Latent regularization for feature selection using kernel methods in tumor classification
Institut Charles Delaunay, Universite de Technologie de Troyes（特鲁瓦理工大学夏尔·德洛纳研究所）；Biomedicine Research Institute of Buenos Aires - Max Planck Partner Institute（布宜诺斯艾利斯生物医学研究所-马克斯·普朗克伙伴研究所）；Universidad Tecnologica Nacional Buenos Aires（布宜诺斯艾利斯国立理工大学）
Martin Palazzo, Patricio Yankilevich, Pierre Beauseroy
The transcriptomics of cancer tumors are characterized with tens of thousands of gene expression features. Patient prognosis or tumor stage can be assessed by machine learning techniques like supervised classification tasks given a gene expression profile. Feature selection is a useful approach to select the key genes which helps to classify tumors. In this work we propose a feature selection method based on Multiple Kernel Learning that results in a reduced subset of genes and a custom kernel that improves the classification performance when used in support vector classification. During the feature selection process this method performs a novel latent regularisation by relaxing the supervised target problem by introducing unsupervised structure obtained from the latent space learned by a non linear dimensionality reduction model. An improvement of the generalization capacity is obtained and assessed by the tumor classification performance on new unseen test samples when the classifier is trained with the features selected by the proposed method in comparison with other supervised feature selection approaches.
Universite de Technologie de Troyes（特鲁瓦技术大学）；Instituto de Investigacion en Biomedicina de Buenos Aires (IBioBA)—CONICET Partner Institute of the Max Planck Society（布宜诺斯艾利斯生物医学研究所（IBioBA）—马克斯·普朗克学会合作研究所）
Molecular data from tumor profiles is high dimensional. Tumor profiles can be characterized by tens of thousands of gene expression features. Due to the size of the gene expression feature set machine learning methods are exposed to noisy variables and complexity. Tumor types present heterogeneity and can be subdivided in tumor subtypes. In many cases tumor data does not include tumor subtype labeling thus unsupervised learning methods are necessary for tumor subtype discovery. This work aims to learn meaningful and low dimensional representations of tumor samples and find tumor subtype cluste…
We tackle the challenge of disentangled representation learning in generative adversarial networks (GANs) from the perspective of regularized optimal transport (OT). Specifically, a smoothed OT loss gives rise to an implicit transportation plan between the latent space and the data space. Based on this theoretical observation, we exploit a structured regularization on the transportation plan to encourage a prescribed latent subspace to be informative. This yields the formulation of a novel informative OT-based GAN. By convex duality, we obtain the equivalent view that this leads to perturbed g…
University of Chicago（芝加哥大学）；Fermi National Accelerator Laboratory（费米国家加速器实验室）
Bayesian optimization has been challenged by datasets with large-scale, high-dimensional, and non-stationary characteristics, which are common in real-world scenarios. Recent works attempt to handle such input by applying neural networks ahead of the classical Gaussian process to learn a latent representation. We show that even with proper network design, such learned representation often leads to collision in the latent space: two points with significantly different observations collide in the learned latent space, leading to degraded optimization performance. To address this issue, we propos…
University of Bremen（不来梅大学）；SCiLS, Bruker Daltonik GmbH（布鲁克道尔顿公司SCiLS部门）；Proteopath GmbH（Proteopath公司）；Center for Histology Cytology and Molecular Diagnostic, Trier（特里尔组织学、细胞学与分子诊断中心）
Neural networks have recently been established as a viable classification method for imaging mass spectrometry data for tumor typing. For multi-laboratory scenarios however, certain confounding factors may strongly impede their performance. In this work, we introduce Deep Relevance Regularization, a method of restricting what the neural network can focus on during classification, in order to improve the classification performance. We demonstrate how Deep Relevance Regularization robustifies neural networks against confounding factors on a challenging inter-lab dataset consisting of breast and …
Normandie Univ, INSA Rouen, UNIROUEN, UNIHAVRE, LITIS（诺曼底大学，鲁昂国立应用科学学院，鲁昂大学，勒阿弗尔大学，LITIS）；Department of Nuclear Medicine, Henri Becquerel Cancer Center（亨利·贝克勒尔癌症中心核医学科）
Multimodal MR images can provide complementary information for accurate brain tumor segmentation. However, it's common to have missing imaging modalities in clinical practice. Since there exists a strong correlation between multi modalities, a novel correlation representation block is proposed to specially discover the latent multi-source correlation. Thanks to the obtained correlation representation, the segmentation becomes more robust in the case of missing modalities. The model parameter estimation module first maps the individual representation produced by each encoder to obtain independe…
Three-dimensional (3D) integrated renal structures (IRS) segmentation is important in clinical practice. With the advancement of deep learning techniques, many powerful frameworks focusing on medical image segmentation are proposed. In this challenge, we utilized the nnU-Net framework, which is the state-of-the-art method for medical image segmentation. To reduce the outlier prediction for the tumor label, we combine contour regularization (CR) loss of the tumor label with Dice loss and cross-entropy loss to improve this phenomenon.
