Unsupervised Feature Selection for Tumor Profiles using Autoencoders and Kernel Methods
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）
Martin Palazzo, Pierre Beauseroy, Patricio Yankilevich
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 clusters while keeping biological signatures without using tumor labels. The proposed method named Latent Kernel Feature Selection (LKFS) is an unsupervised approach for gene selection in tumor gene expression profiles. By using Autoencoders a low dimensional and denoised latent space is learned as a target representation to guide a Multiple Kernel Learning model that selects a subset of genes. By using the selected genes a clustering method is used to group samples. In order to evaluate the performance of the proposed unsupervised feature selection method the obtained features and clusters are analyzed by clinical significance. The proposed method has been applied on three tumor datasets which are Brain, Renal and Lung, each one composed by two tumor subtypes. When compared with benchmark unsupervised feature selection methods the results obtained by the proposed method reveal lower redundancy in the selected features and a better clustering performance.
Viterbi Faculty of Electrical Engineering, Technion - Israel Institute of Technology（以色列理工学院维特比电气与电子工程学院）
Autoencoders are widely used for unsupervised learning and as a regularization scheme in semi-supervised learning. However, theoretical understanding of their generalization properties and of the manner in which they can assist supervised learning has been lacking. We utilize recent advances in the theory of deep learning generalization, together with a novel reconstruction loss, to provide generalization bounds for autoencoders. To the best of our knowledge, this is the first such bound. We further show that, under appropriate assumptions, an autoencoder with good generalization properties ca…
University of Bath（巴斯大学）；University of Cambridge（剑桥大学）
Glioblastoma is profoundly heterogeneous in regional microstructure and vasculature. Characterizing the spatial heterogeneity of glioblastoma could lead to more precise treatment. With unsupervised learning techniques, glioblastoma MRI-derived radiomic features have been widely utilized for tumor sub-region segmentation and survival prediction. However, the reliability of algorithm outcomes is often challenged by both ambiguous intermediate process and instability introduced by the randomness of clustering algorithms, especially for data from heterogeneous patients. In this paper, we propose a…
High-dimensional data in many areas such as computer vision and machine learning tasks brings in computational and analytical difficulty. Feature selection which selects a subset from observed features is a widely used approach for improving performance and effectiveness of machine learning models with high-dimensional data. In this paper, we propose a novel AutoEncoder Feature Selector (AEFS) for unsupervised feature selection which combines autoencoder regression and group lasso tasks. Compared to traditional feature selection methods, AEFS can select the most important features by excavatin…
German Cancer Research Center (DKFZ)（德国癌症研究中心（DKFZ））
Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based auto encoders have shown great potential in detecting anomalies in medical images. However, state-of-the-art anomaly scores are still based on the reconstruction error, which lacks in two essential parts: it ignores the model-internal representation employed for reconstruction, and it lacks formal assertions and comparability between samples. We address these shortcomings by proposing the Context-encoding Variational Autoencoder (ceVAE) which combines reconstructio…
Dimensionality reduction is a crucial first step for many unsupervised learning tasks including anomaly detection and clustering. Autoencoder is a popular mechanism to accomplish dimensionality reduction. In order to make dimensionality reduction effective for high-dimensional data embedding nonlinear low-dimensional manifold, it is understood that some sort of geodesic distance metric should be used to discriminate the data samples. Inspired by the success of geodesic distance approximators such as ISOMAP, we propose to use a minimum spanning tree (MST), a graph-based algorithm, to approximat…
Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-re…
