arXiv subjects

Lionel Spinelli

Publications and source records attributed to Lionel Spinelli.

7 recordsLinked to original sources

arXiv2026

On the Promises and Limits of Multi-omics Integration for Deconvolution: The HADACA3 Benchmark

Understanding the cellular composition of complex tissues, such as tumors, is a key challenge in biology and medicine. A common approach, known as deconvolution, aims to estimate the cellular composition from bulk molecular measurements. With the growing availability of multiple types of molecular data, it is often assumed that combining data sources should improve deconvolution performance. Here, we present HADACA3, a community-driven benchmark designed to evaluate this assumption. We conducted a four-day collaborative competition followed by a large-scale computational benchmark, testing more than 250,000 analysis pipelines across nine datasets with matched DNA methylation (DNAm) and RNA profiles, representing a wide range of biological and experimental conditions. Our framework jointly evaluates the impact of preprocessing, feature selection, modeling, and integration strategies. We find that DNAm alone achieves the highest median performance across datasets, making it the most stable and reliable single-modality approach. However, multi-omics integration strategies can regularly achieve higher top performance in specific datasets and pipeline configurations. Among the tested strategies, late integration based on error-weighted averaging provides a strong and reliable baseline, while non-linear early integration methods, such as optimal transport, show promising results on real biological datasets. Overall, our results show that multi-omics integration does not systematically improve average performance over DNAm alone, but can improve best-case performance in specific settings. This highlights a trade-off between robustness and peak performance, and emphasizes the importance of aligning integration strategies with the statistical properties of the data. All data, code, and evaluation tools are publicly available to support reproducible research and future method development.

q-bio.QM↗

arXiv2014

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: Numerical study

The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is shown that when the particles are uniformly distributed throughout the accessible space, the self-diffusion coefficient is always lowered by the considered interparticle interactions, irrespective of their attractive or repulsive character. This fact is also confirmed by a simple model to compute the correction to the Brownian diffusion coefficient due to the interactions among the particles. These interactions are also responsible for the onset of dynamical chaos and an associated chaotic diffusion which still follows an Einstein-Fick like law for the mean square displacement as a function of time. Transitional phenomena are observed for Coulomb-electrostatic (repulsive) and dipole-electrodynamic (attractive) interactions considered both separately and in competition. The outcomes reported in this paper clearly indicate a feasible experimental method to probe the activation of resonant electrodynamic interactions among biomolecules.

physics.bio-ph↗

arXiv2006

Topology and Phase Transitions I. Preliminary Results

In this first paper, we demonstrate a theorem that establishes a first step toward proving a necessary topological condition for the occurrence of first or second order phase transitions: we prove that the topology of certain submanifolds of configuration space must necessarily change at the phase transition point. The theorem applies to smooth, finite-range and confining potentials V bounded below, describing systems confined in finite regions of space with continuously varying coordinates. The relevant configuration space submanifolds are both the level sets {Σ_v := V_N^{-1} (v)}_{v \in R} of the potential function V_N and the configuration space submanifolds enclosed by the Σ_{v} defined by {M_v := V_N^{-1} ((-\infty,v])}_{v \in R}, which are labeled by the potential energy value v, and where N is the number of degrees of freedom. The proof of the theorem proceeds by showing that, under the assumption of diffeomorphicity of the equipotential hypersurfaces {Σ_v}_{v \in R}, as well as of the ${M_v}_{v \in R}, in an arbitrary interval of values for \vb=v/N, the Helmoltz free energy is uniformly convergent in N to its thermodynamic limit, at least within the class of twice differentiable functions, in the corresponding interval of temperature. This preliminary theorem is essential to prove another theorem - in paper II - which makes a stronger statement about the relevance of topology for phase transitions.

math-ph↗

arXiv2005

Topology and Phase Transitions: Theorem on a necessary relation

An emended and improved version of the present paper has been archived in math-ph/0505057, and a preliminary account of its content has been published in Phys.Rev.Lett. 92, 60601, (2004). Moreover, in order to prove the relevance of topology for phase transition phenomena in a broad domain of physically interesting cases, we have proved another theorem which is reported in math-ph/0505058 and which is crucially based on the result of the paper archived in math-ph/0505057.

math-ph↗

arXiv2001

Topology and Phase Transitions: towards a proper mathematical definition of finite N transitions

A new point of view about the deep origin of thermodynamic phase transitions is sketched. The main idea is to link the appearance of phase transitions to some major topology change of suitable submanifolds of phase space instead of linking them to non-analyticity, as is usual in the Yang-Lee and in the Dobrushin-Ruelle-Sinai theories. In the new framework a new possibility appears to properly define a mathematical counterpart of phase transitions also at finite number of degrees of freedom. This is of prospective interest to the study of those systems that challenge the conventional approaches, as is the case of phase transitions in nuclear clusters.

cond-mat.stat-mech↗

arXiv1999

Topology and phase transitions: a paradigmatic evidence

We report upon the numerical computation of the Euler characteristic χ(a topologic invariant) of the equipotential hypersurfaces Σ_v of the configuration space of the two-dimensional lattice $ϕ^4$ model. The pattern χ(Σ_v) vs. v (potential energy) reveals that a major topology change in the family {Σ_v}_{v\in R} is at the origin of the phase transition in the model considered. The direct evidence given here - of the relevance of topology for phase transitions - is obtained through a general method that can be applied to any other model.

cond-mat.stat-mech↗

arXiv1998

Topological aspects of geometrical signatures of phase transitions

Certain geometric properties of submanifolds of configuration space are numerically investigated for classical lattice phi^4 models in one and two dimensions. Peculiar behaviors of the computed geometric quantities are found only in the two-dimensional case, when a phase transition is present. The observed phenomenology strongly supports, though in an indirect way, a recently proposed topological conjecture about a topology change of the configuration space submanifolds as counterpart of a phase transition.

cond-mat.stat-mech↗