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\section{An arithmetic for the polynomial hierarchy}
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%Our base language is $\{ 0, \succ{} , + , \times, \smsh , |\cdot| , \leq \}$.
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Our base language is defined by the set of functions (and constants) symbols $\{ 0, \succ{} , + , \times, \smsh , |\cdot|, \hlf{}.\}$ and the set of predicate symbols
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 $\{\leq, \safe, \normal \}$.
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We use classical logic connectives $\neg$, $\cand$, $\cor$, $\forall$, $\exists$. The formula $A \cimp B$ will be a notation for $\neg A \cor B$.
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We will also use as shorthand notations:
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$$ (s=t) = (s\leq t) \cand (t\leq s), \quad (s\neq t) = \neg(s=t).$$
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We call \textit{atomic formulas} formulas of the form $(s\leq t)$ or $(s=t)$.
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 As we are in classical logic, we will assume, without loss of generality, that formulas are in \textit{De Morgan normal form}, that is to say that in formulas negation can only occur on atomic formulas, and that there is not any occurrence of subformula of the form $\neg \neg A$.
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In the sequel $\succ{0}(x)$ stand for $2\cdot x$ and $\succ{1}(x)$ stand for $\succ{}(2\cdot x)$,
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Now, let us describe the axioms we are considering.The $\basic$ axioms are as follows:
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\[
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\begin{array}{l}
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\safe (0) \\
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\forall x^\safe . \safe (\succ{} x) \\
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\forall x^\safe . 0 \neq \succ{} (x) \\
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\forall x^\safe , y^\safe . (\succ{} x = \succ{} y \cimp x = y) \\
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\forall x^\safe . (x = 0 \cor \exists y^\safe.\  x = \succ{} y   )\\
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\forall x^\safe, y^\safe . \safe(x+y)\\
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\forall u^\normal, x^\safe . \safe(u\times x) \\
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\forall u^\normal , v^\normal . \safe (u \smsh v)\\
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\forall u^\normal \safe(u) \\
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\forall u^\normal \safe(\hlf{u})\\
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\forall x^\safe \safe(|x|)
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\end{array}
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\]
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\patrick{did I type writly the 2 last axioms?}
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and the list of axioms of Appendix \ref{appendix:arithmetic}, coming from \cite{Buss86book}.
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\anupam{in fact, we use essentially the same language, so just take Buss' Basic axioms after proper typing. Should also add the symbol $\hlf{\cdot}$ for binary predecessor then we have the full language of bounded arithmetic.}
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Notation: if $\vec t=t_0,\dots, t_k$, we will denote as $\safe(\vec t)$ the sequence of formulas $\safe(t_0),\dots, \safe(t_k)$. Similarly for $\normal(\vec t)$.
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\begin{definition}
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[Derived functions and notations]
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We write $1,2,3,\dots$ for the terms $\succ{} 0, \succ{} \succ{} 0, \succ{} \succ{} \succ{} 0 \dots$, and frequently omit the $\times$ symbol.
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We define the functions $\succ 0 x , \succ 1 x$ as $2 x$ and $2x +1$ respectively.
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Need $bit$, $\beta$ , $\pair{}{}{}$.
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\end{definition}
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(Here use a variation of S12 with sharply bounded quantifiers and safe quantifiers)
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Use base theory + sharply bounded quantifiers.
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\begin{definition}
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[Quantifier hierarchy]
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$\Sigma^\safe_0 = \Pi^\safe_0 $ is the set of formulae whose only quantifiers are sharply bounded.
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We define $\Sigma^\safe_{i+1}$ as the closure of $\Pi^\safe_i $ under $\cor, \cand $, safe existentials and sharply bounded quantifiers.
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We define $\Pi^\safe_{i+1}$ as the closure of $\Sigma^\safe_i $ under $\cor, \cand $, safe universals and sharply bounded quantifiers.
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\end{definition}
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\anupam{Collection principles for prenexing? Otherwise need to add closure under sharply bounded quantifiers.}
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\begin{definition}\label{def:polynomialinduction}
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[Polynomial induction]
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The \emph{polynomial induction} axiom schema, $\pind$, consists of the following axioms,
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\[
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A(0)
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\cimp (\forall x^{\normal} . ( A(x) \cimp A(\succ{0} x) ) )
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\cimp  (\forall x^{\normal} . ( A(x) \cimp A(\succ{1} x) ) )
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\cimp  \forall x^{\normal} . A(x)
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\]
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for each formula $A(x)$.
