Many problems in machine learning can be formulated as solving entropy-regularized optimal transport on the space of probability measures. The canonical approach involves the Sinkhorn iterates, renowned for their rich mathematical properties. Recently, the Sinkhorn algorithm has been recast within the mirror descent framework, thus benefiting from classical optimization theory insights. Here, we build upon this result by introducing a continuous-time analogue of the Sinkhorn algorithm. This perspective allows us to derive novel variants of Sinkhorn schemes that are robust to noise and bias. Moreover, our continuous-time dynamics offers a unified perspective on several recently discovered dynamics in machine learning and mathematics, such as the "Wasserstein mirror flow" of Deb et al. (2023) or the "mean-field Schrödinger equation" of Claisse et al. (2023).

This work considers the problem of sampling from a probability distribution known up to a normalization constant while satisfying a set of statistical constraints specified by the expected values of general nonlinear functions. This problem finds applications in, e.g., Bayesian inference, where it can constrain moments to evaluate counterfactual scenarios or enforce desiderata such as prediction fairness. Methods developed to handle support constraints, such as those based on mirror maps, barriers, and penalties, are not suited for this task. This work therefore relies on gradient descent-ascent dynamics in Wasserstein space to put forward a discrete-time primal-dual Langevin Monte Carlo algorithm (PD-LMC) that simultaneously constrains the target distribution and samples from it. We analyze the convergence of PD-LMC under standard assumptions on the target distribution and constraints, namely (strong) convexity and log-Sobolev inequalities. To do so, we bring classical optimization arguments for saddle-point algorithms to the geometry of Wasserstein space. We illustrate the relevance and effectiveness of PD-LMC in several applications.

We propose a principled way to define Gaussian process priors on various sets of unweighted graphs: directed or undirected, with or without loops. We endow each of these sets with a geometric structure, inducing the notions of closeness and symmetries, by turning them into a vertex set of an appropriate metagraph. Building on this, we describe the class of priors that respect this structure and are analogous to the Euclidean isotropic processes, like squared exponential or Matérn. We propose an efficient computational technique for the ostensibly intractable problem of evaluating these priors’ kernels, making such Gaussian processes usable within the usual toolboxes and downstream applications. We go further to consider sets of equivalence classes of unweighted graphs and define the appropriate versions of priors thereon. We prove a hardness result, showing that in this case, exact kernel computation cannot be performed efficiently. However, we propose a simple Monte Carlo approximation for handling moderately sized cases. Inspired by applications in chemistry, we illustrate the proposed techniques on a real molecular property prediction task in the small data regime.

Many modern machine learning applications - from online principal component analysis to covariance matrix identification and dictionary learning - can be formulated as minimization problems on Riemannian manifolds, typically solved with a Riemannian stochastic gradient method (or some variant thereof). However, in many cases of interest, the resulting minimization problem is _not_ geodesically convex, so the convergence of the chosen solver to a desirable solution - i.e., a local minimizer - is by no means guaranteed. In this paper, we study precisely this question, that is, whether stochastic Riemannian optimization algorithms are guaranteed to avoid saddle points with probability $1$. For generality, we study a family of retraction-based methods which, in addition to having a potentially much lower per-iteration cost relative to Riemannian gradient descent, include other widely used algorithms, such as natural policy gradient methods and mirror descent in ordinary convex spaces. In this general setting, we show that, under mild assumptions for the ambient manifold and the oracle providing gradient information, the policies under study avoid strict saddle points / submanifolds with probability $1$, from any initial condition. This result provides an important sanity check for the use of gradient methods on manifolds as it shows that, almost always, the end state of a stochastic Riemannian algorithm can only be a local minimizer.

Non-convex sampling is a key challenge in machine learning, central to non-convex optimization in deep learning as well as to approximate probabilistic inference. Despite its significance, theoretically there remain some important challenges: Existing guarantees suffer from the drawback of lacking guarantees for the last-iterates, and little is known beyond the elementary schemes of stochastic gradient Langevin dynamics. To address these issues, we develop a novel framework that lifts the above issues by harnessing several tools from the theory of dynamical systems. Our key result is that, for a large class of state-of-the-art sampling schemes, their last-iterate convergence in Wasserstein distances can be reduced to the study of their continuous-time counterparts, which is much better understood. Coupled with standard assumptions of MCMC sampling, our theory immediately yields the last-iterate Wasserstein convergence of many advanced sampling schemes such as mirror Langevin, proximal, randomized mid-point, and Runge-Kutta methods.

