Bilevel optimization has emerged as a technique for addressing a wide range of machine learning problems that involve an outer objective implicitly determined by the minimizer of an inner problem. While prior works have primarily focused on the parametric setting, a learning-theoretic foundation for bilevel optimization in the nonparametric case remains relatively unexplored. In this paper, we take a first step toward bridging this gap by studying Kernel Bilevel Optimization (KBO), where the inner objective is optimized over a reproducing kernel Hilbert space. This setting enables rich function approximation while providing a foundation for rigorous theoretical analysis. In this context, we derive novel finite-sample generalization bounds for KBO, leveraging tools from empirical process theory. These bounds further allow us to assess the statistical accuracy of gradient-based methods applied to the empirical discretization of KBO. We numerically illustrate our theoretical findings on a synthetic instrumental variable regression task.

We consider stochastic optimization problems where the objective depends on some parameter, as commonly found in hyperparameter optimization for instance. We investigate the behavior of the derivatives of the iterates of Stochastic Gradient Descent (SGD) with respect to that parameter and show that they are driven by an inexact SGD recursion on a different objective function, perturbed by the convergence of the original SGD. This enables us to establish that the derivatives of SGD converge to the derivative of the solution mapping in terms of mean squared error whenever the objective is strongly convex. Specifically, we demonstrate that with constant step-sizes, these derivatives stabilize within a noise ball centered at the solution derivative, and that with vanishing step-sizes they exhibit $O(\log(k)^2 / k)$ convergence rates. Additionally, we prove exponential convergence in the interpolation regime. Our theoretical findings are illustrated by numerical experiments on synthetic tasks.

In appropriate frameworks, automatic differentiation is transparent to the user, at the cost of being a significant computational burden when the number of operations is large. For iterative algorithms, implicit differentiation alleviates this issue but requires custom implementation of Jacobian evaluation. In this paper, we study one-step differentiation, also known as Jacobian-free backpropagation, a method as easy as automatic differentiation and as performant as implicit differentiation for fast algorithms (e.g. superlinear optimization methods). We provide a complete theoretical approximation analysis with specific examples (Newton's method, gradient descent) along with its consequences in bilevel optimization. Several numerical examples illustrate the well-foundness of the one-step estimator.

Differentiation along algorithms, i.e., piggyback propagation of derivatives, is now routinely used to differentiate iterative solvers in differentiable programming. Asymptotics is well understood for many smooth problems but the nondifferentiable case is hardly considered. Is there a limiting object for nonsmooth piggyback automatic differentiation (AD)? Does it have any variational meaning and can it be used effectively in machine learning? Is there a connection with classical derivative? All these questions are addressed under appropriate contractivity conditions in the framework of conservative derivatives which has proved useful in understanding nonsmooth AD. For nonsmooth piggyback iterations, we characterize the attractor set of nonsmooth piggyback iterations as a set-valued fixed point which remains in the conservative framework. This has various consequences and in particular almost everywhere convergence of classical derivatives. Our results are illustrated on parametric convex optimization problems with forward-backward, Douglas-Rachford and Alternating Direction of Multiplier algorithms as well as the Heavy-Ball method.

In theory, the choice of ReLU(0) in [0, 1] for a neural network has a negligible influence both on backpropagation and training. Yet, in the real world, 32 bits default precision combined with the size of deep learning problems makes it a hyperparameter of training methods. We investigate the importance of the value of ReLU'(0) for several precision levels (16, 32, 64 bits), on various networks (fully connected, VGG, ResNet) and datasets (MNIST, CIFAR10, SVHN, ImageNet). We observe considerable variations of backpropagation outputs which occur around half of the time in 32 bits precision. The effect disappears with double precision, while it is systematic at 16 bits. For vanilla SGD training, the choice ReLU'(0) = 0 seems to be the most efficient. For our experiments on ImageNet the gain in test accuracy over ReLU'(0) = 1 was more than 10 points (two runs). We also evidence that reconditioning approaches as batch-norm or ADAM tend to buffer the influence of ReLU'(0)’s value. Overall, the message we convey is that algorithmic differentiation of nonsmooth problems potentially hides parameters that could be tuned advantageously.

