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Question: What are the two ground states observed for indeno[1,2-a]fluorene on NaCl surfaces?

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Context 1: Paper Info

Title: Bistability between π-diradical open-shell and closed-shell states in indeno[1,2-a]fluorene
Publish Date: Unkown
Author List: Shantanu Mishra (from IBM Research Europe -Zurich), Manuel Vilas-Varela (from Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela), Leonard-Alexander Lieske (from IBM Research Europe -Zurich), Ricardo Ortiz (from Donostia International Physics Center (DIPC)), Igor Rončević (from Department of Chemistry, University of Oxford), Florian Albrecht (from IBM Research Europe -Zurich), Diego Peña (from Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela), Leo Gross (from IBM Research Europe -Zurich)

Figure

Fig  1 | Non-benzenoid non-alternant polycyclic conjugated hydrocarbons a, Classical nonbenzenoid non-alternant polycyclic conjugated hydrocarbons: pentalene, azulene and heptalene b, Generation of indacenes and indenoindenes through benzinterposition and benzannelation of pentalene, respectively Gray filled rings represent Clar sextets c, Closed-shell Kekulé (left) and openshell non-Kekulé (right) resonance structures of QDMs Note that meta-QDM is a non-Kekulé molecule All indenofluorene isomers, being derived through benzannelation of indacenes, contain a central QDM moiety d, Closed-shell Kekulé (top) and open-shell non-Kekulé (bottom) resonance structures of indenofluorenes Compared to their closed-shell structures, 1 and 5 gain two Clar sextets in the openshell structure, while 2-4 gain only one Clar sextet in the open-shell structure Colored bonds in d highlight the ortho-and para-QDM moieties in the two closed-shell Kekulé structures of 5  e, Scheme of on-surface generation of 5 by voltage pulse-induced dehydrogenation of 6 (C20H14) Structures 7 and 8 represent the two monoradical species (C20H13) 
Fig  2 | Characterization of open-shell indeno[1,2-a]fluorene on bilayer NaCl/Au(111) a, DFTcalculated wave functions of the frontier orbitals of 5OS in the triplet configuration for the spin up (occupied) level (isovalue: 0 002 e -Å -3 ) Blue and red colors represent opposite phases of the wave function b, Corresponding DFT-calculated spin density of 5OS (isovalue: 0 01 e -Å -3) Blue and orange colors represent spin up and spin down densities, respectively c, Probability density of the SOMOs of 5OS (isovalue: 0 001 e -Å -3 ) d, DFT-calculated bond lengths of 5OS e, Constant-height I(V) spectra acquired on a species of 5 assigned as 5OS, along with the corresponding dI/dV(V) spectra Open feedback parameters: V = -2 V, I = 0 17 pA (negative bias side) and V = 2 V, I = 0 17 pA (positive bias side) Acquisition position of the spectra is shown in Supplementary Fig 7 f, Scheme of many-body transitions associated to the measured ionic resonances of 5OS Also shown are STM images of assigned 5OS at biases where the corresponding transitions become accessible Scanning parameters: I = 0 3 pA (V = -1 2V and -1 5 V) and 0 2 pA (V = 1 3 V and 1 6 V)  g, Laplace-filtered AFM image of assigned 5OS STM set point: V = 0 2 V, I = 0 5 pA on bilayer NaCl, Δz = -0 3Å The tip-height offset Δz for each panel is provided with respect to the STM setpoint, and positive (negative) values of Δz denote tip approach (retraction) from the STM setpoint f and g show the same molecule at the same adsorption site, which is next to a trilayer NaCl island The bright and dark features in the trilayer NaCl island in g correspond to Cl -and Na + ions, respectively Scale bars: 10 Å (f) and 5 Å (g) 
