17,505 research outputs found
Confidence Statements for Ordering Quantiles
This work proposes Quor, a simple yet effective nonparametric method to
compare independent samples with respect to corresponding quantiles of their
populations. The method is solely based on the order statistics of the samples,
and independence is its only requirement. All computations are performed using
exact distributions with no need for any asymptotic considerations, and yet can
be run using a fast quadratic-time dynamic programming idea. Computational
performance is essential in high-dimensional domains, such as gene expression
data. We describe the approach and discuss on the most important assumptions,
building a parallel with assumptions and properties of widely used techniques
for the same problem. Experiments using real data from biomedical studies are
performed to empirically compare Quor and other methods in a classification
task over a selection of high-dimensional data sets
Interpretable Categorization of Heterogeneous Time Series Data
Understanding heterogeneous multivariate time series data is important in
many applications ranging from smart homes to aviation. Learning models of
heterogeneous multivariate time series that are also human-interpretable is
challenging and not adequately addressed by the existing literature. We propose
grammar-based decision trees (GBDTs) and an algorithm for learning them. GBDTs
extend decision trees with a grammar framework. Logical expressions derived
from a context-free grammar are used for branching in place of simple
thresholds on attributes. The added expressivity enables support for a wide
range of data types while retaining the interpretability of decision trees. In
particular, when a grammar based on temporal logic is used, we show that GBDTs
can be used for the interpretable classi cation of high-dimensional and
heterogeneous time series data. Furthermore, we show how GBDTs can also be used
for categorization, which is a combination of clustering and generating
interpretable explanations for each cluster. We apply GBDTs to analyze the
classic Australian Sign Language dataset as well as data on near mid-air
collisions (NMACs). The NMAC data comes from aircraft simulations used in the
development of the next-generation Airborne Collision Avoidance System (ACAS
X).Comment: 9 pages, 5 figures, 2 tables, SIAM International Conference on Data
Mining (SDM) 201
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli
Genetic programming in data mining for drug discovery
Genetic programming (GP) is used to extract from rat oral bioavailability
(OB) measurements simple, interpretable and predictive QSAR models
which both generalise to rats and to marketed drugs in humans. Receiver
Operating Characteristics (ROC) curves for the binary classier produced
by machine learning show no statistical dierence between rats (albeit
without known clearance dierences) and man. Thus evolutionary computing
oers the prospect of in silico ADME screening, e.g. for \virtual"
chemicals, for pharmaceutical drug discovery
Variable selection for the multicategory SVM via adaptive sup-norm regularization
The Support Vector Machine (SVM) is a popular classification paradigm in
machine learning and has achieved great success in real applications. However,
the standard SVM can not select variables automatically and therefore its
solution typically utilizes all the input variables without discrimination.
This makes it difficult to identify important predictor variables, which is
often one of the primary goals in data analysis. In this paper, we propose two
novel types of regularization in the context of the multicategory SVM (MSVM)
for simultaneous classification and variable selection. The MSVM generally
requires estimation of multiple discriminating functions and applies the argmax
rule for prediction. For each individual variable, we propose to characterize
its importance by the supnorm of its coefficient vector associated with
different functions, and then minimize the MSVM hinge loss function subject to
a penalty on the sum of supnorms. To further improve the supnorm penalty, we
propose the adaptive regularization, which allows different weights imposed on
different variables according to their relative importance. Both types of
regularization automate variable selection in the process of building
classifiers, and lead to sparse multi-classifiers with enhanced
interpretability and improved accuracy, especially for high dimensional low
sample size data. One big advantage of the supnorm penalty is its easy
implementation via standard linear programming. Several simulated examples and
one real gene data analysis demonstrate the outstanding performance of the
adaptive supnorm penalty in various data settings.Comment: Published in at http://dx.doi.org/10.1214/08-EJS122 the Electronic
Journal of Statistics (http://www.i-journals.org/ejs/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Convex Optimization for Binary Classifier Aggregation in Multiclass Problems
Multiclass problems are often decomposed into multiple binary problems that
are solved by individual binary classifiers whose results are integrated into a
final answer. Various methods, including all-pairs (APs), one-versus-all (OVA),
and error correcting output code (ECOC), have been studied, to decompose
multiclass problems into binary problems. However, little study has been made
to optimally aggregate binary problems to determine a final answer to the
multiclass problem. In this paper we present a convex optimization method for
an optimal aggregation of binary classifiers to estimate class membership
probabilities in multiclass problems. We model the class membership probability
as a softmax function which takes a conic combination of discrepancies induced
by individual binary classifiers, as an input. With this model, we formulate
the regularized maximum likelihood estimation as a convex optimization problem,
which is solved by the primal-dual interior point method. Connections of our
method to large margin classifiers are presented, showing that the large margin
formulation can be considered as a limiting case of our convex formulation.
Numerical experiments on synthetic and real-world data sets demonstrate that
our method outperforms existing aggregation methods as well as direct methods,
in terms of the classification accuracy and the quality of class membership
probability estimates.Comment: Appeared in Proceedings of the 2014 SIAM International Conference on
Data Mining (SDM 2014
Outlier Detection from Network Data with Subnetwork Interpretation
Detecting a small number of outliers from a set of data observations is
always challenging. This problem is more difficult in the setting of multiple
network samples, where computing the anomalous degree of a network sample is
generally not sufficient. In fact, explaining why the network is exceptional,
expressed in the form of subnetwork, is also equally important. In this paper,
we develop a novel algorithm to address these two key problems. We treat each
network sample as a potential outlier and identify subnetworks that mostly
discriminate it from nearby regular samples. The algorithm is developed in the
framework of network regression combined with the constraints on both network
topology and L1-norm shrinkage to perform subnetwork discovery. Our method thus
goes beyond subspace/subgraph discovery and we show that it converges to a
global optimum. Evaluation on various real-world network datasets demonstrates
that our algorithm not only outperforms baselines in both network and high
dimensional setting, but also discovers highly relevant and interpretable local
subnetworks, further enhancing our understanding of anomalous networks
Distributed classifier based on genetically engineered bacterial cell cultures
We describe a conceptual design of a distributed classifier formed by a
population of genetically engineered microbial cells. The central idea is to
create a complex classifier from a population of weak or simple classifiers. We
create a master population of cells with randomized synthetic biosensor
circuits that have a broad range of sensitivities towards chemical signals of
interest that form the input vectors subject to classification. The randomized
sensitivities are achieved by constructing a library of synthetic gene circuits
with randomized control sequences (e.g. ribosome-binding sites) in the front
element. The training procedure consists in re-shaping of the master population
in such a way that it collectively responds to the "positive" patterns of input
signals by producing above-threshold output (e.g. fluorescent signal), and
below-threshold output in case of the "negative" patterns. The population
re-shaping is achieved by presenting sequential examples and pruning the
population using either graded selection/counterselection or by
fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of
experimental implementation of such system computationally using a realistic
model of the synthetic sensing gene circuits.Comment: 31 pages, 9 figure
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