The Structure and Dynamics of Scientific Theories: A Hierarchical Bayesian Perspective
Author(s): Leah Henderson, Noah D. Goodman, Joshua B. Tenenbaum, and James F. Woodward
Source: Philosophy of Science, Vol. 77, No. 2 (April 2010), pp. 172-200
Published by: The University of Chicago Press on behalf of the Philosophy of Science Association
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The Structure and Dynamics ofScientific Theories: A Hierarchical
Bayesian Perspective*
Leah Henderson, Noah D. Goodman, Joshua B.
Tenenbaum, and James F. Woodward†‡
Hierarchical Bayesian models (HBMs) provide an account of Bayesian inference in ahierarchically structured hypothesis space. Scientific theories are plausibly regarded asorganized into hierarchies in many cases, with higher levels sometimes called ‘paradigms’ and lower levels encoding more specific or concrete hypotheses. Therefore,
HBMs provide a useful model for scientific theory change, showing how higher-level
theory change may be driven by the impact of evidence on lower levels. HBMs capturefeatures described in the Kuhnian tradition, particularly the idea that higher-level
theories guide learning at lower levels. In addition, they help resolve certain issues forBayesians, such as scientific preference for simplicity and the problem of new theories.

1. Introduction. Although there has been considerable disagreement over
specifics, it has been a persistent theme in philosophy of science thatscientific theories are hierarchically structured, with theoretical principles
of an abstract or general nature at higher levels and more concrete or
specific hypotheses at lower levels. This idea has been particularly emphasized by such historically oriented writers as Lakatos (1978), Laudan*Received July 2009; revised October 2009.
†To contact the authors, please write to: Leah Henderson, Massachusetts Instituteof Technology, 77 Massachusetts Avenue, 32D-808, Cambridge, MA 02139; e-mail:lhenders@mit.edu.
‡This work was supported in part by the James S. McDonnell Foundation Causal
Learning Collaborative. Thanks to Zoubin Ghahramani for providing the code that
we modified to produce the results and figures in the section on Bayesian curve fitting.
We are extremely grateful to Charles Kemp for his contributions, especially helpful
discussions of hierarchical Bayesian models in general as well as in connection tophilosophy of science. We thank Alison Gopnik for encouraging and supporting thisproject, and we are grateful to Franz Huber, John Norton, Ken Schaffner, and Jiji
Zhang for reading earlier versions of the manuscript and making helpful criticisms.
Philosophy of Science, 77 (April 2010) pp. 172–200. 0031-8248/2010/7702-0004$10.00
Copyright 2010 by the Philosophy of Science Association. All rights reserved.

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HIERARCHICAL BAYESIAN MODELS

173(1978), and Kuhn (1962), who have used terms such as ‘paradigms’, ‘research programs’, or ‘research traditions’ to refer to higher levels in thehierarchy. In this tradition, the mutual dependence and interactions ofdifferent levels of theory in the process of theory change have been explored in a predominantly qualitative way.
Meanwhile, confirmation theories have tended to ignore the hierarchicalstructure of theories. On a Bayesian view, for example, as in other formal
accounts, scientific theories have typically been regarded as hypotheses inan unstructured hypothesis space of mutually exclusive alternatives, andthere has been a tendency to focus exclusively on confirmation and testingof specific hypotheses.
However, Bayesian models with a hierarchically structured hypothesis
space are now widely used for statistical inference (Gelman et al. 2004)
and have proved particularly fruitful in modeling the development of
individuals’ ‘intuitive theories’ in cognitive science.1 In this article, wesuggest that such hierarchical Bayesian models (HBMs) can be helpful in
illuminating the epistemology of scientific theories.2 They provide a formal
model of theory change at different levels of abstraction and hence help
to clarify how high-level theory change may be rational and evidence
driven. This has been a central topic of debate after the appearance of
Kuhn’s Structure of Scientific Revolutions (1962).
HBMs also help to resolve a number of philosophical worries surrounding Bayesianism. They can explain why logically stronger or simpler
theories may be preferred by scientists and how learning of higher-level
theories is not simply parasitic on learning of lower-level theories but may
play a role in guiding learning of specific theories. They also give a newand more satisfactory Bayesian model of the introduction of new theories.
In this article, we first introduce HBMs in section 2 and argue thatthey capture essential features of the evaluation of scientific theories. The
following three sections explain how HBMs may be used to resolve issues
in Bayesian philosophy of science. Section 3 discusses the objection that
Bayesians cannot account for a preference for logically stronger theories.
Section 4 deals with the Bayesian treatment of simplicity. Section 5 explains how HBMs can overcome many of the problems that the introduction of new theories presents to Bayesians. As well as discussing particular issues, two of these sections also introduce different examples of
HBMs, in order to illustrate the variety of scientific theories to which
1. See Kemp, Griffiths, and Tenenbaum (2004), Mansinghka et al. (2006), Griffiths
and Tenenbaum (2007), Kemp (2007), Tenenbaum, Griffiths, and Nigoyi (2007), andKemp and Tenenbaum (2008).
2. Parallels between intuitive theories and scientific theories are explicitly drawn in
Carey and Spelke (1996), Giere (1996), and Gopnik (1996).

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HBMs may be applicable. Section 4 gives the example of curve fitting,while section 5 shows how HBMs may be used for learning about causal
relations. In the final section, section 6, we consider the implications of
HBMs for some general aspects of theory change.
2. Hierarchical Bayesian Models. The Bayesian model standardly used inphilosophy of science operates with a hypothesis space H, which is justa set of mutually exclusive alternative hypotheses. A ‘prior’ probability
distribution is defined over the hypothesis space p(T ), for T ! H. On
observing data D, the prior distribution is updated to the posterior distribution according to the rule of conditionalization:p(T ) r p(TFD).

(1)

The posterior distribution can be calculated using Bayes’s rule to bep(TFD) p

p(T )p(DFT )
.
p(D)

(2)

Here, p(DFT ) is the ‘likelihood’ of theory T, given data D, and p(D) isthe prior probability of the observed data D that serves as a normalization
constant ensuring that p(TFD) is a valid probability distribution that sums
to 1.3In an HBM, the hypothesis space has a hierarchical structure. Givena particular theory at the i ! 1th level, one has a hypothesis space Hi ofhypotheses or theories at the ith level that are treated as mutually exclusivealternatives. One defines a prior probability for a theory Ti ! Hi at leveli that is conditional on the theory at the next level up, as p(TFT
i i!1 ) for
Ti ! Hi and Ti!1 ! Hi!1. This distribution is updated by conditionalizationin the usual way to give a posterior distribution, again conditional on
Ti!1,
p(TFT
Ti!1 ).
i i!1 ) r p(TFD,i(3)

As in the nonhierarchical case, the posterior can be found using Bayes’s
rule asp(TFD,
Ti!1 ) pip(DFTi , Ti!1 )p(TFT
i i!1 ).
p(DFTi!1 )(4)In many cases, one can assume that p(DFTi , Ti!1 ) p p(DFTi ); that is, Ti!1!