Fig  3 | Characterization of closed-shell indeno[1,2-a]fluorene on bilayer NaCl/Au(111) a, DFTcalculated wave functions of the frontier orbitals of closed-shell 5 0 (isovalue: 0 002 e -Å -3 ) The wave functions shown here are calculated for the 5para geometry b, DFT-calculated bond lengths of 5ortho (top) and 5para (bottom) c, Constant-height I(V) spectra acquired on a species of 5 assigned as 5para, along with the corresponding dI/dV(V) spectra Open feedback parameters: V = -2 V, I = 0 15 pA (negative bias side) and V = 2 2 V, I = 0 15 pA (positive bias side) Acquisition position of the spectra is shown in Supplementary Fig  7  d, Scheme of many-body transitions associated to the measured ionic resonances of 5para Also shown are STM images of assigned 5para at biases where the corresponding transitions become accessible Scanning parameters: I = 0 15 pA (V = -1 5 V) and 0 2 pA (V = 1 7 V)  e, Laplace-filtered AFM image of assigned 5para STM set point: V = 0 2 V, I = 0 5 pA on bilayer NaCl, Δz = -0 7 Å  f, Selected bonds labeled for highlighting bond order differences between 5para and 5ortho For the bond pairs a/b, c/d and e/f, the bonds labeled in bold exhibit a higher bond order than their neighboring labeled bonds in 5para g, Laplace-filtered AFM images of 5 on bilayer NaCl/Cu(111) showing switching between 5OS and 5para as the molecule changes its adsorption position The faint protrusion adjacent to 5 is a defect that stabilizes the adsorption of 5  STM set point: V = 0 2 V, I = 0 5 pA on bilayer NaCl, Δz = -0 3Å  STM and STS data in c and d are acquired on the same species, while the AFM data in e is acquired on a different species Scale bars: 10 Å (d) and 5 Å (e,g) 
NMR (300 MHz, CDCl3) δ: 7 51 (m, 2H), 7 40 -7 28 (m, 5H), 7 27 -7 20 (m, 2H), 7 13 (d, J = 7 7 Hz, 1H), 2 07 (s, 3H), 1 77 (s, 3H) ppm  13C NMR-DEPT (75 MHz, CDCl3, 1:1 mixture of atropisomers) δ: 141 2 (C), 141 1 (C), 140 0 (C), 139 4 (2C), 137 5 (C), 137 4 (C), 136 0 (3C), 134 8 (C), 134 5 (C), 134 1 (C), 134 0 (C), 133 7 (C), 133 6 (C), 131 6 (CH), 131 2 (CH), 131 1 (CH), 130 7 (CH), 129 8 (CH), 129 7 (CH), 129 5 (CH), 129 4 (CH), 129 0 (CH), 128 9 (CH), 128 7 (2CH), 128 6 (2CH), 127 2 (CH), 127 1 (CH), 127 0 (CH), 126 9 (CH), 126 7 (CH), 126 6 (CH), 20 6 (CH3), 20 5 (CH3), 17 7 (CH3), 17 5 (CH3) ppm MS (APCI) m/z (%): 327 (M+1, 100) HRMS: C20H16Cl2; calculated: 327 0702, found: 327 0709 
NMR (500 MHz, CDCl3) δ: 7 93 (d, J = 7 6 Hz, 1H), 7 85 (d, J = 7 5 Hz, 1H), 7 78 (d, J = 7 7 Hz, 1H), 7 65 (d, J = 7 4 Hz, 1H), 7 61 (d, J = 7 5 Hz, 1H), 7 59 (d, J = 7 7 Hz, 1H), 7 47 (ddd, J = 8 4, 7 2, 1 1 Hz, 1H), 7 42 (dd, J = 8 1, 7 0 Hz, 1H), 7 35 (m, 2H), 4 22 (s, 3H), 4 02 (s, 3H) ppm  13C NMR-DEPT (125 MHz, CDCl3) δ: 144 1 (C), 143 3 (C), 142 3 (C), 141 9 (C), 141 8 (C), 141 2 (C), 138 2 (C), 136 5 (C), 127 0 (CH), 126 9 (CH), 126 7 (CH), 126 6 (CH), 125 3 (CH), 125 2 (CH), 123 6 (CH), 122 2 (CH), 119 9 (CH), 118 4 (CH), 37 4 (CH2), 36 3 (CH2) ppm MS (APCI) m/z (%): 254 (M+, 88) HRMS: C20H14; calculated: 254 1090, found: 254 1090 

