jmlr jmlr2012 jmlr2012-56 knowledge-graph by maker-knowledge-mining

56 jmlr-2012-Learning Linear Cyclic Causal Models with Latent Variables


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Author: Antti Hyttinen, Frederick Eberhardt, Patrik O. Hoyer

Abstract: Identifying cause-effect relationships between variables of interest is a central problem in science. Given a set of experiments we describe a procedure that identifies linear models that may contain cycles and latent variables. We provide a detailed description of the model family, full proofs of the necessary and sufficient conditions for identifiability, a search algorithm that is complete, and a discussion of what can be done when the identifiability conditions are not satisfied. The algorithm is comprehensively tested in simulations, comparing it to competing algorithms in the literature. Furthermore, we adapt the procedure to the problem of cellular network inference, applying it to the biologically realistic data of the DREAM challenges. The paper provides a full theoretical foundation for the causal discovery procedure first presented by Eberhardt et al. (2010) and Hyttinen et al. (2010). Keywords: causality, graphical models, randomized experiments, structural equation models, latent variables, latent confounders, cycles

Reference: text


Summary: the most important sentenses genereted by tfidf model

sentIndex sentText sentNum sentScore

1 For instance, some causal discovery methods require assuming that the causal structure is acyclic (has no directed cycles), while others require causal sufficiency, that is, that there are no unmeasured common causes affecting the measured variables. [sent-39, score-0.475]

2 While for certain kinds of experimental data it is easy to identify the full causal structure, we show that significant savings either in the number of experiments or in the number of randomized variables per experiment can be achieved. [sent-69, score-0.412]

3 , n) is determined by a linear combination of the values of its causal parents xi ∈ pa(x j ) and an additive disturbance (‘noise’) term e j : x j := ∑ b ji xi + e j . [sent-102, score-0.339]

4 xi ∈pa(x j ) Representing all the observed variables as a vector x and the corresponding disturbances as a vector e, these structural equations can be represented by a single matrix equation x := Bx + e, (1) where B is the (n × n)-matrix of coefficients b ji . [sent-103, score-0.35]

5 A graphical representation of such a causal model is given by representing any non-zero causal effect b ji by an edge xi → x j in the corresponding graph. [sent-104, score-0.406]

6 Typically, a cyclic model is used to represent a causal process that is collapsed over the time dimension and where it is assumed that the data sample is taken after the causal process has ‘settled down’. [sent-122, score-0.396]

7 , 2000; Pearl, 2000), we consider in this paper randomized “surgical” interventions that break all incoming causal influences to the intervened variables by setting the intervened variables to values determined by an exogenous intervention distribution with mean µk and covariance cov(c) = Σk . [sent-162, score-0.741]

8 (4) For an intervened variable x j ∈ Jk , the manipulated model in Equation 4 replaces the original equation x j := ∑i∈pa( j) b ji xi + e j with the equation x j := c j , while the equations for passively observed variables xu ∈ Uk remain unchanged. [sent-172, score-0.755]

9 Definition 3 (Asymptotic Stability) A linear cyclic model with latent variables (B, Σe ) is asymptotically stable if and only if for every possible experiment Ek = (Jk , Uk ), the eigenvalues λi of the matrix Uk B satisfy ∀i : |λi | < 1. [sent-179, score-0.41]

10 This notational simplification makes the partition into intervened and passively observed variables the only parameter specifying an experiment, and allows us to derive the theory purely in terms of the covariance matrices Ck of an experiment. [sent-189, score-0.358]

11 (8) We can now focus on analyzing the covariance matrix obtained from a canonical experiment Ek = (Jk , Uk ) on a canonical model (B, Σe ). [sent-205, score-0.33]

12 The upper left hand block is the identity matrix I, since in a canonical experiment the intervened variables are randomized independently with unit variance. [sent-208, score-0.384]

13 The lower left hand block Tk consists of covariances that represent the so-called experimental effects of x the intervened xi ∈ Jk on the passively observed xu ∈ Uk . [sent-211, score-0.726]

14 An experimental effect t(xi xu ||Jk ) is the overall causal effect of a variable xi on a variable xu in the experiment Ek = (Jk , Uk ); it corresponds to the coefficient of xi when xu is regressed on the set of intervened variables in this experiment. [sent-212, score-1.337]

