Multi-level discrete models of genetic networks, or the more general piecewise affine differential models, provide qualitative information on the dynamics of the system, based on a small number of parameters (such as synthesis and degradation rates). Boolean models also provide qualitative information, but are based simply on the structure of interconnections. To explore the relationship between the two formalisms, a piecewise affine differential model and a Boolean model are compared, for the carbon starvation response network in (...) E. coli . The asymptotic dynamics of both models are shown to be quite similar. This study suggests new tools for analysis and reduction of biological networks. (shrink)

Medical explanations have often been thought on the model of biological ones and are frequently defined as mechanistic explanations of a biological dysfunction. In this paper, I argue that topological explanations, which have been described in ecology or in cognitive sciences, can also be found in medicine and I discuss the relationships between mechanistic and topological explanations in medicine, through the example of network medicine and medical genetics. Network medicine is a recent discipline that relies on the analysis of (...) various disease networks in order to find organizing principles in disease explanation. My aim is to show how topological explanations in network medicine can help solving the conceptual issues that pure mechanistic explanations of the genetics of disease are currently facing, namely the crisis of the concept of genetic disease, the progressive geneticization of diseases and the dissolution of the distinction between monogenic and polygenic diseases. However, I will also argue that topological explanations should not be considered as independent and radically different from mechanistic explanations for at least two reasons. First, in network medicine, topological explanations depend on and use mechanistic information. Second, they leave out some missing gaps in disease explanation that require, in turn, the development of new mechanistic explanations. Finally, I will insist on the specific contribution of topological explanations in medicine: they push us to develop an explanation of disease in general, instead of focusing on single explanations of individual diseases. This last point may have major consequences for biomedical research. (shrink)

Behaviors are quantitative traits determined through actions of multiple genes and subject to genome–environment interactions. Early studies concentrated on analyzing the effects of single genes on behaviors, often generating views of simplified linear genetic pathways. The genome era has generated a profound paradigm shift enabling us to identify all the genes that contribute to expression of a behavioral phenotype, to investigate how they are organized as functional ensembles and to begin to identify polymorphisms that contribute to phenotypic variation and (...) are targets for natural selection. Recent studies show that the genetic architecture of behavior is determined by dynamic and plastic modular networks of pleiotropic genes and that the behavioral phenotype manifests itself as an emergent property of such networks. Such networks are exquisitely sensitive to genetic background and sex effects. This review describes how Drosophila can serve as a model for uncovering fundamental principles of the genetic architecture of behavior. BioEssays 26:1299–1306, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The potential of the soil to hold plant nutrients is governed by the cation-exchange capacity of any soil. Estimating soil CEC aids in conventional soil management practices to replenish the soil solution that supports plant growth. In this study, a multiple model integration scheme supervised with a hybrid genetic algorithm-neural network was developed and employed to predict the accuracy of soil CEC in Tabriz plain, an arid region of Iran. The standalone models and extreme learning machine ) were (...) implemented for incorporation into the MM-GANN. In addition, it was tested to enhance the prediction accuracy of the standalone models. The soil parameters such as clay, silt, pH, carbonate calcium equivalent, and soil organic matter were used as model inputs to predict soil CEC. With the use of several evaluation criteria, the results showed that the MM-GANN model involving the predictions of ELM and ANN models calibrated by considering all the soil parameters as inputs provided superior soil CEC estimates with a Nash Sutcliffe Efficiency = 0.87, Root Mean Square Error = 2.885, Mean Absolute Error = 2.249, Mean Absolute Percentage Error = 12.072, and coefficient of determination = 0.884. The proposed MM-GANN model is a reliable intelligence-based approach for the assessment of soil quality parameters intended for sustainability and management prospects. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is (...) extended to a Łukasiewicz–Moisil Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

This study is to explore the optimization of the adaptive genetic algorithm in the backpropagation neural network, so as to expand the application of the BPNN model in nonlinear issues. Traffic flow prediction is undertaken as a research case to analyse the performance of the optimized BPNN. Firstly, the advantages and disadvantages of the BPNN and genetic algorithm are analyzed based on their working principles, and the AGA is improved and optimized. Secondly, the optimized AGA is applied (...) to optimize the standard BPNN, and the optimized algorithm is named as OAGA-BPNN. Finally, three different cases are proposed based on the actual scenario of traffic flow prediction to analyse the optimized algorithm on the matrix laboratory platform by simulation. The results show that the average error distribution of the GA-BPNN algorithm is about 1% with small fluctuation range, better calculation accuracy, and generalization performance in contrast to the BPNN. The average output error of the AGA-BPNN fluctuates around 0 and remains in a relatively stable range as a whole in contrast to that of GA-BPNN; the maximum fitness level keeps increasing during the evolution process but approaches the average value in later process, so the population diversity is hard to be guaranteed. The output error of the OAGA-BPNN fluctuates little compared with that of AGA-BPNN, and its maximum fitness continues to increase in the evolution process with guaranteed population diversity. In short, the OAGA-BPNN algorithm can achieve the best performance in terms of calculation accuracy, generalization performance, and population evolution. (shrink)

We deal with the design problem of nonfragile state estimator for discrete-time genetic regulatory networks with time-varying delays and randomly occurring uncertainties. In particular, the norm-bounded uncertainties enter into the GRNs in random ways in order to reflect the characteristic of the modelling errors, and the so-called randomly occurring uncertainties are characterized by certain mutually independent random variables obeying the Bernoulli distribution. The focus of the paper is on developing a new nonfragile state estimation method to estimate the (...) concentrations of the mRNA and the protein for considered uncertain delayed GRNs, where the randomly occurring estimator gain perturbations are allowed. By constructing a Lyapunov-Krasovskii functional, a delay-dependent criterion is obtained in terms of linear matrix inequalities by properly using the discrete-time Wirtinger-based inequality and reciprocally convex combination approach as well as the free-weighting matrix method. It is shown that the proposed method ensures that the estimation error dynamics is globally asymptotically stable and the desired estimator parameter is designed via the solutions to certain LMIs. Finally, we provide two numerical examples to illustrate the feasibility and validity of the proposed estimation results. (shrink)

