Yuichi Ike

Mathieu Carriere, Yuichi Ike, Théo Lacombe et al.

Computational topology provides a tool, persistent homology, to extract quantitative descriptors from structured objects (images, graphs, point clouds, etc). These descriptors can then be involved in optimization problems, typically as a way to incorporate topological priors or to regularize machine learning models. This is usually achieved by minimizing adequate, topologically-informed losses based on these descriptors, which, in turn, naturally raises theoretical and practical questions about the possibility of optimizing such loss functions using gradient-based algorithms. This has been an active research field in the topological data analysis community over the last decade, and various techniques have been developed to enable optimization of persistence-based loss functions with gradient descent schemes. This survey presents the current state of this field, covering its theoretical foundations, the algorithmic aspects, and showcasing practical uses in several applications. It includes a detailed introduction to persistence theory and, as such, aims at being accessible to mathematicians and data scientists newcomers to the field. It is accompanied by an open-source library which implements the different approaches covered in this survey, providing a convenient playground for researchers to get familiar with the field.

Naoki Nishikawa, Yuichi Ike, Kenji Yamanishi

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

Kentaro Kanamori, Takuya Takagi, Ken Kobayashi et al.

This paper proposes a new framework of algorithmic recourse (AR) that works even in the presence of missing values. AR aims to provide a recourse action for altering the undesired prediction result given by a classifier. Existing AR methods assume that we can access complete information on the features of an input instance. However, we often encounter missing values in a given instance (e.g., due to privacy concerns), and previous studies have not discussed such a practical situation. In this paper, we first empirically and theoretically show the risk that a naive approach with a single imputation technique fails to obtain good actions regarding their validity, cost, and features to be changed. To alleviate this risk, we formulate the task of obtaining a valid and low-cost action for a given incomplete instance by incorporating the idea of multiple imputation. Then, we provide some theoretical analyses of our task and propose a practical solution based on mixed-integer linear optimization. Experimental results demonstrated the efficacy of our method in the presence of missing values compared to the baselines.

Ryosuke Masuya, Yuichi Ike, Hiroshi Kera

Vanishing component analysis (VCA) computes approximate generators of vanishing ideals of samples, which are further used for extracting nonlinear features of the samples. Recent studies have shown that normalization of approximate generators plays an important role and different normalization leads to generators of different properties. In this paper, inspired by recent self-supervised frameworks, we propose a contrastive normalization method for VCA, where we impose the generators to vanish on the target samples and to be normalized on the transformed samples. We theoretically show that a contrastive normalization enhances the discriminative power of VCA, and provide the algebraic interpretation of VCA under our normalization. Numerical experiments demonstrate the effectiveness of our method. This is the first study to tailor the normalization of approximate generators of vanishing ideals to obtain discriminative features.

Thibault de Surrel, Felix Hensel, Mathieu Carrière et al.

The use of topological descriptors in modern machine learning applications, such as Persistence Diagrams (PDs) arising from Topological Data Analysis (TDA), has shown great potential in various domains. However, their practical use in applications is often hindered by two major limitations: the computational complexity required to compute such descriptors exactly, and their sensitivity to even low-level proportions of outliers. In this work, we propose to bypass these two burdens in a data-driven setting by entrusting the estimation of (vectorization of) PDs built on top of point clouds to a neural network architecture that we call RipsNet. Once trained on a given data set, RipsNet can estimate topological descriptors on test data very efficiently with generalization capacity. Furthermore, we prove that RipsNet is robust to input perturbations in terms of the 1-Wasserstein distance, a major improvement over the standard computation of PDs that only enjoys Hausdorff stability, yielding RipsNet to substantially outperform exactly-computed PDs in noisy settings. We showcase the use of RipsNet on both synthetic and real-world data. Our open-source implementation is publicly available at https://github.com/hensel-f/ripsnet and will be included in the Gudhi library.

Eduardo Paluzo-Hidalgo, Yuichi Ike

We introduce a theoretical framework that connects multi-chart autoencoders in manifold learning with the classical theory of vector bundles and characteristic classes. Rather than viewing autoencoders as producing a single global Euclidean embedding, we treat a collection of locally trained encoder-decoder pairs as a learned atlas on a manifold. We show that any reconstruction-consistent autoencoder atlas canonically defines transition maps satisfying the cocycle condition, and that linearising these transition maps yields a vector bundle coinciding with the tangent bundle when the latent dimension matches the intrinsic dimension of the manifold. This construction provides direct access to differential-topological invariants of the data. In particular, we show that the first Stiefel-Whitney class can be computed from the signs of the Jacobians of learned transition maps, yielding an algorithmic criterion for detecting orientability. We also show that non-trivial characteristic classes provide obstructions to single-chart representations, and that the minimum number of autoencoder charts is determined by the good cover structure of the manifold. Finally, we apply our methodology to low-dimensional orientable and non-orientable manifolds, as well as to a non-orientable high-dimensional image dataset.

