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**|**Cogn Neurodyn**|**v.6(1); 2012 February**|**PMC3253161

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- Abstract
- Introduction
- Granger causality in time domain
- New causality
- Statistical test for significance
- Asymptotic distribution property
- Conclusions
- References

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Cogn Neurodyn. 2012 February; 6(1): 33–42.

Published online 2011 September 27. doi: 10.1007/s11571-011-9175-8

PMCID: PMC3253161

Sanqing Hu,^{}^{1} Yu Cao,^{2} Jianhai Zhang,^{1} Wanzeng Kong,^{1} Kun Yang,^{1} Yanbin Zhang,^{1} and Xun Li^{1}

Sanqing Hu, Email: moc.oohay@0002uhqs.

Received 2011 March 24; Revised 2011 July 6; Accepted 2011 September 13.

Copyright © Springer Science+Business Media B.V. 2011

This article has been cited by other articles in PMC.

Granger causality (GC) has been widely applied in economics and neuroscience to reveal causality influence of time series. In our previous paper (Hu et al., in IEEE Trans on Neural Netw, 22(6), pp. 829–844, 2011), we proposed new causalities in time and frequency domains and particularly focused on new causality in frequency domain by pointing out the shortcomings/limitations of GC or Granger-alike causality metrics and the advantages of new causality. In this paper we continue our previous discussions and focus on new causality and GC or Granger-alike causality metrics in time domain. Although one strong motivation was introduced in our previous paper (Hu et al., in IEEE Trans on Neural Netw, 22(6), pp. 829–844, 2011) we here present additional motivation for the proposed new causality metric and restate the previous motivation for completeness. We point out one property of conditional GC in time domain and the shortcomings/limitations of conditional GC which cannot reveal the real strength of the directional causality among three time series. We also show the shortcomings/limitations of directed causality (DC) or normalize DC for multivariate time series and demonstrate it cannot reveal real causality at all. By calculating GC and new causality values for an example we demonstrate the influence of one of the time series on the other is linearly increased as the coupling strength is linearly increased. This fact further supports reasonability of new causality metric. We point out that larger instantaneous correlation does not necessarily mean larger true causality (e.g., GC and new causality), or vice versa. Finally we conduct analysis of statistical test for significance and asymptotic distribution property of new causality metric by illustrative examples.

Given a set of time series, the topic of how to define causality influence among them has kept philosophers busy for over two thousand years and has yet to be completely resolved. In the literature one of the most popular definitions for causality is Granger causality (GC). Due to its simplicity and easy implementation, GC has been widely used in economics and recently in neuroscience. The basic idea of GC was originally conceived (Wiener 1956) and later formalized by Granger in the form of linear regression model (Granger 1969; Geweke 1982). It can be simply stated as follows: if the variance of the prediction error for the first time series at the present time is not less than the variance of the prediction error by including past measurements from the second time series in the linear regression model, then the second time series can be said to have a causal (driving) influence on the first time series. Reversing the roles of the two time series one repeats the process to address the question of driving in the opposite direction. GC value of is defined to describe the strength of the causality which the second time series has on the first one (Freiwald et al. 1999; Hesse et al. 2003; Ding et al. 2006; Oya et al. 2007; Bressler and Anil 2010). From GC value, it is clear that (i) when there is no causal influence from the second time series to the first one and when there is. This GC definition was extended to frequency domain to show causal influence from one time series on the other one in different frequencies (Geweke 1982; Ding et al. 2006). Several GC or Granger-alike causality metrics in frequency domain have been developed such as spectral GC (Geweke 1982; Ding et al. 2006), PDC (Baccal and Sameshima 2001), RPC (Yamashita et al. 2005), and DTF (Kaminski et al. 2001). To show whether the influence is a direct component or mediated by the third time series, conditional GC is defined (Geweke 1984; Freiwald et al. 1999; Hesse et al. 2003; Ding et al. 2006; Oya et al. 2007; Bressler and Anil 2010). In recent years there has been significant interest to discuss causal interactions between brain areas which are highly complex neural networks in both time and frequency domains (Freiwald et al. 1999; Hesse et al. 2003; Roebroeck et al. 2005; Oya et al. 2007; Wang et al. 2007, 2008; Atmanspacher and Rotter 2008; Gow et al. 2008, 2009; Rajagovindan and Ding 2008; Seth 2008; Cadotte et al. 2009; Zhang et al. 2010).

