prompt_front: Now, answer the following question based on the text below, only give me the answer and do not output any other words.

Question: How does the performance of the PLM with decimation compare to other methods?

Read the following text and answer briefly.

Context 1: \section{Introduction}
Given a data set and a model with some unknown parameters, the inverse problem aims to find the values of the model parameters that best fit the data   
In this work, in which we focus on systems of interacting elements,
 the inverse problem concerns  the statistical inference
 of the underling interaction network and of its coupling coefficients from observed data on the dynamics  of the system  
 Versions of this problem are encountered in physics, biology (e g , \cite{Balakrishnan11,Ekeberg13,Christoph14}), social sciences and finance (e g ,\cite{Mastromatteo12,yamanaka_15}), neuroscience (e g , \cite{Schneidman06,Roudi09a,tyrcha_13}), just to cite a few, and are becoming more and more important due to the increase in the amount of data available from these fields \\
 \indent 
 A standard approach used in statistical inference is to predict the interaction couplings by maximizing the likelihood function 
 This technique, however, requires the evaluation of the  
 
   partition function that, in the most general case, concerns a number of computations scaling exponentially with the system size 
  
  
    Boltzmann machine learning uses Monte Carlo sampling to compute the gradients of the Log-likelihood looking for stationary points \cite{Murphy12} but this method is computationally manageable only for small systems  A series of faster approximations, such as naive mean-field, independent-pair approximation \cite{Roudi09a, Roudi09b}, inversion of TAP equations \cite{Kappen98,Tanaka98}, small correlations expansion \cite{Sessak09}, adaptive TAP \cite{Opper01}, adaptive  cluster expansion \cite{Cocco12} or Bethe approximations \cite{Ricci-Tersenghi12, Nguyen12}  have, then, been developed  These techniques take as input means and correlations of observed variables and most of them assume a fully connected graph as underlying connectivity network, or expand  around it by perturbative dilution   In most cases, network reconstruction turns out to  be not accurate for small data sizes and/or when couplings are  strong or, else, if the original interaction network is sparse \\
\indent
 A further method, substantially improving performances for small data, is the so-called Pseudo-Likelyhood Method (PLM) \cite{Ravikumar10}  In Ref  \cite{Aurell12} Aurell and Ekeberg performed a comparison between PLM and some of the just mentioned mean-field-based algorithms on the pairwise interacting Ising-spin  ($\sigma = \pm 1$) model, showing how PLM performs sensitively better, especially on sparse graphs and in the high-coupling limit, i e , for low temperature 
 
 In this work, we aim at performing statistical inference  on a model whose interacting variables are continuous $XY$ spins, i e , $\sigma \equiv \left(\cos \phi,\sin \phi\right)$ with $\phi \in [0, 2\pi )$  The developed tools can, actually, be also straightforward applied  to the $p$-clock model  \cite{Potts52} where the phase $\phi$ takes discretely equispaced $p$ values  in the $2 \pi$ interval, $\phi_a =  a 2 \pi/p$, with $a= 0,1,\dots,p-1$  The $p$-clock model, else called vector Potts model, gives a hierarchy of discretization of the $XY$ model as $p$ increases  For $p=2$, one recovers the Ising model, for $p=4$ the Ashkin-Teller model \cite{Ashkin43}, for $p=6$ the ice-type model \cite{Pauling35,Baxter82} and the eight-vertex model \cite{Sutherland70,Fan70,Baxter71} for $p=8$   
It turns out to be very useful also for numerical implementations of the continuous $XY$ model  
Recent analysis on the multi-body $XY$ model has shown that for a limited number of discrete phase values ($p\sim 16, 32$) the thermodynamic critical properties of the $p\to\infty$ $XY$ limit are promptly recovered \cite{Marruzzo15, Marruzzo16}   
Our main motivation to study statistical inference is that these kind of models have recently turned out to be rather useful in describing the behavior of optical systems, 
including standard mode-locking lasers \cite{Gordon02,Gat04,Angelani07,Marruzzo15} and random lasers \cite{Angelani06a,Leuzzi09a,Antenucci15a,Antenucci15b,Marruzzo16}  
In particular, the inverse problem on the pairwise XY model analyzed here might be of help in recovering images from light propagated through random media  


      This paper is organized as follows: in Sec  \ref{sec:model} we introduce the general model  and we discuss its  derivation also  as a model for light transmission through random scattering media  
    In Sec  \ref{sec:plm} we introduce the PLM with $l_2$ regularization  and with decimation, two variants of the PLM respectively introduced in Ref  \cite{Wainwright06} and \cite{Aurell12} for the inverse Ising problem  
    Here, we analyze these techniques for continuous $XY$ spins and we test them on thermalized data generated by Exchange Monte Carlo numerical simulations of the original model dynamics  In Sec  \ref{sec:res_reg} we  present the results related to the PLM-$l_2$  In Sec  \ref{sec:res_dec} the results related to the PLM with decimation are reported and its performances are compared to the PLM-$l_2$ and to a variational mean-field method analyzed in Ref  \cite{Tyagi15}  In Sec  \ref{sec:conc}, we outline conclusive remarks and perspectives 

        \section{The leading $XY$ model}
      \label{sec:model}
 The leading model we are considering is defined, for a system of $N$ angular $XY$ variables, by the Hamiltonian 
 \begin{equation}
  \mathcal{H} = - \sum_{ik}^{1,N} J_{ik} \cos{\left(\phi_i-\phi_k\right)} 
  \label{eq:HXY}
 
  \end{equation} 
  
  The $XY$ model is well known in statistical mechanics, displaying important physical
  insights, starting from the Berezinskii-Kosterlitz-Thouless
  transition in two dimensions\cite{Berezinskii70,Berezinskii71,Kosterlitz72} and moving to, e g , the
  transition of liquid helium to its superfluid state \cite{Brezin82}, the roughening transition of the interface of a crystal in equilibrium with its vapor \cite{Cardy96}  In presence of disorder and frustration \cite{Villain77,Fradkin78} the model has been adopted to describe synchronization problems as the Kuramoto model \cite{Kuramoto75} and in the theoretical modeling of Josephson junction arrays \cite{Teitel83a,Teitel83b} and arrays of coupled lasers \cite{Nixon13} 
  Besides several derivations and implementations of the model in quantum and classical physics, equilibrium or out of equilibrium, ordered or fully frustrated systems, Eq  (\ref{eq:HXY}), in its generic form,
  has found applications also in other fields  A rather fascinating example being the behavior of starlings flocks  \cite{Reynolds87,Deneubourg89,Huth90,Vicsek95, Cavagna13} 
  Our interest on the $XY$ model resides, though, in optics  Phasor and phase models with pairwise and  multi-body interaction terms can, indeed, describe the behavior of electromagnetic modes in both linear and nonlinear optical systems in the analysis of problems such as light propagation and lasing \cite{Gordon02, Antenucci15c, Antenucci15d}  As couplings are strongly frustrated, these models turn out to be especially useful to the study of optical properties in random media \cite{Antenucci15a,Antenucci15b}, as in the noticeable case of random lasers \cite{Wiersma08,Andreasen11,Antenucci15e}  and they might as well be applied to linear scattering problems, e g , propagation of waves in opaque systems or disordered fibers  
  
  
  \subsection{A propagating wave model}
  We briefly mention a derivation of the model as a proxy for the propagation of light through random linear media  
 Scattering of light is held responsible to obstruct our view and make objects opaque  Light rays, once that they enter the material, only exit  after getting scattered multiple times within the material  In such a disordered medium, both the direction and the phase of the propagating waves are random  Transmitted light 
 yields a disordered interference pattern typically  having low intensity, random phase and almost no resolution, called a speckle  Nevertheless, in recent years it has been realized that disorder is rather a blessing in disguise \cite{Vellekoop07,Vellekoop08a,Vellekoop08b}  Several experiments have made it possible to control the behavior of light and other optical processes in a given random disordered medium,  
 by exploiting, e g ,  the tools developed for wavefront shaping to control the propagation of light and to engineer the confinement of light \cite{Yilmaz13,Riboli14} 
 \\
 \indent
 In a linear dielectric medium, light propagation can be described through a part of the scattering matrix, the transmission matrix $\mathbb{T}$, linking the outgoing to the incoming fields  
 Consider the case in which there are $N_I$ incoming channels and $N_O$ outgoing ones; we can indicate with $E^{\rm in,out}_k$ the input/output electromagnetic field phasors of channel $k$  In the most general case, i e , without making any particular assumptions on the field polarizations, each light mode and its polarization polarization state can be represented by means of the $4$-dimensional Stokes vector  Each $ t_{ki}$ element of $\mathbb{T}$, thus, is a $4 \times 4$ M{\"u}ller matrix  If, on the other hand, we know that the source is polarized and the observation is made on the same polarization, one can use a scalar model and adopt Jones calculus \cite{Goodman85,Popoff10a,Akbulut11}:
   \begin{eqnarray}
 E^{\rm out}_k = \sum_{i=1}^{N_I}  t_{ki} E^{\rm in}_i \qquad \forall~ k=1,\ldots,N_O
 \label{eq:transm}
 \end{eqnarray}
  We recall that the elements of the transmission matrix are random complex coefficients\cite{Popoff10a}  For the case of completely unpolarized modes, we can also use a scalar model similar to Eq  \eqref{eq:transm}, but whose variables are  the intensities of the outgoing/incoming fields, rather than the fields themselves \\ 
In the following, for simplicity, we will consider Eq  (\ref{eq:transm}) as our starting point,
where $E^{\rm out}_k$, $E^{\rm in}_i$ and $t_{ki}$ are all complex scalars  
If Eq  \eqref{eq:transm} holds for any $k$, we can write:
  \begin{eqnarray}
  \int \prod_{k=1}^{N_O} dE^{\rm out}_k \prod_{k=1}^{N_O}\delta\left(E^{\rm out}_k - \sum_{j=1}^{N_I}  t_{kj} E^{\rm in}_j \right) = 1
  \nonumber
  \\
  \label{eq:deltas}
  \end{eqnarray}

 Observed data are a noisy representation of the true values of the fields  Therefore, in inference problems it is statistically more meaningful to take that noise into account in a probabilistic way, 
 rather than looking  at the precise solutions of the exact equations (whose parameters are unknown)  
 To this aim we can introduce Gaussian distributions whose limit for zero variance are the Dirac deltas in Eq  (\ref{eq:deltas}) 
 Moreover, we move to consider the ensemble of all possible solutions of Eq  (\ref{eq:transm}) at given $\mathbb{T}$, looking at  all configurations of input fields  We, thus, define the function:
 
   \begin{eqnarray}
  Z &\equiv &\int_{{\cal S}_{\rm in}} \prod_{j=1}^{N_I}  dE^{\rm in}_j \int_{{\cal S}_{\rm out}}\prod_{k=1}^{N_O} dE^{\rm out}_k 
  \label{def:Z}
\\
    \times
  &&\prod_{k=1}^{N_O}
   \frac{1}{\sqrt{2\pi \Delta^2}}  \exp\left\{-\frac{1}{2 \Delta^2}\left|
  E^{\rm out}_k -\sum_{j=1}^{N_I}  t_{kj} E^{\rm in}_j\right|^2
\right\} 
\nonumber
 \end{eqnarray}
   We stress that the integral of Eq  \eqref{def:Z} is not exactly a Gaussian integral  Indeed, starting from Eq  \eqref{eq:deltas}, two constraints on the electromagnetic field intensities must be taken into account  

  The space of solutions is  delimited by the total power ${\cal P}$ received by system, i e , 
  ${\cal S}_{\rm in}: \{E^{\rm in} |\sum_k I^{\rm in}_k = \mathcal{P}\}$, also implying  a constraint on the total amount of energy that is transmitted through the medium, i  e , 
  ${\cal S}_{\rm out}:\{E^{\rm out} |\sum_k I^{\rm out}_k=c\mathcal{P}\}$, where the attenuation factor  $c<1$ accounts for total losses 
  As we will see more in details in the following, being interested in inferring the transmission matrix through the PLM, we can omit to explicitly include these terms in Eq  \eqref{eq:H_J} since they do not depend on $\mathbb{T}$ not adding any information on the gradients with respect to the elements of $\mathbb{T}$ 
  
 Taking the same number of incoming and outcoming channels, $N_I=N_O=N/2$, and  ordering the input fields in the first $N/2$ mode indices and the output fields in the last $N/2$ indices, we can drop the ``in'' and ``out'' superscripts and formally write $Z$  as a partition function
    \begin{eqnarray}
        \label{eq:z}
 && Z =\int_{\mathcal S} \prod_{j=1}^{N} dE_j \left(   \frac{1}{\sqrt{2\pi \Delta^2}} \right)^{N/2} 
 \hspace*{- 4cm} \exp\left\{
  -\frac{ {\cal H} [\{E\};\mathbb{T}] }{2\Delta^2}
  \right\}
  \\
&&{\cal H} [\{E\};\mathbb{T}] =
-  \sum_{k=1}^{N/2}\sum_{j=N/2+1}^{N} \left[E^*_j t_{jk} E_k + E_j t^*_{kj} E_k^* 
\right]
 \nonumber
\\
&&\qquad\qquad \qquad + \sum_{j=N/2+1}^{N} |E_j|^2+ \sum_{k,l}^{1,N/2}E_k
U_{kl} E_l^*
 \nonumber
 \\
 \label{eq:H_J}
 &&\hspace*{1 88cm } = - \sum_{nm}^{1,N} E_n J_{nm} E_m^*
 \end{eqnarray}
 where ${\cal H}$ is a real-valued function by construction, we have introduced the effective input-input coupling matrix
\begin{equation}
U_{kl} \equiv \sum_{j=N/2+1}^{N}t^*_{lj} t_{jk} 
 \label{def:U}
 \end{equation}
 and the whole interaction matrix reads (here $\mathbb{T} \equiv \{ t_{jk} \}$)
 \begin{equation}
 \label{def:J}
 \mathbb J\equiv \left(\begin{array}{ccc|ccc}
 \phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}\\
 \phantom{()}&-\mathbb{U} \phantom{()}&\phantom{()}&\phantom{()}&{\mathbb{T}}&\phantom{()}\\
\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}\\
 \hline
\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}\\
 \phantom{()}& \mathbb   T^\dagger&\phantom{()}&\phantom{()}& - \mathbb{I} &\phantom{()}\\
\phantom{a}&\phantom{a}&\phantom{a}&\phantom{a}&\phantom{a}&\phantom{a}\\
 \end{array}\right)
 \end{equation}
 
 Determining the electromagnetic complex amplitude configurations that minimize the {\em cost function} ${\cal H}$, Eq   (\ref{eq:H_J}),  means to maximize the overall distribution peaked around the solutions of the transmission Eqs  (\ref{eq:transm})  As the variance $\Delta^2\to 0$, eventually, the initial set of Eqs  (\ref{eq:transm}) are recovered  The ${\cal H}$ function, thus, plays the role of an Hamiltonian and  $\Delta^2$ the role of a noise-inducing temperature  The exact numerical problem corresponds to the zero temperature limit of the statistical mechanical problem  Working with real data, though, which are noisy, a finite ``temperature''
  allows for a better representation of the ensemble of solutions to the sets of equations of continuous variables  
  

  
  
