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)

Over the last two decades, a fundamental outline of a theory of causal inference has emerged. However, this theory does not consider the following problem. Sometimes two or more measured variables are deterministic functions of one another, not deliberately, but because of redundant measurements. In these cases, manipulation of an observed defined variable may actually be an ambiguous description of a manipulation of some underlying variables, although the manipulator does not know that this is the case. In this article we (...) revisit the question of precisely characterizing conditions and assumptions under which reliable inference about the effects of manipulations is possible, even when the possibility of “ambiguous manipulations” is allowed. (shrink)

We clarify the status of the so-called causal minimality condition in the theory of causal Bayesian networks, which has received much attention in the recent literature on the epistemology of causation. In doing so, we argue that the condition is well motivated in the interventionist (or manipulability) account of causation, assuming the causal Markov condition which is essential to the semantics of causal Bayesian networks. Our argument has two parts. First, we show that the causal minimality condition, rather than an (...) add-on methodological assumption of simplicity, necessarily follows from the substantive interventionist theses, provided that the actual probability distribution is strictly positive. Second, we demonstrate that the causal minimality condition can fail when the actual probability distribution is not positive, as is the case in the presence of deterministic relationships. But we argue that the interventionist account still entails a pragmatic justification of the causal minimality condition. Our argument in the second part exemplifies a general perspective that we think commendable: when evaluating methods for inferring causal structures and their underlying assumptions, it is relevant to consider how the inferred causal structure will be subsequently used for counterfactual reasoning. (shrink)

While companies are increasingly convinced of the relevance of CSR, many are still struggling to define their responsibility. Part of the answer to this question can be found in the dual approach towards CSR. The authors unravel the concept of CSR into two components: responsibility and responsiveness. Regarding the firm's responsiveness towards society, companies can adopt two positions. They might adopt an inside‐out approach towards CSR and emphasise their own ambitions. Alternatively, they can approach stakeholders from an outside‐in perspective, wherein (...) stakeholder claims dominate. The authors argue that both perspectives are inadequate with regard to complex societal issues. Therefore, a third approach towards societal interaction is proposed. This is characterised by a process of collective sensemaking, aimed at understanding the issue and defining responsibilities. (shrink)

Harmonic Grammar (HG) and Optimality Theory (OT) are closely related formal frameworks for the study of language. In both, the structure of a given language is determined by the relative strengths of a set of constraints. They differ in how these strengths are represented: as numerical weights (HG) or as ranks (OT). Weighted constraints have advantages for the construction of accounts of language learning and other cognitive processes, partly because they allow for the adaptation of connectionist and statistical models. HG (...) has been little studied in generative linguistics, however, largely due to influential claims that weighted constraints make incorrect predictions about the typology of natural languages, predictions that are not shared by the more popular OT. This paper makes the case that HG is in fact a promising framework for typological research, and reviews and extends the existing arguments for weighted over ranked constraints. (shrink)

Health and illness are not objective concepts but rather issues which depend upon cultural and religious traditions. In Islam there are two traditional approaches to these concepts: prophetic medicine and the medicine of the Islamic Middle Ages, which was strongly influenced by Galen and Hippocrates. Tody, Islam is increasingly looking at modern western orthodox medicine. With regard to Muslim patients, however, it is still necessary to take into account the peculiarities of their religious traditions.

Clark Glymour, Richard Scheines, Peter Spirtes and Kevin Kelly. Discovering Causal Structure: Artifical Intelligence, Philosophy of Science and Statistical Modeling.

