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Abstract. My research lies at the intersection of mathematical logic, theoretical computer sci-
ence, and several related fields including complexity theory and combinatorics on words. I have
three papers which have been accepted for publication, one which has been submitted, and others
in preparation. These papers study different aspects of automatic structures: mathematical objects
which can be represented by finite automata. I have ongoing research in this area and collabora-
tions with computable model theorists and number theorists. I am also directing an undergraduate
research project studying classes of trees described by finite automata.

1. Introduction

My focus has been on the representation of mathematical structures by automata. This sub-
ject has numerous interesting and difficult open problems and connects with many branches of
mathematics. Various theorems assert the existence of some mathematical object based on data
supplied in the hypotheses of the theorem. Sometimes there is an algorithm to construct the
object asserted to exist directly from the data of the problem. Whole branches of mathematics
and computer science are devoted to studying the existence and complexity of such algorithms
(recursive function theory [53]; polynomial-time complexity theory [56]; parameterized complexity
theory [16]). These areas inform and are motivated by investigations of the effective content of
theorems. Milestones in such investigations include van der Waerden’s work on effective fields
[55], Kleene and Church’s exploration of computation in the 1930s, and the resulting interactions
between algebraic structures, model theory, and computation seen in the work of Frölich and
Shepherdson [20], Malcev [40], Rabin [48], and the Ershov and Nerode schools.
To understand the effective aspects of mathematical theorems, we study representations of ob-
jects using specific models of computation. A structure (or model) is a general abstraction of any
mathematical object. Given a signature (R1m1 , . . . , Rtmt ), a structure with that signature is a set
(universe or domain) of basic elements along with relations RjA ⊂ Amj interpreting the symbols Rj
of the signature. We can impose effectiveness constraints by requiring the domain and each atomic
relation to be recognized or computed by a machine with specified complexity. Computable model
theory [21] uses Turing machines [54] as the underlying mode of computation. As part of their
feasible mathematics program, Nerode and Remmel [45] suggested the study of polynomial-time
structures, where the Turing machines recognizing the basic objects are required to do so in poly-
nomial time. An important early result by Cenzer and Remmel [9] showed that every computable
purely relational structure is computably isomorphic to a polynomial-time structure. This implies
that solving questions about the class of polynomial-time structures is as hard as solving them
for the class of computable structures. Since polynomial-time structures and computable struc-
tures yielded similar complexity results, greater restrictions on the complexity of computations
were imposed. In 1995, Khoussainov and Nerode suggested bringing in models of computations
that have less computational power than polynomial-time Turing machines. The hope was that
if these weaker machines were used to represent the domain and basic relations, then perhaps
isomorphism invariants could be more easily understood. Specifically, they suggested the use of
finite state machines (automata) as the basic computation model.

Most of my research contributions thus far have come from this perspective: studying math-
ematical objects described by finite automata. Finite automata were first introduced by S.C.
Kleene [36] in his explorations of McCulloch and Pitt’s neural nets. A finite automaton (over a
finite alphabet) is defined by a finite set of states, a designated initial state, a transition relation,
and a distinguished subset of accepting states. For a given input finite word, the automaton starts
at the initial state and then reads each letter of the input sequentially, transitioning to new states
as governed by a transition relation (essentially performing like a computer program). If, after
reading the entire input, the automaton is in an accepting state, it accepts the input word. Finite
automata can be viewed as restricted Turing machines in that there is only one-pass reading of the
input and there is a fixed finite amount of memory. The set of words accepted by the automaton
is called its language. A set of finite words is regular if it is the language of some finite automaton.
The class of regular languages forms a Boolean algebra (it is closed under union, intersection,
and complementation). An automatic structure is one whose domain and basic relations are each
recognizable by finite automata. Note that any structure whose domain is finite is automatic.
Conversely, any automatic structure must have at most a countable domain, because it must be
encodable as a set of finite strings over some finite alphabet.
In the computer science community, an interest in automatic structures comes from problems
related to model checking. Model checking is motivated by the quest to prove correctness of
computer programs, a highly topical endeavour given the ubiquity and complexity of software
controlling many aspects of modern life. The importance of this project is highlighted by the
awarding of the 2007 ACM Turing prize to Clarke, Emerson, and Sifakis for their work in this area.
Given an automaton representing the software program for a particular task and a specification
(formula) in a formal system, the model checking problem asks us to compute all the states of the
system that satisfy the specification. Since the state space may be infinite, a naı̈ve examination of
each state in turn may not terminate. Abstraction methods try to represent the behaviour of the
system in finite form. Model checking then reduces to checking a finite representation of the state
space to identify the states that satisfy the specification. Automatic structures arise naturally in
infinite state model checking since both the state space and the transitions of infinite state systems
are usually recognizable by finite automata.

