Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing

Background: In the analysis of effects by cell treatment such as drug dosing, identifying changes on gene network structures between normal and treated cells is a key task. A possible way for identifying the changes is to compare structures of networks estimated from data on normal and treated cells separately. However, this approach usually fails to estimate accurate gene networks due to the limited length of time series data and measurement noise. Thus, approaches that identify changes on regulations by using time series data on both conditions in an efficient manner are demanded. Methods: We propose a new statistical approach that is based on the state space representation of the vector autoregressive model and estimates gene networks on two different conditions in order to identify changes on regulations between the conditions. In the mathematical model of our approach, hidden binary variables are newly introduced to indicate the presence of regulations on each condition. The use of the hidden binary variables enables an efficient data usage; data on both conditions are used for commonly existing regulations, while for condition specific regulations corresponding data are only applied. Also, the similarity of networks on two conditions is automatically considered from the design of the potential function for the hidden binary variables. For the estimation of the hidden binary variables, we derive a new variational annealing method that searches the configuration of the binary variables maximizing the marginal likelihood. Results: For the performance evaluation, we use time series data from two topologically similar synthetic networks, and confirm that our proposed approach estimates commonly existing regulations as well as changes on regulations with higher coverage and precision than other existing approaches in almost all the experimental settings. For a real data application, our proposed approach is applied to time series data from normal Human lung cells and Human lung cells treated by stimulating EGF-receptors and dosing an anticancer drug termed Gefitinib. In the treated lung cells, a cancer cell condition is simulated by the stimulation of EGF-receptors, but the effect would be counteracted due to the selective inhibition of EGF-receptors by Gefitinib. However, gene expression profiles are actually different between the conditions, and the genes related to the identified changes are considered as possible off-targets of Gefitinib. Conclusions: From the synthetically generated time series data, our proposed approach can identify changes on regulations more accurately than existing methods. By applying the proposed approach to the time series data on normal and treated Human lung cells, candidates of off-target genes of Gefitinib are found. According to the published clinical information, one of the genes can be related to a factor of interstitial pneumonia, which is known as a side effect of Gefitinib.

Estimating Brazilian Monthly GDP: a State-Space Approach

This paper has several original contributions. The first is to employ a superior interpolation method that enables to estimate, nowcast and forecast monthly Brazilian GDP for 1980-2012 in an integrated way; see Bernanke, Gertler and Watson (1997, Brookings Papers on Economic Activity). Second, along the spirit of Mariano and Murasawa (2003, Journal of Applied Econometrics), we propose and test a myriad of interpolation models and interpolation auxiliary series- all coincident with GDP from a business-cycle dating point of view. Based on these results, we finally choose the most appropriate monthly indicator for Brazilian GDP. Third, this monthly GDP estimate is compared to an economic activity indicator widely used by practitioners in Brazil - the Brazilian Economic Activity Index - (IBC-Br). We found that the our monthly GDP tracks economic activity better than IBC-Br. This happens by construction, since our state-space approach imposes the restriction (discipline) that our monthly estimate must add up to the quarterly observed series in any given quarter, which may not hold regarding IBC-Br. Moreover, our method has the advantage to be easily implemented: it only requires conditioning on two observed series for estimation, while estimating IBC-Br requires the availability of hundreds of monthly series. Third, in a nowcasting and forecasting exercise, we illustrate the advantages of our integrated approach. Finally, we compare the chronology of recessions of our monthly estimate with those done elsewhere.

Estimating brazilian monthly GDP: a state-space approach

This paper has several original contributions. The rst is to employ a superior interpolation method that enables to estimate, nowcast and forecast monthly Brazilian GDP for 1980-2012 in an integrated way; see Bernanke, Gertler and Watson (1997, Brookings Papers on Economic Activity). Second, along the spirit of Mariano and Murasawa (2003, Journal of Applied Econometrics), we propose and test a myriad of interpolation models and interpolation auxiliary series all coincident with GDP from a business-cycle dating point of view. Based on these results, we nally choose the most appropriate monthly indicator for Brazilian GDP. Third, this monthly GDP estimate is compared to an economic activity indicator widely used by practitioners in Brazil - the Brazilian Economic Activity Index - (IBC-Br). We found that the our monthly GDP tracks economic activity better than IBC-Br. This happens by construction, since our state-space approach imposes the restriction (discipline) that our monthly estimate must add up to the quarterly observed series in any given quarter, which may not hold regarding IBC-Br. Moreover, our method has the advantage to be easily implemented: it only requires conditioning on two observed series for estimation, while estimating IBC-Br requires the availability of hundreds of monthly series. Third, in a nowcasting and forecasting exercise, we illustrate the advantages of our integrated approach. Finally, we compare the chronology of recessions of our monthly estimate with those done elsewhere.