abstract

Indenofluorenes are non-benzenoid conjugated hydrocarbons that have received great interest owing to their unusual electronic structure and potential applications in nonlinear optics and photovoltaics  Here, we report the generation of unsubstituted indeno[1,2-a]fluorene, the final and yet unreported parent indenofluorene regioisomer, on various surfaces by cleavage of two C-H bonds in 7,12-dihydro indeno[1,2-a]fluorene through voltage pulses applied by the tip of a combined scanning tunneling microscope and atomic force microscope 
On bilayer NaCl on Au(111), indeno[1,2a]fluorene is in the neutral charge state, while it exhibits charge bistability between neutral and anionic states on the lower work function surfaces of bilayer NaCl on Ag(111) and Cu(111)  In the neutral state, indeno[1,2-a]fluorene exhibits either of two ground states: an open-shell π-diradical state, predicted to be a triplet by density functional and multireference many-body perturbation theory calculations, or a closedshell state with a para-quinodimethane moiety in the as-indacene core 
Switching between open-and closed-shell states of a single molecule is observed by changing its adsorption site on NaCl  The inclusion of non-benzenoid carbocyclic rings is a viable route to tune the physicochemical properties of polycyclic conjugated hydrocarbons (PCHs)   Non-benzenoid polycycles may lead to local changes in strain, conjugation, aromaticity, and, relevant to the context of the present work, induce an open-shell ground state of the corresponding PCHs  
Many nonbenzenoid PCHs are also non-alternant, where the presence of odd-membered polycycles breaks the bipartite symmetry of the molecular network   Figure shows classical examples of non-benzenoid non-alternant PCHs, namely, pentalene, azulene and heptalene  Whereas azulene is a stable PCH exhibiting Hückel aromaticity ([4n+2] π-electrons, n = 2), pentalene and heptalene are unstable Hückel antiaromatic compounds with [4n] π-electrons, n = 2 (pentalene) and n = 3 (heptalene) 
Benzinterposition of pentalene generates indacenes, consisting of two isomers s-indacene and as-indacene (Fig  )  Apart from being antiaromatic, indacenes also contain proaromatic quinodimethane (QDM) moieties (Fig  ) , which endows them with potential open-shell character  While the parent s-indacene and asindacene have never been isolated, stable derivatives of s-indacene bearing bulky substituents have been synthesized  
A feasible strategy to isolate congeners of otherwise unstable non-benzenoid non-alternant PCHs is through fusion of benzenoid rings at the ends of the π-system, that is, benzannelation  For example, while the parent pentalene is unstable, the benzannelated congener indeno[2,1-a]indene is stable under ambient conditions (Fig  )  
However, the position of benzannelation is crucial for stability: although indeno[2,1a]indene is stable, its regioisomer indeno[1,2-a]indene (Fig  ) oxidizes under ambient conditions   Similarly, benzannelation of indacenes gives rise to the family of PCHs known as indenofluorenes (Fig  ), which constitute the topic of the present work 
Depending on the benzannelation position and the indacene core, five regioisomers can be constructed, namely, indeno [ Practical interest in indenofluorenes stems from their low frontier orbital gap and excellent electrochemical characteristics that render them as useful components in organic electronic devices  
The potential open-shell character of indenofluorenes has led to several theoretical studies on their use as non-linear optical materials and as candidates for singlet fission in organic photovoltaics   Recent theoretical work has also shown that indenofluorene-based ladder polymers may exhibit fractionalized excitations 
Fundamentally, indenofluorenes represent model systems to study the interplay between aromaticity and magnetism at the molecular scale   Motivated by many of these prospects, the last decade has witnessed intensive synthetic efforts toward the realization of indenofluorenes  Derivatives of 1-4 have been realized in solution , while 1-3 have also been synthesized on surfaces and characterized using scanning tunneling microscopy (STM) and atomic force microscopy (AFM), which provide information on molecular orbital densities , molecular structure and oxidation state  
With regards to the open-shell character of indenofluorenes, 2-4 are theoretically and experimentally interpreted to be closed-shell, while calculations indicate that 1 and 5 should exhibit open-shell ground states   Bulk characterization of mesitylsubstituted 1, including X-ray crystallography, temperature-dependent NMR, and electron spin resonance spectroscopy, provided indications of its open-shell ground state  
Electronic characterization of 1 on Au(111) surface using scanning tunneling spectroscopy (STS) revealed a low electronic gap of 0 4 eV (ref  )  However, no experimental proof of an openshell ground state of 1 on Au(111), such as detection of singly occupied molecular orbitals (SOMOs) or spin excitations and correlations due to unpaired electrons , was shown 