3. This may be expressed as p(D) p T!H p(DFT)p(T). The sum is replaced by an
integral if the hypotheses T are continuously varying quantities.

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HIERARCHICAL BAYESIAN MODELS

175

adds no additional information regarding the likelihood of the data, given
Ti (Ti!1 is ‘screened off’ from D, given Ti).4
Theories at higher levels of the hierarchy may represent more abstract
or general knowledge, while lower levels are more specific or concrete.
For example, the problem of curve fitting can be represented in a hierarchical model. Finding the curve that best represents the relationshipbetween two variables X and Y involves not only fitting particular curves
from some given hypothesis space to the data but also making ‘higher’level decisions about which general family or functional form (linear,quadratic, etc.) is most appropriate. There may be a still higher level
allowing choice between expansions in polynomials and expansions inFourier series. At the lowest level of the hierarchical model representing
curve fitting, theories T0 specify specific curves, such as y p 2x ! 3 ory p x 2 " 4, that we fit to the data. At the next level of the hierarchy,
theories T1 are distinguished by the maximum degree of the polynomial
they assign to curves in the low-level hypothesis space. For instance, T1
could be the theory Poly1, with maximum polynomial degree 1. An alternative T1 is Poly2, with maximum polynomial degree 2, and so on. At
a higher level, there are two possible theories that specify that T1 theories
are either polynomials or Fourier series, respectively. The model also
specifies the conditional probabilities p(T0FT1 ) and p(TFT
12 ) . At each levelof the HBM, the alternative theories are mutually exclusive. In this example, Poly1 and Poly2 are taken to be mutually exclusive alternatives.
We will see soon how this should be understood.
We now suggest that HBMs are particularly apt models in certain respects of scientific inference. They provide a natural way to represent a
broadly Kuhnian picture of the structure and dynamics of scientific theories.
Let us first highlight some of the key features of the structure anddynamics of scientific theories to which historians and philosophers witha historical orientation (Kuhn 1962; Lakatos 1978; Laudan 1978) havebeen particularly attentive and for which HBMs provide a natural model.
It has been common in philosophy of science, particularly in this tradition,
to distinguish at least two levels of hierarchical structure: a higher levelconsisting of a paradigm, research program, or research tradition and alower level of more specific theories or hypotheses.
Paradigms, research programs, and research traditions have been invested with a number of different roles. Kuhn’s paradigms, for instance,
may carry with them a commitment to specific forms of instrumentationand to general theoretical goals and methodologies, such as an emphasis
4. The normalization constant is calculated in a similar way to before as p(DFTi!1) p
Ti!Hi p(DFTi)p(TiFTi!1). Again, it is assumed that Ti!1 is screened off from D, given Ti.

!

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on quantitative prediction or a distaste for unobservable entities. However,
one of the primary functions of paradigms and their like is to containwhat we will call ‘framework theories’, which comprise abstract or generalprinciples specifying the possible alternative hypotheses that it is reasonable to entertain at the more specific level—for example, the possible
variables, concepts, and representational formats that may be used toformulate such alternatives; more general classes or kinds into which more
specific variables fall; and possible relationships, causal and structural,that may obtain among variables.5 More generally, framework theories
provide the raw materials out of which more specific theories may beconstructed and the constraints that these must satisfy. We will summarize
this idea by saying that the relation between levels of theory is one of‘generation’, where a lower-level theory Ti is said to be generated from ahigher-level theory Ti!1, when Ti!1 provides a rule or recipe specifying
constraints on the construction of Ti.
Framework theories are generally taken to define a certain epistemic
situation for the evaluation of the specific theories they generate since
they help to determine the alternative hypotheses at the specific level andhow likely they are with respect to one another. Confirmation of theories
is relative to the framework that generates them. This type of idea may
be illustrated even in the simple case of curve fitting. We can think of ascientist who fits a curve to the data from the set of alternatives characterized by or generated from Poly1, as in a different epistemic or evidential situation from an investigator who fits a curve from the set ofalternatives generated by Poly2, even if the same curve is selected in bothcases. The first investigator selects her curve from a different set of alternatives than does the second and has more free parameters to exploit
in achieving fit. This in turn affects the evidential support the data provide
for the curve she selects. In part, Kuhn’s concept of incommensurability
reflects the idea that scientists working in different paradigms are in different epistemic situations. But the epistemic difference in the two situ5. In discussing the application of HBMs to what we call framework theories, we
intend to suggest relevance to several related notions. In cognitive development, thelabel ‘framework theory’ has been used to refer to the more abstract levels of children’s
intuitive theories of core domains—the organizing principles that structure knowledgeof intuitive physics, intuitive psychology, intuitive biology, and the like (Wellman andGelman 1992). In an earlier era of philosophy of science, Carnap introduced the notionof a ‘linguistic framework’, the metatheoretical language within which a scientific theory
is formulated, which is adopted and evaluated on pragmatic or aesthetic grounds rather
than being subject to empirical confirmation or disconfirmation. To the extent that
there is common ground between Carnap’s linguistic frameworks and the later notionsof paradigms, research programs, or research traditions, as some have suggested (Godfrey-Smith 2003), the term ‘framework theory’ also recalls Carnapian ideas.