  Now, we can express every phasor in Eq  \eqref{eq:z}  as $E_k = A_k e^{\imath \phi_k}$  As a working hypothesis we will consider the intensities $A_k^2$ as either homogeneous or as \textit{quenched} with respect to phases 
The first condition occurs, for instance, to the input intensities $|E^{\rm in}_k|$ produced by a phase-only spatial light modulator (SLM) with homogeneous illumination \cite{Popoff11} 
With \textit{quenched} here we mean, instead, that the intensity of each mode is the same for every solution of Eq  \eqref{eq:transm} at fixed $\mathbb T$ 
We stress that, including intensities in the model does not preclude the inference analysis but it is out of the focus of the present work and will be considered elsewhere  

If all intensities are uniform in input and in output, this amount to a constant rescaling for each one of the four sectors of matrix $\mathbb J$ in Eq  (\ref{def:J}) that will not change the properties of the matrices 
For instance, if the original transmission matrix is unitary, so it will be the rescaled one and the matrix $\mathbb U$ will be  diagonal 
Otherwise, if intensities are \textit{quenched}, i e , they can be considered as constants in Eq  (\ref{eq:transm}),
they are inhomogeneous with respect to phases  The generic Hamiltonian element will, therefore, rescale as 
  \begin{eqnarray}
  E^*_n J_{nm} E_m = J_{nm} A_n A_m e^{\imath (\phi_n-\phi_m)} \to J_{nm} e^{\imath (\phi_n-\phi_m)}
  \nonumber
  \end{eqnarray}
  and the properties of the original  $J_{nm}$ components are not conserved  in the rescaled one  In particular, we have no argument, anymore, to possibly set the rescaled $U_{nm}\propto \delta_{nm}$ 
  Eventually, we end up with the complex couplings $XY$ model, whose real-valued Hamiltonian is written as
 \begin{eqnarray}
  \mathcal{H}& = &  - \frac{1}{2} \sum_{nm} J_{nm} e^{-\imath (\phi_n - \phi_m)}  + \mbox{c c } 
    \label{eq:h_im}
\\    &=&  - \frac{1}{2} \sum_{nm} \left[J^R_{nm} \cos(\phi_n - \phi_m)+
  J^I_{nm}\sin (\phi_n - \phi_m)\right] 
  \nonumber
 \end{eqnarray}
where $J_{nm}^R$ and $J_{nm}^I$ are the real and imaginary parts of $J_{nm}$  Being $\mathbb J$  Hermitian, $J^R_{nm}=J^R_{mn}$ is symmetric and $J_{nm}^I=-J_{mn}^I$ is skew-symmetric 

\begin{comment}
\textcolor{red}{
F: comment about quenched:
I think that to obtain the XY model, it is not necessary that the intensities are strictly quenched (that is also a quite unfeasible situation, I guess) 
Indeed eq (2) does not deal with the dynamics of the modes, but just connect the in and out ones 
For this, what it is necessary to have the XY model, it is that the intensities are always the same on the different samples
(so that the matrix $t_{ij}$ is the same for different phase data)  If the intensities are fixed, then they can be incorporated in $t_{ij}$ and eq (2) can be written just for phases as described  \\
}
\end{comment}


  \section{Pseudolikelihood Maximization}
  \label{sec:plm}
The inverse problem consists in the reconstruction of the parameters $J_{nm}$ of the Hamiltonian, Eq  (\ref{eq:h_im})   
Given a set of $M$ data configurations of $N$ spins
 $\bm\sigma = \{ \cos \phi_i^{(\mu)},\sin \phi_i^{(\mu)} \}$, $i = 1,\dots,N$ and $\mu=1,\dots,M$, we want to \emph{infer} the couplings:
 \begin{eqnarray}
\bm \sigma  \rightarrow  \mathbb{J} 
\nonumber
 \end{eqnarray}
 With this purpose in mind,
 in the rest of this section we implement the working equations for the techniques used  
 In order to test our methods, we generate the input data, i e , the configurations, by Monte-Carlo simulations of the model 
 The joint probability distribution of the $N$ variables $\bm{\phi}\equiv\{\phi_1,\dots,\phi_N\}$, follows the Gibbs-Boltzmann distribution:
 \begin{equation}\label{eq:p_xy}
 P(\bm{\phi}) = \frac{1}{Z} e^{-\beta \mathcal{H\left(\bm{\phi}\right)}} \quad \mbox{ where } \quad Z = \int \prod_{k=1}^N d\phi_k  e^{-\beta \mathcal{H\left(\bm{\phi}\right)}}  
 \end{equation}
 and where we denote $\beta=\left( 2\Delta^2 \right)^{-1}$ with respect to Eq  (\ref{def:Z}) formalism 
 In order to stick to usual statistical inference notation, in the following we will rescale the couplings by a factor $\beta / 2$: $\beta J_{ij}/2 \rightarrow J_{ij}$  
 The main idea of the PLM is to work with the conditional probability distribution of one variable $\phi_i$ given all other variables, 
 $\bm{\phi}_{\backslash i}$:
 
  \begin{eqnarray}
	\nonumber
   P(\phi_i | \bm{\phi}_{\backslash i}) &=& \frac{1}{Z_i} \exp \left \{ {H_i^x (\bm{\phi}_{\backslash i})
  	\cos \phi_i + H_i^y (\bm{\phi}_{\backslash i}) \sin \phi_i } \right \}
	\\
 \label{eq:marginal_xy}
	&=&\frac{e^{H_i(\bm{\phi}_{\backslash i}) \cos{\left(\phi_i-\alpha_i(\bm{\phi}_{\backslash i})\right)}}}{2 \pi I_0(H_i)}
  \end{eqnarray}
  where $H_i^x$ and $H_i^y$ are defined as
   \begin{eqnarray}
   H_i^x (\bm{\phi}_{\backslash i})  &=& \sum_{j (\neq i)} J^R_{ij} \cos \phi_j  - \sum_{j  (\neq i) } J_{ij}^{I} \sin \phi_j \phantom{+  h^R_i} \label{eq:26} \\
   H_i^y  (\bm{\phi}_{\backslash i})  &=&  \sum_{j  (\neq i)} J^R_{ij}  \sin \phi_j  + \sum_{j  (\neq i) } J_{ij}^{I}   \cos \phi_j \phantom{ + h_i^{I} }\label{eq:27}
   \end{eqnarray}
and $H_i= \sqrt{(H_i^x)^2 + (H_i^y)^2}$, $\alpha_i = \arctan H_i^y/H_i^x$   and we introduced the modified Bessel function of the first kind:
  \begin{equation}
  \nonumber
   I_k(x) = \frac{1}{2 \pi}\int_{0}^{2 \pi} d \phi e^{x \cos{ \phi}}\cos{k \phi}
  \end{equation}
  
   Given $M$ observation samples $\bm{\phi}^{(\mu)}=\{\phi^\mu_1,\ldots,\phi^\mu_N\}$, $\mu = 1,\dots, M$, the
   pseudo-loglikelihood for the variable $i$ is given by the logarithm of Eq  (\ref{eq:marginal_xy}),
   \begin{eqnarray}
   \label{eq:L_i}
   L_i &=& \frac{1}{M}  \sum_{\mu = 1}^M  \ln P(\phi_i^{(\mu)}|\bm{\phi}^{(\mu)}_{\backslash i})
   \\
   \nonumber
   & =&  \frac{1}{M}  \sum_{\mu = 1}^M  \left[ H_i^{(\mu)} \cos( \phi_i^{(\mu)} - \alpha_i^{(\mu)}) - \ln  2 \pi I_0\left(H_i^{(\mu)}\right)\right] \,  
    \end{eqnarray}
The underlying idea of PLM is that an approximation of the true parameters of the model is obtained for values that maximize the functions $L_i$ 
The specific maximization scheme differentiates the different techniques 


   
   
   \subsection{PLM with $l_2$ regularization}
   Especially for the case of sparse graphs, it is useful to add a regularizer, which prevents the maximization routine to move towards high values of 
   $J_{ij}$ and $h_i$ without converging  We will adopt an $l_2$ regularization so that the Pseudolikelihood function (PLF) at site $i$  reads:
   \begin{equation}\label{eq:plf_i}
  {\cal L}_i = L_i
  - \lambda \sum_{i \neq j} \left(J_{ij}^R\right)^2 - \lambda \sum_{i \neq j} \left(J_{ij}^I\right)^2  
   \end{equation}
   with $\lambda>0$ 
   Note that the values of $\lambda$ have to be chosen arbitrarily, but not too large, in order not to overcome $L_i$ 
   The standard implementation of the PLM consists in maximizing each ${\cal L}_i$, for $i=1\dots N$, separately  The expected values of the couplings are then:
   \begin{equation}
   \{ J_{i j}^*\}_{j\in \partial i} :=  \mbox{arg max}_{ \{ J_{ij} \}}
    \left[{\cal L}_i\right]
   \end{equation}
   In this way, we obtain two estimates for the coupling $J_{ij}$, one from maximization of ${\cal L}_i$, $J_{ij}^{(i)}$, and another one from ${\cal L}_j$, say $J_{ij}^{(j)}$ 
    Since the original Hamiltonian of the $XY$ model is Hermitian, we know that the real part of the couplings is symmetric while the imaginary part is skew-symmetric  
   
     The final estimate for $J_{ij}$ can then be obtained  averaging the two results:
  
  
  
   \begin{equation}\label{eq:symm}
   J_{ij}^{\rm inferred} = \frac{J_{ij}^{(i)} + \bar{J}_{ij}^{(j)}}{2} 
   \end{equation}
   where with $\bar{J}$ we indicate the complex conjugate 
   It is worth noting that the pseudolikelihood $L_i$, Eq  \eqref{eq:L_i}, is characterized by the
   following properties: (i) the normalization term of Eq \eqref{eq:marginal_xy} can be
   computed analytically at odd with the {\em full} likelihood case that
   in general require a computational time which scales exponentially
   with the size of the systems; (ii) the $\ell_2$-regularized pseudolikelihood
   defined in Eq \eqref{eq:plf_i} is strictly concave (i e  it has a single
   maximizer)\cite{Ravikumar10}; (iii) it is consistent, i e  if $M$ samples are
   generated by a model $P(\phi | J*)$ the maximizer tends to $J*$
   for $M\rightarrow\infty$\cite{besag1975}  Note also that (iii) guarantees that  
   $|J^{(i)}_{ij}-J^{(j)}_{ij}| \rightarrow 0$ for $M\rightarrow \infty$ 
   In Secs  \ref{sec:res_reg}, \ref{sec:res_dec} 
   we report the results obtained and we analyze the performances of the PLM having taken the configurations from Monte-Carlo simulations of models whose details are known 
   

   
   \subsection{PLM with decimation}
   Even though the PLM with $l_2$-regularization allows to dwell the inference towards the low temperature region and in the low sampling case with better performances that mean-field methods, in some situations some couplings are overestimated and not at all symmetric  Moreover, in the technique there is the bias of the $l_2$ regularizer 
   Trying to overcome these problems, Decelle and Ricci-Tersenghi introduced a new method \cite{Decelle14}, known as PLM + decimation: the algorithm maximizes the sum of the $L_i$,
   \begin{eqnarray}
    {\cal L}\equiv \frac{1}{N}\sum_{i=1}^N \mbox{L}_i
    \end{eqnarray}  
    and, then, it recursively set to zero couplings which are estimated very small  We expect that as long as we are setting to zero couplings that are unnecessary to fit the data, there should be not much changing on ${\cal L}$  Keeping on with decimation, a point is reached where ${\cal L}$ decreases abruptly indicating  that relevant couplings are being decimated and under-fitting is taking place 
   Let us define  by $x$  the fraction of non-decimated couplings  To have a quantitative measure for the halt criterion of the decimation process, a tilted ${\cal L}$ is defined as,
   \begin{eqnarray}
  \mathcal{L}_t &\equiv& \mathcal{L}  - x \mathcal{L}_{\textup{max}} - (1-x) \mathcal{L}_{\textup{min}} \label{$t$PLF} 
   \end{eqnarray}
   where 
   \begin{itemize}
   \item $\mathcal{L}_{\textup{min}}$ is the pseudolikelyhood of a model with independent variables  In the XY case: $\mathcal{L}_{\textup{min}}=-\ln{2 \pi}$ 
   \item
   $\mathcal{L}_{\textup{max}}$ is the pseudolikelyhood in the fully-connected model and it is maximized over all the $N(N-1)/2$ possible couplings  
   \end{itemize}
   At the first step, when $x=1$, $\mathcal{L}$ takes value $\mathcal{L}_{\rm max}$ and  $\mathcal{L}_t=0$  On the last step, for an empty graph, i e , $x=0$, $\mathcal{L}$ takes the value $\mathcal{L}_{\rm min}$ and, hence, again $\mathcal{L}_t =0$  
   In the intermediate steps, during the decimation procedure, as $x$ is decreasing from $1$ to $0$, one observes firstly that $\mathcal{L}_t$ increases linearly and, then, it displays an abrupt decrease indicating that from this point on relevant couplings are being decimated\cite{Decelle14}  In Fig  \ref{Jor1-$t$PLF} we give an instance of this behavior for the 2D short-range XY model with ordered couplings  We notice that the maximum point of $\mathcal{L}_t$ coincides with the minimum point of the reconstruction error, the latter defined as 
   \begin{eqnarray}\label{eq:errj}
   \mbox{err}_J \equiv \sqrt{\frac{\sum_{i<j} (J^{\rm inferred}_{ij} -J^{\rm true}_{ij})^2}{N(N-1)/2}} \label{err}
   \end{eqnarray}
  We stress that the ${\cal L}_t$ maximum is obtained ignoring the underlying graph, while the err$_J$ minimum can be evaluated once the true graph has been reconstructed  
   
     \begin{figure}[t!]
   	\centering
   	\includegraphics[width=1\linewidth]{Jor1_dec_tPLF_new eps}
   	\caption{The tilted likelyhood ${\cal L}_t$ curve and the reconstruction error vs the number of decimated couplings  for an ordered, real-valued J on 2D XY model with $N=64$ spins  The peak of ${\cal L}_t$ coincides with the dip of the error }  
   	\label{Jor1-$t$PLF}
   \end{figure} 
       
   
   In the next sections we will show the results obtained on the  $XY$ model analyzing the performances of the two methods and comparing them also with a mean-field method \cite{Tyagi15} 
   
  
    
   \section{Inferred couplings with PLM-$l_2$}
    \label{sec:res_reg}
    \subsection{$XY$ model with real-valued couplings}
    
    In order to obtain the vector of couplings, $J_{ij}^{\rm inferred}$ the function $-\mathcal{L}_i$ is minimized through the vector of derivatives ${\partial \mathcal{L}_i}/\partial J_{ij}$  The process is repeated for all the couplings obtaining then a fully connected adjacency matrix  The results here presented are obtained with $\lambda = 0 01$ 
   For the minimization we have used the MATLAB routine \emph{minFunc\_2012}\cite{min_func}  
      
      \begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{Jor11_2D_l2_JR_soJR_TPJR}
    	\caption{Top panels: instances of single site coupling reconstruction for the case of $N=64$ XY spins on a 2D lattice with ordered $J$ (left column) and bimodal distributed $J$ (right column)  
    	