There exist many forms of deep latent variable models, such as the variational autoencoder and adversarial autoencoder. Regardless of the specific class of model, there exists an implicit consensus that the latent distribution should be regularized towards the prior, even in the case where the prior distribution is learned. Upon investigating the effect of latent regularization on image generation our results indicate that in the case where a sufficiently expressive prior is learned, latent regularization is not necessary and may in fact be harmful insofar as image quality is concerned. We add…
Center for Music Technology, Georgia Institute of Technology（佐治亚理工学院音乐技术中心）
Selective manipulation of data attributes using deep generative models is an active area of research. In this paper, we present a novel method to structure the latent space of a Variational Auto-Encoder (VAE) to encode different continuous-valued attributes explicitly. This is accomplished by using an attribute regularization loss which enforces a monotonic relationship between the attribute values and the latent code of the dimension along which the attribute is to be encoded. Consequently, post-training, the model can be used to manipulate the attribute by simply changing the latent code of …
Université Pierre et Marie Curie（皮埃尔和玛丽·居里大学）；Sony CSL（索尼计算机科学研究所）；École Polytechnique（巴黎综合理工学院）
VAEs (Variational AutoEncoders) have proved to be powerful in the context of density modeling and have been used in a variety of contexts for creative purposes. In many settings, the data we model possesses continuous attributes that we would like to take into account at generation time. We propose in this paper GLSR-VAE, a Geodesic Latent Space Regularization for the Variational AutoEncoder architecture and its generalizations which allows a fine control on the embedding of the data into the latent space. When augmenting the VAE loss with this regularization, changes in the learned latent spa…
Philips Co-Creation Center（飞利浦共创中心）；University of Tsukuba（筑波大学）；I Dragon Corporation（I Dragon公司）；The Tokyo Foundation for Policy Research（东京政策研究基金会）；Lowe’s Services India Pvt. Ltd.（劳氏印度服务私人有限公司）
Virtual Adversarial Training (VAT) has shown impressive results among recently developed regularization methods called consistency regularization. VAT utilizes adversarial samples, generated by injecting perturbation in the input space, for training and thereby enhances the generalization ability of a classifier. However, such adversarial samples can be generated only within a very small area around the input data point, which limits the adversarial effectiveness of such samples. To address this problem we propose LVAT (Latent space VAT), which injects perturbation in the latent space instead …
Latent Adversarial Regularization for Offline Preference Optimization
Department of Computer Science, Stanford University（斯坦福大学计算机科学系）；Siebel School of Computing（塞贝尔计算学院）；Data Science, University of Illinois at Urbana-Champaign（数据科学，伊利诺伊大学厄巴纳-香槟分校）
KTH Royal Institute of Technology（瑞典皇家理工学院）；Research Institutes of Sweden（瑞典研究机构）
Autoencoders and their variations provide unsupervised models for learning low-dimensional representations for downstream tasks. Without proper regularization, autoencoder models are susceptible to the overfitting problem and the so-called posterior collapse phenomenon. In this paper, we introduce a quantization-based regularizer in the bottleneck stage of autoencoder models to learn meaningful latent representations. We combine both perspectives of Vector Quantized-Variational AutoEncoders (VQ-VAE) and classical denoising regularization methods of neural networks. We interpret quantizers as r…
FusionINN: Decomposable Image Fusion for Brain Tumor Monitoring
Technische Universität Dresden（德累斯顿工业大学）；Shandong University of Science and Technology（山东科技大学）；Shanghai Tenth People’s Hospital（上海市第十人民医院）；Tongji University Medical School（同济大学医学院）
Cluster of Excellence – Machine Learning for Science（卓越集群——科学机器学习）
A critical challenge for any intelligent system is to infer structure from continuous data streams. Theories of event-predictive cognition suggest that the brain segments sensorimotor information into compact event encodings, which are used to anticipate and interpret environmental dynamics. Here, we introduce a SUrprise-GAted Recurrent neural network (SUGAR) using a novel form of counterfactual regularization. We test the model on a hierarchical sequence prediction task, where sequences are generated by alternating hidden graph structures. Our model learns to both compress the temporal dynami…
Natural images can be regarded as residing in a manifold that is embedded in a higher dimensional Euclidean space. Generative Adversarial Networks (GANs) try to learn the distribution of the real images in the manifold to generate samples that look real. But the results of existing methods still exhibit many unpleasant artifacts and distortions even for the cases where the desired ground truth target images are available for supervised learning such as in single image super resolution (SISR). We probe for ways to alleviate these problems for supervised GANs in this paper. We explicitly apply t…