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ations need not be realized only in the minds of two different scientists.
It applies also when a single scientist approaches the data from the standpoint of multiple paradigms or higher-level theories, weighing themagainst each other consciously or unconsciously, or when a communityof scientists does likewise as a whole (without any one individual committing solely to a single framework).
Our thesis that HBMs provide a suitable model for the structure anddynamics of scientific theories, and particularly of this Kuhnian picture,rests on three core claims about how HBMs represent the scientific situation. First, we claim that the hierarchical hypothesis space in an HBM
is appropriate for modeling scientific theories with hierarchical structure.
Second, the notion of generation between levels of theory can be modeled
formally in terms of the conditional probabilities p(TFT
i i!1 ) linking levelsof theory in an HBM. The conditional probabilities p(TFT
i i!1 ) reflect thescientific assumptions about how Ti is constructed out of Ti!1, explicitly
marking how the subjective probability of a lower-level theory is specified
relative to, or with respect to the viewpoint of, the higher-level theory
that generates it. And third, updating of the conditional probabilities
p(TFT
i i!1 ) of theories at level i with respect to a particular theory at thei ! 1 level represents confirmation of the level-i theory with respect to theclass of alternatives generated by the i ! 1-level theory.
Before developing these claims in more detail, we first consider a few
motivating examples of how higher-level framework theories may be structured and how they function to constrain more specific theories. The
constraints that framework theories provide may take a variety of more
specific forms: for example, they may reflect causal, structural, or classificatory presuppositions or assumptions about the degree of homogeneity or heterogeneity of data obtained in different circumstances.
In the causal case, a framework theory could provide a ‘causal schema’,representing more abstract causal knowledge, such as that causal relations
are only allowed between relata of certain types. A biological example isprovided by the abstract description of the general principles that are now
thought to govern gene regulation (e.g., see Davidson 2006). For example,
current biological understanding distinguishes between structural and regulatory genes. These are organized into networks in which the regulatory
genes influence the expression of both structural and other regulatory
genes. Regulatory genes are also capable of changing independently of
structural genes (e.g., by mutation). This represents a causal schema,
which needs to be filled in with particular regulatory genes in order toyield a specific theory about the expression of any particular structuralgene. Any alternative to this abstract schema (e.g., an alternative according to which gene expression is controlled by some other biologicalThis content downloaded from 171.66.208.5 on Wed, 1 Apr 2015 16:08:14 PM
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agent apart from regulatory genes) will be represented by a competing
higher-level theory, which is inconsistent with the regulatory gene schema.
Another biological example is the so-called Central Dogma of Molecular Biology, suggested by Crick (1958) as a heuristic to guide research.
According to this principle (in its universal, unqualified form), information flows from DNA to RNA to proteins but not vice versa. This canbe represented by the abstract schema DNA r RNA r protein. Specificlower-level theories would fill in the details of the precise molecules involved. Competing high-level theories to the central dogma would include
schemas that also allow information to flow RNA r DNA or protein rDNA. In fact, the discovery of reverse transcriptase led to the replacementof the central dogma with an alternative schema, allowing information
to flow from RNA to DNA in certain cases. An example of the applicationof HBMs to causal networks is given in section 5.
In other applications, the specific theories of interest may be classifications or descriptions of a certain domain. Then a framework theory
might specify the structure of the classification or description, for example,
whether the entities are organized into a tree, a lattice, clusters, and soon. Classification of living kinds was once thought to be a linear structure—each kind was to be placed in the great chain of being. Later Linnaeus discovered that the data were better organized into a tree, with abranching structure. The linear structure and the tree structure were competing higher-level theories, which were compared indirectly via how well
specific theories of each type could account for the data.6
Higher-level theories may also specify how homogeneous data obtained
from different trials or experimental settings are expected to be. Homogeneity assumptions can be represented as a higher-level theory that canbe learned, and they can help to guide further inference. For example, toa surprising extent genetic and molecular mechanisms are shared among
different species of animals. This helps to make it plausible that, say,results about the molecular mechanisms underlying synaptic plasticity inthe sea slug (aplysia) can be generalized to give an understanding ofsynaptic plasticity in humans.
These examples illustrate that framework theories may take a wide
range of representational forms. For instance, they, and the theories theygenerate, may be directed graphs, structural forms such as trees or lattices,or multidimensional spaces. In principle, HBMs may be applied to theories of any kind of representational form, and current research is making
6. Kemp (2007) and Kemp and Tenenbaum (2008) discuss these and other examples
of structural frameworks, as well as showing how they can be learned in an HBM.

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these applications practical for such diverse representations as grammars,
first-order logic, l calculus, logic programs, and more.7
We now turn to a more detailed discussion of how HBMs represent
the structure and dynamics of scientific theories. Any model of scientificinference will take certain assumptions as given in the setup of the model.
These assumptions are then used as fixed points or common presuppositions in the evaluation of rival theories. For example, standard nonhierarchical Bayesian models presuppose a hypothesis space of rival candidate theories. We may think of this space as specified by the backgroundassumptions that characterize a particular problem area—for example, thatthe hypotheses under consideration have a particular representational form,
such as polynomials in curve fitting or directed graphs in causal contexts.
In an HBM, what has to be fixed in the setup of the model is a hierarchicalstructure comprising the highest-level hypothesis space and the conditional
probabilities p(TF
i Ti!1 ) at each level. As we shall see in section 4.3, thebackground assumptions behind the highest-level hypothesis space can beconsiderably more general and abstract than would typically be the casefor a nonhierarchical Bayesian model. For this reason, in many cases, thesebackground assumptions will be less demanding than the presuppositions
required by nonhierarchical Bayesian models. The conditional probabilities
p(TF
i Ti!1 ) can be thought of as reflecting scientists’ judgments about how
likely various lower-level theories Ti are, given the higher-level theory
Ti!1. As we will see in an example discussed in section 5, the higher-level
theory might specify the types of entities or relations involved in the lowerlevel theories, and the conditional probability p(TFT
i i!1 ) may be put together
out of the probabilities that each entity or relation will take some particularform. The overall probability p(TFT
i i!1 ) then reflects scientists’ understandingof the principles governing how the lower-level theories are to be cognitively
constructed from the higher-level theories. In other words, some assumptions about how Ti!1 generates Ti are built into the setup of the HBM.
As we mentioned earlier, updating the conditional probabilities p(TF
i Ti!1 )of theories at level i with respect to a particular theory at the i ! 1 levelmay be thought of as representing confirmation of the level-i theory withrespect to the class of alternatives generated by the i ! 1-level theory. For
instance, the probability p(2x ! 1FPoly1 ) tells us about how likely the curve
2x ! 1 is relative to a hypothesis space of lines of the form y p v0 !
v1 x. However, the probability p(0x 2 ! 2x ! 1FPoly2 ) tells us about how
likely 0x 2 ! 2x ! 1 is with respect to the hypothesis space of quadratic
curves y p v0 ! v1 x ! v2 x 2. The fact that p(2x ! 1FPoly1 ) and p(0x 2 !
2x ! 1FPoly2 ) may differ, even though we may recognize 2x ! 1 and7. This is current research by J. B. Tenenbaum and N. D. Goodman at MIT.

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0x 2 ! 2x ! 1 as representing the same curve, reflects the framework relativity of confirmation mentioned earlier, namely, that evaluations of theories may depend on the background knowledge or higher-level theory
that frames the inquiry.
Thinking of higher-level theories as generators of lower-level theories
contrasts with a certain traditional picture of higher-level theories. According to this traditional approach, a hierarchy of theories can be regarded as a hierarchy of nested sets. On this view, there is a base set of
all possible lowest-level hypotheses, such as the set of all possible curves.
In this base set, curves such as 2x ! 1 and 0x 2 ! 2x ! 1 are taken to be
the same hypothesis, so that the set contains only mutually exclusive
hypotheses. The base set can be grouped into subsets sharing some common feature, such as the set of all nth-order polynomials. Such subsets
are then regarded as ‘higher-level theories’. Thus, the set LIN of all linear
hypotheses of the form y p v0 ! v1 x could be one higher-level theory, andthe set PAR of all quadratic hypotheses of the form y p v0 ! v1 x !
v2 x 2 would be another. On this view, higher-level theories such as LIN
and PAR are not mutually exclusive. For example, the curve represented
by 2x ! 1 would be contained in both sets LIN and PAR.
By contrast, on the generative picture, higher-level theories are mutually
exclusive alternatives—this is a point stressed by Kuhn (1962, chap. 9).
This is also the case in an HBM, where theories at level i are treated as
mutually exclusive alternatives, given a particular theory at the i ! 1th
level. For instance, the model Poly1, together with the conditional probability p(T0FPoly1 ), represents one way that scientists might think of specific theories T0 as being constructed, or ‘generated’, whereas the model
Poly2 and probability p(T0FPoly2 ) represents an alternative and quite distinct way of producing specific theories. It is true that the sets of curves
that each generates may overlap. However, the higher-level theories Poly1
and Poly2 are not identified with the subset of curves that they generate.
In this particular case, the HBM may be thought of as assigning probabilities to a treelike hierarchy of theories, with arrows indicating a generation relation between a higher-level theory and lower-level theories thatit generates (see fig. 1).
In some circumstances, one wants to evaluate theories without reference
to a particular higher-level theory. In the curve-fitting example, one mightwant to assign probabilities to specific curves from the base set of all
possible curves. These form a mutually exclusive set. This can be doneusing the HBM by summing over the higher-level theories that may generate the particular low-level theory:p(T0 ) p!

