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 many massive star-forming regions were studied?

Read the following text and answer briefly.

Context 1: \section{Introduction}

Spectral line surveys have revealed that high-mass star-forming
regions are rich reservoirs of molecules from simple diatomic species
to complex and larger molecules (e g ,
\citealt{schilke1997b,hatchell1998b,comito2005,bisschop2007}) 
However, there have been rarely studies undertaken to investigate the
chemical evolution during massive star formation from the earliest
evolutionary stages, i e , from High-Mass Starless Cores (HMSCs) and
High-Mass Cores with embedded low- to intermediate-mass protostars
destined to become massive stars, via High-Mass Protostellar Objects
(HMPOs) to the final stars that are able to produce Ultracompact H{\sc
  ii} regions (UCH{\sc ii}s, see \citealt{beuther2006b} for a recent
description of the evolutionary sequence)  The first two evolutionary
stages are found within so-called Infrared Dark Clouds (IRDCs)   While
for low-mass stars the chemical evolution from early molecular
freeze-out to more evolved protostellar cores is well studied (e g ,
\citealt{bergin1997,dutrey1997,pavlyuchenkov2006,joergensen2007}),
it is far from clear whether similar evolutionary patterns are present
during massive star formation 

To better understand the chemical evolution of high-mass star-forming
regions we initiated a program to investigate the chemical properties
from IRDCs to UCH{\sc ii}s from an observational and theoretical
perspective  We start with single-dish line surveys toward a large
sample obtaining their basic characteristics, and then perform
detailed studies of selected sources using interferometers on smaller
scales  These observations are accompanied by theoretical modeling of
the chemical processes   Long-term goals are the chemical
characterization of the evolutionary sequence in massive star
formation, the development of chemical clocks, and the identification
of molecules as astrophysical tools to study the physical processes
during different evolutionary stages  Here, we present an initial
study of the reactive radical ethynyl (C$_2$H) combining single-dish
and interferometer observations with chemical modeling   Although
C$_2$H was previously observed in low-mass cores and Photon Dominated
Regions (e g , \citealt{millar1984,jansen1995}), so far it was not
systematically investigated in the framework of high-mass star
formation 

\section{Observations}
\label{obs}

The 21 massive star-forming regions were observed with the Atacama
Pathfinder Experiment (APEX) in the 875\,$\mu$m window in fall 2006 
We observed 1\,GHz from 338 to 339\,GHz and 1\,GHz in the image
sideband from 349 to 350\,GHz   The spectral resolution was
0 1\,km\,s$^{-1}$, but we smoothed the data to
$\sim$0 9\,km\,s$^{-1}$  The average system temperatures were around
200\,K, each source had on-source integration times between 5 and 16
min  The data were converted to main-beam temperatures with forward
and beam efficiencies of 0 97 and 0 73, respectively
\citep{belloche2006}  The average $1\sigma$ rms was 0 4\,K   The main
spectral features of interest are the C$_2$H lines around 349 4\,GHz
with upper level excitation energies $E_u/k$ of 42\,K (line blends of
C$_2$H$(4_{5,5}-3_{4,4})$ \& C$_2$H$(4_{5,4}-3_{4,3})$ at
349 338\,GHz, and C$_2$H$(4_{4,4}-3_{3,3})$ \&
C$_2$H$(4_{4,3}-3_{3,2})$ at 349 399\,GHz)  The beam size was $\sim
18''$ 

The original Submillimeter Array (SMA) C$_2$H data toward the
HMPO\,18089-1732 were first presented in \citet{beuther2005c}  There
we used the compact and extended configurations resulting in good
images for all spectral lines except of C$_2$H  For this project, we
re-worked on these data only using the compact configuration  Because
the C$_2$H emission is distributed on larger scales (see
\S\ref{results}), we were now able to derive a C$_2$H image  The
integration range was from 32 to 35\,km\,s$^{-1}$, and the achieved
$1\sigma$ rms of the C$_2$H image was 450\,mJy\,beam$^{-1}$   For more
details on these observations see \citet{beuther2005c} 

\section{Results}
\label{results}

The sources were selected to cover all evolutionary stages from IRDCs
via HMPOs to UCH{\sc ii}s  We derived our target list from the samples
of \citet{klein2005,fontani2005,hill2005,beltran2006}   Table
\ref{sample} lists the observed sources, their coordinates, distances,
luminosities and a first order classification into the evolutionary
sub-groups IRDCs, HMPOs and UCH{\sc ii}s based on the previously
available data  Although this classification is only based on a
limited set of data, here we are just interested in general
evolutionary trends  Hence, the division into the three main classes
is sufficient 

Figure \ref{spectra} presents sample spectra toward one source of each
evolutionary group  While we see several CH$_3$OH lines as well as
SO$_2$ and H$_2$CS toward some of the HMPOs and UCH{\sc ii}s but not
toward the IRDCs, the surprising result of this comparison is the
presence of the C$_2$H lines around 349 4\,GHz toward all source types
from young IRDCs via the HMPOs to evolved UCH{\sc ii}s   Table
\ref{sample} lists the peak brightness temperatures, the integrated
intensities and the FWHM line-widths of the C$_2$H line blend at
349 399\,GHz  The separation of the two lines of 1 375\,MHz already
corresponds to a line-width of 1 2\,km\,s$^{-1}$  We have three C$_2$H
non-detections (2 IRDCs and 1 HMPO), however, with no clear trend with
respect to the distances or the luminosities (the latter comparison is
only possible for the HMPOs)  While IRDCs are on average colder than
more evolved sources, and have lower brightness temperatures, the
non-detections are more probable due to the relatively low sensitivity
of the short observations (\S\ref{obs})  Hence, the data indicate
that the C$_2$H lines are detected independent of the evolutionary
stage of the sources in contrast to the situation with other
molecules   When comparing the line-widths between the different
sub-groups, one finds only a marginal difference between the IRDCs and
the HMPOs (the average $\Delta v$ of the two groups are 2 8 and
3 1\,km\,s$^{-1}$)   However, the UCH{\sc ii}s exhibit significantly
broader line-widths with an average value of 5 5\,km\,s$^{-1}$ 