Although there are wide applications of GC and Granger-alike causality metrics in both time and frequency domains, some shortcomings/limitations of these metrics were pointed out in our recent paper (Hu et al. 2011). To overcome these shortcomings/limitations, we proposed new causality metrics in time and frequency domains. In particular, we emphasized that GC or Granger-alike causality metrics in frequency domain cannot reveal real strength of causality at all and new causality metric in frequency domain has advantages over spectral GC or Granger-alike causality metrics.

In this paper we will focus on time domain and show inherent shortcomings of conditional GC and DC or normalized DC. We will demonstrate that the proposed new causality metric better reveal directed real causality from one time series on the other one than conditional GC and DC or normalized DC. Thus, we must be caution in drawing any conclusion based on GC, conditional GC and DC or normalized DC by noting the shortcomings/limitations of GC (Hu et al. 2011). We will show the influence of one of the time series on the other is linearly increased as the coupling strength is linearly increased by computing GC and new causality values via an example. We will also discuss statistical test for significance and asymptotic distribution property of new causality metric.

In this section we introduce the well-known Granger causality and conditional Granger causality.

Given two stochastic process *X*_{1}(*t*) and *X*_{2}(*t*) which are assumed to be jointly stationary. Their autoregressive representations are described as

1

and their joint representations are described as

2

where the noise terms are uncorrelated over time, and η_{i} have zero means and variances of and The covariance between η_{1} and η_{2} is defined by

Now consider the first equalities in Eqs. 1 and 2. According to the original formulations (Wiener 1956; Granger 1969), if is less than in some suitable statistical sense, then *X*_{2} is said to have a causal influence on *X*_{1}. In this case, the first equality in Eq. 2 is more accurate than that in Eq. 1 to estimate *X*_{1}. Otherwise, if then *X*_{2} is said to have no causal influence on *X*_{1}. In this case, the two equalities are almost same. Such kind of causal influence called Granger causality (GC) (Ding et al. 2006; Geweke 1982), can be defined by

3

Obviously, when there is no causal influence from *X*_{2} to *X*_{1} and when there is. Similarly, the causal influence from *X*_{1} to *X*_{2} is defined by

4

To show whether the interaction between two time series is direct or is mediated by another recorded time series, conditional Granger causality (Ding et al. 2006; Geweke 1984), was defined by

5

where and are variances of two noise terms, and η_{3}, of the following two joint autoregressive representations:

6

and *X*_{1,t} =

7

According to this definition, means that no further improvement in the prediction of *X*_{1} can be expected by including past measurements of *X*_{2}. On the other hand, when there is still a direct component from *X*_{2} to *X*_{1}, the past measurements of *X*_{1}, *X*_{2}, *X*_{3} together result in better prediction of *X*_{1}, leading to and

For conditional GC, we point out one important property as follows.

** Property 1** Consider the following model

8

where 0 < *a*_{i1,1}, *a*_{i3,1} < 0.7, *i* = 1, 2, 3 and for simplicity η_{1}, η_{2}, η_{3} are assumed to be independent white noise processes with zero mean and variances Figure 1 shows for Model (8) under different parameters *a*_{i1,1} and *a*_{i3,1}. When we calculate conditional GC it should be pointed out that for each specific Model (8) we generate a data set of 200 realizations of 10,000 time points. For each realization, we estimate AR models (joint representations Model (6) and Model (7)) with the order of 8 by using the least-squares method and calculate conditional GC where the order 8 fits well for all examples throughout the paper (see Fig. Fig.1a1a and b from which one can see keeps steady when the order of the estimated models is >8). Then we obtain the average value across all realizations and get From Fig. Fig.11 one can clearly see that has nothing to do with parameters *a*_{i1,1} and *a*_{i3,1}, *i* = 1, 2, 3 (of course, choices of parameters *a*_{i1,1} and *a*_{i3,1} are such that Model (8) does not diverge).

By the conditional GC definition (5), we know that conditional GC explicitly measures the degree to which *X*_{2} predicts *X*_{1} over and above the degree to which *X*_{1} already predicts itself and *X*_{3} predicts *X*_{1}, the influence of *X*_{1} on itself (i.e. the coefficients *a*_{i1,1}) and *X*_{3} on *X*_{1} (i.e. the coefficients *a*_{i3,1}) are factored out and quite correctly makes no difference to the result. So, according to the conditional GC definition (5) the above property is true.

