6,934 research outputs found
Neuroanatomical and gene expression features of the rabbit accessory olfactory system. Implications of pheromone communication in reproductive behaviour and animal physiology
Mainly driven by the vomeronasal system (VNS), pheromone
communication is involved in many species-specific fundamental innate socio-sexual behaviors such as mating and
fighting, which are essential for animal reproduction and survival. Rabbits are a unique model for studying
chemocommunication due to the discovery of the rabbit mammary pheromone, but paradoxically there has been a
lack of knowledge regarding its VNS pathway. In this work, we aim at filling this gap by approaching the system
from an integrative point of view, providing extensive anatomical and genomic data of the rabbit VNS, as well as
pheromone-mediated reproductive and behavioural studies. Our results build strong foundation for further
translational studies which aim at implementing the use of pheromones to improve animal production and welfare
Learning disentangled speech representations
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
Modeling Uncertainty for Reliable Probabilistic Modeling in Deep Learning and Beyond
[ES] Esta tesis se enmarca en la intersección entre las técnicas modernas de Machine Learning, como las Redes Neuronales Profundas, y el modelado probabilístico confiable. En muchas aplicaciones, no solo nos importa la predicción hecha por un modelo (por ejemplo esta imagen de pulmón presenta cáncer) sino también la confianza que tiene el modelo para hacer esta predicción (por ejemplo esta imagen de pulmón presenta cáncer con 67% probabilidad). En tales aplicaciones, el modelo ayuda al tomador de decisiones (en este caso un médico) a tomar la decisión final. Como consecuencia, es necesario que las probabilidades proporcionadas por un modelo reflejen las proporciones reales presentes en el conjunto al que se ha asignado dichas probabilidades; de lo contrario, el modelo es inútil en la práctica. Cuando esto sucede, decimos que un modelo está perfectamente calibrado.
En esta tesis se exploran tres vias para proveer modelos más calibrados. Primero se muestra como calibrar modelos de manera implicita, que son descalibrados por técnicas de aumentación de datos. Se introduce una función de coste que resuelve esta descalibración tomando como partida las ideas derivadas de la toma de decisiones con la regla de Bayes. Segundo, se muestra como calibrar modelos utilizando una etapa de post calibración implementada con una red neuronal Bayesiana. Finalmente, y en base a las limitaciones estudiadas en la red neuronal Bayesiana, que hipotetizamos que se basan en un prior mispecificado, se introduce un nuevo proceso estocástico que sirve como distribución a priori en un problema de inferencia Bayesiana.[CA] Aquesta tesi s'emmarca en la intersecció entre les tècniques modernes de Machine Learning, com ara les Xarxes Neuronals Profundes, i el modelatge probabilístic fiable. En moltes aplicacions, no només ens importa la predicció feta per un model (per ejemplem aquesta imatge de pulmó presenta càncer) sinó també la confiança que té el model per fer aquesta predicció (per exemple aquesta imatge de pulmó presenta càncer amb 67% probabilitat). En aquestes aplicacions, el model ajuda el prenedor de decisions (en aquest cas un metge) a prendre la decisió final. Com a conseqüència, cal que les probabilitats proporcionades per un model reflecteixin les proporcions reals presents en el conjunt a què s'han assignat aquestes probabilitats; altrament, el model és inútil a la pràctica. Quan això passa, diem que un model està perfectament calibrat.
En aquesta tesi s'exploren tres vies per proveir models més calibrats. Primer es mostra com calibrar models de manera implícita, que són descalibrats per tècniques d'augmentació de dades. S'introdueix una funció de cost que resol aquesta descalibració prenent com a partida les idees derivades de la presa de decisions amb la regla de Bayes. Segon, es mostra com calibrar models utilitzant una etapa de post calibratge implementada amb una xarxa neuronal Bayesiana. Finalment, i segons les limitacions estudiades a la xarxa neuronal Bayesiana, que es basen en un prior mispecificat, s'introdueix un nou procés estocàstic que serveix com a distribució a priori en un problema d'inferència Bayesiana.[EN] This thesis is framed at the intersection between modern Machine Learning techniques, such as Deep Neural Networks, and reliable probabilistic modeling. In many machine learning applications, we do not only care about the prediction made by a model (e.g. this lung image presents cancer) but also in how confident is the model in making this prediction (e.g. this lung image presents cancer with 67% probability). In such applications, the model assists the decision-maker (in this case a doctor) towards making the final decision. As a consequence, one needs that the probabilities provided by a model reflects the true underlying set of outcomes, otherwise the model is useless in practice. When this happens, we say that a model is perfectly calibrated.
