David Danks

In this essay, we examine the use of resting state fMRI data for psychological inferences. We argue that resting state studies hold the paired promises of discovering novel functional brain networks, and of avoiding some of the limitations of task-based fMRI. However, we argue that the very features of experimental design that enable resting state fMRI to support exploratory science also generate a novel confound. We argue that seemingly key features of resting state functional connectivity networks may be artefacts resulting from sampling a ‘mixture distribution’ of diverse brain networks active at different times during the scan. We explore the consequences of this ‘mixture view’ for attempts to theorize about the cognitive or psychological functions of resting state networks, as well as the value of exploratory experiments.

Many investigations into the world, including philosophical ones, aim to discover causal knowledge, and many experimental methods have been developed to assist in causal discovery. More recently, algorithms have emerged that can also learn causal structure from purely or mostly observational data, as well as experimental data. These methods have started to be applied in various philosophical contexts, such as debates about our concepts of free will and determinism. This paper provides a “user's guide” to these methods, though not in the sense of specifying exact button presses in a software package. Instead, we explain the larger “pipeline” within which these methods are used and discuss key steps in moving from initial research idea to validated causal structure.

Many approaches to evidence amalgamation focus on relatively static information or evidence: the data to be amalgamated involve different variables, contexts, or experiments, but not measurements over extended periods of time. However, much of scientific inquiry focuses on dynamical systems; the system’s behavior over time is critical. Moreover, novel problems of evidence amalgamation arise in these contexts. First, data can be collected at different measurement timescales, where potentially none of them correspond to the underlying system’s causal timescale. Second, missing variables have a significantly different impact on time series measurements than they do in the traditional static setting; in particular, they make causal and structural inference much more difficult. In this paper, we argue that amalgamation should proceed by integrating causal knowledge, rather than at the level of “raw” evidence. We defend this claim by first outlining both of these problems, and then showing that they can be solved only if we operate on causal structures. We therefore must use causal discovery methods that are reliable given these problems. Such methods do exist, but their successful application requires careful consideration of the problems that we highlight.

We make constant use of causal beliefs in our everyday lives without giving much thought to the source of those beliefs, even for situations about which we have no specific prior causal knowledge. We can ask two distinct types of questions about these causal judgments: descriptive questions and normative questions. The primary goal of this dissertation is to apply normative research on causal judgment to our descriptive theories. ;I begin this dissertation by describing the primary results of research on the normative question: the framework of Bayesian networks, and algorithms that provably extract maximal causal information from observations and interventions in the environment. I then show that we can use the framework of Bayesian networks to represent the three major descriptive theories of causal judgment. The three theories are not directly comparable, however, since one of them is algorithmic, while the other two are computational. Therefore, I provide a fully general characterization of the Rescorla-Wagner model. ;With this computational description of the Rescorla-Wagner model in hand, we can compare all three of the theories against the known experimental data. Unfortunately, the experimental data has all been obtained using one particular experimental methodology, which contains serious problems. In addition to critiquing the currently dominant methodology, I provide a "proof of concept" of a different methodology that does not face these problems. ;More importantly, the psychological theories all focus on parameter estimation in a fixed causal structure, rather than learning the actual structure. Therefore, I consider the experimental question: can people learn complex causal structures? The data from those experiments reveal that people appear to use a wide array of learning strategies. The epistemology of our causal beliefs is substantially more complex than has previously been thought. ;Finally, at the end of this dissertation, I step back and examine the implications of these experimental results for descriptive theories of causal judgment. I also point towards several open research questions, both descriptive and normative, raised by the work in this dissertation.

Our best sciences are frequently held to be one way, perhaps the optimal way, to learn about the world’s higher-level ontology and structure. I first argue that which scientific theory is “best” depends in part on our goals or purposes. As a result, it is theoretically possible to have two scientific theories of the same domain, where each theory is best for some goal, but where the two theories posit incompatible ontologies. That is, it is possible for us to have goal-dependent pluralism in our scientific ontologies. This ontological pluralism arises simply from our inability to directly know the world’s objects, rather than any particular claims about our cognitive limits, values, or social structures. I then present two case studies in which this possibility actually occurs—one based on simulations and theoretical analyses of constructed causal systems, and one from actual scientific investigations into the proper ontology for ocean regions.

Research on adaptive rationality has focused principally on inference, judgment, and decision-making that lead to behaviors and actions. These processes typically require cognitive representations as input, and these representations must presumably be acquired via learning. Nonetheless, there has been little work on the nature of, and justification for, adaptively rational learning processes. In this paper, we argue that there are strong reasons to believe that some learning is adaptively rational in the same way as judgment and decision-making. Indeed, overall adaptive rationality can only properly be assessed for pairs of learning and decision processes. We thus present a formal framework for modeling such pairs of cognitive processes, and thereby assessing their adaptive rationality relative to the environment and the agent’s goals. We then use this high-level formal framework on specific cases by demonstrating how natural formal constraints on decision-making can lead to substantive predictions about adaptively rational learning and representation; and characterizing adaptively rational learning for fast-and-frugal one-reason decision-making.

