2,979 research outputs found
Pathway-Based Genomics Prediction using Generalized Elastic Net.
We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach
Binary Linear Classification and Feature Selection via Generalized Approximate Message Passing
For the problem of binary linear classification and feature selection, we
propose algorithmic approaches to classifier design based on the generalized
approximate message passing (GAMP) algorithm, recently proposed in the context
of compressive sensing. We are particularly motivated by problems where the
number of features greatly exceeds the number of training examples, but where
only a few features suffice for accurate classification. We show that
sum-product GAMP can be used to (approximately) minimize the classification
error rate and max-sum GAMP can be used to minimize a wide variety of
regularized loss functions. Furthermore, we describe an
expectation-maximization (EM)-based scheme to learn the associated model
parameters online, as an alternative to cross-validation, and we show that
GAMP's state-evolution framework can be used to accurately predict the
misclassification rate. Finally, we present a detailed numerical study to
confirm the accuracy, speed, and flexibility afforded by our GAMP-based
approaches to binary linear classification and feature selection
Multimodal Multipart Learning for Action Recognition in Depth Videos
The articulated and complex nature of human actions makes the task of action
recognition difficult. One approach to handle this complexity is dividing it to
the kinetics of body parts and analyzing the actions based on these partial
descriptors. We propose a joint sparse regression based learning method which
utilizes the structured sparsity to model each action as a combination of
multimodal features from a sparse set of body parts. To represent dynamics and
appearance of parts, we employ a heterogeneous set of depth and skeleton based
features. The proper structure of multimodal multipart features are formulated
into the learning framework via the proposed hierarchical mixed norm, to
regularize the structured features of each part and to apply sparsity between
them, in favor of a group feature selection. Our experimental results expose
the effectiveness of the proposed learning method in which it outperforms other
methods in all three tested datasets while saturating one of them by achieving
perfect accuracy
SUBIC: A Supervised Bi-Clustering Approach for Precision Medicine
Traditional medicine typically applies one-size-fits-all treatment for the
entire patient population whereas precision medicine develops tailored
treatment schemes for different patient subgroups. The fact that some factors
may be more significant for a specific patient subgroup motivates clinicians
and medical researchers to develop new approaches to subgroup detection and
analysis, which is an effective strategy to personalize treatment. In this
study, we propose a novel patient subgroup detection method, called Supervised
Biclustring (SUBIC) using convex optimization and apply our approach to detect
patient subgroups and prioritize risk factors for hypertension (HTN) in a
vulnerable demographic subgroup (African-American). Our approach not only finds
patient subgroups with guidance of a clinically relevant target variable but
also identifies and prioritizes risk factors by pursuing sparsity of the input
variables and encouraging similarity among the input variables and between the
input and target variable
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