Feature selection is a dimensionality reduction technique that selects a subset of representative features from high dimensional data by eliminating irrelevant and redundant features. Recently, feature selection combined with sparse learning has attracted significant attention due to its outstanding performance compared with traditional feature selection methods that ignores correlation between features. These works first map data onto a low-dimensional subspace and then select features by posing a sparsity constraint on the transformation matrix. However, they are restricted by design to line…
PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders
School of Mathematical Sciences, Peking University（北京大学数学科学学院）；Center for Statistical Science, Peking University（北京大学统计科学中心）；Computational Biology Program, Fred Hutchinson Cancer Research Center（弗雷德·哈钦森癌症研究中心计算生物学项目）；Howard Hughes Medical Institute（霍华德·休斯医学研究所）
Feature selection reduces the dimensionality of data by identifying a subset of the most informative features. In this paper, we propose an innovative framework for unsupervised feature selection, called fractal autoencoders (FAE). It trains a neural network to pinpoint informative features for global exploring of representability and for local excavating of diversity. Architecturally, FAE extends autoencoders by adding a one-to-one scoring layer and a small sub-neural network for feature selection in an unsupervised fashion. With such a concise architecture, FAE achieves state-of-the-art perf…
Brain tumor segmentation is a challenging problem in medical image analysis. The endpoint is to generate the salient masks that accurately identify brain tumor regions in an fMRI screening. In this paper, we propose a novel attention gate (AG model) for brain tumor segmentation that utilizes both the edge detecting unit and the attention gated network to highlight and segment the salient regions from fMRI images. This feature enables us to eliminate the necessity of having to explicitly point towards the damaged area(external tissue localization) and classify(classification) as per classical c…
Automatic MRI brain tumor segmentation is of vital importance for the disease diagnosis, monitoring, and treatment planning. In this paper, we propose a two-stage encoder-decoder based model for brain tumor subregional segmentation. Variational autoencoder regularization is utilized in both stages to prevent the overfitting issue. The second-stage network adopts attention gates and is trained additionally using an expanded dataset formed by the first-stage outputs. On the BraTS 2020 validation dataset, the proposed method achieves the mean Dice score of 0.9041, 0.8350, and 0.7958, and Hausdorf…
Symantec Corporation（赛门铁克公司）；University of Central Florida（中佛罗里达大学）；Mayo Clinic（梅奥诊所）
Risk stratification (characterization) of tumors from radiology images can be more accurate and faster with computer-aided diagnosis (CAD) tools. Tumor characterization through such tools can also enable non-invasive cancer staging, prognosis, and foster personalized treatment planning as a part of precision medicine. In this study, we propose both supervised and unsupervised machine learning strategies to improve tumor characterization. Our first approach is based on supervised learning for which we demonstrate significant gains with deep learning algorithms, particularly by utilizing a 3D Co…
According to the National Cancer Institute, there were 9.5 million cancer-related deaths in 2018. A challenge in improving treatment is resistance in genetically unstable cells. The purpose of this study is to evaluate unsupervised machine learning on classifying treatment-resistant phenotypes in heterogeneous tumors through analysis of single cell RNA sequencing(scRNAseq) data with a pipeline and evaluation metrics. scRNAseq quantifies mRNA in cells and characterizes cell phenotypes. One scRNAseq dataset was analyzed (tumor/non-tumor cells of different molecular subtypes and patient identific…
George Mason University（乔治梅森大学）；Sapienza University of Rome（罗马第一大学）；University of L’Aquila（拉奎拉大学）
Autoencoders, as a dimensionality reduction technique, have been recently applied to outlier detection. However, neural networks are known to be vulnerable to overfitting, and therefore have limited potential in the unsupervised outlier detection setting. Current approaches to ensemble-based autoencoders do not generate a sufficient level of diversity to avoid the overfitting issue. To overcome the aforementioned limitations we develop a Boosting-based Autoencoder Ensemble approach (in short, BAE). BAE is an unsupervised ensemble method that, similarly to the boosting approach, builds an adapt…
University of Michigan（密歇根大学）；Technicolor（特艺集团）；Adobe（Adobe公司）