One persistent challenge in scientific practice is that the structure of the world can be unstable: changes in the broader context can alter which model of a phenomenon is preferred, all without any overt signal. Scientific discovery becomes much harder when we have a moving target, and the resulting incorrect understandings of relationships in the world can have significant real-world and practical consequences. In this paper, we argue that it is common (in certain sciences) to have changes of context that lead to changes in the relationships under study, but that standard normative accounts of scientific inquiry have assumed away this problem. At the same time, we show that inference and discovery methods can “protect” themselves in various ways against this possibility by using methods with the novel methodological virtue of “diligence.” Unfortunately, this desirable virtue provably is incompatible with other desirable methodological virtues that are central to reliable inquiry. No scientific method can provide every virtue that we might want

Newsome ((2003). The debate between current versions of covariation and mechanism approaches to causal inference. Philosophical Psychology, 16, 87-107.) recently published a critical review of psychological theories of human causal inference. In that review, he characterized covariation and mechanism theories, the two dominant theory types, as competing, and offered possible ways to integrate them. I argue that Newsome has misunderstood the theoretical landscape, and that covariation and mechanism theories do not directly conflict. Rather, they rely on distinct sets of reliable indicators of causation, and focus on different types of causation (type vs. token). There are certainly debates in the research field, but the theoretical landscape is not as fractured as Newsome suggests, and a potential unifying framework has already emerged using causal Bayes nets. Philosophical work on causal epistemology matters for psychologists, but not in the way Newsome suggests.

Standard time series structure learning algorithms assume that the measurement timescale is approximately the same as the timescale of the underlying system. In many scientific contexts, however, this assumption is violated: the measurement timescale can be substantially slower than the system timescale. This assumption violation can lead to significant learning errors. In this paper, we provide a novel learning algorithm to extract systemtimescale structure from measurement data that undersample the underlying system. We employ multiple algorithmic optimizations that exploit the problem structure in order to achieve computational tractability. The resulting algorithm is highly reliable at extracting system-timescale structure from undersampled data

Debates about the moral permissibility of mass electronic surveillance often turn on whether consequentialist considerations legitimately trump relevant deontological rights and principles. In order to establish such overriding consequences, many proponents of mass surveillance employ a modern analogue of Pascal’s wager: they contend that the consequences of no surveillance are so severe that any probability of such outcomes legitimates the abrogation of the relevant rights. In this paper, I briefly review Pascal’s original wager about whether to live a pious life, including two classes of objections that were almost immediately leveled against his argument. I then show that analogues of those objections apply straightforwardly to the modern versions of Pascal’s wager. Mass electronic surveillance might be ethically permissible or even obligatory in some circumstances, but the details matter in ways that are systematically ignored or assumed away in a Pascal’s wager-type argument. Careful consideration of the complexities of our modern situation is required to decide whether consequentialist considerations override deontological principles in this domain.

In everyday matters, as well as in law, we allow that someone’s reasons can be causes of her actions, and often are. That correct reasoning accords with Bayesian principles is now so widely held in philosophy, psychology, computer science and elsewhere that the contrary is beginning to seem obtuse, or at best quaint. And that rational agents should learn about the world from energies striking sensory inputs nerves in people—seems beyond question. Even rats seem to recognize the difference between correlation and causation,1 and accordingly make different inferences from passive observation than from interventions. A few statisticians aside,” so do most of us. To square these views with the demands of computability, increasing numbers of psychologists and others have embraced a particular formalization, causal Bayes nets, as an account of human reasoning about and to causal connections.111 Such structures can be used by rational agents, including humans in so far as they are rational, to have degrees of belief in various conceptual contents, which they use to reason to expectations, which are realized or defeated by sensory inputs, which cause them to change their degrees of belief in other contents in accord with Bayes Rule, or some generalization of it. How is all of this supposed to be carried out? l. Representing Causal Structures The causal Bayes net framework adopted by a growing number of psychologists goes like this: Our representations of causal relations are captured in a graphical causal.

Models based on causal capacities, or independent causal influences/mechanisms, are widespread in the sciences. This paper develops a natural mathematical framework for representing such capacities by extending and generalizing previous results in cognitive psychology and machine learning, based on observations and arguments from prior philosophical debates. In addition to its substantial generality, the resulting framework provides a theoretical unification of the widely-used noisy-OR/AND and linear models, thereby showing how they are complementary rather than competing. This unification helps to explain many of the shared cognitive and mathematical properties of those models.

