arXiv subjects

Jean-Philippe Vert

Publications and source records attributed to Jean-Philippe Vert.

At least 19 recordsLinked to original sources

arXiv2023

Regression as Classification: Influence of Task Formulation on Neural Network Features

Neural networks can be trained to solve regression problems by using gradient-based methods to minimize the square loss. However, practitioners often prefer to reformulate regression as a classification problem, observing that training on the cross entropy loss results in better performance. By focusing on two-layer ReLU networks, which can be fully characterized by measures over their feature space, we explore how the implicit bias induced by gradient-based optimization could partly explain the above phenomenon. We provide theoretical evidence that the regression formulation yields a measure whose support can differ greatly from that for classification, in the case of one-dimensional data. Our proposed optimal supports correspond directly to the features learned by the input layer of the network. The different nature of these supports sheds light on possible optimization difficulties the square loss could encounter during training, and we present empirical results illustrating this phenomenon.

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arXiv2023

Causal inference methods for combining randomized trials and observational studies: a review

With increasing data availability, causal effects can be evaluated across different data sets, both randomized controlled trials (RCTs) and observational studies. RCTs isolate the effect of the treatment from that of unwanted (confounding) co-occurring effects but they may suffer from unrepresentativeness, and thus lack external validity. On the other hand, large observational samples are often more representative of the target population but can conflate confounding effects with the treatment of interest. In this paper, we review the growing literature on methods for causal inference on combined RCTs and observational studies, striving for the best of both worlds. We first discuss identification and estimation methods that improve generalizability of RCTs using the representativeness of observational data. Classical estimators include weighting, difference between conditional outcome models, and doubly robust estimators. We then discuss methods that combine RCTs and observational data to either ensure uncounfoundedness of the observational analysis or to improve (conditional) average treatment effect estimation. We also connect and contrast works developed in both the potential outcomes literature and the structural causal model literature. Finally, we compare the main methods using a simulation study and real world data to analyze the effect of tranexamic acid on the mortality rate in major trauma patients. A review of available codes and new implementations is also provided.

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arXiv2022

Efficient and Modular Implicit Differentiation

Automatic differentiation (autodiff) has revolutionized machine learning. It allows to express complex computations by composing elementary ones in creative ways and removes the burden of computing their derivatives by hand. More recently, differentiation of optimization problem solutions has attracted widespread attention with applications such as optimization layers, and in bi-level problems such as hyper-parameter optimization and meta-learning. However, so far, implicit differentiation remained difficult to use for practitioners, as it often required case-by-case tedious mathematical derivations and implementations. In this paper, we propose automatic implicit differentiation, an efficient and modular approach for implicit differentiation of optimization problems. In our approach, the user defines directly in Python a function $F$ capturing the optimality conditions of the problem to be differentiated. Once this is done, we leverage autodiff of $F$ and the implicit function theorem to automatically differentiate the optimization problem. Our approach thus combines the benefits of implicit differentiation and autodiff. It is efficient as it can be added on top of any state-of-the-art solver and modular as the optimality condition specification is decoupled from the implicit differentiation mechanism. We show that seemingly simple principles allow to recover many existing implicit differentiation methods and create new ones easily. We demonstrate the ease of formulating and solving bi-level optimization problems using our framework. We also showcase an application to the sensitivity analysis of molecular dynamics.

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arXiv2022

Scaling ResNets in the Large-depth Regime

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.

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arXiv2021

Framing RNN as a kernel method: A neural ODE approach

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.

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arXiv2021

Differentiable Divergences Between Time Series

Computing the discrepancy between time series of variable sizes is notoriously challenging. While dynamic time warping (DTW) is popularly used for this purpose, it is not differentiable everywhere and is known to lead to bad local optima when used as a "loss". Soft-DTW addresses these issues, but it is not a positive definite divergence: due to the bias introduced by entropic regularization, it can be negative and it is not minimized when the time series are equal. We propose in this paper a new divergence, dubbed soft-DTW divergence, which aims to correct these issues. We study its properties; in particular, under conditions on the ground cost, we show that it is a valid divergence: it is non-negative and minimized if and only if the two time series are equal. We also propose a new "sharp" variant by further removing entropic bias. We showcase our divergences on time series averaging and demonstrate significant accuracy improvements compared to both DTW and soft-DTW on 84 time series classification datasets.

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arXiv2020

Noisy Adaptive Group Testing using Bayesian Sequential Experimental Design

When the infection prevalence of a disease is low, Dorfman showed 80 years ago that testing groups of people can prove more efficient than testing people individually. Our goal in this paper is to propose new group testing algorithms that can operate in a noisy setting (tests can be mistaken) to decide adaptively (looking at past results) which groups to test next, with the goal to converge to a good detection, as quickly, and with as few tests as possible. We cast this problem as a Bayesian sequential experimental design problem. Using the posterior distribution of infection status vectors for $n$ patients, given observed tests carried out so far, we seek to form groups that have a maximal utility. We consider utilities such as mutual information, but also quantities that have a more direct relevance to testing, such as the AUC of the ROC curve of the test. Practically, the posterior distributions on $\{0,1\}^n$ are approximated by sequential Monte Carlo (SMC) samplers and the utility maximized by a greedy optimizer. Our procedures show in simulations significant improvements over both adaptive and non-adaptive baselines, and are far more efficient than individual tests when disease prevalence is low. Additionally, we show empirically that loopy belief propagation (LBP), widely regarded as the SoTA decoder to decide whether an individual is infected or not given previous tests, can be unreliable and exhibit oscillatory behavior. Our SMC decoder is more reliable, and can improve the performance of other group testing algorithms.