Water quality prediction is the basis of water environmental planning, evaluation, and management. In this work, a novel intelligent prediction model based on the fuzzy wavelet neural network including the neural network, the fuzzy logic, the wavelet transform, and the genetic algorithm was proposed to simulate the nonlinearity of water quality parameters and water quality predictions. A self-adapted fuzzy c-means clustering was used to determine the number of fuzzy rules. A hybrid learning algorithm based on a genetic (...) algorithm and gradient descent algorithm was employed to optimize the network parameters. Comparisons were made between the proposed FWNN model and the fuzzy neural network, the wavelet neural network, and the neural network. The results indicate that the FWNN made effective use of the self-adaptability of NN, the uncertainty capacity of FL, and the partial analysis ability of WT, so it could handle the fluctuation and the nonseasonal time series data of water quality, while exhibiting higher estimation accuracy and better robustness and achieving better performances for predicting water quality with high determination coefficients R2 over 0.90. The FWNN is feasible and reliable for simulating and predicting water quality in river. (shrink)

This aricle discusses the similarity between the propagation of pathogens (viruses and worms) on computer networks and the proliferation of pathogens in cellular organisms (organisms with genetic material contained within a membrane-encased nucleus). It introduces several biological mechanisms which are used in these organisms to protect against such pathogens and presents security models for networked computers inspired by several biological paradigms, including genomics (RNA interference), proteomics (pathway mapping), and physiology (immune system). In addition, the study of epidemiological models (...) for disease control can inspire methods for controlling the spread of pathogens across multiple nodes of a network. It also presents results based on the authors’ research in immune system modeling. (shrink)

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference‐making causes of phenotypes is re‐examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues (...) that it is appropriate to treat genes as specific actual difference‐makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause‐and‐effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes. (shrink)

The topology optimization of computer communication network is studied based on improved genetic algorithm, a network optimization design model based on the establishment of network reliability maximization under given cost constraints, and the corresponding improved GA is proposed. In this method, the corresponding computer communication network cost model and computer communication network reliability model are established through a specific project, and the genetic intelligence algorithm is used to solve the cost model and computer communication (...) network reliability model, respectively. It has been proved that GA can solve the complex problems of computer working environment better, which is 80% higher than the general algorithm, and can select the optimal scheme pertinently. (shrink)

M. xanthus has a complex multicellular lifestyle including swarming, predation and development. These behaviors depend on the ability of the cells to achieve directed motility across solid surfaces. M. xanthus cells have evolved two motility systems including Type‐IV pili that act as grappling hooks and a controversial engine involving mucus secretion and fixed focal adhesion sites. The necessity for cells to coordinate the motility systems and to respond rapidly to environmental cues is reflected by a complex genetic network involving (...) at least three complete sets of chemosensory systems and eukaryotic‐like signaling proteins. In this review, we discuss recent advances suggesting that motor synchronization results from spatial oscillations of motility proteins. We further propose that these dynamics are modulated by the action of multiple upstream complementary signaling systems. M. xanthus is thus an exciting emerging model system to study the intricate processes of directed cell migration. BioEssays 30:733–743, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Porosity is considered as one of the most important indicators for the characterization of the comprehensive performance of thermal barrier coatings. In this study, the ultrasonic technique and the artificial neural network optimized with the genetic algorithm are combined to develop an intelligent method for automatic detection and accurate prediction of TBCs’s porosity. A series of physical models of plasma-sprayed ZrO2 coating are established with a thickness of 288 μm and porosity varying from 5.71% to 26.59%, and the ultrasonic (...) reflection coefficient amplitude spectrum is constructed based on the time-domain numerical simulation signal. The characteristic features f 1, f 2, A max, Δ A of the URCAS, which are highly dependent on porosity, are extracted as input data to train the GA_BPNN model for predicting the unknown porosity. The average error of the prediction results is 1.45%, which suggests that the proposed method can achieve accurate detection and quantitative characterization of the porosity of TBCs with complex pore morphology. (shrink)

A model predictive control method based on recursive backpropagation neural network and genetic algorithm is proposed for a class of nonlinear systems with time delays and uncertainties. In the offline modeling stage, a multistep-ahead predictor with GA-RBP neural network is designed, where GA-BP neural network is used as a one-step prediction model and GA is employed to train the initial weights and bias of the BP neural network. The incorporation of GA into RBP can reduce the possibility (...) of the BP neural network falling into a local optimum instead of reaching global optimization. In the online optimizing stage, a multistep-ahead GA-RBP neural network predictor and an improved gradient descent method are proposed to efficiently solve the online optimization problem of nonlinear MPC by minimizing a modified quadratic criterion. The designed MPC strategy can avoid information loss while linearizing the controlled system and computing the Hessian matrix and its inverse matrix. Experimental results show that the proposed approach can reduce the computational burden and improve the performance of MPC for the solution of nonlinear controlled systems. (shrink)

Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies to (...) many other types of formal networks and weakens the emergentist claim attached to bio-molecular networks, and by extension to living systems. (shrink)