T1, . . ., TU

p(T0FT1 )p(TFT
12 ) . . . p(TU"1FTU)p(TU).

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Figure 1. Hierarchical Bayesian model for curve fitting. At the highest level of thehierarchy, T2 may represent an expansion either in a Fourier basis or in a polynomial
basis. The polynomial theory generates theories, or models, T1, of different degrees.
Each of these then generates specific curves T0—quadratic curves are depicted. Andeach specific curve gives rise to possible data sets.

Here U indexes the highest level of the HBM. Probabilities for subsets ofthe base set, which on the traditional view comprise higher-level theories,
can also be calculated in this way.
3. Preference for Stronger Theories. We now turn to ways in which HBMs
help to resolve certain challenges to Bayesian philosophy of science. The
first problem we will consider was originally posed by Karl Popper (1934).

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It has recently been repeated by Forster and Sober in the context of curve
fitting (Forster and Sober 1994; Forster 1995).
The problem is as follows. If one theory, T1, entails another, T2, thenthe following inequalities are theorems of the probability calculus:p(T1 ) ≤ p(T2 ),(6)

p(TFD)≤ p(T2FD),
1(7)

for any data D. It would seem then that the Bayesian would always haveto assign lower probability to the logically stronger theory. However, arguably scientists often do regard stronger theories as more probable.
Forster and Sober (1994) advance the argument in the context of curve
fitting. They define LIN to be the family of equations or curves of theform
Y p a 0 ! a1 X ! jU

(8)

and PAR to be the family of equations
Y p b 0 ! b1 X ! b 2 X 2 ! jU,(9)where jU is a noise term. The family LIN is then a subset of PAR since“if the true specific curve is in (LIN), it will also be in (PAR)” (7). Forster
and Sober claim that since LIN entails PAR, the Bayesian cannot explain
how LIN can ever be preferred to PAR because prior and posterior probabilities for LIN must always be less than or equal to the probabilities
for PAR.
As we saw in the previous section, there are two ways to think of higherlevel theories: a set-based way and a generative way. Forster and Soberassume that when scientists show a preference for a stronger theory, they
are comparing sets of specific theories, such as LIN and PAR. However,the picture of high-level theories involved in HBMs offers an alternative.
The theories Poly1 and Poly2 considered at the T1 level are mutually exclusive polynomial models, so it is quite legitimate to assign higher probabilities, whether prior or posterior, to Poly1 as opposed to Poly2. Therefore it is possible to prefer the linear theory Poly1 over the quadratic
theory Poly2.
This is not in conflict with the assignment of lower probability to thetheory LIN as opposed to PAR. Suppose Poly1 has probability 0.6 in the
HBM and Poly2 has probability 0.4 (assuming for the sake of simplicity
that Poly1 and Poly2 are the only alternatives). The probability of LIN is
the probability that the system is described by a linear hypothesis. A
linear hypothesis could be generated by either Poly1, with probability 1,
or Poly2, with some probability p ! 1, depending on what weight Poly2

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gives to linear hypotheses (i.e., those quadratic hypotheses with b 2 p 0).
Suppose p p .1. Then the probability for LIN is given by summing theprobabilities for each generating model multiplied by the probability that
if that model was chosen, a linear hypothesis would be drawn. Thus, inthis example, p(LIN) p .6 # 1 ! .4 # .1 p .64. Similarly, the probability
for PAR is p(PAR) p .6 # 1 ! .4 # 1 p 1 since no matter which way
the lower-level hypothesis is generated, it will be a quadratic curve. Thusp(LIN) ≤ p(PAR), as expected. However, the theories that are comparedin an HBM are not LIN and PAR but Poly1 and Poly2. This is because
higher-level theories are not regarded simply as sets of lower-level possibilities but are alternative generative theories.
The alleged failure of Bayesians to account for a preference for stronger
theories has been associated with another alleged failure: to account forthe preference for simpler theories. This is because the stronger theory
may be the simpler one, as in the curve-fitting case. In the next section,
we will argue that not only do HBMs allow preference for simpler theories,
but they actually automatically incorporate such a preference.
4. Curve Fitting. In fitting curves to data, the problem of fitting parameters to a function of a specified form, such as a polynomial of a certain
degree, can be distinguished from the problem of choosing the right functional form to fit. There are statistical techniques of both Bayesian andnon-Bayesian varieties for the latter problem of ‘model selection’. It has
already been suggested in the philosophy of science literature that particular versions of these methods may give a precise formalization of therole of simplicity in theory choice.8 This section will give a more detailed
account of Bayesian inference in the curve-fitting HBM introduced in
section 2, describing inference at the three levels depicted in figure 1. We
will also show that Bayesian model selection, and hence a certain kindof preference for simplicity, arises automatically in higher-level inferencein HBMs. In doing so, we aim to bridge a gap between philosophicaldiscussions of model selection on the one hand, which have tended tofocus on specific methods and their relative merits, and more general
discussions of the hierarchical structure of scientific theories and the epistemology of higher-level theories on the other hand.
At each level of the hierarchy, the posterior distribution is computedfor hypotheses in the hypothesis space generated by the theory at the nextlevel up the hierarchy.
8. Forster and Sober (1994) suggest this for the non-Bayesian method based on the
Akaike Information Criterion, and Dowe, Gardner, and Oppy (2007) suggest it for
Minimum Message Length, which is a Bayesian form of model selection.

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4.1. Inference at Lowest Level: Bayesian Model Fitting. At the lowest
level of the hierarchy, the hypothesis space H0 comprises specific curves
T0 of the form
fv,M (x) p v0 ! v1 x ! . . . ! vM x M ! !

(10)(where ! ∼ N(0, j ) is the noise term), generated by PolyM at the T1 level.
Let ṽ p (v0 , . . . , vM) be a vector representing the parameters of the curve
to be fitted. For simplicity, we treat the variance j 2 as a fixed quantity
rather than as a parameter to be fitted.
The posterior probability for the parameters ṽ is2

˜ Poly )p(vFPoly
˜p(DFv,MM)
˜p(vFD,
PolyM) p.
p(DFPolyM)(11)

The denominator is given byp(DFPolyM) p"

˜ Poly )p(vFPoly˜˜p(DFv,
M
M)dv.

