5,901 research outputs found
Neural Collaborative Subspace Clustering
We introduce the Neural Collaborative Subspace Clustering, a neural model
that discovers clusters of data points drawn from a union of low-dimensional
subspaces. In contrast to previous attempts, our model runs without the aid of
spectral clustering. This makes our algorithm one of the kinds that can
gracefully scale to large datasets. At its heart, our neural model benefits
from a classifier which determines whether a pair of points lies on the same
subspace or not. Essential to our model is the construction of two affinity
matrices, one from the classifier and the other from a notion of subspace
self-expressiveness, to supervise training in a collaborative scheme. We
thoroughly assess and contrast the performance of our model against various
state-of-the-art clustering algorithms including deep subspace-based ones.Comment: Accepted to ICML 201
Transcription Factor-DNA Binding Via Machine Learning Ensembles
We present ensemble methods in a machine learning (ML) framework combining
predictions from five known motif/binding site exploration algorithms. For a
given TF the ensemble starts with position weight matrices (PWM's) for the
motif, collected from the component algorithms. Using dimension reduction, we
identify significant PWM-based subspaces for analysis. Within each subspace a
machine classifier is built for identifying the TF's gene (promoter) targets
(Problem 1). These PWM-based subspaces form an ML-based sequence analysis tool.
Problem 2 (finding binding motifs) is solved by agglomerating k-mer (string)
feature PWM-based subspaces that stand out in identifying gene targets. We
approach Problem 3 (binding sites) with a novel machine learning approach that
uses promoter string features and ML importance scores in a classification
algorithm locating binding sites across the genome. For target gene
identification this method improves performance (measured by the F1 score) by
about 10 percentage points over the (a) motif scanning method and (b) the
coexpression-based association method. Top motif outperformed 5 component
algorithms as well as two other common algorithms (BEST and DEME). For
identifying individual binding sites on a benchmark cross species database
(Tompa et al., 2005) we match the best performer without much human
intervention. It also improved the performance on mammalian TFs.
The ensemble can integrate orthogonal information from different weak
learners (potentially using entirely different types of features) into a
machine learner that can perform consistently better for more TFs. The TF gene
target identification component (problem 1 above) is useful in constructing a
transcriptional regulatory network from known TF-target associations. The
ensemble is easily extendable to include more tools as well as future PWM-based
information.Comment: 33 page
One-Class Classification: Taxonomy of Study and Review of Techniques
One-class classification (OCC) algorithms aim to build classification models
when the negative class is either absent, poorly sampled or not well defined.
This unique situation constrains the learning of efficient classifiers by
defining class boundary just with the knowledge of positive class. The OCC
problem has been considered and applied under many research themes, such as
outlier/novelty detection and concept learning. In this paper we present a
unified view of the general problem of OCC by presenting a taxonomy of study
for OCC problems, which is based on the availability of training data,
algorithms used and the application domains applied. We further delve into each
of the categories of the proposed taxonomy and present a comprehensive
literature review of the OCC algorithms, techniques and methodologies with a
focus on their significance, limitations and applications. We conclude our
paper by discussing some open research problems in the field of OCC and present
our vision for future research.Comment: 24 pages + 11 pages of references, 8 figure
Random forests with random projections of the output space for high dimensional multi-label classification
We adapt the idea of random projections applied to the output space, so as to
enhance tree-based ensemble methods in the context of multi-label
classification. We show how learning time complexity can be reduced without
affecting computational complexity and accuracy of predictions. We also show
that random output space projections may be used in order to reach different
bias-variance tradeoffs, over a broad panel of benchmark problems, and that
this may lead to improved accuracy while reducing significantly the
computational burden of the learning stage
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
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