2. Automaton Decision Procedures

The idea of using automata to study structures goes back to the work of Büchi. Recall that first-
order logic contains the Boolean connectives along with quantifiers over domain elements; monadic
second-order logic also allows quantification over subsets of the domain. The theory of a structure
with respect to some logic is the set of sentences in that logic which hold of the structure. Büchi
[6], [7] used automata to prove the decidability of the monadic second-order theory of the natural
numbers with one successor. Rabin [49] then used automata to prove his incredibly fruitful result
that the monadic second-order theory of the natural numbers with two successor functions (the
infinite binary tree) is also decidable. In the realm of logic, these results have been used to prove
decidability of first-order and monadic second-order theories. Büchi realized that automata and
Presburger arithmetic (the first-order theory of the natural numbers with addition) are closely
connected. He used automata to give a simple proof (not using quantifier elimination) of the
decidability of Presburger arithmetic. Capturing this notion, Hodgson [25] defined automaton
decidable theories in 1982. While he coined the definition of automatic structures, little was
done in the 1980s to follow up on his work. In 1995, Khoussainov and Nerode [31] rediscovered
the concept of automatic structures and initiated a systematic study of the area. In subsequent

papers [5, 34], it was shown that the extended first-order logic theory of any automatic structure
(obtained by adding sentences with the ∃∞ and ∃n,m quantifiers) is decidable. Thus, to prove
the decidability of this theory for a particular structure, it is sufficient to code the domain of the
structure as a regular set of strings in such a way as all the atomic relations are finite automaton
recognizable. Similar results can be proved for structures which can be represented by automata
whose inputs are infinite strings.
The p-adic numbers are defined as completions of the rational numbers with respect to the p-adic
norms. They were introduced by Hensel in 1897 [23, 24]. The first-order theory of these numbers
with the valuation groups as a distinguished subsets was studied by [3, 2, 18, 11, 57, 58, 17] using
quantifier elimination. In my thesis, I proved the decidability of the first-order theory of Qp with
addition and the distinguished ring of integers using automata techniques.
Theorem 1 (Minnes; 2008, PhD). The first-order theory of (Qp ; Zp , +, 0, 1) is decidable.

PThe elements
of the ring of formal power series over the field K, K[[x]], are the formal sums
n≥0 n x , where addition is defined term-by-term and multiplication is analogous to polynomial
multiplication. The field of formal Laurent series, K((x)), contains formal sums with finitely many
non-zero terms with negative powers of x. In my PhD thesis, I also proved the following theorem
using a representation of formal Laurent series by automata [41].
Theorem 2 (Minnes; 2008, PhD). If p is prime and d is a natural number, the first-order theory
of the structure (Fpd ((x)); Fpd [[x]], +, 0) is decidable.
This result is exciting in the context of Hilbert’s tenth problem: is there an algorithm which
decides whether any given multivariable polynomial with integer coefficients has a solution in the
integers. Davis, Putnam, Robinson, and Matiyasevich’s collaboration led to a negative result [13].
Poonen’s recent AMS Notices article [47] articulates the current state of the art in the study of
Hilbert’s tenth problem over other rings. In particular, it is still unknown whether a decision
procedure exists for the ring of formal Laurent series over a finite field. My work above may give
a new approach to this problem, though a significant hurdle remains in representing the full ring
structure of formal Laurent series. I have been collaborating with Poonen in this direction.

3. Isomorphism Problem for Automatic Structures

Considerable work has been invested in classifying algebraically the automatic members of vari-
ous classes. Historically, these results have come in pairs: first proving that structures which satisfy
certain properties are automatic (the easier direction), and then showing that no other member of
the class can be automatic (harder). The first result of this sort was that the automatic well-orders
are exactly those with order-type less than ω ω (sufficiency given by Khoussainov and Nerode in
[31] and necessity by Delhommé in [14]). Khoussainov, Nies, Rubin and Stephan characterized
the isomorphism types of automatic Boolean algebras [32]. There are partial characterizations of
automatic linear orders, well-founded partial orders, infinite groups and trees in terms of model
theoretic concepts such as Cantor-Bendixson ranks (Khoussainov, Rubin and Stephan [35]; Khous-
sainov and Minnes [30]; and Nies and Thomas [46]). Some of these results have direct algorithmic
implications. For example, the isomorphism problems for automatic well-ordered sets and Boolean
algebras were shown to be decidable using the respective classifications [32]. A large class of auto-
matic structures which has a very good classification is that of unary automatic structures, those
whose domain can be encoded as finite strings over the alphabet {1}. This is a strict subclass of
the automatic structures: for example, the order type of the rational numbers is representable as

