Problem 17
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Identifiability and convexification of a band-limited unassigned distance-geometry problem
Let \(X=(x_1,\dots,x_N)\in(\mathbb{R}^3)^N\) carry labels \(e_i\in E\) and weights \(b_i>0\). Quotient by rigid motions (translations and rotations, but not reflections):
\[ \mathcal{X}=(\mathbb{R}^3)^N/E(3). \]
The weighted pair-distance measure and its measurement are
\[ \rho_X=\sum_{i\lt j} w_{ij}\,\delta_{\|x_i-x_j\|},\quad w_{ij}=b_i b_j\ge 0, \qquad F(X)=R_{Q_{\max},\sigma}\,\rho_X\in Y, \]
where \(R_{Q_{\max},\sigma}\) is a known compact smoothing operator: a band-limit \(Q_{\max}\) (real-space resolution \(\Delta r\approx\pi/Q_{\max}\)) followed by convolution of width \(\sigma>0\). Its information capacity
\[ m_{\mathrm{eff}}(Q_{\max},\sigma) =\dim\operatorname{span}\{R_{Q_{\max},\sigma}\delta_t:t\in[0,R_{\max}]\} \approx\lceil R_{\max}/\Delta r\rceil \]
is finite, with \(m_{\mathrm{eff}}\to\infty\) as \(Q_{\max}\to\infty\) (exact-distance limit) and \(m_{\mathrm{eff}}\to 0\) as \(Q_{\max}\to 0\), and
\[ \operatorname{rank}(DF_X)\le\min(d_C,m_{\mathrm{eff}}). \]
A prior is a closed \(C\subset\mathcal{X}\), a smooth manifold of dimension \(d_C\) realizable in internal coordinates (a graph of fixed edge lengths and angles with \(d_C\) free dihedrals). \(F\) is an instance of the unassigned distance geometry problem (Billinge et al. 2018); in the motivating application \(C\) encodes chemical constraints, which play no formal role below.
Known facts
- For \(R=\mathrm{id}\), injectivity of \(\rho\) up to rigid motion is the global-rigidity problem; in 3D generic global rigidity requires redundant rigidity and stressability and is subtler than edge-counting, and special configurations are generically not globally rigid (flip ambiguities persist).
- In 1D (turnpike/beltway) with unassigned noisy distances, projected gradient descent with a spectral initializer converges locally linearly to the global optimizer under explicit conditions (Huang and Dokmanic 2021); for integer sets, sparsity yields polynomial-time recovery up to shift and reversal with high probability (Jaganathan and Hassibi 2012).
- A configuration and its mirror image have identical \(F(X)\), so identifiability holds at best modulo \(\mathbb{Z}_2\) (fiber \(K\ge2\) for chiral configurations).
Open problem
For \(y=F(X_\star)\) and \(\mathcal{L}_y(X)=\|F(X)-y\|_Y^2|_C\):
- (P1) Identifiability: \(F|_C\) injective modulo reflection (fibers of size \(1\), or \(2\) = the mirror pair).
- (P2) Local identifiability: the Fisher operator \(I_X=(DF_X)^{*}(DF_X)\) has full rank on \(T_XC\) for all \(X\in C\).
- (P3) \(\varepsilon\)-convexity: \(\mathcal{L}_y|_C\) is geodesically \(\varepsilon\)-convex on the component of \(X_\star\) with a unique stationary point (no spurious local minima).
Problem. Characterize the priors \(C\), as a function of \(m_{\mathrm{eff}}\), for which \(\text{(P1)}\Leftrightarrow\text{(P2)}\Leftrightarrow\text{(P3)}\) hold for generic \(X_\star\in C\), and find the minimal such prior. In particular:
- Prove or disprove a sharp threshold at \(m_{\mathrm{eff}}=d_C\) (modulo reflection), with counterexamples at \(m_{\mathrm{eff}}=d_C-1\).