A graphical model is a graph that represents a set of conditional independence relations among the vertices (random variables). The graph is often given a causal interpretation as well. I describe how graphical causal models can be used in an algorithm for constructing partial information about causal graphs from observational data that is reliable in the large sample limit, even when some of the variables in the causal graph are unmeasured. I also describe an algorithm for estimating from observational data (...) (in some cases) the total effect of a given variable on a second variable, and theoretical insights into fundamental limitations on the possibility of certain causal inferences by any algorithm whatsoever, and regardless of sample size. (shrink)

In the causal inference framework of Spirtes, Glymour, and Scheines, inferences about causal relationships are made from samples from probability distributions and a number of assumptions relating causal relations to probability distributions. The most controversial of these assumptions is the Causal Faithfulness Assumption, which roughly states that if a conditional independence statement is true of a probability distribution generated by a causal structure, it is entailed by the causal structure and not just for particular parameter values. In this paper (...) we show that the addition of the Causal Faithfulness Assumption plays three quite different roles in the SGS framework: it reduces the degree of underdetermination of causal structure by probability distribution; computationally, it justifies reliable causal inference algorithms that would otherwise have to be slower in order to be reliable; and statistically, it implies that those algorithms reliably obtain the correct answer at smaller sample sizes than would otherwise be the case. We also consider a number of variations on the Causal Faithfulness Assumption, and show how they affect each of these three roles. (shrink)

We have examined only a few of the basic questions about causal inference that result from Reichenbach's two principles. We have not considered what happens when the probability distribution is a mixture of distributions from different causal structures, or how unmeasured common causes can be detected, or what inferences can reliably be drawn about causal relations among unmeasured variables, or the exact advantages that experimental control offers. A good deal is known about these questions, and there is a good deal (...) more to find out. (shrink)

While companies are increasingly convinced of the relevance of CSR, many are still struggling to define their responsibility. Part of the answer to this question can be found in the dual approach towards CSR. The authors unravel the concept of CSR into two components: responsibility and responsiveness. Regarding the firm's responsiveness towards society, companies can adopt two positions. They might adopt an inside‐out approach towards CSR and emphasise their own ambitions. Alternatively, they can approach stakeholders from an outside‐in perspective, wherein (...) stakeholder claims dominate. The authors argue that both perspectives are inadequate with regard to complex societal issues. Therefore, a third approach towards societal interaction is proposed. This is characterised by a process of collective sensemaking, aimed at understanding the issue and defining responsibilities. (shrink)

It is well known that there may be many causal explanations that are consistent with a given set of data. Recent work has been done to represent the common aspects of these explanations into one representation. In this paper, we address what is less well known: how do the relationships common to every causal explanation among the observed variables of some DAG process change in the presence of latent variables? Ancestral graphs provide a class of graphs that can encode conditional (...) independence relations that arise in DAG models with latent and selection variables. In this paper we present a set of orientation rules that construct the Markov equivalence class representative for ancestral graphs, given a member of the equivalence class. These rules are sound and complete. We also show that when the equivalence class includes a DAG, the equivalence class representative is the essential graph for the said DAG. (shrink)

S There is a long tradition of representing causal relationships by directed acyclic graphs (Wright, 1934 ). Spirtes ( 1994), Spirtes et al. ( 1993) and Pearl & Verma ( 1991) describe procedures for inferring the presence or absence of causal arrows in the graph even if there might be unobserved confounding variables, and/or an unknown time order, and that under weak conditions, for certain combinations of directed acyclic graphs and probability distributions, are asymptotically, in sample size, consistent. (...) These results are surprising since they seem to contradict the standard statistical wisdom that consistent estimators of causal effects do not exist for nonrandomised studies if there are potentially unobserved confounding variables. We resolve the apparent incompatibility of these views by closely examining the asymptotic properties of these causal inference procedures. We show that the asymptotically consistent procedures are ‘pointwise consistent’, but ‘uniformly consistent’ tests do not exist. Thus, no finite sample size can ever be guaranteed to approximate the asymptotic results. We also show the nonexistence of valid, consistent confidence intervals for causal effects and the nonexistence of uniformly consistent point estimators. Our results make no assumption about the form of the tests or estimators. In particular, the tests could be classical independence tests, they could be Bayes tests or they could be tests based on scoring methods such as  or . The implications of our results for observational studies are controversial and are discussed briefly in the last section of the paper. The results hinge on the following fact: it is possible to find, for each sample size n, distributions P and Q such that P and Q are empirically indistinguishable and yet P and Q correspond to different causal effects. (shrink)

Worst case complexity analyses of algorithms are sometimes held to be less informative about the real difficulty of computation than are expected complexity analyses. We show that the two most common representations of problem solving in cognitive science each admit aigorithms that have constant expected complexity, and for one of these representations we obtain constant expected complexity bounds under a variety of probability measures.