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arXiv2020

Supervised Quantile Normalization for Low-rank Matrix Approximation

Low rank matrix factorization is a fundamental building block in machine learning, used for instance to summarize gene expression profile data or word-document counts. To be robust to outliers and differences in scale across features, a matrix factorization step is usually preceded by ad-hoc feature normalization steps, such as \texttt{tf-idf} scaling or data whitening. We propose in this work to learn these normalization operators jointly with the factorization itself. More precisely, given a $d\times n$ matrix $X$ of $d$ features measured on $n$ individuals, we propose to learn the parameters of quantile normalization operators that can operate row-wise on the values of $X$ and/or of its factorization $UV$ to improve the quality of the low-rank representation of $X$ itself. This optimization is facilitated by the introduction of a new differentiable quantile normalization operator built using optimal transport, providing new results on top of existing work by (Cuturi et al. 2019). We demonstrate the applicability of these techniques on synthetic and genomics datasets.

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arXiv2020

On Mixup Regularization

Mixup is a data augmentation technique that creates new examples as convex combinations of training points and labels. This simple technique has empirically shown to improve the accuracy of many state-of-the-art models in different settings and applications, but the reasons behind this empirical success remain poorly understood. In this paper we take a substantial step in explaining the theoretical foundations of Mixup, by clarifying its regularization effects. We show that Mixup can be interpreted as standard empirical risk minimization estimator subject to a combination of data transformation and random perturbation of the transformed data. We gain two core insights from this new interpretation. First, the data transformation suggests that, at test time, a model trained with Mixup should also be applied to transformed data, a one-line change in code that we show empirically to improve both accuracy and calibration of the prediction. Second, we show how the random perturbation of the new interpretation of Mixup induces multiple known regularization schemes, including label smoothing and reduction of the Lipschitz constant of the estimator. These schemes interact synergistically with each other, resulting in a self calibrated and effective regularization effect that prevents overfitting and overconfident predictions. We corroborate our theoretical analysis with experiments that support our conclusions.

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arXiv2020

Learning with Differentiable Perturbed Optimizers

Machine learning pipelines often rely on optimization procedures to make discrete decisions (e.g., sorting, picking closest neighbors, or shortest paths). Although these discrete decisions are easily computed, they break the back-propagation of computational graphs. In order to expand the scope of learning problems that can be solved in an end-to-end fashion, we propose a systematic method to transform optimizers into operations that are differentiable and never locally constant. Our approach relies on stochastically perturbed optimizers, and can be used readily together with existing solvers. Their derivatives can be evaluated efficiently, and smoothness tuned via the chosen noise amplitude. We also show how this framework can be connected to a family of losses developed in structured prediction, and give theoretical guarantees for their use in learning tasks. We demonstrate experimentally the performance of our approach on various tasks.

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arXiv2020

MissDeepCausal: Causal Inference from Incomplete Data Using Deep Latent Variable Models

Inferring causal effects of a treatment, intervention or policy from observational data is central to many applications. However, state-of-the-art methods for causal inference seldom consider the possibility that covariates have missing values, which is ubiquitous in many real-world analyses. Missing data greatly complicate causal inference procedures as they require an adapted unconfoundedness hypothesis which can be difficult to justify in practice. We circumvent this issue by considering latent confounders whose distribution is learned through variational autoencoders adapted to missing values. They can be used either as a pre-processing step prior to causal inference but we also suggest to embed them in a multiple imputation strategy to take into account the variability due to missing values. Numerical experiments demonstrate the effectiveness of the proposed methodology especially for non-linear models compared to competitors.

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arXiv2019

Differentiable Ranks and Sorting using Optimal Transport

Sorting an array is a fundamental routine in machine learning, one that is used to compute rank-based statistics, cumulative distribution functions (CDFs), quantiles, or to select closest neighbors and labels. The sorting function is however piece-wise constant (the sorting permutation of a vector does not change if the entries of that vector are infinitesimally perturbed) and therefore has no gradient information to back-propagate. We propose a framework to sort elements that is algorithmically differentiable. We leverage the fact that sorting can be seen as a particular instance of the optimal transport (OT) problem on $\mathbb{R}$, from input values to a predefined array of sorted values (e.g. $1,2,\dots,n$ if the input array has $n$ elements). Building upon this link , we propose generalized CDFs and quantile operators by varying the size and weights of the target presorted array. Because this amounts to using the so-called Kantorovich formulation of OT, we call these quantities K-sorts, K-CDFs and K-quantiles. We recover differentiable algorithms by adding to the OT problem an entropic regularization, and approximate it using a few Sinkhorn iterations. We call these operators S-sorts, S-CDFs and S-quantiles, and use them in various learning settings: we benchmark them against the recently proposed neuralsort [Grover et al. 2019], propose applications to quantile regression and introduce differentiable formulations of the top-k accuracy that deliver state-of-the art performance.