In general GC is useful to show whether or not theoretically there is directional interaction between two neurons or among three neurons. When there exists causal influence, a question is arising: does GC value reveals the real strength of causality? to answer this question, let’s consider the following simple model

9

where η_{1} and η_{2} are two independent white noise processes with zero mean and *a*_{12,1}*a*_{21,1} ≠ 0. From Model (9) one can get

10

So, GC value

11

or equivalently,

12

which is only related to the last two noise terms and has nothing to do with the first term. It is noted that all of three terms make contributions to current *X*_{1,t}, and *a*_{12,1}*a*_{21,1}*X*_{1,t−2} must have causal influence on *X*_{1,t} and must be considered to illustrate real causality. Especially, when we have *X*_{1,t} = *a*_{12,1}*a*_{21,1}*X*_{1,t−2} + η_{1,t} and Since *a*_{21,1}*X*_{1,t−2} comes from *X*_{2,t−1} we can surely know that *X*_{2} has real nonzero causality on *X*_{1} due to *a*_{12,1}*a*_{21,1} ≠ 0. Thus, GC value may not reveal real causality at all. As such, the definition has its inherent shortcomings and/or limitations to illustrate the real strength of causality. Please refer to Remark 1 (Hu et al. 2011) for the detailed discussions.

Due to the shortcomings and/or limitations of GC, we next give a new definition for causality anaylsis of multivariate time series. Let’s consider the following general model:

13

where are *n* time series, has zero mean and variance of and Based on Eq. 13, Fig. Fig.22 clearly shows contributions to *X*_{k,t}, which includes and the noise term η_{k,t} where the influence from is causality from *X*_{k}’s own past values. Each contribution plays an important role in determining *X*_{k,t}. If occupies larger portion among all those contributions, then *X*_{i} has stronger causality on *X*_{k}, or vice versa. Thus, a good definition for causality from *X*_{i} to *X*_{k} in time domain should be able to describe what proportion *X*_{i} occupies among all these contributions. This is a general guideline for proposing any causality method (i.e., all contributions must be considered). For Eq. 10, let’s define

14

which is summation of two noise terms and each noise term makes contributions to To describe what proportion η_{2} occupies in we define

15

which is the same as GC defined in Eq. 12. Therefore, here in nature GC is actually defined based on the noise model (14) and follows the above guideline. Motivated by this idea, we can naturally extend the noise model (14) to the *k*th equation of Model (13) and define a new direct causality from *X*_{i} to *X*_{k} as follows:

16

When *N* is large enough,

Then, Eq. 16 can be approximated as

17

Throughout the paper, we always assume that *N* is large enough so that is always defined as Eq. 17.

New causality based on Eq. 10 can be written as

18

which describes what proportion *X*_{2} occupies among two contributions in *X*_{1} (see Eq. 10). Note that for (10) GC is proposed based on Model (14) and describes what proportion η_{2} occupies among two contributions in (see Eq. 15). Thus GC actually reveals causal influence from η_{2} to it does not reveal causal influence from *X*_{2} to *X*_{1} at all by noting that is only partial information of *X*_{1}, i.e., the noise terms *a*_{12,1}η_{2,t−1} + η_{1,t}. One can see that new causality definition based on Eq. 10 is a natural extension of GC definition based on Eq. 14 as far as the concept of proportion is concerned (in this way, our new causality definition has a rather sound conceptual or theoretical basis). But, as said above, the equivalent GC describes what the proportion η_{2} occupies in of Eq. 14 and new causality describes what the proportion *X*_{2} occupies in *X*_{1} of Eq. 10. Thus, they are two totally different concepts, that is, the equivalent GC reveals causal influence from η_{2} to but new causality indeed reveals causal influence from *X*_{2} to *X*_{1}. Obviously, one cannot use causal influence value from η_{2} to (involving partial information of *X*_{1}, i.e., the noise terms *a*_{12,1}η_{2,t−1} + η_{1,t}) to express causality influence value from *X*_{2} to *X*_{1} (involving complete information, i.e.,the noise terms *a*_{12,1}η_{2,t−1} + η_{1,t} plus *a*_{12,1}*a*_{21,1}*X*_{1,t−2}). Any causality definition (like traditional GC) only using partial information of *X*_{1} inevitably leads to misinterpretation result. In addition to some important points shown in Remark 2 (Hu et al. 2011), next we give some more comments for new causality in the following remark.