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For a class $\Xi$ of formulae, $\cax{\Xi}{\pind}$ denotes the set of induction axioms when $A(x) \in \Xi$.
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%We write $I\Xi$ to denote the theory consisting of $\basic$ and $\cax{\Xi}{\ind}$.
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\end{definition}
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\begin{definition}\label{def:ariththeory}
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Define the theory $\arith^i$ consisting of the following axioms:
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\begin{itemize}
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	\item $\basic$;
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	\item $\cpind{\Sigma^\safe_i } $:
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\end{itemize}
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and an inference rule, called $\rais$, for closed formulas $\exists y^\normal . A$:
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\[
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 \dfrac{\forall \vec x^\normal . \exists  y^\safe .  A }{ \forall \vec x^\normal .\exists y^\normal . A}
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\]
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\end{definition}
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\patrick{I think in the definition of  $\arith^i$ we should impose that the formulas considered are \textit{integer positive}, that is to say that the only negative occurrences of atoms $\safe(t)$, $\normal(t)$ are those occurring in $\forall^{\safe}$ and $\forall^{\normal}$.  Indeed I don't think this can be just proved to be a consequence of a kind of 'normal form' of proofs, as we had discussed (see sect 4.4)}
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\anupam{In induction,for inductive cases, need $u\neq 0$ for $\succ 0$ case.}
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It is often useful for us to work with \emph{length-induction}, which is equivalent to polynomial induction and well known from bounded arithmetic:
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\begin{proposition}
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	[Length induction]
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	The axiom schema of formulae,
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\begin{equation}
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\label{eqn:lind}
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	( A(0) \cand \forall x^\normal . (A(x) \cimp A(\succ{} x)) ) \cimp \forall x^\safe. A(|x|)
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\end{equation}
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	for formulae $A \in \Sigma^\safe_i$
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	is equivalent to $\cpind{\Sigma^\safe_i}$.
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\end{proposition}
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\begin{proof}
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	Suppose we have $A(0)$ and $A(a) \cimp A(\succ{} a)$ for each $a \in \normal$.
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	Then, by $\basic$, we have that $A(|a|) \cimp A(|2a|)$ and $A(|a|) \cimp A(|2a+1|)$ for each $a \in \normal$, whence we may conclude $\forall x. A(|x|)$ by polynomial induction on $A(|x|)$.
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\end{proof}
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Let us refer to the axiom schema in \eqref{eqn:lind} as $\clind{\mathcal C}$, when $A \in \mathcal C$.
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We will freely use this in place of polynomial induction whenever it is convenient.
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\begin{lemma}
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[Sharply bounded lemma]
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Let $f_A$ be the characteristic function of a predicate $A(u , \vec u ; \vec x)$.
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Then the characteristic functions of $\forall u \prefix v . A(u,\vec u ; \vec x)$ and $\exists u \prefix v . A(u , \vec u ; \vec x)$ are in $\bc(f_A)$.
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\end{lemma}
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\begin{proof}
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	We give the $\forall$ case, the $\exists$ case being dual.
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	The characteristic function $f(v , \vec u ; \vec x)$ is defined by predicative recursion on $v$ as:
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	\[
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	\begin{array}{rcl}
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	f(0, \vec u ; \vec x) & \dfn & f_A (0 , \vec u ; \vec x) \\
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	f(\succ i v , \vec u ; \vec x) & \dfn & \cond ( ; f_A (\succ i v, \vec u ; \vec x) , 0 , f(v , \vec u ; \vec x) )
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	\end{array}
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	\]
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\end{proof}
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Notice that $\prefix$ suffices to encode usual sharply bounded inequalities,
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since $\forall u \leq |t| . A(u , \vec u ; \vec x) \ciff \forall u \prefix t . A(|u|, \vec u ; \vec x)$.