Intrigued by this finding, we wanted to understand the C$_2$H spatial
structure during the different evolutionary stages   Therefore, we
went back to a dataset obtained with the Submillimeter Array toward
the hypercompact H{\sc ii} region IRAS\,18089-1732 with a much higher
spatial resolution of $\sim 1''$ \citep{beuther2005c}   Albeit this
hypercompact H{\sc ii} region belongs to the class of HMPOs, it is
already in a relatively evolved stage and has formed a hot core with a
rich molecular spectrum   \citet{beuther2005c} showed the spectral
detection of the C$_2$H lines toward this source, but they did not
present any spatially resolved images  To recover large-scale
structure, we restricted the data to those from the compact SMA
configuration (\S\ref{obs})  With this refinement, we were able to
produce a spatially resolved C$_2$H map of the line blend at
349 338\,GHz with an angular resolution of $2 9''\times 1 4''$
(corresponding to an average linear resolution of 7700\,AU at the
given distance of 3 6\,kpc)  Figure \ref{18089} presents the
integrated C$_2$H emission with a contour overlay of the 860\,$\mu$m
continuum source outlining the position of the massive protostar  In
contrast to almost all other molecular lines that peak along with the
dust continuum \citep{beuther2005c}, the C$_2$H emission surrounds the
continuum peak in a shell-like fashion 

\section{Discussion and Conclusions}

To understand the observations, we conducted a simple chemical
modeling of massive star-forming regions  A 1D cloud model with a mass
of 1200\,M$_\sun$, an outer radius of 0 36\,pc and a power-law density
profile ($\rho\propto r^p$ with $p=-1 5$) is the initially assumed
configuration  Three cases are studied: (1) a cold isothermal cloud
with $T=10$\,K, (2) $T=50$\,K, and (3) a warm model with a temperature
profile $T\propto r^q$ with $q=-0 4$ and a temperature at the outer
radius of 44\,K  The cloud is illuminated by the interstellar UV
radiation field (IRSF, \citealt{draine1978}) and by cosmic ray
particles (CRP)  The ISRF attenuation by single-sized $0 1\mu$m
silicate grains at a given radius is calculated in a plane-parallel
geometry following \citet{vandishoeck1988}  The CRP ionization rate is
assumed to be $1 3\times 10^{-17}$~s$^{-1}$ \citep{spitzer1968}  The
gas-grain chemical model by \citet{vasyunin2008} with the desorption
energies and surface reactions from \citet{garrod2006} is used 
Gas-phase reaction rates are taken from RATE\,06 \citep{woodall2007},
initial abundances, were adopted from the ``low metal'' set of
\citet{lee1998} 

Figure \ref{model} presents the C$_2$H abundances for the three models
at two different time steps: (a) 100\,yr, and (b) in a more evolved
stage after $5\times10^4$\,yr  The C$_2$H abundance is high toward the
core center right from the beginning of the evolution, similar to
previous models (e g , \citealt{millar1985,herbst1986,turner1999}) 
During the evolution, the C$_2$H abundance stays approximately
constant at the outer core edges, whereas it decreases by more than
three orders of magnitude in the center, except for the cold $T=10$~K
model   The C$_2$H abundance profiles for all three models show
similar behavior 

The chemical evolution of ethynyl is determined by relative removal
rates of carbon and oxygen atoms or ions into molecules like CO, OH,
H$_2$O  Light ionized hydrocarbons CH$^+_{\rm n}$ (n=2  5) are quickly
formed by radiative association of C$^+$ with H$_2$ and hydrogen
addition reactions: C$^+$ $\rightarrow$ CH$_2^+$ $\rightarrow$
CH$_3^+$ $\rightarrow$ CH$_5^+$   The protonated methane reacts with
electrons, CO, C, OH, and more complex species at later stage and
forms methane   The CH$_4$ molecules undergo reactive collisions with
C$^+$, producing C$_2$H$_2^+$ and C$_2$H$_3^+$  An alternative way to
produce C$_2$H$_2^+$ is the dissociative recombination of CH$_5^+$
into CH$_3$ followed by reactions with C$^+$   Finally, C$_2$H$_2^+$
and C$_2$H$_3^+$ dissociatively recombine into CH, C$_2$H, and
C$_2$H$_2$  The major removal for C$_2$H is either the direct
neutral-neutral reaction with O that forms CO, or the same reaction
but with heavier carbon chain ions that are formed from C$_2$H by
subsequent insertion of carbon  At later times, depletion and
gas-phase reactions with more complex species may enter into this
cycle   At the cloud edge the interstellar UV radiation
instantaneously dissociates CO despite its self-shielding,
re-enriching the gas with elemental carbon 

The transformation of C$_2$H into CO and other species proceeds
efficiently in dense regions, in particular in the ``warm'' model
where endothermic reactions result in rich molecular complexity of the
gas (see Fig ~\ref{model})   In contrast, in the ``cold'' 10\,K model
gas-grain interactions and surface reactions become important   As a
result, a large fraction of oxygen is locked in water ice that is hard
to desorb ($E_{\rm des} \sim 5500$~K), while half of the elemental
carbon goes to volatile methane ice ($E_{\rm des} \sim 1300$~K)  Upon
CRP heating of dust grains, this leads to much higher gas-phase
abundance of C$_2$H in the cloud core for the cold model compared to
the warm model  The effect is not that strong for less dense regions
at larger radii from the center 

Since the C$_2$H emission is anti-correlated with the dust continuum
emission in the case of IRAS\,18089-1732 (Fig \,\ref{18089}), we do
not have the H$_2$ column densities to quantitatively compare the
abundance profiles of IRAS\,18089-1732 with our model  However, data
and model allow a qualitative comparison of the spatial structures 
Estimating an exact evolutionary time for IRAS\,18089-1732 is hardly
possible, but based on the strong molecular line emission, its high
central gas temperatures and the observed outflow-disk system
\citep{beuther2004a,beuther2004b,beuther2005c}, an approximate age of
$5\times10^4$\,yr appears reasonable   Although dynamical and chemical
times are not necessarily exactly the same, in high-mass star
formation they should not differ to much: Following the models by
\citet{mckee2003} or \citet{krumholz2006b}, the luminosity rises
strongly right from the onset of collapse which can be considered as a
starting point for the chemical evolution  At the same time disks and
outflows evolve, which should hence have similar time-scales   The
diameter of the shell-like C$_2$H structure in IRAS\,18089-1732 is
$\sim 5''$ (Fig \,\ref{18089}), or $\sim$9000\,AU in radius at the
given distance of 3 6\,kpc   This value is well matched by the modeled
region with decreased C$_2$H abundance (Fig \,\ref{model})   Although
in principle optical depths and/or excitation effects could mimic the
C$_2$H morphology, we consider this as unlikely because the other
observed molecules with many different transitions all peak toward the
central submm continuum emission in IRAS\,18089-1732
\citep{beuther2005c}  Since C$_2$H is the only exception in that rich
dataset, chemical effects appear the more plausible explanation 