    	Bottom panels: sorted couplings }
    	\label{PL-Jor1}
    \end{figure}

   
To produce the data by means of numerical Monte Carlo simulations a system with $N=64$  spin variables  is considered on a deterministic 2D lattice with periodic boundary conditions  
Each spin has then connectivity $4$, i e , we expect to infer an adjacency matrix with $N c = 256$ couplings different from zero  
The dynamics of the simulated model is based on the Metropolis algorithm and parallel tempering\cite{earl05} is used to speed up the thermalization of the system 
The thermalization is tested looking at the average energy over logarithmic time windows and
the acquisition of independent configurations
starts only after the system is well thermalized 

   For the values of the couplings we considered two cases: an ordered case, indicated in the figure as  $J$ ordered (e g , left column of Fig  \ref{PL-Jor1}) where the couplings can take values $J_{ij}=0,J$, with $J=1$, 
   and a quenched disordered case, indicated in the figures as  $J$ disordered (e g , right column of Fig  \ref{PL-Jor1})
   where the couplings can take also  negative values, i e , 
    $J_{ij}=0,J,-J$, with a certain probability   The results here presented were obtained with bimodal distributed $J$s: 
   
    $P(J_{ij}=J)=P(J_{ij}=-J)=1/2$   The performances of the PLM have shown not to depend on $P(J)$  
   
    We recall that in Sec  \ref{sec:plm} we used the temperature-rescaled notation, i e , $J_{ij}$ stands for $J_{ij}/T$  
   
    To analyze the performances of the PLM, in Fig  \ref{PL-Jor1} the inferred couplings, $\mathbb{J}^R_{\rm inf}$, are shown on top of the original couplings,  $\mathbb{J}^R_{\rm true}$ 
     The first figure (from top) in the left column shows  the $\mathbb{J}^R_{\rm inf}$ (black) and the $\mathbb{J}^R_{\rm tru}$ (green) for a given spin
     at temperature $T/J=0 7$ and number of samples  $M=1024$  PLM appears to reconstruct the correct couplings, though zero couplings are always given a small inferred non-zero value  
     In the left column of Fig   \ref{PL-Jor1},  both the $\mathbb{J}^R_{\rm{inf}}$ and the $\mathbb{J}^R_{\rm{tru}}$ are sorted in decreasing order and plotted on top of each other  
     We can clearly see that $\mathbb{J}^R_{\rm inf}$ reproduces the expected step function  Even though the jump is smeared, the difference between inferred couplings corresponding to the set of non-zero couplings 
     and to the set of zero couplings can be clearly appreciated 
     Similarly, the plots in the right column of Fig  \ref{PL-Jor1} show the results obtained for the case with  bimodal disordered couplings, for the same working temperature and number of samples  
     In particular, note that the algorithm infers half positive and half negative couplings, as expected 
     
     
\begin{figure}
\centering
\includegraphics[width=1\linewidth]{Jor11_2D_l2_errJ_varT_varM}
\caption{Reconstruction error $\mbox{err}_J$, cf  Eq  (\ref{eq:errj}), plotted as a function of temperature (left) for three values of the number of samples $M$ and  as a function $M$ (right) for three values of temperature in the ordered system, i e , $J_{ij}=0,1$  
The system size is $N=64$ }
\label{PL-err-Jor1}
\end{figure}

In order to analyze the effects of the number of samples and of the temperature regimes, we plot in Fig  \ref{PL-err-Jor1} the reconstruction error, Eq  (\ref{err}), as a function of temperature for three different sample sizes $M=64,128$ and $512$  
The error is seen to sharply rise al low temperature, incidentally, in the ordered case, for  $T<T_c \sim 0 893$, which is the Kosterlitz-Thouless transition temperature of the 2XY model\cite{Olsson92}  
 However, we can see that if only $M=64$ samples are considered, $\mbox{err}_J$ remains high independently on the working temperature  
 In the right plot of Fig  \ref{PL-err-Jor1},  $\mbox{err}_J$ is plotted as a function of $M$ for three different working temperatures $T/J=0 4,0 7$ and $1 3$  As we expect, 
 $\mbox{err}_J$  decreases as $M$ increases  This effect was observed also with mean-field inference techniques on the same model\cite{Tyagi15} 

To better understand the performances of the algorithms, in Fig  \ref{PL-varTP-Jor1} we show several True Positive (TP) curves obtained for various values of $M$ at three different temperatures $T$  As $M$ is large and/or temperature is not too small,  we are able to reconstruct correctly all the couplings present in the system (see bottom plots) 
The True Positive curve displays how many times the inference method finds a true link of the original network  as a function of the index of the vector of sorted absolute value of reconstructed couplings $J_{ij}^{\rm inf}$  
The index $n_{(ij)}$ represents the related spin couples $(ij)$  The TP curve is obtained as follows: 
first  the values $|J^{\rm inf}_{ij}|$ are sorted in descending order and  the spin pairs $(ij)$ are ordered according to the sorting position of $|J^{\rm inf}_{ij}|$  Then,
     	a cycle over the ordered set of pairs $(ij)$, indexed by $n_{(ij)}$, is performed, comparing with the original network coupling $J^{\rm true}_{ij}$ and verifying whether it is zero or not  The true positive curve is computed as
\begin{equation}
\mbox{TP}[n_{(ij)}]= \frac{\mbox{TP}\left[n_{(ij)}-1\right] (n_{ij}-1)+ 1 -\delta_{J^{\rm true}_{ij},0}}{n_{(ij)}}
\end{equation}
As far as $J^{\rm true}_{ij} \neq 0$, TP$=1$  As soon as the true coupling of a given $(ij)$ couple in the sorted list is zero, the TP curve departs from one  
In our case, where the connectivity per spin of the original system is  $c=4$ and there are $N=64$ spins, we know that we will have  $256$ non-zero couplings   
     	If the inverse problem is successful, hence, we expect a steep decrease of the TP curve when  $n_{ij}=256$ is overcome 

In Fig  \ref{PL-varTP-Jor1}
it is  shown that,  almost independently of $T/J$, the TP score improves as $M$ increases  Results are plotted for three different temperatures, $T=0 4,1$ and $2 2$, with increasing number of samples $M = 64, 128,512$ and $1024$ (clockwise)  
We can clearly appreciate the improvement in temperature if the size of the data-set is not very large: for small $M$, $T=0 4$ performs better  
When $M$ is high enough (e g , $M=1024$), instead, the TP curves do not appear to be strongly influenced by the temperature 

\begin{figure}[t!]
	\centering
	\includegraphics[width=1\linewidth]{Jor11_2D_l2_TPJR_varT_varM}
	\caption{TP  curves  for 2D short-range ordered $XY$ model with $N=64$ spins at three different values of $T/J$ with increasing - clockwise from top - $M$ }
	\label{PL-varTP-Jor1} 
\end{figure} 

\subsection{$XY$ model with complex-valued couplings}
For the complex $XY$ we have to contemporary  infer $2$ apart coupling matrices,  $J^R_{i j}$ and $J^I_{i j}$   As before, a system of $N=64$ spins is considered on a 2D lattice 
For the couplings we have considered both ordered and bimodal disordered cases 
In Fig  \ref{PL-Jor3}, a single row of the matrix $J$ (top) and the whole sorted couplings (bottom) are displayed for the ordered model (same legend as in Fig  \ref{PL-Jor1}) for the real, $J^R$ (left column), and the imaginary part, $J^I$   

\begin{figure}[t!]
	\centering
\includegraphics[width=1\linewidth]{Jor3_l2_JRJI_soJRJI_TPJRJI}
	\caption{Results related to the ordered complex XY model with $N=64$ spins on a  2D lattice  Top: instances of  single site reconstruction for the real, JR (left column), and
		the imaginary, JI (right column), part of $J_{ij}$  Bottom: sorted values of JR (left) and JI (right) }
		
	\label{PL-Jor3}
\end{figure}
 
 
  \section{PLM with Decimation}
 \label{sec:res_dec}
 

\begin{figure}[t!]
   	\centering
   	\includegraphics[width=1\linewidth]{Jor1_dec_tPLF_varT_varM}
    	\caption{Tilted Pseudolikelyhood, ${\cal L}_t$, plotted as a function of decimated couplings  Top: Different ${\cal L}_t$ curves obtained for different values of $M$ plotted on top of each other  Here $T=1 3$  The black line indicates the expected number of decimated couplings, $x^*=(N (N-1) - N c)/2=1888$  As we can see, as $M$ increases, the maximum point of ${\cal L}_t$ approaches $x^*$  Bottom: Different ${\cal L}_t$ curves obtained for different values of T with $M=2048$  We can see that, with this value of $M$, no differences can be appreciated on the maximum points of the different  ${\cal L}_t$ curves }
   	\label{var-$t$PLF}
   \end{figure}

\begin{figure}[t!]
    \centering
    \includegraphics[width=1\linewidth]{Jor1_dec_tPLF_peak_statistics_varM_prob eps}
    	\caption{Number of most likely decimated couplings, estimated by the maximum point of $\mathcal{L}_t$, as a function of the number of samples $M$  We can clearly see that the maximum point of $\mathcal{L}_t$ tends toward $x^*$, which is the right expected number of zero couplings in the system }  
    	\label{PLF_peak_statistics}
    \end{figure}
      
      For the ordered real-valued XY model we show in Fig  \ref{var-$t$PLF}, top panel, the outcome on the tilted pseudolikelyhood, $\mathcal{L}_t$ Eq  \eqref{$t$PLF}, of the progressive decimation: from a fully connected lattice  down to an empty lattice  The figure shows the behaviour of $\mathcal{L}_t$ for three different data sizes $M$  A clear data size dependence of the maximum point of  $\mathcal{L}_t$, signalling the most likely value for decimation, is shown  For small $M$ the most likely number of  couplings is overestimated and for increasing $M$ it tends to the true value, as displayed in Fig  \ref{PLF_peak_statistics}   In the bottom panel of Fig  \ref{var-$t$PLF} we display instead different 
 $\mathcal{L}_t$ curves obtained for three different values of $T$ 
  Even though the values of $\mathcal{L}_t$ decrease with increasing temperature, the value of the most likely number of decimated couplings appears to be quite independent on $T$ with $M=2048$ number of samples 
In Fig  \ref{fig:Lt_complex} we eventually display the tilted pseudolikelyhood for a 2D network with complex valued ordered couplings, where the decimation of the real and imaginary coupling matrices proceeds in parallel, that is, 
when a real coupling is small enough to be decimated its imaginary part is also decimated, and vice versa 
One can see that though the apart errors for the real and imaginary parts are different in absolute values, they display the same dip, to be compared with the maximum point of $\mathcal{L}_t$ 
     
       \begin{figure}[t!]
    	\centering
      	\includegraphics[width=1\linewidth]{Jor3_dec_tPLF_new}
      	\caption{Tilted Pseudolikelyhood, ${\cal L}_t$, plotted with the reconstruction errors for the XY model with $N=64$ spins on a 2D lattice  These results refer to the case of  ordered and complex valued couplings  The full (red) line indicates ${\cal L}_t$  The dashed (green) 
      		and the dotted (blue) lines show the reconstruction errors (Eq  \eqref{eq:errj}) obtained for the real and the imaginary couplings respectively  We can see that both ${\rm err_{JR}}$ and ${\rm err_{JI}}$ have a minimum at $x^*$ }
          	\label{fig:Lt_complex}
    \end{figure}

\begin{figure}[t!]
   	\centering
   	\includegraphics[width=1\linewidth]{Jor1_dec_JR_soJR_TPJR}
   	\caption{XY model on a 2D lattice with $N=64$ sites and real valued couplings  The graphs show the inferred (dashed black lines) and true couplings (full green lines) plotted on top of each other  The left and right columns refer to the
   		 cases of ordered and bimodal disordered couplings, respectively  Top figures: single site reconstruction, i e , one row of the matrix $J$  Bottom figures: couplings are plotted sorted in descending order }  
   	\label{Jor1_dec}
   \end{figure}
   
\begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{Jor3_dec_JRJI_soJRJI_TPJRJI}
    	\caption{XY model on a 2D lattice with $N=64$ sites and ordered complex-valued couplings 
    		The inferred and true couplings are plotted on top of each other  The left and right columns show the real and imaginary parts, respectively, of the couplings  Top figures refer to a single site reconstruction, i e , one row of the matrix $J$  Bottom figures report the couplings sorted in descending order }
    	\label{Jor3_dec}
    \end{figure}
    
       







       \begin{figure}[t!]
     	\centering
     	\includegraphics[width=1\linewidth]{MF_PL_Jor1_2D_TPJR_varT}
     	\caption{True Positive curves obtained with the three techniques: PLM with decimation, (blue) dotted line,  PLM with $l_2$ regularization, (greed) dashed line, and mean-field, (red) full line   These results refer to real valued ordered couplings with $N=64$ spins on a 2D lattice  The temperature is here $T=0 7$ while the four graphs refer to different sample sizes: $M$ increases clockwise }
     	\label{MF_PL_TP}
     \end{figure}
    
    \begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{MF_PL_Jor1_2D_errJ_varT_varM}
    	\caption{Variation of reconstruction error, ${\rm err_J}$, with respect to temperature as obtained with the three different techniques, see Fig  \ref{MF_PL_TP}, for four different sample size:  clockwise from top   $M=512,1024, 2048$ and $4096$ } 
    	\label{MF_PL_err}
    \end{figure}
    
     Once the most likely network has been identified through the decimation procedure, we perform the same analysis displayed in Fig  \ref{Jor1_dec}  for ordered and then quenched disordered real-valued couplings
and in Fig  \ref{Jor3_dec} for  complex-valued ordered couplings   In comparison to the results shown in Sec  \ref{sec:res_reg},
  the PLM with decimation leads to rather cleaner results  In Figs  \ref{MF_PL_err} and \ref{MF_PL_TP} we compare the performances of the PLM with decimation in respect to ones of the PLM with $l_2$-regularization  These two techniques are also analysed in respect to a mean-field technique previously implemented on the same XY systems\cite{Tyagi15} 
  
    For what concerns the network of connecting links, in Fig  \ref{MF_PL_TP} we compare the TP curves obtained with the three techniques  The results refer to the case of ordered and real valued couplings, but similar behaviours were obtained for the other cases analysed  
  The four graphs are related to different sample sizes, with $M$ increasing clockwise  When $M$ is high enough, all techniques reproduce the true network  
  However, for lower values of $M$ the performances of the PLM with $l_2$ regularization and with decimation drastically overcome those ones of the previous mean field technique  
  In particular, for $M=256$ the PLM techniques still reproduce the original network while the mean-field method fails to find more than half of the couplings  
  When $M=128$, the network is clearly reconstructed only through the PLM with decimation while the PLM with $l_2$ regularization underestimates the couplings  
  Furthermore, we notice that the PLM method with decimation is able to clearly infer the network of interaction even when $M=N$ signalling that it could be considered also in the under-sampling regime $M<N$   
 
 
In Fig  \ref{MF_PL_err} we compare the temperature behaviour of the reconstruction error 
In can be observed that for all temperatures and for all sample sizes  the reconstruction error, ${\rm err_J}$, (plotted here in log-scale) obtained with the PLM+decimation is always smaller than 
that one obtained with the other techniques  The temperature behaviour of ${\rm err_J}$ agrees with the one already observed for Ising spins in \cite{Nguyen12b} and for XY spins  in \cite{Tyagi15} with a mean-field approach:  ${\rm err_J}$ displays a minimum around $T\simeq 1$ and then it increases for very lower $T$; however,
 the error obtained with the PLM with decimation is several times smaller  than the error estimated by the other methods 



 
 

