In recent years, a comprehensive study of multi-view datasets (e.g., multi-omics and imaging scans) has been a focus and forefront in biomedical research. State-of-the-art biomedical technologies are enabling us to collect multi-view biomedical datasets for the study of complex diseases. While all the views of data tend to explore complementary information of a disease, multi-view data analysis with complex interactions is challenging for a deeper and holistic understanding of biological systems. In this paper, we propose a novel generalized kernel machine approach to identify higher-order composite effects in multi-view biomedical datasets. This generalized semi-parametric (a mixed-effect linear model) approach includes the marginal and joint Hadamard product of features from different views of data. The proposed kernel machine approach considers multi-view data as predictor variables to allow more thorough and comprehensive modeling of a complex trait. The proposed method can be applied to the study of any disease model, where multi-view datasets are available. We applied our approach to both synthesized datasets and real multi-view datasets from adolescence brain development and osteoporosis study, including an imaging scan dataset and five omics datasets. Our experiments demonstrate that the proposed method can effectively identify higher-order composite effects and suggest that corresponding features (genes, region of interests, and chemical taxonomies) function in a concerted effort. We show that the proposed method is more generalizable than existing ones.
In many artificial intelligence and computer vision systems, the same object can be observed at distinct viewpoints or by diverse sensors, which raises the challenges for recognizing objects from different, even heterogeneous views. Multi-view discriminant analysis (MvDA) is an effective multi-view subspace learning method, which finds a discriminant common subspace by jointly learning multiple view-specific linear projections for object recognition from multiple views, in a non-pairwise way. In this paper, we propose the kernel version of multi-view discriminant analysis, called kernel multi-…
This paper introduces a novel framework for generative models based on Restricted Kernel Machines (RKMs) with joint multi-view generation and uncorrelated feature learning, called Gen-RKM. To enable joint multi-view generation, this mechanism uses a shared representation of data from various views. Furthermore, the model has a primal and dual formulation to incorporate both kernel-based and (deep convolutional) neural network based models within the same setting. When using neural networks as explicit feature-maps, a novel training procedure is proposed, which jointly learns the features and s…
Recent research on multiple kernel learning has lead to a number of approaches for combining kernels in regularized risk minimization. The proposed approaches include different formulations of objectives and varying regularization strategies. In this paper we present a unifying general optimization criterion for multiple kernel learning and show how existing formulations are subsumed as special cases. We also derive the criterion's dual representation, which is suitable for general smooth optimization algorithms. Finally, we evaluate multiple kernel learning in this framework analytically usin…
Positive definite kernels and their associated Reproducing Kernel Hilbert Spaces provide a mathematically compelling and practically competitive framework for learning from data. In this paper we take the approximation theory point of view to explore various aspects of smooth kernels related to their inferential properties. We analyze eigenvalue decay of kernels operators and matrices, properties of eigenfunctions/eigenvectors and "Fourier" coefficients of functions in the kernel space restricted to a discrete set of data points. We also investigate the fitting capacity of kernels, giving expl…
TU Dortmund University（多特蒙德工业大学）；Washington University in St. Louis（圣路易斯华盛顿大学）；TU Darmstadt（达姆施塔特工业大学）
Non-linear kernel methods can be approximated by fast linear ones using suitable explicit feature maps allowing their application to large scale problems. We investigate how convolution kernels for structured data are composed from base kernels and construct corresponding feature maps. On this basis we propose exact and approximative feature maps for widely used graph kernels based on the kernel trick. We analyze for which kernels and graph properties computation by explicit feature maps is feasible and actually more efficient. In particular, we derive approximative, explicit feature maps for …
In this paper, we propose a unified view of gradient-based algorithms for stochastic convex composite optimization by extending the concept of estimate sequence introduced by Nesterov. This point of view covers the stochastic gradient descent method, variants of the approaches SAGA, SVRG, and has several advantages: (i) we provide a generic proof of convergence for the aforementioned methods; (ii) we show that this SVRG variant is adaptive to strong convexity; (iii) we naturally obtain new algorithms with the same guarantees; (iv) we derive generic strategies to make these algorithms robust to…
Indian Statistical Institute（印度统计研究所）；University of California, Berkeley（加州大学伯克利分校）；Duke University（杜克大学）
Kernel $k$-means clustering is a powerful tool for unsupervised learning of non-linearly separable data. Since the earliest attempts, researchers have noted that such algorithms often become trapped by local minima arising from non-convexity of the underlying objective function. In this paper, we generalize recent results leveraging a general family of means to combat sub-optimal local solutions to the kernel and multi-kernel settings. Called Kernel Power $k$-Means, our algorithm makes use of majorization-minimization (MM) to better solve this non-convex problem. We show the method implicitly …
In this paper, we propose a unified view of gradient-based algorithms for stochastic convex composite optimization by extending the concept of estimate sequence introduced by Nesterov. More precisely, we interpret a large class of stochastic optimization methods as procedures that iteratively minimize a surrogate of the objective, which covers the stochastic gradient descent method and variants of the incremental approaches SAGA, SVRG, and MISO/Finito/SDCA. This point of view has several advantages: (i) we provide a simple generic proof of convergence for all of the aforementioned methods; (ii…
