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Nicolas Tremblay

Publications and source records attributed to Nicolas Tremblay.

At least 19 recordsLinked to original sources

A Generalized Tikhonov Layer for Interpretable-by-design Graph Neural Networks

We propose the Tikhonov layer, a graph neural network layer that is interpretable by design: once trained, its learned parameters directly reveal which node features and which aspects of the graph topology were leveraged for prediction. In practice, the layer's propagation matrix takes the closed-form $R = (p(L)+Q)^{-1} Q$, where $L$ is the normalized graph Laplacian, $Q = diag(q_1,...,q_n)$ a learnable diagonal matrix of positive node-importance scores, and $p(\cdot)$ a learnable polynomial. For any input feature $x$, the layer output $Rx$ is the exact minimizer of a generalized graph Tikhonov problem that trades off node-level data fidelity against a topology-driven regularization penalty. The learned pair $\{\{q_i\},p\}$ constitutes a built-in explanation: large $q_i$ indicates that node $i$'s own features drive the prediction, while small $q_i$ signals reliance on the local graph topology; the shape of $p$ reveals whether homophily, heterophily, or a band-pass response is exploited. Expressivity is preserved by routing complexity through a dedicated, arbitrarily deep Q-network that produces the importance scores, while the Tikhonov layer itself remains transparent. We prove that distinct node-importance matrices yield distinct propagation operators, structurally coupling the explanation to the computation. Additionally, the Tikhonov layer provides, in a single layer, a global receptive field, mitigating both oversmoothing and oversquashing. Experiments on standard graph classification benchmarks confirm that the model matches (and sometimes outperforms) opaque baselines while producing interpretable and faithful explanations.

cs.LG

Biology-driven assessment of deep learning super-resolution imaging of the porosity network in dentin

The mechanosensory system of teeth is currently believed to partly rely on Odontoblast cells stimulation by fluid flow through a porosity network extending through dentin. Visualizing the smallest sub-microscopic porosity vessels therefore requires the highest achievable resolution from confocal fluorescence microscopy, the current gold standard. This considerably limits the extent of the field of view to very small sample regions. To overcome this limitation, we tested different deep learning (DL) super-resolution (SR) models to allow faster experimental acquisitions of lower resolution images and restore optimal image quality by post-processing. Three supervised 2D SR models (RCAN, pix2pix, FSRCNN) and one unsupervised (CycleGAN) were applied to a unique set of experimentally paired high- and low-resolution confocal images acquired with different sampling schemes, resulting in a pixel size increase of x2, x4, x8. Model performance was quantified using a broad set of similarity and distribution-based image quality assessment (IQA) metrics, which yielded inconsistent results that mostly contradicted our visual perception. This raises the question of the relevance of such generic metrics to efficiently target the specific structure of dental porosity. To resolve this conflicting information, the generated SR images were segmented taking into account the specific scales and morphology of the porosity network and analysed by comparing connected components. Additionally, the capacity of the SR models to preserve 3D porosity connectivity throughout the confocal image stacks was evaluated using graph analysis. This biology-driven assessment allowed a far better mechanistic interpretation of SR performance, highlighting differences in model sensitivity to weak intensity features and the impact of non-linearity in image generation, which explains the failure of standard IQA metrics.

cs.LG

Spectrum Estimation through Kirchhoff Random Forests

Given a non-oriented edge-weighted graph, we show how to make some estimation of the associated Laplacian eigenvalues through Monte Carlo evaluation of spectral quantities computed along Kirchhoff random rooted spanning forest trajectories. The sampling cost of this estimation is only linear in the node number, up to a logarithmic factor. By associating a double cover of such a graph with any symmetric real matrix, we can then perform spectral estimation in the same way for the latter.

math.PR

Estimating a graph's spectrum via random Kirchhoff forests

Exact eigendecomposition of large matrices is very expensive, and it is practically impossible to compute exact eigenvalues. Instead, one may set a more modest goal of approaching the empirical distribution of the eigenvalues, recovering the overall shape of the eigenspectrum. Current approaches to spectral estimation typically work with \emph{moments} of the spectral distribution. These moments are first estimated using Monte Carlo trace estimators, then the estimates are combined to approximate the spectral density. In this article we show how \emph{Kirchhoff forests}, which are random forests on graphs, can be used to estimate certain non-linear moments of very large graph Laplacians. We show how to combine these moments into an estimate of the spectral density. If the estimate's desired precision isn't too high, our approach paves the way to the estimation of a graph's spectrum in time sublinear in the number of links.