** Remark 1** (1) Let the transfer function of Model (13) be

19

where the power spectrum

20

Equation 20 indicates that the power spectrum of *X*_{i,t} at frequency *f* can be decomposed as to *n* terms each of which can be interpreted as the power contribution of the *j*th innovation η_{j,t} transferring to *X*_{i,t} via the transfer function *H*_{ij}(*f*). RPC can be regarded as a ratio of the power contribution of the innovation η_{j,t} on the power spectrum of *X*_{i,t} to the power spectrum From this point of view, this ratio also provides a strong motivation (or theoretical basis) to define the proposed new causality metric Eq. 16 for multivariate time series. However, as pointed out in Remark 6 (Hu et al. 2011) RPC has inherent shortcomings/limitations and cannot reveal real causality influence at all.(2) Consider the following two models

21

and

22

where η_{1}, η_{2} and η_{3} are three independent white noise processes with zero mean and variances and the initial conditions and From both of Models (21) and (22) it can be seen that there are no direct causality from *X*_{3} to *X*_{1}, so, Moreover, based on Property 1, are same for both of Models (21) and (22). We can obtain for both of Models (21) and (22), for Model (21), and for Model (22). Figure 3 shows trajectories and η_{1} for one realization of Model (21) and Model (22). From Fig. Fig.3a3a and c one can clearly see that amplitudes of −0.99*X*_{2} are much larger than that of η_{1} and the contribution from −0.99*X*_{2,t−1} occupies much larger portion compared to that from η_{1,t}, as a result, the causal influence from *X*_{2} to *X*_{1} occupies a major portion compared to the influence from η_{1} and the real strength of causality from *X*_{2} to *X*_{1} should have higher value. This fact is real. Our causality value for Model (21) is consistent with this fact. Similarly, from Fig. Fig.3b3b and c one can clearly see that amplitude of is much smaller than that of η_{1} and the contribution from occupies much smaller portion compared to that from η_{1,t}, as a result, the causal influence from to occupies a rather small portion compared to the influence from η_{1} and the real strength of causality from to should have smaller value. This fact is also real. Our causality value for Model (22) is consistent with this fact. However, conditional GC always equals to 0.092 for both of Models (21) and Eq. 22 and does not reflect such kind of changes at all, and violates above two real facts. These results show that the conditional GC definition (5) does not reveal real strength of direct causality from *X*_{2} to *X*_{1} at all for Models (21) and (22), our new causality definition very reasonably reflects the real strength of the direct causality.(3) An alternate time-domain metric namely direct causality (DC) has been proposed earlier (Kaminski et al. 2001) which quantifies causality based on the AR coefficients

or the following normalized measure

23

Since the AR coefficients themselves represent the coupling strength, now a question is arising: would this normalized measure suffice to reveal the real causality of two time series? Unfortunately, the answer is no. Let’s take a look at the following model:

24

where η_{1}, η_{2} and η_{3} are three independent white noise processes with zero mean and variances For Models (24) we can obtain and Figure 4 shows trajectories of *X*_{1,t}, 0.9(− *X*_{2,t−1} + *X*_{2,t−2} − *X*_{2,t−3} + *X*_{2,t−4}), 0.9*X*_{3,t}, and η_{1,t} for one realization of Model (24). From Fig. Fig.4a–d4a–d one can clearly see that amplitudes of 0.9*X*_{3} are much larger than that of η_{1,t} and 0.9(− *X*_{2,t−1} + *X*_{2,t−2} − *X*_{2,t−3} + *X*_{2,t−4}), and the contribution from 0.9*X*_{3} occupies much larger portion compared to that from η_{1,t} and 0.9(− *X*_{2,t−1} + *X*_{2,t−2} − *X*_{2,t−3} + *X*_{2,t−4}). As a result, the causal influence from *X*_{2} to *X*_{1} occupies a small portion compared to the influence from 0.9*X*_{3} and the real strength of causality from *X*_{2} to *X*_{1} should have smaller value. This fact is real. Our causality value for Model (24) is consistent with this fact. However, for Model (24) violates the real fact. These results show that the direct causality definition (23) does not reveal real strength of direct causality from *X*_{2} to *X*_{1} at all for Model (24), our new causality definition reflects the real strength of the direct causality very reasonably.(4) It should be noted that the influence of one of the time series on the other is linearly increased as the coupling strength is linearly increased. Let’s consider the following bivariate AR process with 5 levels of coupling strength:

25

where η_{1} and η_{2} are two independent white noise processes with zero mean and variances From Eq. 25 one can see that the coupling strength of *X*_{2} on *X*_{1} is linearly increased as the parameter *c* increases. The true causality of *X*_{2} on *X*_{1} should increase as the parameter *c* increases. The estimated causality measures (new causality and GC) against the parameter *c* are shown in Fig. Fig.5a5a and b, respectively, from which one can clearly see that both of two metrics indicate the increasing true causality as the true coupling strength (i.e., the parameter *c*) increases.(5) Figure 5c shows the increasing instantaneous correlation (i.e., zero-lag influence) of two time series as the parameter *c* increases. Combining Fig. Fig.5a5a and b with c we can conclude that the increasing instantaneous correlation leads to the reasonable increasing new causality and GC. However, in general this conclusion may not be true. It is well known that in general there may be no relationship between true causality and correlation. In other words, larger correlation does not necessarily mean larger true causality, or vice versa. Therefore, it is meaningless to discuss whether new causality or GC will be affected by correlation.