In this paper, we propose a novel unsupervised clustering approach exploiting the hidden information that is indirectly introduced through a pseudo classification objective. Specifically, we randomly assign a pseudo parent-class label to each observation which is then modified by applying the domain specific transformation associated with the assigned label. Generated pseudo observation-label pairs are subsequently used to train a neural network with Auto-clustering Output Layer (ACOL) that introduces multiple softmax nodes for each pseudo parent-class. Due to the unsupervised objective based …
Mila（米拉人工智能研究所）；DIRO, Université de Montréal（蒙特利尔大学计算机科学与运筹学系）；ServiceNow Research（ServiceNow研究院）；Tübingen AI Center, University of Tübingen（蒂宾根大学蒂宾根人工智能中心）；Google Research（谷歌研究院）
This work introduces a novel principle we call disentanglement via mechanism sparsity regularization, which can be applied when the latent factors of interest depend sparsely on past latent factors and/or observed auxiliary variables. We propose a representation learning method that induces disentanglement by simultaneously learning the latent factors and the sparse causal graphical model that relates them. We develop a rigorous identifiability theory, building on recent nonlinear independent component analysis (ICA) results, that formalizes this principle and shows how the latent variables ca…
Existing Bayesian models, especially nonparametric Bayesian methods, rely on specially conceived priors to incorporate domain knowledge for discovering improved latent representations. While priors can affect posterior distributions through Bayes' rule, imposing posterior regularization is arguably more direct and in some cases more natural and general. In this paper, we present regularized Bayesian inference (RegBayes), a novel computational framework that performs posterior inference with a regularization term on the desired post-data posterior distribution under an information theoretical f…
School of Computer Science（计算机科学学院）；The Interdisciplinary Center, Herzliya（赫兹利亚跨学科中心）
Autoencoders represent an effective approach for computing the underlying factors characterizing datasets of different types. The latent representation of autoencoders have been studied in the context of enabling interpolation between data points by decoding convex combinations of latent vectors. This interpolation, however, often leads to artifacts or produces unrealistic results during reconstruction. We argue that these incongruities are due to the structure of the latent space and because such naively interpolated latent vectors deviate from the data manifold. In this paper, we propose a r…
School of Software, Northwestern Polytechnical University（西北工业大学软件学院）
Generative Adversarial Networks (GAN) is currently widely used as an unsupervised image generation method. Current state-of-the-art GANs can generate photorealistic images with high resolution. However, a large amount of data is required, or the model would prone to generate images with similar patterns (mode collapse) and bad quality. I proposed an additional structure and loss function for GANs called LFM, trained to maximize the feature diversity between the different dimensions of the latent space to avoid mode collapse without affecting the image quality. Orthogonal latent vector pairs ar…
University of Minnesota（明尼苏达大学）；IQVIA（艾昆纬）；University of Virginia（弗吉尼亚大学）；Temple University（天普大学）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Accurate prediction of the transmission of epidemic diseases such as COVID-19 is crucial for implementing effective mitigation measures. In this work, we develop a tensor method to predict the evolution of epidemic trends for many regions simultaneously. We construct a 3-way spatio-temporal tensor (location, attribute, time) of case counts and propose a nonnegative tensor factorization with latent epidemiological model regularization named STELAR. Unlike standard tensor factorization methods which cannot predict slabs ahead, STELAR enables long-term prediction by incorporating latent temporal …
Variational Autoencoder (VAE), a simple and effective deep generative model, has led to a number of impressive empirical successes and spawned many advanced variants and theoretical investigations. However, recent studies demonstrate that, when equipped with expressive generative distributions (aka. decoders), VAE suffers from learning uninformative latent representations with the observation called KL Varnishing, in which case VAE collapses into an unconditional generative model. In this work, we introduce mutual posterior-divergence regularization, a novel regularization that is able to cont…
Duke University（杜克大学）；Infinia ML Inc.（Infinia ML公司）