Kentaro Kanamori, Takuya Takagi, Ken Kobayashi et al.

This paper proposes a new algorithm for learning accurate tree-based models while ensuring the existence of recourse actions. Algorithmic Recourse (AR) aims to provide a recourse action for altering the undesired prediction result given by a model. Typical AR methods provide a reasonable action by solving an optimization task of minimizing the required effort among executable actions. In practice, however, such actions do not always exist for models optimized only for predictive performance. To alleviate this issue, we formulate the task of learning an accurate classification tree under the constraint of ensuring the existence of reasonable actions for as many instances as possible. Then, we propose an efficient top-down greedy algorithm by leveraging the adversarial training techniques. We also show that our proposed algorithm can be applied to the random forest, which is known as a popular framework for learning tree ensembles. Experimental results demonstrated that our method successfully provided reasonable actions to more instances than the baselines without significantly degrading accuracy and computational efficiency.

Charles Arnal, Felix Hensel, Mathieu Carrière et al.

Despite their successful application to a variety of tasks, neural networks remain limited, like other machine learning methods, by their sensitivity to shifts in the data: their performance can be severely impacted by differences in distribution between the data on which they were trained and that on which they are deployed. In this article, we propose a new family of representations, called MAGDiff, that we extract from any given neural network classifier and that allows for efficient covariate data shift detection without the need to train a new model dedicated to this task. These representations are computed by comparing the activation graphs of the neural network for samples belonging to the training distribution and to the target distribution, and yield powerful data- and task-adapted statistics for the two-sample tests commonly used for data set shift detection. We demonstrate this empirically by measuring the statistical powers of two-sample Kolmogorov-Smirnov (KS) tests on several different data sets and shift types, and showing that our novel representations induce significant improvements over a state-of-the-art baseline relying on the network output.

Théo Lacombe, Yuichi Ike, Mathieu Carriere et al.

Although neural networks are capable of reaching astonishing performances on a wide variety of contexts, properly training networks on complicated tasks requires expertise and can be expensive from a computational perspective. In industrial applications, data coming from an open-world setting might widely differ from the benchmark datasets on which a network was trained. Being able to monitor the presence of such variations without retraining the network is of crucial importance. In this article, we develop a method to monitor trained neural networks based on the topological properties of their activation graphs. To each new observation, we assign a Topological Uncertainty, a score that aims to assess the reliability of the predictions by investigating the whole network instead of its final layer only, as typically done by practitioners. Our approach entirely works at a post-training level and does not require any assumption on the network architecture, optimization scheme, nor the use of data augmentation or auxiliary datasets; and can be faithfully applied on a large range of network architectures and data types. We showcase experimentally the potential of Topological Uncertainty in the context of trained network selection, Out-Of-Distribution detection, and shift-detection, both on synthetic and real datasets of images and graphs.

Kentaro Kanamori, Takuya Takagi, Ken Kobayashi et al.

Post-hoc explanation methods for machine learning models have been widely used to support decision-making. One of the popular methods is Counterfactual Explanation (CE), also known as Actionable Recourse, which provides a user with a perturbation vector of features that alters the prediction result. Given a perturbation vector, a user can interpret it as an "action" for obtaining one's desired decision result. In practice, however, showing only a perturbation vector is often insufficient for users to execute the action. The reason is that if there is an asymmetric interaction among features, such as causality, the total cost of the action is expected to depend on the order of changing features. Therefore, practical CE methods are required to provide an appropriate order of changing features in addition to a perturbation vector. For this purpose, we propose a new framework called Ordered Counterfactual Explanation (OrdCE). We introduce a new objective function that evaluates a pair of an action and an order based on feature interaction. To extract an optimal pair, we propose a mixed-integer linear optimization approach with our objective function. Numerical experiments on real datasets demonstrated the effectiveness of our OrdCE in comparison with unordered CE methods.

Mathieu Carrière, Frédéric Chazal, Yuichi Ike et al.

Persistence diagrams, the most common descriptors of Topological Data Analysis, encode topological properties of data and have already proved pivotal in many different applications of data science. However, since the (metric) space of persistence diagrams is not Hilbert, they end up being difficult inputs for most Machine Learning techniques. To address this concern, several vectorization methods have been put forward that embed persistence diagrams into either finite-dimensional Euclidean space or (implicit) infinite dimensional Hilbert space with kernels. In this work, we focus on persistence diagrams built on top of graphs. Relying on extended persistence theory and the so-called heat kernel signature, we show how graphs can be encoded by (extended) persistence diagrams in a provably stable way. We then propose a general and versatile framework for learning vectorizations of persistence diagrams, which encompasses most of the vectorization techniques used in the literature. We finally showcase the experimental strength of our setup by achieving competitive scores on classification tasks on real-life graph datasets.