The fact that we see C$_2$H at the earliest and the later evolutionary
stages can be explained by the reactive nature of C$_2$H: it is
produced quickly early on and gets replenished at the core edges by
the UV photodissociation of CO  The inner ``chemical'' hole observed
toward IRAS\,18089-1732 can be explained by C$_2$H being consumed in
the chemical network forming CO and more complex molecules like larger
carbon-hydrogen complexes and/or depletion 

The data show that C$_2$H is not suited to investigate the central gas
cores in more evolved sources, however, our analysis indicates that
C$_2$H may be a suitable tracer of the earliest stages of (massive)
star formation, like N$_2$H$^+$ or NH$_3$ (e g ,
\citealt{bergin2002,tafalla2004,beuther2005a,pillai2006})  While a
spatial analysis of the line emission will give insights into the
kinematics of the gas and also the evolutionary stage from chemical
models, multiple C$_2$H lines will even allow a temperature
characterization  With its lowest $J=1-0$ transitions around 87\,GHz,
C$_2$H has easily accessible spectral lines in several bands between
the 3\,mm and 850\,$\mu$m   Furthermore, even the 349\,GHz lines
presented here have still relatively low upper level excitation
energies ($E_u/k\sim42$\,K), hence allowing to study cold cores even
at sub-millimeter wavelengths   This prediction can further be proved
via high spectral and spatial resolution observations of different
C$_2$H lines toward young IRDCs 

\acknowledgments{H B  acknowledges financial support
  by the Emmy-Noether-Programm of the Deutsche Forschungsgemeinschaft
  (DFG, grant BE2578)  }



Context 2: \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 3: \section{Introduction}

Ultracold neutral plasmas studied in the laboratory offer access to a regime of plasma physics that scales to describe thermodynamic aspects of important high-energy-density systems, including strongly coupled astrophysical plasmas \cite{VanHorn,Burrows}, as well as terrestrial sources of neutrons \cite{Hinton,Ichimaru_fusion,Atzeni,Boozer} and x-ray radiation \cite{Rousse,Esarey}   Yet, under certain conditions, low-temperature laboratory plasmas evolve with dynamics that are governed by the quantum mechanical properties of their constituent particles, and in some cases by coherence with an external electromagnetic field    

The relevance of ultracold plasmas to such a broad scope of problems in classical and quantum many-body physics has given rise to a great deal of experimental and theoretical research on these systems since their discovery in the late 90s   A series of reviews affords a good overview of progress in the last twenty years \cite{Gallagher,Killian_Science,PhysRept,Lyon}   Here, we focus on the subset of ultracold neutral plasmas that form via kinetic rate processes from state-selected Rydberg gases, and emphasize in particular the distinctive dynamics found in the evolution of molecular ultracold plasmas   

While molecular beam investigations of threshold photoionization spectroscopy had uncovered relevant effects a few years earlier \cite{Scherzer,Alt}, the field of ultracold plasma physics began in earnest with the 1999 experiment of Rolston and coworkers on metastable xenon atoms cooled in a magneto optical trap (MOT) \cite{Killian}   

This work and many subsequent efforts tuned the photoionization energy as a means to form a plasma of very low electron temperature built on a strongly coupled cloud of ultracold ions   Experiment and theory soon established that fast processes associated with disorder-induced heating and longer-time electron-ion collisional rate processes act to elevate the ion temperatures to around one degree Kelvin, and constrain the effective initial electron temperature to a range above 30 K \cite{Kuzmin,Hanson,Laha}   

This apparent limit on the thermal energy of the electrons can be more universally expressed for an expanding plasma by saying that the electron correlation parameter, $\Gamma_e$, does not exceed 0 25, where, 
\begin{equation}
\Gamma_e = \frac{e^2}{4\pi \epsilon_0 a_{ws}}\frac{1}{k_B T_e}
\label{eqn:gamma_e}
\end{equation}
defines the ratio of the average unscreened electron-electron potential energy to the electron kinetic energy   $a_{ws}$ is the Wigner-Seitz radius, related to the electron density by, $\rho_e = 1/(\frac{4}{3} \pi a_{ws}^3)$   These plasmas of weakly coupled electrons and strongly coupled ions have provided an important testing ground for ion transport theory and the study of electron-ion collision physics \cite{Strickler} 

Soon after the initial reports of ultracold plasmas formed by direct photoionization, a parallel effort began with emphasis on the plasma that forms spontaneously by Penning ionization and electron-impact avalanche in a dense ultracold Rydberg gas \cite{Mourachko}   This process affords less apparent control of the initial electron temperature   But, pulsed field-ionization measurements soon established that the photoionized plasma and that formed by the avalanche of a Rydberg gas both evolve to quasi-equilibria of electrons, ions and high-Rydberg neutrals \cite{Rolston_expand,Gallagher}   

Early efforts to understand plasmas formed by Rydberg gas avalanche paid particular attention to the process of initiation   Evolution to plasma in effusive atomic beams was long known for high-Rydberg gases of caesium and well explained by coupled rate equations \cite{Vitrant}   But, low densities and ultracold velocity distributions were thought to exclude Rydberg-Rydberg collisional mechanisms in a MOT   

In work on ultracold Rydberg gases of Rb and Cs, Gallagher, Pillet and coworkers describe the initial growth of electron signal by a model that includes ionization by blackbody radiation and collisions with a background of uncooled Rydberg atoms \cite{Mourachko,Gallagher,Li,Comparat,Tanner}  This picture was subsequently refined to include many-body excitation and autoionization, as well as attractive dipole-dipole interactions \cite{Viteau,Pillet}, later confirmed by experiments at Rice \cite{Mcquillen}   

The Orsay group also studied the effect of adding Rydberg atoms to an established ultracold plasma   They found that electron collisions in this environment completely ionize added atoms, even when selected to have deep binding energies \cite{Vanhaecke}   They concluded from estimates of electron trapping efficiency that the addition of Rydberg atoms does not significantly alter the electron temperature of the plasma   