Estimating Brazilian monthly GDP: a state-space approach

This paper has several original contributions. The rst is to employ a superior interpolation method that enables to estimate, nowcast and forecast monthly Brazilian GDP for 1980-2012 in an integrated way; see Bernanke, Gertler and Watson (1997, Brookings Papers on Economic Activity). Second, along the spirit of Mariano and Murasawa (2003, Journal of Applied Econometrics), we propose and test a myriad of interpolation models and interpolation auxiliary series all coincident with GDP from a business-cycle dating point of view. Based on these results, we nally choose the most appropriate monthly indicator for Brazilian GDP. Third, this monthly GDP estimate is compared to an economic activity indicator widely used by practitioners in Brazil- the Brazilian Economic Activity Index - (IBC-Br). We found that the our monthly GDP tracks economic activity better than IBC-Br. This happens by construction, since our state-space approach imposes the restriction (discipline) that our monthly estimate must add up to the quarterly observed series in any given quarter, whichmay not hold regarding IBC-Br. Moreover, our method has the advantage to be easily implemented: it only requires conditioning on two observed series for estimation, while estimating IBC-Br requires the availability of hundreds of monthly series. Third, in a nowcasting and forecasting exercise, we illustrate the advantages of our integrated approach. Finally, we compare the chronology of recessions of our monthly estimate with those done elsewhere.

A squeezed state holomorphic phase space representation of equations of motion

A mapping scheme is presented which takes quantum operators associated to bosonic degrees of freedom into complex phase space integral kernel representatives. The procedure consists of using the Schrödinger squeezed state as the starting point for the construction of the integral mapping kernel which, due to its inherent structure, is suited for the description of second quantized operators. Products and commutators of operators have their representatives explicitly written which reveal new details when compared to the usual q-p phase space description. The classical limit of the equations of motion for the canonical pair q-p is discussed in connection with the effect of squeezing the quantum phase space cellular structure. © 1993.

Fractional State Space Analysis of Temperature Time Series

Atmospheric temperatures characterize Earth as a slow dynamics spatiotemporal system, revealing long-memory and complex behavior. Temperature time series of 54 worldwide geographic locations are considered as representative of the Earth weather dynamics. These data are then interpreted as the time evolution of a set of state space variables describing a complex system. The data are analyzed by means of multidimensional scaling (MDS), and the fractional state space portrait (fSSP). A centennial perspective covering the period from 1910 to 2012 allows MDS to identify similarities among different Earth’s locations. The multivariate mutual information is proposed to determine the “optimal” order of the time derivative for the fSSP representation. The fSSP emerges as a valuable alternative for visualizing system dynamics.

Estimating Brazilian monthly GDP: a state-space approach

The first contribution of this paper is to employ a superior interpolation method that enables to estimate, nowcast and forecast monthly Brazilian GDP for 1980-2012 in an integrated way; see Bernanke, Gertler and Watson (1997, Brookings Papers on Economic Activity). The second contribution, along the spirit of Mariano and Murasawa (2003, Journal of Applied Econometrics), is to propose and test a myriad of inter-polation models and interpolation auxiliary series all coincident with GDP from a business-cycle dating point of view. Based on these results, we finally choose the most appropriate monthly indicator for Brazilian GDP. Third, this monthly GDP estimate is compared to an economic activity indicator widely used by practitioners in Brazil - the Brazilian Economic Activity Index - (IBC-Br). We found that our monthly GDP tracks economic activity better than IBC-Br. This happens by construction, since our state-space approach imposes the restriction (discipline) that our monthly estimate must add up to the quarterly observed series in any given quarter, which may not hold regarding IBC-Br. Moreover, our method has the advantage to be easily implemented: it only requires conditioning on two observed series for estimation, while estimating IBC-Br requires the availability of hundreds of monthly series. The third contribution is to illustrate, in a nowcasting and forecasting exercise, the advantages of our integrated approach. Finally, we compare the chronology of recessions of our monthly estimate with those done elsewhere.

A Bayesian state space modelling approach to probabilistic quantitative precipitation forecasting

The generation of very short range forecasts of precipitation in the 0-6 h time window is traditionally referred to as nowcasting. Most existing nowcasting systems essentially extrapolate radar observations in some manner, however, very few systems account for the uncertainties involved. Thus deterministic forecast are produced, which have a limited use when decisions must be made, since they have no measure of confidence or spread of the forecast. This paper develops a Bayesian state space modelling framework for quantitative precipitation nowcasting which is probabilistic from conception. The model treats the observations (radar) as noisy realisations of the underlying true precipitation process, recognising that this process can never be completely known, and thus must be represented probabilistically. In the model presented here the dynamics of the precipitation are dominated by advection, so this is a probabilistic extrapolation forecast. The model is designed in such a way as to minimise the computational burden, while maintaining a full, joint representation of the probability density function of the precipitation process. The update and evolution equations avoid the need to sample, thus only one model needs be run as opposed to the more traditional ensemble route. It is shown that the model works well on both simulated and real data, but that further work is required before the model can be used operationally. © 2004 Elsevier B.V. All rights reserved.

