Reverse Engineering of Dynamic

Networks
B. STIGLER,a A. JARRAH,b M. STILLMAN,c AND R. LAUBENBACHERb
a Mathematical Biosciences Institute, The Ohio State University, Columbus,
Ohio, USA
b Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
c Mathematics Department, Cornell University, Ithaca, New York, USA

ABSTRACT: We consider the problem of reverse-engineering dynamic

models of biochemical networks from experimental data using polyno-
mial dynamic systems. In earlier work, we developed an algorithm to
identify minimal wiring diagrams, that is, directed graphs that represent
the causal relationships between network variables. Here we extend this
algorithm to identify a most likely dynamic model from the set of all
possible dynamic models that fit the data over a fixed wiring diagram.
To illustrate its performance, the method is applied to simulated time-
course data from a published gene regulatory network in the fruitfly
Drosophila melanogaster.

KEYWORDS: gene regulatory networks; reverse engineering; wiring di-

agrams; dynamic models

INTRODUCTION

Available reverse-engineering methods for biochemical networks span a

range of techniques and modeling frameworks, from statistical methods to
algorithms that have systems of ordinary differential equations as output. They
require different types and amounts of experimental data to perform well. The
goal of the DREAM effort is to provide a rigorous basis on which to assess and
compare the performance of individual methods. This paper proposes a new
reverse-engineering method within the framework of time-discrete dynamic
systems over finite-state sets. Such systems can be considered to form a
subclass of the class of dynamic Bayesian networks. In order to bring to bear
sophisticated mathematical tools we make the additional assumption that the
set of variable states can be equipped with the structure of a finite number
system. This assumption is familiar in the case of Boolean networks, where

Address for correspondence: A. Jarrah, Virginia Tech, Virginia Bioinformatics Institute, Washington
Street (0477), Blacksburg VA 24061. Voice: 540-231-9456; fax: 540-231-2606.
ajarrah@vbi.vt.edu

Ann. N.Y. Acad. Sci. 1115: 168–177 (2007). 

C 2007 New York Academy of Sciences.

doi: 10.1196/annals.1407.012
168
STIGLER et al. 169

Boolean algebra exploits the fact that the set {0, 1} is endowed with an
algebraic structure. Namely, we have an addition (1 + 1 = 0) and an obvious
multiplication, both of which satisfy the usual rules of arithmetic. It is natural
to consider more general finite number systems, such as the integers Z modulo
a prime integer, allowing for data discretization that is finer than the binary
ON/OFF discretization.
In this paper we assume that the set k of possible variable states forms a
finite number system called a finite field. It is well-known that every function
f : k n → k on a finite field k can be represented by a polynomial function.
Therefore we call the vector-valued function f = ( f 1 , . . . , f n ) : k n → k n
a polynomial dynamical system (PDS), where each f i : k n → k is called a
transition function. Note that each f i ∈ k[x 1 , . . . , xn ] is a polynomial in n
variables. This construction allows us to apply a rich collection of algorithms
from computational algebra and algebraic geometry.
Suppose we are given a data set D of state transition pairs (s i , t i ) for a network
on n nodes. Here, the inputs s i and the outputs t i are n-tuples of elements in
the finite field k, obtained by discretizing the real-valued measurements into
finitely many states (Dimitrova et al., manuscript submitted for publication). In
applications, k typically has less than 20 elements, depending on the dynamic
range of the data. We consider the following problem: find a PDS f : k n →
k n such that f (s i ) =t i . Note that as a consequence one also obtains a wiring
diagram for the network. In fact, the proposed algorithm consists of two parts,
the first of which infers one or a small family of most likely wiring diagrams
for the network. The second part infers a most likely dynamic model for each
of these wiring diagrams. While the second step in the algorithm could be used
as a stand-alone inference algorithm for dynamic modeling, coupling it with
the first part to provide constraints significantly improves its performance.
We present an algorithm, previously described in Jarrah et al.,1 which com-
putes all possible minimal wiring diagrams for a given data set of measure-
ments from a biochemical network and scores the diagrams. The algorithm
uses computational algebra, namely primary decomposition of monomial ide-
als, as the principal tool. By assigning a probability distribution on the set of
all minimal diagrams, we identify a single wiring diagram or a small fam-
ily of most likely diagrams. We have extended the algorithm to construct all
possible dynamic models on that wiring diagram and a most likely one is
identified by assigning a probability distribution on the set of all dynamic
models. The algorithm to compute a most likely dynamic model involves a
parameter choice, namely a total ordering on all terms of all appearing poly-
nomials. There are infinitely many such orderings. A geometric construct,
called the Gröbner fan, divides these infinitely many choices into finitely
many segments, each of which gives rise to a dynamic model. The probability
distribution is constructed on these finitely many models. We validated the
method on a Boolean data set from a published segment polarity network in
Drosophila melanogaster.
170 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES

NETWORK INFERENCE

In this discussion, we will focus on the reverse engineering of a gene

regulatory network; however, the proposed methods can be applied to more
general settings.
The method we describe below computes the solution of the problem one
gene at a time, so we can consider the outputs to be measurements for a single
gene, which we will denote by t i .

Inference of Network Topology

Let Dl = {(s1 , t1 ), . . . , (sm , tm )} be the data set for gene , where s i ∈ k n and
ti ∈ k. We first consider the problem of identifying all sets of variables V =
{xe1 , . . . , xeh } such that there exists a polynomial function f ∈ k[xe1 , . . . , xeh ]
where f (si ) = ti for all i = 1, . . . , r and V is minimal in the sense that if we
remove any variable x from V , there is no such function on V −{x}. Any set
that satisfies these criteria we call a minimal set.
We briefly describe the minimal-sets algorithm that finds and scores all such
minimal sets, and identifies one as the most likely by assigning a probability
distribution on the set of minimal sets. While a detailed description is available
in Jarrah et al.,1 we include it here for completeness.
We first partition the inputs {s 1 , . . . , s m } as follows. For a ∈ k, let
X a = {si ∈ k n : ti = a}.

Next we encode this information in a monomial ideal, that is, a set of

monomials closed under addition and multiplication.
Definition 1. Given the partition {Xa : a ∈ k } of the inputs {s 1 , . . . , s m },
define M ⊂ k[x 1 , . . . , xn ] to be the square-free monomial ideal generated by
{m(p, q) : p ∈ X a , q ∈ X b , and a = b ∈ k},

where m(p, q) := xi .
pi =qi
In other words, the monomial m(p,q) encodes the coordinates in which p
and q differ.
The following proposition is the key technical result underlying the algo-
rithm.
Proposition 2. Let V = {xe1 , . . . , xeh } be a subset of {x 1 , . . . , xn }. Then,
there is a function f ∈ k[xe1 , . . . , xeh ] such that f (s i ) = ti for all i if and only
if the ideal xe1 , . . . , xeh  contains M. Furthermore, the ideals xe1 , . . . , xeh 
are precisely the associated primes in the primary decomposition of the
ideal M.
STIGLER et al. 171

In particular, to find all minimal sets, it is enough to find the so-called

minimal primary decomposition of M, which is a decomposition of an ideal
into an intersection of “irreducible” components analogous to decomposing a
number into a product of factors. Such decompositions can easily be found
using methods from computational algebra.2
Each minimal set V is a candidate set of inputs for gene  and there may
potentially be a very large number of possible minimal sets. If additional
information about the network is available (e.g., about the existence or absence
of certain interactions), then it can be used for model selection (see Jarrah
et al.,1 for more details). Next we describe a statistical measure for model
selection in the case where no additional information about the network is
available.
Let D  be as above and let V be the collection of all minimal sets from
Proposition 2. For 1 ≤ i, j ≤ n, let Z j be the number of sets V in V of length j,
and let Wi ( j) be the number of sets V in V of length j such that xi ∈V . That is,
Z j = |{V ∈ V : |V | = j}| and Wi ( j) = |{V ∈ V : xi ∈ V and |V | = j}|.

