Canalization and control in automata networks: body segmentation in Drosophila melanogaster

We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic of automata. This results in straightforward measures to quantify canalization in an automaton (micro-level), which is in turn integrated into a highly scalable framework to characterize the collective dynamics of large-scale automata networks (macro-level). This way, our approach provides a method to link micro- to macro-level dynamics -- a crux of complexity. Several new results ensue from this methodology: uncovering of dynamical modularity (modules in the dynamics rather than in the structure of networks), identification of minimal conditions and critical nodes to control the convergence to attractors, simulation of dynamical behaviour from incomplete information about initial conditions, and measures of macro-level canalization and robustness to perturbations. We exemplify our methodology with a well-known model of the intra- and inter cellular genetic regulation of body segmentation in Drosophila melanogaster. We use this model to show that our analysis does not contradict any previous findings. But we also obtain new knowledge about its behaviour: a better understanding of the size of its wild-type attractor basin (larger than previously thought), the identification of novel minimal conditions and critical nodes that control wild-type behaviour, and the resilience of these to stochastic interventions. Our methodology is applicable to any complex network that can be modelled using automata, but we focus on biochemical regulation and signalling, towards a better understanding of the (decentralized) control that orchestrates cellular activity -- with the ultimate goal of explaining how do cells and tissues 'compute'

PTPARL-D: Annotated Corpus of 44 years of Portuguese Parliament debates

In a representative democracy, some decide in the name of the rest, and these elected officials are commonly gathered in public assemblies, such as parliaments, where they discuss policies, legislate, and vote on fundamental initiatives. A core aspect of such democratic processes are the plenary debates, where important public discussions take place. Many parliaments around the world are increasingly keeping the transcripts of such debates, and other parliamentary data, in digital formats accessible to the public, increasing transparency and accountability. Furthermore, some parliaments are bringing old paper transcripts to semi-structured digital formats. However, these records are often only provided as raw text or even as images, with little to no annotation, and inconsistent formats, making them difficult to analyze and study, reducing both transparency and public reach. Here, we present PTPARL-D, an annotated corpus of debates in the Portuguese Parliament, from 1976 to 2019, covering the entire period of Portuguese democracy

Projecto, montagem e teste de uma unidade modular de detecção de radiação Geiger-Muller

Dissertação para obtenção do grau de Mestre em Engenharia Electrotécnica Ramo de Automação e Electrónica IndustrialEsta dissertação apresenta o estudo e o projecto de uma fonte de alimentação para um detector de radiação Geiger-Muller. A fonte de alimentação tanto pode funcionar com a tensão da rede como pode ser integrada em sistemas de electrónica modular NIM de modo a ser facilmente integrada em qualquer tipo de laboratório. A fonte de alimentação inclui os seguintes módulos: 1) rectificador controlado; 2) conversor boost; 3) inversor de tensão; 4) transformador de impulsos; 5) ponte rectificadora de díodos e 6) separador de Alta Tensão – Sinal. Os resultados obtidos experimentalmente estão de acordo com resultados obtidos por simulações usando o Matlab/Simulink ou o OrCAD. Estes resultados permitem demonstrar a fiabilidade e a validade da fonte de alimentação proposta para alimentar o detector Geiger-Muller. A fonte de alimentação foi testada em condições reais de funcionamento com fontes de isótopos radioactivos escolhidos.Abstract: This MSc thesis presents the research and project of a power supply for a Geiger-Muller radiation detector. The power supply may work with mains voltage or may be integrated in a NIM module so that can be easily integrated in any kind of laboratory. The power supply includes the following modules: 1) single-phase full wave controlled rectifier; 2) Boost converter; 3) Voltage inverter; 4) pulse transformer; 5) single-phase bridge rectifier and 6) separador de Alta Tensão – Sinal. The results obtained experimentally match the results obtained by simulations using Matlab/Simulink or OrCAD. This results allow to demonstrate the fiability and validate the proposed power supply to connect to the Geiger-Muller detector. The power supply was tested in real conditions of functioning with chosen sources of radioactive isotopes

Shift-Symmetric Configurations in Two-Dimensional Cellular Automata: Irreversibility, Insolvability, and Enumeration

The search for symmetry as an unusual yet profoundly appealing phenomenon, and the origin of regular, repeating configuration patterns have long been a central focus of complexity science and physics. To better grasp and understand symmetry of configurations in decentralized toroidal architectures, we employ group-theoretic methods, which allow us to identify and enumerate these inputs, and argue about irreversible system behaviors with undesired effects on many computational problems. The concept of so-called configuration shift-symmetry is applied to two-dimensional cellular automata as an ideal model of computation. Regardless of the transition function, the results show the universal insolvability of crucial distributed tasks, such as leader election, pattern recognition, hashing, and encryption. By using compact enumeration formulas and bounding the number of shift-symmetric configurations for a given lattice size, we efficiently calculate the probability of a configuration being shift-symmetric for a uniform or density-uniform distribution. Further, we devise an algorithm detecting the presence of shift-symmetry in a configuration. Given the resource constraints, the enumeration and probability formulas can directly help to lower the minimal expected error and provide recommendations for system's size and initialization. Besides cellular automata, the shift-symmetry analysis can be used to study the non-linear behavior in various synchronous rule-based systems that include inference engines, Boolean networks, neural networks, and systolic arrays.Comment: 22 pages, 9 figures, 2 appendice

The Influence of Canalization on the Robustness of Boolean Networks

Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by $k$-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to $c$-sensitivity and provides formulas for the activities and $c$-sensitivity of general $k$-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the $c$-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally efficient way to obtain Derrida values of Boolean networks, deterministic or stochastic, that does not involve simulation.Comment: 16 pages, 2 figures, 3 table

Adaptive Tutorial Dialogue Systems Using Deep NLP Techniques

We present tutorial dialogue systems in two different domains that demonstrate the use of dialogue management and deep natural language processing techniques. Generation techniques are used to produce natural sounding feedback adapted to student performance and the dialogue history, and context is used to interpret tentative answers phrased as questions

The Beetle and BeeDiff Tutoring Systems

We describe two tutorial dialogue systems that adapt techniques from task-oriented dialogue systems to tutorial dialogue. Both systems employ the same reusable deep natural language understanding and generation components to interpret students ' written utterances and to automatically generate adaptive tutorial responses, with separate domain reasoners to provide the necessary knowledge about the correctness of student answers and hinting strategies. We focus on integrating the domain-independent language processing components with domain-specific reasoning and tutorial components in order to improve the dialogue interaction, and present a preliminary analysis of BeeDiff's evaluation

Drivers of survival in a small mammal of conservation concern : An assessment using extensive genetic non-invasive sampling in fragmented farmland

This study was supported by the Portuguese Foundation for Science and Technology (FCT) under projects NETPERSIST (PTDC/AAG-MAA/3227/2012) and MATEFRAG (PTDC/BIA-BIC/6582/2014). APF was supported by FCT grant SFRH/BD/109242/2015. JP was supported by the project ‘Genomics and Evolutionary Biology’ co-financed by North Portugal Regional Operational Programme 2007/2013 (ON.2 - O Novo Norte), under the National Strategic Reference Framework, through the ERDF and by the European Union's Horizon 2020 research and innovation programme under project EnvMetaGen (grant agreement no 668981). HSM was supported by FCT grant SFRH/BD/73765/2010. PB was supported by EDP Biodiversity Chair. FM was supported by IF/01053/2015. RP was supported by FCT grants SFRH/BPD/73478/2010 and SFRH/BPD/109235/2015.Peer reviewedPostprin