Previous asymptotically correct algorithms for recovering causal structure from sample probabilities have been limited even in sparse graphs to a few variables. We describe an asymptotically correct algorithm whose complexity for fixed graph connectivity increases polynomially in the number of vertices, and may in practice recover sparse graphs with several hundred variables. From..

Whenever the use of non-experimental data for discovering causal relations or predicting the outcomes of experiments or interventions is contemplated, two difficulties are routinely faced. One is the problem of latent variables, or confounders: factors influencing two or more measured variables may not themselves have been measured or recorded. The other is the problem of sample selection bias: values of the variables or features under study may themselves influence whether a unit is included in the data sample.

We describe anytime search procedures that (1) find disjoint subsets of recorded variables for which the members of each subset are d-separated by a single common unrecorded cause, if such exists; (2) return information about the causal relations among the latent factors so identified. We prove the procedure is point-wise consistent assuming (a) the causal relations can be represented by a directed acyclic graph (DAG) satisfying the Markov Assumption and the Faithfulness Assumption; (b) unrecorded variables are not caused by recorded (...) variables; and (c) dependencies are linear. We compare the procedure with standard approaches over a variety of simulated structures and sample sizes, and illustrate its practical value with brief studies of social science data sets. Finally, we consider generalizations for non-linear systems. Keywords: latent variable models, causality, graphical models.. (shrink)

Spirtes, Glymour and Scheines [Causation, Prediction, and Search Springer] described a pointwise consistent estimator of the Markov equivalence class of any causal structure that can be represented by a directed acyclic graph for any parametric family with a uniformly consistent test of conditional independence, under the Causal Markov and Causal Faithfulness assumptions. Robins et al. [Biometrika 90 491–515], however, proved that there are no uniformly consistent estimators of Markov equivalence classes of causal structures under those assumptions. Subsequently, Kalisch and (...) B¨uhlmann [J. Mach. Learn. Res. 8 613–636] described a uniformly consistent estimator of the Markov equivalence class of a linear Gaussian causal structure under the Causal Markov and Strong Causal Faithfulness assumptions. However, the Strong Faithfulness assumption may be false with high probability in many domains. We describe a uniformly consistent estimator of both the Markov equivalence class of a linear Gaussian causal structure and the identifiable structural coefficients in the Markov equivalence class under the Causal Markov assumption and the considerably weaker k-Triangle-Faithfulness assumption. (shrink)

Much of the recent work on the epistemology of causation has centered on two assumptions, known as the Causal Markov Condition and the Causal Faithfulness Condition. Philosophical discussions of the latter condition have exhibited situations in which it is likely to fail. This paper studies the Causal Faithfulness Condition as a conjunction of weaker conditions. We show that some of the weaker conjuncts can be empirically tested, and hence do not have to be assumed a priori. Our results lead to (...) two methodologically significant observations: (1) some common types of counterexamples to the Faithfulness condition constitute objections only to the empirically testable part of the condition; and (2) some common defenses of the Faithfulness condition do not provide justification or evidence for the testable parts of the condition. It is thus worthwhile to study the possibility of reliable causal inference under weaker Faithfulness conditions. As it turns out, the modification needed to make standard procedures work under a weaker version of the Faithfulness condition also has the practical effect of making them more robust when the standard Faithfulness condition actually holds. This, we argue, is related to the possibility of controlling error probabilities with finite sample size (“uniform consistency”) in causal inference. (shrink)

In the last several decades, a confluence of work in the social sciences, philosophy, statistics, and computer science has developed a theory of causal inference using directed graphs. This theory typically rests either explicitly or implicitly on two major assumptions.