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\subsection{Graphs of some basic functions}\label{sect:graphsbasicfunctions}
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Todo: $+1$,
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\subsection{Encoding sequences in the arithmetic}
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\todo{}
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\anupam{Assume we have a $\Sigma^\safe_1$ predicate $\beta(i,x,y)$, expressing that the $i$th element of the sequence $x$ is $y$, such that $\arith^1 \proves \forall i^\normal , x^\safe . \exists ! y^\safe . \beta (i,x,y)$.}
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\subsection{A sequent calculus presentation}
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\begin{figure}
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\[
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\small
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\begin{array}{l}
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\begin{array}{cccc}
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%\vlinf{\lefrul{\bot}}{}{p, \lnot{p} \seqar }{}
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%& \vlinf{\id}{}{p \seqar p}{}
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%& \vlinf{\rigrul{\bot}}{}{\seqar p, \lnot{p}}{}
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%& \vliinf{\cut}{}{\Gamma, \Sigma \seqar \Delta , \Pi}{ \Gamma \seqar \Delta, A }{\Sigma, A \seqar \Pi}
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 \vlinf{id}{}{\Gamma, p \seqar p, \Delta }{}
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& \vliinf{cut}{}{\Gamma \seqar \Delta }{ \Gamma \seqar \Delta, A }{\Gamma, A \seqar \Delta}
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&&
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\\
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\noalign{\bigskip}
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%\noalign{\bigskip}
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\vliinf{\lefrul{\cor}}{}{\Gamma, A \cor B \seqar \Delta}{\Gamma , A \seqar \Delta}{\Gamma, B \seqar \Delta}
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&
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\vlinf{\lefrul{\cand}}{}{\Gamma, A\cand B \seqar \Delta}{\Gamma, A , B \seqar \Delta}
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&
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%\vlinf{\lefrul{\laand}}{}{\Gamma, A\laand B \seqar \Delta}{\Gamma, B \seqar \Delta}
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%\quad
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\vlinf{\rigrul{\cor}}{}{\Gamma \seqar \Delta, A \cor B}{\Gamma \seqar \Delta, A, B}
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&
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%\vlinf{\rigrul{\laor}}{}{\Gamma \seqar \Delta, A\laor B}{\Gamma \seqar \Delta, B}
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%\quad
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\vliinf{\rigrul{\cand}}{}{\Gamma \seqar \Delta, A \cand B }{\Gamma \seqar \Delta, A}{\Gamma \seqar \Delta, B}
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\\
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\noalign{\bigskip}
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\vlinf{\lefrul{\neg}}{}{\Gamma, \neg A \seqar \Delta}{\Gamma \seqar A, \Delta}
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&
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\vlinf{\lefrul{\neg}}{}{\Gamma, \seqar \neg A, \Delta}{\Gamma, A \seqar  \Delta}
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&
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&
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%\vliinf{\lefrul{\cimp}}{}{\Gamma, A \cimp B \seqar \Delta}{\Gamma \seqar A, \Delta}{\Gamma, B \seqar \Delta}
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%&
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%
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%\vlinf{\rigrul{\cimp}}{}{\Gamma \seqar \Delta, A \cimp B}{\Gamma, A \seqar \Delta,  B}
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\\
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\noalign{\bigskip}
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%\text{Structural:} & & & \\
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%\noalign{\bigskip}
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%\vlinf{\lefrul{\wk}}{}{\Gamma, A \seqar \Delta}{\Gamma \seqar \Delta}
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%&
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\vlinf{\lefrul{\cntr}}{}{\Gamma, A \seqar \Delta}{\Gamma, A, A \seqar \Delta}
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%&
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%\vlinf{\rigrul{\wk}}{}{\Gamma \seqar \Delta, A }{\Gamma \seqar \Delta}
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&
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\vlinf{\rigrul{\cntr}}{}{\Gamma \seqar \Delta, A}{\Gamma \seqar \Delta, A, A}
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&
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&
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\\
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\noalign{\bigskip}
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\vlinf{\lefrul{\exists}}{}{\Gamma, \exists x . A(x) \seqar \Delta}{\Gamma, A(a) \seqar \Delta}
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&
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\vlinf{\lefrul{\forall}}{}{\Gamma, \forall x. A(x) \seqar \Delta}{\Gamma, A(t) \seqar \Delta}
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&
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\vlinf{\rigrul{\exists}}{}{\Gamma \seqar \Delta, \exists x . A(x)}{ \Gamma \seqar \Delta, A(t)}
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&
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\vlinf{\rigrul{\forall}}{}{\Gamma \seqar \Delta, \forall x . A(x)}{ \Gamma \seqar \Delta, A(a) } \\
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%\noalign{\bigskip}
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% \vliinf{mix}{}{\Gamma, \Sigma \seqar \Delta , \Pi}{ \Gamma \seqar \Delta}{\Sigma \seqar \Pi} &&&
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\end{array}
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\end{array}
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\]
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\caption{Sequent calculus rules}\label{fig:sequentcalculus}
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\end{figure}
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 We denote sequence as $\Gamma \seqar \Delta$ where $\Gamma$, $\Delta$ are multi sets of formulas. The sequent calculus rules are displayed on Fig. \ref{fig:sequentcalculus},  where $p$ is atomic, $i \in \{ 1,2 \}$, $t$ is a term and the eigenvariable $a$ does not occur free in $\Gamma$ or $\Delta$.