Tuning pair distributions by varying the wavelength of the excitation laser, Weidem\"uller and coworkers confirmed the mechanical effects of van der Waals interactions on the rates of Penning ionization in ultracold $^{87}$Rb Rydberg gases \cite{Amthor_mech}   They recognized blackbody radiation as a possible means of final-state redistribution, and extended this mechanical picture to include long-range repulsive interactions \cite{Amthor_model}   This group later studied the effects of spatial correlations in the spontaneous avalanche of Rydberg gases in a regime of strong blockade, suggesting a persistence of initial spatial correlations \cite{RobertdeSaintVincent}   

Robicheaux and coworkers have recently investigated the question of prompt many-body ionization from the point of view of Monte Carlo classical trajectory calculations \cite{Goforth}   For atoms on a regular or random grid driven classically by an electromagnetic field, they find that many-body excitation enhances prompt ionization by about twenty percent for densities greater than $5 6 \times 10^{-3}/(n_0^2 a_0)^3$, where $n_0$ is the principal quantum number of the Rydberg gas and $a_0$ is the Bohr radius   They observed that density fluctuations (sampled from the distribution of nearest neighbour distances) have a greater effect, and point to the possible additional influence of secondary electron-Rydberg collisions and the Penning production of fast atoms not considered by the model, but already observed by Raithel and coworkers \cite{Knuffman}   

The Raithel group also found direct evidence for electron collisional $\ell$-mixing in a Rb MOT \cite{Dutta}, and used selective field ionization to monitor evolution to plasma on a microsecond timescale in ultracold $^{85}$Rb $65d$ Rydberg gases with densities as low as $10^8$ cm$^{-3}$ \cite{WalzFlannigan}   Research by our group at UBC has observed very much the same dynamics in the relaxation of Xe Rydberg gases of similar density prepared in a molecular beam \cite{Hung2014}   In both cases, the time evolution to avalanche is well-described by coupled rate equations (see below), assuming an initializing density of Penning electrons determined by Robicheaux's criterion \cite{Robicheaux05}, applied to an Erlang distribution of Rydberg-Rydberg nearest neighbours   

Theoretical investigations of ultracold plasma physics have focused for the most part on the long- and short-time dynamics of plasmas formed by direct photoionization \cite{PhysRept,Lyon}   In addition to studies mentioned above, key insights on the evolution dynamics of Rydberg gases have been provided by studies of Pohl and coworkers exploring the effects of ion correlations and recombination-reionization on the hydrodynamics of plasma expansion \cite{Pohl:2003,PPR}   Further research has drawn upon molecular dynamics (MD) simulations to reformulate rate coefficients for the transitions driven by electron impact between highly excited Rydberg states \cite{PVS}, and describe an effect of strong coupling as it suppresses three-body recombination \cite{Bannasch:2011}   MD simulations confirm the accuracy of coupled rate equation descriptions for systems with $\Gamma$ as large as 0 3   Newer calculations suggest a strong connection between the order created by dipole blockade in Rydberg gases and the most favourable correlated distribution of ions in a corresponding strongly coupled ultracold plasma \cite{Bannasch:2013}   

Tate and coworkers have studied ultracold plasma avalanche and expansion theoretically as well as experimentally   Modelling observed expansion rates, they recently found that $^{85}$Rb atoms in a MOT form plasmas with effective initial electron temperatures determined by initial Rydberg density and the selected initial binding energy, to the extent that these parameters determine the fraction of the excited atoms that ionize by electron impact in the avalanche to plasma \cite{Forest}   This group also returned to the question of added Rydberg atoms, and managed to identify a crossover in $n_0$, depending on the initial electron temperature, that determines whether added Rydberg atoms of a particular initial binding energy act to heat or cool the electron temperature \cite{Crockett}    

Our group has focused on the plasma that evolves from a Rydberg gas under the low-temperature conditions of a skimmed, seeded supersonic molecular beam   In work on nitric oxide starting in 2008 \cite{Morrison2008,Plasma_expan,Morrison_shock,PCCP}, we established an initial kinetics of electron impact avalanche ionization that conforms with coupled rate equation models \cite{Saquet2011,Saquet2012,Scaling,haenelCP} and agrees at early times with the properties of ultracold plasmas that evolve from ultracold atoms in a MOT   We have also observed unique properties of the NO ultracold plasma owing to the fact that its Rydberg states dissociate \cite{Haenel2017}, and identified relaxation pathways that may give rise to quantum effects \cite{SousMBL,SousNJP}   The remainder of this review focuses on the nitric oxide ultracold plasma and the unique characteristics conferred by its evolution from a Rydberg gas in a laser-crossed molecular beam   


\section{Avalanche to strong coupling in a molecular Rydberg gas}

\subsection{The molecular beam ultracold plasma compared with a MOT}

When formed with sufficient density, a Rydberg gas of principal quantum number $n_0>30$ undergoes a spontaneous avalanche to form an ultracold plasma \cite{Li,Morrison2008,RobertdeSaintVincent}   Collisional rate processes combine with ambipolar hydrodynamics to govern the properties of the evolving plasma   For a molecular Rydberg gas, neutral fragmentation, occurs in concert with electron-impact ionization, three-body recombination and electron-Rydberg inelastic scattering   Neutral dissociation combined with radial expansion in a shaped distribution of charged particles, can give rise to striking effects of self-assembly and spatial correlation \cite{Schulz-Weiling2016,Haenel2017}    

The formation of a molecular ultracold plasma requires the conditions of local temperature and density afforded by a high mach-number skimmed supersonic molecular beam   Such a beam propagates at high velocity in the laboratory, with exceedingly well-defined hydrodynamic properties, including a propagation-distance-dependent density and sub-Kelvin temperature in the moving frame \cite{MSW_tutorial}   The low-temperature gas in a supersonic molecular beam differs in three important ways from the atomic gas laser-cooled in a magneto-optical trap (MOT) 

The milli-Kelvin temperature of the gas of ground-state NO molecules entrained in a beam substantially exceeds the sub-100 micro-Kelvin temperature of laser-cooled atoms in a MOT   However, the evolution to plasma tends to erase this distinction, and the two further characteristics that distinguish a beam offer important advantages for ultracold plasma physics:  Charged-particle densities in a molecular beam can exceed those attainable in a MOT by orders of magnitude   A great many different chemical substances can be seeded in a free-jet expansion, and the possibility this affords to form other molecular ultracold plasmas, introduces interesting and potentially important new degrees of freedom governing the dynamics of their evolution 