- Find the maximal admissible \(d_C\) (least external information) and the trade-off curve \(d_C^{\,*}(Q_{\max})\).
- Show the threshold coincides with vanishing of \(I_{\mathrm{deficit}}=h(X\mid C)-I(F(X);X\mid C)\) (up to \(\log 2\)).
This is generic-global-rigidity theory for band-limited, weighted, soft data on a constraint manifold - the regime open at the intersection of Huang and Dokmanic (2021), Jaganathan and Hassibi (2012), and Billinge et al. (2018).
Remark. For more details on the chemical side of the problem, see the project repository: grebenyyk/pdf-convexification.
References
S. Huang and I. Dokmanic, Reconstructing Point Sets from Distance Distributions, IEEE Transactions on Signal Processing, 69 (2021), 1811-1827. arXiv:1804.02465.
K. Jaganathan and B. Hassibi, Reconstruction of Integers from Pairwise Distances, arXiv:1212.2386 (2012).
S. J. L. Billinge, P. M. Duxbury, D. S. Goncalves, C. Lavor, and A. Mucherino, Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures, Annals of Operations Research, 271(1) (2018), 161-203. doi:10.1007/s10479-018-2989-6.
S. J. L. Billinge and M. G. Kanatzidis, Beyond crystallography: the study of disorder, nanocrystallinity and crystallographically challenged materials with pair distribution functions, Chemical Communications (2004), 749-760. doi:10.1039/b311073n.
Source: Dimitry Grebenyuk.
LaTeX source
\section*{Identifiability and Convexification of a Band-Limited Unassigned Distance-Geometry Problem}
Let \(X=(x_1,\dots,x_N)\in(\mathbb{R}^3)^N\) carry labels \(e_i\in E\) and weights
\(b_i>0\). Quotient by rigid motions (translations and rotations, but
\emph{not} reflections):
\[
\mathcal{X}=(\mathbb{R}^3)^N/E(3).
\]
The weighted pair-distance measure and its measurement are
\[
\rho_X=\sum_{i\lt j} w_{ij}\,\delta_{\|x_i-x_j\|},\quad w_{ij}=b_i b_j\ge 0,
\qquad
F(X)=R_{Q_{\max},\sigma}\,\rho_X\in Y,
\]
where \(R_{Q_{\max},\sigma}\) is a known compact smoothing operator: a
band-limit \(Q_{\max}\) (real-space resolution \(\Delta r\approx\pi/Q_{\max}\))
followed by convolution of width \(\sigma>0\). Its \emph{information capacity}
\[
m_{\mathrm{eff}}(Q_{\max},\sigma)
=\dim\operatorname{span}\{R_{Q_{\max},\sigma}\delta_t:t\in[0,R_{\max}]\}
\approx\lceil R_{\max}/\Delta r\rceil
\]
is finite, with \(m_{\mathrm{eff}}\to\infty\) as \(Q_{\max}\to\infty\)
(exact-distance limit) and \(m_{\mathrm{eff}}\to 0\) as \(Q_{\max}\to 0\), and
\[
\operatorname{rank}(DF_X)\le\min(d_C,m_{\mathrm{eff}}).
\]
A \emph{prior} is a closed \(C\subset\mathcal{X}\), a smooth manifold of
dimension \(d_C\) realizable in internal coordinates (a graph of fixed edge
lengths and angles with \(d_C\) free dihedrals). \(F\) is an instance of the
unassigned distance geometry problem \cite{Billinge2018}; in the motivating
application \(C\) encodes chemical constraints, which play no formal role below.
\paragraph{Known facts.}
\begin{enumerate}
\item For \(R=\mathrm{id}\), injectivity of \(\rho\) up to rigid motion is the
global-rigidity problem; in \(3\)D generic global rigidity requires redundant
rigidity and stressability and is subtler than edge-counting, and special
configurations are generically \emph{not} globally rigid (flip ambiguities
persist).