stat.CO

Random Multi-Type Spanning Forests for Synchronization on Sparse Graphs

Random diffusions are a popular tool in Monte-Carlo estimations, with well established algorithms such as Walk-on-Spheres (WoS) going back several decades. In this work, we introduce diffusion estimators for the problems of angular synchronization and smoothing on graphs, in the presence of a rotation associated to each edge. Unlike classical WoS algorithms that are point-wise estimators, our diffusion estimators allow for global estimations by propagating along the branches of random spanning subgraphs called multi-type spanning forests. Building upon efficient samplers based on variants of Wilson's algorithm, we show that our estimators outperform standard numerical-linear-algebra solvers in challenging instances, depending on the topology and density of the graph.

math.PR

Convergence of Message Passing Graph Neural Networks with Generic Aggregation On Large Random Graphs

We study the convergence of message passing graph neural networks on random graph models to their continuous counterpart as the number of nodes tends to infinity. Until now, this convergence was only known for architectures with aggregation functions in the form of normalized means, or, equivalently, of an application of classical operators like the adjacency matrix or the graph Laplacian. We extend such results to a large class of aggregation functions, that encompasses all classically used message passing graph neural networks, such as attention-based message passing, max convolutional message passing, (degree-normalized) convolutional message passing, or moment-based aggregation message passing. Under mild assumptions, we give non-asymptotic bounds with high probability to quantify this convergence. Our main result is based on the McDiarmid inequality. Interestingly, this result does not apply to the case where the aggregation is a coordinate-wise maximum. We treat this case separately and obtain a different convergence rate.

stat.ML

A Faster Sampler for Discrete Determinantal Point Processes

Discrete Determinantal Point Processes (DPPs) have a wide array of potential applications for subsampling datasets. They are however held back in some cases by the high cost of sampling. In the worst-case scenario, the sampling cost scales as O(n^3) where n is the number of elements of the ground set. A popular workaround to this prohibitive cost is to sample DPPs defined by low-rank kernels. In such cases, the cost of standard sampling algorithms scales as O(np^2 + nm^2) where m is the (average) number of samples of the DPP (usually m << n) and p the rank of the kernel used to define the DPP (m \leq p \leq n). The first term, O(np^2), comes from a SVD-like step. We focus here on the second term of this cost, O(nm^2), and show that it can be brought down to O(nm + m^3 log m) without loss on the sampling's exactness. In practice, we observe very substantial speedups compared to the classical algorithm as soon as n > 1000. The algorithm described here is a close variant of the standard algorithm for sampling continuous DPPs, and uses rejection sampling. In the specific case of projection DPPs, we also show that any additional sample can be drawn in time O(m^3 log m). Finally, an interesting by-product of the analysis is that a realisation from a DPP is typically contained in a subset of size O(m log m) formed using leverage score i.i.d. sampling.

cs.LG

Smoothing complex-valued signals on Graphs with Monte-Carlo

We introduce new smoothing estimators for complex signals on graphs, based on a recently studied Determinantal Point Process (DPP). These estimators are built from subsets of edges and nodes drawn according to this DPP, making up trees and unicycles, i.e., connected components containing exactly one cycle. We provide a Julia implementation of these estimators and study their performance when applied to a ranking problem.

stat.ME

Variance Reduction for Inverse Trace Estimation via Random Spanning Forests

The trace $\tr(q(\ma{L} + q\ma{I})^{-1})$, where $\ma{L}$ is a symmetric diagonally dominant matrix, is the quantity of interest in some machine learning problems. However, its direct computation is impractical if the matrix size is large. State-of-the-art methods include Hutchinson's estimator combined with iterative solvers, as well as the estimator based on random spanning forests (a random process on graphs). In this work, we show two ways of improving the forest-based estimator via well-known variance reduction techniques, namely control variates and stratified sampling. Implementing these techniques is easy, and provides substantial variance reduction, yielding comparable or better performance relative to state-of-the-art algorithms.