\subsection{Supersonic molecular beam temperature and particle density}

Seeded in a skimmed supersonic molecular beam, nitric oxide forms different phase-space distributions in the longitudinal (propagation) and transverse coordinate dimensions   As it propagates in $z$, the NO molecules reach a terminal laboratory velocity, $u_{\parallel}$, of about 1400 ${\rm ms^{-1}}$, which varies with the precise seeding ratio   

The distribution of $v_{\parallel}$, narrows to define a local temperature, $T_{\parallel}$, of approximately 0 5 K   The beam forms a Gaussian spatial distribution in the transverse coordinates, $x$ and $y$   In this plane, the local velocity, $v_{\perp}(r)$ is defined for any radial distance almost entirely by the divergence velocity of the beam, $u_{\perp}(r)$   Phase-space sorting cools the temperature in the transverse coordinates, $T_{\perp}$ to a value as low as $\sim 5$ mK \cite{MSW_tutorial}   

The stagnation pressure and seeding ratio determine the local density distribution as a function of $z$   For example, expanding from a stagnation pressure of 500 kPa with a 1:10 seeding ratio, a molecular beam propagates 2 5 cm to a skimmer and then 7 5 cm to a point of laser interaction, where it contains NO at a peak density of $1 6 \times 10^{14}$ cm$^{-3}$   

Here, crossing the molecular beam with a laser beam tuned to the transition sequence, ${\rm X} ~^2 \Pi_{1/2} ~N'' = 1 \xrightarrow{\omega_1} {\rm A} ~^2\Sigma^+ ~N'=0  \xrightarrow{\omega_2} n_0 f(2)$ forms a Gaussian ellipsoidal volume of Rydberg gas in a single selected principal quantum number, $n_0$, orbital angular momentum, $\ell = 3$, NO$^+$ core rotational quantum number, $N^+ = 2$ and total angular momentum neglecting spin, $N=1$   

A typical $\omega_1$ pulse energy of 2 $\mu$J and a Gaussian width of 0 2 mm serves to drive the first step of this sequence in a regime of linear absorption   Overlapping this volume by an $\omega_2$ pulse with sufficient fluence to saturate the second step forms a Rydberg gas ellipsoid with a nominal peak density of $5 \times 10^{12}$ cm$^{-3}$  \cite{Morrison2008,MSW_tutorial}   Fluctuations in the pulse energy and longitudinal mode of $\omega_1$ cause the real density to vary



ground_truth: 21.

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 3:   For certain experiments, we find it convenient to saturate the $\omega_1$ transition, and vary the density of Rydberg gas by delaying $\omega_2$   An $\omega_1$-$\omega_2$ delay, $\Delta t$, reduces the Rydberg gas density by a precise factor, $e^{-\Delta t/\tau}$, where $\tau$ is the 200 ns radiative lifetime of NO ${\rm A} ~^2\Sigma^+ ~N'=0$ \cite{Carter,Hancock} 


\subsection{Penning ionization}

The density distribution of a Rydberg gas defines a local mean nearest neighbour distance, or Wigner-Seitz radius of $ a_{ws} =  \left(3/4 \pi \rho \right)^{1/3} $, where $\rho$ refers to the local Rydberg gas density   For example, a Rydberg gas with a density of $ \rho_0=0 5 \times 10^{12}$ cm$^{-3} $ forms an Erlang distribution \cite{Torquato 1990} of nearest neighbour separations with a mean value of $ 2 a_{ws}=1 6$  $\mu$m   

A semi-classical model \cite{Robicheaux05} suggests that 90 percent of Rydberg molecule pairs separated by a critical distance, $ r_c = 1 8 \cdot 2 n_0^2 a_0 $ or less undergo Penning ionization within 800 Rydberg periods   We can integrate the Erlang distribution from $ r=0 $ to the critical distance $r = r_c$ for a Rydberg gas of given $n_0$, to define the local density of Penning electrons ($ \rho_e$ at $t=0$) produced by this prompt interaction, for any given initial local density, $\rho_0$ by the expression:
\begin{equation}
\rho_e(\rho_0,n_0) = \frac{0 9}{2} \cdot 4 \pi \rho_0 ^2\int_0^{r_{c}} r^2 \mathrm{e}^{-\frac{4\pi}{3}\rho_0 r^3}\mathrm{d}r \quad 
\label{eqn:Erlang}
\end{equation}

Evaluating this definite integral yields an equation in closed form that predicts the Penning electron density for any particular initial Rydberg density and principal quantum number 
\begin{equation}
\rho_e(\rho_0,n_0) =\frac{0 9 \rho_0}{2}(1-\mathrm{e}^{-\frac{4\pi}{3}\rho_0 r_c^3}) \quad 
\label{Eq:PenDens}
\end{equation}
\begin{figure}[h!]
\centering
\includegraphics[scale=0 33]{Penning_Latice pdf}
\caption{Distributions of ion-ion nearest neighbours following Penning ionization and electron-impact avalanche simulated for a predissociating molecular Rydberg gas of initial principal quantum number, $n_0$, from 30 to 80, and density of 10$^{12}$ cm$^{-3}$   Dashed lines mark corresponding values of $a_{ws}$  Calculated by counting ion distances after relaxation to plasma in 10$^6$-particle stochastic simulations  Integrated areas proportional to populations surviving neutral dissociation }
\label{fig:PL}
\end{figure}

Prompt Penning ionization acts on the portion of the initial nearest-neighbour distribution in the Rydberg gas that lies within $r_c$   When a molecule ionizes, its collision partner relaxes to a lower principal quantum number, $n'<n_0/\sqrt{2}$   This close-coupled interaction disrupts the separability of Rydberg orbital configurations in the Penning partner   This causes mixing with core penetrating states that are strongly dissociative   Penning partners are thus very likely to dissociate, leaving a spatially isolated distribution of ions   We refer to the spatial correlation that results as a Penning lattice \cite{Sadeghi:2014}   The extent of this effect varies depending on the local density and the selected initial principal quantum number   Figure \ref{fig:PL} shows the degree to which Rydberg gases with initial principal quantum numbers from 30 to 80 form a Penning lattice for an initial density of $1 \times 10^{12} ~{\rm cm}^{-3}$   

