Advances in sequencing technologies have enabled the generation of large amounts of data, offering new possibilities to identify relationships between biological units (e.g. genes) and phenotypic traits (e.g. disease outcomes). Yet, identifying these associations using variable selection methods remains challenging due to the high dimension ($p \gg n$) and the correlation structure of the data. To address these challenges, we study the applicability of the knockoff (KO) procedure. Introduced by Barber and Candès in 2015, the KO variable selection procedure has shown promising results on real biological data, such as Genome-Wide Association Studies. This method seeks to identify the truly important predictors by overcoming the correlation structure between variables while controlling the false discovery rate. Here, we study the applicability of the KO procedure on transcriptomic data in a classification setting. We conduct an extensive simulation study using real transcriptomic data to evaluate the performance of the KO framework in the context of high-dimensional classification. We find that the KO framework outperforms widely used variable selection models, and that using KO aggregation to mitigate the effect of KO stochasticity improves stability while maintaining the same power. Finally, applied to three real transcriptomic datasets, the KO framework made very few discoveries, highlighting its conservative nature and suggesting that other methods may substantially overestimate the number of relevant features.

Deep ResNets are recognized for achieving state-of-the-art results in complex machine learning tasks. However, the remarkable performance of these architectures relies on a training procedure that needs to be carefully crafted to avoid vanishing or exploding gradients, particularly as the depth $L$ increases. No consensus has been reached on how to mitigate this issue, although a widely discussed strategy consists in scaling the output of each layer by a factor $\alpha_L$. We show in a probabilistic setting that with standard i.i.d. initializations, the only non-trivial dynamics is for $\alpha_L = \frac{1}{\sqrt{L}}$---other choices lead either to explosion or to identity mapping. This scaling factor corresponds in the continuous-time limit to a neural stochastic differential equation, contrarily to a widespread interpretation that deep ResNets are discretizations of neural ordinary differential equations. By contrast, in the latter regime, stability is obtained with specific correlated initializations and $\alpha_L = \frac{1}{L}$. Our analysis suggests a strong interplay between scaling and regularity of the weights as a function of the layer index. Finally, in a series of experiments, we exhibit a continuous range of regimes driven by these two parameters, which jointly impact performance before and after training.

We consider the task of learning individual-specific intensities of counting processes from a set of static variables and irregularly sampled time series. We introduce a novel modelization approach in which the intensity is the solution to a controlled differential equation. We first design a neural estimator by building on neural controlled differential equations. In a second time, we show that our model can be linearized in the signature space under sufficient regularity conditions, yielding a signature-based estimator which we call CoxSig. We provide theoretical learning guarantees for both estimators, before showcasing the performance of our models on a vast array of simulated and real-world datasets from finance, predictive maintenance and food supply chain management.

Stochastic Gradient Descent (SGD) with adaptive steps is widely used to train deep neural networks and generative models. Most theoretical results assume that it is possible to obtain unbiased gradient estimators, which is not the case in several recent deep learning and reinforcement learning applications that use Monte Carlo methods. This paper provides a comprehensive non-asymptotic analysis of SGD with biased gradients and adaptive steps for non-convex smooth functions. Our study incorporates time-dependent bias and emphasizes the importance of controlling the bias of the gradient estimator. In particular, we establish that Adagrad, RMSProp, and AMSGRAD, an exponential moving average variant of Adam, with biased gradients, converge to critical points for smooth non-convex functions at a rate similar to existing results in the literature for the unbiased case. Finally, we provide experimental results using Variational Autoenconders (VAE) and applications to several learning frameworks that illustrate our convergence results and show how the effect of bias can be reduced by appropriate hyperparameter tuning.

We address the problem of learning the dynamics of an unknown non-parametric system linking a target and a feature time series. The feature time series is measured on a sparse and irregular grid, while we have access to only a few points of the target time series. Once learned, we can use these dynamics to predict values of the target from the previous values of the feature time series. We frame this task as learning the solution map of a controlled differential equation (CDE). By leveraging the rich theory of signatures, we are able to cast this non-linear problem as a high-dimensional linear regression. We provide an oracle bound on the prediction error which exhibits explicit dependencies on the individual-specific sampling schemes. Our theoretical results are illustrated by simulations which show that our method outperforms existing algorithms for recovering the full time series while being computationally cheap. We conclude by demonstrating its potential on real-world epidemiological data.

Building on the interpretation of a recurrent neural network (RNN) as a continuous-time neural differential equation, we show, under appropriate conditions, that the solution of a RNN can be viewed as a linear function of a specific feature set of the input sequence, known as the signature. This connection allows us to frame a RNN as a kernel method in a suitable reproducing kernel Hilbert space. As a consequence, we obtain theoretical guarantees on generalization and stability for a large class of recurrent networks. Our results are illustrated on simulated datasets.