In view of training increasingly complex learning architectures, we establish a nonsmooth implicit function theorem with an operational calculus. Our result applies to most practical problems (i.e., definable problems) provided that a nonsmooth form of the classical invertibility condition is fulfilled. This approach allows for formal subdifferentiation: for instance, replacing derivatives by Clarke Jacobians in the usual differentiation formulas is fully justified for a wide class of nonsmooth problems. Moreover this calculus is entirely compatible with algorithmic differentiation (e.g., backpropagation). We provide several applications such as training deep equilibrium networks, training neural nets with conic optimization layers, or hyperparameter-tuning for nonsmooth Lasso-type models. To show the sharpness of our assumptions, we present numerical experiments showcasing the extremely pathological gradient dynamics one can encounter when applying implicit algorithmic differentiation without any hypothesis.

Deep equilibrium models are based on implicitly defined functional relations and have shown competitive performance compared with the traditional deep networks. Monotone operator equilibrium networks (monDEQ) retain interesting performance with additional theoretical guaranties. Existing certification tools for classical deep networks cannot directly be applied to monDEQs for which much fewer tools exist. We introduce a semialgebraic representation for ReLU based monDEQs which allow to approximate the corresponding input output relation by semidefinite programs (SDP). We present several applications to network certification and obtain SDP models for the following problems : robustness certification, Lipschitz constant estimation, ellipsoidal uncertainty propagation. We use these models to certify robustness of monDEQs with respect to a general $L_p$ norm. Experimental results show that the proposed models outperform existing approaches for monDEQ certification. Furthermore, our investigations suggest that monDEQs are much more robust to $L_2$ perturbations than $L_{\infty}$ perturbations.

We introduce a new second-order inertial optimization method for machine learning called INNA. It exploits the geometry of the loss function while only requiring stochastic approximations of the function values and the generalized gradients. This makes INNA fully implementable and adapted to large-scale optimization problems such as the training of deep neural networks. The algorithm combines both gradient-descent and Newton-like behaviors as well as inertia. We prove the convergence of INNA for most deep learning problems. To do so, we provide a well-suited framework to analyze deep learning loss functions involving tame optimization in which we study a continuous dynamical system together with its discrete stochastic approximations. We prove sublinear convergence for the continuous-time differential inclusion which underlies our algorithm. Additionally, we also show how standard optimization mini-batch methods applied to non-smooth non-convex problems can yield a certain type of spurious stationary points never discussed before. We address this issue by providing a theoretical framework around the new idea of $D$-criticality; we then give a simple asymptotic analysis of INNA. Our algorithm allows for using an aggressive learning rate of $o(1/\log k)$. From an empirical viewpoint, we show that INNA returns competitive results with respect to state of the art (stochastic gradient descent, ADAGRAD, ADAM) on popular deep learning benchmark problems.

The Lipschitz constant of a network plays an important role in many applications of deep learning, such as robustness certification and Wasserstein Generative Adversarial Network. We introduce a semidefinite programming hierarchy to estimate the global and local Lipschitz constant of a multiple layer deep neural network. The novelty is to combine a polynomial lifting for ReLU functions derivatives with a weak generalization of Putinar's positivity certificate. This idea could also apply to other, nearly sparse, polynomial optimization problems in machine learning. We empirically demonstrate that our method provides a trade-off with respect to state of the art linear programming approach, and in some cases we obtain better bounds in less time.

Automatic differentiation, as implemented today, does not have a simple mathematical model adapted to the needs of modern machine learning. In this work we articulate the relationships between differentiation of programs as implemented in practice, and differentiation of nonsmooth functions. To this end we provide a simple class of functions, a nonsmooth calculus, and show how they apply to stochastic approximation methods. We also evidence the issue of artificial critical points created by algorithmic differentiation and show how usual methods avoid these points with probability one.

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.