Since new causality metric has a highly nonlinear relation to the time series data, it makes tests of significance difficult to perform. In this section, we use the same technology (Kaminski et al. 2001) to deal with this problem; that is, we first create a surrogate data set (Theiler et al. 1992) for each channel, we then fit a model to this surrogate data set and calculate new causality metric. Repeating this process many time, we can obtain an empirical distribution for the metric. Based on this distribution we can then evaluate the significance of the causal metric derived from the actual data. We use the following model to illustrate the process.

26

where η_{1} and η_{2} are two independent white noise processes with standard normal distribution. For a simulated data of a realization of Model (26), we produce surrogate data (i.e., perform random and independent shuffling of *X*_{1} and *X*_{2}). We then estimate a joint regression model (2) with *m* = 6 to fit the shuffled data and calculate new causality value. Carrying out the procedure for 1,000 such independently shuffled data sets we can construct an empirical distribution for the new causality values. Since the shuffling procedure destroys all the temporal structure in the data, this empirical distribution gives the variability for the new causality values when the null hypothesis of no causal influence is true.

Figure 6 shows Histogram of new causality values based on the original simulated data and 1000 surrogate data. One can see that the new causality value (=0.275) based on the original simulated data is statistically significant (*P* < 0.001).

It is well known that the asymptotic distribution of GC metric under the null hypothesis of zero causality is known (it is a χ ^{2}-distribution) (Geweke 1982). Now a question is arising: what is asymptotic distribution for new causality metric under the null hypothesis of zero causality? For new causality metric can we derive the similar asymptotic distribution property as GC metric? In general it is difficult to discuss this issue because of complexity of new causality definition. But in the following example we find that new causality metric has χ^{2}(1)-distribution as GC metric.

27

where η_{1} and η_{2} are two independent white noise processes with standard normal distribution, (i.e., *N* = 10,000). For each realization of Model (27) we set *m* = 1 to estimate the autoregression Model (1) and the joint regression Model (2), then based on the two estimated models we calculate new causalty and GC This process is repeated by *N* = 10,000 times. Finally we plot large-sample distributions for and in Fig. Fig.7a7a and b, respectively. One can see probability density functions for both new causality and GC follow χ^{2}(1)-distribution. In general, as for whether or not follows a χ^{2}-distribution under the null hypothesis of zero causality keeps unknown and is left for further study in near future.

In this paper, we further make more discussions for GC or Granger-alike causality and new causality metrics by following our previous paper (Hu et al. 2011) and focus on time domain. In addition to the previous motivation for introducing new causality metric in time domain, we provide additional strong motivation (or theoretical basis) to the proposed metric for multivariate time series. After introducing one property for conditional GC, we point out the inherent shortcomings/limitations of conditional GC and demonstrate that it cannot reveal directed causal influence from one time series to the other one among three time series. We also point out the shortcomings/limitations of Granger-alike causality, i.e., DC or normalized DC metric and show that it cannot disclose directed causality influence at all for multivariate time series. Furthermore, all these shortcomings/limitations demonstrate reasonability and advantages of new causality metric. Therefore, researchers must be caution in drawing any conclusion based on DC (or normalized DC) value and conditional GC value. By calculating GC and new causality values for an example we show the influence of one of the time series on the other is linearly increased as the coupling strength is linearly increased. Finally for new causality metric in time domain we analyze statistical test for significance and show significance level for a simulated data, meanwhile we conduct analysis for asymptotic distribution property by an examples in which both GC and new causality metrics follow χ^{2}(1)-distribution. However, in general, as for whether or not new causality metric follows a χ^{2}-distribution under the null hypothesis of zero causality keeps unknown and is left for further study in near future. Thus our proposed new causality metrics in time and frequency domains may have wide applications in economics and neuroscience.

This work was supported in part by the National Natural Science Foundation of China under Grant 61070127, and the International Cooperation Project of Zhejiang Province, China, under Grant 2009C14013, Qianjiang Project of Zhejiang Province, China, under Grant 2011R10063, U.S. National Science Foundation (NSF) under Grant 0821820, and Tennessee Higher Education Commission, the State of Tennessee, USA.

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