15 If only variable xi is intervened on in the experiment, then the experimental effect t(xi xu ||{xi }) is standardly called the total effect and denoted simply as t(xi xu ). [sent-213, score-0.744]

16 If all observed variables except for xu are intervened on, then an experimental effect is called a direct effect: t(xi xu ||V \ {xu }) = b(xi → xu ) = (B)ui = bui . [sent-214, score-1.072]

17 In our case, these trekrules imply that the experimental effect t(xi xu ||Jk ) can be expressed as the sum of contributions by all directed paths starting at xi and ending in xu in the manipulated graph, denoted by the set P (xi xu ||Jk ). [sent-217, score-0.934]

18 Any directed paths through ˜ marginalized variables are transformed into directed edges in B, and any confounding effect of the ˜ marginalized variables is integrated into the covariance matrix Σe of the disturbances. [sent-248, score-0.479]

19 We term this assumption weak stability: Definition 6 (Weak Stability) A linear cyclic causal model with latent variables (B, Σe ) is weakly stable if and only if for every experiment Ek = (Jk , Uk ), the matrix I − Uk B is invertible. [sent-267, score-0.585]

20 The interpretation of any learned weakly stable model (B, Σe ) is then only that the distribution over the observed variables produced at equilibrium by the true underlying asymptotically stable model has mean and covariance as described by Equations 7 and 8. [sent-276, score-0.47]

21 4 In the following two Lemmas, we give the details of how the canonical model over the observed variables is related to the original linear cyclic model in the case of hidden variables and self-cycles (respectively). [sent-278, score-0.329]

22 3397 H YTTINEN , E BERHARDT AND H OYER ˜ ˜ ˜ ized model (B, Σe ) over variables V = V \ M defined by ˜ B = BV V + BV M (I − BM M )−1 BM V , ˜ ˜ ˜ ˜ ˜ e = (I − B) (I − B)−1 Σe (I − B)−T ˜ ˜ (I − B)T ˜ ˜ Σ VV is also a weakly stable linear cyclic causal model with latent variables. [sent-286, score-0.488]

23 The marginalized covariance matrix of the original model and the covariance matrix of the marginalized model are equal in ˜ any experiments where any subset of the variables in V are intervened on. [sent-287, score-0.626]

24 First, the coefficient matrix B ˜ in the of the marginalized model is given by the existing coefficients between the variables in V ˜ original model plus any paths in the original model from variables in V through variables in M ˜ ˜ and back to variables in V . [sent-289, score-0.417]

25 For a weakly stable model (B, Σe ) containing a self-loop for variable xi with coefficient bii , we can define a model without that self-loop given by bii Ui (I − B), 1 − bii bii bii Ui )Σe (I + Ui )T . [sent-296, score-0.933]

26 = (I + 1 − bii 1 − bii ˜ B = B− ˜ Σe ˜ ˜ The resulting model (B, Σe ) is also weakly stable and yields the same observations at equilibrium in all experiments. [sent-297, score-0.501]

27 Note that Equation 12 relates the experimental effects of intervening on {x1 , x2 } to the experimental effects of intervening on {x1 , x2 , x4 }. [sent-327, score-0.522]

28 Thus, if we had a set of experiments that allowed us to infer all the experimental effects of all the experiments that intervene on all but one variable, then we would have determined all the direct effects and would thereby have identified the B-matrix. [sent-332, score-0.393]

29 On the other hand, Equation 12 shows how the measured experimental effects can be used to construct 3399 H YTTINEN , E BERHARDT AND H OYER linear constraints on the (unknown) direct effects b ji . [sent-333, score-0.377]

30 The example in Equation 12 can be generalized in the following way: As stated earlier, for an asymptotically stable model, the experimental effect t(xi xu ||Jk ) of xi ∈ Jk on xu ∈ Uk in experiment Ek = (Jk , Uk ) is the sum-product of coefficients on all directed paths from xi to xu . [sent-339, score-1.135]

31 The sum-product of all those paths is equal to the experimental effect t(xi xu ||Jk ∪ {x j }), since all paths through x j are intercepted by additionally intervening on x j . [sent-342, score-0.44]