an automatic structure over the alphabet {0, 1} but not as a unary automatic structure [33, 4].
The structure of a unary automaton can be described in terms of modular relations and has led to
a classification of all unary automatic graphs as eventually periodic chains of finite graphs [33, 4].
In recent work with Liu [38], we have used this classification to give polynomial-time algorithms
for the isomorphism problem of various classes of unary automatic structures. Moreover, we have
shown that, relative to natural isomorphism invariants, there are very concise (polynomial-space)
automata representing any such structure.
Theorem 3 (Liu, Minnes 2009). The isomorphism problem for unary automatic linear orders,
equivalence structures, and trees can be decided in polynomial-time (with respect to the size of
the automaton). In particular, this implies that the state complexity of these classes is low. The
isomorphism problem for unary automatic graphs of finite degree is solved in elementary time.

Because of ubiquitous applications of graphs and their intrinsic interest in mathematics and
computer science, Khoussainov, Liu, and I [29] studied the complexity of natural graph questions
on unary automatic graphs of finite degree. We introduced the concept of the edge path of a finite
directed path, which interfaces well with the periodic characterization of unary automatic graphs.
Theorem (Khoussainov, Liu, Minnes 2007). For a unary automatic graph of finite degree, there
are polynomial-time algorithms which decide each of the following questions: is the graph infinite?
does the graph have an infinite component? is the graph connected? given two elements of the
graph, is there a path between them?

4. High complexity of automatic structures

The results about automatic structures can be seen to pull in two opposite directions. One
body of work demonstrates that automatic structures are simple from a logical and computational
point of view. However, many recent results have demonstrated richness in the class of automatic
structures. In particular, there is a strong sense in which computable structures can be encoded
into automatic structures using their Turing machine presentations. In [30], we proved that each
computable structure A can be embedded into an automatic structure B in such a way that A is
Lω1 ,ω -definable in B, and the embedding preserves the isomorphism type A.
Since every automaton is a (restricted) Turing machine, any structure that can be represented
by automata can also be represented by Turing machines. Hence, they are computable structures.
Within the context of computable model theory, sharp bounds on the complexity of computable
structures have been established. These bounds are given as ordinal values of various complexity
measures. Not surprisingly, most of these bounds occur at the boundary between the computable
ordinals and the non-computable ordinals. The question now becomes: does passing to the smaller
subclass of automatic structures lead to lower complexity (as measured by the various complexity
metrics)? In [30], we answered this question for three complexity measures: ordinal height of
well-founded binary relations, Cantor-Bendixson ranks of trees, and Scott ranks. A well-founded
binary relation is one where each subset has a minimal element. The ordinal height is defined
inductively on elements of a well-founded relation in such a way that the height of any ordinal
is itself. The first non-computable ordinal, ω1CK , is thus a sharp bound on the ordinal heights of
computable well-founded relations. Vardi asked whether the bound remains tight when we restrict
to automatic structures. The following theorem answers this question.
Theorem 4 (Khoussainov, Minnes 2007). For each computable ordinal α, there is an automatic
well-founded relation A such that α ≤ r(A) ≤ ω + α.

Corollary. Ordinal heights of automatic well-founded relations are unbounded below ω1CK .

As a key tool in proving his famous isomorphism theorem for countable structures, Scott defined
an infinitary sentence which describes the isomorphism type of each structure [52]. The Scott rank
of a structure is essentially the quantifier rank of this sentence and describes the complexity of
its automorphism orbits. Over the past forty years, there has been interest in the Scott ranks of
computable structures. Nadel [44] showed that the bound on Scott rank for computable structures
is ω1CK +1. Harrison’s work [22] gave the first example of a computable structure with the maximal
Scott rank. More recently, Cholak, Downey, and Harrington [10] gave a natural example of a
(hyperarithmetical) structure with Scott rank ω1CK + 1. It took considerable effort (Makkai [39];
Knight and J. Millar [37]; Calvert, Goncharov, Knight [8]) to show that there are computable
structures whose Scott rank is the limit ordinal ω1CK . The following theorem transfers any result
about Scott ranks of computable structures to the setting of automatic structures.
Theorem (Khoussainov, Minnes 2007). For each computable structure, there is an automatic
structure with the same Scott rank.
Corollary. There are automatic structures with Scott ranks any computable ordinal, ω1CK , ω1CK +1.