In the multidisciplinary field of developmental cognitive neuroscience, statistical associations between levels of description play an increasingly important role. One example of such associations is the observation of correlations between relatively common gene variants and individual differences in behavior. It is perhaps surprising that such associations can be detected despite the remoteness of these levels of description, and the fact that behavior is the outcome of an extended developmental process involving interaction of the whole organism with a variable environment. Given (...) that they have been detected, how do such associations inform cognitive-level theories? To investigate this question, we employed a multiscale computational model of development, using a sample domain drawn from the field of language acquisition. The model comprised an artificial neural network model of past-tense acquisition trained using the backpropagation learning algorithm, extended to incorporate population modeling and genetic algorithms. It included five levels of description—four internal: genetic, network, neurocomputation, behavior; and one external: environment. Since the mechanistic assumptions of the model were known and its operation was relatively transparent, we could evaluate whether cross-level associations gave an accurate picture of causal processes. We established that associations could be detected between artificial genes and behavioral variation, even under polygenic assumptions of a many-to-one relationship between genes and neurocomputational parameters, and when an experience-dependent developmental process interceded between the action of genes and the emergence of behavior. We evaluated these associations with respect to their specificity, to their developmental stability, and to their replicability, as well as considering issues of missing heritability and gene–environment interactions. We argue that gene–behavior associations can inform cognitive theory with respect to effect size, specificity, and timing. The model demonstrates a means by which researchers can undertake multiscale modeling with respect to cognition and develop highly specific and complex hypotheses across multiple levels of description. (shrink)

Chronic myeloid leukemia (CML) is a cancer of the hematopoietic system initiated by a single genetic mutation which results in the oncogenic fusion protein Bcr-Abl. Untreated, patients pass through different phases of the disease beginning with the rather asymptomatic chronic phase and ultimately culminating into blast crisis, an acute leukemia resembling phase with a very high mortality. Although many processes underlying the chronic phase are well understood, the exact mechanisms of disease progression to blast crisis are not yet revealed. (...) In this paper we develop a mathematical model of CML based on causal Bayesian networks in order to study possible disease progression mechanisms. Our results indicate that an increase of Bcr-Abl levels alone is not sufficient to explain the phenotype of blast crisis and that secondary changes such as additional mutations are necessary to explain disease progression and the poor therapy response of patients in blast crisis. (shrink)

Behaving presents an overview of the recent history and methodology of behavioral genetics and psychiatric genetics, informed by a philosophical perspective. Kenneth F. Schaffner addresses a wide range of issues, including genetic reductionism and determinism, "free will," and quantitative and molecular genetics. The latter covers newer genome-wide association studies that have produced a paradigm shift in the subject, and generated the problem of "missing heritability." Schaffner also presents cases involving pro and con arguments for genetic testing for IQ (...) and for Attention Deficit Hyperactivity Disorder. Schaffner examines the nature-nurture controversy and Developmental Systems Theory using C. elegans or "worm" studies as a test case, concluding that genes are special and provide powerful tools, including "deep homology," for investigating behavior. He offers a novel account of biological knowledge emphasizing the importance of models, mechanisms, pathways, and networks, which clarifies how partial reductions provide explanations of traits and disorders. The book also includes examinations of personality genetics and of schizophrenia and its etiology, alongside interviews with prominent researchers in the area, and discusses debates about psychosis that led to changes in the DSM-5 in 2013.Schaffner concludes by discussing additional philosophical implications of the genetic analyses in the book, some major worries about "free will," and arguments pro and con about why genes and DNA are so special. Though genes are special, newer perspectives presented in this book will be needed for progress in behavioral genetics- perspectives that situate genes in complex multilevel prototypic pathways and networks. With a mix of optimism and pessimism about the state of the field and the subject, Schaffner's book will be of interest to scholars in the history and philosophy of science, medicine, and psychiatry. (shrink)

This paper examines processes of translation through which molecular genetic technologies and practices are incorporated into environmental health research and regulation. Specifically, it considers how scientists, risk assessors, and regulators have used genetically modified mouse models to translate across scientific disciplines, articulate emergent molecular forms, standards, and practices with the extant? gold standard,? and establish roles for molecular knowledge in risk assessment and regulation. Noting variation both within and between regulatory agencies in responses to data from these models, the (...) article describes also the role of public-private networks and their effects on professional and institutional imperatives which shape regulators? responses to the potential applications of these models. The conclusions address the importance of translation for understanding the wider implications of the molecularization of environmental health science. (shrink)

This study aims to develop a hybrid model to represent the human mind from a functionalist point of view that can be adapted to artificial intelligence. The model is not a realistic theory of the neural network of the brain but an instrumentalist AI model, which means that there can be some other representative models too. It had been thought that the provability of an axiomatic system requires the completeness of a formal system. However, Gödel proved that (...) no consistent formal system can prove its own consistency. There is a paradoxical limit to provability. Both consistency and completeness are impossible together. These formal limits form the basis of our model: the hybrid model of the mind consists of a formal axiomatic system and an evolutionary algorithm (EA) of intelligence, which also includes the genetic algorithm (GA) of consciousness. The GA of consciousness operates based on intentions, functioning in conjunction with the principles of EA. This collaboration allows it to transcend the paradoxical formal limits of intelligence. However, GA overcomes the problem of paradoxicality at the cost of producing illusions. Following this collaboration gives us a GA operating system. After all, if the rational optimization task of the GA in question produces illusions, then the rationality must lie elsewhere in the paradox. (shrink)

