31,268 research outputs found
A Provable Smoothing Approach for High Dimensional Generalized Regression with Applications in Genomics
In many applications, linear models fit the data poorly. This article studies
an appealing alternative, the generalized regression model. This model only
assumes that there exists an unknown monotonically increasing link function
connecting the response to a single index of explanatory
variables . The generalized regression model is flexible and
covers many widely used statistical models. It fits the data generating
mechanisms well in many real problems, which makes it useful in a variety of
applications where regression models are regularly employed. In low dimensions,
rank-based M-estimators are recommended to deal with the generalized regression
model, giving root- consistent estimators of . Applications of
these estimators to high dimensional data, however, are questionable. This
article studies, both theoretically and practically, a simple yet powerful
smoothing approach to handle the high dimensional generalized regression model.
Theoretically, a family of smoothing functions is provided, and the amount of
smoothing necessary for efficient inference is carefully calculated.
Practically, our study is motivated by an important and challenging scientific
problem: decoding gene regulation by predicting transcription factors that bind
to cis-regulatory elements. Applying our proposed method to this problem shows
substantial improvement over the state-of-the-art alternative in real data.Comment: 53 page
Mining Frequent Neighborhood Patterns in Large Labeled Graphs
Over the years, frequent subgraphs have been an important sort of targeted
patterns in the pattern mining literatures, where most works deal with
databases holding a number of graph transactions, e.g., chemical structures of
compounds. These methods rely heavily on the downward-closure property (DCP) of
the support measure to ensure an efficient pruning of the candidate patterns.
When switching to the emerging scenario of single-graph databases such as
Google Knowledge Graph and Facebook social graph, the traditional support
measure turns out to be trivial (either 0 or 1). However, to the best of our
knowledge, all attempts to redefine a single-graph support resulted in measures
that either lose DCP, or are no longer semantically intuitive.
This paper targets mining patterns in the single-graph setting. We resolve
the "DCP-intuitiveness" dilemma by shifting the mining target from frequent
subgraphs to frequent neighborhoods. A neighborhood is a specific topological
pattern where a vertex is embedded, and the pattern is frequent if it is shared
by a large portion (above a given threshold) of vertices. We show that the new
patterns not only maintain DCP, but also have equally significant semantics as
subgraph patterns. Experiments on real-life datasets display the feasibility of
our algorithms on relatively large graphs, as well as the capability of mining
interesting knowledge that is not discovered in prior works.Comment: 9 page
A novel dimensionality reduction technique based on independent component analysis for modeling microarray gene expression data
DNA microarray experiments generating thousands of gene
expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. But one challenge of microarray studies is the fact that the number n of samples collected is relatively small compared to the number p of genes per sample which are usually in thousands. In statistical terms this very large number of predictors compared to a small number of samples or observations makes the classification problem difficult. This is known as the ācurse of dimensionality problemā. An efficient way to solve this problem is by using dimensionality reduction techniques. Principle Component Analysis(PCA) is a leading method for dimensionality reduction of gene expression data which is optimal in the sense of least square error. In this paper we propose a new dimensionality reduction technique for specific bioinformatics applications based on Independent component Analysis(ICA). Being able to exploit higher order statistics to identify a linear model result, this ICA based dimensionality reduction technique
outperforms PCA from both statistical and biological
significance aspects. We present experiments on NCI 60
dataset to show this result
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