Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Interpretable statistics for complex modelling: quantile and topological learning

As the complexity of our data increased exponentially in the last decades, so has our need for interpretable features. This thesis revolves around two paradigms to approach this quest for insights. In the first part we focus on parametric models, where the problem of interpretability can be seen as a “parametrization selection”. We introduce a quantile-centric parametrization and we show the advantages of our proposal in the context of regression, where it allows to bridge the gap between classical generalized linear (mixed) models and increasingly popular quantile methods. The second part of the thesis, concerned with topological learning, tackles the problem from a non-parametric perspective. As topology can be thought of as a way of characterizing data in terms of their connectivity structure, it allows to represent complex and possibly high dimensional through few features, such as the number of connected components, loops and voids. We illustrate how the emerging branch of statistics devoted to recovering topological structures in the data, Topological Data Analysis, can be exploited both for exploratory and inferential purposes with a special emphasis on kernels that preserve the topological information in the data. Finally, we show with an application how these two approaches can borrow strength from one another in the identification and description of brain activity through fMRI data from the ABIDE project

Integrating knowledge accross disciplines. Experiences from the NeWater project

The starting question for this deliverable was how to create a new adaptive management concept that can integrate insights from various disciplines and connect people from different institutional backgrounds. From literature research and empirical research on the NeWater project we identified challenges for cross-disciplinary knowledge integration, we evaluated interventions for connecting multiple knowledge frames, we analyzed the process of group model building with UML and formulated recommendations. Cross-disciplinary research has arisen from a growing number of complex problems for which knowledge of a single scientific discipline or societal field is insufficient, but presents important challenges: (1) collaboration and integration of knowledge requires in depth discussions that are timeconsuming; (2) the recursive process of problem structuring and restructuring is often at odds with the sequential planning of project activities; (3) participation and mutual learning are crucial but need to be carefully structured and sequenced; and (4) management and leadership faces the difficult challenge of balancing in depth exploration with timely delivery of tangible results. We conclude with the following general recommendations for large cross-disciplinary projects: (1) including a preparatory proposal phase for thorough exploration of opportunities of between researchers and stakeholders (2) flexible funding, planning and operational arrangements to allow for a recursive research process; (3) a project size that allows frequent interaction opportunities between researchers and between researchers and stakeholders to allow for mutual learning and in depth exploration; and (4) enhancing learning opportunities from one project to the next

Harnessing machine learning for fiber-induced nonlinearity mitigation in long-haul coherent optical OFDM

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Coherent optical orthogonal frequency division multiplexing (CO-OFDM) has attracted a lot of interest in optical fiber communications due to its simplified digital signal processing (DSP) units, high spectral-efficiency, flexibility, and tolerance to linear impairments. However, CO-OFDM’s high peak-to-average power ratio imposes high vulnerability to fiber-induced non-linearities. DSP-based machine learning has been considered as a promising approach for fiber non-linearity compensation without sacrificing computational complexity. In this paper, we review the existing machine learning approaches for CO-OFDM in a common framework and review the progress in this area with a focus on practical aspects and comparison with benchmark DSP solutions.Peer reviewe

An overview of decision table literature 1982-1995.

This report gives an overview of the literature on decision tables over the past 15 years. As much as possible, for each reference, an author supplied abstract, a number of keywords and a classification are provided. In some cases own comments are added. The purpose of these comments is to show where, how and why decision tables are used. The literature is classified according to application area, theoretical versus practical character, year of publication, country or origin (not necessarily country of publication) and the language of the document. After a description of the scope of the interview, classification results and the classification by topic are presented. The main body of the paper is the ordered list of publications with abstract, classification and comments.

Adaptive-Rate Compressive Sensing Using Side Information

We provide two novel adaptive-rate compressive sensing (CS) strategies for sparse, time-varying signals using side information. Our first method utilizes extra cross-validation measurements, and the second one exploits extra low-resolution measurements. Unlike the majority of current CS techniques, we do not assume that we know an upper bound on the number of significant coefficients that comprise the images in the video sequence. Instead, we use the side information to predict the number of significant coefficients in the signal at the next time instant. For each image in the video sequence, our techniques specify a fixed number of spatially-multiplexed CS measurements to acquire, and adjust this quantity from image to image. Our strategies are developed in the specific context of background subtraction for surveillance video, and we experimentally validate the proposed methods on real video sequences

Methodologies synthesis

This deliverable deals with the modelling and analysis of interdependencies between critical infrastructures, focussing attention on two interdependent infrastructures studied in the context of CRUTIAL: the electric power infrastructure and the information infrastructures supporting management, control and maintenance functionality. The main objectives are: 1) investigate the main challenges to be addressed for the analysis and modelling of interdependencies, 2) review the modelling methodologies and tools that can be used to address these challenges and support the evaluation of the impact of interdependencies on the dependability and resilience of the service delivered to the users, and 3) present the preliminary directions investigated so far by the CRUTIAL consortium for describing and modelling interdependencies

A Formal Approach based on Fuzzy Logic for the Specification of Component-Based Interactive Systems

Formal methods are widely recognized as a powerful engineering method for the specification, simulation, development, and verification of distributed interactive systems. However, most formal methods rely on a two-valued logic, and are therefore limited to the axioms of that logic: a specification is valid or invalid, component behavior is realizable or not, safety properties hold or are violated, systems are available or unavailable. Especially when the problem domain entails uncertainty, impreciseness, and vagueness, the appliance of such methods becomes a challenging task. In order to overcome the limitations resulting from the strict modus operandi of formal methods, the main objective of this work is to relax the boolean notion of formal specifications by using fuzzy logic. The present approach is based on Focus theory, a model-based and strictly formal method for componentbased interactive systems. The contribution of this work is twofold: i) we introduce a specification technique based on fuzzy logic which can be used on top of Focus to develop formal specifications in a qualitative fashion; ii) we partially extend Focus theory to a fuzzy one which allows the specification of fuzzy components and fuzzy interactions. While the former provides a methodology for approximating I/O behaviors under imprecision, the latter enables to capture a more quantitative view of specification properties such as realizability.Comment: In Proceedings FESCA 2015, arXiv:1503.0437