arXiv subjects

Leo Liberti

Publications and source records attributed to Leo Liberti.

At least 19 recordsLinked to original sources

arXiv2026

A computational comparison of handling distance constraints in MINLP

Minimum distance constraints (minDCs) appear in many geometric optimization problems. They pose major challenges for mixed-integer nonlinear programming (MINLP) due to their reverse-convexity. We develop new algorithms for tightening variable bounds in general MINLPs with minDCs. Because many such problems exhibit substantial symmetry, we further discuss an approach for handling rotation symmetries. In a computational study, we examine the performance of the various methods and determine the scenarios in which each approach demonstrates superiority.

math.OC↗

arXiv2026

Hardness of some optimization problems over correlation polyhedra

We prove the \textbf{NP}-hardness, using Karp reductions, of some problems related to the correlation polytope and its corresponding cone, spanned by all of the $n\times n$ rank-one matrices over $\{0,1\}$. The problems are: membership, rank of the decomposition, and a ``relaxed rank'' obtained from relaxing the zero-norm expression for the rank to an $\ell_1$ norm. While membership and rank are natural problems for any matrix cone, the relaxed rank problem occurs in some signal processing and statistical applications.

math.OC↗

arXiv2025

A hybrid combinatorial-continuous strategy for solving molecular distance geometry problems

The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact combinatorial formulation that enables efficient exploration of the search space. However, in practical settings such as Nuclear Magnetic Resonance (NMR) spectroscopy, distances are available only within uncertainty bounds, leading to the interval variant (\emph{i}DMDGP). We propose a hybrid combinatorial--continuous framework for solving the \emph{i}DMDGP. The method combines an enumeration process derived from the DMDGP with a continuous refinement stage that minimizes a nonconvex stress function that penalizes deviations from admissible distance intervals. This integration supports a systematic exploration guided by discrete structure and local optimization. The formulation incorporates torsion-angle intervals and chirality constraints through a refined atom ordering that preserves protein-backbone geometry. Numerical experiments show that the approach efficiently reconstructs geometrically valid conformations even under wide distance bounds, whereas most existing studies assume narrow ones.

math.OC↗

arXiv2025

On Saxe's theorems about the complexity of the Distance Geometry Problem

In 1979, James B.~Saxe published an extended summary on the complexity of the Distance Geometry Problem in the proceedings of the 17th Allerton Conference. Many of the proofs in his paper are sketches, and even the whole proofs do not have all the details. In this paper we provide a commentary to Saxe's results and hopefully more understandable versions thereof.

cs.CC↗

arXiv2025

Mathematics with large language models as provers and verifiers

During 2024 and 2025 the discussion about the theorem-proving capabilities of large language models started reporting interesting success stories, mostly to do with difficult exercises (such as problems from the International Mathematical Olympiad), but also with conjectures [Feldman & Karbasi, arXiv:2509.18383v1] formulated for the purpose of verifying whether the artificial intelligence could prove it. In this paper we report a theorem proving feat achieved by ChatGPT by using a protocol involving different prover and verifier instances of the gpt-5 model working collaboratively. To make sure that the produced proofs do not suffer from hallucinations, the final proof is formally verified by the lean proof assistant, and the conformance of premises and conclusion of the lean code is verified by a human. Our methodology is by no means complete or exact. It was nonetheless able to solve five out of six 2025 IMO problems, and close about a third of the sixty-six number theory conjectures in [Cohen, Journal of Integer Sequences, 2025].

cs.CL↗

arXiv2025

An Angle-Based Algorithmic Framework for the Interval Discretizable Distance Geometry Problem

Distance Geometry plays a central role in determining protein structures from Nuclear Magnetic Resonance (NMR) data, a task known as the Molecular Distance Geometry Problem (MDGP). A subclass of this problem, the Discretizable Distance Geometry Problem (DDGP), allows a recursive solution via the combinatorial Branch-and-Prune (BP) algorithm by exploiting specific vertex orderings in protein backbones. To accommodate the inherent uncertainty in NMR data, the interval Branch-and-Prune (\textit{i}BP) algorithm was introduced, incorporating interval distance constraints through uniform sampling. In this work, we propose two new algorithmic frameworks for solving the three-dimensional interval DDGP (\textit{i}DDGP): the interval Angular Branch-and-Prune (\textit{i}ABP), and its extension, the interval Torsion-angle Branch-and-Prune (\textit{i}TBP). These methods convert interval distances into angular constraints, enabling structured sampling over circular arcs. The \textit{i}ABP method guarantees feasibility by construction and removes the need for explicit constraint checking. The \textit{i}TBP algorithm further incorporates known torsion angle intervals, enforcing local chirality and planarity conditions critical for protein geometry. We present formal mathematical foundations for both methods and a systematic strategy for generating biologically meaningful \textit{i}DDGP instances from the Protein Data Bank (PDB) structures. Computational experiments demonstrate that both \textit{i}ABP and \textit{i}TBP consistently outperform \textit{i}BP in terms of solution rate and computational efficiency. In particular, \textit{i}TBP yields solutions with lower RMSD variance relative to the original PDB structures, better reflecting biologically plausible conformations.