(12)

Figure 2 shows the polynomial of each degree with highest posterior
probability for a small data set, together with samples from the posterior
that illustrate the ‘spread’ of the posterior distribution.
The posterior is used by the Bayesian for the task of fitting the parameters to the data, given a model—the problem of ‘model fitting’. Strictly
speaking, Bayesian assessment of hypotheses involves only the posterior
probability distribution. However, one could also ‘select’ the best hypothesis, for example, by choosing the one with the highest posterior
probability.
4.2. Inference at Second Level: Bayesian Model Selection. At the nextlevel of the hierarchy, the hypothesis space H1 consists of the polynomial#
models {PolyM}Mp1
with different degrees M. These models may be compared by calculating their posterior probabilities, given by9P(PolyMFD) ∝ P(PolyM)P(DFPolyM),
where
P(DFPolyM) p

"

˜ ˜
˜
P(DFv)P(vFPoly
M)dv.

(13)

ṽ

9. Once the parameters ṽ of the polynomial are defined, so is the maximum degree ofthe polynomial. Therefore, the screening-off assumption mentioned after eq. (4) holds,
˜ Poly ) p p(DFv)˜.
and p(DFv,
M

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Figure 2. Polynomial of each degree with highest posterior (dark gray), with otherpolynomials sampled from the posterior (light gray). Data are sampled from the polynomial f(x) p 100(x " 3)(x " 12)(x " 17), plus normally distributed noise.

Computing the posterior distribution over models in this way is the way
models at the second level of the HBM are assessed, and it is also thestandard Bayesian approach to the problem of model selection (or ‘modelcomparison’, if the Bayesian strictly restricts herself to the posterior probability distribution). Although the posterior indicates the relative support
for a theory PolyM, the model is not directly supported by the data but
is indirectly confirmed through support for the specific functions fv,M (x)that it generates.
It has been observed by a number of authors that, with a certain natural
choice of priors, the Bayesian posterior reflects a preference for simpler
models, and Bayesian model selection involves a trade-off between thecomplexity of the model and fit to the data, similar to that seen in other
non-Bayesian approaches to model selection.10
10. Rosenkrantz (1977) discusses the role of simplicity in Bayesian evaluations offamilies of curves and other examples (see his discussion of what he calls ‘sample
coverage’). Similar ideas are discussed for a simple case in White (2005). Jefferys andThis content downloaded from 171.66.208.5 on Wed, 1 Apr 2015 16:08:14 PM
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Figure 3. Posterior probability of models with different M (horizontal axis) for boththe polynomial case and the Fourier case discussed in sec. 4.3. The Bayesian Ockham’srazor is evident in the favoring of simpler models when the amount of data is small.

We illustrate this in figure 3, which shows the posterior probabilities
for each model and how they change as data accumulate (this is shownfor both polynomial and Fourier models). The prior probability overmodels has been assumed to be uniform, and the probability has also
been distributed uniformly between specific polynomials in each hypothesis space. This choice does not imply equal probability for specific polynomials generated by different theories: individual polynomials have priorprobability that decreases as degree increases since they must ‘share’ theprobability mass with more competitors.11 With these priors, when theamount of data is small, the linear model Poly1 is preferred over the higherBerger (1992) and MacKay (2003) highlight the trade-off between simplicity and fit in
Bayesian model selection.
11. Technically, this is captured by the Jacobian of the natural embedding of the smaller
model class into the larger. Results shown in fig. 3 were produced using a uniform
prior over a finite number of models. If the number of model classes is countably
infinite, one could use a geometric or exponential distribution over model classes.

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order polynomial models. As the amount of data increases, the higherorder models become more probable. If linear models may be regarded
as ‘simpler’ than higher-order models, then the Bayesian posterior has atendency to favor simpler models, at least until there is an accumulationof data supporting a more complex theory. This is a Bayesian Ockham’srazor: when there are only a few data points, the data can be fitted either
by a line or by a quadratic (cubic, etc.); however, the linear model Poly1
is preferred because it is ‘simpler’.
This simplicity preference arises because the posterior on models, equation (13), involves an integral over all the polynomials generated by themodel, not just the best fitting. Since there are more quadratics that fit
poorly than there are lines (indeed, there are more quadratics than lines,
period), the quadratic model is penalized.
This effect is manifested generally in the posterior probability for a higherlevel theory Ti. The likelihood p(DFTi ) for this theory is obtained by integrating over all the possible specific models Ti"1 that Ti generates:12p(DFTi ) p"

p(DFTi"1 )p(Ti"1FTi )dTi"1.

(14)

That is, the likelihood of a high-level theory is the expected likelihood of
the specific theories that it generates. This will be large when there are
relatively many specific theories, with high prior, that fit the data well—since complex higher-level theories tend to have many specific theories
that fit the data poorly, even when they have a few that fit the data very
well, simplicity is preferred. For this preference, it is not essential that thepriors p(Ti"1FTi ) be exactly uniform, as they were in our illustration. All
that is needed is that the priors for lower-level theories are not weighted
heavily in favor of those theories that fit the data best. Intuitively, thelikelihood p(DFTi ) penalizes complexity of the model: if the model is more
complex, then it will have greater flexibility in fitting the data and could
also generate a number of other data sets; thus, the probability assigned
to this particular data set will be lower than that assigned by a less flexible
model (which would spread its probability mass over fewer potential data
sets; see fig. 4). This simplicity preference balances against fit to the data,rather than overriding them: as we see in figure 3, an initial simplicity
bias can be overcome by the accumulation of data supporting a more
complex theory.
12. If screening off does not hold, p(DFTi"1) should be replaced by p(DFTi"1, Ti).

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Figure 4. Probability distributions p(DFHi ) over a one-dimensional data set D for threedifferent theories. The more complex theory H1 spreads the probability mass over a
wider range of possible data sets than the simpler theories H2 and H3. For the observed
data D*, the complex theory H1 has lower likelihood than H2. The simpler theory H3does not spread its mass so widely but misses the observed data D*. In this case, thetheory of intermediate complexity, H2, will be favored.

4.3. Inference at Higher Levels: Bayesian ‘Framework Theory’ Selection. We have seen how at the second level of the HBM, we can compare
or select the appropriate degree M for a polynomial model. Each polynomial model PolyM generates a set of specific hypotheses differing onlyin parameter values. All the polynomial models are expansions to different
degrees in terms of polynomial functions. However, this is not the only
way that models could be constructed. Models could also be expansions
to degree M in terms of Fourier-basis functions. The model FouriM, forexample, would generate specific functions of the form fv,M (x) p v0 !
v1 sin (x) ! . . . ! vM sin (Mx) ! !.
In an HBM, comparison between the type of basis functions used cantake place at a third level of the hierarchy. The principles are the sameas those behind comparison of models at the second level. One finds theposterior probability:
P(BasisFD) ∝ P(Basis)P(DFBasis),with
P(DFBasis) p!