We study a surprising phenomenon related to the representation of a cloud of data points using polynomials. We start with the previously unnoticed empirical observation that, given a collection (a cloud) of data points, the sublevel sets of a certain distinguished polynomial capture the shape of the cloud very accurately. This distinguished polynomial is a sum-of-squares (SOS) derived in a simple manner from the inverse of the empirical moment matrix. In fact, this SOS polynomial is directly related to orthogonal polynomials and the Christoffel function. This allows to generalize and interpret extremality properties of orthogonal polynomials and to provide a mathematical rationale for the observed phenomenon. Among diverse potential applications, we illustrate the relevance of our results on a network intrusion detection task for which we obtain performances similar to existing dedicated methods reported in the literature.

MOTIVATION: Identifying the emergence and underlying mechanisms of drug side effects is a challenging task in the drug development process. This underscores the importance of system-wide approaches for linking different scales of drug actions; namely drug-protein interactions (molecular scale) and side effects (phenotypic scale) toward side effect prediction for uncharacterized drugs. RESULTS: We performed a large-scale analysis to extract correlated sets of targeted proteins and side effects, based on the co-occurrence of drugs in protein-binding profiles and side effect profiles, using sparse canonical correlation analysis. The analysis of 658 drugs with the two profiles for 1368 proteins and 1339 side effects led to the extraction of 80 correlated sets. Enrichment analyses using KEGG and Gene Ontology showed that most of the correlated sets were significantly enriched with proteins that are involved in the same biological pathways, even if their molecular functions are different. This allowed for a biologically relevant interpretation regarding the relationship between drug-targeted proteins and side effects. The extracted side effects can be regarded as possible phenotypic outcomes by drugs targeting the proteins that appear in the same correlated set. The proposed method is expected to be useful for predicting potential side effects of new drug candidate compounds based on their protein-binding profiles. SUPPLEMENTARY INFORMATION: Datasets and all results are available at http://web.kuicr.kyoto-u.ac.jp/supp/smizutan/target-effect/. AVAILABILITY: Software is available at the above supplementary website. CONTACT: [email protected], or [email protected].

MOTIVATION: Drug effects are mainly caused by the interactions between drug molecules and their target proteins including primary targets and off-targets. Identification of the molecular mechanisms behind overall drug-target interactions is crucial in the drug design process. RESULTS: We develop a classifier-based approach to identify chemogenomic features (the underlying associations between drug chemical substructures and protein domains) that are involved in drug-target interaction networks. We propose a novel algorithm for extracting informative chemogenomic features by using L(1) regularized classifiers over the tensor product space of possible drug-target pairs. It is shown that the proposed method can extract a very limited number of chemogenomic features without loosing the performance of predicting drug-target interactions and the extracted features are biologically meaningful. The extracted substructure-domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein families. AVAILABILITY: Softwares are available at the supplemental website. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/l1binary/ .

BACKGROUND: Drug side-effects, or adverse drug reactions, have become a major public health concern. It is one of the main causes of failure in the process of drug development, and of drug withdrawal once they have reached the market. Therefore, in silico prediction of potential side-effects early in the drug discovery process, before reaching the clinical stages, is of great interest to improve this long and expensive process and to provide new efficient and safe therapies for patients. RESULTS: In the present work, we propose a new method to predict potential side-effects of drug candidate molecules based on their chemical structures, applicable on large molecular databanks. A unique feature of the proposed method is its ability to extract correlated sets of chemical substructures (or chemical fragments) and side-effects. This is made possible using sparse canonical correlation analysis (SCCA). In the results, we show the usefulness of the proposed method by predicting 1385 side-effects in the SIDER database from the chemical structures of 888 approved drugs. These predictions are performed with simultaneous extraction of correlated ensembles formed by a set of chemical substructures shared by drugs that are likely to have a set of side-effects. We also conduct a comprehensive side-effect prediction for many uncharacterized drug molecules stored in DrugBank, and were able to confirm interesting predictions using independent source of information. CONCLUSIONS: The proposed method is expected to be useful in various stages of the drug development process.