A new algorithmic framework is proposed for learning autoencoders of data distributions. We minimize the discrepancy between the model and target distributions, with a \emph{relational regularization} on the learnable latent prior. This regularization penalizes the fused Gromov-Wasserstein (FGW) distance between the latent prior and its corresponding posterior, allowing one to flexibly learn a structured prior distribution associated with the generative model. Moreover, it helps co-training of multiple autoencoders even if they have heterogeneous architectures and incomparable latent spaces. W…
University of Cambridge（剑桥大学）；Mila, Université de Montréal（蒙特利尔大学米拉（Mila）实验室）；Alan Turing Institute（艾伦·图灵研究所）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
This paper considers the problem of unsupervised 3D object reconstruction from in-the-wild single-view images. Due to ambiguity and intrinsic ill-posedness, this problem is inherently difficult to solve and therefore requires strong regularization to achieve disentanglement of different latent factors. Unlike existing works that introduce explicit regularizations into objective functions, we look into a different space for implicit regularization -- the structure of latent space. Specifically, we restrict the structure of latent space to capture a topological causal ordering of latent factors …
There have been many recent advances in representation learning; however, unsupervised representation learning can still struggle with model identification issues related to rotations of the latent space. Variational Auto-Encoders (VAEs) and their extensions such as $β$-VAEs have been shown to improve local alignment of latent variables with PCA directions, which can help to improve model disentanglement under some conditions. Borrowing inspiration from Independent Component Analysis (ICA) and sparse coding, we propose applying an $L_1$ loss to the VAE's generative Jacobian during training to …
LIT-LVM: Structured Regularization for Interaction Terms in Linear Predictors using Latent Variable Models
Department of Computer and Data Sciences（计算机与数据科学系）；Case Western Reserve University（凯斯西储大学）；Department of Mathematics and Computer Science（数学与计算机科学系）；Suffolk University（索尔福德大学）
Latent Variable Models (LVMs) are a large family of machine learning models providing a principled and effective way to extract underlying patterns, structure and knowledge from observed data. Due to the dramatic growth of volume and complexity of data, several new challenges have emerged and cannot be effectively addressed by existing LVMs: (1) How to capture long-tail patterns that carry crucial information when the popularity of patterns is distributed in a power-law fashion? (2) How to reduce model complexity and computational cost without compromising the modeling power of LVMs? (3) How t…
Most practical data science problems encounter missing data. A wide variety of solutions exist, each with strengths and weaknesses that depend upon the missingness-generating process. Here we develop a theoretical framework for training and inference using only observed variables enabling modeling of incomplete datasets without imputation. Using an information and measure-theoretic argument we construct models with latent space representations that regularize against the potential bias introduced by missing data. The theoretical properties of this approach are demonstrated empirically using a …
We propose a novel method for emotion conversion in speech based on a chained encoder-decoder-predictor neural network architecture. The encoder constructs a latent embedding of the fundamental frequency (F0) contour and the spectrum, which we regularize using the Large Diffeomorphic Metric Mapping (LDDMM) registration framework. The decoder uses this embedding to predict the modified F0 contour in a target emotional class. Finally, the predictor uses the original spectrum and the modified F0 contour to generate a corresponding target spectrum. Our joint objective function simultaneously optim…
When designing variational autoencoders (VAEs) or other types of latent space models, the dimensionality of the latent space is typically defined upfront. In this process, it is possible that the number of dimensions is under- or overprovisioned for the application at hand. In case the dimensionality is not predefined, this parameter is usually determined using time- and resource-consuming cross-validation. For these reasons we have developed a technique to shrink the latent space dimensionality of VAEs automatically and on-the-fly during training using Generalized ELBO with Constrained Optimi…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；University at Buffalo（布法罗大学）；Amazon（亚马逊）