32 Second, the remaining paths are all of the form xi x j xu , where x j is the ˜ ˜ last occurrence of x j on the path (recall that paths may contain cycles, so there may be multiple occurrences of x j on the path). [sent-343, score-0.365]

33 The sum-product of coefficients on all subpaths xi x j is given ˜ by t(xi x j || Jk ) and the sum-product of coefficients on all subpaths x j xu is t(x j xu || Jk ∪ {x j }). [sent-344, score-0.547]

34 ˜ Taking all combinations of subpaths xi x j and x j xu , we obtain the contribution of all the paths ˜ ˜ through x j as the product t(xi x j || Jk )t(x j xu || Jk ∪ {x j }). [sent-345, score-0.579]

35 We thus obtain t(xi xu || Jk ) = t(xi xu || Jk ∪ {x j }) + t(xi x j || Jk )t(x j xu || Jk ∪ {x j }). [sent-346, score-0.738]

36 Now, if the matrix on the left is invertible, we can directly solve for the experimental effects of the third experiment just from the experimental effects in the first two. [sent-354, score-0.506]

37 / Since there are no experimental effects in experiments intervening on 0 or V , the experimental effects are considered to be determined trivially in those cases. [sent-358, score-0.489]

38 x In a canonical model the coefficients b(• → xu ) on the arcs into variable xu (the direct effects of the other variables on that variable) are equal to the experimental effects when intervening on everything except xu , that is, b(• → xu ) = t(• xu ||V \ {xu }). [sent-361, score-1.752]

39 ,K satisfies the pair condition for an ordered pair of variables (xi , xu ) ∈ V × V (with xi = xu ) whenever there is an experiment Ek = (Jk , Uk ) in {Ek }k=1,. [sent-371, score-0.864]

40 ,K such that xi ∈ Jk (xi is intervened on) and xu ∈ Uk (xu is passively observed). [sent-374, score-0.489]

41 From a set of experiments satisfying the pair condition for all ordered pairs, we can find for all xi = xu an experiment satisfying the pair condition for the ˜ ˜ ˜ pair (xi , xu ). [sent-377, score-0.925]

42 Now, by iteratively ˜ ˜ ˜ using Lemma 9, we can determine the experimental effects in the union experiment E∪ = (J∪ , U∪ ) ˜ i }i=u , where variables in set J∪ = i=u Ji are intervened on. [sent-379, score-0.481]

43 Variable xu was passively observed in each experiment, thus xu ∈ J∪ . [sent-381, score-0.569]

44 The experimental effects of this union experiment intervening on / ˜ ˜∪ = V \ {xu } are thus the direct effects b(• → xu ). [sent-382, score-0.733]

45 ,K a weakly stable canonical model (B, Σe ) over the variables V is identifiable if the set of experiments satisfies the pair condition for each ordered pair of variables (xi , x j ) ∈ V × V (with xi = x j ) and the covariance condition for each unordered pair of variables {xi , x j } ⊆ V . [sent-401, score-0.779]

46 Then a model with coefficient ˜ matrix B defined by ˜ BK V = BK V , ˜ BLL = 0 bi j b ji + δ 0 , ˜ ˜ BLK = (I − BLL )(I − BLL )−1 BLK will produce the same experimental effects as B for any experiment that does not satisfy the pair ˜ condition for the pair (xi , x j ). [sent-431, score-0.524]

47 As in our example, it is generally the ˜ case that for δ = 0 the models B and B will produce different experimental effects in any experiment that satisfies the pair condition for the pair (xi , x j ). [sent-434, score-0.428]

48 To see the effect of the perturbation more clearly, we can write it explicitly as follows: ˜ ∀l = j, ∀k : blk = blk , ˜ b ji = b ji + δ, ˜ b j j = 0, bik + bi j b jk ˜ ∀k ∈ {i, j} : b jk = b jk − δ / . [sent-436, score-1.717]

49 If the pair condition is not satisfied for several pairs, then Lemma 13 can be applied iteratively for each missing pair to arrive at a model with different coefficients, that produces the same experimental effects as the original for all experiments not satisfying the pairs in question. [sent-442, score-0.413]

50 However, the following lemma shows that the covariance matrix of disturbances can always be perturbed such that the two models become completely indistinguishable for any experiment that does not satisfy the pair condition for some pair (xi , x j ), as was the case in Figure 6. [sent-445, score-0.421]