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We consider \emph{systems} of `nonlogical' rules extending this sequent calculus, which we write as follows,
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 \[
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 \begin{array}{cc}
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    \vlinf{(R)}{}{ \Gamma , \Sigma' \seqar \Delta' , \Pi  }{ \{\Gamma , \Sigma_i \seqar \Delta_i , \Pi \}_{i \in I} }
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\end{array}
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\]
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 where, in each rule $(R)$, $I$ is a finite possibly empty set (indicating the number of premises) and we assume the following conditions and terminology:
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 \begin{enumerate}
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 \item In $(R)$ the formulas of $\Sigma', \Delta'$  are called \textit{principal}, those of $\Sigma_i, \Delta_i$ are called \textit{active}, and those of
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$ \Gamma,  \Pi$ are called \textit{context formulas}.
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\item Each rule $(R)$ comes with a list $a_1$, \dots, $a_k$ of eigenvariables such that each $a_j$ appears in exactly one $\Sigma_i, \Delta_i$ (so in some active formulas of exactly one premise)  and does not appear in  $\Sigma', \Delta'$ or $ \Gamma,  \Pi$.
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    \item A system $\mathcal{S}$ of rules must be closed under substitutions of free variables by terms (where these substitutions do not contain the eigenvariables $a_j$ in their domain or codomain).
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   \end{enumerate}
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%The distinction between modal and nonmodal formulae in $(R)$ induces condition 1
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 Conditions 2 and 3 are standard requirements for nonlogical rules, independently of the logical setting, cf.\ \cite{Beckmann11}. Condition 2 reflects the intuitive idea that, in our nonlogical rules, we often need a notion of \textit{bound} variables in the active formulas (typically for induction rules), for which we rely on eigenvariables. Condition 3 is needed for our proof system to admit elimination of cuts on quantified formulas.
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%\begin{definition}
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%[Polynomial induction]
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%The \emph{polynomial induction} axiom schema, $\pind$, consists of the following axioms,
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%\[
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%A(0)
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%\cimp (\forall x^{\normal} . ( A(x) \cimp A(\succ{0} x) ) )
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%\cimp  (\forall x^{\normal} . ( A(x) \cimp A(\succ{1} x) ) )
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%\cimp  \forall x^{\normal} . A(x)
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%\]
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%for each formula $A(x)$.
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%
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%For a class $\Xi$ of formulae, $\cax{\Xi}{\pind}$ denotes the set of induction axioms when $A(x) \in \Xi$.
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%
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%We write $I\Xi$ to denote the theory consisting of $\basic$ and $\cax{\Xi}{\ind}$.
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%\end{definition}
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As an example any axiom can be represented by such a nonlogical rule $(R)$, with no premise ($I=\emptyset$), $\Delta'$ equal to the axiom and $\Gamma=\Sigma'=\Pi$. For instance the axiom $\pind$ of Def. \ref{def:polynomialinduction}.