C.H. Waddington is today remembered chiefly as a Drosophila developmental geneticist who developed the concepts of “canalization” and “the epigenetic landscape.” In his lifetime, however, he was widely perceived primarily as a critic of Neo-Darwinian evolutionary theory. His criticisms of Neo-Darwinian evolutionary theory were focused on what he saw as unrealistic, “atomistic” models of both gene selection and trait evolution. In particular, he felt that the Neo-Darwinians badly neglected the phenomenon of extensive gene interactions and that the “randomness” of mutational (...) effects, posited in the theory, was a false postulate. This last criticism dealt with the phenomenon known today as “developmental constraints.” Although population genetics itself has evolved considerably from its form at mid-20th century, much of Waddington’s critique, it is argued here, retains cogency. Yet, he did not attempt to develop a full-fledged alternative theory himself. Perhaps most surprisingly, in retrospect, is that he did not try to marry his work on gene interactions in development with his evolutionary interests, to create a theory of “genetic networks” and their evolution. Whether evolutionary genetics today will incorporate “network thinking” as a central element or whether there will be a general retreat to the more atomistic approach offered by genomics, remains an open question. (shrink)

Complex diseases involve both a genetic component and a response to environmental factors or lifestyle changes. Recently, genome-wide association studies (GWAS) have succeeded in identifying hundreds of polymorphisms that are statistically associated with complex diseases. However, the association is usually weak and none of the associated allelic forms is either necessary or sufficient for the disease occurrence. We argue that this promotes a network view, centred on functional redundancy. We adapted reliability theory to the concerned sub-network, modelled as a (...) parallel array of functional modules. In our model, as long as one module remains active, the function correlated with the respective disease is ensured and disease does not occur. Genetic factors reduce the initial number of available modules while environment, contingent surroundings, personal history, epigenetics, and some intrinsic stochasticity influence their persistence time. This model reproduces age-specific incidence curves and explains the influence of environmental changes. It offers a new paradigm, according to which disease occurs due to a lack of functional elements, depending on many idiosyncratic factors. Genetic risk assessed from GWAS is only a statistical notion with no direct interpretation at the individual level. However, genomic profiling could be useful at population level in devising models to guide decisions in health care policy. (shrink)

As one of the key technologies for accelerating the construction of the ubiquitous Internet of Things, demand response not only guides users to participate in power market operations but also increases the randomness of grid operations and the difficulty of load forecasting. In order to solve the problem of rough feature engineering processing and low prediction accuracy, a short-term load forecasting model of LSTM neural network considering demand response is proposed. First of all, in view of the strong randomness (...) and complexity of input features, the weighted method is used to process multiple input features to strengthen the contribution of effective features and tap the potential value of features. Secondly, an improved genetic algorithm is used to obtain the best LSTM parameters; finally, the special gate structure of the LSTM model is used to selectively control the influence of input variables on the model parameters and perform load forecasting. The experimental results show that the research has high prediction accuracy and application value and provides a new way for the development of power load forecasting. (shrink)

Through their transcript products genes regulate the rates at which an immense variety of transcripts and subsequent proteins occur. Understanding the mechanisms that determine which genes are expressed, and when they are expressed, is one of the keys to genetic manipulation for many purposes, including the development of new treatments for disease. Viewing each gene in a genome as a distinct variable that is either on or off, or more realistically as a continuous variable, the values of some of (...) these variables influence the values of others through the regulatory proteins they express, including, of course, the possibility that the rate of expression of a gene at one time may, in various circumstances, influence the rate of expression of that same gene at a later time. If we imagine an arrow drawn from each gene expression variable at a given time to a gene variable whose expression it influences a short while after, the result is a network, technically a directed acyclic graph. For example, the DAG in Figure 1 is a representation of a system in which the expression level of gene G1 at time 1 ) causes the expression level of G2, which in turn causes the expression level of G3. The arrows in Figure 1 which do not have a variable at their tails are “error terms” which represent all of the causes of a variable other than the ones explicitly represented in the DAG. The DAG describes more than associations—it describes causal connections among gene expression rates. A shock to a cell—by mutation, heating, chemical treatment, etc. may alter the DAG describing the relations among gene expressions, for example by activating a gene that was otherwise not expressed, producing a cascade of new expression effects. Although “knockout” experiments can reveal some of the underlying causal network of gene expression levels, unless guided by information from other sources, such experiments are limited in how much of the network structure they can reveal, due to the sheer number of possible combinations of experimental manipulations of genes necessary to reveal the complete causal network. Recent developments have made it possible to compare quantitatively the expression of tens of thousands of genes in cells from different sources in a single experiment, and to trace gene expression over time in thousands of genes simultaneously. cDNA microarrays are already producing extensive data, much of it available on the web. Thus there are calls for analytic software that can be applied to microarray and other data to help infer regulatory networks. In this paper we will review current techniques that are available for searching for the causal relations between variables, describe algorithmic and data gathering obstacles to applying these techniques to gene expression levels, and describe the prospects for overcoming these obstacles. (shrink)

This book provides an elaboration and evaluation of the dominant conceptions of genetic counseling as they are accounted for in three different models: the teaching model; the psychotherapeutic model; and the responsibility model. The elaboration of these models involves an identification of the larger traditions, visions and theories of communication that underwrite them; the evaluation entails an assessment of each model’s theses and ultimately a comparison of their adequacy in response to two important concerns in (...) genetic counseling: the contested values of non-directiveness and the recognition of differences across perspectives, with special focus on how religious and spiritual beliefs of patients are coordinated with the networks of meaning in genetics. Several insights are made explicit in this project through the work of Robert Brandom. Brandom’s deontic scorekeeping model demonstrates how dialogue is at the root of grasping a conceptual content. Against this backdrop, professional communications such as genetic counseling can be seen as late developments in linguistic practices that have structural challenges. Brandom’s model reminds us that the professional needs the client’s understanding to grasp conceptual content in a particular context. (shrink)

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, (...) motivation and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels, and network hierarchies. (shrink)

