5,088 research outputs found
EC3: Combining Clustering and Classification for Ensemble Learning
Classification and clustering algorithms have been proved to be successful
individually in different contexts. Both of them have their own advantages and
limitations. For instance, although classification algorithms are more powerful
than clustering methods in predicting class labels of objects, they do not
perform well when there is a lack of sufficient manually labeled reliable data.
On the other hand, although clustering algorithms do not produce label
information for objects, they provide supplementary constraints (e.g., if two
objects are clustered together, it is more likely that the same label is
assigned to both of them) that one can leverage for label prediction of a set
of unknown objects. Therefore, systematic utilization of both these types of
algorithms together can lead to better prediction performance. In this paper,
We propose a novel algorithm, called EC3 that merges classification and
clustering together in order to support both binary and multi-class
classification. EC3 is based on a principled combination of multiple
classification and multiple clustering methods using an optimization function.
We theoretically show the convexity and optimality of the problem and solve it
by block coordinate descent method. We additionally propose iEC3, a variant of
EC3 that handles imbalanced training data. We perform an extensive experimental
analysis by comparing EC3 and iEC3 with 14 baseline methods (7 well-known
standalone classifiers, 5 ensemble classifiers, and 2 existing methods that
merge classification and clustering) on 13 standard benchmark datasets. We show
that our methods outperform other baselines for every single dataset, achieving
at most 10% higher AUC. Moreover our methods are faster (1.21 times faster than
the best baseline), more resilient to noise and class imbalance than the best
baseline method.Comment: 14 pages, 7 figures, 11 table
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
Bag-Level Aggregation for Multiple Instance Active Learning in Instance Classification Problems
A growing number of applications, e.g. video surveillance and medical image
analysis, require training recognition systems from large amounts of weakly
annotated data while some targeted interactions with a domain expert are
allowed to improve the training process. In such cases, active learning (AL)
can reduce labeling costs for training a classifier by querying the expert to
provide the labels of most informative instances. This paper focuses on AL
methods for instance classification problems in multiple instance learning
(MIL), where data is arranged into sets, called bags, that are weakly labeled.
Most AL methods focus on single instance learning problems. These methods are
not suitable for MIL problems because they cannot account for the bag structure
of data. In this paper, new methods for bag-level aggregation of instance
informativeness are proposed for multiple instance active learning (MIAL). The
\textit{aggregated informativeness} method identifies the most informative
instances based on classifier uncertainty, and queries bags incorporating the
most information. The other proposed method, called \textit{cluster-based
aggregative sampling}, clusters data hierarchically in the instance space. The
informativeness of instances is assessed by considering bag labels, inferred
instance labels, and the proportion of labels that remain to be discovered in
clusters. Both proposed methods significantly outperform reference methods in
extensive experiments using benchmark data from several application domains.
Results indicate that using an appropriate strategy to address MIAL problems
yields a significant reduction in the number of queries needed to achieve the
same level of performance as single instance AL methods
Digging into acceptor splice site prediction : an iterative feature selection approach
Feature selection techniques are often used to reduce data dimensionality, increase classification performance, and gain insight into the processes that generated the data. In this paper, we describe an iterative procedure of feature selection and feature construction steps, improving the classification of acceptor splice sites, an important subtask of gene prediction.
We show that acceptor prediction can benefit from feature selection, and describe how feature selection techniques can be used to gain new insights in the classification of acceptor sites. This is illustrated by the identification of a new, biologically motivated feature: the AG-scanning feature.
The results described in this paper contribute both to the domain of gene prediction, and to research in feature selection techniques, describing a new wrapper based feature weighting method that aids in knowledge discovery when dealing with complex datasets
A Deep and Autoregressive Approach for Topic Modeling of Multimodal Data
Topic modeling based on latent Dirichlet allocation (LDA) has been a
framework of choice to deal with multimodal data, such as in image annotation
tasks. Another popular approach to model the multimodal data is through deep
neural networks, such as the deep Boltzmann machine (DBM). Recently, a new type
of topic model called the Document Neural Autoregressive Distribution Estimator
(DocNADE) was proposed and demonstrated state-of-the-art performance for text
document modeling. In this work, we show how to successfully apply and extend
this model to multimodal data, such as simultaneous image classification and
annotation. First, we propose SupDocNADE, a supervised extension of DocNADE,
that increases the discriminative power of the learned hidden topic features
and show how to employ it to learn a joint representation from image visual
words, annotation words and class label information. We test our model on the
LabelMe and UIUC-Sports data sets and show that it compares favorably to other
topic models. Second, we propose a deep extension of our model and provide an
efficient way of training the deep model. Experimental results show that our
deep model outperforms its shallow version and reaches state-of-the-art
performance on the Multimedia Information Retrieval (MIR) Flickr data set.Comment: 24 pages, 10 figures. A version has been accepted by TPAMI on Aug
4th, 2015. Add footnote about how to train the model in practice in Section
5.1. arXiv admin note: substantial text overlap with arXiv:1305.530
Multiple Instance Learning: A Survey of Problem Characteristics and Applications
Multiple instance learning (MIL) is a form of weakly supervised learning
where training instances are arranged in sets, called bags, and a label is
provided for the entire bag. This formulation is gaining interest because it
naturally fits various problems and allows to leverage weakly labeled data.
Consequently, it has been used in diverse application fields such as computer
vision and document classification. However, learning from bags raises
important challenges that are unique to MIL. This paper provides a
comprehensive survey of the characteristics which define and differentiate the
types of MIL problems. Until now, these problem characteristics have not been
formally identified and described. As a result, the variations in performance
of MIL algorithms from one data set to another are difficult to explain. In
this paper, MIL problem characteristics are grouped into four broad categories:
the composition of the bags, the types of data distribution, the ambiguity of
instance labels, and the task to be performed. Methods specialized to address
each category are reviewed. Then, the extent to which these characteristics
manifest themselves in key MIL application areas are described. Finally,
experiments are conducted to compare the performance of 16 state-of-the-art MIL
methods on selected problem characteristics. This paper provides insight on how
the problem characteristics affect MIL algorithms, recommendations for future
benchmarking and promising avenues for research
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