvio de dados acima mencionado, desenvolvemos dois compressores de dados sem perda para dados genómicos e um para dados proteómicos. Os métodos funcionam com base em (a) uma combinação de FCMs e STMMs ou (b) na combinação mencionada, juntamente com modelos de repetição e um modelo de previsão competitiva. Testados em vários dados sintéticos e reais mostraram a sua eficiência sobre os métodos do estado-de-arte em termos de taxa de compressão. A privacidade dos dados genómicos é um tópico recentemente focado nos desenvolvimentos do campo da medicina personalizada. Propomos uma ferramenta capaz de representar dados genómicos de maneira criptografada com segurança e, ao mesmo tempo, compactando as sequencias FASTA e FASTQ para um fator de três. Emprega criptografia AES acompanhada de um mecanismo de embaralhamento para melhorar a segurança dos dados. Os resultados mostram que ´e mais rápido que os algoritmos de uso geral e específico. As técnicas de compressão podem ser exploradas para análise de dados ómicos. Tendo isso em mente, investigamos a identificação de regiões únicas em uma espécie em relação a espécies próximas, que nos podem dar uma visão das características evolutivas. Para esse fim, desenvolvemos duas ferramentas livres de alinhamento que podem encontrar e visualizar com precisão regiões distintas entre duas coleções de sequências de DNA ou proteínas. Testados em humanos modernos em relação a neandertais, encontrámos várias regiões ausentes nos neandertais que podem expressar novas funcionalidades associadas à evolução dos humanos modernos. Por último, investigamos a identificação de rearranjos genómicos, que têm papéis importantes em desordens genéticas e cancro, empregando uma técnica de compressão. Para esse fim, desenvolvemos uma ferramenta capaz de localizar e visualizar com precisão os rearranjos em pequena e grande escala entre duas sequências genómicas. Os resultados da aplicação da ferramenta proposta, em vários dados sintéticos e reais, estão em conformidade com os resultados parcialmente relatados por abordagens laboratoriais, por exemplo, análise FISH.Programa Doutoral em Engenharia Informátic

Cognición y representación interna de entornos dinámicos en el cerebro de los mamíferos

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias Biológicas, leída el 07/05/2021El tiempo es una de las dimensiones fundamentales de la realidad. Paradójicamente, los fenómenos temporales del mundo natural contienen ingentes cantidades de información redundante, y a pesar de ello, codificar internamente el tiempo en el cerebro es imprescindible para anticiparse a peligros en ambientes dinámicos. No obstante, dedicar grandes cantidades de recursos cognitivos a procesar las características espacio-temporales de entornos complejos debería ser incompatible con la supervivencia, que requiere respuestas rápidas. Aun así, los animales son capaces de tomar decisiones en intervalos de tiempo muy estrechos. ¿Cómo consigue hacer esto el cerebro? Como respuesta al balance entre complejidad y velocidad, la hipótesis de la compactación del tiempo propone que el cerebro no codifica el tiempo explícitamente, sino que lo integra en el espacio. En teoría, la compactación del tiempo simplifica las representaciones internas del entorno, reduciendo significativamente la carga de trabajo dedicada a la planificación y la toma de decisiones. La compactación del tiempo proporciona un marco operativo que pretende explicar cómo las situaciones dinámicas, percibidas o producidas, se representan cognitivamente en forma de predicciones espaciales o representaciones internas compactas (CIR), que pueden almacenarse en la memoria y recuperarse más adelante para generar respuestas. Aunque la compactación del tiempo ya ha sido implementada en robots, hasta ahora no se había comprobado su existencia como mecanismo biológico y cognitivo en el cerebro...Time is one of the most prominent dimensions that organize reality. Paradoxically, there are loads of redundant information contained within the temporal features of the natural world, and yet internal coding of time in the brain seems to be crucial for anticipating time-changing, dynamic hazards. Allocating such significant brain resources to process spatiotemporal aspects of complex environments should apparently be incompatible with survival, which requires fast and accurate responses. Nonetheless, animals make decisions under pressure and in narrow time windows. How does the brain achieve this? An effort to resolve the complexity-velocity trade-off led to a hypothesis called time compaction, which states the brain does not encode time explicitly but embeds it into space. Theoretically, time compaction can significantly simplify internal representations of the environment and hence ease the brain workload devoted to planning and decision-making. Time compaction also provides an operational framework that aims to explain how perceived and produced dynamic situations are cognitively represented, in the form of spatial predictions or compact internal representations (CIRs) that can be stored in memory and be used later on to guide behaviour and generate action. Although successfully implemented in robots, time compaction still lacked assessment of its biological soundness as an actual cognitive mechanism in the brain...Fac. de Ciencias BiológicasTRUEunpu