As a brand-new marketing method, network marketing has gradually become one of the main ways and means for enterprises to improve profitability and competitiveness with its unique advantages. Using these marketing data to build a model can dig out useful information that the business is concerned about, and the company can then formulate marketing strategies based on this information. Sales forecasting is to speculate on the future based on historical sales. It is a tool for companies to determine production (...) volume and ensure the balance of product supply and sales. It can help companies make correct business decisions to maximize profits. The neural network can approximate the nonlinear function with arbitrary precision, and the time series prediction model based on the neural network can well reflect the nonlinear development trend of information. Based on the analysis of the shortcomings of the traditional BP network, this paper uses a genetic algorithm with good global search capabilities to improve the neural network. The thought and theory of optimizing the initial weight and threshold of the neural network of the GA algorithm are discussed in detail. While expounding the forecasting method, it uses specific examples to analyze the performance and characteristics of the GA-BP network in the enterprise network marketing forecasting. The results show that the GA-BP neural network is higher than the traditional BP neural network in terms of prediction accuracy and adaptability. (shrink)

Over the last two decades, network-focused approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While the network approach continues to grow very rapidly, some of its conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. Consequently, the central focus of this theme issue will be (...) on the definition, motivation and application of key concepts in biological network science, such as levels, hierarchies, and explanatory directionality. A unification will be achieved by formulating norms for delimiting the distinctively network-topological class of explanations that connect general as well as very specific biological research questions. The impact of this theme issue is broad and encompassing, as it is highly interdisciplinary and opens a uniquely normative perspective on the foundational aspects of network-based explanations and modelling. This theme issue is intended to become a landmark publication for practical research as well as funding policy decisions, by unifying network approaches in biological sciences in terms of fundamental concepts and informing the public understanding of the network science. (shrink)

Genes are gained and lost over the course of evolution. A recent study found that over 1,800 new genes have appeared during primate evolution and that an unexpectedly high proportion of these genes are expressed in the human brain. But what are the molecular functions of newly evolved genes and what is their impact on an organism's fitness? The acquisition of new genes may provide a rich source of genetic diversity that fuels evolutionary innovation. Although gene manipulation experiments are (...) not feasible in humans, studies in model organisms, such as Drosophila melanogaster, have shown that new genes can quickly become integrated into genetic networks and become essential for survival or fertility. Future studies of new genes, especially chimeric genes, and their functions will help determine the role of genetic novelty in the adaptation and diversification of species. (shrink)

Predicting the phenotype of an organism from its genotype is a central question in genetics. Most importantly, we would like to find out if the perturbation of a single gene may be the cause of a disease. However, our current ability to predict the phenotypic effects of perturbations of individual genes is limited. Network models of genes are one tool for tackling this problem. In a recent study, (Lee et al.) it has been shown that network models covering the majority (...) of genes of an organism can be used for accurately predicting phenotypic effects of gene perturbations in multicellular organisms. BioEssays 30:707–710, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Emergency scheduling of public resources on the cloud computing platform network can effectively improve the network emergency rescue capability of the cloud computing platform. To schedule the network common resources, it is necessary to generate the initial population through the Hamming distance constraint and improve the objective function as the fitness function to complete the emergency scheduling of the network common resources. The traditional method, from the perspective of public resource fairness and priority mapping, uses incremental optimization algorithm to realize (...) emergency scheduling of public resources, neglecting the improvement process of the objective function, which leads to unsatisfactory scheduling effect. An emergency scheduling method of cloud computing platform network public resources based on genetic algorithm is proposed. With emergency public resource scheduling time cost and transportation cost minimizing target, initial population by Hamming distance constraints, emergency scheduling model, and the corresponding objective function improvement as the fitness function, the genetic algorithm to individual selection and crossover and mutation probability were optimized and complete the public emergency resources scheduling. Experimental results show that the proposed method can effectively improve the efficiency of emergency resource scheduling, and the reliability of emergency scheduling is better. (shrink)

At the interface of developmental biology and evolutionary biology, the very criteria of scientific knowledge are up for grabs. A central issue is the status of evolutionary genetics models, which some argue cannot coherently be used with complex gene regulatory network (GRN) models to explain the same evolutionary phenomena. Despite those claims, many researchers use evolutionary genetics models jointly with GRN models to study evolutionary phenomena. This dissertation compares two recent research projects in which researchers jointly use the two kinds (...) of models. I use methods from the empirical social sciences, such as digital corpus analysis, content analysis, and structured case analysis. I infer three primary conclusions about projects of the kind studied. First, they employ an implicit concept of gene that enables the joint use of both kinds of models. Second, they pursue more epistemic aims besides mechanistic explanation of phenomena. Third, they don’t work to create and export broad synthesized theories. Rather, they focus on phenomena too complex to be understood by a common general theory, they distinguish parts of the phenomena, and they apply models from different theories to the different parts. For such projects, seemingly incompatible models are synthesized largely through mediated representations of complex phenomena. (shrink)

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for (...) understanding the evolution of the biological categories development-heredity; plasticity-evolvability; and epigenetic-genetic. (shrink)

This volume maps the areas of ethical concern in the debate regarding the governance of genetic information, and suggests alternative ethical frameworks and models of regulation in order to inform its restructuring. Genetic governance is at the heart of medical and scientific developments, and is connected to global exploitation, issues of commodification, commercialisation and ownership, the concepts of property and intellectual property and concerns about individual and communal identity. Thus the decisions that are made in the next few (...) years about appropriate models of genetic governance will have knock-on effects for other areas of governance. In short the final answer to 'Who Decides?' in the context of genetic governance will fundamentally shape the ethical constructs of individuals and their networks and relationships in the public sphere. (shrink)