This paper presents a general vector-valued reproducing kernel Hilbert spaces (RKHS) framework for the problem of learning an unknown functional dependency between a structured input space and a structured output space. Our formulation encompasses both Vector-valued Manifold Regularization and Co-regularized Multi-view Learning, providing in particular a unifying framework linking these two important learning approaches. In the case of the least square loss function, we provide a closed form solution, which is obtained by solving a system of linear equations. In the case of Support Vector Mach…
In this study, we tested the interaction effect of multimodal datasets using a novel method called the kernel method for detecting higher order interactions among biologically relevant mulit-view data. Using a semiparametric method on a reproducing kernel Hilbert space (RKHS), we used a standard mixed-effects linear model and derived a score-based variance component statistic that tests for higher order interactions between multi-view data. The proposed method offers an intangible framework for the identification of higher order interaction effects (e.g., three way interaction) between genetic…
Learning on graph structured data has drawn increasing interest in recent years. Frameworks like Graph Convolutional Networks (GCNs) have demonstrated their ability to capture structural information and obtain good performance in various tasks. In these frameworks, node aggregation schemes are typically used to capture structural information: a node's feature vector is recursively computed by aggregating features of its neighboring nodes. However, most of aggregation schemes treat all connections in a graph equally, ignoring node feature similarities. In this paper, we re-interpret node aggreg…
The problem of graph learning concerns the construction of an explicit topological structure revealing the relationship between nodes representing data entities, which plays an increasingly important role in the success of many graph-based representations and algorithms in the field of machine learning and graph signal processing. In this paper, we propose a novel graph learning framework that incorporates the node-side and observation-side information, and in particular the covariates that help to explain the dependency structures in graph signals. To this end, we consider graph signals as fu…
Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所（HIIT））；Aalto University（阿尔托大学）；Aix-Marseille University（艾克斯-马赛大学）；CNRS（法国国家科学研究中心）；Turing Center for Living Systems (CENTURI)（图灵生命系统中心（CENTURI））
We consider the kernel completion problem with the presence of multiple views in the data. In this context the data samples can be fully missing in some views, creating missing columns and rows to the kernel matrices that are calculated individually for each view. We propose to solve the problem of completing the kernel matrices with Cross-View Kernel Transfer (CVKT) procedure, in which the features of the other views are transformed to represent the view under consideration. The transformations are learned with kernel alignment to the known part of the kernel matrix, allowing for finding gene…
Ulsan National Institute of Science and Technology（蔚山国立科学技术院）
Gaussian Processes (GPs) provide a general and analytically tractable way of modeling complex time-varying, nonparametric functions. The Automatic Bayesian Covariance Discovery (ABCD) system constructs natural-language description of time-series data by treating unknown time-series data nonparametrically using GP with a composite covariance kernel function. Unfortunately, learning a composite covariance kernel with a single time-series data set often results in less informative kernel that may not give qualitative, distinctive descriptions of data. We address this challenge by proposing two re…
Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所（HIIT））；Aalto University School of Science and Technology（阿尔托大学科学与技术学院）
In this paper, we introduce the first method that (1) can complete kernel matrices with completely missing rows and columns as opposed to individual missing kernel values, (2) does not require any of the kernels to be complete a priori, and (3) can tackle non-linear kernels. These aspects are necessary in practical applications such as integrating legacy data sets, learning under sensor failures and learning when measurements are costly for some of the views. The proposed approach predicts missing rows by modelling both within-view and between-view relationships among kernel values. We show, b…
Centre for Artificial Intelligence, University College London（大学学院伦敦大学人工智能中心）；Gatsby Computational Neuroscience Unit, University College London（大学学院伦敦大学盖茨比计算神经科学单位）；Department of Statistical Science, University College London（大学学院伦敦大学统计科学系）；Faculty of Engineering and Science, Adolfo Ibañez University（工程与科学学院，阿道弗·伊巴涅斯大学）
Aix Marseille Univ（艾克斯-马赛大学）；Université de Toulon（土伦大学）；CNRS（法国国家科学研究中心）；LIS（信息科学实验室）
We consider the problem of metric learning for multi-view data and present a novel method for learning within-view as well as between-view metrics in vector-valued kernel spaces, as a way to capture multi-modal structure of the data. We formulate two convex optimization problems to jointly learn the metric and the classifier or regressor in kernel feature spaces. An iterative three-step multi-view metric learning algorithm is derived from the optimization problems. In order to scale the computation to large training sets, a block-wise Nystr{ö}m approximation of the multi-view kernel matrix is …
Multiple Kernel Learning, or MKL, extends (kernelized) SVM by attempting to learn not only a classifier/regressor but also the best kernel for the training task, usually from a combination of existing kernel functions. Most MKL methods seek the combined kernel that performs best over every training example, sacrificing performance in some areas to seek a global optimum. Localized kernel learning (LKL) overcomes this limitation by allowing the training algorithm to match a component kernel to the examples that can exploit it best. Several approaches to the localized kernel learning problem have…
Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；Institute of Software, Chinese Academy of Sciences（中国科学院软件研究所）；Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）
