1,755 research outputs found
Denoising Adversarial Autoencoders: Classifying Skin Lesions Using Limited Labelled Training Data
We propose a novel deep learning model for classifying medical images in the
setting where there is a large amount of unlabelled medical data available, but
labelled data is in limited supply. We consider the specific case of
classifying skin lesions as either malignant or benign. In this setting, the
proposed approach -- the semi-supervised, denoising adversarial autoencoder --
is able to utilise vast amounts of unlabelled data to learn a representation
for skin lesions, and small amounts of labelled data to assign class labels
based on the learned representation. We analyse the contributions of both the
adversarial and denoising components of the model and find that the combination
yields superior classification performance in the setting of limited labelled
training data.Comment: Under consideration for the IET Computer Vision Journal special issue
on "Computer Vision in Cancer Data Analysis
Multi-Channel Stochastic Variational Inference for the Joint Analysis of Heterogeneous Biomedical Data in Alzheimer's Disease
The joint analysis of biomedical data in Alzheimer's Disease (AD) is
important for better clinical diagnosis and to understand the relationship
between biomarkers. However, jointly accounting for heterogeneous measures
poses important challenges related to the modeling of the variability and the
interpretability of the results. These issues are here addressed by proposing a
novel multi-channel stochastic generative model. We assume that a latent
variable generates the data observed through different channels (e.g., clinical
scores, imaging, ...) and describe an efficient way to estimate jointly the
distribution of both latent variable and data generative process. Experiments
on synthetic data show that the multi-channel formulation allows superior data
reconstruction as opposed to the single channel one. Moreover, the derived
lower bound of the model evidence represents a promising model selection
criterion. Experiments on AD data show that the model parameters can be used
for unsupervised patient stratification and for the joint interpretation of the
heterogeneous observations. Because of its general and flexible formulation, we
believe that the proposed method can find important applications as a general
data fusion technique.Comment: accepted for presentation at MLCN 2018 workshop, in Conjunction with
MICCAI 2018, September 20, Granada, Spai
VAESim: A probabilistic approach for self-supervised prototype discovery
In medical image datasets, discrete labels are often used to describe a continuous spectrum of conditions, making unsupervised image stratification a challenging task. In this work, we propose VAESim, an architecture for image stratification based on a conditional variational autoencoder. VAESim learns a set of prototypical vectors during training, each associated with a cluster in a continuous latent space. We perform a soft assignment of each data sample to the clusters and reconstruct the sample based on a similarity measure between the sample embedding and the prototypical vectors. to update the prototypical embeddings, we use an exponential moving average of the most similar representations between actual prototypes and samples in the batch size. We test our approach on the MNIST handwritten digit dataset and the pneumoniaMNIST medical benchmark dataset, where we show that our method outperforms baselines in terms of kNN accuracy (up to +15% improvement in performance) and performs at par with classification models trained in a fully supervised way. our model also outperforms current end-to-end models for unsupervised stratification
Machine Learning Models for High-dimensional Biomedical Data
abstract: The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to help understand the data, discover the patterns and improve the decision making. All the proposed methods can generalize to other industrial fields.
The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.
The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.
The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.
The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201
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