Mathematical modelling plant signalling networks

During the last two decades, molecular genetic studies and the completion of the sequencing of the Arabidopsis thaliana genome have increased knowledge of hormonal regulation in plants. These signal transduction pathways act in concert through gene regulatory and signalling networks whose main components have begun to be elucidated. Our understanding of the resulting cellular processes is hindered by the complex, and sometimes counter-intuitive, dynamics of the networks, which may be interconnected through feedback controls and cross-regulation. Mathematical modelling provides a valuable tool to investigate such dynamics and to perform in silico experiments that may not be easily carried out in a laboratory. In this article, we firstly review general methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This sub-cellular analysis paves the way for more comprehensive mathematical studies of hormonal transport and signalling in a multi-scale setting

Potentials and Limits of Bayesian Networks to Deal with Uncertainty in the Assessment of Climate Change Adaptation Policies

Bayesian networks (BNs) have been increasingly applied to support management and decision-making processes under conditions of environmental variability and uncertainty, providing logical and holistic reasoning in complex systems since they succinctly and effectively translate causal assertions between variables into patterns of probabilistic dependence. Through a theoretical assessment of the features and the statistical rationale of BNs, and a review of specific applications to ecological modelling, natural resource management, and climate change policy issues, the present paper analyses the effectiveness of the BN model as a synthesis framework, which would allow the user to manage the uncertainty characterising the definition and implementation of climate change adaptation policies. The review will let emerge the potentials of the model to characterise, incorporate and communicate the uncertainty, with the aim to provide an efficient support to an informed and transparent decision making process. The possible drawbacks arising from the implementation of BNs are also analysed, providing potential solutions to overcome them.Adaptation to Climate Change, Bayesian Network, Uncertainty

An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems

The authors would like to thank the support on this research by the CRISP project (Combinatorial Responses In Stress Pathways) funded by the BBSRC (BB/F00513X/1) under the Systems Approaches to Biological Research (SABR) Initiative.Peer reviewedPublisher PD

A general framework for quantifying the effects of land-use history on ecosystem dynamics

Land-use legacies are important for explaining present-day ecological patterns and processes. However, an overarching approach to quantify land-use history effects on ecosystem properties is lacking, mainly due to the scarcity of high-quality, complete and detailed data on past land use. We propose a general framework for quantifying the effects of land-use history on ecosystem properties, which is applicable (i) to different ecological processes in various ecosystem types and across trophic levels; and (ii) when historical data are incomplete or of variable quality. The conceptual foundation of our framework is that past land use affects current (and future) ecosystem properties through altering the past values of resources and conditions that are the driving variables of ecosystem responses. We describe and illustrate how Markov chains can be applied to derive past time series of driving variables, and how these time series can be used to improve our understanding of present-day ecosystem properties. We present our framework in a stepwise manner, elucidating its general nature. We illustrate its application through a case study on the importance of past light levels for the contemporary understorey composition of temperate deciduous forest. We found that the understorey shows legacies of past forest management: high past light availability lead to a low proportion of typical forest species in the understorey. Our framework can be a useful tool for quantifying the effect of past land use on ecological patterns and processes and enhancing our understanding of ecosystem dynamics by including legacy effects which have often been ignored

Loan maturity aggregation in interbank lending networks obscures mesoscale structure and economic functions

Since the 2007-2009 financial crisis, substantial academic effort has been dedicated to improving our understanding of interbank lending networks (ILNs). Because of data limitations or by choice, the literature largely lacks multiple loan maturities. We employ a complete interbank loan contract dataset to investigate whether maturity details are informative of the network structure. Applying the layered stochastic block model of Peixoto (2015) and other tools from network science on a time series of bilateral loans with multiple maturity layers in the Russian ILN, we find that collapsing all such layers consistently obscures mesoscale structure. The optimal maturity granularity lies between completely collapsing and completely separating the maturity layers and depends on the development phase of the interbank market, with a more developed market requiring more layers for optimal description. Closer inspection of the inferred maturity bins associated with the optimal maturity granularity reveals specific economic functions, from liquidity intermediation to financing. Collapsing a network with multiple underlying maturity layers or extracting one such layer, common in economic research, is therefore not only an incomplete representation of the ILN's mesoscale structure, but also conceals existing economic functions. This holds important insights and opportunities for theoretical and empirical studies on interbank market functioning, contagion, stability, and on the desirable level of regulatory data disclosure

Neuro-fuzzy knowledge processing in intelligent learning environments for improved student diagnosis

In this paper, a neural network implementation for a fuzzy logic-based model of the diagnostic process is proposed as a means to achieve accurate student diagnosis and updates of the student model in Intelligent Learning Environments. The neuro-fuzzy synergy allows the diagnostic model to some extent "imitate" teachers in diagnosing students' characteristics, and equips the intelligent learning environment with reasoning capabilities that can be further used to drive pedagogical decisions depending on the student learning style. The neuro-fuzzy implementation helps to encode both structured and non-structured teachers' knowledge: when teachers' reasoning is available and well defined, it can be encoded in the form of fuzzy rules; when teachers' reasoning is not well defined but is available through practical examples illustrating their experience, then the networks can be trained to represent this experience. The proposed approach has been tested in diagnosing aspects of student's learning style in a discovery-learning environment that aims to help students to construct the concepts of vectors in physics and mathematics. The diagnosis outcomes of the model have been compared against the recommendations of a group of five experienced teachers, and the results produced by two alternative soft computing methods. The results of our pilot study show that the neuro-fuzzy model successfully manages the inherent uncertainty of the diagnostic process; especially for marginal cases, i.e. where it is very difficult, even for human tutors, to diagnose and accurately evaluate students by directly synthesizing subjective and, some times, conflicting judgments

Tracking by Prediction: A Deep Generative Model for Mutli-Person localisation and Tracking

Current multi-person localisation and tracking systems have an over reliance on the use of appearance models for target re-identification and almost no approaches employ a complete deep learning solution for both objectives. We present a novel, complete deep learning framework for multi-person localisation and tracking. In this context we first introduce a light weight sequential Generative Adversarial Network architecture for person localisation, which overcomes issues related to occlusions and noisy detections, typically found in a multi person environment. In the proposed tracking framework we build upon recent advances in pedestrian trajectory prediction approaches and propose a novel data association scheme based on predicted trajectories. This removes the need for computationally expensive person re-identification systems based on appearance features and generates human like trajectories with minimal fragmentation. The proposed method is evaluated on multiple public benchmarks including both static and dynamic cameras and is capable of generating outstanding performance, especially among other recently proposed deep neural network based approaches.Comment: To appear in IEEE Winter Conference on Applications of Computer Vision (WACV), 201