51 ,K and all xi ∈ Jk and x j ∈ Uk it produces the ˜ ˜ ˜ ˜ same experimental effects t(xi x j || Jk ), then the model (B, Σe ) with Σe = (I − B)(I − B)−1 Σe (I − −T (I − B)T produces data covariance matrices Ck = Ck for all k = 1, . [sent-454, score-0.359]

52 ,K over the variables in V , all coefficients b(xi → x j ) of a weakly stable canonical model are identified if and only if the pair condition is satisfied for all ordered pairs of variables with respect to these experiments. [sent-466, score-0.429]

53 ,K satisfies the pair condition for all ordered pairs (xi , x j ) ∈ V × V (such that xi = x j ) and the covariance condition for all unordered pairs {xi , x j } ⊆ V . [sent-478, score-0.335]

54 ) Since the covariance matrix Ck of an experiment Ek contains the experimental effects for all x pairs (xi , x j ) with xi ∈ Jk and x j ∈ Uk , each experiment generates mk = |Jk | × |Uk | constraints of the form of Equation 16. [sent-497, score-0.576]

55 ) We thus have a matrix equation T b = t, (17) where T is a ((∑K mk ) × (n2 − n))-matrix of (measured) experimental effects, b is the (n2 − n)k=1 vector of unknown b ji and t is a (∑K mk )-ary vector corresponding to the (measured) experimental k=1 effects on the left-hand side of Equation 16. [sent-503, score-0.361]

56 , Equation 16) only includes unknowns of the type bu• , corresponding to edge-coefficients for edges into some node xu ∈ Uk , we can rearrange the equations such that the system of equations can be presented in the following form      T11 b1 t1   b2    t2  T22      (18)  . [sent-507, score-0.347]

57 Instead of solving the equation system in Equation 17 with (n2 − n) unknowns, Equation 18 allows us to separate the system into n blocks each constraining direct effects bu• into a different xu . [sent-517, score-0.406]

58 For example, in the case of the experiment intervening on Jk = {x1 , x2 } of the 4-variable model in Figure 3, we obtain the following experimental covariance matrix:   1 0 t(x1 x3 ||{x1 , x2 }) t(x1 x4 ||{x1 , x2 })  0 1 t(x2 x3 ||{x1 , x2 }) t(x2 x4 ||{x1 , x2 })  . [sent-520, score-0.335]

59 When the covariance condition is not satisfied for a particular pair, then the covariance of the disturbances for that pair remains undefined. [sent-537, score-0.338]

60 One can take a more conservative approach and treat any b jk as undetermined for all k whenever there exists an i such that the pair condition is not fulfilled for the ordered pair (xi , x j ). [sent-560, score-0.679]

61 Similarly, the fifth step of the algorithm implements a conservative condition for the identifiability of the covariance matrix: covariance σi j can be treated as determined if the covariance condition is satisfied for the pair {xi , x j } and the direct effects B{xi ,x j },V are determined. [sent-562, score-0.514]

62 ,K , determine which ordered pairs of variables satisfy the pair condition and which pairs of variables satisfy the covariance condition. [sent-582, score-0.365]

63 x (b) From the estimated covariance matrix, extract the experimental effects t(xi xu ||Jk ) for all (xi , xu ) ∈ Jk × Uk . [sent-585, score-0.775]

64 (c) For each pair (xi , xu ) ∈ Jk × Uk add an equation bui + ∑ t(xi x j ||Jk )bu j = t(xi xu ||Jk ) x j ∈Uk \{xu } into the system Tb = t. [sent-586, score-0.631]

65 Output the estimated model (B, Σe ), a list of ordered pairs of variables for which the pair condition is not satisfied, and a list of pairs of variables for which the covariance condition is not satisfied. [sent-593, score-0.417]

66 experimental effects or the entire covariance matrix for union- or intersection7 experiments of the available experiments even if the set of experiments does not satisfy the identifiability conditions. [sent-594, score-0.408]

67 , the set of four experiments on six variables above versus a set of six experiments each intervening on a single variable), the sequence of experiments intervening on multiple variables simultaneously will provide a better estimate of the underlying model even if the total sample size is the same. [sent-632, score-0.373]