We now score each variable x i as follows:

n
Wi ( j)
S(xi ) =
j=1
j · Zj

Using the scores of the variables, we score each set V ∈ V as follows:


T (V ) = S(xi ).
xi ∈V

We then obtain a probability distribution on the set V by normalizing the

scores of all sets in V. That is, for V ∈ V, we assign the normalized score
T (V )
T̄ (V ) =  .
T (G)
G∈V

The minimal sets with the highest score are returned by the algorithm. By
repeating this process for each gene, we obtain a family of minimal wiring
diagrams for the biochemical network.
Heuristically speaking, the minimal-sets algorithm captures minimal sets of
variable dependencies that allow for an explanation of the data as a functional
relationship, without actually computing that functional relationship. This is
left to the second part of the algorithm. If more than one possible minimal
set is returned, the family of them can be viewed as a set of experimental
hypotheses to be tested. A strength of the algorithm is that it does in fact find
ALL possible minimal wiring diagrams by completely surveying the space
172 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES

of possible diagrams rather than searching it heuristically. In practice, the

collection of highest-scoring minimal sets is quite small.

Inference of Network Dynamics

For each of the minimal wiring diagrams returned by the first part of the
algorithm we now infer a unique most likely dynamic model which has this
wiring diagram as the collection of variable dependencies. As explained ear-
lier, this can be done a variable at a time, by inferring the most likely transition
function for this variable. Suppose, for a fixed gene  in the network, the mini-
mal set for x  is Vl = {xe1 , . . . , xeh } ⊂ {x1 , . . . , xn }. Then we are interested in
the set of all transition functions on V l given D l , that is, the set of polynomial
functions such that
Fl = { f ∈ k[xe1 , . . . , xeh ] : f ( pe1 , . . . , peh ) = a, for all p ∈ X a , a ∈ k}.

The set F  can be computed similarly to how one solves a linear sys-
tem of equations.3 First, a particular solution f is computed, typically us-
ing the Lagrange interpolation formula. Then, by means of computational
algebra, the set of homogenous solutions is characterized as the ideal
I = {g ∈ k[xe1 , . . . , xeh ] : g( pe1 , . . . , peh ) = 0}. The set f + I represents the
model space, from which we can select a minimal model as follows. Compute
the normal form of f , denoted by f% I, by taking the remainder of f upon
division by the elements of I. This can be accomplished by first computing
a Gröbner basis of I, which is required for multivariate polynomial division.
However, the construction of a Gröbner basis requires fixing a term order, that
is, a total ordering on all possible monomials. Selecting a different term order
possibly results in a different normal form, thereby changing the model.
There is a geometric construction, called the Gröbner fan, which captures
the number of different forms by partitioning the set of all term orders into
cones where two term orders in the same cone give rise to the same normal
form (For more information about the Gröbner fan, see Sturmfels.4 ) Thus it is
enough to compute the normal form of f with respect to only one term order
from each cone. Then we pick the normal form that shows up most often as
the transition function for x  . To be precise, suppose the Gröbner fan of I has
q cones and the distinct normal forms are { f 1 , . . . , f s } where f i is the normal
form of f with respect to only h of the q cones. Then the score of the normal
form f i is qh . This gives a probability distribution on the set of normal forms.
The normal form with the maximum score is chosen as the transition function
for x l . Repeating this for each gene in the network we obtain a dynamic model
of the network.
In essence, the Gröbner fan approach reduces the infinitely many possible
choices of term order to finitely many choices of a normal form and makes the
STIGLER et al. 173