\subsection{Spontaneous electron-impact avalanche}

The electrons produced by prompt Penning ionization start an electron impact avalanche   The kinetics of this process are well described by a set of coupled rate equations that account for state-to-state electron-Rydberg inelastic scattering, electron-impact ionization and three-body ion-electron recombination \cite{PPR,Saquet2011,Saquet2012,Scaling} using detailed rate coefficients,  $k_{ij}$, $k_{i,ion}$ and $k_{i,tbr}$ validated by MD simulations \cite{PVS}   
\begin{eqnarray}
-\frac{d\rho_i}{dt}&=&\sum_{j}{k_{ij}\rho_e\rho_i}-\sum_{j}{k_{ji}\rho_e\rho_j} \nonumber\\
&& +k_{i,ion}\rho_e\rho_i-k_{i,tbr}\rho^3_e 
  \label{level_i}
\end{eqnarray}
\noindent and,
\begin{equation}
\frac{d\rho_e}{dt}=\sum_{i}{k_{i,ion}\rho_e^2}-\sum_{i}{k_{i,tbr}\rho^3_e}
  \label{electron}
\end{equation}

The relaxation of Rydberg molecules balances with collisional ionization to determine an evolving temperature of avalanche electrons to conserve total energy per unit volume  
\begin{equation}
E_{tot}=\frac{3}{2}k_BT_e(t)\rho_e(t)-R\sum_i{\frac{\rho_i(t)}{n_i^2}},
  \label{energy}
\end{equation}
Here, for simplicity, we neglect the longer-time effects of Rydberg predissociation and electron-ion dissociative recombination \cite{Saquet2012} 

Such calculations show that the conversion from Rydberg gas to plasma occurs on a timescale determined largely by the local Penning electron density, or Penning fraction, $P_f = \rho_e/\rho_0$, which depends on the local density of Rydberg molecules and their initial principal quantum number   

Avalanche times predicted by coupled rate equation calculations range widely   For example, in a model developed for experiments on xenon, simulations predict that a Rydberg gas with $n_0 = 42$ at a density of $8 8 \times 10^8 ~{\rm cm}^{-3}$ ($P_f = 6 \times 10^{-5}$) avalanches with a half time of  40 $\mu$s \cite{Hung2014}   At an opposite extreme, rate equations estimate that a Rydberg gas of NO with $n_0=60$ at a density of $1 \times 10^{12} ~{\rm cm}^{-3}$ ($P_f = 0 3$) rises to plasma in about 2 ns \cite{Saquet2012}   

\begin{figure}[h!]
\centering
\includegraphics[width=  49 \textwidth]{SFI_n=49 pdf}
   \caption{Contour plots showing SFI signal as a function the applied field for an $nf(2)$ Rydberg gas with an initial principal quantum number, $n_0=49$   Each frame represents 4,000 SFI traces, sorted by initial Rydberg gas density   Ramp field beginning at 0 and 150 ns (top, left to right), and  300 and 450 ns (bottom) after the $\omega_2$ laser pulse   The two bars of signal most evident at early ramp field delay times represent the field ionization of the $49f(2)$ Rydberg state respectively to NO$^+$ X $^1\Sigma^+$ cation rotational states, $N^+=0$ and 2   The signal waveform extracted near zero applied field represents the growing population of plasma electrons   
   }
\label{fig:SFI}
\end{figure}

Selective field ionization (SFI) probes the spectrum of binding energies in a Rydberg gas   Applied as a function of time after photoexcitation, SFI maps the evolution from a state of selected initial principal quantum number, $n_0$, to plasma \cite{Haenel2017}   Figure \ref{fig:SFI} shows SFI spectra taken at a sequence of delays after the formation of $49f(2)$ Rydberg gases of varying density     

Here, we can see that a $49f(2)$ Rydberg gas with an estimated initial density $\rho_0 = 3 \times 10^{11} ~{\rm cm}^{-3}$ relaxes to plasma on a timescale of about 500 ns   Observations such as these agree well with the predictions of coupled rate-equation calculations   We can understand this variation in relaxation dynamics with $\rho_0$ and $n_0$ quite simply in terms of the corresponding density of prompt Penning electrons these conditions afford to initiate the avalanche to plasma   

Figure \ref{fig:scaled_rise} illustrates this, showing how rise times predicted by coupled rate-equation simulations for a large range of initial densities and principal quantum number match when plotted as a function of time scaled by the ultimate plasma frequency and fraction of prompt Penning electrons   The dashed line gives an approximate account of the scaled rate of avalanche under all conditions of Rydberg gas density and initial principal quantum number in terms of the simple sigmoidal function:

\begin{equation}
\frac{\rho_e}{\rho_0} = \frac{a}{b+e^{-c\tau}},
  \label{scaledEq1}
\end{equation}
where,
\begin{equation}
\tau = t \omega_e P_f^{3/4},
  \label{scaledEq2}
\end{equation}
in which $\omega_e$ is the plasma frequency after avalanche, $P_f$ is the fraction of prompt Penning electrons, and $a = 0 00062$,  $b =   0 00082$ and $c =     0 075$ are empirical coefficients   

\begin{figure}[h!]
\centering
\includegraphics[width=  4 \textwidth]{sim_analytical_density pdf}
   \caption{Rise in fractional electron density as a function of time scaled by the plasma frequency, $\omega_e$ and fraction, $\rho_e(t=0)/\rho_0 = P_f$, of prompt Penning electrons   Simulation results shown for $n_0 = 30$, 50 and 70 with initial densities, $\rho_0 = 10^9,~10^{10},~10^{11},~{\rm and}~10^{12}~{\rm cm}^{-3}$   
   }
\label{fig:scaled_rise}
\end{figure}


\subsection{Evolution to plasma in a Rydberg gas Gaussian ellipsoid}

As outlined above, the local density and principal quantum number together determine the rate at which a Rydberg gas avalanches to plasma   Our experiment crosses a 2 mm wide cylindrically Gaussian molecular beam with a 1 mm diameter TEM$_{00}$ $\omega_1$ laser beam to produce a Gaussian ellipsoidal distribution of molecules excited to the A $^2\Sigma^+$ $v=0, ~N'=0$ intermediate state   A larger diameter $\omega_2$ pulse then drives a second step that forms a Rydberg gas in a single $n_0f(2)$ state with the spatial distribution of the intermediate state   

We model this shaped Rydberg gas as a system of 100 concentric ellipsoidal shells of varying density \cite{haenelCP}   Coupled rate equations within each shell describe the avalanche to plasma   This rate process proceeds from shell to shell with successively longer induction periods, determined by the local density as detailed above   The rising conversion of Rydberg molecules to ions plus neutral dissociation products conserves the particle number in each shell   We assume that local space charge confines electrons to shells, conserving quasi-neutrality   Electrons exchange kinetic energy at the boundaries of each shell, which determines a single plasma electron temperature   

\begin{figure}[h!]
\centering
\includegraphics[width=  5 \textwidth]{shell_model_100}
   \caption{(top frame) Cross-sectional contour diagram in the $x,y$ plane for $z=0$ describing the distribution of ion plus electron density over 100 shells of Gaussian ellipsoid with initial dimensions, $\sigma_x= 0 75$ mm and $\sigma_y= \sigma_z = 0 42$ mm and an initial $n_0 = 50$ Rydberg gas density, $\rho_0 = 2 \times 10^{11}$ cm$^{3}$ after an evolution time of 100 ns



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

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 is the electron correlation parameter, $\Gamma_e$?