Unsupervised clustering is one of the most fundamental challenges in machine learning. A popular hypothesis is that data are generated from a union of low-dimensional nonlinear manifolds; thus an approach to clustering is identifying and separating these manifolds. In this paper, we present a novel approach to solve this problem by using a mixture of autoencoders. Our model consists of two parts: 1) a collection of autoencoders where each autoencoder learns the underlying manifold of a group of similar objects, and 2) a mixture assignment neural network, which takes the concatenated latent vec…
University of Science and Technology of China（中国科学技术大学）；The Fourth Affiliated Hospital of Anhui Medical University（安徽医科大学第四附属医院）；Genmab Inc.（Genmab公司）
Deep learning has become the mainstream methodological choice for analyzing and interpreting whole-slide digital pathology images (WSIs). It is commonly assumed that tumor regions carry most predictive information. In this paper, we proposed an unsupervised clustering-based multiple-instance learning, and apply our method to develop deep-learning models for prediction of gene mutations using WSIs from three cancer types in The Cancer Genome Atlas (TCGA) studies (CRC, LUAD, and HNSCC). We showed that unsupervised clustering of image patches could help identify predictive patches, exclude patche…
We propose an unsupervised method using self-clustering convolutional adversarial autoencoders to classify prostate tissue as tumor or non-tumor without any labeled training data. The clustering method is integrated into the training of the autoencoder and requires only little post-processing. Our network trains on hematoxylin and eosin (H&E) input patches and we tested two different reconstruction targets, H&E and immunohistochemistry (IHC). We show that antibody-driven feature learning using IHC helps the network to learn relevant features for the clustering task. Our network achieves a F1 s…
This paper proposes an autoencoder (AE) that is used for improving the performance of once-class classifiers for the purpose of detecting anomalies. Traditional one-class classifiers (OCCs) perform poorly under certain conditions such as high-dimensionality and sparsity. Also, the size of the training set plays an important role on the performance of one-class classifiers. Autoencoders have been widely used for obtaining useful latent variables from high-dimensional datasets. In the proposed approach, the AE is capable of deriving meaningful features from high-dimensional datasets while doing …
University of Cambridge（剑桥大学）；Alan Turing Institute（艾伦·图灵研究所）；Microsoft Research（微软研究院）
Despite their successes, deep neural networks may make unreliable predictions when faced with test data drawn from a distribution different to that of the training data, constituting a major problem for AI safety. While this has recently motivated the development of methods to detect such out-of-distribution (OoD) inputs, a robust solution is still lacking. We propose a new probabilistic, unsupervised approach to this problem based on a Bayesian variational autoencoder model, which estimates a full posterior distribution over the decoder parameters using stochastic gradient Markov chain Monte …
We present a new flavor of Variational Autoencoder (VAE) that interpolates seamlessly between unsupervised, semi-supervised and fully supervised learning domains. We show that unlabeled datapoints not only boost unsupervised tasks, but also the classification performance. Vice versa, every label not only improves classification, but also unsupervised tasks. The proposed architecture is simple: A classification layer is connected to the topmost encoder layer, and then combined with the resampled latent layer for the decoder. The usual evidence lower bound (ELBO) loss is supplemented with a supe…
Nanyang Technological University（南洋理工大学）；Salesforce Research Asia（赛富时亚洲研究院）
Adversarial training has shown impressive success in learning bilingual dictionary without any parallel data by mapping monolingual embeddings to a shared space. However, recent work has shown superior performance for non-adversarial methods in more challenging language pairs. In this work, we revisit adversarial autoencoder for unsupervised word translation and propose two novel extensions to it that yield more stable training and improved results. Our method includes regularization terms to enforce cycle consistency and input reconstruction, and puts the target encoders as an adversary again…
Lawrence Livermore National Laboratory（劳伦斯利弗莫尔国家实验室）
