10,111 research outputs found
A study of hierarchical and flat classification of proteins
Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area
On Machine-Learned Classification of Variable Stars with Sparse and Noisy Time-Series Data
With the coming data deluge from synoptic surveys, there is a growing need
for frameworks that can quickly and automatically produce calibrated
classification probabilities for newly-observed variables based on a small
number of time-series measurements. In this paper, we introduce a methodology
for variable-star classification, drawing from modern machine-learning
techniques. We describe how to homogenize the information gleaned from light
curves by selection and computation of real-numbered metrics ("feature"),
detail methods to robustly estimate periodic light-curve features, introduce
tree-ensemble methods for accurate variable star classification, and show how
to rigorously evaluate the classification results using cross validation. On a
25-class data set of 1542 well-studied variable stars, we achieve a 22.8%
overall classification error using the random forest classifier; this
represents a 24% improvement over the best previous classifier on these data.
This methodology is effective for identifying samples of specific science
classes: for pulsational variables used in Milky Way tomography we obtain a
discovery efficiency of 98.2% and for eclipsing systems we find an efficiency
of 99.1%, both at 95% purity. We show that the random forest (RF) classifier is
superior to other machine-learned methods in terms of accuracy, speed, and
relative immunity to features with no useful class information; the RF
classifier can also be used to estimate the importance of each feature in
classification. Additionally, we present the first astronomical use of
hierarchical classification methods to incorporate a known class taxonomy in
the classifier, which further reduces the catastrophic error rate to 7.8%.
Excluding low-amplitude sources, our overall error rate improves to 14%, with a
catastrophic error rate of 3.5%.Comment: 23 pages, 9 figure
Online Robot Introspection via Wrench-based Action Grammars
Robotic failure is all too common in unstructured robot tasks. Despite
well-designed controllers, robots often fail due to unexpected events. How do
robots measure unexpected events? Many do not. Most robots are driven by the
sense-plan act paradigm, however more recently robots are undergoing a
sense-plan-act-verify paradigm. In this work, we present a principled
methodology to bootstrap online robot introspection for contact tasks. In
effect, we are trying to enable the robot to answer the question: what did I
do? Is my behavior as expected or not? To this end, we analyze noisy wrench
data and postulate that the latter inherently contains patterns that can be
effectively represented by a vocabulary. The vocabulary is generated by
segmenting and encoding the data. When the wrench information represents a
sequence of sub-tasks, we can think of the vocabulary forming a sentence (set
of words with grammar rules) for a given sub-task; allowing the latter to be
uniquely represented. The grammar, which can also include unexpected events,
was classified in offline and online scenarios as well as for simulated and
real robot experiments. Multiclass Support Vector Machines (SVMs) were used
offline, while online probabilistic SVMs were are used to give temporal
confidence to the introspection result. The contribution of our work is the
presentation of a generalizable online semantic scheme that enables a robot to
understand its high-level state whether nominal or abnormal. It is shown to
work in offline and online scenarios for a particularly challenging contact
task: snap assemblies. We perform the snap assembly in one-arm simulated and
real one-arm experiments and a simulated two-arm experiment. This verification
mechanism can be used by high-level planners or reasoning systems to enable
intelligent failure recovery or determine the next most optima manipulation
skill to be used.Comment: arXiv admin note: substantial text overlap with arXiv:1609.0494
Multi-TGDR: a regularization method for multi-class classification in microarray experiments
Background
With microarray technology becoming mature and popular, the selection and use
of a small number of relevant genes for accurate classification of samples is a
hot topic in the circles of biostatistics and bioinformatics. However, most of
the developed algorithms lack the ability to handle multiple classes, which
arguably a common application. Here, we propose an extension to an existing
regularization algorithm called Threshold Gradient Descent Regularization
(TGDR) to specifically tackle multi-class classification of microarray data.
When there are several microarray experiments addressing the same/similar
objectives, one option is to use meta-analysis version of TGDR (Meta-TGDR),
which considers the classification task as combination of classifiers with the
same structure/model while allowing the parameters to vary across studies.
However, the original Meta-TGDR extension did not offer a solution to the
prediction on independent samples. Here, we propose an explicit method to
estimate the overall coefficients of the biomarkers selected by Meta-TGDR. This
extension permits broader applicability and allows a comparison between the
predictive performance of Meta-TGDR and TGDR using an independent testing set.
Results
Using real-world applications, we demonstrated the proposed multi-TGDR
framework works well and the number of selected genes is less than the sum of
all individualized binary TGDRs. Additionally, Meta-TGDR and TGDR on the
batch-effect adjusted pooled data approximately provided same results. By
adding Bagging procedure in each application, the stability and good predictive
performance are warranted.
Conclusions
Compared with Meta-TGDR, TGDR is less computing time intensive, and requires
no samples of all classes in each study. On the adjusted data, it has
approximate same predictive performance with Meta-TGDR. Thus, it is highly
recommended
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