68 linear acyclic models without latent variables, linear cyclic models without latent variables, linear acyclic models with latent variables, linear cyclic models with latent variables, and non-linear acyclic models without latent variables. [sent-666, score-0.517]

69 We can estimate the values of the variables xu such that u = i, j using the interpretation of the experimental effects as regression coefficients: i, xu j,ko = t(xi xu ||{xi , x j }) · xii,ko + t(x j j,ko xu ||{xi , x j }) · x j . [sent-810, score-1.236]

70 Following Lauritzen and Richardson (2002) we refer to this most common interpretation of cyclic models as the deterministic equilibrium interpretation, since the value of the observed variables x at equilibrium is a deterministic function of the disturbances e. [sent-829, score-0.417]

71 However, interventions needn’t be “surgical” in this sense, but could instead only add an additional influence to the intervened variable without breaking the relations between the intervened variable and its causal parents. [sent-855, score-0.464]

72 Assuming that the influence of the soft interventions on the intervened variables is known, that is, that c is measured, and that multiple simultaneous soft interventions are performed independently, it can be shown that one can still determine the experimental effects of the intervened variables. [sent-860, score-0.634]

73 Lastly, it is worth noting that the LLC-Algorithm presented here uses the measured experimental effects t(xi xu ||J ) to linearly constrain the unknown direct effects b ji of B. [sent-865, score-0.623]

74 There may be circumstances in which it might be beneficial to instead use the experimental effects to linearly constrain the total effects t(xi xu ). [sent-866, score-0.571]

75 Given an experiment Ek = (Jk , Uk ), the linear constraint of the measured experimental effects on the unknown total effects t(xi xu ) is then given by t(xi xu ) = t(xi xu ||Jk ) + ∑ t(xi x j )t(x j xu ||Jk ). [sent-869, score-1.404]

76 Recall that the total effect corresponds to the experimental effect in the single-intervention experiment where only the cause is subject to intervention, that is, t(xi xu ) = t(xi xu ||{xi }). [sent-875, score-0.65]

77 The ¯x x x x centering of Equation 27 implies that instead of randomizing the intervened variables in Jk with mean (µk )Jk and covariance (Σk )Jk Jk , the centered variables are considered to be randomized with c c ¯c mean (µk )Jk = (µk − µ0 )Jk and covariance (Σk )Jk Jk = (Σk )Jk Jk . [sent-911, score-0.451]

78 The theory in the paper can be used to estimate the direct effects matrix B and covariance matrix Σe , as the data covariance matrices are independent of the mean of the disturbances. [sent-917, score-0.355]

79 1 Weak Stability ˜ ˜ We show that if the full model (B, Σe ) is weakly stable then the marginalized model (B, Σe ) is also ˜ ˜ Σe ) is weakly unstable, thus there exists an weakly stable. [sent-946, score-0.333]

80 V Jk V Jk (28) (29) (30) (31) The goal is to derive Equation 31, which means that both models produce the same experimental ˜ ˜ effects from xi ∈ Jk to xu ∈ Uk . [sent-957, score-0.495]

81 If xi ∈ Jk we have that Uk Ui = 0n×n , then ˜ ˜ Uk B = Uk (I − bii Ui )B + bii Uk Ui = Uk B ˜ and Uk Bv = Uk Bv = v. [sent-983, score-0.347]

82 Alternatively if xi ∈ Uk , we have that Uk Ui = Ui , then ˜ Uk Bv = Uk (I − bii Ui )Bv + bii Uk Ui v ||Multiplication of diagonal matrices commutes ˜ = (I − bii Ui )Uk Bv + bii Uk Ui v = (I − bii Ui )v + bii Ui v = v. [sent-984, score-0.931]

83 First, if variable xi ∈ Jk , then Uk Ui = 0n×n , Uk B = Uk B (as shown above) and ˜ Uk Σe Uk = Uk (I + bii bii Ui )Σe (I + Ui )T Uk = Uk Σe Uk . [sent-989, score-0.347]

84 1 − bii 1 − bii 3429 H YTTINEN , E BERHARDT AND H OYER The covariance matrices are trivially equal: ˜x ˜ ˜ ˜ Ck = (I − Uk B)−1 (Jk + Uk Σe Uk )(I − Uk B)−T = (I − Uk B)−1 (Jk + Uk Σe Uk )(I − Uk B)−T = Ck . [sent-990, score-0.381]