Gene expression profiles have been widely used to characterize patterns of cellular responses to diseases. As data becomes available, scalable learning toolkits become essential to processing large datasets using deep learning models to model complex biological processes. We present an autoencoder to capture nonlinear relationships recovered from gene expression profiles. The autoencoder is a nonlinear dimension reduction technique using an artificial neural network, which learns hidden representations of unlabeled data. We train the autoencoder on a large collection of tumor samples from the …
This paper aims to improve the explainability of Autoencoder's (AE) predictions by proposing two explanation methods based on the mean and epistemic uncertainty of log-likelihood estimate, which naturally arise from the probabilistic formulation of the AE called Bayesian Autoencoders (BAE). To quantitatively evaluate the performance of explanation methods, we test them in sensor network applications, and propose three metrics based on covariate shift of sensors : (1) G-mean of Spearman drift coefficients, (2) G-mean of sensitivity-specificity of explanation ranking and (3) sensor explanation q…
Exemplar-based methods rely on informative data points or prototypes to guide the optimization of learning algorithms. Such data facilitate interpretable model design and prediction. Of particular interest is the utility of exemplars in learning unsupervised deep representations. In this paper, we leverage hubs, which emerge as frequent neighbors in high-dimensional spaces, as exemplars to regularize a variational autoencoder and to learn a discriminative embedding for unsupervised down-stream tasks. We propose an unsupervised, data-driven regularization of the latent space with a mixture of h…
Text autoencoders are often used for unsupervised conditional text generation by applying mappings in the latent space to change attributes to the desired values. Recently, Mai et al. (2020) proposed Emb2Emb, a method to learn these mappings in the embedding space of an autoencoder. However, their method is restricted to autoencoders with a single-vector embedding, which limits how much information can be retained. We address this issue by extending their method to Bag-of-Vectors Autoencoders (BoV-AEs), which encode the text into a variable-size bag of vectors that grows with the size of the t…
We aim to build image generation models that generalize to new domains from few examples. To this end, we first investigate the generalization properties of classic image generators, and discover that autoencoders generalize extremely well to new domains, even when trained on highly constrained data. We leverage this insight to produce a robust, unsupervised few-shot image generation algorithm, and introduce a novel training procedure based on recovering an image from data augmentations. Our Augmentation-Interpolative AutoEncoders synthesize realistic images of novel objects from only a few re…
Precision medicine is a paradigm shift in healthcare relying heavily on genomics data. However, the complexity of biological interactions, the large number of genes as well as the lack of comparisons on the analysis of data, remain a tremendous bottleneck regarding clinical adoption. In this paper, we introduce a novel, automatic and unsupervised framework to discover low-dimensional gene biomarkers. Our method is based on the LP-Stability algorithm, a high dimensional center-based unsupervised clustering algorithm, that offers modularity as concerns metric functions and scalability, while bei…
Seoul National University（首尔国立大学）；Hanyang University（汉阳大学）；University of Birmingham（伯明翰大学）
We propose a symmetric graph convolutional autoencoder which produces a low-dimensional latent representation from a graph. In contrast to the existing graph autoencoders with asymmetric decoder parts, the proposed autoencoder has a newly designed decoder which builds a completely symmetric autoencoder form. For the reconstruction of node features, the decoder is designed based on Laplacian sharpening as the counterpart of Laplacian smoothing of the encoder, which allows utilizing the graph structure in the whole processes of the proposed autoencoder architecture. In order to prevent the numer…
Seoul National University（首尔大学）；Samsung Electronics Co. Ltd.（三星电子株式会社）
In this paper, we propose Squeezed Convolutional Variational AutoEncoder (SCVAE) for anomaly detection in time series data for Edge Computing in Industrial Internet of Things (IIoT). The proposed model is applied to labeled time series data from UCI datasets for exact performance evaluation, and applied to real world data for indirect model performance comparison. In addition, by comparing the models before and after applying Fire Modules from SqueezeNet, we show that model size and inference times are reduced while similar levels of performance is maintained.
