35,123 research outputs found
A transfer-learning approach to feature extraction from cancer transcriptomes with deep autoencoders
Publicado en Lecture Notes in Computer Science.The diagnosis and prognosis of cancer are among the more
challenging tasks that oncology medicine deals with. With the main aim
of fitting the more appropriate treatments, current personalized medicine
focuses on using data from heterogeneous sources to estimate the evolu-
tion of a given disease for the particular case of a certain patient. In recent
years, next-generation sequencing data have boosted cancer prediction by
supplying gene-expression information that has allowed diverse machine
learning algorithms to supply valuable solutions to the problem of cancer
subtype classification, which has surely contributed to better estimation
of patient’s response to diverse treatments. However, the efficacy of these
models is seriously affected by the existing imbalance between the high
dimensionality of the gene expression feature sets and the number of sam-
ples available for a particular cancer type. To counteract what is known
as the curse of dimensionality, feature selection and extraction methods
have been traditionally applied to reduce the number of input variables
present in gene expression datasets. Although these techniques work by
scaling down the input feature space, the prediction performance of tradi-
tional machine learning pipelines using these feature reduction strategies
remains moderate. In this work, we propose the use of the Pan-Cancer
dataset to pre-train deep autoencoder architectures on a subset com-
posed of thousands of gene expression samples of very diverse tumor
types. The resulting architectures are subsequently fine-tuned on a col-
lection of specific breast cancer samples. This transfer-learning approach
aims at combining supervised and unsupervised deep learning models
with traditional machine learning classification algorithms to tackle the
problem of breast tumor intrinsic-subtype classification.Universidad de Málaga. Campus de Excelencia Internacional AndalucĂa Tech
Simultaneous Spectral-Spatial Feature Selection and Extraction for Hyperspectral Images
In hyperspectral remote sensing data mining, it is important to take into
account of both spectral and spatial information, such as the spectral
signature, texture feature and morphological property, to improve the
performances, e.g., the image classification accuracy. In a feature
representation point of view, a nature approach to handle this situation is to
concatenate the spectral and spatial features into a single but high
dimensional vector and then apply a certain dimension reduction technique
directly on that concatenated vector before feed it into the subsequent
classifier. However, multiple features from various domains definitely have
different physical meanings and statistical properties, and thus such
concatenation hasn't efficiently explore the complementary properties among
different features, which should benefit for boost the feature
discriminability. Furthermore, it is also difficult to interpret the
transformed results of the concatenated vector. Consequently, finding a
physically meaningful consensus low dimensional feature representation of
original multiple features is still a challenging task. In order to address the
these issues, we propose a novel feature learning framework, i.e., the
simultaneous spectral-spatial feature selection and extraction algorithm, for
hyperspectral images spectral-spatial feature representation and
classification. Specifically, the proposed method learns a latent low
dimensional subspace by projecting the spectral-spatial feature into a common
feature space, where the complementary information has been effectively
exploited, and simultaneously, only the most significant original features have
been transformed. Encouraging experimental results on three public available
hyperspectral remote sensing datasets confirm that our proposed method is
effective and efficient
Optimized kernel minimum noise fraction transformation for hyperspectral image classification
This paper presents an optimized kernel minimum noise fraction transformation (OKMNF) for feature extraction of hyperspectral imagery. The proposed approach is based on the kernel minimum noise fraction (KMNF) transformation, which is a nonlinear dimensionality reduction method. KMNF can map the original data into a higher dimensional feature space and provide a small number of quality features for classification and some other post processing. Noise estimation is an important component in KMNF. It is often estimated based on a strong relationship between adjacent pixels. However, hyperspectral images have limited spatial resolution and usually have a large number of mixed pixels, which make the spatial information less reliable for noise estimation. It is the main reason that KMNF generally shows unstable performance in feature extraction for classification. To overcome this problem, this paper exploits the use of a more accurate noise estimation method to improve KMNF. We propose two new noise estimation methods accurately. Moreover, we also propose a framework to improve noise estimation, where both spectral and spatial de-correlation are exploited. Experimental results, conducted using a variety of hyperspectral images, indicate that the proposed OKMNF is superior to some other related dimensionality reduction methods in most cases. Compared to the conventional KMNF, the proposed OKMNF benefits significant improvements in overall classification accuracy
Joint & Progressive Learning from High-Dimensional Data for Multi-Label Classification
Despite the fact that nonlinear subspace learning techniques (e.g. manifold
learning) have successfully applied to data representation, there is still room
for improvement in explainability (explicit mapping), generalization
(out-of-samples), and cost-effectiveness (linearization). To this end, a novel
linearized subspace learning technique is developed in a joint and progressive
way, called \textbf{j}oint and \textbf{p}rogressive \textbf{l}earning
str\textbf{a}teg\textbf{y} (J-Play), with its application to multi-label
classification. The J-Play learns high-level and semantically meaningful
feature representation from high-dimensional data by 1) jointly performing
multiple subspace learning and classification to find a latent subspace where
samples are expected to be better classified; 2) progressively learning
multi-coupled projections to linearly approach the optimal mapping bridging the
original space with the most discriminative subspace; 3) locally embedding
manifold structure in each learnable latent subspace. Extensive experiments are
performed to demonstrate the superiority and effectiveness of the proposed
method in comparison with previous state-of-the-art methods.Comment: accepted in ECCV 201
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
Complex biological systems have been successfully modeled by biochemical and
genetic interaction networks, typically gathered from high-throughput (HTP)
data. These networks can be used to infer functional relationships between
genes or proteins. Using the intuition that the topological role of a gene in a
network relates to its biological function, local or diffusion based
"guilt-by-association" and graph-theoretic methods have had success in
inferring gene functions. Here we seek to improve function prediction by
integrating diffusion-based methods with a novel dimensionality reduction
technique to overcome the incomplete and noisy nature of network data. In this
paper, we introduce diffusion component analysis (DCA), a framework that plugs
in a diffusion model and learns a low-dimensional vector representation of each
node to encode the topological properties of a network. As a proof of concept,
we demonstrate DCA's substantial improvement over state-of-the-art
diffusion-based approaches in predicting protein function from molecular
interaction networks. Moreover, our DCA framework can integrate multiple
networks from heterogeneous sources, consisting of genomic information,
biochemical experiments and other resources, to even further improve function
prediction. Yet another layer of performance gain is achieved by integrating
the DCA framework with support vector machines that take our node vector
representations as features. Overall, our DCA framework provides a novel
representation of nodes in a network that can be used as a plug-in architecture
to other machine learning algorithms to decipher topological properties of and
obtain novel insights into interactomes.Comment: RECOMB 201
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
- …