arXiv subjects

Jean-Baptiste Masson

Publications and source records attributed to Jean-Baptiste Masson.

17 recordsLinked to original sources

arXiv2026

Optimal transport unlocks end-to-end learning for single-molecule localization

Single-molecule localization microscopy (SMLM) allows reconstructing biology-relevant structures beyond the diffraction limit by detecting and localizing individual fluorophores -- fluorescent molecules stained onto the observed specimen -- over time to reconstruct super-resolved images. Currently, efficient SMLM requires non-overlapping emitting fluorophores, leading to long acquisition times that hinders live-cell imaging. Recent deep-learning approaches can handle denser emissions, but they rely on variants of non-maximum suppression (NMS) layers, which are unfortunately non-differentiable and may discard true positives with their local fusion strategy. In this presentation, we reformulate the SMLM training objective as a set-matching problem, deriving an optimal-transport loss that eliminates the need for NMS during inference and enables end-to-end training. Additionally, we propose an iterative neural network that integrates knowledge of the microscope's optical system inside our model. Experiments on synthetic benchmarks and real biological data show that both our new loss function and architecture surpass the state of the art at moderate and high emitter densities. Code is available at https://github.com/RSLLES/SHOT.

cs.CV↗

arXiv2025

Objective comparison of methods to decode anomalous diffusion

Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers.

physics.data-an↗

arXiv2025

Information maximization for a broad variety of multi-armed bandit games

Information and free-energy maximization are physics principles that provide general rules for an agent to optimize actions in line with specific goals and policies. These principles are the building blocks for designing decision-making policies capable of efficient performance with only partial information. Notably, the information maximization principle has shown remarkable success in the classical bandit problem and has recently been shown to yield optimal algorithms for Gaussian and sub-Gaussian reward distributions. This article explores a broad extension of physics-based approaches to more complex and structured bandit problems. To this end, we cover three distinct types of bandit problems, where information maximization is adapted and leads to strong performance. Since the main challenge of information maximization lies in avoiding over-exploration, we highlight how information is tailored at various levels to mitigate this issue, paving the way for more efficient and robust decision-making strategies.

cs.LG↗

arXiv2024

Approximate information maximization for bandit games

Entropy maximization and free energy minimization are general physical principles for modeling the dynamics of various physical systems. Notable examples include modeling decision-making within the brain using the free-energy principle, optimizing the accuracy-complexity trade-off when accessing hidden variables with the information bottleneck principle (Tishby et al., 2000), and navigation in random environments using information maximization (Vergassola et al., 2007). Built on this principle, we propose a new class of bandit algorithms that maximize an approximation to the information of a key variable within the system. To this end, we develop an approximated analytical physics-based representation of an entropy to forecast the information gain of each action and greedily choose the one with the largest information gain. This method yields strong performances in classical bandit settings. Motivated by its empirical success, we prove its asymptotic optimality for the two-armed bandit problem with Gaussian rewards. Owing to its ability to encompass the system's properties in a global physical functional, this approach can be efficiently adapted to more complex bandit settings, calling for further investigation of information maximization approaches for multi-armed bandit problems.

stat.ML↗

arXiv2024

Compression-based inference of network motif sets

Physical and functional constraints on biological networks lead to complex topological patterns across multiple scales in their organization. A particular type of higher-order network feature that has received considerable interest is network motifs, defined as statistically regular subgraphs. These may implement fundamental logical and computational circuits and are referred as "building blocks of complex networks". Their well-defined structures and small sizes also enables the testing of their functions in synthetic and natural biological experiments. The statistical inference of network motifs is however fraught with difficulties, from defining and sampling the right null model to accounting for the large number of possible motifs and their potential correlations in statistical testing. Here we develop a framework for motif mining based on lossless network compression using subgraph contractions. The minimum description length principle allows us to select the most significant set of motifs as well as other prominent network features in terms of their combined compression of the network. The approach inherently accounts for multiple testing and correlations between subgraphs and does not rely on a priori specification of an appropriate null model. This provides an alternative definition of motif significance which guarantees more robust statistical inference. Our approach overcomes the common problems in classic testing-based motif analysis. We apply our methodology to perform comparative connectomics by evaluating the compressibility and the circuit motifs of a range of synaptic-resolution neural connectomes.

