3,729 research outputs found
Multiclass discovery in array data
BACKGROUND: A routine goal in the analysis of microarray data is to identify genes with expression levels that correlate with known classes of experiments. In a growing number of array data sets, it has been shown that there is an over-abundance of genes that discriminate between known classes as compared to expectations for random classes. Therefore, one can search for novel classes in array data by looking for partitions of experiments for which there are an over-abundance of discriminatory genes. We have previously used such an approach in a breast cancer study. RESULTS: We describe the implementation of an unsupervised classification method for class discovery in microarray data. The method allows for discovery of more than two classes. We applied our method on two published microarray data sets: small round blue cell tumors and breast tumors. The method predicts relevant classes in the data sets with high success rates. CONCLUSIONS: We conclude that the proposed method is accurate and efficient in finding biologically relevant classes in microarray data. Additionally, the method is useful for quality control of microarray experiments. We have made the method available as a computer program
Detection of Dispersed Radio Pulses: A machine learning approach to candidate identification and classification
Searching for extraterrestrial, transient signals in astronomical data sets
is an active area of current research. However, machine learning techniques are
lacking in the literature concerning single-pulse detection. This paper
presents a new, two-stage approach for identifying and classifying dispersed
pulse groups (DPGs) in single-pulse search output. The first stage identified
DPGs and extracted features to characterize them using a new peak
identification algorithm which tracks sloping tendencies around local maxima in
plots of signal-to-noise ratio vs. dispersion measure. The second stage used
supervised machine learning to classify DPGs. We created four benchmark data
sets: one unbalanced and three balanced versions using three different
imbalance treatments.We empirically evaluated 48 classifiers by training and
testing binary and multiclass versions of six machine learning algorithms on
each of the four benchmark versions. While each classifier had advantages and
disadvantages, all classifiers with imbalance treatments had higher recall
values than those with unbalanced data, regardless of the machine learning
algorithm used. Based on the benchmarking results, we selected a subset of
classifiers to classify the full, unlabelled data set of over 1.5 million DPGs
identified in 42,405 observations made by the Green Bank Telescope. Overall,
the classifiers using a multiclass ensemble tree learner in combination with
two oversampling imbalance treatments were the most efficient; they identified
additional known pulsars not in the benchmark data set and provided six
potential discoveries, with significantly less false positives than the other
classifiers.Comment: 13 pages, accepted for publication in MNRAS, ref. MN-15-1713-MJ.R
Unconventional machine learning of genome-wide human cancer data
Recent advances in high-throughput genomic technologies coupled with
exponential increases in computer processing and memory have allowed us to
interrogate the complex aberrant molecular underpinnings of human disease from
a genome-wide perspective. While the deluge of genomic information is expected
to increase, a bottleneck in conventional high-performance computing is rapidly
approaching. Inspired in part by recent advances in physical quantum
processors, we evaluated several unconventional machine learning (ML)
strategies on actual human tumor data. Here we show for the first time the
efficacy of multiple annealing-based ML algorithms for classification of
high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas.
To assess algorithm performance, we compared these classifiers to a variety of
standard ML methods. Our results indicate the feasibility of using
annealing-based ML to provide competitive classification of human cancer types
and associated molecular subtypes and superior performance with smaller
training datasets, thus providing compelling empirical evidence for the
potential future application of unconventional computing architectures in the
biomedical sciences
API design for machine learning software: experiences from the scikit-learn project
Scikit-learn is an increasingly popular machine learning li- brary. Written
in Python, it is designed to be simple and efficient, accessible to
non-experts, and reusable in various contexts. In this paper, we present and
discuss our design choices for the application programming interface (API) of
the project. In particular, we describe the simple and elegant interface shared
by all learning and processing units in the library and then discuss its
advantages in terms of composition and reusability. The paper also comments on
implementation details specific to the Python ecosystem and analyzes obstacles
faced by users and developers of the library
Interpretable multiclass classification by MDL-based rule lists
Interpretable classifiers have recently witnessed an increase in attention
from the data mining community because they are inherently easier to understand
and explain than their more complex counterparts. Examples of interpretable
classification models include decision trees, rule sets, and rule lists.
Learning such models often involves optimizing hyperparameters, which typically
requires substantial amounts of data and may result in relatively large models.
In this paper, we consider the problem of learning compact yet accurate
probabilistic rule lists for multiclass classification. Specifically, we
propose a novel formalization based on probabilistic rule lists and the minimum
description length (MDL) principle. This results in virtually parameter-free
model selection that naturally allows to trade-off model complexity with
goodness of fit, by which overfitting and the need for hyperparameter tuning
are effectively avoided. Finally, we introduce the Classy algorithm, which
greedily finds rule lists according to the proposed criterion. We empirically
demonstrate that Classy selects small probabilistic rule lists that outperform
state-of-the-art classifiers when it comes to the combination of predictive
performance and interpretability. We show that Classy is insensitive to its
only parameter, i.e., the candidate set, and that compression on the training
set correlates with classification performance, validating our MDL-based
selection criterion
Innovative Hybridisation of Genetic Algorithms and Neural Networks in Detecting Marker Genes for Leukaemia Cancer
Methods for extracting marker genes that trigger the growth
of cancerous cells from a high level of complexity microarrays are of much interest from the computing community. Through the identified genes, the pathology of cancerous cells can be revealed and early precaution
can be taken to prevent further proliferation of cancerous cells. In this paper, we propose an innovative hybridised gene identification framework based on genetic algorithms and neural networks to identify marker genes for leukaemia disease. Our approach confirms that high classification
accuracy does not ensure the optimal set of genes have been identified and our model delivers a more promising set of genes even with a lower classification accurac
Scalable Solutions for Automated Single Pulse Identification and Classification in Radio Astronomy
Data collection for scientific applications is increasing exponentially and
is forecasted to soon reach peta- and exabyte scales. Applications which
process and analyze scientific data must be scalable and focus on execution
performance to keep pace. In the field of radio astronomy, in addition to
increasingly large datasets, tasks such as the identification of transient
radio signals from extrasolar sources are computationally expensive. We present
a scalable approach to radio pulsar detection written in Scala that
parallelizes candidate identification to take advantage of in-memory task
processing using Apache Spark on a YARN distributed system. Furthermore, we
introduce a novel automated multiclass supervised machine learning technique
that we combine with feature selection to reduce the time required for
candidate classification. Experimental testing on a Beowulf cluster with 15
data nodes shows that the parallel implementation of the identification
algorithm offers a speedup of up to 5X that of a similar multithreaded
implementation. Further, we show that the combination of automated multiclass
classification and feature selection speeds up the execution performance of the
RandomForest machine learning algorithm by an average of 54% with less than a
2% average reduction in the algorithm's ability to correctly classify pulsars.
The generalizability of these results is demonstrated by using two real-world
radio astronomy data sets.Comment: In Proceedings of the 47th International Conference on Parallel
Processing (ICPP 2018). ACM, New York, NY, USA, Article 11, 11 page
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