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Actually  $\pind$ is equivalent to the following rule:
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\begin{equation}
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\label{eqn:ind-rule}
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\small
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\vliinf{\pind}{}{ \normal(t) , \Gamma , A(0) \seqar A(t), \Delta }{ \normal(a) , \Gamma, A(a) \seqar A(\succ{0} a) , \Delta }{ \normal(a) , \Gamma, A(a) \seqar A(\succ{1} a) , \Delta  }
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\end{equation}
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where $I=2$ and  in all cases, $t$ varies over arbitrary terms and the eigenvariable $a$ does not occur in the lower sequent of the $\pind$ rule.
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Similarly the $\rais$ inference rule of Def. \ref{def:ariththeory} is represented by the nonlogical rule:
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 \[
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 \begin{array}{cc}
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    \vlinf{\rais}{}{  \normal(t_1), \dots, \normal(t_k) \seqar  \exists  y^\normal .  A }{  \normal(t_1), \dots, \normal(t_k) \seqar \exists  y^\safe .  A}
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\end{array}
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\]
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%\patrick{In fact, I think we rather need the following nonlogical rule, which implies the previous one but is I guess more general:
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%\[
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% \begin{array}{cc}
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%    \vlinf{\rais}{}{  \normal(t_1), \dots, \normal(t_k) \seqar  \normal(t) }{  \normal(t_1), \dots, \normal(t_k) \seqar \safe(t)}
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%\end{array}
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%\]
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%}
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The $\basic$ axioms are equivalent to the following nonlogical rules, that we will also designate by $\basic$:
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\[
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\small
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\begin{array}{l}
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\begin{array}{cccc}
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\vlinf{}{}{\seqar \safe (0)}{}&
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\vlinf{}{}{\safe(t) \seqar \safe(\succ{} t)}{}&
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\vlinf{}{}{ \safe (t)   \seqar 0 \neq \succ{} t}{} &
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\vlinf{}{}{\safe (s) , \safe (t)  , \succ{} s = \succ{} t\seqar s = t }{}\\
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\end{array}
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\\
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\vlinf{}{}{\safe (t) \seqar t = 0 \cor \exists y^\safe . t = \succ{} y  }{}
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\qquad
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\vlinf{}{}{\safe(s), \safe(t) \seqar \safe(s+t) }{}\\
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\vlinf{}{}{\normal (s), \safe(t) \seqar \safe(s \times t)  }{}
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\qquad
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\vlinf{}{}{\normal (s), \normal(t) \seqar \safe(s \smsh t)  }{}\\
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\vlinf{}{}{\normal(t) \seqar \safe(t)  }{}
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\end{array}
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\]
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 The sequent calculus for $\arith^i$ is that of Fig. \ref{fig:sequentcalculus} extended with the $\basic$,  $\cpind{\Sigma^\safe_i } $ and $\rais$ nonlogical rules.
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 \begin{lemma}
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 For any term $t$, its free variables can be split in two sets $\vec{x}$ and $\vec{y}$ such  that the sequent $\normal(\vec x), \safe(\vec y) \seqar \safe(t)$ is provable.
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 \end{lemma}
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\subsection{Free-cut free normal form of proofs}
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\todo{State theorem, with references (Takeuti, Cook-Nguyen) and present the important corollaries for this work.}
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Since our nonlogical rules may have many principal formulae on which cuts may be anchored, we need a slightly more general notion of principality.
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    \begin{definition}\label{def:anchoredcut}
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  We define the notions of \textit{hereditarily principal formula} and \textit{anchored cut} in a $\system$-proof, for a system $\system$, by mutual induction as follows:
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  \begin{itemize}
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  \item A formula $A$ in a sequent $\Gamma \seqar \Delta$ is \textit{hereditarily principal} for a rule instance (S) if either (i) the sequent is in the conclusion of (S) and $A$ is principal in it, or
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(ii)  the sequent is in the conclusion of an anchored cut, the direct ancestor of $A$ in the corresponding premise is hereditarily principal for the rule instance (S), and the rule (S) is nonlogical.
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  \item A cut-step is an \textit{anchored cut} if the two occurrences of its cut-formula $A$ in each premise are hereditarily principal for nonlogical steps, or one is hereditarily principal for a nonlogical step and the other one is principal for a logical step.
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  \end{itemize}
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     A cut which is not anchored will also be called a \textit{free-cut}.