Emotionally arousing events reach awareness more easily and evoke greater visual cortex activation than more mundane events. Recent studies have shown that they are also perceived more vividly and that emotionally enhanced perceptual vividness predicts memory vividness. We propose that affect-biased attention (ABA) – selective attention to emotionally salient events – is an endogenous attentional system tuned by an individual's history of reward and punishment. We present the Biased Attention via Norepinephrine (BANE) model, which unifies genetic, neuromodulatory, neural (...) and behavioural evidence to account for ABA. We review evidence supporting BANE's proposal that a key mechanism of ABA is locus coeruleus–norepinephrine (LC–NE) activity, which interacts with activity in hubs of affective salience networks to modulate visual cortex activation and heighten the subjective vividness of emotionally salient stimuli. We further review literature on biased competition and look at initial evidence for its potential as a neural mechanism behind ABA. We also review evidence supporting the role of the LC–NE system as a driving force of ABA. Finally, we review individual differences in ABA and memory including differences in sensitivity to stimulus category and valence. We focus on differences arising from a variant of the ADRA2b gene, which codes for the alpha2b adrenoreceptor as a way of investigating influences of NE availability on ABA in humans. (shrink)

Some philosophers suggest that the development of scientificknowledge is a kind of Darwinian process. The process of discovery,however, is one problematic element of this analogy. I compare HerbertSimon's attempt to simulate scientific discovery in a computer programto recent connectionist models that were not designed for that purpose,but which provide useful cases to help evaluate this aspect of theanalogy. In contrast to the classic A.I. approach Simon used, ``neuralnetworks'' contain no explicit protocols, but are generic learningsystems built on the model (...) of the interconnections of neurons in thebrain. I describe two cases that take the connectionist approach a stepfurther by using genetic algorithms, a form of evolutionary computationthat explicitly models Darwinian mechanisms. These cases show thatDarwinian mechanisms can make novel discoveries of complex, previouslyunknown patterns. With some caveats, they lend support to evolutionaryepistemology. (shrink)

Beyond belief change and meme adoption, both genetics and infection have been spoken of in terms of information transfer. What we examine here, concentrating on the specific case of transfer between sub-networks, are the differences in network dynamics in these cases: the different network dynamics of germs, genes, and memes. Germs and memes, it turns out, exhibit a very different dynamics across networks. For infection, measured in terms of time to total infection, it is network type rather than (...) degree of linkage between sub-networks that is of primary importance. For belief transfer, measured in terms of time to consensus, it is degree of linkage rather than network type that is crucial. Genes model each of these other dynamics in part, but match neither in full. For genetics, like belief transfer and unlike infection, network type makes little difference. Like infection and unlike belief, on the other hand, the dynamics of genetic information transfer within single and between linked networks are much the same. In ways both surprising and intriguing, transfer of genetic information seems to be robust across network differences crucial for the other two. (shrink)

Scientific anomalies are observations and facts that contradict current scientific theories and they are instrumental in scientific theory change. Philosophers of science have approached scientific theory change from different perspectives as Darden (Theory change in science: Strategies from Mendelian genetics, 1991) observes: Lakatos (In: Lakatos, Musgrave (eds) Criticism and the growth of knowledge, 1970) approaches it as a progressive “research programmes” consisting of incremental improvements (“monster barring” in Lakatos, Proofs and refutations: The logic of mathematical discovery, 1976), Kuhn (The structure (...) of scientific revolutions, 1996) observes that changes in “paradigms” are instigated by a crisis from some anomaly, and Hanson (In: Feigl, Maxwell (eds) Current issues in the philosophy of science, 1961) proposes that discovery does not begin with hypothesis but with some “problematic phenomena requiring explanation”. Even though anomalies are important in all of these approaches to scientific theory change, there have been only few investigations into the specific role anomalies play in scientific theory change. Furthermore, much of these approaches focus on the theories themselves and not on how the scientists and their experiments bring about scientific change (Gooding, Experiment and the making of meaning: Human agency in scientific observation and experiment, 1990). To address these issues, this paper approaches scientific anomaly resolution from a meaning construction point of view. Conceptual integration theory (Fauconnier and Turner, Cogn Sci 22:133–187, 1996; The way we think: Conceptual blending and mind’s hidden complexities, 2002) from cognitive linguistics describes how one constructs meaning from various stimuli, such as text and diagrams, through conceptual integration or blending. The conceptual integration networks that describe the conceptual integration process characterize cognition that occurs unconsciously during meaning construction. These same networks are used to describe some of the cognition while resolving an anomaly in molecular genetics called RNA interference (RNAi) in a case study. The RNAi case study is a cognitive-historical reconstruction (Nersessian, In: Giere (ed) Cognitive models of science, 1992) that reconstructs how the RNAi anomaly was resolved. This reconstruction traces four relevant molecular genetics publications in describing the cognition necessary in accounting for how RNAi was resolved through strategies (Darden 1991), abductive reasoning (Peirce, In: Hartshorne, Weiss (eds) Collected papers, 1958), and experimental reasoning (Gooding 1990). The results of the case study show that experiments play a crucial role in formulating an explanation of the RNAi anomaly and the integration networks describe the experiments’ role. Furthermore, these results suggest that RNAi anomaly resolution is embodied. It is embodied in a sense that cognition described in the cognitive-historical reconstruction is experientially based. (shrink)

