Jean-Baptiste Masson

Hippolyte Verdier, François Laurent, Alhassan Cassé et al.

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.

Alex Barbier-Chebbah, Christian L. Vestergaard, Jean-Baptiste Masson

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.

Alex Barbier-Chebbah, Christian L. Vestergaard, Jean-Baptiste Masson et al.

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.

Romain Seailles, Jean-Baptiste Masson, Jean Ponce et al.

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.

Alex Barbier-Chebbah, Christian L. Vestergaard, Jean-Baptiste Masson

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.

Hippolyte Verdier, Maxime Duval, François Laurent et al.

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.