Biomedical subjects

Yan Karklin

Publications and source records attributed to Yan Karklin.

3 recordsLinked to original sources

PubMed2005

A hierarchical Bayesian model for learning nonlinear statistical regularities in nonstationary natural signals.

Capturing statistical regularities in complex, high-dimensional data is an important problem in machine learning and signal processing. Models such as principal component analysis (PCA) and independent component analysis (ICA) make few assumptions about the structure in the data and have good scaling properties, but they are limited to representing linear statistical regularities and assume that the distribution of the data is stationary. For many natural, complex signals, the latent variables often exhibit residual dependencies as well as nonstationary statistics. Here we present a hierarchical Bayesian model that is able to capture higher-order nonlinear structure and represent nonstationary data distributions. The model is a generalization of ICA in which the basis function coefficients are no longer assumed to be independent; instead, the dependencies in their magnitudes are captured by a set of density components. Each density component describes a common pattern of deviation from the marginal density of the pattern ensemble; in different combinations, they can describe nonstationary distributions. Adapting the model to image or audio data yields a nonlinear, distributed code for higher-order statistical regularities that reflect more abstract, invariant properties of the signal.

Bayes Theorem↗

PubMed2005

Classification of non-coding RNA using graph representations of secondary structure.

Some genes produce transcripts that function directly in regulatory, catalytic, or structural roles in the cell. These non-coding RNAs are prevalent in all living organisms, and methods that aid the understanding of their functional roles are essential. RNA secondary structure, the pattern of base-pairing, contains the critical information for determining the three dimensional structure and function of the molecule. In this work we examine whether the basic geometric and topological properties of secondary structure are sufficient to distinguish between RNA families in a learning framework. First, we develop a labeled dual graph representation of RNA secondary structure by adding biologically meaningful labels to the dual graphs proposed by Gan et al [1]. Next, we define a similarity measure directly on the labeled dual graphs using the recently developed marginalized kernels [2]. Using this similarity measure, we were able to train Support Vector Machine classifiers to distinguish RNAs of known families from random RNAs with similar statistics. For 22 of the 25 families tested, the classifier achieved better than 70% accuracy, with much higher accuracy rates for some families. Training a set of classifiers to automatically assign family labels to RNAs using a one vs. all multi-class scheme also yielded encouraging results. From these initial learning experiments, we suggest that the labeled dual graph representation, together with kernel machine methods, has potential for use in automated analysis and classification of uncharacterized RNA molecules or efficient genome-wide screens for RNA molecules from existing families.

Base Sequence↗

PubMed2003

Learning higher-order structures in natural images.

The theoretical principles that underlie the representation and computation of higher-order structure in natural images are poorly understood. Recently, there has been considerable interest in using information theoretic techniques, such as independent component analysis, to derive representations for natural images that are optimal in the sense of coding efficiency. Although these approaches have been successful in explaining properties of neural representations in the early visual pathway and visual cortex, because they are based on a linear model, the types of image structure that can be represented are very limited. Here, we present a hierarchical probabilistic model for learning higher-order statistical regularities in natural images. This non-linear model learns an efficient code that describes variations in the underlying probabilistic density. When applied to natural images the algorithm yields coarse-coded, sparse-distributed representations of abstract image properties such as object location, scale and texture. This model offers a novel description of higher-order image structure and could provide theoretical insight into the response properties and computational functions of lower level cortical visual areas.

Learning↗