     
     \section{Conclusions}
     \label{sec:conc}


Different statistical inference methods have been applied to the inverse problem of the XY model 
After a short review of techniques based on pseudo-likelihood and their formal generalization to the model we have tested their performances against data generated by means of Monte Carlo numerical simulations of known instances
with diluted, sparse, interactions 

The main outcome is that the best performances are obtained by means of the  pseudo-likelihood method combined with decimation  Putting to zero (i e , decimating) very weak bonds, this technique turns out to be very precise for  problems whose real underlying interaction network is sparse, i e , the number of couplings per variable does not scale with number of variables 
The PLM + decimation method is compared to the PLM + regularization method, with $\ell_2$ regularization and to a mean-field-based method  The behavior of the quality of the network reconstruction is analyzed by looking at the overall sorted couplings and at the single site couplings, comparing them with the real network, and at the true positive curves in all three approaches  In the PLM +decimation method, moreover, the identification of the number of decimated bonds at which the tilted pseudo-likelihood is maximum allows for a precise estimate of the total number of bonds  Concerning this technique, it is also shown that the network with the most likely number of bonds is also the one of least reconstruction error, where not only the prediction of the presence of a bond is estimated but also its value 

The behavior of the inference quality in temperature and in the size of data samples is also investigated, basically confirming the low $T$ behavior hinted by Nguyen and Berg \cite{Nguyen12b} for the Ising model  In temperature, in particular, the reconstruction error curve displays a minimum at a low temperature, close to the critical point in those cases in which a critical behavior occurs, and a sharp increase as temperature goes to zero  The decimation method, once again, appears to enhance this minimum of the reconstruction error of almost an order of magnitude with respect to other methods 
 
The techniques displayed and the results obtained in this work can be of use in any of the many systems whose theoretical representation is given by Eq  \eqref{eq:HXY} or Eq  \eqref{eq:h_im}, some of which are recalled in Sec  \ref{sec:model}  In particular, a possible application can be the field of light waves propagation through random media and the corresponding problem of the  reconstruction of an object seen through an opaque medium or a disordered optical fiber \cite{Vellekoop07,Vellekoop08a,Vellekoop08b, Popoff10a,Akbulut11,Popoff11,Yilmaz13,Riboli14} 

 	
Context 2: Hugh Hilton Goodwin (December 21, 1900 – February 25, 1980) was a decorated officer in the United States Navy with the rank of Vice Admiral  A veteran of both World Wars, he commanded escort carrier  during the Mariana Islands campaign  Goodwin then served consecutively as Chief of Staff, Carrier Strike Group 6 and as Air Officer, Philippine Sea Frontier and participated in the Philippines campaign in the later part of the War 

Following the War, he remained in the Navy and rose to the flag rank and held several important commands including Vice Commander, Military Air Transport Service, Commander, Carrier Division Two and Commander, Naval Air Forces, Continental Air Defense Command 

Early life and career

Hugh H  Goodwin was born on December 21, 1900, in Monroe, Louisiana and attended Monroe High School there (now Neville High School)  Following the United States' entry into World War I in April 1917, Goodwin left the school without receiving the diploma in order to see some combat and enlisted the United States Navy on May 7, 1917  He completed basic training and was assigned to the battleship   Goodwin participated in the training of armed guard crews and engine room personnel as the Atlantic Fleet prepared to go to war and in November 1917, he sailed with the rest of Battleship Division 9, bound for Britain to reinforce the Grand Fleet in the North Sea 

Although he did not complete the last year of high school, Goodwin was able to earn an appointment to the United States Naval Academy at Annapolis, Maryland in June 1918  While at the academy, he earned a nickname "Huge" and among his classmates were several future admirals and generals including: Hyman G  Rickover, Milton E  Miles, Robert E  Blick Jr , Herbert S  Duckworth, Clayton C  Jerome, James P  Riseley, James A  Stuart, Frank Peak Akers, Sherman Clark, Raymond P  Coffman, Delbert S  Cornwell, Frederick J  Eckhoff, Ralph B  DeWitt, John Higgins, Vernon Huber, Albert K  Morehouse, Harold F  Pullen, Michael J  Malanaphy, William S  Parsons, Harold R  Stevens, John P  Whitney, Lyman G  Miller and George J  O'Shea 

Goodwin graduated with Bachelor of Science degree on June 3, 1922, and was commissioned Ensign in the United States Navy  He was subsequently assigned to the battleship  and took part in the voyage to Rio de Janeiro, Brazil, before he was ordered to the Naval Torpedo Station at Newport, Rhode Island for submarine instruction in June 1923  Goodwin completed the training several weeks later and was attached to the submarine   He then continued his further training aboard submarine  and following his promotion to Lieutenant (junior grade) on June 3, 1925, he qualified as submariner 

He then served aboard submarine  off the coast of California, before he was ordered for the recruiting duty to San Francisco in September 1927  While in this capacity, Goodwin applied for naval aviation training which was ultimately approved and he was ordered to the Naval Air Station Pensacola, Florida in August 1928  Toward the end of the training, he was promoted to lieutenant on December 11, 1928, and upon the completion of the training in January 1929, he was designated Naval aviator 

Goodwin was subsequently attached to the Observation Squadron aboard the aircraft carrier  and participated in the Fleet exercises in the Caribbean  He was transferred to the Bureau of Aeronautics in Washington, D C  in August 1931 and served consecutively under the architect of naval aviation William A  Moffett and future Chief of Naval Operations Ernest J  King 

In June 1933, Goodwin was ordered to the Naval War College at Newport, Rhode Island, where he completed junior course in May of the following year  He subsequently joined the crew of aircraft carrier  and served under Captain Arthur B  Cook and took part in the Fleet exercises in the Caribbean and off the East Coast of the United States 

He was ordered back to the Naval Air Station Pensacola, Florida in June 1936 and was attached to the staff of the Base Commandant, then-Captain Charles A  Blakely  When Blakely was succeeded by William F  Halsey in June 1937, Goodwin remained in Halsey's staff and was promoted to Lieutenant Commander on December 1, 1937  He also completed correspondence course in International law at the Naval War College 

Goodwin was appointed Commanding officer of the Observation Squadron 1 in June 1938 and attached to the battleship  he took part in the patrolling of the Pacific and 
West Coast of the United States until September 1938, when he assumed command of the Observation Squadron 2 attached to the battleship  

When his old superior from Lexington, now Rear Admiral Arthur B  Cook, was appointed Commander Aircraft, Scouting Force in June 1939, he requested Goodwin as his Aide and Flag Secretary  He became Admiral Cook's protégé and after year and half of service in the Pacific, he continued as his Aide and Flag Secretary, when Cook was appointed Commander Aircraft, Atlantic Fleet in November 1940 

World War II

Following the United States' entry into World War II, Goodwin was promoted to the temporary rank of Commander on January 1, 1942, and assumed duty as advisor to the Argentine Navy  His promotion was made permanent two months later and he returned to the United States in early 1943 for duty as assistant director of Planning in the Bureau of Aeronautics under Rear admiral John S  McCain  While still in Argentina, Goodwin was promoted to the temporary rank of Captain on June 21, 1942 

By the end of December 1943, Goodwin was ordered to Astoria, Oregon, where he assumed command of newly commissioned escort carrier USS Gambier Bay  He was responsible for the initial training of the crew and was known as a strict disciplinarian, but the crew appreciated the skills he taught them that prepared them for combat  Goodwin insisted that everyone aboard has to do every job right every time and made us fight our ship at her best 

During the first half of 1944, Gambier Bay was tasked with ferrying aircraft for repairs and qualified carrier pilots from San Diego to Pearl Harbor, Hawaii, before departed on May 1, 1944, to join Rear admiral Harold B



ground_truth: It outperforms mean-field methods and the PLM with $l_2$ regularization in terms of reconstruction error and true positive rate.

prompt_front: Now, answer the following question based on the text below, only give me the answer and do not output any other words.

Question: What was Hugh H. Goodwin's rank in the United States Navy?

Read the following text and answer briefly.

Context 2:  Sallada's Carrier Support Group 2, staging in the Marshalls for the invasion of the Marianas 

The air unit, VC-10 Squadron, under Goodwin's command gave close air support to the initial landings of Marines on Saipan on June 15, 1944, destroying enemy gun emplacements, troops, tanks, and trucks  On the 17th, her combat air patrol (CAP) shot down or turned back all but a handful of 47 enemy planes headed for her task group and her gunners shot down two of the three planes that did break through to attack her 

Goodwin's carrier continued in providing of close ground support operations at Tinian during the end of July 1944, then turned her attention to Guam, where she gave identical aid to invading troops until mid-August that year  For his service during the Mariana Islands campaign, Goodwin was decorated with Bronze Star Medal with Combat "V" 

He was succeeded by Captain Walter V  R  Vieweg on August 18, 1944, and appointed Chief of Staff, Carrier Division Six under Rear admiral Arthur W  Radford  The Gambier Bay was sunk in the Battle off Samar on October 25, 1944, during the Battle of Leyte Gulf after helping turn back a much larger attacking Japanese surface force 

Goodwin served with Carrier Division Six during the Bonin Islands raids, the naval operations at Palau and took part in the Battle of Leyte Gulf and operations supporting Leyte landings in late 1944  He was later appointed Air Officer of the Philippine Sea Frontier under Rear admiral James L  Kauffman and remained with that command until the end of hostilities  For his service in the later part of World War II, Goodwin was decorated with Legion of Merit with Combat "V"  He was also entitled to wear two Navy Presidential Unit Citations and Navy Unit Commendation 

Postwar service

Following the surrender of Japan, Goodwin assumed command of Light aircraft carrier  on August 24, 1945  The ship was tasked with air missions over Japan became mercy flights over Allied prisoner-of-war camps, dropping food and medicine until the men could be rescued  She was also present at Tokyo Bay for the Japanese surrender on September 2, 1945 

Goodwin returned with San Jacinto to the United States in mid-September 1945 and he was detached in January 1946  He subsequently served in the office of the Chief of Naval Operations until May that year, when he entered the instruction at National War College  Goodwin graduated in June 1947 and served on Secretary's committee for Research on Reorganization  Upon promotion to Rear admiral on April 1, 1949, Goodwin was appointed Chief of Staff and Aide to Commander-in-Chief, Atlantic Fleet under Admiral William H  P  Blandy 

Revolt of the Admirals

In April 1949, the budget's cuts and proposed reorganization of the United States Armed Forces by the Secretary of Defense Louis A  Johnson launched the wave of discontent between senior commanders in the United States Navy  Johnson proposed the merging of the Marine Corps into the Army, and reduce the Navy to a convoy-escort force 

Goodwin's superior officer, Admiral Blandy was call to testify before the House Committee on Armed Services and his harsh statements for the defense of the Navy, costed him his career  Goodwin shared his views and openly criticized Secretary Johnson for having power concentrated in a single civilian executive, who is an appointee of the Government and not an elected representative of the people  He also criticized aspects of defense unification which permitted the Joint Chiefs of Staff to vote on arms policies of individual services, and thus "rob" the branches of autonomy 

The outbreak of the Korean War in summer 1950 proved the proposal of Secretary Johnson as incorrect and he resigned in September that year  Also Secretary of the Navy, Francis P  Matthews resigned one month earlier 

Later service

Due to the Revolts of the admirals, Blandy was forced to retire in February 1950 and Goodwin was ordered to Newport, Rhode Island for temporary duty as Chief of Staff and Aide to the President of the Naval War College under Vice admiral Donald B  Beary in April 1950  Goodwin was detached from that assignment two months and appointed member of the General Board of the Navy  He was shortly thereafter appointed acting Navy Chief of Public Information, as the substitute for Rear Admiral Russell S  Berkey, who was relieved of illness, but returned to the General Board of the Navy in July that year  Goodwin served in that capacity until February 1951, when he relieved his Academy class, Rear admiral John P  Whitney as Vice Commander, Military Air Transport Service (MATS) 

While in this capacity, Goodwin served under Lieutenant general Laurence S  Kuter and was co-responsible for the logistical support of United Nations troops fighting in Korea  The MATS operated from the United States to Japan and Goodwin served in this capacity until August 1953, when he was appointed Commander Carrier Division Two  While in this assignment, he took part in the Operation Mariner, Joint Anglo-American exercise which encountered very heavy seas over a two-week period in fall 1953 

Goodwin was ordered to the Philippines in May 1954 and assumed duty as Commander, U S  Naval Forces in the Philippines with headquarters at Naval Station Sangley Point near Cavite  He held that command in the period of tensions between Taiwan and China and publicly declared shortly after his arrival, that any attack on Taiwan by the Chinese Communists on the mainland would result in US participation in the conflict  The naval fighter planes under his command also provided escort for passing commercial planes  Goodwin worked together with retired Admiral Raymond A  Spruance, then-Ambassador to the Philippines, and accompanied him during the visits to Singapore, Bangkok and Saigon in January 1955 

On December 18, 1955, Goodwin's classmate Rear admiral Albert K  Morehouse, then serving as Commander, Naval Air Forces, Continental Air Defense Command (CONAD), died of heart attack and Goodwin was ordered to CONAD headquarters in Colorado Springs, Colorado to assume Morehouse's position  While in this capacity, he was subordinated to Army General Earle E  Partridge and was responsible for the Naval and Marine Forces allocated to the command designated for the defense of the Continental United States 

Retirement

Goodwin retired on June 1, 1957, after 40 years of active service and was advanced to the rank of Vice admiral on the retired list for having been specially commended in combat  A week later, he was invited back to his Monroe High School (now Neville High School) and handed a diploma showing that he had been graduated with the class of 1918  He then settled in Monterey, California where he taught American history at Stevenson school and was a member of the Naval Order of the United States 

Vice admiral Hugh H  Goodwin died at his home on February 25, 1980, aged 79  He was survived by his wife, Eleanor with whom he had two children, a daughter Sidney and a son Hugh Jr , who graduated from the Naval Academy in June 1948, but died one year later, when the Hellcat fighter he was piloting collided with another over the Gulf of Mexico during training 

Decorations

Here is the ribbon bar of Vice admiral Hugh H  Goodwin:

References

1900 births
1980 deaths
People from Monroe, Louisiana
Military personnel from Louisiana
United States Naval Academy alumni
Naval War College alumni
United States Naval Aviators
United States Navy personnel of World War I
United States Navy World War II admirals
United States Navy vice admirals
United States submarine commanders
Recipients of the Legion of Merit
Context 3: \section{Introduction}
Given a data set and a model with some unknown parameters, the inverse problem aims to find the values of the model parameters that best fit the data   
In this work, in which we focus on systems of interacting elements,
 the inverse problem concerns  the statistical inference
 of the underling interaction network and of its coupling coefficients from observed data on the dynamics  of the system  
 Versions of this problem are encountered in physics, biology (e g , \cite{Balakrishnan11,Ekeberg13,Christoph14}), social sciences and finance (e g ,\cite{Mastromatteo12,yamanaka_15}), neuroscience (e g , \cite{Schneidman06,Roudi09a,tyrcha_13}), just to cite a few, and are becoming more and more important due to the increase in the amount of data available from these fields \\
 \indent 
 A standard approach used in statistical inference is to predict the interaction couplings by maximizing the likelihood function 
 This technique, however, requires the evaluation of the  
 
   partition function that, in the most general case, concerns a number of computations scaling exponentially with the system size 
  
