arXiv subjects

Frédéric Cazals

Publications and source records attributed to Frédéric Cazals.

6 recordsLinked to original sources

arXiv2026

Circula-based multivariate distributions on the flat torus, with applications in structural biology

Modeling dependencies between random variables independently from their marginals is fundamental in applications ranging from finance to (structural) biology. In this work, we undertake this problem using circula to model data living on the $d$-dimensional flat torus $\mathbb{T}^d$, making two contributions. First, using a low rank covariance structure to define circulae based on a latent variable model, we design the first closed-form normalized distribution on the flat torus $\mathbb{T}^d$--with covariance structure. Second, building on this framework, we propose the first models for joint distributions of torsion angles (backbone and side-chains) for neighboring amino-acids in proteins. In practice, we fit mixtures on flat torii from $\mathbb{T}^{2}$ to $\mathbb{T}^{14}$, and show they are SOTA in terms of likelihood and sparsity. We anticipate that these models will prove fundamental to move from discrete structural studies like in AlphaFold2, to thermodynamics and kinetics, which are the ultimate goals in theoretical biophysics.

stat.AP↗

arXiv2026

A Unified, Cross-Platform Framework for Automatic GUI and Plugin Generation in Structural Bioinformatics and Beyond

We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step 2) the formal (platform independent) specification of the GUI, and (Step 3) the plugin code generation for the targeted platforms. Our architecture is aligned with the Model--View--Presenter (MVP) pattern: steps one and two build the Model and View descriptions, while step three implements the Presenter layer that binds inputs, invokes the CLI, and updates outputs. Once Step one has been (manually) completed, steps two and three are fully automated. The decoupled MVP design and platform-specific generator modules enable reuse of logic, portability across ecosystems, and significant reductions in engineering effort for complex interactive applications. We primarily use our workflow to generate GUI in structural bioinformatics for CLI executables from the Structural Bioinformatics Library (SBL), targeting three platforms, namely VMD, Pymol and Web servers. The workflow can be used as a guideline, while its implementation available in the package Plugin_manager from the SBL, see https://sbl.inria.fr/doc/Plugin_manager-user-manual.html.

cs.HC↗

arXiv2025

Modeling high dimensional point clouds with the spherical cluster model

A parametric cluster model is a statistical model providing geometric insights onto the points defining a cluster. The {\em spherical cluster model} (SC) approximates a finite point set $P\subset \mathbb{R}^d$ by a sphere $S(c,r)$ as follows. Taking $r$ as a fraction $η\in(0,1)$ (hyper-parameter) of the std deviation of distances between the center $c$ and the data points, the cost of the SC model is the sum over all data points lying outside the sphere $S$ of their power distance with respect to $S$. The center $c$ of the SC model is the point minimizing this cost. Note that $η=0$ yields the celebrated center of mass used in KMeans clustering. We make three contributions. First, we show fitting a spherical cluster yields a strictly convex but not smooth combinatorial optimization problem. Second, we present an exact solver using the Clarke gradient on a suitable stratified cell complex defined from an arrangement of hyper-spheres. Finally, we present experiments on a variety of datasets ranging in dimension from $d=9$ to $d=10,000$, with two main observations. First, the exact algorithm is orders of magnitude faster than BFGS based heuristics for datasets of small/intermediate dimension and small values of $η$, and for high dimensional datasets (say $d>100$) whatever the value of $η$. Second, the center of the SC model behave as a parameterized high-dimensional median. The SC model is of direct interest for high dimensional multivariate data analysis, and the application to the design of mixtures of SC will be reported in a companion paper.

stat.ME↗

arXiv2025

Improved seeding strategies for k-means and k-GMM

We revisit the randomized seeding techniques for k-means clustering and k-GMM (Gaussian Mixture model fitting with Expectation-Maximization), formalizing their three key ingredients: the metric used for seed sampling, the number of candidate seeds, and the metric used for seed selection. This analysis yields novel families of initialization methods exploiting a lookahead principle--conditioning the seed selection to an enhanced coherence with the final metric used to assess the algorithm, and a multipass strategy to tame down the effect of randomization. Experiments show a consistent constant factor improvement over classical contenders in terms of the final metric (SSE for k-means, log-likelihood for k-GMM), at a modest overhead. In particular, for k-means, our methods improve on the recently designed multi-swap strategy, which was the first one to outperform the greedy k-means++ seeding. Our experimental analysis also shed light on subtle properties of k-means often overlooked, including the (lack of) correlations between the SSE upon seeding and the final SSE, the variance reduction phenomena observed in iterative seeding methods, and the sensitivity of the final SSE to the pool size for greedy methods. Practically, our most effective seeding methods are strong candidates to become one of the--if not the--standard techniques. From a theoretical perspective, our formalization of seeding opens the door to a new line of analytical approaches.

cs.LG↗

arXiv2022

Efficient computation of the volume of a polytope in high-dimensions using Piecewise Deterministic Markov Processes

Computing the volume of a polytope in high dimensions is computationally challenging but has wide applications. Current state-of-the-art algorithms to compute such volumes rely on efficient sampling of a Gaussian distribution restricted to the polytope, using e.g. Hamiltonian Monte Carlo. We present a new sampling strategy that uses a Piecewise Deterministic Markov Process. Like Hamiltonian Monte Carlo, this new method involves simulating trajectories of a non-reversible process and inherits similar good mixing properties. However, importantly, the process can be simulated more easily due to its piecewise linear trajectories - and this leads to a reduction of the computational cost by a factor of the dimension of the space. Our experiments indicate that our method is numerically robust and is one order of magnitude faster (or better) than existing methods using Hamiltonian Monte Carlo. On a single core processor, we report computational time of a few minutes up to dimension 500.

stat.CO↗

arXiv2020

Low-Complexity Nonparametric Bayesian Online Prediction with Universal Guarantees

We propose a novel nonparametric online predictor for discrete labels conditioned on multivariate continuous features. The predictor is based on a feature space discretization induced by a full-fledged k-d tree with randomly picked directions and a recursive Bayesian distribution, which allows to automatically learn the most relevant feature scales characterizing the conditional distribution. We prove its pointwise universality, i.e., it achieves a normalized log loss performance asymptotically as good as the true conditional entropy of the labels given the features. The time complexity to process the $n$-th sample point is $O(\log n)$ in probability with respect to the distribution generating the data points, whereas other exact nonparametric methods require to process all past observations. Experiments on challenging datasets show the computational and statistical efficiency of our algorithm in comparison to standard and state-of-the-art methods.

cs.LG↗