A state-space modeling approach for active structural acoustic control

The demands for improvement in sound quality and reduction of noise generated by vehicles are constantly increasing, as well as the penalties for space and weight of the control solutions. A promising approach to cope with this challenge is the use of active structural-acoustic control. Usually, the low frequency noise is transmitted into the vehicle`s cabin through structural paths, which raises the necessity of dealing with vibro-acoustic models. This kind of models should allow the inclusion of sensors and actuators models, if accurate performance indexes are to be accessed. The challenge thus resides in deriving reasonable sized models that integrate structural, acoustic, electrical components and the controller algorithm. The advantages of adequate active control simulation strategies relies on the cost and time reduction in the development phase. Therefore, the aim of this paper is to present a methodology for simulating vibro-acoustic systems including this coupled model in a closed loop control simulation framework that also takes into account the interaction between the system and the control sensors/actuators. It is shown that neglecting the sensor/actuator dynamics can lead to inaccurate performance predictions.

Infinite horizon MPC with non-minimal state space feedback

In the MPC literature, stability is usually assured under the assumption that the state is measured. Since the closed-loop system may be nonlinear because of the constraints, it is not possible to apply the separation principle to prove global stability for the Output feedback case. It is well known that, a nonlinear closed-loop system with the state estimated via an exponentially converging observer combined with a state feedback controller can be unstable even when the controller is stable. One alternative to overcome the state estimation problem is to adopt a non-minimal state space model, in which the states are represented by measured past inputs and outputs [P.C. Young, M.A. Behzadi, C.L. Wang, A. Chotai, Direct digital and adaptative control by input-output, state variable feedback pole assignment, International journal of Control 46 (1987) 1867-1881; C. Wang, P.C. Young, Direct digital control by input-output, state variable feedback: theoretical background, International journal of Control 47 (1988) 97-109]. In this case, no observer is needed since the state variables can be directly measured. However, an important disadvantage of this approach is that the realigned model is not of minimal order, which makes the infinite horizon approach to obtain nominal stability difficult to apply. Here, we propose a method to properly formulate an infinite horizon MPC based on the output-realigned model, which avoids the use of an observer and guarantees the closed loop stability. The simulation results show that, besides providing closed-loop stability for systems with integrating and stable modes, the proposed controller may have a better performance than those MPC controllers that make use of an observer to estimate the current states. (C) 2008 Elsevier Ltd. All rights reserved.

On state representations of time-varying nonlinear systems

This work considers a nonlinear time-varying system described by a state representation, with input u and state x. A given set of functions v, which is not necessarily the original input u of the system, is the (new) input candidate. The main result provides necessary and sufficient conditions for the existence of a local classical state space representation with input v. These conditions rely on integrability tests that are based on a derived flag. As a byproduct, one obtains a sufficient condition of differential flatness of nonlinear systems. (C) 2009 Elsevier Ltd. All rights reserved.

IOPT Petri Net State Space Generation Algorithm with Maximal-Step Execution Semantics

This paper presents an algorithm to efficiently generate the state-space of systems specified using the IOPT Petri-net modeling formalism. IOPT nets are a non-autonomous Petri-net class, based on Place-Transition nets with an extended set of features designed to allow the rapid prototyping and synthesis of system controllers through an existing hardware-software co-design framework. To obtain coherent and deterministic operation, IOPT nets use a maximal-step execution semantics where, in a single execution step, all enabled transitions will fire simultaneously. This fact increases the resulting state-space complexity and can cause an arc "explosion" effect. Real-world applications, with several million states, will reach a higher order of magnitude number of arcs, leading to the need for high performance state-space generator algorithms. The proposed algorithm applies a compilation approach to read a PNML file containing one IOPT model and automatically generate an optimized C program to calculate the corresponding state-space.

ECG biometrics using a dissimilarity space representation

Electrocardiogram (ECG) biometrics are a relatively recent trend in biometric recognition, with at least 13 years of development in peer-reviewed literature. Most of the proposed biometric techniques perform classifi-cation on features extracted from either heartbeats or from ECG based transformed signals. The best representation is yet to be decided. This paper studies an alternative representation, a dissimilarity space, based on the pairwise dissimilarity between templates and subjects' signals. Additionally, this representation can make use of ECG signals sourced from multiple leads. Configurations of three leads will be tested and contrasted with single-lead experiments. Using the same k-NN classifier the results proved superior to those obtained through a similar algorithm which does not employ a dissimilarity representation. The best Authentication EER went as low as 1:53% for a database employing 503 subjects. However, the employment of extra leads did not prove itself advantageous.

State Space Analysis of Forest Fires

This paper studies forest fires from the perspective of dynamical systems. Burnt area, precipitation and atmospheric temperatures are interpreted as state variables of a complex system and the correlations between them are investigated by means of different mathematical tools. First, we use mutual information to reveal potential relationships in the data. Second, we adopt the state space portrait to characterize the system’s behavior. Third, we compare the annual state space curves and we apply clustering and visualization tools to unveil long-range patterns. We use forest fire data for Portugal, covering the years 1980–2003. The territory is divided into two regions (North and South), characterized by different climates and vegetation. The adopted methodology represents a new viewpoint in the context of forest fires, shedding light on a complex phenomenon that needs to be better understood in order to mitigate its devastating consequences, at both economical and environmental levels.