\item In \(1\)D (turnpike/beltway) with unassigned noisy distances, projected
gradient descent with a spectral initializer converges locally linearly to the
global optimizer under explicit conditions \cite{HuangDokmanic2021}; for
integer sets, sparsity yields polynomial-time recovery up to shift and reversal
with high probability \cite{JaganathanHassibi2012}.
\item A configuration and its mirror image have identical \(F(X)\), so
identifiability holds at best modulo \(\mathbb{Z}_2\) (fiber \(K\ge2\) for
chiral configurations).
\end{enumerate}
\paragraph{Open problem.}
For \(y=F(X_\star)\) and \(\mathcal{L}_y(X)=\|F(X)-y\|_Y^2|_C\):
\begin{itemize}
\item[\textbf{(P1)}] \emph{Identifiability:} \(F|_C\) injective modulo
reflection (fibers of size \(1\), or \(2\) = the mirror pair).
\item[\textbf{(P2)}] \emph{Local identifiability:} the Fisher operator
\(I_X=(DF_X)^{*}(DF_X)\) has full rank on \(T_XC\) for all \(X\in C\).
\item[\textbf{(P3)}] \emph{\(\varepsilon\)-convexity:} \(\mathcal{L}_y|_C\) is
geodesically \(\varepsilon\)-convex on the component of \(X_\star\) with a
unique stationary point (no spurious local minima).
\end{itemize}
\begin{problem}
Characterize the priors \(C\), as a function of \(m_{\mathrm{eff}}\), for which
\(\text{(P1)}\Leftrightarrow\text{(P2)}\Leftrightarrow\text{(P3)}\) hold for
generic \(X_\star\in C\), and find the \emph{minimal} such prior. In particular:
\begin{enumerate}
\item[\textbf{(a)}] Prove or disprove a sharp threshold at
\(m_{\mathrm{eff}}=d_C\) (modulo reflection), with counterexamples at
\(m_{\mathrm{eff}}=d_C-1\).
\item[\textbf{(b)}] Find the maximal admissible \(d_C\) (least external
information) and the trade-off curve \(d_C^{\,*}(Q_{\max})\).
\item[\textbf{(c)}] Show the threshold coincides with vanishing of
\(I_{\mathrm{deficit}}=h(X\mid C)-I(F(X);X\mid C)\) (up to \(\log 2\)).
\end{enumerate}
\end{problem}
This is generic-global-rigidity theory for band-limited, weighted, soft data
on a constraint manifold - the regime open at the intersection of
\cite{HuangDokmanic2021,JaganathanHassibi2012,Billinge2018}.
\paragraph{Remark.}
For more details on the chemical side of the problem, see
\url{https://github.com/grebenyyk/pdf-convexification}.
\begin{thebibliography}{99}
\bibitem{HuangDokmanic2021} S.~Huang, I.~Dokmanic, \emph{Reconstructing Point
Sets from Distance Distributions}, IEEE Trans.\ Signal Process.\ \textbf{69}
(2021), 1811--1827. arXiv:1804.02465.
\bibitem{JaganathanHassibi2012} K.~Jaganathan, B.~Hassibi, \emph{Reconstruction
of Integers from Pairwise Distances}, arXiv:1212.2386 (2012).
\bibitem{Billinge2018} S.~J.~L.~Billinge, P.~M.~Duxbury, D.~S.~Goncalves,
C.~Lavor, A.~Mucherino, \emph{Recent results on assigned and unassigned
distance geometry with applications to protein molecules and nanostructures},
Ann.\ Oper.\ Res.\ \textbf{271}(1) (2018), 161--203. DOI:10.1007/s10479-018-2989-6.
\bibitem{Billinge2004} S.~J.~L.~Billinge, M.~G.~Kanatzidis, \emph{Beyond
crystallography: the study of disorder, nanocrystallinity and
crystallographically challenged materials with pair distribution functions},
Chem.\ Commun.\ (2004), 749--760. DOI:10.1039/b311073n.
\end{thebibliography}
Added June 23, 2026.