Research on human causal learning has largely focused on strength learning, or on computational-level theories; there are few formal algorithmic models of how people learn causal structure from covariations. We introduce a model that learns causal structure in a local manner via prediction-error learning. This local learning is then integrated dynamically into a unified representation of causal structure. The model uses computationally plausible approximations of rational learning, and so represents a hybrid between the associationist and rational paradigms in causal learning research. We conclude by showing that the model provides a good fit to data from a previous experiment

Structure learning algorithms for graphical models have focused almost exclusively on stable environments in which the underlying generative process does not change; that is, they assume that the generating model is globally stationary. In real-world environments, however, such changes often occur without warning or signal. Real-world data often come from generating models that are only locally stationary. In this paper, we present LoSST, a novel, heuristic structure learning algorithm that tracks changes in graphical model structure or parameters in a dynamic, real-time manner. We show by simulation that the algorithm performs comparably to batch-mode learning when the generating graphical structure is globally stationary, and significantly better when it is only locally stationary

Many different, seemingly mutually exclusive, theories of categorization have been proposed in recent years. The most notable theories have been those based on prototypes, exemplars, and causal models. This chapter provides “representation theorems” for each of these theories in the framework of probabilistic graphical models. More specifically, it shows for each of these psychological theories that the categorization judgments predicted and explained by the theory can be wholly captured using probabilistic graphical models. In other words, probabilistic graphical models provide a lingua franca for these disparate categorization theories, and so we can quite directly compare the different types of theories. These formal results are used to explain a variety of surprising empirical results, and to propose several novel theories of categorization.

It is “well known” that in linear models: (1) testable constraints on the marginal distribution of observed variables distinguish certain cases in which an unobserved cause jointly influences several observed variables; (2) the technique of “instrumental variables” sometimes permits an estimation of the influence of one variable on another even when the association between the variables may be confounded by unobserved common causes; (3) the association (or conditional probability distribution of one variable given another) of two variables connected by a path or pair of paths with a single common vertex (a trek) can be computed directly from the parameter values associated with each edge in the trek; (4) the association of two variables produced by multiple treks can be computed from the parameters associated with each trek; and (5) the independence of two variables conditional on a third implies the corresponding independence of the sums of the variables over all units conditional on the sums over all units of each of the original conditioning variables.

The Rescorla–Wagner model has been a leading theory of animal causal induction for nearly 30 years, and human causal induction for the past 15 years. Recent theories 367) have provided alternative explanations of how people draw causal conclusions from covariational data. However, theoretical attempts to compare the Rescorla–Wagner model with more recent models have been hampered by the fact that the Rescorla–Wagner model is an algorithmic theory, while the more recent theories are all computational. This paper provides a detailed derivation of the long-run behavior of the Rescorla– Wagner model under a wide range of parameters and experimental setups, so that the model can be compared with computational theories. It also shows that the model agrees with competing theories on a wider range of cases than had previously been thought. The paper concludes by showing how recently suggested modifications of the Rescorla–Wagner model impact the long-run behavior of the model.

Causal structure learning from time series data is a major scientific challenge. Existing algorithms assume that measurements occur sufficiently quickly; more precisely, they assume that the system and measurement timescales are approximately equal. In many scientific domains, however, measurements occur at a significantly slower rate than the underlying system changes. Moreover, the size of the mismatch between timescales is often unknown. This paper provides three distinct causal structure learning algorithms, all of which discover all dynamic graphs that could explain the observed measurement data as arising from undersampling at some rate. That is, these algorithms all learn causal structure without assuming any particular relation between the measurement and system timescales; they are thus rate-agnostic. We apply these algorithms to data from simulations. The results provide insight into the challenge of undersampling

It is the height of banality to observe that people, not bullets, fight kinetic wars. The machinery of kinetic warfare is obviously relevant to the conduct of each particular act of warfare, but the reasons for, and meanings of, those acts depend critically on the fact that they are done by humans. Any attempt to understand warfare—its causes, strategies, legitimacy, dynamics, and resolutions—must incorporate humans as an intrinsic part, both descriptively and normatively. Humans from general staff to “boots on the ground” play key roles in all aspects of kinetic warfare, and the literature about it reflects this focus. 2 In contrast, many discussions of cyberwarfare and cyber-conflict focus principally on the technical aspects of machines, systems, and data, 3 and human agents are included only as collateral effects, or as loci of moral responsibility.

Various causal details of the genetic process of translation have been singled out to account for its privileged status as a ‘code'. We explicate the biological uses of coding talk by characterizing a class of special causal processes in which topological properties are the causally relevant ones. This class contains both the process of translation and communication theoretic coding processes as special cases. We propose a formalism in terms of graphs for expressing our theory of biological codes and discuss its utility in understanding biological systems. *Received May 2007; revised May 2008. †To contact the authors, please write to: Department of Philosophy, Baker Hall 135, Carnegie Mellon University, Pittsburgh, PA 15213; e-mail: [email protected] or [email protected].