Autoencoder Implementations in the predictive coding framework

Abstract. We study the implementation and functionality of autoencoders based on the predictive coding model and the free energy framework, which have seen relatively little experimentation. This framework offers an alternative approach to constructing artificial neural networks in place of traditional backpropagation networks. The limited number of studies published on the subject indicate that the framework could provide better solutions to applications employing artificial intelligence. This work is meant to accessible to any university student wishing to gain a preliminary understanding for the concepts involved. To this end we provide a detailed walkthrough of the core mathematical ideas behind the implementation using Bogacz’s great tutorial as a guide. We document the implementation process of two autoencoders that learn to recreate handwritten digits from the MNIST dataset in an unsupervised learning scenario. Both of these implementations utilize fully connected layers and are tasked with encoding and decoding of handwritten digits from the MNIST dataset. We analyze graphs of the different variable values and compare the final images produced by the autoencoder to the original ones. The first implementation is an attempt at constructing an original network and serves as an example of how error sensitive the construction of these networks from the ground up can be. We study the applicability of the theory of predictive coding in practice and diagnose the issues that we encounter. In particular, we showcase problems relating to the update of variances within the network and general difficulties in achieving convergence for all nodes in the network. The second implementation is built on top of a predictive coding library built by B. Millidge and A. Tschantz and showcases the potential of predictive coding model as a basis for a functional autoencoder. We partially replicate the results obtained by Millidge to establish a baseline for the network’s performance. Furthermore, we study the effects of tuning different aspects of these networks to better understand the function of these types of networks. These aspects include the network depth, number of nodes per layer and activation functions. Subjective evaluation on the effects of these modifications is conducted. Our findings regarding the second implementation indicate that the most important factor in determining final image quality and classification capability is the width of the code layer of the autoencoder. Our experiments using different activation functions do not reveal significant performance gains for any of the functions used. Lastly, we look at the effects of deepening the network but find equal or worse performance when compared to shallow networks

A low-complexity beamforming design for multiuser wireless energy transfer

Wireless energy transfer (WET) is a green enabler of low-power Internet of Things (IoT). Therein, traditional optimization schemes relying on full channel state information (CSI) are often too costly to implement due to excessive energy consumption and high processing complexity. This letter proposes a simple, yet effective, energy beamforming scheme that allows a multi-antenna power beacon (PB) to fairly power a set of IoT devices by only relying on the first-order statistics of the channels. In addition to low complexity, the proposed scheme performs favorably as compared to benchmarking schemes and its performance improves as the number of PB’s antennas increases. Finally, it is shown that further performance improvement can be achieved through proper angular rotations of the PB.info:eu-repo/semantics/acceptedVersio

Strain-controlled criticality governs the nonlinear mechanics of fibre networks

Disordered fibrous networks are ubiquitous in nature as major structural components of living cells and tissues. The mechanical stability of networks generally depends on the degree of connectivity: only when the average number of connections between nodes exceeds the isostatic threshold are networks stable (Maxwell, J. C., Philosophical Magazine 27, 294 (1864)). Upon increasing the connectivity through this point, such networks undergo a mechanical phase transition from a floppy to a rigid phase. However, even sub-isostatic networks become rigid when subjected to sufficiently large deformations. To study this strain-controlled transition, we perform a combination of computational modeling of fibre networks and experiments on networks of type I collagen fibers, which are crucial for the integrity of biological tissues. We show theoretically that the development of rigidity is characterized by a strain-controlled continuous phase transition with signatures of criticality. Our experiments demonstrate mechanical properties consistent with our model, including the predicted critical exponents. We show that the nonlinear mechanics of collagen networks can be quantitatively captured by the predictions of scaling theory for the strain-controlled critical behavior over a wide range of network concentrations and strains up to failure of the material

Predicting Skeletal Muscle and Whole-Body Insulin Sensitivity Using NMR-Metabolomic Profiling

Purpose: Abnormal lipoprotein and amino acid profiles are associated with insulin resistance and may help to identify this condition. The aim of this study was to create models estimating skeletal muscle and whole-body insulin sensitivity using fasting metabolite profiles and common clinical and laboratory measures.Material and Methods: The cross-sectional study population included 259 subjects with normal or impaired fasting glucose or type 2 diabetes in whom skeletal muscle and whole-body insulin sensitivity (M-value) were measured during euglycemic hyperinsulinemic clamp. Muscle glucose uptake (GU) was measured directly using [F-18]FDG-PET. Serum metabolites were measured using nuclear magnetic resonance (NMR) spectroscopy. We used linear regression to build the models for the muscle GU (Muscle-insulin sensitivity index [ISI]) and M-value (whole-body [WB]-ISI). The models were created and tested using randomly selected training (n = 173) and test groups (n = 86). The models were compared to common fasting indices of insulin sensitivity, homeostatic model assessment-insulin resistance (HOMA-IR) and the revised quantitative insulin sensitivity check index (QUICKI).Results: WB-ISI had higher correlation with actual M-value than HOMA-IR or revised QUICKI (rho = 0.83 vs -0.67 and 0.66; P < 0.05 for both comparisons), whereas the correlation of Muscle-ISI with the actual skeletal muscle GU was not significantly stronger than HOMA-IR's or revised QUICKI's (rho = 0.67 vs -0.58 and 0.59; both nonsignificant) in the test dataset.Conclusion: Muscle-ISI and WB-ISI based on NMR-metabolomics and common laboratory measurements from fasting serum samples and basic anthropometrics are promising rapid and inexpensive tools for determining insulin sensitivity in at-risk individuals. (C) Endocrine Society 2020