method independent of the term-order parameter by algorithmically exploring

the result for all possible parameter choices. Again, this is done by systemat-
ically, taking into account all possibilities rather than heuristically exploring
the parameter space.
This algorithm has been implemented in the computer algebra system
Macaulay25 and the Gröbner fan computations are done using the program
Gfan.6
Algorithm-1
Input: Data set D = {(si , ti ) : i = 1, . . . , m}
Output: Minimal PDS(s) that fit D
For each  ∈ {1, . . . , n} do
1. Compute the minimal sets for D  and select the highest-scoring set(s) V .
2. For each V do
(a) Compute the ideal I of inputs in D V , the restriction of D  to the
coordinates defined by V .
(b) Compute the Gröbner fan G of I.
(c) Compute a transition function fl .
(d) Compute NF = { fl % G : G ∈ G} and select the highest-scoring
normal form(s) f  .
3. Return the normal form(s) f  for D  .
The output of the above algorithm is a collection of PDSs, whose transition
functions are most representative among all possible transition functions.

AN APPLICATION TO A GENE REGULATORY NETWORK

In this section, we consider a segment polarity gene network in the

D. melanogaster embryo, for which a bottom-up Boolean model was proposed
by Albert and Othmer.7 The authors constructed a dynamic model consisting
of 15 Boolean functions based on known connectivity structure of the network.
Laubenbacher and Sigler3 aimed to reconstruct this Boolean model of the net-
work from data generated by this model. While these authors demonstrated
favorable performance of their reverse-engineering method (84% identifica-
tion with 20% false positives and 15% false negatives), it relies heavily on
the choice of a total ordering of the variables. Jarrah et al.1 reconstructed the
wiring diagram, based on the minimal-sets algorithm. We have extended these
results to include a dynamic model of the network.

METHODS AND RESULTS

We generated 168 state transitions from the Boolean model in Albert and
Othmer7 and applied Algorithm-1 to these data. We note that the data make
up < 0.01% of all possible state transitions.
174 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES

FIGURE 1. The reverse-engineered wiring diagram for the Boolean network. Solid and
dashed edges make up the wiring diagram returned from the minimal-sets algorithm. Solid
edges represent true positives; dotted edges, true negatives; and boldface, false positives
(x11). Dashed edges arise from multiple minimal sets. For example, x8 has two highest-
scoring minimal sets: one involving x4, the other x16.

Each node had a unique highest-scoring minimal set, with the exception of
nodes 8 and 10: the data for x8 and x10 admitted two highest-scoring minimal
sets each. FIGURE 1 shows the reconstructed wiring diagram. We identified 38
edges, with all but 1 being correct, namely, the self-loop on x11, and missed 9
edges. While we failed to discover the remaining edges, all have been identified
as nonidentifiable interactions. For more details, see Jarrah et al.1
For each node, the highest-scoring normal forms associated to a choice
of minimal set, were returned. In this example, each minimal set admitted a
unique normal form, producing four distinct PDSs. The transition functions
are given below. Notice that each of the nodes 8 and 10 could take one of two
local transitions, since each of x8 and x10 has two highest-scoring minimal
STIGLER et al. 175

sets. Underlined terms represent false positives and terms in brackets are true
negatives.

f1 = x1
f 2 = x 1x 14 + x 2x 14 + x 2x 15 + x 2 + [12 terms]
f3 = x2
f 4 = x 16 + [5 terms]
f5 = x4
f 6 = x 5 + [1 terms]
f7 = x6
f 8 = x 11x 13x 20 + x 11x 13x 21 + x 4x 13 + x 11x 13 +
x 13x 20 + x 13x 21 + [37 terms]
f 8 = x 11x 13x 20 + x 11x 13x 21 + x 11x 13 + x 13x 16 +
x 13x 20 + x 13x 21 + [37 terms]
f 9 = x 8x 9 + x 8x 18 + x 8x 19 + x 8 + x 9 + x 18 + x 19
+ [6 terms]
f 10 = x 8x 9x 20 + x 8x 9x 21 + x 8x 20 + x 9x 20 + x 8x 21
+ x 9x 21 + [21 terms]
f 10 = x 8x 10x 20 + x 8x 10x 21 + x 8x 20 + x 10x 20 +
x 8x 21 + x 10x 21 + [25 terms]
f 11 = x 8x 9x 11 + x 8x 9 + x 9x 11 + x 8x 20 + x 8x 21 +
x 8 + x 9 + 1 + [31 terms]
f 12 = x 5 + 1
f 13 = x 12
f 14 = x 11x 13x 20 + x 11x 13x 21 + x 11x 13 + x 13x 20 +
x 13x 21 + [2 terms]
f 15 = x 11x 13x 20 + x 11x 13x 21 + x 11x 13 + x 13x 20 +
x 13x 21 + x 13 + [2 terms]