  
    Boltzmann machine learning uses Monte Carlo sampling to compute the gradients of the Log-likelihood looking for stationary points \cite{Murphy12} but this method is computationally manageable only for small systems  A series of faster approximations, such as naive mean-field, independent-pair approximation \cite{Roudi09a, Roudi09b}, inversion of TAP equations \cite{Kappen98,Tanaka98}, small correlations expansion \cite{Sessak09}, adaptive TAP \cite{Opper01}, adaptive  cluster expansion \cite{Cocco12} or Bethe approximations \cite{Ricci-Tersenghi12, Nguyen12}  have, then, been developed  These techniques take as input means and correlations of observed variables and most of them assume a fully connected graph as underlying connectivity network, or expand  around it by perturbative dilution   In most cases, network reconstruction turns out to  be not accurate for small data sizes and/or when couplings are  strong or, else, if the original interaction network is sparse \\
\indent
 A further method, substantially improving performances for small data, is the so-called Pseudo-Likelyhood Method (PLM) \cite{Ravikumar10}  In Ref  \cite{Aurell12} Aurell and Ekeberg performed a comparison between PLM and some of the just mentioned mean-field-based algorithms on the pairwise interacting Ising-spin  ($\sigma = \pm 1$) model, showing how PLM performs sensitively better, especially on sparse graphs and in the high-coupling limit, i e , for low temperature 
 
 In this work, we aim at performing statistical inference  on a model whose interacting variables are continuous $XY$ spins, i e , $\sigma \equiv \left(\cos \phi,\sin \phi\right)$ with $\phi \in [0, 2\pi )$  The developed tools can, actually, be also straightforward applied  to the $p$-clock model  \cite{Potts52} where the phase $\phi$ takes discretely equispaced $p$ values  in the $2 \pi$ interval, $\phi_a =  a 2 \pi/p$, with $a= 0,1,\dots,p-1$  The $p$-clock model, else called vector Potts model, gives a hierarchy of discretization of the $XY$ model as $p$ increases  For $p=2$, one recovers the Ising model, for $p=4$ the Ashkin-Teller model \cite{Ashkin43}, for $p=6$ the ice-type model \cite{Pauling35,Baxter82} and the eight-vertex model \cite{Sutherland70,Fan70,Baxter71} for $p=8$   
It turns out to be very useful also for numerical implementations of the continuous $XY$ model  
Recent analysis on the multi-body $XY$ model has shown that for a limited number of discrete phase values ($p\sim 16, 32$) the thermodynamic critical properties of the $p\to\infty$ $XY$ limit are promptly recovered \cite{Marruzzo15, Marruzzo16}   
Our main motivation to study statistical inference is that these kind of models have recently turned out to be rather useful in describing the behavior of optical systems, 
including standard mode-locking lasers \cite{Gordon02,Gat04,Angelani07,Marruzzo15} and random lasers \cite{Angelani06a,Leuzzi09a,Antenucci15a,Antenucci15b,Marruzzo16}  
In particular, the inverse problem on the pairwise XY model analyzed here might be of help in recovering images from light propagated through random media  


      This paper is organized as follows: in Sec  \ref{sec:model} we introduce the general model  and we discuss its  derivation also  as a model for light transmission through random scattering media  
    In Sec  \ref{sec:plm} we introduce the PLM with $l_2$ regularization  and with decimation, two variants of the PLM respectively introduced in Ref  \cite{Wainwright06} and \cite{Aurell12} for the inverse Ising problem  
    Here, we analyze these techniques for continuous $XY$ spins and we test them on thermalized data generated by Exchange Monte Carlo numerical simulations of the original model dynamics  In Sec  \ref{sec:res_reg} we  present the results related to the PLM-$l_2$  In Sec  \ref{sec:res_dec} the results related to the PLM with decimation are reported and its performances are compared to the PLM-$l_2$ and to a variational mean-field method analyzed in Ref  \cite{Tyagi15}  In Sec  \ref{sec:conc}, we outline conclusive remarks and perspectives 

        \section{The leading $XY$ model}
      \label{sec:model}
 The leading model we are considering is defined, for a system of $N$ angular $XY$ variables, by the Hamiltonian 
 \begin{equation}
  \mathcal{H} = - \sum_{ik}^{1,N} J_{ik} \cos{\left(\phi_i-\phi_k\right)} 
  \label{eq:HXY}
 
  \end{equation} 
  
  The $XY$ model is well known in statistical mechanics, displaying important physical
  insights, starting from the Berezinskii-Kosterlitz-Thouless
  transition in two dimensions\cite{Berezinskii70,Berezinskii71,Kosterlitz72} and moving to, e g , the
  transition of liquid helium to its superfluid state \cite{Brezin82}, the roughening transition of the interface of a crystal in equilibrium with its vapor \cite{Cardy96}  In presence of disorder and frustration \cite{Villain77,Fradkin78} the model has been adopted to describe synchronization problems as the Kuramoto model \cite{Kuramoto75} and in the theoretical modeling of Josephson junction arrays \cite{Teitel83a,Teitel83b} and arrays of coupled lasers \cite{Nixon13} 
  Besides several derivations and implementations of the model in quantum and classical physics, equilibrium or out of equilibrium, ordered or fully frustrated systems, Eq  (\ref{eq:HXY}), in its generic form,
  has found applications also in other fields  A rather fascinating example being the behavior of starlings flocks  \cite{Reynolds87,Deneubourg89,Huth90,Vicsek95, Cavagna13} 
  Our interest on the $XY$ model resides, though, in optics  Phasor and phase models with pairwise and  multi-body interaction terms can, indeed, describe the behavior of electromagnetic modes in both linear and nonlinear optical systems in the analysis of problems such as light propagation and lasing \cite{Gordon02, Antenucci15c, Antenucci15d}  As couplings are strongly frustrated, these models turn out to be especially useful to the study of optical properties in random media \cite{Antenucci15a,Antenucci15b}, as in the noticeable case of random lasers \cite{Wiersma08,Andreasen11,Antenucci15e}  and they might as well be applied to linear scattering problems, e g , propagation of waves in opaque systems or disordered fibers  
  
  
  \subsection{A propagating wave model}
  We briefly mention a derivation of the model as a proxy for the propagation of light through random linear media  
 Scattering of light is held responsible to obstruct our view and make objects opaque  Light rays, once that they enter the material, only exit  after getting scattered multiple times within the material  In such a disordered medium, both the direction and the phase of the propagating waves are random  Transmitted light 
 yields a disordered interference pattern typically  having low intensity, random phase and almost no resolution, called a speckle  Nevertheless, in recent years it has been realized that disorder is rather a blessing in disguise \cite{Vellekoop07,Vellekoop08a,Vellekoop08b}  Several experiments have made it possible to control the behavior of light and other optical processes in a given random disordered medium,  
 by exploiting, e g ,  the tools developed for wavefront shaping to control the propagation of light and to engineer the confinement of light \cite{Yilmaz13,Riboli14} 
 \\
 \indent
 In a linear dielectric medium, light propagation can be described through a part of the scattering matrix, the transmission matrix $\mathbb{T}$, linking the outgoing to the incoming fields  
 Consider the case in which there are $N_I$ incoming channels and $N_O$ outgoing ones; we can indicate with $E^{\rm in,out}_k$ the input/output electromagnetic field phasors of channel $k$  In the most general case, i e , without making any particular assumptions on the field polarizations, each light mode and its polarization polarization state can be represented by means of the $4$-dimensional Stokes vector  Each $ t_{ki}$ element of $\mathbb{T}$, thus, is a $4 \times 4$ M{\"u}ller matrix  If, on the other hand, we know that the source is polarized and the observation is made on the same polarization, one can use a scalar model and adopt Jones calculus \cite{Goodman85,Popoff10a,Akbulut11}:
   \begin{eqnarray}
 E^{\rm out}_k = \sum_{i=1}^{N_I}  t_{ki} E^{\rm in}_i \qquad \forall~ k=1,\ldots,N_O
 \label{eq:transm}
 \end{eqnarray}
  We recall that the elements of the transmission matrix are random complex coefficients\cite{Popoff10a}  For the case of completely unpolarized modes, we can also use a scalar model similar to Eq  \eqref{eq:transm}, but whose variables are  the intensities of the outgoing/incoming fields, rather than the fields themselves \\ 
In the following, for simplicity, we will consider Eq  (\ref{eq:transm}) as our starting point,
where $E^{\rm out}_k$, $E^{\rm in}_i$ and $t_{ki}$ are all complex scalars  
If Eq  \eqref{eq:transm} holds for any $k$, we can write:
  \begin{eqnarray}
  \int \prod_{k=1}^{N_O} dE^{\rm out}_k \prod_{k=1}^{N_O}\delta\left(E^{\rm out}_k - \sum_{j=1}^{N_I}  t_{kj} E^{\rm in}_j \right) = 1
  \nonumber
  \\
  \label{eq:deltas}
  \end{eqnarray}

 Observed data are a noisy representation of the true values of the fields  Therefore, in inference problems it is statistically more meaningful to take that noise into account in a probabilistic way, 
 rather than looking  at the precise solutions of the exact equations (whose parameters are unknown)  
 To this aim we can introduce Gaussian distributions whose limit for zero variance are the Dirac deltas in Eq  (\ref{eq:deltas}) 
 Moreover, we move to consider the ensemble of all possible solutions of Eq  (\ref{eq:transm}) at given $\mathbb{T}$, looking at  all configurations of input fields  We, thus, define the function:
 
   \begin{eqnarray}
  Z &\equiv &\int_{{\cal S}_{\rm in}} \prod_{j=1}^{N_I}  dE^{\rm in}_j \int_{{\cal S}_{\rm out}}\prod_{k=1}^{N_O} dE^{\rm out}_k 
  \label{def:Z}
\\
    \times
  &&\prod_{k=1}^{N_O}
   \frac{1}{\sqrt{2\pi \Delta^2}}  \exp\left\{-\frac{1}{2 \Delta^2}\left|
  E^{\rm out}_k -\sum_{j=1}^{N_I}  t_{kj} E^{\rm in}_j\right|^2
\right\} 
\nonumber
 \end{eqnarray}
   We stress that the integral of Eq  \eqref{def:Z} is not exactly a Gaussian integral  Indeed, starting from Eq  \eqref{eq:deltas}, two constraints on the electromagnetic field intensities must be taken into account  

  The space of solutions is  delimited by the total power ${\cal P}$ received by system, i e , 
  ${\cal S}_{\rm in}: \{E^{\rm in} |\sum_k I^{\rm in}_k = \mathcal{P}\}$, also implying  a constraint on the total amount of energy that is transmitted through the medium, i  e , 
  ${\cal S}_{\rm out}:\{E^{\rm out} |\sum_k I^{\rm out}_k=c\mathcal{P}\}$, where the attenuation factor  $c<1$ accounts for total losses 
  As we will see more in details in the following, being interested in inferring the transmission matrix through the PLM, we can omit to explicitly include these terms in Eq  \eqref{eq:H_J} since they do not depend on $\mathbb{T}$ not adding any information on the gradients with respect to the elements of $\mathbb{T}$ 
  
 Taking the same number of incoming and outcoming channels, $N_I=N_O=N/2$, and  ordering the input fields in the first $N/2$ mode indices and the output fields in the last $N/2$ indices, we can drop the ``in'' and ``out'' superscripts and formally write $Z$  as a partition function
    \begin{eqnarray}
        \label{eq:z}
 && Z =\int_{\mathcal S} \prod_{j=1}^{N} dE_j \left(   \frac{1}{\sqrt{2\pi \Delta^2}} \right)^{N/2} 
 \hspace*{- 4cm} \exp\left\{
  -\frac{ {\cal H} [\{E\};\mathbb{T}] }{2\Delta^2}
  \right\}
  \\
&&{\cal H} [\{E\};\mathbb{T}] =
-  \sum_{k=1}^{N/2}\sum_{j=N/2+1}^{N} \left[E^*_j t_{jk} E_k + E_j t^*_{kj} E_k^* 
\right]
 \nonumber
\\
&&\qquad\qquad \qquad + \sum_{j=N/2+1}^{N} |E_j|^2+ \sum_{k,l}^{1,N/2}E_k
U_{kl} E_l^*
 \nonumber
 \\
 \label{eq:H_J}
 &&\hspace*{1 88cm } = - \sum_{nm}^{1,N} E_n J_{nm} E_m^*
 \end{eqnarray}
 where ${\cal H}$ is a real-valued function by construction, we have introduced the effective input-input coupling matrix
\begin{equation}
U_{kl} \equiv \sum_{j=N/2+1}^{N}t^*_{lj} t_{jk} 
 \label{def:U}
 \end{equation}
 and the whole interaction matrix reads (here $\mathbb{T} \equiv \{ t_{jk} \}$)
 \begin{equation}
 \label{def:J}
 \mathbb J\equiv \left(\begin{array}{ccc|ccc}
 \phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}\\
 \phantom{()}&-\mathbb{U} \phantom{()}&\phantom{()}&\phantom{()}&{\mathbb{T}}&\phantom{()}\\
\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}\\
 \hline
\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}&\phantom{()}\\
 \phantom{()}& \mathbb   T^\dagger&\phantom{()}&\phantom{()}& - \mathbb{I} &\phantom{()}\\
\phantom{a}&\phantom{a}&\phantom{a}&\phantom{a}&\phantom{a}&\phantom{a}\\
 \end{array}\right)
 \end{equation}
 
 Determining the electromagnetic complex amplitude configurations that minimize the {\em cost function} ${\cal H}$, Eq   (\ref{eq:H_J}),  means to maximize the overall distribution peaked around the solutions of the transmission Eqs  (\ref{eq:transm})  As the variance $\Delta^2\to 0$, eventually, the initial set of Eqs  (\ref{eq:transm}) are recovered  The ${\cal H}$ function, thus, plays the role of an Hamiltonian and  $\Delta^2$ the role of a noise-inducing temperature  The exact numerical problem corresponds to the zero temperature limit of the statistical mechanical problem  Working with real data, though, which are noisy, a finite ``temperature''
  allows for a better representation of the ensemble of solutions to the sets of equations of continuous variables  
  

  
  
  Now, we can express every phasor in Eq  \eqref{eq:z}  as $E_k = A_k e^{\imath \phi_k}$  As a working hypothesis we will consider the intensities $A_k^2$ as either homogeneous or as \textit{quenched} with respect to phases 
The first condition occurs, for instance, to the input intensities $|E^{\rm in}_k|$ produced by a phase-only spatial light modulator (SLM) with homogeneous illumination \cite{Popoff11} 
With \textit{quenched} here we mean, instead, that the intensity of each mode is the same for every solution of Eq  \eqref{eq:transm} at fixed $\mathbb T$ 
We stress that, including intensities in the model does not preclude the inference analysis but it is out of the focus of the present work and will be considered elsewhere  