q-bio.BM↗

arXiv2024

Distance geometry with and without the graph

We survey theoretical, algorithmic, and computational results at the intersection of distance geometry problems and mathematical programming, both with and without adjacencies as part of the input. While mathematical programming methods can solve large-scale distance geometry problems with adjacencies, they are severely challenged in the absence thereof.

math.OC↗

arXiv2024

Unassigned distance geometry and the Buckminsterfullerene

The Buckminsterfullerene is an inorganic molecule consisting of 60 carbon atoms in the shape of a soccer ball. It was used in [Juhas et al., Nature 2006] to showcase algorithms that find the correct shape of a protein from limited data (length of inter-atomic distances) without any further chemical experiment: in that case, by means of a complicated constructive heuristic based on genetic algorithms. In this paper we show that we can reconstruct the Buckminsterfullerene structure by means of mathematical programming, standard solver software, and little else.

math.OC↗

arXiv2024

Relaxations for binary polynomial optimization via signed certificates

We consider the problem of minimizing a polynomial $f$ over the (binary) hypercube. We show that, for a specific set of polynomials, their binary non-negativity (i.e. on the hypercube) can be checked in polynomial time via minimum cut algorithms, from which we construct a linear programming representation for this set of polynomials. We categorize binary polynomials according to their signed support patterns and develop parameterized linear programming representations for binary non-negative polynomials. This allows the construction of signed certificates of binary non-negativity with adjustable signed support patterns and representation complexities; and we propose a method for minimizing $f$ by decomposing it as a sum of signed certificates. This method yields new hierarchies of linear programming relaxations for binary polynomial optimization. Moreover, since our decomposition depends only on the support of $f$, the new hierarchies are sparsity-preserving.

math.OC↗

arXiv2024

The Algorithm Configuration Problem

The field of algorithmic optimization has significantly advanced with the development of methods for the automatic configuration of algorithmic parameters. This article delves into the Algorithm Configuration Problem, focused on optimizing parametrized algorithms for solving specific instances of decision/optimization problems. We present a comprehensive framework that not only formalizes the Algorithm Configuration Problem, but also outlines different approaches for its resolution, leveraging machine learning models and heuristic strategies. The article categorizes existing methodologies into per-instance and per-problem approaches, distinguishing between offline and online strategies for model construction and deployment. By synthesizing these approaches, we aim to provide a clear pathway for both understanding and addressing the complexities inherent in algorithm configuration.

cs.AI↗

arXiv2024

Learning to Configure Mathematical Programming Solvers by Mathematical Programming

We discuss the issue of finding a good mathematical programming solver configuration for a particular instance of a given problem, and we propose a two-phase approach to solve it. In the first phase we learn the relationships between the instance, the configuration and the performance of the configured solver on the given instance. A specific difficulty of learning a good solver configuration is that parameter settings may not all be independent; this requires enforcing (hard) constraints, something that many widely used supervised learning methods cannot natively achieve. We tackle this issue in the second phase of our approach, where we use the learnt information to construct and solve an optimization problem having an explicit representation of the dependency/consistency constraints on the configuration parameter settings. We discuss computational results for two different instantiations of this approach on a unit commitment problem arising in the short-term planning of hydro valleys. We use logistic regression as the supervised learning methodology and consider CPLEX as the solver of interest.

math.OC↗

arXiv2024

A learning-based mathematical programming formulation for the automatic configuration of optimization solvers

We propose a methodology, based on machine learning and optimization, for selecting a solver configuration for a given instance. First, we employ a set of solved instances and configurations in order to learn a performance function of the solver. Secondly, we formulate a mixed-integer nonlinear program where the objective/constraints explicitly encode the learnt information, and which we solve, upon the arrival of an unknown instance, to find the best solver configuration for that instance, based on the performance function. The main novelty of our approach lies in the fact that the configuration set search problem is formulated as a mathematical program, which allows us to a) enforce hard dependence and compatibility constraints on the configurations, and b) solve it efficiently with off-the-shelf optimization tools.