eess.SP

Determinantal Point Processes in the Flat Limit: Extended L-ensembles, Partial-Projection DPPs and Universality Classes

Determinantal point processes (DPPs) are repulsive point processes where the interaction between points depends on the determinant of a positive-semi definite matrix. The contributions of this paper are two-fold. First of all, we introduce the concept of extended L-ensemble, a novel representation of DPPs. These extended L-ensembles are interesting objects because they fix some pathologies in the usual formalism of DPPs, for instance the fact that projection DPPs are not L-ensembles. Every (fixed-size) DPP is an (fixed-size) extended L-ensemble, including projection DPPs. This new formalism enables to introduce and analyze a subclass of DPPs, called partial-projection DPPs. Secondly, with these new definitions in hand, we first show that partial-projection DPPs arise as perturbative limits of L-ensembles, that is, limits in $\varepsilon \rightarrow 0$ of L-ensembles based on matrices of the form $\varepsilon \mathbf{A} + \mathbf{B}$ where $\mathbf{B}$ is low-rank. We generalise this result by showing that partial-projection DPPs also arise as the limiting process of L-ensembles based on kernel matrices, when the kernel function becomes flat (so that every point interacts with every other point, in a sense). We show that the limiting point process depends mostly on the smoothness of the kernel function. In some cases, the limiting process is even universal, meaning that it does not depend on specifics of the kernel function, but only on its degree of smoothness.

math.PR

Extended L-ensembles: a new representation for Determinantal Point Processes

Determinantal point processes (DPPs) are a class of repulsive point processes, popular for their relative simplicity. They are traditionally defined via their marginal distributions, but a subset of DPPs called "L-ensembles" have tractable likelihoods and are thus particularly easy to work with. Indeed, in many applications, DPPs are more naturally defined based on the L-ensemble formulation rather than through the marginal kernel. The fact that not all DPPs are L-ensembles is unfortunate, but there is a unifying description. We introduce here extended L-ensembles, and show that all DPPs are extended L-ensembles (and vice-versa). Extended L-ensembles have very simple likelihood functions, contain L-ensembles and projection DPPs as special cases. From a theoretical standpoint, they fix some pathologies in the usual formalism of DPPs, for instance the fact that projection DPPs are not L-ensembles. From a practical standpoint, they extend the set of kernel functions that may be used to define DPPs: we show that conditional positive definite kernels are good candidates for defining DPPs, including DPPs that need no spatial scale parameter. Finally, extended L-ensembles are based on so-called ``saddle-point matrices'', and we prove an extension of the Cauchy-Binet theorem for such matrices that may be of independent interest.

math.ST

Determinantal Point Processes in the Flat Limit

Determinantal point processes (DPPs) are repulsive point processes where the interaction between points depends on the determinant of a positive-semi definite matrix. In this paper, we study the limiting process of L-ensembles based on kernel matrices, when the kernel function becomes flat (so that every point interacts with every other point, in a sense). We show that these limiting processes are best described in the formalism of extended L-ensembles and partial projection DPPs, and the exact limit depends mostly on the smoothness of the kernel function. In some cases, the limiting process is even universal, meaning that it does not depend on specifics of the kernel function, but only on its degree of smoothness. Since flat-limit DPPs are still repulsive processes, this implies that practically useful families of DPPs exist that do not require a spatial length-scale parameter.

math.PR

Graph Tikhonov Regularization and Interpolation via Random Spanning Forests

Novel Monte Carlo estimators are proposed to solve both the Tikhonov regularization (TR) and the interpolation problems on graphs. These estimators are based on random spanning forests (RSF), the theoretical properties of which enable to analyze the estimators' theoretical mean and variance. We also show how to perform hyperparameter tuning for these RSF-based estimators. TR is a component in many well-known algorithms, and we show how the proposed estimators can be easily adapted to avoid expensive intermediate steps in generalized semi-supervised learning, label propagation, Newton's method and iteratively reweighted least squares. In the experiments, we illustrate the proposed methods on several problems and provide observations on their run time.