Read the following text and answer briefly.

Context 3:   (bottom frame) Curves describing the (dashed) ascending ion and (solid) descending Rydberg gas densities of each shell as functions of evolution time, for $t=20$, 40, 60, 80 and 100 ns   
   }
\label{fig:shell}
\end{figure}

The upper frame of Figure \ref{fig:shell} shows contours of NO$^+$ ion density after 100 ns obtained from a shell-model coupled rate-equation simulation of the avalanche of a Gaussian ellipsoidal Rydberg gas of nitric oxide with a selected initial state, $50f(2)$ and a density of $2 \times 10^{11}$ cm$^{-3}$   Here, we simulate a relaxation that includes channels of predissociation at every Rydberg level and redistributes the energy released to electrons, which determines a uniform rising electron temperature for all shells   

For comparison, the lower frame plots curves describing the ion density of each shell as a function of time from 20 to 100 ns, as determined by applying Eq \ref{scaledEq1} for the local conditions of initial Rydberg gas density   This numerical approximation contains no provision for predissociation   Coupled rate-equation simulations for uniform volumes show that predissociation depresses yield to some degree, but has less effect on the avalanche kinetics \cite{Saquet2012}   Therefore, we can expect sets of numerically estimated shell densities, scaled to agree with the simulated ion density at the elapsed time of 100 ns to provide a reasonable account of the earlier NO$^+$ density profiles as a function of time    


\begin{figure}[h!]
\centering
\includegraphics[width=  4 \textwidth]{Shell_pop}
   \caption{Global population fractions of particles as they evolve in the avalanche of a shell-model ellipsoidal Rydberg gas with the initial principal quantum number and density distribution of Figure \ref{fig:shell}
   }
\label{fig:shell_yields}
\end{figure}

For each time step, the difference, $\rho_0 - \rho_e$ defines the neutral population of each shell   We assign a fraction of this population to surviving Rydberg molecules, such that the total population of NO$^*$ as a function of time agrees with the prediction of the shell-model simulation, as shown in Figure \ref{fig:shell_yields}   We consider the balance of this neutral population to reflect NO$^*$ molecules that have dissociated to form N($^4$S) $+$ O($^3$P)   Figure \ref{fig:shell} plots these surviving Rydberg densities as a function of radial distance for each evolution time   At the initial density of this simulation, note at each time step that a higher density of Rydberg molecules encloses the tail of the ion density distribution in $x$    

\subsection{Plasma expansion and NO$^+$ - NO$^*$ charge exchange as an avenue of quench}

We regard the ions as initially stationary   The release of electrons creates a radial electric potential gradient, which gives rise to a force, $-e\nabla \phi_{k,j}(t)$, that accelerates the ions in shell $j$ in direction $k$ according to \cite{Sadeghi 2012}:

\begin{align}
\frac{-e}{m'}\nabla \phi_{k,j}(t) = & \frac{\partial u_{k,j}(t)}{\partial t} \notag  \\
= & \frac{k_BT_e(t)}{m'\rho_j(t)} \frac{\rho_{j+1}(t) - \rho_j(t)}{r_{k,j+1}(t) - r_{k,j}(t)},
  \label{dr_dt}
\end{align}

\noindent where $\rho_j(t)$ represents the density of ions in shell $j$   

The instantaneous velocity, $u_{k,j}(t)$ determines the change in the radial coordinates of each shell, $r_{k,j}(t)$, 
\begin{equation}
\frac{\partial r_{k,j}(t)}{\partial t}=u_{k,j}(t) = \gamma_{k,j}(t) r_{k,j}(t),
  \label{dr_dt}
\end{equation}
\noindent which in turn determines shell volume and thus its density, $ \rho_j(t)$    
The electron temperature supplies the thermal energy that drives this ambipolar expansion   Ions accelerate and $T_e$ falls according to: 

\begin{equation}
\frac{3k_B}{2}\frac{\partial T_e(t)}{\partial t}= -\frac{m'}{\sum_{j}{N_j}}\sum_{k,j}{N_j u_{k,j}(t)\frac{\partial u_{k,j}(t)}{\partial t}},
  \label{dr_dt}
\end{equation}
\noindent where we define an effective ion mass, $m'$, that recognizes the redistribution of the electron expansion force over all the NO$^+$ charge centres by resonant ion-Rydberg charge exchange, which occurs with a very large cross section \cite{PPR}   
\begin{equation}
m' =\left (1+ \frac{\rho^*_{j}(t)}{ \rho_j(t)}\right) m ,
  \label{dr_dt}
\end{equation}
\noindent in which $\rho^*_{j}(t)$ represents the instantaneous Rydberg density in shell $j$ 

The initial avalanche in the high-density core of the ellipsoid leaves few Rydberg molecules, so this term has little initial effect   Rydberg molecules predominate in the lower-density wings   There, momentum sharing by charge exchange assumes a greater importance   

We see this most directly in the $\omega_2$ absorption spectrum of transitions to states in the $n_0 f(2)$ Rydberg series, detected as the long-lived signal that survives a flight time of 400 $\mu$s to reach the imaging detector   The balance between the rising density of ions and the falling density of Rydberg molecules depends on the initial density of electrons produced by prompt Penning ionization   As clear from Eq \ref{Eq:PenDens}, this Penning fraction depends sensitively on the principal quantum number, and for all principal quantum numbers, on the initial Rydberg gas density   

\begin{figure}[h!]
\centering
\includegraphics[width=  4 \textwidth]{w2_spectra}
   \caption{Double-resonant spectra of nitric oxide Rydberg states in the $nf$ series converging to NO$^+$ $v=0$, $N^+=2$ (designated, $nf(2)$), derived from the late-peak signal obtained after a flight time of 400 $\mu$s by scanning $\omega_2$ for $\omega_1$ tuned to NO A $^2\Sigma^+$ $v=0$, $N'=0$ for initial $nf(2)$ densities from top to bottom of 0 07, 0 10, 0 13, 0 19, 0 27, 0 30, 0 32 and $3 \times 10^{12}$ cm$^{3}$   
  }
\label{fig:w2_spectra}
\end{figure}