We also measure the complexity of trees. Trees may be thought of as partial orders with
minimal elements, and which satisfy the property that the set of predecessors of any element is
linearly ordered. We consider successor trees: instead of having access to the full partial order,
only the immediate successor relation is given. (Note that, computability considerations aside,
successor trees form the same class as partial order trees.) The Cantor-Bendixson rank quantifies
the branching of the tree via isolated paths (this is related to the notion of a Cantor-Bendixson
derivative in topology, see [28]). As before, ω1CK is the sharp bound on Cantor-Bendixson ranks
of computable trees. Restricting to automatic successor trees does not decrease this bound.
Theorem (Khoussainov, Minnes 2007). For each computable ordinal α, there is an automatic
successor tree whose Cantor-Bendixson rank is α.

The three theorems above involve fundamentally different measure of complexity. However,
their proofs are similar: to transfer a result about computable structures to one about automatic
structures, we consider the Turing machine presentations of the computable structures. Associated
with each Turing machine is its configuration graph, which captures the transition relation between
states of the machine. This configuration graph is an automatic structure. Thus, proving the
theorems above involves connecting configuration graphs of Turing machines in such a way as to
preserve automaticity of the resulting structure, while maintaining high complexity. However, this
is challenging because the complexity of any configuration graph by itself is very low.

5. Ongoing Projects

5.1. Classifications and embeddings of automatic structures. It is not hard to see that
any infinite linear order contains either an infinite increasing sequence or an infinite decreasing
sequence. The computable version of this theorem fails [51]: there is a computable linear order
with no computable suborder isomorphic to ω and no computable suborder isomorphic to ω ∗ . I
have recently proved the automatic analogue of the classical result [42].
Theorem 5 (Minnes; 2008). There is a computable procedure that, given an automatic infinite
linear order L, produces (an index for) a regular subset of order type ω or order type ω ∗ .

Blumensath and Grädel showed that every structure first-order interpretable in an automatic
structure has an automatic presentation [5]. Therefore, the sum of any two automatic linear orders
is itself automatic. The converse of this would generalize Theorem 5 for arbitrary summands of an
automatic linear order. This line of work parallels investigations of linear orders in the computable
setting (see [15] for a survey or [12] for investigations into initial segment complexity).
Project 1. Given an automatic linear order L which can be expressed as L1 +L2 , what conditions
guarantee that either L1 or L2 has an automatic presentation?

Recently, Kach and Miller [27] and Kach and Levin [26] further explored the question of em-
beddings in the context of computable structures. In my ongoing collaboration with Kach, we are
studying the behaviour of automatic structures under embeddings.
Project 2. Let C be the class of automatic permutation structures, automatic equivalence struc-
tures, or automatic trees. Is it true that for any A1 , A2 ∈ C, if A1 embeds classically into A2 there
is an automatic copy of A1 in A2 ? Can this copy be found computably? uniformly computably?

5.2. Parameterized complexity. A relatively recent and very exciting application of automata
theory is in the area of paramterized complexity. This field was initiated by Downey and Fellows
[16]. Their insight was that many instances of NP-complete problems which arise in practice (for
example, travelling salesman or satisifability) are actually feasible. Therefore, they suggest that
the intractability can be traced back to some feature of the input, described by some parameter
which, when sufficiently small, makes the problem tractable. Some of the deepest theorems in this
field connect Robertson and Seymour’s celebrated Graph Minors Theorem [50] with automata
theory to formulate (fixed-parameter) tractable algorithms [19].
Project 3. It has already been observed that different choices of parameter lead to different
tractability results. What is the theory of multi-parameter complexity? In particular, is there a
notion of joint complexity distribution? This is an ongoing joint project with Nerode.

5.3. Output automata, trees, and real numbers. So far, we have treated automata as recog-
nition or acceptance machines. However, there are similar computation models (finite state trans-
ducers, deterministic finite automata with output) which are functional; that is, they convert input
strings to output strings. The class of functions represented by such machines is different from
the class of functions whose graphs are automaton recognizable. Mohri’s group at AT&T Labs
has already applied finite-state transducers with great effect to the problem of natural language
processing [43].
Project 4. In order to connect automaton representations with actual numerical problems, we
need to work over the real numbers. What is the correct definition of an automaton computable
real-valued function? Which closure properties apply the class of such function? This is an ongoing
joint project with Khoussainov and Cenzer.

Allouche and Shallit [1] use deterministic finite automata with output to study combinatorics
on infinite words. Words represented in this way have been connected to morphic words and to
algebraicity of real numbers.
Project 5. The current automata-theoretic definition used by the combinatorialists is highly
base-dependent. Is there a way to elucidate this using trees and automata on trees as the basic
structures? This is one of the goals of the undergraduate research project I am supervising.

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Department of Mathematics, MIT, Cambridge MA, 0213

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