If all intensities are uniform in input and in output, this amount to a constant rescaling for each one of the four sectors of matrix $\mathbb J$ in Eq  (\ref{def:J}) that will not change the properties of the matrices 
For instance, if the original transmission matrix is unitary, so it will be the rescaled one and the matrix $\mathbb U$ will be  diagonal 
Otherwise, if intensities are \textit{quenched}, i e , they can be considered as constants in Eq  (\ref{eq:transm}),
they are inhomogeneous with respect to phases  The generic Hamiltonian element will, therefore, rescale as 
  \begin{eqnarray}
  E^*_n J_{nm} E_m = J_{nm} A_n A_m e^{\imath (\phi_n-\phi_m)} \to J_{nm} e^{\imath (\phi_n-\phi_m)}
  \nonumber
  \end{eqnarray}
  and the properties of the original  $J_{nm}$ components are not conserved  in the rescaled one  In particular, we have no argument, anymore, to possibly set the rescaled $U_{nm}\propto \delta_{nm}$ 
  Eventually, we end up with the complex couplings $XY$ model, whose real-valued Hamiltonian is written as
 \begin{eqnarray}
  \mathcal{H}& = &  - \frac{1}{2} \sum_{nm} J_{nm} e^{-\imath (\phi_n - \phi_m)}  + \mbox{c c } 
    \label{eq:h_im}
\\    &=&  - \frac{1}{2} \sum_{nm} \left[J^R_{nm} \cos(\phi_n - \phi_m)+
  J^I_{nm}\sin (\phi_n - \phi_m)\right] 
  \nonumber
 \end{eqnarray}
where $J_{nm}^R$ and $J_{nm}^I$ are the real and imaginary parts of $J_{nm}$  Being $\mathbb J$  Hermitian, $J^R_{nm}=J^R_{mn}$ is symmetric and $J_{nm}^I=-J_{mn}^I$ is skew-symmetric 

\begin{comment}
\textcolor{red}{
F: comment about quenched:
I think that to obtain the XY model, it is not necessary that the intensities are strictly quenched (that is also a quite unfeasible situation, I guess) 
Indeed eq (2) does not deal with the dynamics of the modes, but just connect the in and out ones 
For this, what it is necessary to have the XY model, it is that the intensities are always the same on the different samples
(so that the matrix $t_{ij}$ is the same for different phase data)  If the intensities are fixed, then they can be incorporated in $t_{ij}$ and eq (2) can be written just for phases as described  \\
}
\end{comment}


  \section{Pseudolikelihood Maximization}
  \label{sec:plm}
The inverse problem consists in the reconstruction of the parameters $J_{nm}$ of the Hamiltonian, Eq  (\ref{eq:h_im})   
Given a set of $M$ data configurations of $N$ spins
 $\bm\sigma = \{ \cos \phi_i^{(\mu)},\sin \phi_i^{(\mu)} \}$, $i = 1,\dots,N$ and $\mu=1,\dots,M$, we want to \emph{infer} the couplings:
 \begin{eqnarray}
\bm \sigma  \rightarrow  \mathbb{J} 
\nonumber
 \end{eqnarray}
 With this purpose in mind,
 in the rest of this section we implement the working equations for the techniques used  
 In order to test our methods, we generate the input data, i e , the configurations, by Monte-Carlo simulations of the model 
 The joint probability distribution of the $N$ variables $\bm{\phi}\equiv\{\phi_1,\dots,\phi_N\}$, follows the Gibbs-Boltzmann distribution:
 \begin{equation}\label{eq:p_xy}
 P(\bm{\phi}) = \frac{1}{Z} e^{-\beta \mathcal{H\left(\bm{\phi}\right)}} \quad \mbox{ where } \quad Z = \int \prod_{k=1}^N d\phi_k  e^{-\beta \mathcal{H\left(\bm{\phi}\right)}}  
 \end{equation}
 and where we denote $\beta=\left( 2\Delta^2 \right)^{-1}$ with respect to Eq  (\ref{def:Z}) formalism 
 In order to stick to usual statistical inference notation, in the following we will rescale the couplings by a factor $\beta / 2$: $\beta J_{ij}/2 \rightarrow J_{ij}$  
 The main idea of the PLM is to work with the conditional probability distribution of one variable $\phi_i$ given all other variables, 
 $\bm{\phi}_{\backslash i}$:
 
  \begin{eqnarray}
	\nonumber
   P(\phi_i | \bm{\phi}_{\backslash i}) &=& \frac{1}{Z_i} \exp \left \{ {H_i^x (\bm{\phi}_{\backslash i})
  	\cos \phi_i + H_i^y (\bm{\phi}_{\backslash i}) \sin \phi_i } \right \}
	\\
 \label{eq:marginal_xy}
	&=&\frac{e^{H_i(\bm{\phi}_{\backslash i}) \cos{\left(\phi_i-\alpha_i(\bm{\phi}_{\backslash i})\right)}}}{2 \pi I_0(H_i)}
  \end{eqnarray}
  where $H_i^x$ and $H_i^y$ are defined as
   \begin{eqnarray}
   H_i^x (\bm{\phi}_{\backslash i})  &=& \sum_{j (\neq i)} J^R_{ij} \cos \phi_j  - \sum_{j  (\neq i) } J_{ij}^{I} \sin \phi_j \phantom{+  h^R_i} \label{eq:26} \\
   H_i^y  (\bm{\phi}_{\backslash i})  &=&  \sum_{j  (\neq i)} J^R_{ij}  \sin \phi_j  + \sum_{j  (\neq i) } J_{ij}^{I}   \cos \phi_j \phantom{ + h_i^{I} }\label{eq:27}
   \end{eqnarray}
and $H_i= \sqrt{(H_i^x)^2 + (H_i^y)^2}$, $\alpha_i = \arctan H_i^y/H_i^x$   and we introduced the modified Bessel function of the first kind:
  \begin{equation}
  \nonumber
   I_k(x) = \frac{1}{2 \pi}\int_{0}^{2 \pi} d \phi e^{x \cos{ \phi}}\cos{k \phi}
  \end{equation}
  
   Given $M$ observation samples $\bm{\phi}^{(\mu)}=\{\phi^\mu_1,\ldots,\phi^\mu_N\}$, $\mu = 1,\dots, M$, the
   pseudo-loglikelihood for the variable $i$ is given by the logarithm of Eq  (\ref{eq:marginal_xy}),
   \begin{eqnarray}
   \label{eq:L_i}
   L_i &=& \frac{1}{M}  \sum_{\mu = 1}^M  \ln P(\phi_i^{(\mu)}|\bm{\phi}^{(\mu)}_{\backslash i})
   \\
   \nonumber
   & =&  \frac{1}{M}  \sum_{\mu = 1}^M  \left[ H_i^{(\mu)} \cos( \phi_i^{(\mu)} - \alpha_i^{(\mu)}) - \ln  2 \pi I_0\left(H_i^{(\mu)}\right)\right] \,  
    \end{eqnarray}
The underlying idea of PLM is that an approximation of the true parameters of the model is obtained for values that maximize the functions $L_i$ 
The specific maximization scheme differentiates the different techniques 


   
   
   \subsection{PLM with $l_2$ regularization}
   Especially for the case of sparse graphs, it is useful to add a regularizer, which prevents the maximization routine to move towards high values of 
   $J_{ij}$ and $h_i$ without converging  We will adopt an $l_2$ regularization so that the Pseudolikelihood function (PLF) at site $i$  reads:
   \begin{equation}\label{eq:plf_i}
  {\cal L}_i = L_i
  - \lambda \sum_{i \neq j} \left(J_{ij}^R\right)^2 - \lambda \sum_{i \neq j} \left(J_{ij}^I\right)^2  
   \end{equation}
   with $\lambda>0$ 
   Note that the values of $\lambda$ have to be chosen arbitrarily, but not too large, in order not to overcome $L_i$ 
   The standard implementation of the PLM consists in maximizing each ${\cal L}_i$, for $i=1\dots N$, separately  The expected values of the couplings are then:
   \begin{equation}
   \{ J_{i j}^*\}_{j\in \partial i} :=  \mbox{arg max}_{ \{ J_{ij} \}}
    \left[{\cal L}_i\right]
   \end{equation}
   In this way, we obtain two estimates for the coupling $J_{ij}$, one from maximization of ${\cal L}_i$, $J_{ij}^{(i)}$, and another one from ${\cal L}_j$, say $J_{ij}^{(j)}$ 
    Since the original Hamiltonian of the $XY$ model is Hermitian, we know that the real part of the couplings is symmetric while the imaginary part is skew-symmetric  
   
     The final estimate for $J_{ij}$ can then be obtained  averaging the two results:
  
  
  
   \begin{equation}\label{eq:symm}
   J_{ij}^{\rm inferred} = \frac{J_{ij}^{(i)} + \bar{J}_{ij}^{(j)}}{2} 
   \end{equation}
   where with $\bar{J}$ we indicate the complex conjugate 
   It is worth noting that the pseudolikelihood $L_i$, Eq  \eqref{eq:L_i}, is characterized by the
   following properties: (i) the normalization term of Eq \eqref{eq:marginal_xy} can be
   computed analytically at odd with the {\em full} likelihood case that
   in general require a computational time which scales exponentially
   with the size of the systems; (ii) the $\ell_2$-regularized pseudolikelihood
   defined in Eq \eqref{eq:plf_i} is strictly concave (i e  it has a single
   maximizer)\cite{Ravikumar10}; (iii) it is consistent, i e  if $M$ samples are
   generated by a model $P(\phi | J*)$ the maximizer tends to $J*$
   for $M\rightarrow\infty$\cite{besag1975}  Note also that (iii) guarantees that  
   $|J^{(i)}_{ij}-J^{(j)}_{ij}| \rightarrow 0$ for $M\rightarrow \infty$ 
   In Secs  \ref{sec:res_reg}, \ref{sec:res_dec} 
   we report the results obtained and we analyze the performances of the PLM having taken the configurations from Monte-Carlo simulations of models whose details are known 
   

   
   \subsection{PLM with decimation}
   Even though the PLM with $l_2$-regularization allows to dwell the inference towards the low temperature region and in the low sampling case with better performances that mean-field methods, in some situations some couplings are overestimated and not at all symmetric  Moreover, in the technique there is the bias of the $l_2$ regularizer 
   Trying to overcome these problems, Decelle and Ricci-Tersenghi introduced a new method \cite{Decelle14}, known as PLM + decimation: the algorithm maximizes the sum of the $L_i$,
   \begin{eqnarray}
    {\cal L}\equiv \frac{1}{N}\sum_{i=1}^N \mbox{L}_i
    \end{eqnarray}  
    and, then, it recursively set to zero couplings which are estimated very small  We expect that as long as we are setting to zero couplings that are unnecessary to fit the data, there should be not much changing on ${\cal L}$  Keeping on with decimation, a point is reached where ${\cal L}$ decreases abruptly indicating  that relevant couplings are being decimated and under-fitting is taking place 
   Let us define  by $x$  the fraction of non-decimated couplings  To have a quantitative measure for the halt criterion of the decimation process, a tilted ${\cal L}$ is defined as,
   \begin{eqnarray}
  \mathcal{L}_t &\equiv& \mathcal{L}  - x \mathcal{L}_{\textup{max}} - (1-x) \mathcal{L}_{\textup{min}} \label{$t$PLF} 
   \end{eqnarray}
   where 
   \begin{itemize}
   \item $\mathcal{L}_{\textup{min}}$ is the pseudolikelyhood of a model with independent variables  In the XY case: $\mathcal{L}_{\textup{min}}=-\ln{2 \pi}$ 
   \item
   $\mathcal{L}_{\textup{max}}$ is the pseudolikelyhood in the fully-connected model and it is maximized over all the $N(N-1)/2$ possible couplings  
   \end{itemize}
   At the first step, when $x=1$, $\mathcal{L}$ takes value $\mathcal{L}_{\rm max}$ and  $\mathcal{L}_t=0$  On the last step, for an empty graph, i e , $x=0$, $\mathcal{L}$ takes the value $\mathcal{L}_{\rm min}$ and, hence, again $\mathcal{L}_t =0$  
   In the intermediate steps, during the decimation procedure, as $x$ is decreasing from $1$ to $0$, one observes firstly that $\mathcal{L}_t$ increases linearly and, then, it displays an abrupt decrease indicating that from this point on relevant couplings are being decimated\cite{Decelle14}  In Fig  \ref{Jor1-$t$PLF} we give an instance of this behavior for the 2D short-range XY model with ordered couplings  We notice that the maximum point of $\mathcal{L}_t$ coincides with the minimum point of the reconstruction error, the latter defined as 
   \begin{eqnarray}\label{eq:errj}
   \mbox{err}_J \equiv \sqrt{\frac{\sum_{i<j} (J^{\rm inferred}_{ij} -J^{\rm true}_{ij})^2}{N(N-1)/2}} \label{err}
   \end{eqnarray}
  We stress that the ${\cal L}_t$ maximum is obtained ignoring the underlying graph, while the err$_J$ minimum can be evaluated once the true graph has been reconstructed  
   
     \begin{figure}[t!]
   	\centering
   	\includegraphics[width=1\linewidth]{Jor1_dec_tPLF_new eps}
   	\caption{The tilted likelyhood ${\cal L}_t$ curve and the reconstruction error vs the number of decimated couplings  for an ordered, real-valued J on 2D XY model with $N=64$ spins  The peak of ${\cal L}_t$ coincides with the dip of the error }  
   	\label{Jor1-$t$PLF}
   \end{figure} 
       
   
   In the next sections we will show the results obtained on the  $XY$ model analyzing the performances of the two methods and comparing them also with a mean-field method \cite{Tyagi15} 
   
  
    
   \section{Inferred couplings with PLM-$l_2$}
    \label{sec:res_reg}
    \subsection{$XY$ model with real-valued couplings}
    
    In order to obtain the vector of couplings, $J_{ij}^{\rm inferred}$ the function $-\mathcal{L}_i$ is minimized through the vector of derivatives ${\partial \mathcal{L}_i}/\partial J_{ij}$  The process is repeated for all the couplings obtaining then a fully connected adjacency matrix  The results here presented are obtained with $\lambda = 0 01$ 
   For the minimization we have used the MATLAB routine \emph{minFunc\_2012}\cite{min_func}  
      
      \begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{Jor11_2D_l2_JR_soJR_TPJR}
    	\caption{Top panels: instances of single site coupling reconstruction for the case of $N=64$ XY spins on a 2D lattice with ordered $J$ (left column) and bimodal distributed $J$ (right column)  
    	
    	Bottom panels: sorted couplings }
    	\label{PL-Jor1}
    \end{figure}

   
To produce the data by means of numerical Monte Carlo simulations a system with $N=64$  spin variables  is considered on a deterministic 2D lattice with periodic boundary conditions  
Each spin has then connectivity $4$, i e , we expect to infer an adjacency matrix with $N c = 256$ couplings different from zero  
The dynamics of the simulated model is based on the Metropolis algorithm and parallel tempering\cite{earl05} is used to speed up the thermalization of the system 
The thermalization is tested looking at the average energy over logarithmic time windows and
the acquisition of independent configurations
starts only after the system is well thermalized 

   For the values of the couplings we considered two cases: an ordered case, indicated in the figure as  $J$ ordered (e g , left column of Fig  \ref{PL-Jor1}) where the couplings can take values $J_{ij}=0,J$, with $J=1$, 
   and a quenched disordered case, indicated in the figures as  $J$ disordered (e g , right column of Fig  \ref{PL-Jor1})
   where the couplings can take also  negative values, i e , 
    $J_{ij}=0,J,-J$, with a certain probability   The results here presented were obtained with bimodal distributed $J$s: 
   
    $P(J_{ij}=J)=P(J_{ij}=-J)=1/2$   The performances of the PLM have shown not to depend on $P(J)$  
   
    We recall that in Sec  \ref{sec:plm} we used the temperature-rescaled notation, i e , $J_{ij}$ stands for $J_{ij}/T$  
   