Pathways to emotional closeness in neonatal units – a cross-national qualitative study

Background: Research shows evidence for the importance of physical and emotional closeness for the infant, the parent and the infant-parent dyad. Less is known about how, when and why parents experience emotional closeness to their infants in a neonatal unit (NU), which was the aim of this study. Methods: A qualitative study using a salutogenic approach to focus on positive health and wellbeing was undertaken in three NUs: one in Sweden, England and Finland. An ‘emotional closeness’ form was devised, which asked parents to describe moments/situations when, how and why they had felt emotionally close to their infant. Data for 23 parents of preterm infants were analyzed using thematic networks analysis. Results: A global theme of ‘pathways for emotional closeness’ emerged from the data set. This concept related to how emotional, physical, cognitive and social influences led to feelings of emotional closeness between parents and their infants. The five underpinning organising themes relate to the: Embodied recognition through the power of physical closeness; Reassurance of, and contributing to, infant wellness; Understanding the present and the past; Feeling engaged in the day to day and Spending time and bonding as a family. Conclusion: These findings generate important insights into why, how and when parents feel emotionally close. This knowledge contributes to an increased awareness of how to support parents of premature infants to form positive and loving relationships with their infants. Health care staff should create a climate where parents’ emotions and their emotional journey are individually supported

Mãe, cadê o bebê? Repercussões do nascimento prematuro de um irmão

O objetivo deste artigo foi investigar as repercussões do nascimento prematuro do bebê sobre o(s) seu(s) irmão(s), sob a perspectiva materna, durante a internação do recém-nascido na Unidade de Terapia Intensiva Neonatal. O estudo contou com a participação de 37 mães, entrevistadas no 15º dia após o parto. Elas responderam a instrumentos que contemplaram dados demográficos familiares, informações clínicas do bebê e da mãe, e a experiência da maternidade no contexto da prematuridade. A entrevista sobre maternidade continha questões acerca do irmão do bebê, cujas respostas foram examinadas a partir de análise de conteúdo qualitativa. Os resultados revelaram alteração na rotina dos irmãos em razão da maior ausência materna. Os sentimentos e reações dos irmãos incluíram questionamentos, preocupações, ciúme e ansiedade, ao lado de contentamento e curiosidade. A visita do irmão ao bebê prematuro não foi permitida por alguns hospitais. Evidencia-se a importância de os irmãos serem atendidos em suas necessidades de cuidado nesse período de hospitalização do bebê

Capillary filling with pseudo-potential binary Lattice-Boltzmann model

We present a systematic study of capillary filling for a binary fluid by using a mesoscopic lattice Boltzmann model for immiscible fluids describing a diffusive interface moving at a given contact angle with respect to the walls. The phenomenological way to impose a given contact angle is analysed. Particular attention is given to the case of complete wetting, that is contact angle equal to zero. Numerical results yield quantitative agreement with the theoretical Washburn law, provided that the correct ratio of the dynamic viscosities between the two fluids is used. Finally, the presence of precursor films is experienced and it is shown that these films advance in time with a square-root law but with a different prefactor with respect to the bulk interface.Comment: 13 pages, 8 figures, accepted for publication on The European journal of physics

Lanthanide-based time-resolved luminescence immunoassays

The sensitive and specific detection of analytes such as proteins in biological samples is critical for a variety of applications, for example disease diagnosis. In immunoassays a signal in response to the concentration of analyte present is generated by use of antibodies labeled with radioisotopes, luminophores, or enzymes. All immunoassays suffer to some extent from the problem of the background signal observed in the absence of analyte, which limits the sensitivity and dynamic range that can be achieved. This is especially the case for homogeneous immunoassays and surface measurements on tissue sections and membranes, which typically have a high background because of sample autofluorescence. One way of minimizing background in immunoassays involves the use of lanthanide chelate labels. Luminescent lanthanide complexes have exceedingly long-lived luminescence in comparison with conventional fluorophores, enabling the short-lived background interferences to be removed via time-gated acquisition and delivering greater assay sensitivity and a broader dynamic range. This review highlights the potential of using lanthanide luminescence to design sensitive and specific immunoassays. Techniques for labeling biomolecules with lanthanide chelate tags are discussed, with aspects of chelate design. Microtitre plate-based heterogeneous and homogeneous assays are reviewed and compared in terms of sensitivity, dynamic range, and convenience. The great potential of surface-based time-resolved imaging techniques for biomolecules on gels, membranes, and tissue sections using lanthanide tracers in proteomics applications is also emphasized