In this thesis three ways are explored to provide more calibrated models. First, it is shown how to calibrate models implicitly, which are decalibrated by data augmentation techniques. A cost function is introduced that solves this decalibration taking as a starting point the ideas derived from decision making with Bayes' rule. Second, it shows how to calibrate models using a post-calibration stage implemented with a Bayesian neural network. Finally, and based on the limitations studied in the Bayesian neural network, which we hypothesize that came from a mispecified prior, a new stochastic process is introduced that serves as a priori distribution in a Bayesian inference problem.Maroñas Molano, J. (2022). Modeling Uncertainty for Reliable Probabilistic Modeling in Deep Learning and Beyond [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/181582TESI
Towards A Graphene Chip System For Blood Clotting Disease Diagnostics
Point of care diagnostics (POCD) allows the rapid, accurate measurement of analytes near to a patient. This enables faster clinical decision making and can lead to earlier diagnosis and better patient monitoring and treatment. However, despite many prospective POCD devices being developed for a wide range of diseases this promised technology is yet to be translated to a clinical setting due to the lack of a cost-effective biosensing platform.This thesis focuses on the development of a highly sensitive, low cost and scalable biosensor platform that combines graphene with semiconductor fabrication tech-niques to create graphene field-effect transistors biosensor. The key challenges of designing and fabricating a graphene-based biosensor are addressed. This work fo-cuses on a specific platform for blood clotting disease diagnostics, but the platform has the capability of being applied to any disease with a detectable biomarker.Multiple sensor designs were tested during this work that maximised sensor ef-ficiency and costs for different applications. The multiplex design enabled different graphene channels on the same chip to be functionalised with unique chemistry. The Inverted MOSFET design was created, which allows for back gated measurements to be performed whilst keeping the graphene channel open for functionalisation. The Shared Source and Matrix design maximises the total number of sensing channels per chip, resulting in the most cost-effective fabrication approach for a graphene-based sensor (decreasing cost per channel from £9.72 to £4.11).The challenge of integrating graphene into a semiconductor fabrication process is also addressed through the development of a novel vacuum transfer method-ology that allows photoresist free transfer. The two main fabrication processes; graphene supplied on the wafer “Pre-Transfer” and graphene transferred after met-allisation “Post-Transfer” were compared in terms of graphene channel resistance and graphene end quality (defect density and photoresist). The Post-Transfer pro-cess higher quality (less damage, residue and doping, confirmed by Raman spec-troscopy).Following sensor fabrication, the next stages of creating a sensor platform involve the passivation and packaging of the sensor chip. Different approaches using dielec-tric deposition approaches are compared for passivation. Molecular Vapour Deposi-tion (MVD) deposited Al2O3 was shown to produce graphene channels with lower damage than unprocessed graphene, and also improves graphene doping bringing the Dirac point of the graphene close to 0 V. The packaging integration of microfluidics is investigated comparing traditional soft lithography approaches and the new 3D printed microfluidic approach. Specific microfluidic packaging for blood separation towards a blood sampling point of care sensor is examined to identify the laminar approach for lower blood cell count, as a method of pre-processing the blood sample before sensing.To test the sensitivity of the Post-Transfer MVD passivated graphene sensor de-veloped in this work, real-time IV measurements were performed to identify throm-bin protein binding in real-time on the graphene surface. The sensor was function-alised using a thrombin specific aptamer solution and real-time IV measurements were performed on the functionalised graphene sensor with a range of biologically relevant protein concentrations. The resulting sensitivity of the graphene sensor was in the 1-100 pg/ml concentration range, producing a resistance change of 0.2% per pg/ml. Specificity was confirmed using a non-thrombin specific aptamer as the neg-ative control. These results indicate that the graphene sensor platform developed in this thesis has the potential as a highly sensitive POCD. The processes developed here can be used to develop graphene sensors for multiple biomarkers in the future
Annals [...].