85 commutes 1 − bii 1 − bii bii bii ˜ Ui )Σe (I + Ui )T Uk )(I − Uk B)−T +Uk (I + 1 − bii 1 − bii bii bii ˜ ˜ Ui )(Jk + Uk Σe Uk )(I + Ui )T (I − Uk B)−T ||id. [sent-994, score-1.168]

86 Derivation of Equation 13 Lemma 7 (Marginalization) showed that weak stability and experimental effects from an intervened variable xi ∈ Jk to an observed variable xu ∈ Uk are preserved (as part of the covariance matrix) when some variables in Uk are marginalized. [sent-997, score-0.83]

87 Then, it is sufficient to show that Equation 13 applies in a weakly stable model where variables Uk \ {x j , xu } are marginalized. [sent-998, score-0.431]

88 Examine experiment Ek = (Jk , Uk ) where Uk = {x j , xu } in the marginalized model (B, Σe ). [sent-1000, score-0.429]

89 The experimental effects in the experiment intervening on Jk ∪ {x j } are just the direct effects t(xi xu ||Jk ∪ {x j }) = bui and t(x j xu ||Jk ∪ {x j }) = bu j . [sent-1001, score-1.094]

90 1 Generalizations of Equation 13 Equation 13 can be generalized to relate some experimental effects in Ek = (Jk , Uk ) to some experimental effects in Ek∪l = (Jk ∪ Jl , Uk ∩ Ul ) by applying Equation 13 iteratively: t(xi xu ||Jk ) = t(xi ∑ xu ||Jk ∪ Jl ) + t(xi x j ||Jk )t(x j xu ||Jk ∪ Jl ). [sent-1007, score-1.126]

91 Another way of writing the generalization relates some experimental effects in Ek = (Jk , Uk ) to experimental effects in Ek∩l = (Jk ∩ Jl , Uk ∪ Ul ): t(xi xu ||Jk ∩ Jl ) = t(xi xu ||Jk ) + ∑ t(xi x j ||Jk ∩ Jl )t(x j xu ||Jk ). [sent-1009, score-1.126]

92 For each pair (xk , xu ) with xk ∈ K and xu ∈ O we can form an equation of the form of Equation 34 using experimental effects from experiment Ek : t(xk xu ||Jk ∪ Jl ) + ∑ t(xk x j ||Jk )t(x j xu ||Jk ∪ Jl ) = t(xk xu ||Jk ). [sent-1013, score-1.602]

93 x Similarly, equations can be formed for all pairs (xk , xu ) with xk ∈ L and xu ∈ O using experimental effects from experiment El . [sent-1015, score-0.841]

94 For pairs (xk , xu ) with xk ∈ I and xu ∈ O , equations could be formed using the experimental effects from either experiments, but it turns out that only equations using the experimental effects of experiment Ek are needed. [sent-1016, score-1.07]

95 Earlier we showed that experimental effects are equal when x j is intervened on, this holds in particular for experiment (Jk ∪ L , Uk \ L ). [sent-1047, score-0.423]

96 By Lemma 9 (Union/Intersection Experiment) the effects of an intersection experiment Ek are defined by the experimental effects of the two original experiments, so the experimental effects must be equal in experiment Ek . [sent-1048, score-0.709]

97 Say we have conducted experiment Ek observing covariance matrix Ck and experiment El observing covariance matrix Cl . [sent-1067, score-0.414]

98 x To predict the whole covariance matrix in the intersection experiment, we need the passive observational data covariance matrix C0 in addition to the observations in experiments Ek and El . [sent-1074, score-0.34]

99 In an arbitrary experiment Ek , equations for all pairs (xi , xu ) with xi ∈ Jk and xu ∈ Uk , can be represented neatly in matrix notation: B{xu }Jk + B{xu }(Uk \{xu }) (Tk )(Uk \{xu })Jk x (B{xu }Jk )T + ((Tk )(Uk \{xu })Jk )T (B{xu }(Uk \{xu }) )T x = (Tk ){xu }Jk x ⇔ = ((Tk ){xu }Jk )T . [sent-1085, score-0.725]

100 As we considered arbitrary xu ∈ O , the same procedure can be repeated for each xu ∈ O . [sent-1099, score-0.492]


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