In this work, we report the generation and characterization of unsubstituted 5  Our research is motivated by theoretical calculations that indicate 5 to exhibit the largest diradical character among all indenofluorene isomers   The same calculations also predict that 5 should possess a triplet ground state 
Therefore, 5 would qualify as a Kekulé triplet, of which only a handful of examples exist   However, definitive synthesis of 5 has never been reported so far  Previously, Dressler et al  reported transient isolation of mesityl-substituted 5, where it decomposed both in the solution and in solid state , and only the structural proof of the corresponding dianion was obtained 
On-surface generation of a derivative of 5, starting from truxene as a precursor, was recently reported   STM data on this compound, containing the indeno[1,2-a]fluorene moiety as part of a larger PCH, was interpreted to indicate its open-shell ground state  However, the results did not imply the ground state of unsubstituted 5  Here, we show that on insulating surfaces 5 can exhibit either of two ground states: an open-shell or a closed-shell 
We infer the existence of these two ground states based on high-resolution AFM imaging with bond-order discrimination and STM imaging of molecular orbital densities   AFM imaging reveals molecules with two different geometries  Characteristic bond-order differences in the two geometries concur with the geometry of either an open-or a closed-shell state 
Concurrently, STM images at ionic resonances show molecular orbital densities corresponding to SOMOs for the open-shell geometry, but orbital densities of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) for the closed-shell geometry  Our experimental results are in good agreement with density functional theory (DFT) and multireference perturbation theory calculations 
Finally, we observe switching between open-and closed-shell states of a single molecule by changing its adsorption site on the surface  Synthetic strategy toward indeno[1,2-a]fluorene  The generation of 5 relies on the solution-phase synthesis of the precursor 7,12-dihydro indeno[1,2-a]fluorene (6)  Details on synthesis and characterization of 6 are reported in Supplementary Figs 
  Single molecules of 6 are deposited on coinage metal (Au(111), Ag(111) and Cu(111)) or insulator surfaces  In our work, insulating surfaces correspond to two monolayer-thick (denoted as bilayer) NaCl on coinage metal surfaces  Voltage pulses ranging between 4-6 V are applied by the tip of a combined STM/AFM system, which result in cleavage of one C-H bond at each of the pentagonal apices of 6, thereby leading to the generation of 5 (Fig  ) 
In the main text, we focus on the generation and characterization of 5 on insulating surfaces  Generation and characterization of 5 on coinage metal surfaces is shown in Supplementary Fig    )  Blue and orange colors represent spin up and spin down densities, respectively  c, Probability density of the SOMOs of 5OS (isovalue: 0 001 e -Å -3 ) 
d, DFT-calculated bond lengths of 5OS  e, Constant-height I(V) spectra acquired on a species of 5 assigned as 5OS, along with the corresponding dI/dV(V) spectra  Open feedback parameters: V = -2 V, I = 0 17 pA (negative bias side) and V = 2 V, I = 0 17 pA (positive bias side)  Acquisition position of the spectra is shown in Supplementary Fig    f, Scheme of many-body transitions associated to the measured ionic resonances of 5OS 
Also shown are STM images of assigned 5OS at biases where the corresponding transitions become accessible  Scanning parameters: I = 0 3 pA (V = -1 2 V and -1 5 V) and 0 2 pA (V = 1 3 V and 1 6 V)  g, Laplace-filtered AFM image of assigned 5OS  STM set point: V = 0 2 V, I = 0 5 pA on bilayer NaCl, Δz = -0 3
Å  The tip-height offset Δz for each panel is provided with respect to the STM setpoint, and positive (negative) values of Δz denote tip approach (retraction) from the STM setpoint  f and g show the same molecule at the same adsorption site, which is next to a trilayer NaCl island  The bright and dark features in the trilayer NaCl island in g correspond to Cl -and Na + ions, respectively 
Scale bars: 10 Å (f) and 5 Å (g)  To experimentally explore the electronic structure of 5, we used bilayer NaCl films on coinage metal surfaces to electronically decouple the molecule from the metal surfaces  Before presenting the experimental findings, we summarize the results of our theoretical calculations performed on 5 in the neutral charge state (denoted as 5 0 ) 
We start by performing DFT calculations on 5 0 in the gas phase  Geometry optimization performed at the spin-unrestricted UB3LYP/6-31G level of theory leads to one local minimum, 5OS, the geometry of which corresponds to the open-shell resonance structure of 5 (Fig  , the label OS denotes open-shell) 