    To analyze the performances of the PLM, in Fig  \ref{PL-Jor1} the inferred couplings, $\mathbb{J}^R_{\rm inf}$, are shown on top of the original couplings,  $\mathbb{J}^R_{\rm true}$ 
     The first figure (from top) in the left column shows  the $\mathbb{J}^R_{\rm inf}$ (black) and the $\mathbb{J}^R_{\rm tru}$ (green) for a given spin
     at temperature $T/J=0 7$ and number of samples  $M=1024$  PLM appears to reconstruct the correct couplings, though zero couplings are always given a small inferred non-zero value  
     In the left column of Fig   \ref{PL-Jor1},  both the $\mathbb{J}^R_{\rm{inf}}$ and the $\mathbb{J}^R_{\rm{tru}}$ are sorted in decreasing order and plotted on top of each other  
     We can clearly see that $\mathbb{J}^R_{\rm inf}$ reproduces the expected step function  Even though the jump is smeared, the difference between inferred couplings corresponding to the set of non-zero couplings 
     and to the set of zero couplings can be clearly appreciated 
     Similarly, the plots in the right column of Fig  \ref{PL-Jor1} show the results obtained for the case with  bimodal disordered couplings, for the same working temperature and number of samples  
     In particular, note that the algorithm infers half positive and half negative couplings, as expected 
     
     
\begin{figure}
\centering
\includegraphics[width=1\linewidth]{Jor11_2D_l2_errJ_varT_varM}
\caption{Reconstruction error $\mbox{err}_J$, cf  Eq  (\ref{eq:errj}), plotted as a function of temperature (left) for three values of the number of samples $M$ and  as a function $M$ (right) for three values of temperature in the ordered system, i e , $J_{ij}=0,1$  
The system size is $N=64$ }
\label{PL-err-Jor1}
\end{figure}

In order to analyze the effects of the number of samples and of the temperature regimes, we plot in Fig  \ref{PL-err-Jor1} the reconstruction error, Eq  (\ref{err}), as a function of temperature for three different sample sizes $M=64,128$ and $512$  
The error is seen to sharply rise al low temperature, incidentally, in the ordered case, for  $T<T_c \sim 0 893$, which is the Kosterlitz-Thouless transition temperature of the 2XY model\cite{Olsson92}  
 However, we can see that if only $M=64$ samples are considered, $\mbox{err}_J$ remains high independently on the working temperature  
 In the right plot of Fig  \ref{PL-err-Jor1},  $\mbox{err}_J$ is plotted as a function of $M$ for three different working temperatures $T/J=0 4,0 7$ and $1 3$  As we expect, 
 $\mbox{err}_J$  decreases as $M$ increases  This effect was observed also with mean-field inference techniques on the same model\cite{Tyagi15} 

To better understand the performances of the algorithms, in Fig  \ref{PL-varTP-Jor1} we show several True Positive (TP) curves obtained for various values of $M$ at three different temperatures $T$  As $M$ is large and/or temperature is not too small,  we are able to reconstruct correctly all the couplings present in the system (see bottom plots) 
The True Positive curve displays how many times the inference method finds a true link of the original network  as a function of the index of the vector of sorted absolute value of reconstructed couplings $J_{ij}^{\rm inf}$  
The index $n_{(ij)}$ represents the related spin couples $(ij)$  The TP curve is obtained as follows: 
first  the values $|J^{\rm inf}_{ij}|$ are sorted in descending order and  the spin pairs $(ij)$ are ordered according to the sorting position of $|J^{\rm inf}_{ij}|$  Then,
     	a cycle over the ordered set of pairs $(ij)$, indexed by $n_{(ij)}$, is performed, comparing with the original network coupling $J^{\rm true}_{ij}$ and verifying whether it is zero or not  The true positive curve is computed as
\begin{equation}
\mbox{TP}[n_{(ij)}]= \frac{\mbox{TP}\left[n_{(ij)}-1\right] (n_{ij}-1)+ 1 -\delta_{J^{\rm true}_{ij},0}}{n_{(ij)}}
\end{equation}
As far as $J^{\rm true}_{ij} \neq 0$, TP$=1$  As soon as the true coupling of a given $(ij)$ couple in the sorted list is zero, the TP curve departs from one  
In our case, where the connectivity per spin of the original system is  $c=4$ and there are $N=64$ spins, we know that we will have  $256$ non-zero couplings   
     	If the inverse problem is successful, hence, we expect a steep decrease of the TP curve when  $n_{ij}=256$ is overcome 

In Fig  \ref{PL-varTP-Jor1}
it is  shown that,  almost independently of $T/J$, the TP score improves as $M$ increases  Results are plotted for three different temperatures, $T=0 4,1$ and $2 2$, with increasing number of samples $M = 64, 128,512$ and $1024$ (clockwise)  
We can clearly appreciate the improvement in temperature if the size of the data-set is not very large: for small $M$, $T=0 4$ performs better  
When $M$ is high enough (e g , $M=1024$), instead, the TP curves do not appear to be strongly influenced by the temperature 

\begin{figure}[t!]
	\centering
	\includegraphics[width=1\linewidth]{Jor11_2D_l2_TPJR_varT_varM}
	\caption{TP  curves  for 2D short-range ordered $XY$ model with $N=64$ spins at three different values of $T/J$ with increasing - clockwise from top - $M$ }
	\label{PL-varTP-Jor1} 
\end{figure} 

\subsection{$XY$ model with complex-valued couplings}
For the complex $XY$ we have to contemporary  infer $2$ apart coupling matrices,  $J^R_{i j}$ and $J^I_{i j}$   As before, a system of $N=64$ spins is considered on a 2D lattice 
For the couplings we have considered both ordered and bimodal disordered cases 
In Fig  \ref{PL-Jor3}, a single row of the matrix $J$ (top) and the whole sorted couplings (bottom) are displayed for the ordered model (same legend as in Fig  \ref{PL-Jor1}) for the real, $J^R$ (left column), and the imaginary part, $J^I$   

\begin{figure}[t!]
	\centering
\includegraphics[width=1\linewidth]{Jor3_l2_JRJI_soJRJI_TPJRJI}
	\caption{Results related to the ordered complex XY model with $N=64$ spins on a  2D lattice  Top: instances of  single site reconstruction for the real, JR (left column), and
		the imaginary, JI (right column), part of $J_{ij}$  Bottom: sorted values of JR (left) and JI (right) }
		
	\label{PL-Jor3}
\end{figure}
 
 
  \section{PLM with Decimation}
 \label{sec:res_dec}
 

\begin{figure}[t!]
   	\centering
   	\includegraphics[width=1\linewidth]{Jor1_dec_tPLF_varT_varM}
    	\caption{Tilted Pseudolikelyhood, ${\cal L}_t$, plotted as a function of decimated couplings  Top: Different ${\cal L}_t$ curves obtained for different values of $M$ plotted on top of each other  Here $T=1 3$  The black line indicates the expected number of decimated couplings, $x^*=(N (N-1) - N c)/2=1888$  As we can see, as $M$ increases, the maximum point of ${\cal L}_t$ approaches $x^*$  Bottom: Different ${\cal L}_t$ curves obtained for different values of T with $M=2048$  We can see that, with this value of $M$, no differences can be appreciated on the maximum points of the different  ${\cal L}_t$ curves }
   	\label{var-$t$PLF}
   \end{figure}

\begin{figure}[t!]
    \centering
    \includegraphics[width=1\linewidth]{Jor1_dec_tPLF_peak_statistics_varM_prob eps}
    	\caption{Number of most likely decimated couplings, estimated by the maximum point of $\mathcal{L}_t$, as a function of the number of samples $M$  We can clearly see that the maximum point of $\mathcal{L}_t$ tends toward $x^*$, which is the right expected number of zero couplings in the system }  
    	\label{PLF_peak_statistics}
    \end{figure}
      
      For the ordered real-valued XY model we show in Fig  \ref{var-$t$PLF}, top panel, the outcome on the tilted pseudolikelyhood, $\mathcal{L}_t$ Eq  \eqref{$t$PLF}, of the progressive decimation: from a fully connected lattice  down to an empty lattice  The figure shows the behaviour of $\mathcal{L}_t$ for three different data sizes $M$  A clear data size dependence of the maximum point of  $\mathcal{L}_t$, signalling the most likely value for decimation, is shown  For small $M$ the most likely number of  couplings is overestimated and for increasing $M$ it tends to the true value, as displayed in Fig  \ref{PLF_peak_statistics}   In the bottom panel of Fig  \ref{var-$t$PLF} we display instead different 
 $\mathcal{L}_t$ curves obtained for three different values of $T$ 
  Even though the values of $\mathcal{L}_t$ decrease with increasing temperature, the value of the most likely number of decimated couplings appears to be quite independent on $T$ with $M=2048$ number of samples 
In Fig  \ref{fig:Lt_complex} we eventually display the tilted pseudolikelyhood for a 2D network with complex valued ordered couplings, where the decimation of the real and imaginary coupling matrices proceeds in parallel, that is, 
when a real coupling is small enough to be decimated its imaginary part is also decimated, and vice versa 
One can see that though the apart errors for the real and imaginary parts are different in absolute values, they display the same dip, to be compared with the maximum point of $\mathcal{L}_t$ 
     
       \begin{figure}[t!]
    	\centering
      	\includegraphics[width=1\linewidth]{Jor3_dec_tPLF_new}
      	\caption{Tilted Pseudolikelyhood, ${\cal L}_t$, plotted with the reconstruction errors for the XY model with $N=64$ spins on a 2D lattice  These results refer to the case of  ordered and complex valued couplings  The full (red) line indicates ${\cal L}_t$  The dashed (green) 
      		and the dotted (blue) lines show the reconstruction errors (Eq  \eqref{eq:errj}) obtained for the real and the imaginary couplings respectively  We can see that both ${\rm err_{JR}}$ and ${\rm err_{JI}}$ have a minimum at $x^*$ }
          	\label{fig:Lt_complex}
    \end{figure}

\begin{figure}[t!]
   	\centering
   	\includegraphics[width=1\linewidth]{Jor1_dec_JR_soJR_TPJR}
   	\caption{XY model on a 2D lattice with $N=64$ sites and real valued couplings  The graphs show the inferred (dashed black lines) and true couplings (full green lines) plotted on top of each other  The left and right columns refer to the
   		 cases of ordered and bimodal disordered couplings, respectively  Top figures: single site reconstruction, i e , one row of the matrix $J$  Bottom figures: couplings are plotted sorted in descending order }  
   	\label{Jor1_dec}
   \end{figure}
   
\begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{Jor3_dec_JRJI_soJRJI_TPJRJI}
    	\caption{XY model on a 2D lattice with $N=64$ sites and ordered complex-valued couplings 
    		The inferred and true couplings are plotted on top of each other  The left and right columns show the real and imaginary parts, respectively, of the couplings  Top figures refer to a single site reconstruction, i e , one row of the matrix $J$  Bottom figures report the couplings sorted in descending order }
    	\label{Jor3_dec}
    \end{figure}
    
       







       \begin{figure}[t!]
     	\centering
     	\includegraphics[width=1\linewidth]{MF_PL_Jor1_2D_TPJR_varT}
     	\caption{True Positive curves obtained with the three techniques: PLM with decimation, (blue) dotted line,  PLM with $l_2$ regularization, (greed) dashed line, and mean-field, (red) full line   These results refer to real valued ordered couplings with $N=64$ spins on a 2D lattice  The temperature is here $T=0 7$ while the four graphs refer to different sample sizes: $M$ increases clockwise }
     	\label{MF_PL_TP}
     \end{figure}
    
    \begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{MF_PL_Jor1_2D_errJ_varT_varM}
    	\caption{Variation of reconstruction error, ${\rm err_J}$, with respect to temperature as obtained with the three different techniques, see Fig  \ref{MF_PL_TP}, for four different sample size:  clockwise from top   $M=512,1024, 2048$ and $4096$ } 
    	\label{MF_PL_err}
    \end{figure}
    
     Once the most likely network has been identified through the decimation procedure, we perform the same analysis displayed in Fig  \ref{Jor1_dec}  for ordered and then quenched disordered real-valued couplings
and in Fig  \ref{Jor3_dec} for  complex-valued ordered couplings   In comparison to the results shown in Sec  \ref{sec:res_reg},
  the PLM with decimation leads to rather cleaner results  In Figs  \ref{MF_PL_err} and \ref{MF_PL_TP} we compare the performances of the PLM with decimation in respect to ones of the PLM with $l_2$-regularization  These two techniques are also analysed in respect to a mean-field technique previously implemented on the same XY systems\cite{Tyagi15} 
  
    For what concerns the network of connecting links, in Fig  \ref{MF_PL_TP} we compare the TP curves obtained with the three techniques  The results refer to the case of ordered and real valued couplings, but similar behaviours were obtained for the other cases analysed  
  The four graphs are related to different sample sizes, with $M$ increasing clockwise  When $M$ is high enough, all techniques reproduce the true network  
  However, for lower values of $M$ the performances of the PLM with $l_2$ regularization and with decimation drastically overcome those ones of the previous mean field technique  
  In particular, for $M=256$ the PLM techniques still reproduce the original network while the mean-field method fails to find more than half of the couplings  
  When $M=128$, the network is clearly reconstructed only through the PLM with decimation while the PLM with $l_2$ regularization underestimates the couplings  
  Furthermore, we notice that the PLM method with decimation is able to clearly infer the network of interaction even when $M=N$ signalling that it could be considered also in the under-sampling regime $M<N$   
 
 
In Fig  \ref{MF_PL_err} we compare the temperature behaviour of the reconstruction error 
In can be observed that for all temperatures and for all sample sizes  the reconstruction error, ${\rm err_J}$, (plotted here in log-scale) obtained with the PLM+decimation is always smaller than 
that one obtained with the other techniques  The temperature behaviour of ${\rm err_J}$ agrees with the one already observed for Ising spins in \cite{Nguyen12b} and for XY spins  in \cite{Tyagi15} with a mean-field approach:  ${\rm err_J}$ displays a minimum around $T\simeq 1$ and then it increases for very lower $T$; however,
 the error obtained with the PLM with decimation is several times smaller  than the error estimated by the other methods 



 
 

     
     \section{Conclusions}
     \label{sec:conc}


Different statistical inference methods have been applied to the inverse problem of the XY model 
After a short review of techniques based on pseudo-likelihood and their formal generalization to the model we have tested their performances against data generated by means of Monte Carlo numerical simulations of known instances
with diluted, sparse, interactions 

The main outcome is that the best performances are obtained by means of the  pseudo-likelihood method combined with decimation  Putting to zero (i e , decimating) very weak bonds, this technique turns out to be very precise for  problems whose real underlying interaction network is sparse, i e , the number of couplings per variable does not scale with number of variables 
The PLM + decimation method is compared to the PLM + regularization method, with $\ell_2$ regularization and to a mean-field-based method  The behavior of the quality of the network reconstruction is analyzed by looking at the overall sorted couplings and at the single site couplings, comparing them with the real network, and at the true positive curves in all three approaches  In the PLM +decimation method, moreover, the identification of the number of decimated bonds at which the tilted pseudo-likelihood is maximum allows for a precise estimate of the total number of bonds  Concerning this technique, it is also shown that the network with the most likely number of bonds is also the one of least reconstruction error, where not only the prediction of the presence of a bond is estimated but also its value 

The behavior of the inference quality in temperature and in the size of data samples is also investigated, basically confirming the low $T$ behavior hinted by Nguyen and Berg \cite{Nguyen12b} for the Ising model  In temperature, in particular, the reconstruction error curve displays a minimum at a low temperature, close to the critical point in those cases in which a critical behavior occurs, and a sharp increase as temperature goes to zero  The decimation method, once again, appears to enhance this minimum of the reconstruction error of almost an order of magnitude with respect to other methods 
 
The techniques displayed and the results obtained in this work can be of use in any of the many systems whose theoretical representation is given by Eq  \eqref{eq:HXY} or Eq  \eqref{eq:h_im}, some of which are recalled in Sec  \ref{sec:model}  In particular, a possible application can be the field of light waves propagation through random media and the corresponding problem of the  reconstruction of an object seen through an opaque medium or a disordered optical fiber \cite{Vellekoop07,Vellekoop08a,Vellekoop08b, Popoff10a,Akbulut11,Popoff11,Yilmaz13,Riboli14} 

 	



ground_truth: Vice Admiral.

prompt_front: Now, answer the following question based on the text below, only give me the answer and do not output any other words.