Existing multi-view learning methods based on kernel function either require the user to select and tune a single predefined kernel or have to compute and store many Gram matrices to perform multiple kernel learning. Apart from the huge consumption of manpower, computation and memory resources, most of these models seek point estimation of their parameters, and are prone to overfitting to small training data. This paper presents an adaptive kernel nonlinear max-margin multi-view learning model under the Bayesian framework. Specifically, we regularize the posterior of an efficient multi-view la…
Universidad Carlos III de Madrid（马德里卡洛斯三世大学）；Gregorio Marañón Health Research Institute（格雷戈里奥·马拉尼翁健康研究所）
Multi-view problems can be faced with latent variable models since they are able to find low-dimensional projections that fairly capture the correlations among the multiple views that characterise each datum. On the other hand, high-dimensionality and non-linear issues are traditionally handled by kernel methods, inducing a (non)-linear function between the latent projection and the data itself. However, they usually come with scalability issues and exposition to overfitting. Here, we propose merging both approaches into single model so that we can exploit the best features of multi-view laten…
The input data features set for many data driven tasks is high-dimensional while the intrinsic dimension of the data is low. Data analysis methods aim to uncover the underlying low dimensional structure imposed by the low dimensional hidden parameters by utilizing distance metrics that consider the set of attributes as a single monolithic set. However, the transformation of the low dimensional phenomena into the measured high dimensional observations might distort the distance metric, This distortion can effect the desired estimated low dimensional geometric structure. In this paper, we sugges…
Multi-View Oriented GPLVM: Expressiveness and Efficiency
School of Computing and Data Science University of Hong Kong（计算与数据科学学院 香港大学）；Department of Signal Theory and Communications Universidad Carlos III de Madrid（信号理论与通信系 马德里卡洛斯三世大学）
As a subset of unsupervised representation learning, self-supervised representation learning adopts self-defined signals as supervision and uses the learned representation for downstream tasks, such as object detection and image captioning. Many proposed approaches for self-supervised learning follow naturally a multi-view perspective, where the input (e.g., original images) and the self-supervised signals (e.g., augmented images) can be seen as two redundant views of the data. Building from this multi-view perspective, this paper provides an information-theoretical framework to better underst…
RJ Research Consulting（RJ研究咨询公司）；Tencent AI Lab（腾讯人工智能实验室）
This paper first presents a theory for generative adversarial methods that does not rely on the traditional minimax formulation. It shows that with a strong discriminator, a good generator can be learned so that the KL divergence between the distributions of real data and generated data improves after each functional gradient step until it converges to zero. Based on the theory, we propose a new stable generative adversarial method. A theoretical insight into the original GAN from this new viewpoint is also provided. The experiments on image generation show the effectiveness of our new method.
The primary hyperparameter in kernel regression (KR) is the choice of kernel. In most theoretical studies of KR, one assumes the kernel is fixed before seeing the training data. Under this assumption, it is known that the optimal kernel is equal to the prior covariance of the target function. In this note, we consider KR in which the kernel may be updated after seeing the training data. We point out that an analogous choice of kernel using the posterior of the target function is optimal in this setting. Connections to the view of deep neural networks as data-dependent kernel learners are discu…
Non-parametric goodness-of-fit testing procedures based on kernel Stein discrepancies (KSD) are promising approaches to validate general unnormalised distributions in various scenarios. Existing works focused on studying kernel choices to boost test performances. However, the choices of (non-unique) Stein operators also have considerable effect on the test performances. Inspired by the standardisation technique that was originally developed to better derive approximation properties for normal distributions, we present a unifying framework, called standardisation-function kernel Stein discrepan…
Bayesian Optimization (BO) has become a core method for solving expensive black-box optimization problems. While much research focussed on the choice of the acquisition function, we focus on online length-scale adaption and the choice of kernel function. Instead of choosing hyperparameters in view of maximum likelihood on past data, we propose to use the acquisition function to decide on hyperparameter adaptation more robustly and in view of the future optimization progress. Further, we propose a particular kernel function that includes non-stationarity and local anisotropy and thereby implici…
We develop a general duality between neural networks and compositional kernels, striving towards a better understanding of deep learning. We show that initial representations generated by common random initializations are sufficiently rich to express all functions in the dual kernel space. Hence, though the training objective is hard to optimize in the worst case, the initial weights form a good starting point for optimization. Our dual view also reveals a pragmatic and aesthetic perspective of neural networks and underscores their expressive power.
The amount of data collected from patients involved in clinical trials is continuously growing. All patient characteristics are potential covariates that could be used to improve clinical trial analysis and power. However, the restricted number of patients in phases I and II studies limits the possible number of covariates included in the analyses. In this paper, we investigate the cost/benefit ratio of including covariates in the analysis of clinical trials. Within this context, we address the long-running question "What is the optimum number of covariates to include in a clinical trial?" To …
