As the problem of minimizing functionals on the Wasserstein space encompasses many applications in machine learning, different optimization algorithms on $\mathbb{R}^d$ have received their counterpart analog on the Wasserstein space. We focus here on lifting two explicit algorithms: mirror descent and preconditioned gradient descent. These algorithms have been introduced to better capture the geometry of the function to minimize and are provably convergent under appropriate (namely relative) smoothness and convexity conditions. Adapting these notions to the Wasserstein space, we prove guarantees of convergence of some Wasserstein-gradient-based discrete-time schemes for new pairings of objective functionals and regularizers. The difficulty here is to carefully select along which curves the functionals should be smooth and convex. We illustrate the advantages of adapting the geometry induced by the regularizer on ill conditioned optimization tasks, and showcase the improvement of choosing different discrepancies and geometries in a computational biology task of aligning single-cells.

Many problems in machine learning can be formulated as optimizing a convex functional over a vector space of measures. This paper studies the convergence of the mirror descent algorithm in this infinite-dimensional setting. Defining Bregman divergences through directional derivatives, we derive the convergence of the scheme for relatively smooth and convex pairs of functionals. Such assumptions allow to handle non-smooth functionals such as the Kullback--Leibler (KL) divergence. Applying our result to joint distributions and KL, we show that Sinkhorn's primal iterations for entropic optimal transport in the continuous setting correspond to a mirror descent, and we obtain a new proof of its (sub)linear convergence. We also show that Expectation Maximization (EM) can always formally be written as a mirror descent. When optimizing only on the latent distribution while fixing the mixtures parameters -- which corresponds to the Richardson--Lucy deconvolution scheme in signal processing -- we derive sublinear rates of convergence.

Shape constraints, such as non-negativity, monotonicity, convexity or supermodularity, play a key role in various applications of machine learning and statistics. However, incorporating this side information into predictive models in a hard way (for example at all points of an interval) for rich function classes is a notoriously challenging problem. We propose a unified and modular convex optimization framework, relying on second-order cone (SOC) tightening, to encode hard affine SDP constraints on function derivatives, for models belonging to vector-valued reproducing kernel Hilbert spaces (vRKHSs). The modular nature of the proposed approach allows to simultaneously handle multiple shape constraints, and to tighten an infinite number of constraints into finitely many. We prove the convergence of the proposed scheme and that of its adaptive variant, leveraging geometric properties of vRKHSs. Due to the covering-based construction of the tightening, the method is particularly well-suited to tasks with small to moderate input dimensions. The efficiency of the approach is illustrated in the context of shape optimization, safety-critical control, robotics and econometrics.

Among dissimilarities between probability distributions, the Kernel Stein Discrepancy (KSD) has received much interest recently. We investigate the properties of its Wasserstein gradient flow to approximate a target probability distribution $\pi$ on $\mathbb{R}^d$, known up to a normalization constant. This leads to a straightforwardly implementable, deterministic score-based method to sample from $\pi$, named KSD Descent, which uses a set of particles to approximate $\pi$. Remarkably, owing to a tractable loss function, KSD Descent can leverage robust parameter-free optimization schemes such as L-BFGS; this contrasts with other popular particle-based schemes such as the Stein Variational Gradient Descent algorithm. We study the convergence properties of KSD Descent and demonstrate its practical relevance. However, we also highlight failure cases by showing that the algorithm can get stuck in spurious local minima.

Shape constraints (such as non-negativity, monotonicity, convexity) play a central role in a large number of applications, as they usually improve performance for small sample size and help interpretability. However enforcing these shape requirements in a hard fashion is an extremely challenging problem. Classically, this task is tackled (i) in a soft way (without out-of-sample guarantees), (ii) by specialized transformation of the variables on a case-by-case basis, or (iii) by using highly restricted function classes, such as polynomials or polynomial splines. In this paper, we prove that hard affine shape constraints on function derivatives can be encoded in kernel machines which represent one of the most flexible and powerful tools in machine learning and statistics. Particularly, we present a tightened second-order cone constrained reformulation, that can be readily implemented in convex solvers. We prove performance guarantees on the solution, and demonstrate the efficiency of the approach in joint quantile regression with applications to economics and to the analysis of aircraft trajectories, among others.

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) offers new possibilities to infer gene regulatory network (GRNs) for biological processes involving a notion of time, such as cell differentiation or cell cycles. It also raises many challenges due to the destructive measurements inherent to the technology. RESULTS: In this work, we propose a new method named GRISLI for de novo GRN inference from scRNA-seq data. GRISLI infers a velocity vector field in the space of scRNA-seq data from profiles of individual cells, and models the dynamics of cell trajectories with a linear ordinary differential equation to reconstruct the underlying GRN with a sparse regression procedure. We show on real data that GRISLI outperforms a recently proposed state-of-the-art method for GRN reconstruction from scRNA-seq data. AVAILABILITY AND IMPLEMENTATION: The MATLAB code of GRISLI is available at: https://github.com/PCAubin/GRISLI. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.