Figure \ref{fig:w2_spectra} shows a series of $\omega_2$ late-signal excitation spectra for a set of initial densities   Here, we see a clear consequence of the higher-order dependence of Penning fraction - and thus the NO$^+$ ion - NO$^*$ Rydberg molecule balance - on $n_0$, the $\omega_2$-selected Rydberg gas initial principal quantum number   This Penning-regulated NO$^+$ ion - NO$^*$ Rydberg molecule balance appears necessary as a critical factor in achieving the long ultracold plasma lifetime required to produce this signal   We are progressing in theoretical work that explains the stability apparently conferred by this balance   


\subsection{Bifurcation and arrested relaxation}

Ambipolar expansion quenches electron kinetic energy as the initially formed plasma expands   Core ions follow electrons into the wings of the Rydberg gas   There, recurring charge exchange between NO$^+$ ions and NO$^*$ Rydberg molecules redistributes the ambipolar force of the expanding electron gas, equalizing ion and Rydberg velocities   This momentum matching effectively channels electron energy through ion motion into the overall $\pm x$ motion of gas volumes in the laboratory   The internal kinetic energy of the plasma, which at this point is defined almost entirely by the ion-Rydberg relative motion, falls   Spatial correlation develops, and over a period of 500 ns, the system forms the plasma/high-Rydberg quasi-equilibrium dramatically evidenced by the SFI results in Figure \ref{fig:SFI}   

\begin{figure}[h!]
\centering
\includegraphics[width=  4 \textwidth]{Bifurcation pdf}
   \caption{$x,y$ detector images of ultracold plasma volumes produced by 2:1 aspect ratio ellipsoidal Rydberg gases with selected initial state, $40f(2)$ after a flight time of 402 $\mu$s over a distance of 575 mm   Lower frame displays the distribution in $x$ of the charge integrated in $y$ and $z$   Both images represent the unadjusted raw signal acquired in each case after 250 shots   
   }
\label{fig:bifurcation}
\end{figure}

In the wings, momentum redistribution owing to cycles of ion-Rydberg charge transfer retards radial expansion \cite{Pohl2003,PPR}   By redirecting electron energy from ambipolar acceleration to $\pm x$ plasma motion, NO$^+$ to NO$^*$ charge exchange dissipates electron thermal energy   This redistribution of energy released in the avalanche of the Rydberg gas to plasma, causes the ellipsoidal Rydberg gas to bifurcate \cite{Schulz-Weiling2016,Haenel2017}, forming very long-lived, separating charged-particle distributions   We capture the electron signal from these recoiling volumes on an imaging detector as pictured in Figure \ref{fig:bifurcation}   Here, momentum matching preserves density and enables ions and Rydberg molecules to relax to positions that minimize potential energy, building spatial correlation   

The semi-classical description of avalanche and relaxation outlined above forms an important point of reference from which to interpret our experimental observations   The laser crossed molecular beam illumination geometry creates a Rydberg gas with a distinctively shaped high-density spatial distribution   This initial condition has an evident effect on the evolution dynamics   We have developed semi-classical models that explicitly consider the coupled rate and hydrodynamic processes governing the evolution from Rydberg gas to plasma using a realistic, ellipsoidal representation of the ion/electron and Rydberg densities \cite{haenelCP}   No combination of initial conditions can produce a simulation that conforms classically with the state of arrested relaxation we observe experimentally  


\subsection{A molecular ultracold plasma state of arrested relaxation}

Thus, we find that spontaneous avalanche to plasma splits the core of an ellipsoidal Rydberg gas of nitric oxide  As ambipolar expansion quenches the electron temperature of this core plasma, long-range, resonant charge transfer from ballistic ions to frozen Rydberg molecules in the wings of the ellipsoid quenches the ion-Rydberg molecule relative velocity distribution  This sequence of steps gives rise to a remarkable mechanics of self-assembly, in which the kinetic energy of initially formed hot electrons and ions drives an observed separation of plasma volumes  These dynamics redistribute ion momentum, efficiently channeling electron energy into a reservoir of mass-transport  This starts a process that evidently anneals separating volumes to a state of cold, correlated ions, electrons and Rydberg molecules  

We have devised a three-dimensional spin model to describe this arrested state of the ultracold plasma in terms of two, three and four-level dipole-dipole energy transfer interactions (spin flip-flops), together with Ising interactions that arise from the concerted pairwise coupling of resonant pairs of dipoles \cite{SousMBL,SousNJP}   

The Hamiltonian includes the effects of onsite disorder owing to the broad spectrum of states populated in the ensemble and the unique electrostatic environment of every dipole   Extending ideas developed for simpler systems \cite{Burin1,Sondhi}, one can make a case for slow dynamics, including an arrest in the relaxation of NO Rydberg molecules to predissociating states of lower principal quantum number 

Systems of higher dimension ought to thermalize by energy transfer that spreads from rare but inevitable ergodic volumes (Griffiths regions) \cite{Sarang2, Roeck_griffith, RareRegions_rev, Thermal_inclusions}   However, a feature in the self-assembly of the molecular ultracold plasma may preclude destabilization by rare thermal domains:  Whenever the quenched plasma develops a delocalizing Griffiths region, the local predissociation of relaxing NO molecules promptly proceeds to deplete that region to a void of no consequence 

In summary, the classical dynamics of avalanche and bifurcation appear to create a quenched condition of low temperature and high disorder in which dipole-dipole interactions drive self-assembly to a localized state purified by the predissociation of thermal regions   We suggest that this state of the quenched ultracold plasma offers an experimental platform for studying quantum many-body physics of disordered systems  \\

\section{Acknowledgments}
This work was supported by the US Air Force Office of Scientific Research (Grant No  FA9550-17-1-0343), together with the Natural Sciences and Engineering research Council of Canada (NSERC), the Canada Foundation for Innovation (CFI) and the British Columbia Knowledge Development Fund (BCKDF)  





ground_truth: It is the ratio of the average unscreened electron-electron potential energy to kinetic energy.