The triplet electronic configuration of 5OS is the lowest-energy state, with the openshell singlet configuration 90 meV higher in energy  Geometry optimization performed at the restricted closed-shell RB3LYP/6-31G level reveals two local minima, 5para and 5ortho, the geometries of which (Fig  ) exhibit bond length alternations in line with the presence of a para-or an ortho-QDM moiety, respectively, in the as-indacene core of the closed-shell resonance structures of 5 (Fig  )  
Relative to 5OS in the triplet configuration, 5para and 5ortho are 0 40 and 0 43 eV higher in energy, respectively  Additional DFT results are shown in Supplementary Fig    To gain more accurate insights into the theoretical electronic structure of 5, we performed multireference perturbation theory calculations (Supplementary Fig  ) based on quasi-degenerate second-order n-electron valence state perturbation theory (QD-NEVPT2) 
In so far as the order of the ground and excited states are concerned, the results of QD-NEVPT2 calculations qualitatively match with DFT calculations  For 5OS, the triplet configuration remains the lowest-energy state, with the open-shell singlet configuration 60 meV higher in energy  The energy differences between the open-and closed-shell states are substantially reduced in QD-NEVPT2 calculations, with 5para and 5ortho only 0 11 and 0 21 eV higher in energy, respectively, compared to 5OS in the triplet configuration 
We also performed nucleus-independent chemical shift calculations to probe local aromaticity of 5 in the openand closed-shell states  While 5OS in the triplet configuration exhibits local aromaticity at the terminal benzenoid rings, 5OS in the open-shell singlet configuration, 5para and 5ortho all display antiaromaticity (Supplementary Fig  ) 
The choice of the insulating surface determines the charge state of 5: while 5 adopts neutral charge state on the high work function bilayer NaCl/Au(111) surface (irrespective of its openor closed-shell state, Supplementary Fig  ), 5 exhibits charge bistability between 5 0 and the anionic state 5 -1 on the lower work function bilayer NaCl/Ag(111) and Cu(111) surfaces (Supplementary Figs  ) 
In the main text, we focus on the characterization of 5 on bilayer NaCl/Au(111)  Characterization of charge bistable 5 is reported in Supplementary Figs    We first describe experiments on 5 on bilayer NaCl/Au(111), where 5 exhibits a geometry corresponding to the calculated 5OS geometry, and an open-shell electronic configuration 
We compare the experimental data on this species to calculations on 5OS with a triplet configuration, as theory predicts a triplet ground state for 5OS  For 5OS, the calculated frontier orbitals correspond to the SOMOs ψ1 and ψ2 (Fig  ), whose spin up levels are occupied and the spin down levels are empty 
Figure shows the DFT-calculated bond lengths of 5OS, where the two salient features, namely, the small difference in the bond lengths within each ring and the notably longer bond lengths in the pentagonal rings, agree with the open-shell resonance structure of 5 (Fig  )  Figure shows an AFM image of 5 adsorbed on bilayer NaCl/Au(111) that we assign as 5OS, where the bond-order differences qualitatively correspond to the calculated 5OS geometry (discussed and compared to the closed-shell state below) 
Differential conductance spectra (dI/dV(V), where I and V denote the tunneling current and bias voltage, respectively) acquired on assigned 5OS exhibit two peaks centered at -1 5 V and 1 6 V (Fig  ), which we assign to the positive and negative ion resonances (PIR and NIR), respectively  Figure shows the corresponding STM images acquired at the onset (V = -1 2
V/1 3 V) and the peak (V = -1 5 V/1 6 V) of the ionic resonances  To draw a correspondence between the STM images and the molecular orbital densities, we consider tunneling events as many-body electronic transitions between different charge states of 5OS (Fig  )  Within this framework, the PIR corresponds to transitions between 5 0 and the cationic state 5  
At the onset of the PIR at -1 2 V, an electron can only be detached from the SOMO ψ1 and the corresponding STM image at -1 2 V shows the orbital density of ψ1  Increasing the bias to the peak of the PIR at -1 5 V, it becomes possible to also empty the SOMO ψ2, such that the corresponding STM image shows the superposition of ψ1 and ψ2, that is, |ψ1| 2 + |ψ2| 2 (ref 
)  Similarly, the NIR corresponds to transitions between 5 0 and 5 -1   At the NIR onset of 1 3 V, only electron attachment to ψ2 is energetically possible  At 1 6 V, electron attachment to ψ1 also becomes possible, and the corresponding STM image shows the superposition of ψ1 and ψ2  The observation of the orbital densities of SOMOs, and not the hybridized HOMO and LUMO, proves the open-shell ground state of assigned 5OS 
Measurements of the monoradical species with a doublet ground state are shown in Supplementary Fig    Unexpectedly, another species of 5 was also experimentally observed that exhibited a closedshell ground state  In contrast to 5OS, where the frontier orbitals correspond to the SOMOs ψ1 and ψ2, DFT calculations predict orbitals of different shapes and symmetries for 5para and 5ortho, denoted as α and β and shown in Fig   