Artificial neural networks, in interaction with fuzzy logic, genetic algorithms, and fuzzy neural networks, represent an example of a modern interdisciplinary field, especially when it comes to solving certain types of engineering problems that could not be solved using traditional modeling methods and statistical methods. They represent a modern trend in practical developments within the prognostic modeling field and, with acceptable limitations, enjoy a generally recognized perspective for application in construction. Results obtained from numerical analysis, which includes (...) analysis of the behavior of reinforced concrete elements and linear structures exposed to actions of standard fire, were used for the development of a prognostic model with the application of fuzzy neural networks. As fire resistance directly affects the functionality and safety of structures, the significance which new methods and computational tools have on enabling quick, easy, and simple prognosis of the same is quite clear. This paper will consider the application of fuzzy neural networks by creating prognostic models for determining fire resistance of eccentrically loaded reinforced concrete columns. (shrink)

A crucial question for artificial cognition systems is what meaning is and how it arises. In pursuit of that question, this paper extends earlier work in which we show that emergence of simple signaling in biologically inspired models using arrays of locally interactive agents. Communities of "communicators" develop in an environment of wandering food sources and predators using any of a variety of mechanisms: imitation of successful neighbors, localized genetic algorithms and partial neural net training on successful neighbors. Here (...) we focus on environmental variability, comparing results for environments with (a) constant resources, (b) random resources, and (c) cycles of "boom and bust." In both simple and complex models across all three mechanisms of strategy change, the emergence of communication is strongly favored by cycles of "boom and bust." These results are particularly intriguing given the importance of environmental variability in fields as diverse as psychology, ecology and cultural anthropology. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Setting the Scientific Bar for the Genetics of BehaviorEric Turkheimer, PhD (bio) and Sarah Rodock Greer, BA (bio)We are grateful for the opportunity to respond to such a varied and challenging set of commentaries. They range from highly supportive to quite disputatious; we will repay the supportive ones ironically, by discussing them only briefly. That will allow us to expand a bit on the more difficult comments, and of (...) course the thoughtful reply from Dr. Dick.Knox, Allen, and DownesKnox, Allen, and Downes imagine a world in which effective polygenic scores for alcohol use exist and conclude that even then there would be no way to use them ethically. We agree, for the most part, but there are several distinctions to consider. The first is among physical, medical, psychiatric, and normal-range behavioral phenotypes. Effective polygenic scores exist for height, and to a somewhat lesser extent for medical conditions like coronary heart disease. Whether or not it is a good idea to deploy them in embryo selection or clinical medicine, that is already happening.We do not think an R2 of 0.35 polygenic scores for complex behavioral phenotypes will ever exist, for all the reasons we outlined in the original paper. If we allow ourselves to imagine it happening, however, there are two explanatory pathways to follow. The first is the raw R2, and let’s stipulate that with more enormous samples or exome sequencing or whatever, respectable values are eventually achieved. The second involves the causal validity underlying black-box prediction. Scientists are taking the first step down that path (although not in Spit for Science [S4S], see the reply below to Lee and Morris) by investigating direct and indirect effects between and within families and examining the portability of polygenic scores (PGS) across environments and ancestries. The most convincing causal evidence would involve the kind of mechanistic causal biology about which enthusiasts like to speculate, but there is little sign of that.We will grant another possibility. Suppose there was a PGS for alcohol at an R2 of 0.35 that worked between families and within them, in [End Page 455] North America, South Asia, Central America, and West Africa. Animal models confirmed that it is related to specific metabolic pathways involved in alcohol. It was related but not identical to other successful PGS that predict cannabis use and other addictions. Ancient DNA studies find that it is high in human remains that were preserved next to the casks of wine that they apparently loved. Pharmacologists use it to develop effective medications for withdrawal. This hypothetical PGS, mechanistically opaque though it might remain, would exist in what Cronbach and Meehl (1955) called a nomological network. It would have construct validity, similar to a good self-report questionnaire. Like PGS for coronary heart disease, people would want to have access to construct valid PGS, and there would probably be no way to prevent people from obtaining them. We repeat that we do not expect this to happen, and as we discuss in the response to Dick below, hypothetical discussions of future scientific outcomes usually turn out to be unscientific wishcasting. It is like insisting that cities need to develop traffic control systems for flying cars.SadlerSadler is probably correct that the exigencies of grant funding explain much of what we have observed in S4S. It is certainly a more charitable explanation than the alternatives. It is interesting to consider that one of several revolutions that have occurred in the years since S4S was conceived is in the realm of scientific design and reporting. Preregistration of research hypotheses might have prevented many of the more dubious outcomes of S4S. Yet those ideas have never been applied to grant proposals, as far as we know. Grant reviews reward grandiose promises. No one has ever received funding for announcing that they hope to make incremental progress at the margins of a difficult and perhaps intractable problem. There is no mechanism to check on whether the big promises in proposals were ever fulfilled. What does get checked is whether and where investigators have published, often without regard to what the... (shrink)

Forecasting blood glucose values for patients can help prevent hypoglycemia and hyperglycemia events in advance. To this end, this study proposes an intelligent ensemble deep learning system to predict BG values in 15, 30, and 60 min prediction horizons based on historical BG values collected via continuous glucose monitoring devices as an endogenous factor and carbohydrate intake and insulin administration information as exogenous factors. Although there are numerous deep learning algorithms available, this study applied five algorithms, namely, recurrent neural network, (...) which is optimized for sequence data, and RNN-based algorithms, stacked LSTM, bidirectional LSTM, and gated recurrent unit). Then, a genetic algorithm was applied to the five prediction models to optimize their weights through ensemble techniques and to yield the final predicted BG values. The performance of the proposed model was compared to that of the autoregressive integrated moving average model as a baseline. The results show that the proposed model significantly outperforms the baseline in terms of the root mean square error and continuous glucose error grid analysis. For the valid 29 diabetic patients for the multivariate models, the RMSE was 11.08, 19.25, and 31.30 mg/DL for 15, 30, and 60 min PH, respectively. When the same data were applied to univariate models, the RMSE was 11.28, 19.99, and 33.13 mg/DL for 15, 30, and 60 min PH, respectively. Both the univariate and multivariate models showed a statistically significant difference compared with the baseline at a 5% statistical significance level. Instead of using a model with a single algorithm, applying a GA based on each output of a model with multiple algorithms was found to play a significant role in improving model performance. (shrink)

