Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adaptively Weighted Large Margin Classifiers.

ABSTRACT: Large margin classifiers have been shown to be very useful in many applications. The Support Vector Machine is a canonical example of large margin classifiers. Despite their flexibility and ability in handling high dimensional data, many large margin classifiers have serious drawbacks when the data are noisy, especially when there are outliers in the data. In this paper, we propose a new weighted large margin classification technique. The weights are chosen adaptively with data. The proposed classifiers are shown to be robust to outliers and thus are able to produce more accurate classification results.

SUBMITTER: Wu Y

PROVIDER: S-EPMC3867158 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Adaptively Weighted Large Margin Classifiers.

Wu Yichao Y Liu Yufeng Y

Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America 20130101 2

Large margin classifiers have been shown to be very useful in many applications. The Support Vector Machine is a canonical example of large margin classifiers. Despite their flexibility and ability in handling high dimensional data, many large margin classifiers have serious drawbacks when the data are noisy, especially when there are outliers in the data. In this paper, we propose a new weighted large margin classification technique. The weights are chosen adaptively with data. The proposed cla ...[more]

PMID: 24363545

Similar Datasets

Adaptively weighted association statistics.

Project description:We investigate methods for testing gene-disease outcome associations in situations where the genetic relationship potentially varies among subjects with differing environmental or clinical attributes. We propose a strategy which modestly increases multiple testing by evaluating weighted test statistics which focus (or enrich) association tests within subgroups and use a Monte-Carlo method, based on simulating from the approximate large sample distribution of the statistics, to control type 1 error. We also introduce a stage-wise calculated test statistic which allows more complex weighting on multiple environmental variables. Results from simulation studies confirm improved power of the proposed approaches compared to marginal testing in many situations.

| S-EPMC3571103 | biostudies-literature

Multicategory angle-based large-margin classification.

Project description:Large-margin classifiers are popular methods for classification. Among existing simultaneous multicategory large-margin classifiers, a common approach is to learn k different functions for a k-class problem with a sum-to-zero constraint. Such a formulation can be inefficient. We propose a new multicategory angle-based large-margin classification framework. The proposed angle-based classifiers consider a simplex-based prediction rule without the sum-to-zero constraint, and enjoy more efficient computation. Many binary large-margin classifiers can be naturally generalized for multicategory problems through the angle-based framework. Theoretical and numerical studies demonstrate the usefulness of the angle-based methods.

| S-EPMC4629508 | biostudies-literature

Large-Margin Classification in Hyperbolic Space.

Project description:Representing data in hyperbolic space can effectively capture latent hierarchical relationships. To enable accurate classification of points in hyperbolic space while respecting their hyperbolic geometry, we introduce hyperbolic SVM, a hyperbolic formulation of support vector machine classifiers, and describe its theoretical connection to the Euclidean counterpart. We also generalize Euclidean kernel SVM to hyperbolic space, allowing nonlinear hyperbolic decision boundaries and providing a geometric interpretation for a certain class of indefinite kernels. Hyperbolic SVM improves classification accuracy in simulation and in real-world problems involving complex networks and word embeddings. Our work enables end-to-end analyses based on the inherent hyperbolic geometry of the data without resorting to ill-fitting tools developed for Euclidean space.

| S-EPMC7434093 | biostudies-literature

Adaptively Weighted and Robust Mathematical Programming for the Discovery of Driver Gene Sets in Cancers.

Project description:High coverage and mutual exclusivity (HCME), which are considered two combinatorial properties of mutations in a collection of driver genes in cancers, have been used to develop mathematical programming models for distinguishing cancer driver gene sets. In this paper, we summarize a weak HCME pattern to justify the description of practical mutation datasets. We then present AWRMP, a method for identifying driver gene sets through the adaptive assignment of appropriate weights to gene candidates to tune the balance between coverage and mutual exclusivity. It embeds the genetic algorithm into the subsampling strategy to provide the optimization results robust against the uncertainty and noise in the data. Using biological datasets, we show that AWRMP can identify driver gene sets that satisfy the weak HCME pattern and outperform the state-of-arts methods in terms of robustness.

| S-EPMC6459865 | biostudies-literature

Multicategory Outcome Weighted Margin-based Learning for Estimating Individualized Treatment Rules.

Project description:Due to heterogeneity for many chronic diseases, precise personalized medicine, also known as precision medicine, has drawn increasing attentions in the scientific community. One main goal of precision medicine is to develop the most effective tailored therapy for each individual patient. To that end, one needs to incorporate individual characteristics to detect a proper individual treatment rule (ITR), by which suitable decisions on treatment assignments can be made to optimize patients' clinical outcome. For binary treatment settings, outcome weighted learning (OWL) and several of its variations have been proposed recently to estimate the ITR by optimizing the conditional expected outcome given patients' information. However, for multiple treatment scenarios, it remains unclear how to use OWL effectively. It can be shown that some direct extensions of OWL for multiple treatments, such as one-versus-one and one-versus-rest methods, can yield suboptimal performance. In this paper, we propose a new learning method, named Multicategory Outcome weighted Margin-based Learning (MOML), for estimating ITR with multiple treatments. Our proposed method is very general and covers OWL as a special case. We show Fisher consistency for the estimated ITR, and establish convergence rate properties. Variable selection using the sparse l 1 penalty is also considered. Analysis of simulated examples and a type 2 diabetes mellitus observational study are used to demonstrate competitive performance of the proposed method.

| S-EPMC7731977 | biostudies-literature

Parallel reinforcement learning for weighted multi-criteria model with adaptive margin.