q-bio.QM↗

arXiv2024

Multi-Center Fetal Brain Tissue Annotation (FeTA) Challenge 2022 Results

Segmentation is a critical step in analyzing the developing human fetal brain. There have been vast improvements in automatic segmentation methods in the past several years, and the Fetal Brain Tissue Annotation (FeTA) Challenge 2021 helped to establish an excellent standard of fetal brain segmentation. However, FeTA 2021 was a single center study, and the generalizability of algorithms across different imaging centers remains unsolved, limiting real-world clinical applicability. The multi-center FeTA Challenge 2022 focuses on advancing the generalizability of fetal brain segmentation algorithms for magnetic resonance imaging (MRI). In FeTA 2022, the training dataset contained images and corresponding manually annotated multi-class labels from two imaging centers, and the testing data contained images from these two imaging centers as well as two additional unseen centers. The data from different centers varied in many aspects, including scanners used, imaging parameters, and fetal brain super-resolution algorithms applied. 16 teams participated in the challenge, and 17 algorithms were evaluated. Here, a detailed overview and analysis of the challenge results are provided, focusing on the generalizability of the submissions. Both in- and out of domain, the white matter and ventricles were segmented with the highest accuracy, while the most challenging structure remains the cerebral cortex due to anatomical complexity. The FeTA Challenge 2022 was able to successfully evaluate and advance generalizability of multi-class fetal brain tissue segmentation algorithms for MRI and it continues to benchmark new algorithms. The resulting new methods contribute to improving the analysis of brain development in utero.

eess.IV↗

arXiv2023

Approximate information for efficient exploration-exploitation strategies

This paper addresses the exploration-exploitation dilemma inherent in decision-making, focusing on multi-armed bandit problems. The problems involve an agent deciding whether to exploit current knowledge for immediate gains or explore new avenues for potential long-term rewards. We here introduce a novel algorithm, approximate information maximization (AIM), which employs an analytical approximation of the entropy gradient to choose which arm to pull at each point in time. AIM matches the performance of Infomax and Thompson sampling while also offering enhanced computational speed, determinism, and tractability. Empirical evaluation of AIM indicates its compliance with the Lai-Robbins asymptotic bound and demonstrates its robustness for a range of priors. Its expression is tunable, which allows for specific optimization in various settings.

stat.ML↗

arXiv2022

Variational inference of fractional Brownian motion with linear computational complexity

We introduce a simulation-based, amortised Bayesian inference scheme to infer the parameters of random walks. Our approach learns the posterior distribution of the walks' parameters with a likelihood-free method. In the first step a graph neural network is trained on simulated data to learn optimized low-dimensional summary statistics of the random walk. In the second step an invertible neural network generates the posterior distribution of the parameters from the learnt summary statistics using variational inference. We apply our method to infer the parameters of the fractional Brownian motion model from single trajectories. The computational complexity of the amortized inference procedure scales linearly with trajectory length, and its precision scales similarly to the Cram{é}r-Rao bound over a wide range of lengths. The approach is robust to positional noise, and generalizes well to trajectories longer than those seen during training. Finally, we adapt this scheme to show that a finite decorrelation time in the environment can furthermore be inferred from individual trajectories.

cs.LG↗

arXiv2021

Learning physical properties of anomalous random walks using graph neural networks

Single particle tracking allows probing how biomolecules interact physically with their natural environments. A fundamental challenge when analysing recorded single particle trajectories is the inverse problem of inferring the physical model or class of models of the underlying random walks. Reliable inference is made difficult by the inherent stochastic nature of single particle motion, by experimental noise, and by the short duration of most experimental trajectories. Model identification is further complicated by the fact that main physical properties of random walk models are only defined asymptotically, and are thus degenerate for short trajectories. Here, we introduce a new, fast approach to inferring random walk properties based on graph neural networks (GNNs). Our approach consists in associating a vector of features with each observed position, and a sparse graph structure with each observed trajectory. By performing simulation-based supervised learning on this construct [1], we show that we can reliably learn models of random walks and their anomalous exponents. The method can naturally be applied to trajectories of any length. We show its efficiency in analysing various anomalous random walks of biological relevance that were proposed in the AnDi challenge [2]. We explore how information is encoded in the GNN, and we show that it learns relevant physical features of the random walks. We furthermore evaluate its ability to generalize to types of trajectories not seen during training, and we show that the GNN retains high accuracy even with few parameters. We finally discuss the possibility to leverage these networks to analyse experimental data.