Pedometrics: innovation in tropics; Legacy data: how turn it useful?; Advances in soil sensing; Pedometric guidelines to systematic soil surveys.Evento online. Coordenado por: Waldir de Carvalho Junior, Helena Saraiva Koenow Pinheiro, Ricardo Simão Diniz Dalmolin
Um modelo para suporte automatizado ao reconhecimento, extração, personalização e reconstrução de gráficos estáticos
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
AIUCD 2022 - Proceedings
L’undicesima edizione del Convegno Nazionale dell’AIUCD-Associazione di Informatica Umanistica ha per titolo Culture digitali. Intersezioni: filosofia, arti, media. Nel titolo è presente, in maniera esplicita, la richiesta di una riflessione, metodologica e teorica, sull’interrelazione tra tecnologie digitali, scienze dell’informazione, discipline filosofiche, mondo delle arti e cultural studies
Flexographic printed nanogranular LBZA derived ZnO gas sensors: Synthesis, printing and processing
Within this document, investigations of the processes towards the production of a flexographic printed ZnO gas sensor for breath H2 analysis are presented. Initially, a hexamethylenetetramine (HMTA) based, microwave assisted, synthesis method of layered basic zinc acetate (LBZA) nanomaterials was investigated. Using the synthesised LBZA, a dropcast nanogranular ZnO gas sensor was produced. The testing of the sensor showed high sensitivity towards hydrogen with response (Resistanceair/ Resistancegas) to 200 ppm H2 at 328 °C of 7.27. The sensor is highly competitive with non-catalyst surface decorated sensors and sensitive enough to measure current H2 guideline thresholds for carbohydrate malabsorption (Positive test threshold: 20 ppm H2, Predicted response: 1.34). Secondly, a novel LBZA synthesis method was developed, replacing the HMTA by NaOH. This resulted in a large yield improvement, from a [OH-] conversion of 4.08 at% to 71.2 at%. The effects of [OH-]/[Zn2+] ratio, microwave exposure and transport to nucleation rate ratio on purity, length, aspect ratio and polydispersity were investigated in detail. Using classical nucleation theory, analysis of the basal layer charge symmetries, and oriented attachment theory, a dipole-oriented attachment reaction mechanism is presented. The mechanism is the first theory in literature capable of describing all observed morphological features along length scales. The importance of transport to nucleation rate ratio as the defining property that controls purity and polydispersity is then shown. Using the NaOH derived LBZA, a flexographic printing ink was developed, and proof-of-concept sensors printed. Gas sensing results showed a high response to 200 ppm H2 at 300 °C of 60.2. Through IV measurements and SEM analysis this was shown to be a result of transfer of silver between the electrode and the sensing layer during the printing process. Finally, Investigations into the intense pulsed light treatment of LBZA were conducted. The results show that dehydration at 150 °C prior to exposure is a requirement for successful calcination, producing ZnO quantum dots (QDs) in the process. SEM measurements show mean radii of 1.77-2.02 nm. The QDs show size confinement effects with the exciton blue shifting by 0.105 eV, and exceptionally low defect emission in photoluminescence spectra, indicative of high crystalline quality, and high conductivity. Due to the high crystalline quality and amenity to printing, the IPL ZnO QDs have numerous potential uses ranging from sensing to opto-electronic devices
Engineering Tools to Probe and Manipulate the Immune System at Single-Cell Resolution
My thesis focuses on developing experimental and computational tools to probe and manipulate cellular transcriptomes in the context of human health and disease. Chapter 1 and 2 focus on published work where we leverage single-cell RNA sequencing (scRNA-seq) to understand human immune variability, characterize cell-type specific biases of multiple viral variants within an animal, and assess temporal immune response in the brain to delivery of genetic cargo via an adeno-associated virus (AAV). Chapter 3 and 4 present progress I have made on tools for exporting RNA extracellularly and engineering of a transcription factor for modulating macrophage state.
For probing cellular transcriptome states, we have developed a platform using multiplexed single-cell sequencing and out-of-clinic capillary blood extraction to understand temporal and inter-individual variability of gene expression within immune cell types. Our platform enables simplified, cost-effective profiling of the human immune system across subjects and time at single-cell resolution. To demonstrate the power of our platform, we performed a three day time-of-day study of four healthy individuals, generating gene expression data for 24,087 cells across 22 samples. We detected genes with cell type-specific time-of-day expression and identified robust genes and pathways particular to each individual, all of which could have been missed if analyzed with bulk RNA-sequencing. Also, using scRNA-seq, we have developed a method to screen and characterize cellular tropism of multiple AAV variants. Additionally, I have looked at AAV-mediated transcriptomic changes in animals injected with AAV-PHP.eB three days and twenty-five days post-injection. I have found that there is an upregulation of genes involved in p53 signaling in endothelial cells three days post-injection.
In the context of manipulating cellular transcriptomic states, I demonstrate that a fusion between RNA targeting enzyme, dCas13, and capsid-forming neuronal protein, Arc, is able to form a capsid-like structure capable of encapsulating RNA. I also present methods and preliminary data for tuning macrophage states through mutations in transcription factor EB (TFEB) using scRNA-seq as a readout.</p
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