Project description:Reinforcement learning (RL) for a linear family of tasks is described in this paper. The key of our discussion is nonlinearity of the optimal solution even if the task family is linear; we cannot obtain the optimal policy using a naive approach. Although an algorithm exists for calculating the equivalent result to Q-learning for each task simultaneously, it presents the problem of explosion of set sizes. We therefore introduce adaptive margins to overcome this difficulty.

| S-EPMC2645492 | biostudies-other

P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications.

Project description:MotivationMeta-analysis methods have been widely used to combine results from multiple clinical or genomic studies to increase statistical powers and ensure robust and accurate conclusions. The adaptively weighted Fisher's method (AW-Fisher), initially developed for omics applications but applicable for general meta-analysis, is an effective approach to combine P-values from K independent studies and to provide better biological interpretability by characterizing which studies contribute to the meta-analysis. Currently, AW-Fisher suffers from the lack of fast P-value computation and variability estimate of AW weights. When the number of studies K is large, the 3K - 1 possible differential expression pattern categories generated by AW-Fisher can become intractable. In this paper, we develop an importance sampling scheme with spline interpolation to increase the accuracy and speed of the P-value calculation. We also apply bootstrapping to construct a variability index for the AW-Fisher weight estimator and a co-membership matrix to categorize (cluster) differentially expressed genes based on their meta-patterns for intuitive biological investigations.ResultsThe superior performance of the proposed methods is shown in simulations as well as two real omics meta-analysis applications to demonstrate its insightful biological findings.Availability and implementationAn R package AWFisher (calling C++) is available at Bioconductor and GitHub (https://github.com/Caleb-Huo/AWFisher), and all datasets and programing codes for this paper are available in the Supplementary Material.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC7867999 | biostudies-literature

scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data.

Project description:MotivationTechnological advances have enabled us to profile single-cell multi-omics data from the same cells, providing us with an unprecedented opportunity to understand the cellular phenotype and links to its genotype. The available protocols and multi-omics datasets [including parallel single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data profiled from the same cell] are growing increasingly. However, such data are highly sparse and tend to have high level of noise, making data analysis challenging. The methods that integrate the multi-omics data can potentially improve the capacity of revealing the cellular heterogeneity.ResultsWe propose an adaptively weighted multi-view learning (scAWMV) method for the integrative analysis of parallel scRNA-seq and scATAC-seq data profiled from the same cell. scAWMV considers both the difference in importance across different modalities in multi-omics data and the biological connection of the features in the scRNA-seq and scATAC-seq data. It generates biologically meaningful low-dimensional representations for the transcriptomic and epigenomic profiles via unsupervised learning. Application to four real datasets demonstrates that our framework scAWMV is an efficient method to dissect cellular heterogeneity for single-cell multi-omics data.Availability and implementationThe software and datasets are available at https://github.com/pengchengzeng/scAWMV.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC9805575 | biostudies-literature

Large landslides cluster at the margin of a deglaciated mountain belt.

Project description:Landslides in deglaciated and deglaciating mountains represent a major hazard, but their distribution at the spatial scale of entire mountain belts has rarely been studied. Traditional models of landslide distribution assume that landslides are concentrated in the steepest, wettest, and most tectonically active parts of the orogens, where glaciers reached their greatest thickness. However, based on mapping large landslides (> 0.9 km2) over an unprecedentedly large area of Southern Patagonia (~ 305,000 km2), we show that the distribution of landslides can have the opposite trend. We show that the largest landslides within the limits of the former Patagonian Ice Sheet (PIS) cluster along its eastern margins occupying lower, tectonically less active, and arid part of the Patagonian Andes. In contrast to the heavily glaciated, highest elevations of the mountain range, the peripheral regions have been glaciated only episodically, leaving a larger volume of unstable sedimentary and volcanic rocks that are subject to ongoing slope instability.

| S-EPMC8983719 | biostudies-literature

Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation.

Project description:BackgroundWith the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent results of the exploratory analysis on the web in an easy-to-comprehend form and to facilitate convenient information retrieval.ResultsWe developed an approach to visualize large phylogenetic trees in an aggregated form with a special representation of subscale details. The initial aggregated tree representation is built with a level of resolution automatically selected to fit into the available screen space, with terminal groups selected based on sequence similarity. The default aggregated representation can be refined by users interactively.Structure and data variability within terminal groups are displayed using small trees that have the same vertical size as the text annotation of the group. These subscale representations are calculated using systematic sampling from the corresponding terminal group. The aggregated tree containing terminal groups can be annotated using aggregation of structured metadata, such as seasonal distribution, geographic locations, etc.AvailabilityThe algorithms are implemented in JavaScript within the NCBI Influenza Virus Resource 1.

| S-EPMC2416652 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data