arXiv subjects

Fabrice Delbary

Publications and source records attributed to Fabrice Delbary.

7 recordsLinked to original sources

arXiv2026

VertAX: a differentiable vertex model for learning epithelial tissue mechanics

Epithelial tissues dynamically reshape through local mechanical interactions among cells, a process well captured by vertex models. Yet their many tunable parameters make inference and optimization challenging, motivating computational frameworks that flexibly model and learn tissue mechanics. We introduce VertAX, a differentiable JAX-based framework for vertex-modeling of confluent epithelia. VertAX provides automatic differentiation, GPU acceleration, and end-to-end bilevel optimization for forward simulation, parameter inference, and inverse mechanical design. Users can define arbitrary energy and cost functions in pure Python, enabling seamless integration with machine-learning pipelines. We demonstrate VertAX on three representative tasks: (i) forward modeling of tissue morphogenesis, (ii) mechanical parameter inference, and (iii) inverse design of tissue-scale behaviors. We benchmark three differentiation strategies-automatic differentiation, implicit differentiation, and equilibrium propagation-showing that the latter can approximate gradients using repeated forward, adjoint-free simulations alone, offering a simple route for extending inverse biophysical problems to non-differentiable simulators with limited additional engineering effort.

cs.LG↗

arXiv2025

Inverse 3D Microscopy Rendering for Cell Shape Inference with Active Mesh

Traditional methods for biological shape inference, such as deep learning (DL) and active contour models, face important limitations in 3D. DL approaches require large annotated datasets, which are often impractical to obtain, while active contour methods depend on carefully tuned heuristics for intensity attraction and shape regularization. We introduce deltaMic, a novel differentiable 3D renderer for fluorescence microscopy that formulates shape inference as an inverse problem. By leveraging differentiable convolutions, deltaMic simulates the image formation process, integrating a parameterized point spread function (PSF) with a triangle mesh-based representation of biological structures. Unlike DL- or contour-based segmentation, deltaMic directly optimizes both shape and optical parameters to align synthetic and real microscopy images, removing the need for large datasets or sample-specific fine-tuning. To ensure scalability, we implement a GPU-accelerated Fourier transform for triangle meshes along with narrow-band spectral filtering. We show that deltaMic accurately reconstructs cell geometries from both synthetic and diverse experimental 3D microscopy data, while remaining robust to noise and initialization. This establishes a new physics-informed framework for biophysical image analysis and inverse modeling.

physics.bio-ph↗

arXiv2025

Physical configurations of a cell doublet with line tension, a theoretical study

As a first approximation, early embryos may be modeled as foams whose shape depends on the surface tensions of each cell. However it has been remarked that exist line tensions at polarized exterior cellular interfaces (apical). In order to understand the changes it may imply on the usual foam model, a simple case study is considered: a double cell with line tension. Phase diagrams, bifurcations, possible new configurations are studied.

math.NA↗

arXiv2025

Stable soap bubble clusters with multiple torus bubbles

In the last two centuries and more particularly in the last decades, the geometry of foams has become an important research domain, in mathematics, physics, material sciences and biology. Most of the simplest geometrical observations of bubble clusters have long resisted rigorous mathematical proofs. Geometries can even get more complicated if immiscible fluids are considered. Although they have to fulfill Plateau's laws like soap bubble clusters if the surface tensions are close to unity, this is not the case in general. In 1996, Frederick J. Almgren asked whether there is "any stable cluster of bubbles in $\mathbb{R}^3$ with some bubble being topologically a torus". We propose to answer the latter numerically with simple numerical examples. We build stable soap bubble clusters with a triple torus bubble, a fivefold torus bubble or an elevenfold torus bubble. The construction uses the geometry of a simple immiscible fluids cluster with a torus bubble.

math-ph↗

arXiv2018

A generalized Newton iteration for computing the solution of the inverse Henderson problem

We develop a generalized Newton scheme IHNC for the construction of effective pair potentials for systems of interacting point-like particles.The construction is made in such a way that the distribution of the particles matches a given radial distribution function. The IHNC iteration uses the hypernetted-chain integral equation for an approximate evaluation of the inverse of the Jacobian of the forward operator. In contrast to the full Newton method realized in the Inverse Monte Carlo (IMC) scheme, the IHNC algorithm requires only a single molecular dynamics computation of the radial distribution function per iteration step, and no further expensive cross-correlations. Numerical experiments are shown to demonstrate that the method is as efficient as the IMC scheme, and that it easily allows to incorporate thermodynamical constraints.

math.NA↗

arXiv2016

The Radon transform and the Hough transform: a unifying perspective

The Radon transform is a linear integral transform that mimics the data formation process in medical imaging modalities like X-ray Computerized Tomography and Positron Emission Tomography. The Hough transform is a pattern recognition technique, which is mainly used to detect straight lines in digital images and which has been recently extended to the automatic recognition of algebraic plane curves. Although defined in very different ways, in numerical applications both transforms ultimately take an image as an input and provide, as an output, a function defined on a parameter space. The parameters in this space describe a family of curves, which represent either the integration domains considered in the (generalized) Radon transform, or the curves to be detected by means of the Hough transform. In both cases, the 2D plot of the intensity values of the output function is the so-called (Radon or Hough) sinogram. While the Hough sinogram is produced by an algorithm whose implementation requires that the parameter space be discretized in cells, the Radon sinogram is mathematically defined on a continuous parameter space, which in turn may need to be discretized just for physical or numerical reasons. In this paper, by considering a more general and n-dimensional setting, we prove that, whether the input image is described as a set of points (possibly with different intensity values) or as a piecewise constant function, its (rescaled) Hough sinogram converges to the corresponding Radon sinogram as the discretization step in the parameter space tends to zero. We also show that this result may have a notable impact on the image reconstruction problem of inverting the Radon sinogram recorded by a medical imaging scanner, and that the description of the Hough transform problem within the framework of regularization theory for inverse problems is worth investigating.

math.NA↗

arXiv2016

Compartmental analysis of dynamic nuclear medicine data: models and identifiability

Compartmental models based on tracer mass balance are extensively used in clinical and pre-clinical nuclear medicine in order to obtain quantitative information on tracer metabolism in the biological tissue. This paper is the first of a series of two that deal with the problem of tracer coefficient estimation via compartmental modelling in an inverse problem framework. Specifically, here we discuss the identifiability problem for a general n-dimension compartmental system and provide uniqueness results in the case of two-compartment and three-compartment compartmental models. The second paper will utilize this framework in order to show how non-linear regularization schemes can be applied to obtain numerical estimates of the tracer coefficients in the case of nuclear medicine data corresponding to brain, liver and kidney physiology.

q-bio.QM↗