We consider metabolic networks with reversible enzymatic reactions. The model is written as a system of ordinary differential equations, possibly with inputs and outputs. We prove the global stability of the equilibrium , using techniques of monotone systems and compartmental matrices. We show that the equilibrium does not always exist. Finally, we consider a metabolic system coupled with a genetic network, and we study the dependence of the metabolic equilibrium with respect to concentrations of enzymes. We give (...) some conclusions concerning the dynamical behavior of coupled genetic/metabolic systems. (shrink)

The deterministic economic system will also produce chaotic dynamic behaviour, so economic chaos is getting more and more attention, and the research of economic chaos forecasting methods has become an important topic at present. The traditional economic chaos forecasting models are mostly based on large samples, but in actual production activities, there are a large number of small-sample economic chaos problems, and there is still no effective solution. This paper proposes a combined forecasting model based on the traditional economic (...) chaos forecasting method. First of all, through the decision tree classification, priority selection of features, rough prediction is achieved. Secondly, we use BP neural network to make secondary prediction. Because the initial weight is randomly selected, it is easy to fall into the defect of local minimum. This paper optimizes the BP neural network. Finally, the decision tree model and the BP neural network model optimized by the improved genetic algorithm are combined, and the combined model is optimized by the improved GA. This method can take advantage of many prediction models and combine the prediction information of multiple different prediction models to effectively improve the fitting ability of the model and improve the prediction accuracy. (shrink)

Partner selection is the primary aspect of the formation of knowledge collaboration teams. We propose a method of partner selection for KCTs based on a weighted social network analysis method in which the individual knowledge competence and the collaboration performance of candidates are both considered. To select the desired partners, a biobjective 0-1 model is built, integrating the knowledge competence and collaboration performance, which is an NP-hard problem. Then, a multiobjective genetic algorithm is developed to solve the proposed (...) model. Finally, a real-world example is provided to illustrate the applicability of the model, and the MOGA is implemented to search for Pareto solutions of partner selection for KCT in this case. Moreover, some simulation examples are used to test the efficiency of the algorithm. The results suggest that the proposed method can support effective and practical partner selection. (shrink)

The majority of commentators agree on one thing: Our network approach might be the prime candidate for offering a new perspective on the origins of mental disorders. In our response, we elaborate on refinements (e.g., cognitive and genetic levels) and extensions (e.g., to Axis II disorders) of the network model, as well as discuss ways to test its validity.

The BP neural network model is a hot issue in recent academic research, and it has been successfully applied to many other fields, but few researchers apply the BP neural network model to the field of automobile insurance. The main method that has been used in the prediction of the total claim amount in automobile insurance is the generalized linear model, where the BP neural network model could provide a different approach to estimate the total claim (...) loss. This paper uses a genetic algorithm to optimize the structure of the BP neural network at first, and the calculation speed is significantly improved. At the same time, by considering the overfitting problem, an early stop method is introduced to avoid the overfitting problem. In the model, a three-layer BP neural network model, which includes the input layer, hidden layer, and output layer, is trained. With consideration of various factors, a total claim amount prediction model is established, and the trained BP neural network model is used to predict the total claim amount of automobile insurance based on the data of the training set. The results show that the accuracy of the prediction by using the BP neural network model to both the data of Shandong Province and to the data of six cities is over 95%. Then, the predicted total claim amount is used to calculate premiums for five cities in Shandong Province according to credibility theory. The results show that the average premium of the five cities is slightly higher than the actual claim amount of the city. The combination of BP neural network and credibility theory can perform accurate claim amount estimation and pricing for automobile insurance, which can effectively improve the current situation of the automobile insurance business and promote the development of insurance industry. (shrink)

We are living in a time of meta-organics and post-biology, where we perceive everything in our world as customizable and changeable. Modelling biology within a technological context allows us to investigate GEO-volutionary alternatives/alterations to our original natural systems, where augmentation and transmutation become standards in search of overall betterment (Genetically Engineered Organics). Our expectations for technology exceeds ubiquitous access and functional perfection and enters the world of technoetics, where our present hyper-functional, immersively multi-apped, borderline-prosthetic, global village devices fail to satiate (...) our desires to be synaptically surpassed. Most real-time interactive behavioural systems in art utilize two and three dimensions. Artificial neural networks and prediction (Latin: from pr- before plus dicere to say) systems give rise to experimentation within the third-plus-one (3+1) dimension of the spacetime continuum. Spacetime in accordance with string theory requires the where and when to describe something in existence, rather than mere points in space. It explains the workings of the universe from both super-galactic and subatomic levels. Physical cosmology studies the motions of the celestial bodies in relation to the first cause (ie. primum movens) or the source of all-being. In book 12 of Metaphysics, Aristotle spoke of something which moves without (itself) being moved (by anything), and referred to being as motion. In quantum mechanics, a particle is described by a wave. Physiognomy is an evolving area of psychological research that describes a direct correlation between human gesture (or movement) and thought. Early twentieth-century Persian philosopher Abdul-Baha mentioned that the reality of man is his thought, not his material body. Prediction systems apply models of the mind, or artificial neural networks and machine learning strategies, to use the recorded past with the present to anticipate the future. This article investigates existing human and artificial psychic systems in hopes of identifying tools necessary in building a gesture prediction system. The relationship of intent to gesture and whether intent can be perceived without the evidence of gesture are two factors that must be tested. (shrink)