math.OC↗

arXiv2023

Cycle-based formulations in Distance Geometry

The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension K, where the edges are realized as straight segments of lengths equal (or as close as possible) to the edge weights. The problem is often modelled as a mathematical programming formulation involving decision variables that determine the position of the vertices in the given Euclidean space. Solution algorithms are generally constructed using local or global nonlinear optimization techniques. We present a new modelling technique for this problem where, instead of deciding vertex positions, formulations decide the length of the segments representing the edges in each cycle in the graph, projected in every dimension. We propose an exact formulation and a relaxation based on a Eulerian cycle. We then compare computational results from protein conformation instances obtained with stochastic global optimization techniques on the new cycle-based formulation and on the existing edge-based formulation. While edge-based formulations take less time to reach termination, cycle-based formulations are generally better on solution quality measures.

math.OC↗

arXiv2023

Submodular maximization and its generalization through an intersection cut lens

We study a mixed-integer set $S:=\{(x,t) \in \{0,1\}^n \times \mathbb{R}: f(x) \ge t\}$ arising in the submodular maximization problem, where $f$ is a submodular function defined over $\{0,1\}^n$. We use intersection cuts to tighten a polyhedral outer approximation of $S$. We construct a continuous extension $F$ of $f$, which is convex and defined over the entire space $\mathbb{R}^n$. We show that the epigraph of $F$ is an $S$-free set, and characterize maximal $S$-free sets including the epigraph. We propose a hybrid discrete Newton algorithm to compute an intersection cut efficiently and exactly. Our results are generalized to the hypograph or the superlevel set of a submodular-supermodular function, which is a model for discrete nonconvexity. A consequence of these results is intersection cuts for Boolean multilinear constraints. We evaluate our techniques on max cut, pseudo Boolean maximization, and Bayesian D-optimal design problems within a MIP solver.

math.OC↗

arXiv2022

Cutting planes for signomial programming

Cutting planes are of crucial importance when solving nonconvex nonlinear programs to global optimality, for example using the spatial branch-and-bound algorithms. In this paper, we discuss the generation of cutting planes for signomial programming. Many global optimization algorithms lift signomial programs into an extended formulation such that these algorithms can construct relaxations of the signomial program by outer approximations of the lifted set encoding nonconvex signomial term sets, i.e., hypographs, or epigraphs of signomial terms. We show that any signomial term set can be transformed into the subset of the difference of two concave power functions, from which we derive two kinds of valid linear inequalities. Intersection cuts are constructed using signomial term-free sets which do not contain any point of the signomial term set in their interior. We show that these signomial term-free sets are maximal in the nonnegative orthant, and use them to derive intersection sets. We then convexify a concave power function in the reformulation of the signomial term set, resulting in a convex set containing the signomial term set. This convex outer approximation is constructed in an extended space, and we separate a class of valid linear inequalities by projection from this approximation. We implement the valid inequalities in a global optimization solver and test them on MINLPLib instances. Our results show that both types of valid inequalities provide comparable reductions in running time, number of search nodes, and duality gap.

math.OC↗

arXiv2022

Decoding noisy messages: a method that just shouldn't work

This paper is about receiving text messages through a noisy and costly line. Because the line is noisy we need redundancy, but because it is costly we can afford very little of it. I start by using well-known machinery for decoding noisy messages (compressed sensing), then I attempt to reduce the redundancy (using random projections), until I get to a point where I use more orthogonal vectors than the space dimension allows. Instead of grinding to a halt or spurting out noise, this method is still able to decode messages correctly or almost correctly. I have no idea why the method works: this is my first reason for writing this paper using a narrative instead of formal scientific style (the second one is that I am tired of writing semi-formal prose, and long for a change).

math.OC↗

arXiv2021

An impossible utopia in distance geometry

The Distance Geometry Problem asks for a realization of a given weighted graph in $\mathbb{R}^K$. Two variants of this problem, both originating from protein conformation, are based on a given vertex order (which abstracts the protein backbone). Both variants involve an element of discrete decision in the realization of the next vertex in the order using $K$ preceding (already realized) vertices. The difference between these variants is that one requires the $K$ preceding vertices to be contiguous. The presence of this constraint allows one to prove, via a combinatorial counting of the number of solutions, that the realization algorithm is fixed-parameter tractable. Its absence, on the other hand, makes it possible to efficiently construct the vertex order directly from the graph. Deriving a combinatorial counting method without using the contiguity requirement would therefore be desirable. In this paper we prove that, unfortunately, such a counting method cannot be devised in general.

cs.CG↗

arXiv2021

Random projections for conic programs

We discuss the application of random projections to conic programming: notably linear, second-order and semidefinite programs. We prove general approximation results on feasibility and optimality using the framework of formally real Jordan algebras. We then discuss some computational experiments on randomly generated semidefinite programs in order to illustrate the practical applicability of our ideas

math.OC↗