P(DFModel)P(ModelFBasis),

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Figure 5. Log-posterior probability ratio between bases for curve fitting (positive numbers indicate support for Fourier basis, negative for polynomial basis). Error bars
represent standard error over 20 data sets randomly sampled from the polynomial
f(x) p 100(x " 3)(x " 12)(x " 17), plus normally distributed noise. When the numberof observations is small, the Fourier basis is favored; eventually enough evidence
accumulates to confirm the (correct) polynomial basis.

where Model will be one of the PolyM or FouriM, depending on the basis.13
Just as the models receive support from the evidence through the specificfunctions below them, the curve-fitting bases receive support through themodels they generate. In figure 5 the posterior probability values for eachbasis are plotted against the number of data points observed (the data
are actually sampled from a cubic polynomial with noise). Note that there
is a great deal of uncertainty when only a few data points are observed—
indeed, the Fourier basis has higher posterior—but the correct (polynomial) basis gradually becomes confirmed. Since there are only two hypotheses at the highest level (polynomial or Fourier), we have made thenatural assumption that the two are a priori equally likely (P(Basis) p.5).
13. Once the model is specified, the basis is also given, so p(DFModel) pp(DFModel, Basis).

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In some respects, the choice of a basis in this simple curve-fitting example is analogous to a choice between ‘framework theories’ (see sec. 2).
Framework theories frame the possibilities for how theories are expressedat lower levels. They may even be, as in Carnap’s picture of linguistic
frameworks, something like a language for expressing theories. In thisexample, we have a natural comparison between the ‘language of polynomials’, with a simple ‘grammar’ built from variables and constants,
addition, multiplication, and exponentiation and an alternative ‘Fourier
language’ built from trigonometric functions, addition, constants, andvariables. Since any function may be approximated arbitrarily well bypolynomials or sinusoids (a standard result of analysis), the two languages
are equally powerful in allowing fit to the data, so the main determinantof choice between them is simplicity as reflected in the likelihood of theframework theories. Simplicity here is a criterion that arises naturally
from assessing the empirical support of a high-level hypothesis.
5. The Problem of New Theories. One of the most pressing challenges forBayesian philosophy of science is to account for the discovery or introduction of new theories. When a genuinely new theory is introduced, thehypothesis space changes, and the Bayesian will have to reassign the priordistribution over the new hypothesis space. This has been called the ‘problem of new theories’ for Bayesians because the adoption of a new prior
is not governed by conditionalization and so is, strictly speaking, a nonBayesian process (Earman 1992).
The main Bayesian proposal to deal with the problem has been to usea ‘catchall’ hypothesis to represent as-yet-unformulated theories and then‘shave off’ probability mass from the catchall to assign to new theories.
This is an unsatisfactory solution since there is no particularly principled
way to decide how much initial probability should be assigned to thecatchall or how to update the probabilities when a new theory is introduced.
Given the inadequacy of this proposal, even would-be-full-time Bayesians like Earman have given up on a Bayesian solution and turned to aqualitative account of the introduction of new theories, such as that proposed by Kuhn (1962). Earman (1992) appeals to the process of coming
to community consensus and suggests that the redistribution of probabilities over the competing theories is accomplished by a process of “persuasions rather than proof” (197).
Difficulties in describing changes to the hypothesis space have also led
to another alleged problem. Donald Gillies claims that Bayesians must
limit themselves to situations in which the theoretical framework—by
which he means the space of possible theories—can be fixed in advance.
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are in a situation in which there is a fixed and known theoretical framework that it is reasonable to suppose will not be altered in the course of
the investigation,” where “theoretical framework” refers to “the set oftheories under consideration” (Gillies 2001, 364). Gillies claims that thisposes an enormous problem of practicality since it would not be feasible
to consider the “whole series of arcane possible hypotheses” (368) inadvance. He thinks that for the Bayesian to “begin every investigationby considering all possible hypotheses that might be encountered in thecourse of the investigation” would be a “waste of time” (376). This claim
is motivated by consideration of the potentially enormous size of adequate
hypothesis spaces, even for simple examples.
We will argue that both the problem of new theories and the practicality
problem for large hypothesis spaces are alleviated if assignment of a priorprobability distribution does not depend on an explicit enumeration of
the hypothesis space. As we said in section 2, just as the application ofnonhierarchical Bayesianism is restricted to a particular fixed hypothesis
space, so HBM Bayesianism can be validly applied only if we are in asituation in which there is a fixed and known hierarchy that it is reasonable
to suppose will not be altered in the course of the investigation. However,part of this hierarchy (the conditional probabilities p(TFT
i i!1 )) represent
background assumptions about how lower-level theories are generated
from higher-level theories. Given these assumptions, there is no need toenumerate the lower-level theories. In fact Bayesian inference in an HBM
can be performed over very large and even infinite hypothesis spaces.
These considerations provide a solution to the problem of practicalitythat Gillies raises. Also, there can be theories implicit in the hypothesis
space, initially with very low probability, which come to get high probability as the data accumulate. This provides a way of effectively modelingthe introduction of theories that are ‘new’ in the sense that they may be
regarded as implicit in assumptions about how the lower-level theories
are generated, although not explicitly enumerated or recognized as possible hypotheses.
To illustrate, we will use an example of an HBM that represents scientifictheories about causal relations (Tenenbaum and Nigoyi 2003; Griffiths
and Tenenbaum 2007). The example also serves to illustrate another application of HBMs. Directed graphs in which the arrows are given a causal
interpretation are now a popular way to represent different possible systems of causal relationships between certain variables. These are calledcausal graphs. More abstract causal knowledge may be represented by a‘causal graph schema’ that generates lower-level causal graphs.
Consider a family of causal graphs representing different possible systems of causal relationships among such variables as smoking, lung cancer,
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Figure 6. Causal networks illustrating different possible relationships between behaviors, diseases, and symptoms; N0, N1, and N2 are based on the same abstract graphschema Gdis, whereas N3 is not. The network N2 contains an extra disease node.

or node X directed into another Y means that X causes Y. Compare thegraphs in figure 6. The three graphs N0, N1, and N2 employ the same setof variables. Although these graphs posit different causal links among
the variables, they differ in a systematic way from graph N3. In N0, N1,
and N2, the variables fall into three more general classes that might bedescribed as behaviors, diseases, and symptoms. Furthermore, there is amore abstract pattern that governs possible causal relationships among
variables in these classes. Direct causal links run only from behaviors todiseases and from diseases to symptoms. Other possible causal links (e.g.,
direct causal links from behaviors to symptoms or causal links between
symptoms) do not occur. By contrast, N3 does not follow this pattern—in this graph, for example, the disease variable flu causes the behavior
variable smoking.
The particular graphs N0, N1, and N2 (but not N3) are generated by amore abstract graph schema Gdis that is characterized by the following
features:i)

There are three node classes B, D, and S into which specific nodes
fall. Each node class is open in the sense that additional variables
may be added to that class.

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193

Possible causal relationships take the form B r D and D r S only.