Contrastive loss has been increasingly used in learning representations from multiple modalities. In the limit, the nature of the contrastive loss encourages modalities to exactly match each other in the latent space. Yet it remains an open question how the modality alignment affects the downstream task performance. In this paper, based on an information-theoretic argument, we first prove that exact modality alignment is sub-optimal in general for downstream prediction tasks. Hence we advocate that the key of better performance lies in meaningful latent modality structures instead of perfect m…
Latent Manifold Reconstruction and Representation with Topological and Geometrical Regularization
Southern University of Science and Technology（南方科技大学）；Shenzhen University of Advanced Technology（深圳先进技术大学）；Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences（深圳先进技术研究所，中国科学院）
Tsinghua University（清华大学）；Beijing University of Posts and Telecommunications（北京邮电大学）
Deep speaker embedding has achieved state-of-the-art performance in speaker recognition. A potential problem of these embedded vectors (called `x-vectors') are not Gaussian, causing performance degradation with the famous PLDA back-end scoring. In this paper, we propose a regularization approach based on Variational Auto-Encoder (VAE). This model transforms x-vectors to a latent space where mapped latent codes are more Gaussian, hence more suitable for PLDA scoring.
Several regularization methods have recently been introduced which force the latent activations of an autoencoder or deep neural network to conform to either a Gaussian or hyperspherical distribution, or to minimize the implicit rank of the distribution in latent space. In the present work, we introduce a novel regularizing loss function which simulates a pairwise repulsive force between items and an attractive force of each item toward the origin. We show that minimizing this loss function in isolation achieves a hyperspherical distribution. Moreover, when used as a regularizing term, the sca…
University at Buffalo, The State University of New York（纽约州立大学布法罗分校）
Many segmentation tasks for biomedical images can be modeled as the minimization of an energy function and solved by a class of max-flow and min-cut optimization algorithms. However, the segmentation accuracy is sensitive to the contrasting of semantic features of different segmenting objects, as the traditional energy function usually uses hand-crafted features in their energy functions. To address these limitations, we propose to incorporate end-to-end trainable neural network features into the energy functions. Our deep neural network features are extracted from the down-sampling and up-sam…
Approximating distributions over complicated manifolds, such as natural images, are conceptually attractive. The deep latent variable model, trained using variational autoencoders and generative adversarial networks, is now a key technique for representation learning. However, it is difficult to unify these two models for exact latent-variable inference and parallelize both reconstruction and sampling, partly due to the regularization under the latent variables, to match a simple explicit prior distribution. These approaches are prone to be oversimplified, and can only characterize a few modes…
Beihang University（北京航空航天大学）；University of Sheffield（谢菲尔德大学）；Ping An Technology（平安科技）
Variational autoencoders (VAEs) are one of the powerful unsupervised learning frameworks in NLP for latent representation learning and latent-directed generation. The classic optimization goal of VAEs is to maximize the Evidence Lower Bound (ELBo), which consists of a conditional likelihood for generation and a negative Kullback-Leibler (KL) divergence for regularization. In practice, optimizing ELBo often leads the posterior distribution of all samples converge to the same degenerated local optimum, namely posterior collapse or KL vanishing. There are effective ways proposed to prevent poster…
In representation learning and non-linear dimension reduction, there is a huge interest to learn the 'disentangled' latent variables, where each sub-coordinate almost uniquely controls a facet of the observed data. While many regularization approaches have been proposed on variational autoencoders, heuristic tuning is required to balance between disentanglement and loss in reconstruction accuracy -- due to the unsupervised nature, there is no principled way to find an optimal weight for regularization. Motivated to completely bypass regularization, we consider a projection strategy: modifying …
Autodesk AI Lab（欧特克人工智能实验室）；Imperial College London（伦敦帝国理工学院）
Learning interpretable and human-controllable representations that uncover factors of variation in data remains an ongoing key challenge in representation learning. We investigate learning group-disentangled representations for groups of factors with weak supervision. Existing techniques to address this challenge merely constrain the approximate posterior by averaging over observations of a shared group. As a result, observations with a common set of variations are encoded to distinct latent representations, reducing their capacity to disentangle and generalize to downstream tasks. In contrast…