For 5ortho, α and β correspond to HOMO and LUMO, respectively  The orbitals are inverted in energy and occupation for 5para, where β is the HOMO and α is the LUMO  Fig  shows an AFM image of 5 that we assign as 5para  We experimentally infer its closed-shell state first by using qualitative bond order discrimination by AFM 
In high-resolution AFM imaging, chemical bonds with higher bond order are imaged brighter (that is, with higher frequency shift Δf) due to stronger repulsive forces, and they appear shorter   In Fig  , we label seven bonds whose bond orders show significant qualitative differences in the calculated 5ortho, 5para (Fig  ) and 5OS (Fig  ) geometries 
In 5para, the bonds b and d exhibit a higher bond order than a and c, respectively  This pattern is reversed for 5ortho, while the bond orders of the bonds a-d are all similar and small for 5OS  Furthermore, in 5para bond f exhibits a higher bond order than e, while in 5ortho and 5OS bonds e and f exhibit similar bond order (because they belong to Clar sextets) 
Finally, the bond labeled g shows a higher bond order in 5para than in 5ortho and 5OS  The AFM image of assigned 5para shown in Fig  indicates higher bond orders of the bonds b, d and f compared to a, c and e, respectively  In addition, the bond g appears almost point-like and with enhanced Δf contrast compared to its neighboring bonds, indicative of a high bond order (see Supplementary Fig  for height-dependent measurements) 
These observations concur with the calculated 5para geometry (Fig  )  Importantly, all these distinguishing bond-order differences are distinctly different in the AFM image of 5OS shown in Fig  , which is consistent with the calculated 5OS geometry (Fig  )  In the AFM images of 5OS (Fig  and Supplementary Fig  ), the bonds a-d at the pentagon apices appear with similar contrast and apparent bond length 
The bonds e and f at one of the terminal benzenoid rings also exhibit similar contrast and apparent bond length, while the central bond g appears longer compared to assigned 5para  Further compelling evidence for the closed-shell state of assigned 5para is obtained by STM and STS  dI/dV(V) spectra acquired on an assigned 5para species exhibit two peaks centered at -1 4 V (PIR) and 1 6 V (NIR) (Fig  ) 
STM images acquired at these biases (Fig  ) show the orbital densities of β (-1 4 V) and α (1 6 V)  First, the observation of α and β as the frontier orbitals of this species, and not the SOMOs, strongly indicates its closed-shell state  Second, consistent with AFM measurements that indicate good correspondence to the calculated 5para geometry, we observe β as the HOMO and α as the LUMO 
For 5ortho, α should be observed as the HOMO and β as the LUMO  We did not observe molecules with the signatures of 5ortho in our experiments  We observed molecules in open-(5OS, Fig  ) and closed-shell (5para, Fig  ) states in similar occurrence after their generation from 6 on the surface  We could also switch individual molecules between open-and closed-shell states as shown in Fig  and Supplementary Fig   
To this end, a change in the adsorption site of a molecule was induced by STM imaging at ionic resonances, which often resulted in movement of the molecule  The example presented in Fig  shows a molecule that was switched from 5para to 5OS and back to 5para  The switching is not directed, that is, we cannot choose which of the two species will be formed when changing the adsorption site, and we observed 5OS and 5para in approximately equal yields upon changing the adsorption site 
The molecule in Fig  is adsorbed on top of a defect that stabilizes its adsorption geometry on bilayer NaCl  At defect-free adsorption sites on bilayer NaCl, that is, without a third layer NaCl island or atomic defects in the vicinity of the molecule, 5 could be stably imaged neither by AFM nor by STM at ionic resonances (Supplementary Fig  ) 
Without changing the adsorption site, the state of 5 (open-or closedshell) never changed, including the experiments on bilayer NaCl/Ag(111) and Cu(111), on which the charge state of 5 could be switched (Supplementary Figs  )  Also on these lower work function surfaces, both open-and closed-shell species were observed for 5 0 and both showed charge bistability between 5 0 (5OS or 5para) and 5 -1 (Supplementary Figs  ) 
The geometrical structure of 5 -1 probed by AFM, and its electronic structure probed by STM imaging at the NIR (corresponding to transitions between 5 -1 and the dianionic state 5 -2 ), are identical within the measurement accuracy for the charged species of both 5OS and 5para  When cycling the charge state of 5 between 5 0 and 5 -1 several times, we always observed the same state (5OS or 5para) when returning to 5 0 , provided the molecule did not move during the charging/discharging process 
Based on our experimental observations we conclude that indeno[1,2-a]fluorene (5), the last unknown indenofluorene isomer, can be stabilized in and switched between an open-shell (5OS) and a closed-shell (5para) state on NaCl  For the former, both DFT and QD-NEVPT2 calculations predict a triplet electronic configuration 