This paper introduces a class of graphical independence models that is closed under marginalization and conditioning but that contains all DAG independence models. This class of graphs, called maximal ancestral graphs, has two attractive features: there is at most one edge between each pair of vertices; every missing edge corresponds to an independence relation. These features lead to a simple parameterization of the corresponding set of distributions in the Gaussian case.

Reflectance spectroscopy is a standard tool for studying the mineral composition of rock and soil samples and for remote sensing of terrestrial and extraterrestrial surfaces. We describe research on automated methods of mineral identification from reflectance spectra and give evidence that a simple algorithm, adapted from a well-known search procedure for Bayes nets, identifies the most frequently occurring classes of carbonates with reliability equal to or greater than that of human experts. We compare the reliability of the procedure to the (...) reliability of several other automated methods adapted to the same purpose. Evidence is given that the procedure can be applied to some other mineral classes as well. Since the procedure is fast with low memory requirements, it is suitable for on- board scientific analysis by orbiters or surface rovers. (shrink)

Data analysis that merely fits an empirical covariance matrix or that finds the best least squares linear estimator of a variable is not of itself a reliable guide to judgements about policy, which inevitably involve causal conclusions. The policy implications of empirical data can be completely reversed by alternative hypotheses about the causal relations of variables, and the estimates of a particular causal influence can be radically altered by changes in the assumptions made about other dependencies.2 For these reasons, one (...) of the common aims of empirical research in the.. (shrink)

Researchers routinely face the problem of inferring causal relationships from large amounts of data, sometimes involving hundreds of variables. Often, it is the causal relationships between "latent" (unmeasured) variables that are of primary interest. The problem is how causal relationships between unmeasured variables can be inferred from measured data. For example, naval manpower researchers have been asked to infer the causal relations among psychological traits such as job satisfaction and job challenge from a data base in which neither trait is (...) measured directly, but in which answers to interview questions are plausibly associated with each trait. By combining background knowledge with an algorithm that searches for causal structure among the unobserved variables, we have created a tool that can reliably extract useful causal information about latent variables from large data bases. In what follows we describe the class of causal models to which our.. (shrink)

Peter Spirtes, Clark Glymour and Richard Scheines. Causality From Probability.

Peter Spirtes and Thomas Verma. Equivalence of Causal Models with Latent Variables.

Most causal discovery algorithms in the literature exploit an assumption usually referred to as the Causal Faithfulness or Stability Condition. In this paper, we highlight two components of the condition used in constraint-based algorithms, which we call “Adjacency-Faithfulness” and “Orientation- Faithfulness.” We point out that assuming Adjacency-Faithfulness is true, it is possible to test the validity of Orientation- Faithfulness. Motivated by this observation, we explore the consequence of making only the Adjacency-Faithfulness assumption. We show that the familiar PC algorithm has (...) to be modified to be correct under the weaker, Adjacency-Faithfulness assumption. The modified algorithm, called Conservative PC (CPC), checks whether Orientation- Faithfulness holds in the orientation phase, and if not, avoids drawing certain causal conclusions the PC algorithm would draw. Howtion: ever, if the stronger, standard causal Faith-. (shrink)