Cross-dataset transfer learning is an important problem in person re-identification (Re-ID). Unfortunately, not too many deep transfer Re-ID models exist for realistic settings of practical Re-ID systems. We propose a purely deep transfer Re-ID model consisting of a deep convolutional neural network and an autoencoder. The latent code is divided into metric embedding and nuisance variables. We then utilize an unsupervised training method that does not rely on co-training with non-deep models. Our experiments show improvements over both the baseline and competitors' transfer learning models.
Learning disentangled representation from any unlabelled data is a non-trivial problem. In this paper we propose Information Maximising Autoencoder (InfoAE) where the encoder learns powerful disentangled representation through maximizing the mutual information between the representation and given information in an unsupervised fashion. We have evaluated our model on MNIST dataset and achieved 98.9 ($\pm .1$) $\%$ test accuracy while using complete unsupervised training.
RWTH Aachen University（亚琛工业大学）；Human Language Technology and Pattern Recognition Group（人类语言技术与模式识别小组）
Unsupervised learning of cross-lingual word embedding offers elegant matching of words across languages, but has fundamental limitations in translating sentences. In this paper, we propose simple yet effective methods to improve word-by-word translation of cross-lingual embeddings, using only monolingual corpora but without any back-translation. We integrate a language model for context-aware search, and use a novel denoising autoencoder to handle reordering. Our system surpasses state-of-the-art unsupervised neural translation systems without costly iterative training. We also analyze the eff…
University of Maryland College Park（马里兰大学帕克分校）；IBM Research（IBM研究院）
Detecting out of distribution (OOD) samples is of paramount importance in all Machine Learning applications. Deep generative modeling has emerged as a dominant paradigm to model complex data distributions without labels. However, prior work has shown that generative models tend to assign higher likelihoods to OOD samples compared to the data distribution on which they were trained. First, we propose Adversarial Mirrored Autoencoder (AMA), a variant of Adversarial Autoencoder, which uses a mirrored Wasserstein loss in the discriminator to enforce better semantic-level reconstruction. We also pr…
School of Computing（计算机学院）；NUS Graduate School（新加坡国立大学研究生院）；National University of Singapore（新加坡国立大学）
We propose the Motion Capsule Autoencoder (MCAE), which addresses a key challenge in the unsupervised learning of motion representations: transformation invariance. MCAE models motion in a two-level hierarchy. In the lower level, a spatio-temporal motion signal is divided into short, local, and semantic-agnostic snippets. In the higher level, the snippets are aggregated to form full-length semantic-aware segments. For both levels, we represent motion with a set of learned transformation invariant templates and the corresponding geometric transformations by using capsule autoencoders of a novel…
Anomalous sound detection (ASD) is, nowadays, one of the topical subjects in machine listening discipline. Unsupervised detection is attracting a lot of interest due to its immediate applicability in many fields. For example, related to industrial processes, the early detection of malfunctions or damage in machines can mean great savings and an improvement in the efficiency of industrial processes. This problem can be solved with an unsupervised ASD solution since industrial machines will not be damaged simply by having this audio data in the training stage. This paper proposes a novel framewo…
This paper presents a novel framework for unsupervised anomaly detection on masked objects called ODDObjects, which stands for Out-of-Distribution Detection on Objects. ODDObjects is designed to detect anomalies of various categories using unsupervised autoencoders trained on COCO-style datasets. The method utilizes autoencoder-based image reconstruction, where high reconstruction error indicates the possibility of an anomaly. The framework extends previous work on anomaly detection with autoencoders, comparing state-of-the-art models trained on object recognition datasets. Various model archi…
CCG ZGDV Institute（CCG ZGDV研究所）；Bosch Car Multimedia, Portugal（博世汽车多媒体（葡萄牙）公司）
This technical report describes two methods that were developed for Task 2 of the DCASE 2020 challenge. The challenge involves an unsupervised learning to detect anomalous sounds, thus only normal machine working condition samples are available during the training process. The two methods involve deep autoencoders, based on dense and convolutional architectures that use melspectogram processed sound features. Experiments were held, using the six machine type datasets of the challenge. Overall, competitive results were achieved by the proposed dense and convolutional AE, outperforming the basel…