For any choice of model, we correctly identified 6 of the 15 Boolean func-

tions. In the PDS with f 8 and f 10, on average 90% of the terms in the transition
functions are correct; however, 39% of the terms in the Boolean functions were
not identified. These terms are not recoverable since they vanish on the given
data and are divided out in the computation of the normal forms.
For any choice of model, we correctly identified 6 of the 15 Boolean func-
tions. In the PDS with f 8 and f 10, on average 90% of the terms in the transition
functions are correct; however, 39% of the terms in the Boolean functions were
not identified. These terms are not recoverable since they vanish on the given
data and are divided out in the computation of the normal forms. For similar
analysis for the other three models, see TABLE 1.
This result is very interesting for two reasons. First, it is extremely surprising
that the method performs as well as it does on the given data set. On a
random Boolean network of comparable size and with a comparable dataset
the method would very likely have performed extremely poorly, since the input
176 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES

TABLE 1. A summary for the 4 PDSs for the Boolean network. Each value represents an
average over the terms in the transitions functions
TP FP TN
M1 (f 8, f10) 0.90 0.10 0.39
M2 (f 8 , f10) 0.90 0.10 0.39
M3 (f 8, f10 ) 0.86 0.14 0.40
M4 (f 8 , f10 ) 0.86 0.14 0.40
TP = true positives; FP = false positives; TN = true negatives.

is a vanishingly small part of the model’s state space. It would be interesting

to explore rigorously what is special about biological models that lead to
comparatively easy identifiability. Second, it is because of the mathematical
foundation of the method that we are able to assess the specific reason for
the algorithm’s failure to infer certain features of the network. In this case
the dataset does not contain enough information to infer some of the network
connections and, therefore, some of the transition functions. This fact points
to the difficulty of assessing the absolute performance of reverse-engineering
methods without having a way to measure the information content of the data
set used. It is possible to include more data that allow the algorithm to correctly
identify all features of the network.

DISCUSSION

We have presented an algorithm that identifies most likely polynomial dy-

namical systems for the most likely wiring diagrams. The method is an ex-
tension of the minimal-sets algorithm described in Jarrah et al.1 in which we
incorporate the Gröbner fan, a geometric object to encode the dynamic model
space. The use of Gröbner fans for modeling was first introduced by Dimitrova
et al.8 In their paper, the authors used the Gröbner fan to compute the model
space globally, that is, in the full ring k[x 1 , . . . , xn ]. We have adapted it to
perform a local computation of the model space, that is, over a smaller ring
k[x 1 , . . . , xr ], for r ≤ n. The advantage to this approach is that we reduce the
model space dimension by restricting the ring to the variables in a minimal
set. This allows us to rigorously analyze the space of PDSs as opposed to
performing random sampling as was done in Allen et al.9 and Laubenbacher
and Stigler.3
As with all other system-identification methods of this type, a rigorous
validation requires techniques to measure the quality of the given input data.
No such methods have been proposed at this time for this modeling framework,
an important open problem, so validation rests on individual case studies. Also,
it is important to use simulated data sets rather than actual experimental data,
since the underlying regulatory networks are not completely known in almost
all cases.
STIGLER et al. 177

ACKNOWLEDGMENTS

B.S. was supported by NSF Grant 0112050 and NIH Grant RO1 GM068947-
01. A.J. was partially supported by NSF Grant DMS-0511441. R.L. was par-
tially supported by NIH Grant RO1 GM068947-01 and NSF Grant DMS-
0511441. M.S. was partially supported by NSF Grant DMS-0311806.

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