cs.DM

Gaussian Process Regression in the Flat Limit

Gaussian process (GP) regression is a fundamental tool in Bayesian statistics. It is also known as kriging and is the Bayesian counterpart to the frequentist kernel ridge regression. Most of the theoretical work on GP regression has focused on a large-$n$ asymptotics, i.e. as the amount of data increases. Fixed-sample analysis is much more difficult outside of simple cases, such as locations on a regular grid. In this work we perform a fixed-sample analysis that was first studied in the context of approximation theory by Driscoll & Fornberg (2002), called the ``flat limit''. In flat-limit asymptotics, the goal is to characterise kernel methods as the length-scale of the kernel function tends to infinity, so that kernels appear flat over the range of the data. Surprisingly, this limit is well-defined, and displays interesting behaviour: Driscoll & Fornberg showed that radial basis interpolation converges in the flat limit to polynomial interpolation, if the kernel is Gaussian. Subsequent work showed that this holds true in the multivariate setting as well, but that kernels other than the Gaussian may have (polyharmonic) splines as the limit interpolant. Leveraging recent results on the spectral behaviour of kernel matrices in the flat limit, we study the flat limit of Gaussian process regression. Results show that Gaussian process regression tends in the flat limit to (multivariate) polynomial regression, or (polyharmonic) spline regression, depending on the kernel. Importantly, this holds for both the predictive mean and the predictive variance, so that the posterior predictive distributions become equivalent. Our results have practical consequences: for instance, they show that optimal GP predictions in the sense of leave-one-out loss may occur at very large length-scales, which would be invisible to current implementations because of numerical difficulties.

math.ST

Variance reduction in stochastic methods for large-scale regularised least-squares problems

Large dimensional least-squares and regularised least-squares problems are expensive to solve. There exist many approximate techniques, some deterministic (like conjugate gradient), some stochastic (like stochastic gradient descent). Among the latter, a new class of techniques uses Determinantal Point Processes (DPPs) to produce unbiased estimators of the solution. In particular, they can be used to perform Tikhonov regularization on graphs using random spanning forests, a specific DPP. While the unbiasedness of these algorithms is attractive, their variance can be high. We show here that variance can be reduced by combining the stochastic estimator with a deterministic gradient-descent step, while keeping the property of unbiasedness. We apply this technique to Tikhonov regularization on graphs, where the reduction in variance is found to be substantial at very small extra cost.

eess.SP

A unified framework for spectral clustering in sparse graphs

This article considers spectral community detection in the regime of sparse networks with heterogeneous degree distributions, for which we devise an algorithm to efficiently retrieve communities. Specifically, we demonstrate that a conveniently parametrized form of regularized Laplacian matrix can be used to perform spectral clustering in sparse networks, without suffering from its degree heterogeneity. Besides, we exhibit important connections between this proposed matrix and the now popular non-backtracking matrix, the Bethe-Hessian matrix, as well as the standard Laplacian matrix. Interestingly, as opposed to competitive methods, our proposed improved parametrization inherently accounts for the hardness of the classification problem. These findings are summarized under the form of an algorithm capable of both estimating the number of communities and achieving high-quality community reconstruction.

stat.ML

Nishimori meets Bethe: a spectral method for node classification in sparse weighted graphs

This article unveils a new relation between the Nishimori temperature parametrizing a distribution P and the Bethe free energy on random Erdos-Renyi graphs with edge weights distributed according to P. Estimating the Nishimori temperature being a task of major importance in Bayesian inference problems, as a practical corollary of this new relation, a numerical method is proposed to accurately estimate the Nishimori temperature from the eigenvalues of the Bethe Hessian matrix of the weighted graph. The algorithm, in turn, is used to propose a new spectral method for node classification in weighted (possibly sparse) graphs. The superiority of the method over competing state-of-the-art approaches is demonstrated both through theoretical arguments and real-world data experiments.

stat.ML

Community detection in sparse time-evolving graphs with a dynamical Bethe-Hessian

This article considers the problem of community detection in sparse dynamical graphs in which the community structure evolves over time. A fast spectral algorithm based on an extension of the Bethe-Hessian matrix is proposed, which benefits from the positive correlation in the class labels and in their temporal evolution and is designed to be applicable to any dynamical graph with a community structure. Under the dynamical degree-corrected stochastic block model, in the case of two classes of equal size, we demonstrate and support with extensive simulations that our proposed algorithm is capable of making non-trivial community reconstruction as soon as theoretically possible, thereby reaching the optimal detectability threshold and provably outperforming competing spectral methods.

cs.SI