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arXiv2019

Differentiable Deep Clustering with Cluster Size Constraints

Clustering is a fundamental unsupervised learning approach. Many clustering algorithms -- such as $k$-means -- rely on the euclidean distance as a similarity measure, which is often not the most relevant metric for high dimensional data such as images. Learning a lower-dimensional embedding that can better reflect the geometry of the dataset is therefore instrumental for performance. We propose a new approach for this task where the embedding is performed by a differentiable model such as a deep neural network. By rewriting the $k$-means clustering algorithm as an optimal transport task, and adding an entropic regularization, we derive a fully differentiable loss function that can be minimized with respect to both the embedding parameters and the cluster parameters via stochastic gradient descent. We show that this new formulation generalizes a recently proposed state-of-the-art method based on soft-$k$-means by adding constraints on the cluster sizes. Empirical evaluations on image classification benchmarks suggest that compared to state-of-the-art methods, our optimal transport-based approach provide better unsupervised accuracy and does not require a pre-training phase.

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arXiv2019

ASNI: Adaptive Structured Noise Injection for shallow and deep neural networks

Dropout is a regularisation technique in neural network training where unit activations are randomly set to zero with a given probability \emph{independently}. In this work, we propose a generalisation of dropout and other multiplicative noise injection schemes for shallow and deep neural networks, where the random noise applied to different units is not independent but follows a joint distribution that is either fixed or estimated during training. We provide theoretical insights on why such adaptive structured noise injection (ASNI) may be relevant, and empirically confirm that it helps boost the accuracy of simple feedforward and convolutional neural networks, disentangles the hidden layer representations, and leads to sparser representations. Our proposed method is a straightforward modification of the classical dropout and does not require additional computational overhead.

stat.ML↗

arXiv2019

Deep multi-class learning from label proportions

We propose a learning algorithm capable of learning from label proportions instead of direct data labels. In this scenario, our data are arranged into various bags of a certain size, and only the proportions of each label within a given bag are known. This is a common situation in cases where per-data labeling is lengthy, but a more general label is easily accessible. Several approaches have been proposed to learn in this setting with linear models in the multiclass setting, or with nonlinear models in the binary classification setting. Here we investigate the more general nonlinear multiclass setting, and compare two differentiable loss functions to train end-to-end deep neural networks from bags with label proportions. We illustrate the relevance of our methods on an image classification benchmark, and demonstrate the possibility to learn accurate image classifiers from bags of images.

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arXiv2018

Relating Leverage Scores and Density using Regularized Christoffel Functions

Statistical leverage scores emerged as a fundamental tool for matrix sketching and column sampling with applications to low rank approximation, regression, random feature learning and quadrature. Yet, the very nature of this quantity is barely understood. Borrowing ideas from the orthogonal polynomial literature, we introduce the regularized Christoffel function associated to a positive definite kernel. This uncovers a variational formulation for leverage scores for kernel methods and allows to elucidate their relationships with the chosen kernel as well as population density. Our main result quantitatively describes a decreasing relation between leverage score and population density for a broad class of kernels on Euclidean spaces. Numerical simulations support our findings.

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arXiv2018

The Weighted Kendall and High-order Kernels for Permutations

We propose new positive definite kernels for permutations. First we introduce a weighted version of the Kendall kernel, which allows to weight unequally the contributions of different item pairs in the permutations depending on their ranks. Like the Kendall kernel, we show that the weighted version is invariant to relabeling of items and can be computed efficiently in $O(n \ln(n))$ operations, where $n$ is the number of items in the permutation. Second, we propose a supervised approach to learn the weights by jointly optimizing them with the function estimated by a kernel machine. Third, while the Kendall kernel considers pairwise comparison between items, we extend it by considering higher-order comparisons among tuples of items and show that the supervised approach of learning the weights can be systematically generalized to higher-order permutation kernels.

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arXiv2018

Robust Seriation and Applications to Cancer Genomics

The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a global ordering consistent with the similarity information exists, an exact spectral solution recovers it in the noiseless case and seriation is equivalent to the combinatorial 2-SUM problem over permutations, for which several relaxations have been derived. However, in applications such as DNA assembly, similarity values are often heavily corrupted, and the solution of 2-SUM may no longer yield an approximate serial structure on the elements. We introduce the robust seriation problem and show that it is equivalent to a modified 2-SUM problem for a class of similarity matrices modeling those observed in DNA assembly. We explore several relaxations of this modified 2-SUM problem and compare them empirically on both synthetic matrices and real DNA data. We then introduce the problem of seriation with duplications, which is a generalization of Seriation motivated by applications to cancer genome reconstruction. We propose an algorithm involving robust seriation to solve it, and present preliminary results on synthetic data sets.

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