Therefore, 5 can be considered to exhibit the spin-crossover effect, involving magnetic switching between high-spin (5OS) and low-spin (5para) states, coupled with a reversible structural transformation  So far, the spin-crossover effect has mainly only been observed in transition-metal-based coordination compounds with a near-octahedral geometry  
The observation that the switching between open-and closedshell states is related to changes in the adsorption site but is not achieved by charge-state cycling alone, indicates that the NaCl surface and local defects facilitate different electronic configurations of 5 depending on the adsorption site 
Gas-phase QD-NEVPT2 calculations predict that 5OS is the ground state, and the closed-shell 5para and 5ortho states are 0 11 and 0 21 eV higher in energy  The experiments, showing bidirectional switching between 5OS and 5para, indicate that a change in the adsorption site can induce sufficient change in the geometry of 5 (leading to a corresponding change in the ground state electronic configuration) and thus induce switching 
Switching between open-and closed-shell states in 5 does not require the breaking or formation of covalent bonds , but a change of adsorption site on NaCl where the molecule is physisorbed  Our results should have implications for single-molecule devices, capitalizing on the altered electronic and chemical properties of a system in π-diradical open-shell and closed-shell states such as frontier orbital and singlet-triplet gaps, and chemical reactivity 
For possible future applications as a single-molecule switch, it might be possible to also switch between open-and closed-shell states by changing the local electric field, such as by using chargeable adsorbates   Scanning probe microscopy measurements and sample preparation  STM and AFM measurements were performed in a home-built system operating at base pressures below 1×10 -10 mbar and a base temperature of 5 K  Bias voltages are provided with respect to the sample 
All STM, AFM and spectroscopy measurements were performed with carbon monoxide (CO) functionalized tips  AFM measurements were performed in non-contact mode with a qPlus sensor   The sensor was operated in frequency modulation mode with a constant oscillation amplitude of 0 5 Å  STM measurements were performed in constantcurrent mode, AFM measurements were performed in constant-height mode with V = 0 V, and I(V) and Δf(V) spectra were acquired in constant-height mode 
Positive (negative) values of the tip-height offset Δz represent tip approach (retraction) from the STM setpoint  All dI/dV(V) spectra are obtained by numerical differentiation of the corresponding I(V) spectra  STM and AFM images, and spectroscopy curves, were post-processed using Gaussian low-pass filters 
Au(111), Ag(111) and Cu(111) surfaces were cleaned by iterative cycles of sputtering with Ne + ions and annealing up to 800 K  NaCl was thermally evaporated on Au(111), Ag(111) and Cu(111) surfaces held at 323 K, 303 K and 283 K, respectively  This protocol results in the growth of predominantly bilayer (100)-terminated islands, with a minority of trilayer islands 
Sub-monolayer coverage of 6 on surfaces was obtained by flashing an oxidized silicon wafer containing the precursor molecules in front of the cold sample in the microscope  CO molecules for tip functionalization were dosed from the gas phase on the cold sample  Density functional theory calculations  DFT was employed using the PSI4 program package  
All molecules with different charge (neutral and anionic) and electronic (open-and closed-shell) states were independently investigated in the gas phase  The B3LYP exchangecorrelation functional with 6-31G basis set was employed for structural relaxation and singlepoint energy calculations  The convergence criteria were set to 10 −4 eV Å −1 for the total forces and 10 −6 eV for the total energies 
Multireference calculations  Multireference calculations were performed on the DFToptimized geometries using the QD-NEVPT2 level of theory , with three singlet roots and one triplet root included in the state-averaged calculation  A (10,10) active space (that is, 10 electrons in 10 orbitals) was used along with the def2-TZVP basis set  
Increasing either the active space size or expanding the basis set resulted in changes of about 50 meV for relative energies of the singlet and triplet states  These calculations were performed using the ORCA program package   Nucleus-independent chemical shift (NICS) calculations  Isotropic nucleus-independent chemical shift values were evaluated at the centre of each ring using the B3LYP exchangecorrelation functional with def2-TZVP basis set using the Gaussian 16 software package  
Starting materials (reagent grade) were purchased from TCI and Sigma-Aldrich and used without further purification  Reactions were carried out in flame-dried glassware and under an inert atmosphere of purified Ar using Schlenk techniques  Thin-layer chromatography (TLC) was performed on Silica Gel 60 F-254 plates (Merck) 
