663 research outputs found
From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification
<p>Abstract</p> <p>Background</p> <p>Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification.</p> <p>Results</p> <p>In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model.</p> <p>Conclusions</p> <p>FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context.</p
A Route Confidence Evaluation Method for Reliable Hierarchical Text Categorization
Hierarchical Text Categorization (HTC) is becoming increasingly important
with the rapidly growing amount of text data available in the World Wide Web.
Among the different strategies proposed to cope with HTC, the Local Classifier
per Node (LCN) approach attains good performance by mirroring the underlying
class hierarchy while enforcing a top-down strategy in the testing step.
However, the problem of embedding hierarchical information (parent-child
relationship) to improve the performance of HTC systems still remains open. A
confidence evaluation method for a selected route in the hierarchy is proposed
to evaluate the reliability of the final candidate labels in an HTC system. In
order to take into account the information embedded in the hierarchy, weight
factors are used to take into account the importance of each level. An
acceptance/rejection strategy in the top-down decision making process is
proposed, which improves the overall categorization accuracy by rejecting a few
percentage of samples, i.e., those with low reliability score. Experimental
results on the Reuters benchmark dataset (RCV1- v2) confirm the effectiveness
of the proposed method, compared to other state-of-the art HTC methods
Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data
Microbial identification is a central issue in microbiology, in particular in
the fields of infectious diseases diagnosis and industrial quality control. The
concept of species is tightly linked to the concept of biological and clinical
classification where the proximity between species is generally measured in
terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the
information provided by this well-known hierarchical structure is rarely used
by machine learning-based automatic microbial identification systems.
Structured machine learning methods were recently proposed for taking into
account the structure embedded in a hierarchy and using it as additional a
priori information, and could therefore allow to improve microbial
identification systems. We test and compare several state-of-the-art machine
learning methods for microbial identification on a new Matrix-Assisted Laser
Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset.
We include in the benchmark standard and structured methods, that leverage the
knowledge of the underlying hierarchical structure in the learning process. Our
results show that although some methods perform better than others, structured
methods do not consistently perform better than their "flat" counterparts. We
postulate that this is partly due to the fact that standard methods already
reach a high level of accuracy in this context, and that they mainly confuse
species close to each other in the tree, a case where using the known hierarchy
is not helpful
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