22 research outputs found
Hierarchical Multi-Bottleneck Classification Method And Its Application to DNA Microarray Expression Data
The recent development of DNA microarray technology is creating a wealth of gene expression data. Typically these datasets have high dimensionality and a lot of varieties. Analysis of DNA microarray expression data is a fast growing research area that interfaces various disciplines such as biology, biochemistry, computer science and statistics. It is concluded that clustering and classification techniques can be successfully employed to group genes based on the similarity of their expression patterns. In this paper, a hierarchical multi-bottleneck classification method is proposed, and it is applied to classify a publicly available gene microarray expression data of budding yeast Saccharomyces cerevisiae.Singapore-MIT Alliance (SMA
Deep Divergence-Based Approach to Clustering
A promising direction in deep learning research consists in learning
representations and simultaneously discovering cluster structure in unlabeled
data by optimizing a discriminative loss function. As opposed to supervised
deep learning, this line of research is in its infancy, and how to design and
optimize suitable loss functions to train deep neural networks for clustering
is still an open question. Our contribution to this emerging field is a new
deep clustering network that leverages the discriminative power of
information-theoretic divergence measures, which have been shown to be
effective in traditional clustering. We propose a novel loss function that
incorporates geometric regularization constraints, thus avoiding degenerate
structures of the resulting clustering partition. Experiments on synthetic
benchmarks and real datasets show that the proposed network achieves
competitive performance with respect to other state-of-the-art methods, scales
well to large datasets, and does not require pre-training steps
Optimal Kullback-Leibler Aggregation via Information Bottleneck
In this paper, we present a method for reducing a regular, discrete-time
Markov chain (DTMC) to another DTMC with a given, typically much smaller number
of states. The cost of reduction is defined as the Kullback-Leibler divergence
rate between a projection of the original process through a partition function
and a DTMC on the correspondingly partitioned state space. Finding the reduced
model with minimal cost is computationally expensive, as it requires an
exhaustive search among all state space partitions, and an exact evaluation of
the reduction cost for each candidate partition. Our approach deals with the
latter problem by minimizing an upper bound on the reduction cost instead of
minimizing the exact cost; The proposed upper bound is easy to compute and it
is tight if the original chain is lumpable with respect to the partition. Then,
we express the problem in the form of information bottleneck optimization, and
propose using the agglomerative information bottleneck algorithm for searching
a sub-optimal partition greedily, rather than exhaustively. The theory is
illustrated with examples and one application scenario in the context of
modeling bio-molecular interactions.Comment: 13 pages, 4 figure