Items i and ii thus represent structural features that characterize an entire
class of more specific theories. These structural features have to do withcausal relationships (or their absence) that are determined by the classes
into which variables fall.
In an HBM we may regard Gdis as a general theory, T1, generating
specific networks Ni as specific theories T0. It divides the variables ofinterest into classes or kinds and specifies that only a limited set of causal
relationships may hold among these variables, in much the same way that
the Central Dogma of molecular biology restricts the set of possible informational relationships among DNA, RNA, and proteins. In order tospecify the HBM completely, we need to define the prior p(NFGidis ) (i.e.,p(T0FT1 )), which encapsulates probabilistic information about how the specific networks Ni depend on, or are generated by, the causal schema Gdis.
As an illustration, in Griffiths and Tenenbaum (2007), the prior p(NFGidis )was specified by giving probability distributions for the number of nodes
in each class (B, D, or S) in the network Ni and distributions for the
probability of causal links between pairs of nodes from classes B and D
and from classes D and S. More specifically, the number of nodes in eachclass was assumed to follow a power law distribution p(N ) ∼ 1/N a withan exponent specific to each class (so that, other things being equal, graphswith more nodes have lower prior probability). There was also assumed
to be a fixed probability hBD of a causal link from b to d for any nodes
b ! B and d ! D and a fixed probability hDS of a causal link from d tos for any nodes d ! D and s ! S. Thus, the probability of a causal linkdepends only on the classes to which the nodes belong. A specific causal
graph such as N0 may then be generated by randomly drawing individual
nodes from each node class and then randomly generating causal links
between each pair of nodes. The result is a probability p(NFGidis ) for eachspecific causal graph Ni, which is nonzero if and only if Gdis generates Ni.
At the outset of the investigation, the range of graphs to be considered
need not be explicitly enumerated. The range of hypotheses is implicitly
determined by the causal schema (or schemas) under consideration andthe ‘instructions’ we have just given for building hypotheses and theirprior probabilities at the lower level based on the schema. At first, a highprobability is assigned to certain of the possible causal graphs—for instance, those with fewer disease variables. However, a causal network
containing a new disease can be discovered, given the right data, eventhough initially all the networks with nonnegligible prior probability do
not contain this disease. Suppose, for example, that a correlation is observed between a previously known behavior b such as working in afactory and a previously known symptom s such as chest pain. To ac-

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commodate this correlation, the logically simplest possibility is simply to
add another causal link directly from b to s, but the schema Gdis rules out
this possibility: any link between a behavior and symptom must passthrough a disease as an intermediate link. Another possibility that isallowed by Gdis is to add links from b to one of the known diseases andfrom this disease to s. This has the advantage that no new disease nodeneeds to be introduced. But it may be that any new links from working
in a factory to existing disease nodes and from these to symptoms generatecorrelations that are inconsistent with what is observed. In such circumstances, one will eventually learn that the correct causal graph is one that
introduces a new disease node Y that is causally between b and s as shownin N2. The rules associated with the graph schema Gdis for constructing
specific graphs tell us what the prior is for this new graph, and as we
update on the basis of the data, this new graph may acquire a higher
posterior than any of its competitors (Griffiths and Tenenbaum 2007).
In general, HBMs can provide a Bayesian model of the introductionof new theories.14 New theories that were implicit in the hypothesis space,but that initially received very low prior probability, can be explicitly
introduced and come to receive high posterior probability as the appropriate supporting data accumulate. The example also illustrates how thehigher-level theory may play a role in guiding the construction of more
specific theories. What Gdis in effect does is to provide a sort of abstract
recipe for the construction or generation of more specific theories. By
restricting the range of possible hypotheses among which the learner has
to search, Gdis makes it possible to learn the correct hypothesis from amuch smaller body of data than would be required if one were instead
searching a much larger space of possible alternatives. So the adoptionof the schema represented by Gdis greatly facilitates learning.
The lack of need to explicitly enumerate hypotheses also removes thepractical problem for large hypothesis spaces posed by Gillies. In thecontext of HBMs, one might be concerned that the evaluation of posterior
14. Earman suggests distinguishing ‘weak revolutions’, which involve the introductionof theories in which the new theory is a possibility that was within the space of theories,
previously unarticulated, from revolutions proper or ‘strong revolutions’, where a completely new possibility is introduced. HBMs provide a Bayesian treatment of weak
revolutions. This is important for at least two reasons. First, given the ubiquity of
weak revolutions in day-to-day science, it would be a serious limitation if the Bayesianaccount could not deal with them without making the implausible assumption that all
weakly new hypotheses need to be explicitly enumerated before inference begins. Second, it is far from clear how common ‘pure’ strong revolutions are. Detailed investigation of putative examples of such revolutions typically reveals a major guiding rolefrom previously accepted frameworks, suggesting that at least some aspects of such
episodes can be modeled as weak revolutions.

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probabilities, although possible in principle, is too computationally challenging. However, Bayesian inference in large HBMs is made practical by
the existence of algorithms for producing good approximations to theposterior probabilities. Indeed, there are a number of ways to efficiently
approximate Bayesian inference that appear, prima facie, very different
from the usual method of explicit enumeration and computation that
Gillies criticizes. For instance, in Markov Chain Monte Carlo (MCMC)
the posterior distribution is approximated by sequentially sampling hypotheses as follows. From the current hypothesis, a ‘proposal’ for a new
hypothesis is made using some heuristic—usually by randomly altering
the current hypothesis. Next, the current hypothesis is compared to the
proposed hypothesis, resulting in a stochastic decision to accept or reject
the proposal. This comparison involves evaluation of the ratio of priorand likelihood functions but not the (properly normalized) posterior probability. With a proper choice of proposals, the resulting sequence of hypotheses is guaranteed to comprise a set of samples from the posterior
distribution over hypotheses that can be used to approximate the distribution itself.15
In the case of an HBM in which one level of theory generates the
hypotheses of a lower level, each step of sequential sampling that changes
the higher level can allow access to entirely different hypotheses at thelower level. Thus, while an arbitrary variety of alternative specific theories
is available, only a small portion need be considered at any one time.
Indeed, the sequence of local moves used to approximate posterior inference may never reach most of the hypothesis space—although in principle these hypotheses could be accessed if the evidence warranted.
It has been demonstrated that MCMC provides an effective way toimplement Bayesian learning in a computational model of the diseasesymptom example (Mansinghka et al. 2006). The MCMC method is used
to learn both the specific causal graph and the division of variables into
the classes that appear in the higher-level graph schema. For instance, tolearn the causal schema Gdis it would have to be discovered that thevariables can be divided into three classes (‘behaviors’ B, ‘diseases’ D,and ‘symptoms’ S) with causal links from B to D and from D to S. The
size of the hypothesis space is extremely large in this example, but themodel can still effectively find an appropriate theory in a reasonable time.
The MCMC method can even be regarded as a suggestive metaphor
for the process of scientific discovery. It highlights two ways in which theBayesian approach to science may be more realistic than has often been
assumed. First, as just described, it is possible to efficiently approximate
15. For more details, see, e.g., MacKay (2003).