Aalborg University（奥尔堡大学）；Huawei Cloud Database Innovation Lab（华为云数据库创新实验室）；University of Electronic Science and Technology of China（电子科技大学）
Time series data occurs widely, and outlier detection is a fundamental problem in data mining, which has numerous applications. Existing autoencoder-based approaches deliver state-of-the-art performance on challenging real-world data but are vulnerable to outliers and exhibit low explainability. To address these two limitations, we propose robust and explainable unsupervised autoencoder frameworks that decompose an input time series into a clean time series and an outlier time series using autoencoders. Improved explainability is achieved because clean time series are better explained with eas…
Philips Medical Systems Technologies Ltd.（飞利浦医疗系统科技有限公司）
Deep sparse auto-encoders with mixed structure regularization (MSR) in addition to explicit sparsity regularization term and stochastic corruption of the input data with Gaussian noise have the potential to improve unsupervised abnormality detection. Unsupervised abnormality detection based on identifying outliers using deep sparse auto-encoders is a very appealing approach for medical computer aided detection systems as it requires only healthy data for training rather than expert annotated abnormality. In the task of detecting coronary artery disease from Coronary Computed Tomography Angiogr…
Institute for Theoretical Particle Physics and Cosmology (TTK), RWTH Aachen University（亚琛工业大学理论粒子物理与宇宙学研究所（TTK））
Autoencoders are widely used in machine learning applications, in particular for anomaly detection. Hence, they have been introduced in high energy physics as a promising tool for model-independent new physics searches. We scrutinize the usage of autoencoders for unsupervised anomaly detection based on reconstruction loss to show their capabilities, but also their limitations. As a particle physics benchmark scenario, we study the tagging of top jet images in a background of QCD jet images. Although we reproduce the positive results from the literature, we show that the standard autoencoder se…
The problem of estimating event truths from conflicting agent opinions in a social network is investigated. An autoencoder learns the complex relationships between event truths, agent reliabilities and agent observations. A Bayesian network model is proposed to guide the learning process by modeling the relationship of the autoencoder's outputs with different variables. At the same time, it also models the social relationships between agents in the network. The proposed approach is unsupervised and is applicable when ground truth labels of events are unavailable. A variational inference method…
Binary change detection in bi-temporal co-registered hyperspectral images is a challenging task due to a large number of spectral bands present in the data. Researchers, therefore, try to handle it by reducing dimensions. The proposed work aims to build a novel feature extraction system using a feature fusion deep convolutional autoencoder for detecting changes between a pair of such bi-temporal co-registered hyperspectral images. The feature fusion considers features across successive levels and multiple receptive fields and therefore adds a competitive edge over the existing feature extracti…
Institute of Computer Science, University of Wrocław（弗罗茨瓦夫大学计算机科学研究所）；Google Research（谷歌研究院）；DeepMind
We consider the task of unsupervised extraction of meaningful latent representations of speech by applying autoencoding neural networks to speech waveforms. The goal is to learn a representation able to capture high level semantic content from the signal, e.g.\ phoneme identities, while being invariant to confounding low level details in the signal such as the underlying pitch contour or background noise. Since the learned representation is tuned to contain only phonetic content, we resort to using a high capacity WaveNet decoder to infer information discarded by the encoder from previous samp…
Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院）；Harvard University（哈佛大学）
In this paper, we propose Normality-Calibrated Autoencoder (NCAE), which can boost anomaly detection performance on the contaminated datasets without any prior information or explicit abnormal samples in the training phase. The NCAE adversarially generates high confident normal samples from a latent space having low entropy and leverages them to predict abnormal samples in a training dataset. NCAE is trained to minimise reconstruction errors in uncontaminated samples and maximise reconstruction errors in contaminated samples. The experimental results demonstrate that our method outperforms sha…