cs.LG↗

arXiv2020

Statistical Tests for Force Inference in Heterogeneous Environments

We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed drift includes a "spurious" force term when the diffusivity varies in space. We show how Bayesian inference can be leveraged to reliably infer forces by taking into account such spurious forces of unknown amplitude as well as experimental sources of error. The method is based on marginalizing the force posterior over all possible spurious force contributions. The approach is combined with a Bayes factor statistical test for the presence of forces. The performance of our method is investigated analytically, numerically and tested on experimental data sets. The main results are obtained in a closed form allowing for direct exploration of their properties and fast computation. The method is incorporated into TRamWAy, an open-source software platform for automated analysis of biomolecule trajectories.

physics.bio-ph↗

arXiv2016

Single-Molecule Imaging of Nav1.6 on the Surface of Hippocampal Neurons Reveals Somatic Nanoclusters

Voltage-gated sodium (Na$_\mathrm{v}$) channels are responsible for the depolarizing phase of the action potential in most nerve cells, and Na$_\mathrm{v}$ channel localization to the axon initial segment is vital to action potential initiation. Na$_\mathrm{v}$ channels in the soma play a role in the transfer of axonal output information to the rest of the neuron and in synaptic plasticity, although little is known about Na$_\mathrm{v}$ channel localization and dynamics within this neuronal compartment. This study uses single-particle tracking and photoactivation localization microscopy to analyze cell-surface Na$_\mathrm{v}$1.6 within the soma of cultured hippocampal neurons. Mean-square displacement analysis of individual trajectories indicated that half of the somatic Na$_\mathrm{v}$1.6 channels localized to stable nanoclusters $\sim$230 nm in diameter. Strikingly, these domains were stabilized at specific sites on the cell membrane for >30 min, notably via an ankyrin-independent mechanism, indicating that the means by which Na$_\mathrm{v}$1.6 nanoclusters are maintained in the soma is biologically different from axonal localization. Nonclustered Na$_\mathrm{v}$1.6 channels showed anomalous diffusion, as determined by mean-square-displacement analysis. High-density single-particle tracking of Na$_\mathrm{v}$ channels labeled with photoactivatable fluorophores in combination with Bayesian inference analysis was employed to characterize the surface nanoclusters. A subpopulation of mobile Na$_\mathrm{v}$1.6 was observed to be transiently trapped in the nanoclusters. Somatic Na$_\mathrm{v}$1.6 nanoclusters represent a new, to our knowledge, type of Na$_\mathrm{v}$ channel localization, and are hypothesized to be sites of localized channel regulation.

physics.bio-ph↗

arXiv2015

InferenceMAP: Mapping of Single-Molecule Dynamics with Bayesian Inference

Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to understand the multi-scale nature of single-molecule dynamics in biological systems. We have previously shown that with high-density SPT, spatial maps of the parameters that dictate molecule motion can be generated to intricately describe cellular environments [2,3,4]. To date, however, there exist no publically available tools that reconcile trajectory data to generate the aforementioned maps. We address this void in the SPT community with InferenceMAP: an interactive software package that uses a powerful Bayesian method to map the dynamic cellular space experienced by individual biomolecules.

q-bio.QM↗

arXiv2015

Bayesian Decision Tree for the Classification of the Mode of Motion in Single-Molecule Trajectories

Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to improve our knowledge of the membrane architecture and to understand the nature of interactions between membrane proteins and their environments. Here, we present an analysis technique for single molecule tracking (SMT) trajectories that can determine the preferred model of motion that best matches observed trajectories. Information theory criteria, such as the Bayesian information criterion (BIC), the Akaike information criterion (AIC), and modified AIC (AICc), are used to select the preferred model. The considered group of models includes free Brownian motion, and confined motion in 2nd or 4th order potentials. We determine the best information criteria for classifying trajectories. We tested its limits through simulations matching large sets of experimental conditions and built a decision tree. This decision tree first uses the BIC to distinguish between free Brownian motion and confined motion. In a second step, it classifies the confining potential further using the AIC. We apply the method to experimental Clostridium Perfingens epsilon-toxin (CPepsilonT) receptor trajectories to show that these receptors are confined by a spring-like potential. An adaptation of this technique was applied on a sliding window in the temporal dimension along the trajectory. We applied this adaptation to experimental CPepsilonT trajectories that lose confinement due to disaggregation of confining domains. This new technique adds another dimension to the discussion of SMT data. The mode of motion of a receptor holds more biologically relevant information than the diffusion coefficient or domain size and may be a better tool to classify and compare different SMT experiments.

physics.bio-ph↗

arXiv2015

Pitfalls in the quantitative analysis of random walks and the mapping of single-molecule dynamics at the cellular scale

In recent years Bayesian Inference has become an efficient tool to analyse single molecule trajectories. Recently, high density single molecule tagging, Langevin Equation modelling and Bayesian Inference [10] have been used to infer diffusion, force and potential fields at the full cell scale. In this short comment, we point out pitfalls [1, 2] to avoid in single molecule analysis in order to get unbiased results and reliable fields at various scales.

physics.bio-ph↗

arXiv2015

Mapping the energy and diffusion landscapes of membrane proteins at the cell surface using high-density single-molecule imaging and Bayesian inference: application to the multi-scale dynamics of glycine receptors in the neuronal membrane

Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions governing the motion. Here, we present a method combining high-density single-molecule imaging and statistical inference to separately map the diffusion and energy landscapes of membrane proteins across the cell surface at ~100 nm resolution (with acquisition of a few minutes). When applying these analytical tools to glycine neurotransmitter receptors (GlyRs) at inhibitory synapses, we find that gephyrin scaffolds act as shallow energy traps (~3 kBT) for GlyRs, with a depth modulated by the biochemical properties of the receptor-gephyrin interaction loop. In turn, the inferred maps can be used to simulate the dynamics of proteins in the membrane, from the level of individual receptors to that of the population, and thereby, to model the stochastic fluctuations of physiological parameters (such as the number of receptors at synapses). Overall, our approach provides a powerful and comprehensive framework with which to analyze biochemical interactions in living cells and to decipher the multi-scale dynamics of biomolecules in complex cellular environments.

physics.bio-ph↗

arXiv2007

Extra energy coupling through subwavelength hole arrays via stochastic resonance

Interaction between metal surface waves and periodic geometry of subwavelength structures is at the core of the recent but crucial renewal of interest in plasmonics. One of the most intriguing points is the observation of abnormal strong transmission through these periodic structures, which can exceed by orders of magnitude the classical transmission given by the filling factor of the plate. The actual paradigm is that this abnormal transmission arises from the periodicity, and then that such high transmission should disappear in random geometries. Here, we show that extra energy can be coupled through the subwavelength structure by adding a controlled quantity of noise to the position of the apertures. This result can be modelled in the statistical framework of stochastic resonance. The evolution of the coupled energy with respect to noise gives access to the extra energy coupled at the surface of the subwavelength array.

cond-mat.other↗

arXiv2006

Experimental evidence of percolation phase transition in surface plasmons generation

Carrying digital information in traditional copper wires is becoming a major issue in electronic circuits. Optical connections such as fiber optics offers unprecedented transfer capacity, but the mismatch between the optical wavelength and the transistors size drastically reduces the coupling efficiency. By merging the abilities of photonics and electronics, surface plasmon photonics, or 'plasmonics' exhibits strong potential. Here, we propose an original approach to fully understand the nature of surface electrons in plasmonic systems, by experimentally demonstrating that surface plasmons can be modeled as a phase of surface waves. First and second order phase transitions, associated with percolation transitions, have been experimentally observed in the building process of surface plasmons in lattice of subwavelength apertures. Percolation theory provides a unified framework for surface plasmons description.

cond-mat.other↗