Stochastic Coordinate Coding and Its Application for Drosophila Gene Expression Pattern Annotation

\textit{Drosophila melanogaster} has been established as a model organism for investigating the fundamental principles of developmental gene interactions. The gene expression patterns of \textit{Drosophila melanogaster} can be documented as digital images, which are annotated with anatomical ontology terms to facilitate pattern discovery and comparison. The automated annotation of gene expression pattern images has received increasing attention due to the recent expansion of the image database. The effectiveness of gene expression pattern annotation relies on the quality of feature representation. Previous studies have demonstrated that sparse coding is effective for extracting features from gene expression images. However, solving sparse coding remains a computationally challenging problem, especially when dealing with large-scale data sets and learning large size dictionaries. In this paper, we propose a novel algorithm to solve the sparse coding problem, called Stochastic Coordinate Coding (SCC). The proposed algorithm alternatively updates the sparse codes via just a few steps of coordinate descent and updates the dictionary via second order stochastic gradient descent. The computational cost is further reduced by focusing on the non-zero components of the sparse codes and the corresponding columns of the dictionary only in the updating procedure. Thus, the proposed algorithm significantly improves the efficiency and the scalability, making sparse coding applicable for large-scale data sets and large dictionary sizes. Our experiments on Drosophila gene expression data sets demonstrate the efficiency and the effectiveness of the proposed algorithm.

Minimum Message Length Clustering Using Gibbs Sampling

The K-Mean and EM algorithms are popular in clustering and mixture modeling, due to their simplicity and ease of implementation. However, they have several significant limitations. Both coverage to a local optimum of their respective objective functions (ignoring the uncertainty in the model space), require the apriori specification of the number of classes/clsuters, and are inconsistent. In this work we overcome these limitations by using the Minimum Message Length (MML) principle and a variation to the K-Means/EM observation assignment and parameter calculation scheme. We maintain the simplicity of these approaches while constructing a Bayesian mixture modeling tool that samples/searches the model space using a Markov Chain Monte Carlo (MCMC) sampler known as a Gibbs sampler. Gibbs sampling allows us to visit each model according to its posterior probability. Therefore, if the model space is multi-modal we will visit all models and not get stuck in local optima. We call our approach multiple chains at equilibrium (MCE) MML sampling.

On Constrained Spectral Clustering and Its Applications

Constrained clustering has been well-studied for algorithms such as $K$-means and hierarchical clustering. However, how to satisfy many constraints in these algorithmic settings has been shown to be intractable. One alternative to encode many constraints is to use spectral clustering, which remains a developing area. In this paper, we propose a flexible framework for constrained spectral clustering. In contrast to some previous efforts that implicitly encode Must-Link and Cannot-Link constraints by modifying the graph Laplacian or constraining the underlying eigenspace, we present a more natural and principled formulation, which explicitly encodes the constraints as part of a constrained optimization problem. Our method offers several practical advantages: it can encode the degree of belief in Must-Link and Cannot-Link constraints; it guarantees to lower-bound how well the given constraints are satisfied using a user-specified threshold; it can be solved deterministically in polynomial time through generalized eigendecomposition. Furthermore, by inheriting the objective function from spectral clustering and encoding the constraints explicitly, much of the existing analysis of unconstrained spectral clustering techniques remains valid for our formulation. We validate the effectiveness of our approach by empirical results on both artificial and real datasets. We also demonstrate an innovative use of encoding large number of constraints: transfer learning via constraints.

A Reconstruction Error Formulation for Semi-Supervised Multi-task and Multi-view Learning

A significant challenge to make learning techniques more suitable for general purpose use is to move beyond i) complete supervision, ii) low dimensional data, iii) a single task and single view per instance. Solving these challenges allows working with "Big Data" problems that are typically high dimensional with multiple (but possibly incomplete) labelings and views. While other work has addressed each of these problems separately, in this paper we show how to address them together, namely semi-supervised dimension reduction for multi-task and multi-view learning (SSDR-MML), which performs optimization for dimension reduction and label inference in semi-supervised setting. The proposed framework is designed to handle both multi-task and multi-view learning settings, and can be easily adapted to many useful applications. Information obtained from all tasks and views is combined via reconstruction errors in a linear fashion that can be efficiently solved using an alternating optimization scheme. Our formulation has a number of advantages. We explicitly model the information combining mechanism as a data structure (a weight/nearest-neighbor matrix) which allows investigating fundamental questions in multi-task and multi-view learning. We address one such question by presenting a general measure to quantify the success of simultaneous learning of multiple tasks or from multiple views. We show that our SSDR-MML approach can outperform many state-of-the-art baseline methods and demonstrate the effectiveness of connecting dimension reduction and learning.