Question: What are some fields in which the inverse problem is encountered?

Read the following text and answer briefly.

Context 4: [49]
In the spring of 1774, William Hewson died unexpectedly of septicemia two weeks after cutting himself while dissecting a cadaver  Polly was left to care for their two young sons and was pregnant with a daughter she would give birth to in August of the same year  Is it possible that Margaret and Benjamin moved back into No  27 to assist Polly after the death of her husband as suggested in The Americanization of Benjamin Franklin?[50]
If the Westminster Rate Books are to be believed, the answer is no  For the year 1774, the Rate Books list Margaret Stevenson at No  1 and William Hewson at No  27  For the year 1775, they list Margaret Stevenson at No  1 and Magnus Falkner (Falconer/Falconar) at No  27  Magnus was William’s assistant at the anatomy school and fiancé to William’s sister, Dorothy  On his death bed, William instructed Polly, “let Mr  Falconar be my successor ”[51] Magnus would immediately take over the running of the anatomy school and continue William’s unfinished research  Four months later, he and Dorothy would marry [52] Essentially only two things changed at 27 Craven Street after William’s death: Polly gave birth to her daughter, and Magnus replaced William as the lease holder, so even if Margaret and Benjamin had wished to move back into No  27, there would have been no room for them  It is also interesting to note that considering the multiple times Benjamin wrote of his move out of No  27 (and complained of it), he never once mentioned moving back into No  27 in any of his correspondence after Mr  Hewson’s death 
Figure 6  No  36 Craven Street  (Photo courtesy of David Ross, britainexpress com)
In sum, based on the Westminster Rate Books[53] and Franklin’s correspondence, Mrs  Stevenson is known to have resided at No  27 (36) Craven Street from 1748 to 1772  It follows that, aside from the two years Franklin spent in Philadelphia from 1762 to 1764, he resided there from 1757 to 1772  Franklin’s correspondence also reveals that in the autumn of 1772, he and Mrs  Stevenson moved to another house on Craven Street  The 1773 Westminster Rate Books show her name crossed off at No  27 and William Hewson’s inserted  The following year the Rate Books list her at No  1 Craven Street  Evidence for Mrs  Stevenson and Benjamin remaining at No  1 after William’s death appears in the Westminster Rate Books for 1775 which have Mrs  Stevenson still residing at No  1 and Magnus Falkner residing at No  27  Further evidence can be construed from the lack of any mention of a move back into No  27 in Franklin’s correspondence  Despite the many theories one could devise as to why Franklin was thought to have lived at No  7 Craven Street by so many guide books and Franklin biographers of the nineteenth century, one thing is certain; at some point after Franklin’s departure to America in March of 1775, and no later than 1807, someone mistakenly associated him with No  7 on the west side of Craven Street, and it soon became his de facto residence  Credit must go to D  H  Montgomery in 1896 and Sir George in 1913 for setting the record partially straight by placing Franklin at No  27(36)  In 1937, the London County Council gave us the first accurate account of Franklin’s residences on Craven Street in the Survey of London at No  27(36) and No  1  It has been shown conclusively that No  27 was never previously numbered 7  It was, however, renumbered 36 in 1792 after ten additional houses were built at the southern end of the street and remains No  36 to this day 
[1] “Craven Street and Hungerford Lane”, in Survey of London: Volume 18, St Martin-in-the-Fields II: the Strand, ed  G H Gater and E P Wheeler (London, 1937), 27-39, Early History of the Site 
http://www british-history ac uk/survey-london/vol18/pt2/pp27-39
[2] “England, Westminster Rate Books, 1634-1900,” from database with images, Craven Street – 1735, FamilySearch from database by FindMyPast and images digitized by FamilySearch; citing Westminster City Archives, London 
[3] Ibid , Craven Street – 1748 
[4] The Statutes at Large, From Magna Charta to the End of the Eleventh Parliament of Great Britain  Anno 1761 Continued, Vol  XXVII, ed  Danby Pickering, (Cambridge, John Archdeacon, 1767), 96 
[6] James Raven, Publishing Business in Eighteenth-Century England, (Woodbridge: The Boydell Press, 2014), 201 
[7] The London Directory For the Year 1776, Ninth Edition, (London: T  Lowndes, 1776), title page 
[8] Kent’s Directory For the Year 1778, Forty-Sixth Edition, (London: Richard and Henry Causton, 1778), title page 
[9] A listing in Kent’s Directory for the Year 1882 on p  28 reveals, “Brown Sarah, Leather-seller, 1, Westmoreland-buildings, Aldersgate-street”, and in Kent’s Directory for the Year 1883 on p  175, “Whiteland Mary, Wine & Brandy Mercht  Jermyn-str  St  James ”
[10] “The Papers of Benjamin Franklin,” Sponsored by The American Philosophical Society and Yale University, Digital Edition by The Packard Humanities Institute, 22:263a 
http://franklinpapers org/franklin
Mrs  Stevenson wrote to Benjamin Franklin a letter from her new home at 75 Northumberland Court on November 16, 1775: “In this Court I have a kind friend, Mr  Lechmoen he comes and seats with me and talks of you with a hiy regard and friendship ”
[11] Survey of London, Early History of the Site 
[12] Survey of London, Footnotes/n 10 
[13] Survey of London, Historical Notes/No  31 
[14] David Hughson, LL D , London; Being An Accurate History And Description Of The British Metropolis And Its Neighbourhood, To Thirty Miles Extent, From An Actual Perambulation, Vol  IV, (London: W  Stratford, 1807), 227 
[15] The Reverend Joseph Nightingale, The Beauties of England and Wales: Or, Original Delineations, Topographical, Historical, and Descriptive, of Each County, Vol  X, Part III, Vol  II (London: J  Harris; Longman and Co ; J  Walker; R  Baldwin; Sherwood and Co ; J  and J  Cundee; B  and R  Crosby and Co ; J Cuthell; J  and J  Richardson; Cadell and Davies; C  and J  Rivington; and G  Cowie and Co , 1815), 245 
[16] John Britton, F S A  & Co , ed , The Original Picture of London, Enlarged and Improved: Being A Correct Guide For The Stranger, As Well As For the Inhabitant, To The Metropolis Of The British Empire Together With A Description Of The Environs, The Twenty-Fourth Edition (London: Longman, Rees, Orme, Brown, and Green, 1826), 479 
[17] Jared Sparks, The Works of Benjamin Franklin, Vol  VII, (Philadelphia: Childs & Peterson, 1840), 151 
[18] George Gulliver, F R S , The Works of William Hewson, F  R  S , (London: Printed for the Sydenham Society, MDCCCXLVI), xx 
[19] Peter Cunningham, Handbook for London; Past and Present, Vol  I, (London: John Murray, 1849), 245 
[20] F  Saunders, Memories of the Great Metropolis: or, London, from the Tower to the Crystal Palace, (New York: G P  Putnam, MDCCCLII), 138 
[21] Leigh Hunt, The Town; Its Memorable Characters and Events, (London: Smith, Elder and Co , 1859), 185 
[22] K  Baedeker, London and Its Environs, Including Excursions To Brighton, The Isle of Wight, Etc : Handbook For Travelers, Second Edition, (London: Dulau and Co , 1879), 133 
[23] Herbert Fry, London In 1880 Illustrated With Bird’s-Eye Views of the Principal Streets, Sixth Edition, (New York: Scribner, Welford, & Co , 1880), 50 
[24] Herbert Fry, London  Illustrated By Eighteen Bird’s-Eye Views of the Principal Streets, (London: W  H  Allen and Co , 1886), 40 
[25] Henry B  Wheatley, F S A , London Past and Present; Its History, Associations, and Traditions, Vol  1, (London: John Murray, New York: Scribner & Welford, 1891), 473 
[26] The Journal of the Society of Arts, Vol  XV, No  778, (October 18, 1867): 717 
[27] D  G  C  Allen, “Dear and Serviceable to Each Other: Benjamin Franklin and the Royal Society of Arts,” American Philosophical Society, Vol  144, No  3, (September 2000): 248-249 
Franklin was a corresponding member in 1756 because he was still residing in Philadelphia  He became an active member the following year when he moved to London 
[28] The Journal of the Society of Arts, Vol  XVIII, No  894, (Jan  7, 1870): 137 
“Since the last announcement, the following tablets have been affixed on houses formerly occupied by – Benjamin Franklin, 7 Craven-street, Strand, W C ”
[29] Franklin in His Own Time, eds  Kevin J  Haytes and Isabelle Bour, (Iowa City, University of Iowa Press, 2011), xxxvii 
“Takes lodgings with Margaret Stevenson at No  7 Craven Street ” It is unknown if the editors are referring to No  7 on the west side of Craven Street or No  36 on the east side using Sir George’s explanation of No  36 being previously numbered 7 
[30] Henry C  Shelly, “American Shrines on English Soil, III  In the Footprints of Benjamin Franklin,” in The Book News Monthly, September, 1913 to August, 1914, (Philadelphia: John Wanamaker, 1914), 325 
[31] The Journal of the Royal Society of Arts, Vol  LVI, No  2,880, (Jan  31, 1908): 245 
http://babel hathitrust org/cgi/pt?id=mdp 39015058423073;view=1up;seq=251
“His Majesty the King, who is Patron of the Society, has granted permission to the Society to prefix to its title the term ‘Royal,’ and the Society will consequently be known in future as the ‘Royal Society of Arts ’”
[32] Nineteenth Annual Report, 1914, of the American Scenic and Historic Preservation Society, (Albany: J  B  Lyon Company, 1914), 293 
http://babel hathitrust org/cgi/pt?id=wu 89072985302;view=1up;seq=4;size=150
[33] The Journal of the Society of Arts, Vol  LXII, No  3,183, (Nov  21, 1913): 18 
http://babel hathitrust org/cgi/pt?id=mdp 39015058422968;view=1up;seq=26
[36] Allen, “Dear and Serviceable,” 263-264 
[37] Papers of Benjamin Franklin, 19:20 
[38] Thomas Joseph Pettigrew, F  L  S , Memoirs of the Life and Writings of the Late John Coakley Lettsom With a Selection From His Correspondence, Vol  I, (London: Nichols, Son, and Bentley, 1817), 144 of Correspondence 
[39] Papers of Benjamin Franklin, 19:321b 
[40] Ibid , 19:314 
[41] Ibid , 19:353a 
[43] Simon David John Chaplin, John Hunter and the ‘museum oeconomy’, 1750-1800, Department of History, King’s College London  Thesis submitted for the degree of Doctor of Philosophy of the University of London , 202 
“Following Falconar’s death [1778] the lease [27 Craven Street] was advertised, and the buildings were described as:
A genteel and commodious house, in good Repair, with Coach-house and Stabling for two Horses…consisting of two rooms and light closets on each floor, with outbuildings in the Yard, a Museum, a Compleat Theatre, and other conveniences  (Daily Advertiser, 27 August 1778)”
[44] Simon Chaplin, “Dissection and Display in Eighteenth-Century London,” in Anatomical Dissection in Enlightenment England and Beyond: Autopsy, Pathology and Display, ed  Dr  Piers Mitchell, (Burlington: Ashgate Publishing Company, 2012), 108 
“Given that a nearby building at 35 [ No  26 in Franklin’s time] was occupied by the man-midwife John Leake, who advertised lectures – including lessons in the art of making preparations – at his ‘theatre’ between 1764 and 1788, it is possible that some facilities were shared  In both cases, however, the buildings [Leake’s residence at No  26 and Hewson’s residence next door at 27] served a dual function as domestic accommodation and as sites for lecturing and dissection ”
[45] George Gulliver, F R S , The Works of William Hewson, F  R  S , (London: Printed for the Sydenham Society, MDCCCXLVI), xviii 
[46] Westminster Rate Books, Craven Street – 1773, courtesy of the City of Westminster Archives 
[47] S W  Hillson et al , “Benjamin Franklin, William Hewson, and the Craven Street Bones,” Archaeology International, Vol  2, (Nov  22, 1998): 14-16 
http://dx doi org/10 5334/ai 0206
[48] Westminster Rate Books, Craven Street – 1774, 1775, courtesy of the City of Westminster Archives 
[49] Survey of London, Historical Notes/No  36, Craven Street (not sourced) 
[50] Gordon S  Wood, The Americanization of Benjamin Franklin, (New York: The Penguin Press, 2004), 261 
[51] Pettigrew, Memoirs, 146 of Correspondence 
[52] http://founders archives gov/documents/Franklin/01-22-02-0178, note 7  “Falconar married Hewson’s sister five months after the Doctor’s death; most of the Craven Street circle attended the wedding, and BF gave away the bride: Polly to Barbara Hewson, Oct  4, 1774, APS” (American Philosophical Society); “England Marriages, 1538–1973 ,” database, FamilySearch (https://familysearch org/ark:/61903/1:1:V52W-TGS : accessed September 15, 2015), Magnus Falconar and Dorothy Hewson, September 12, 1774; citing Saint Martin In The Fields, Westminster, London, England, reference ; FHL microfilm 561156, 561157, 561158, 942 B4HA V  25, 942 B4HA V  66 
[53] I chose to rely on the Westminster Rate Books for the numbering system on Craven Street  The books were consistent throughout the eighteenth century in the ordering of residents on the street and were used as the basis for the 1792 re-numbering  For the most part, commercial directories aligned with them as well  If by chance a directory didn’t initially align, it would inevitably produce future editions that did 
Benjamin Franklin, Benjamin Franklin House, London
More from David Turnquist
If one looked into Benjamin Franklin’s time on Craven Street, they might   
I think it’s very ironic that on the street maps included in your excellent article, Craven Street is so close to Scotland Yard  Because following the back and forth juxtapositions of numbers 7, 27 and 36 Craven Street (throw in 75 Northumberland Court and 1 Craven Street, too) was a case that could confound Sherlock Holmes 
Excellent job of deciphering street renumbering material spanning sixty years, including that of a wrong house number (# 7) being erroneously identified and then perpetuated in subsequent street map printings  It’s gratifying at least to know that the present day #36 Craven Street is the correct house for Ben Franklin tourists to visit  Except for #1 Craven Street for the last three years Franklin was in London, but we won’t get into that 
Again, excellent article, David!



ground_truth: Physics, biology, social sciences, finance, and neuroscience are some fields in which the inverse problem is encountered.