Column chromatography was performed on silica gel (40-60 µm)  Nuclear magnetic resonance (NMR) spectra were recorded on a Bruker Varian Mercury 300 or Bruker Varian Inova 500 spectrometers  Mass spectrometry (MS) data were recorded in a Bruker Micro-TOF spectrometer  The synthesis of compound 6 was developed following the two-step synthetic route shown in Supplementary Fig  , which is based on the preparation of methylene-bridge polyarenes by means of Pd-catalyzed activation of benzylic C-H bonds  
Supplementary Figure | Synthetic route to obtain compound 6  The complex Pd2(dba)3 (20 mg, 0 02 mmol) was added over a deoxygenated mixture of 1,3-dibromo-2,4-dimethylbenzene (9, 100 mg, 0 38 mmol), boronic acid 10 (178 mg, 1 14 mmol), K2CO3 (314 mg, 2 28 mmol) and XPhos (35 mg, 0 08 mmol) in toluene (1:1, 10 mL), and the resulting mixture was heated at 90 °C for 2 h 
After cooling to room temperature, the solvents were evaporated under reduced pressure  The reaction crude was purified by column chromatography (SiO2; hexane:CH2Cl2 9:1) affording 11 (94 mg, 76%) as a colorless oil  The complex Pd(OAc)2 (7 mg, 0 03 mmol) was added over a deoxygenated mixture of terphenyl 11 (90 mg, 0 27 mmol), K2CO3 (114 mg, 0 83 mmol) and ligand L (26 mg, 0 06 mmol) in NMP (2 mL) 
The resulting mixture was heated at 160 °C for 4 h  After cooling to room temperature, H2O (30 mL) was added, and the mixture was extracted with EtOAc (3x15 mL)  The combined organic extracts were dried over anhydrous Na2SO4, filtered, and evaporated under reduced pressure  The reaction crude was purified by column chromatography (SiO2; hexane:CH2Cl2 9:1) affording compound 6 (8 mg, 11%) as a white solid  in AFM imaging due to their reduced adsorption height compared to the rest of the carbon atoms 
We attribute this observation to the significantly different lattice parameter of Cu(111) (2 57 Å) compared to Au(111) and Ag(111) (2 95 Å and 2 94 Å, respectively) , such that the apical carbon atoms of the pentagonal rings of 5 adsorb on the on-top atomic sites on Au(111) and Ag(111), but not on Cu(111) 
Our speculation is based on a previous study of polymers of 1 on Au(111) by Di Giovannantonio et al  , where both tilted and planar individual units of 1 were observed depending on whether the apical carbon atoms of the pentagonal rings in 1 adsorbed on the on-top or hollow sites of the surface, respectively 
Given the strong molecule-metal interaction, we found no electronic state signatures of 5 on all three metal surfaces  STM set point for AFM images: V = 0  e, Frontier orbital spectrum of 5 -1   In the anionic state, ψ2 becomes doubly occupied and ψ1 is the SOMO  Filled and empty circles denote occupied and empty orbitals, respectively 
For each panel, zero of the energy axis has been aligned to the respective highest-energy occupied orbital 
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 ${\partial \mathcal{L}_i}/\partial J_{ij}$



ground_truth: Open-shell π-diradical state and closed-shell state with a para-quinodimethane moiety.

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

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

Read the following text and answer briefly.

Context 2:  The process is repeated for all the couplings obtaining then a fully connected adjacency matrix  The results here presented are obtained with $\lambda = 0 01$ 
   For the minimization we have used the MATLAB routine \emph{minFunc\_2012}\cite{min_func}  
      
      \begin{figure}[t!]
    	\centering
    	\includegraphics[width=1\linewidth]{Jor11_2D_l2_JR_soJR_TPJR}
    	\caption{Top panels: instances of single site coupling reconstruction for the case of $N=64$ XY spins on a 2D lattice with ordered $J$ (left column) and bimodal distributed $J$ (right column)  
    	
    	Bottom panels: sorted couplings }
    	\label{PL-Jor1}
    \end{figure}

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

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

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

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

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

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

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

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

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

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

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







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



 
 

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


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

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

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

 	



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

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

Question: How many massive star-forming regions were studied?

Read the following text and answer briefly.

Context 3: \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)  }






ground_truth: 21.