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  \end{definition}
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  As a consequence of this definition, an anchored cut on a formula $A$ has the following properties:
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  \begin{itemize}
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  \item At least one of the two premises of the cut has above it a sub-branch of the proof which starts (top-down) with a nonlogical step (R) with $A$ as one of its principal formulas, and then a sequence of anchored cuts in which $A$ is part of the context.
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  \item The other premise is either of the same form or is a logical step with principal formula $A$.
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  \end{itemize}
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   Now we have (see \cite{Takeuti87}):
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   \begin{theorem}
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   [Free-cut elimination]\label{thm:freecutelimination}
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   \label{thm:free-cut-elim}
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    Given a system  $\mathcal{S}$, any  $\mathcal{S}$-proof $\pi$ can be transformed into a $\system$-proof $\pi'$ with same end sequent and without any free-cut.
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   \end{theorem}
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   Now we want to deduce from that theorem a normal form property for proofs of certain formulas. But before that let us define some particular classes of sequents and proofs.
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   Say that a sequent $\Gamma \seqar \Delta$ is \textit{well-typed} if for any free variable $x$ occurring in $\Gamma$ or $\Delta$, there exists a formula $\safe(x)$ or $\normal(x)$ in $\Gamma$. A proof is well-typed if its sequence are.
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   \begin{lemma}\label{lem:welltyped}
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   If a well-typed sequent $\Gamma \seqar \Delta$ is provable, then there exists $\vec u$  such that
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 the sequent $\normal(\vec u), \Gamma \seqar \Delta$ admits a well-typed proof.
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   \end{lemma}
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   \patrick{It seems to me the statement had to be modified so as to prove the lemma. Maybe I misunderstand something.}
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   \begin{proof}[Proof sketch]
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   First by Thm \ref{thm:freecutelimination} we know that $\Gamma \seqar \Delta$ admits a proof $\pi$ without any free-cut. Let us then prove that $\pi$ can be transformed in a proof $\pi'$ of conclusion of the form  $\normal(\vec u), \Gamma \seqar \Delta$ and such that, for any sequent, if it is well-typed then its premises are well-typed.
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   Observe first that by definition of $\arith^i$ and the absence of free cut, all quantifiers occurring in a formula of the proof are of one of the forms
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   $\forall^{\safe}$,   $\exists^{\safe}$,  $\forall^{\normal}$,   $\exists^{\normal}$, and for the last two ones they are sharply bounded.
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  Then, one can check that for all rules but the quantifier rules and the cut rule, if the conclusion is well-typed, then so are the two premises.  For the remaining rules, $\forall-r$ and $\exists-l$ are unproblematic, because of the observation above. Let us now examine the case of $\exists-r$, with a $\safe$ label, and the other rules can be treated in the same way. In the premise we get a formula $\safe(t) \cand A(t)$. Then what we do is that, if  $\vec u$ denote the free variables of $t$, we add to the context of all sequents of the proof $\normal(\vec u)$. We obtain in this way a valid proof new proof,  and the premises of the rule have become well-typed.
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       \end{proof}
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     \patrick{As mentioned after Def 14, I don't think that we can prove that the proofs we consider are equivalent to integer positive proofs, by arguing that negative occurrences $\neg \safe(t)$ could be replaced by 'false', by using the lemma above. Indeed even if for all its free variables we have $\safe(\vec x)$, $\normal(\vec u)$ on the l.h.s. of the sequent, it is not clear to me why that would prove $\safe(t)$. My proposition is thus to restrict 'by definition' of $\arith^i$ to integer positive formulas.}
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 \begin{theorem}
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   Assume the $\arith^i$ sequent calculus proves a closed formula $\forall \vec u^\normal . \forall \vec x^\safe . \exists y^\safe . A(\vec u ; \vec x , y)$. Then there exists a proof $\pi$ of the sequent
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   $\normal(\vec u), \safe(\vec x) \seqar \exists y^\safe . A(\vec u ; \vec x , y)$ satisfying:
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   \begin{enumerate}
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    \item $\pi$  only contains  $\Sigma^\safe_{i}$ formulas,
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    \item $\pi$ is a well-typed and integer-positive proof.
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   \end{enumerate}
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   \end{theorem}