The Fast Casual Inference (FCI) algorithm searches for features common to observationally equivalent sets of causal directed acyclic graphs. It is correct in the large sample limit with probability one even if there is a possibility of hidden variables and selection bias. In the worst case, the number of conditional independence tests performed by the algorithm grows exponentially with the number of variables in the data set. This affects both the speed of the algorithm and the accuracy of the algorithm (...) on small samples, because tests of independence conditional on large numbers of variables have very low power. In this paper, I prove that the FCI algorithm can be interrupted at any stage and asked for output. The output from the interrupted algorithm is still correct with probability one in the large sample limit, although possibly less informative (in the sense that it answers “Can’t tell” for a larger number of questions) than if the FCI algorithm had been allowed to continue uninterrupted. (shrink)

if and only if for every W in V, W is independent of the set of all its non-descendants conditional on the set of its parents. One natural question that arises with respect to DAGs is when two DAGs are “statistically equivalent”. One interesting sense of “statistical equivalence” is “d-separation equivalence” (explained in more detail below.) In the case of DAGs, d-separation equivalence is also corresponds to a variety of other natural senses of statistical equivalence (such as representing the same (...) set of distributions). Theorems characterizing d-separation equivalence for directed acyclic graphs and that can be used as the basis for polynomial time algorithms for checking d-separation equivalence were provided by Verma and Pearl (1990), and Frydenberg (1990). The question we will examine is how to extend these results to cases where a DAG may have latent (unmeasured) variables or selection bias (i.e. some of the variables in the DAG have been conditioned on.) D-separation equivalence is of interest in part because there are algorithms for constructing DAGs with latent variables and selection bias that are based on observed conditional independence relations. For this class of algorithms, it is impossible to determine which of two d-separation equivalent causal structures generated a given probability distribution, given only the set of conditional independence and dependence relations true of the observed distribution. We will describe a polynomial (in the number of vertices) time algorithm for determining when two DAGs which may have latent variables or selection bias are d-separation equivalent. (shrink)

Linear structural equation models (SEMs) are widely used in sociology, econometrics, biology, and other sciences. A SEM (without free parameters) has two parts: a probability distribution (in the Normal case specified by a set of linear structural equations and a covariance matrix among the “error” or “disturbance” terms), and an associated path diagram corresponding to the functional composition of variables specified by the structural equations and the correlations among the error terms. It is often thought that the path diagram is (...) nothing more than a heuristic device for illustrating the assumptions of the model. However, in this paper, we will show how path diagrams can be used to solve a number of important problems in structural equation modelling. (shrink)

Peter Spirtes, Clark Glymour, Richard Scheines, Christopher Meek, S. Fineberg, E. Slate. Prediction and Experimental Design with Graphical Causal Models.

Les conferences dont se compose le present ouvrage furent ecrites au profit de jeunes etudiants en philosophie. Par le terme de Platonisme ne s'entend certes pas ici un quelconque Neoplatonisme mais les seuls principes fondateurs de la doctrine de Platon, doctrine que nous avons tente d'observer en un rapport direct avec son auteur tel qu'il se presente au travers de ses propres ecrits. Plongeant aux racines antiques avec une decision toute nitzscheenne, Pater en revient pourtant conforte dans sa distance: (...) pour lui l'esthetique forme bien le primum mobile de l'histoire de l'esprit. Cet ouvrage permet, bien mieux qu'un manuel, d'acquerir une solide connaissance de Platon et d'interessants elements touchant aussi ses deux antipodes: les presocratiques et, comme nous le suggerons, Nietzsche. (shrink)

Studies in the History of the Renaissance is a highly influential defence of aestheticism. Pater redefined the practice of criticism through his readings of some of the paintings, sculptures, and poems of the Renaissance, and shocked contemporaries for sponsoring a hedonistic ethic with his infamous 'Conclusion'.

Peter Spirtes. Building Causal Graphs from Statistical Data in the Presence of Latent Variables.

Peter Spirtes. Conditional Independence in Directed Cyclical Graphical Models Representing Feedback or Mixtures.

Peter Spirtes. Conditional Independence in Directed Cyclic Graphical Models for Feedback.

Peter Spirtes and Clark Glymour. Casual Structure Among Measured Variables Preserved with Unmeasured Variables.

Peter Spirtes. Calculating TETRAD Constraints Implied by Directed Acyclic Graphs.