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Bayesian models, even over infinite hypothesis spaces, without ‘wasting’an inordinate amount of time considering very unlikely hypotheses. These
approximation methods provide for an orderly, rule-governed process bywhich new possibilities are introduced and considered. Second, such approximation can have a qualitative character that is very different fromexact Bayesian computation: the approximate search may look locally
arbitrary, even irrational, mixing elements of hypothesis testing and heuristic change, but it still arrives at the rational Bayesian answer in thelong run.
6. Broader Implications for Theory Change. We have argued so far that
HBMs help to resolve certain issues for Bayesian philosophy of science.
In particular, they give a Bayesian account of high-level theory change
and of the introduction of new theories. In addition, they allow us toresolve puzzles associated with the preference for stronger or simpler theories.
HBMs also have implications for general discussions of theory construction and theory change that are not specifically Bayesian. A numberof traditional accounts of how abstract knowledge may be learned proceed‘bottom up’. For instance, in the logical empiricist tradition, more ‘observational’ hypotheses must be learned first, with the acquisition of themore theoretical level following rather than guiding learning at the observational level. Such a bottom-up picture has led to puzzlement about
why we need theories at all (Hempel 1958). It has been alleged that thisis a particularly pressing problem for a Bayesian since a theory presumably
should always receive lower probability than its observational consequences (Glymour 1980, 83–84).
This problem is dissolved in the HBM analysis, which validates theintuition—central in Kuhn’s program but more generally appealing—that
higher-level theories play a role in guiding lower-level learning.16 In section
5 we saw how higher-level theories may guide the search through a large
lower-level hypothesis space by ‘spotlighting’ the particular subset oflower-level hypotheses to be under active consideration. In both the curvefitting and the causal-network problems discussed in previous sections, it
is possible for a hierarchical Bayesian learner given a certain sample ofevidence to be more confident about higher-level hypotheses than lowerlevel knowledge and to use the constraints provided by these higher-level
hypotheses to facilitate faster and more accurate learning at the lower
16. Also, since the relation between levels in an HBM is not logical entailment but
generation, probability assignments are not constrained by entailment relations between
levels. Indeed, theories at different levels of an HBM are not in the same hypothesis
space and so are not directly compared in probabilistic terms.

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level. In one representative case study, Mansinghka et al. (2006) studied
learning of a causal network with 16 variables according to a simple‘disease theory’ schema (variables divided into two classes corresponding
to ‘diseases’ and ‘symptoms’, with causal links connecting each disease
to several symptoms). A hierarchical Bayesian learner needed only a few
tens of examples to learn this abstract structure. It was found that after
only 20 examples, the correct schema dominated in posterior probability—
most of the posterior probability was placed on causal links from diseases
to symptoms—even though specific causal links (between specific pairs ofvariables) were impossible to identify. After seeing a few more examples,the hierarchical Bayesian learner was able to use the learned schema toprovide strong inductive constraints on lower-level inferences, detecting
the presence or absence of specific causal links between conditions withnear-perfect accuracy. In contrast, a purely bottom-up, empiricist learner(using a uniform prior over all causal networks) made a number of ‘false
alarm’ inferences, assigning significant posterior probability to causal links
that do not exist and indeed should not exist under the correct abstract
theory because they run from symptoms to diseases or from one symptom
to another. Only the hierarchical Bayesian learner can acquire these principles as inductive constraints and simultaneously use them to guide causal
learning.17
HBMs illuminate aspects of theory change that have been controversialin the aftermath of Kuhn’s The Structure of Scientific Revolutions (1962).
A number of commentators have contended that on Kuhn’s characterization, high-level theory change, or paradigm shift, was a largely irrational
process, even a matter of “mob psychology” (Lakatos 1978, 91). Considerable effort was devoted to providing accounts that showed that suchchanges could be ‘rational’. However, these accounts were handicappedby the absence of a formal account of how confirmation of higher-level
theories might work. HBMs provide such an account.
HBMs also help to resolve an ongoing debate between ‘one-process’and ‘two-process’ accounts of scientific theory change (as described in
Godfrey-Smith 2003, chap. 7). If scientific knowledge is organized intolevels, this opens up the possibility that different processes of change might
be operative at the different levels—for example, the processes governingchange at the level of specific theories or the way in which these arecontrolled by evidence might be quite different from the processes governing change at the higher levels of theory. Carnap held a version of thistwo-process view—he held that changes to a ‘framework’ were quite different from changes within the framework. Similarly, Kuhn thought that
17. See Mansinghka et al. (2006), esp. fig. 4.

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the processes at work when there was a paradigm change were quite
different from the processes governing change within a paradigm (i.e.,
choice of one specific theory or another). Part of the motivation for twoprocess views has been the idea that change at lower levels of theory isdriven by empirical observations, whereas change at higher levels is driven
more by pragmatic, social, or conventional criteria. Carnap, for example,
thought that changes to a ‘framework’ were mostly governed by virtues
such as simplicity that were primarily pragmatic, not empirical.
However, there have been those who favor a single general account oftheory change. Popper and Quine may plausibly be regarded as proponents of this one-process view. According to Popper (1934, 1963), change
at every level of science from the most specific to the most general andabstract proceeds (or at least as a normative matter ought to proceed) inaccord with a single process of conjecture and refutation. According toQuine (1970), all changes to our ‘web of belief’ involve the same generalprocess in which we accommodate new experience via a holistic processof adjustment guided by considerations of simplicity and a desire to keepchanges ‘small’ when possible.
HBMs allow us to make sense of valuable insights from both the oneprocess and the two-process viewpoints, which previously seemed contradictory. Within the HBM formalism, there is a sense in which evaluation at higher framework levels is the same as evaluation at lower levels
and also a sense in which it is different. It is the same in the sense that
it is fundamentally empirical, resting on the principle of Bayesian updating. This reflects the judgment of the one-process school that all theorychange ultimately has an empirical basis. Yet evaluation of framework
theories is different from that of specific hypotheses, in the sense that it
is more indirect. In HBMs, framework theories, unlike more specific hypotheses, cannot be directly tested against data. Instead they are judged
on whether the hypotheses they give rise to do well on the data—or more
precisely, whether the specific theories they generate with high probability
themselves tend to assign high probability to the observations. As we haveseen, when this Bayesian principle of inference is applied to higher levelsof a hierarchy of theories, it can lead to effects that would seem to dependon ostensibly nonempirical criteria such as simplicity and pragmatic utility.
Thus, HBMs also reflect the judgment of the two-process school thatcriteria such as simplicity can be the immediate drivers of frameworkchange, although in this picture those criteria are ultimately grounded inempirical considerations in a hierarchical context. In place of the oneprocess versus two-process debate that animated much of twentieth-century philosophy of science, we might consider a new slogan for understanding the structure of scientific theories and the dynamics by which
they change: ‘Many levels, one dynamical principle’.

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