Interacting particle systems have proven highly successful in various machine learning tasks, including approximate Bayesian inference and neural network optimization. However, the analysis of these systems often relies on the simplifying assumption of the \emph{mean-field} limit, where particle numbers approach infinity and infinitesimal step sizes are used. In practice, discrete time steps, finite particle numbers, and complex integration schemes are employed, creating a theoretical gap between continuous-time and discrete-time processes. In this paper, we present a novel framework that establishes a precise connection between these discrete-time schemes and their corresponding mean-field limits in terms of convergence properties and asymptotic behavior. By adopting a dynamical system perspective, our framework seamlessly integrates various numerical schemes that are typically analyzed independently. For example, our framework provides a unified treatment of optimizing an infinite-width two-layer neural network and sampling via Stein Variational Gradient descent, which were previously studied in isolation.

Many important learning algorithms, such as stochastic gradient methods, are often deployed to solve nonlinear problems on Riemannian manifolds. Motivated by these applications, we propose a family of Riemannian algorithms generalizing and extending the seminal stochastic approximation framework of Robbins and Monro (1951). Compared to their Euclidean counterparts, Riemannian iterative algorithms are much less understood due to the lack of a global linear structure on the manifold. We overcome this difficulty by introducing an extended Fermi coordinate frame which allows us to map the asymptotic behavior of the proposed Riemannian Robbins–Monro (RRM) class of algorithms to that of an associated deterministic dynamical system under very mild assumptions on the underlying manifold. In so doing, we provide a general template of almost sure convergence results that mirrors and extends the existing theory for Euclidean Robbins-Monro schemes, albeit with a significantly more involved analysis that requires a number of new geometric ingredients. We showcase the flexibility of the proposed RRM framework by using it to establish the convergence of a retraction-based analogue of the popular optimistic / extra-gradient methods for solving minimization problems and games, and we provide a unified treatment for their convergence.

It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.

Given $k$ pre-trained classifiers and a stream of unlabeled data examples, how can we actively decide when to query a label so that we can distinguish the best model from the rest while making a small number of queries? Answering this question has a profound impact on a range of practical scenarios. In this work, we design an online selective sampling approach that actively selects informative examples to label and outputs the best model with high probability at any round. Our algorithm can also be used for online prediction tasks for both adversarial and stochastic streams. We establish several theoretical guarantees for our algorithm and extensively demonstrate its effectiveness in our experimental studies.

Modern online learning algorithms achieve low (sublinear) regret in a variety of diverse settings. These algorithms, however, update their solution at every time step. While these updates are computationally efficient, the very requirement of frequent updates makes the algorithms untenable in some practical applications. In this work we develop online learning algorithms that update a sublinear number of times. We give a meta algorithm based on non-homogeneous Poisson Processes that gives a smooth trade-off between regret and frequency of updates. Empirically, we show that in many cases, we can significantly reduce updates at a minimal increase in regret.

Stochastic optimization of continuous objectives is at the heart of modern machine learning. However, many important problems are of discrete nature and often involve submodular objectives. We seek to unleash the power of stochastic continuous optimization, namely stochastic gradient descent and its variants, to such discrete problems. We first introduce the problem of stochastic submodular optimization, where one needs to optimize a submodular objective which is given as an expectation. Our model captures situations where the discrete objective arises as an empirical risk (e.g., in the case of exemplar-based clustering), or is given as an explicit stochastic model (e.g., in the case of influence maximization in social networks). By exploiting that common extensions act linearly on the class of submodular functions, we employ projected stochastic gradient ascent and its variants in the continuous domain, and perform rounding to obtain discrete solutions. We focus on the rich and widely used family of weighted coverage functions. We show that our approach yields solutions that are guaranteed to match the optimal approximation guarantees, while reducing the computational cost by several orders of magnitude, as we demonstrate empirically.

Many users in online social networks are constantly trying to gain attention from their followers by broadcasting posts to them. These broadcasters are likely to gain greater attention if their posts can remain visible for a longer period of time among their followers' most recent feeds. Then when to post? In this paper, we study the problem of smart broadcasting using the framework of temporal point processes, where we model users feeds and posts as discrete events occurring in continuous time. Based on such continuous-time model, then choosing a broadcasting strategy for a user becomes a problem of designing the conditional intensity of her posting events. We derive a novel formula which links this conditional intensity with the visibility of the user in her followers' feeds. Furthermore, by exploiting this formula, we develop an efficient convex optimization framework for the when-to-post problem. Our method can find broadcasting strategies that reach a desired visibility level with provable guarantees. We experimented with data gathered from Twitter, and show that our framework can consistently make broadcasters' post more visible than alternatives.