Applications of regularized least squares to pattern classification

AbstractWe survey a number of recent results concerning the behaviour of algorithms for learning classifiers based on the solution of a regularized least-squares problem

A machine learning strategy to identify candidate binding sites in human protein-coding sequence

BACKGROUND: The splicing of RNA transcripts is thought to be partly promoted and regulated by sequences embedded within exons. Known sequences include binding sites for SR proteins, which are thought to mediate interactions between splicing factors bound to the 5' and 3' splice sites. It would be useful to identify further candidate sequences, however identifying them computationally is hard since exon sequences are also constrained by their functional role in coding for proteins. RESULTS: This strategy identified a collection of motifs including several previously reported splice enhancer elements. Although only trained on coding exons, the model discriminates both coding and non-coding exons from intragenic sequence. CONCLUSION: We have trained a computational model able to detect signals in coding exons which seem to be orthogonal to the sequences' primary function of coding for proteins. We believe that many of the motifs detected here represent binding sites for both previously unrecognized proteins which influence RNA splicing as well as other regulatory elements

Graphical Models: Modeling, Optimization, and Hilbert Space Embedding

Over the past two decades graphical models have been widely used as a powerful tool for compactly representing distributions. On the other hand, kernel methods have also been used extensively to come up with rich representations. This thesis aims to combine graphical models with kernels to produce compact models with rich representational abilities. The following four areas are our focus. 1. Conditional random fields for multi-agent reinforcement learning. Conditional random fields (CRFs) are graphical models for modeling the probability of labels given the observations. They have traditionally assumed that, conditioned on the training data, the label sequences of different training examples are independent and identically distributed (iid). We extended the use of CRFs to a class of temporal learning algorithms, namely policy gradient reinforcement learning (RL). Now the labels are no longer iid. They are actions that update the environment and affect the next observation. From an RL point of view, CRFs provide a natural way to model joint actions in a decentralized Markov decision process. Using tree sampling for inference, our experiment shows the RL methods employing CRFs clearly outperform those which do not model the proper joint policy. 2. Bayesian online multi-label classification. Gaussian density filtering provides fast and effective inference for graphical models (Maybeck, 1982). Based on it, we propose a Bayesian online multi-label classification (BOMC) framework which learns a probabilistic model of the linear classifier. The training labels are incorporated to update the posterior of the classifiers via a graphical model similar to TrueSkill (Herbrich et al, 2007). Using samples from the posterior, we label the test data by maximizing the expected F1-score. In our experiments, BOMC delivers significantly higher macro-averaged F1-score than the state-of-the-art online maximum margin learners. 3. Hilbert space embedment of distributions. Graphical models are also an essential tool in kernel measures of independence for non-iid data. Traditional information theory often requires density estimation, which makes it unideal for statistical estimation. Motivated by the fact that distributions often appear in machine learning via expectations, we can characterize the distance between distributions in terms of distances between means, especially means in reproducing kernel Hilbert spaces which are called kernel embeddings. Under this framework, the undirected graphical models further allow us to factorize the kernel embeddings onto cliques, which yields efficient measures of independence for non-iid data (Zhang et al, 2009). 4. Optimization in maximum margin models for structured data. Maximum margin estimation for structured data is an important task where graphical models also play a key role. They are special cases of regularized risk minimization, for which bundle methods (BMRM, Teo et al, 2007) are a state-of-the-art general purpose solver. Smola et al (2007) proved that BMRM requires O(1/epsilon) iterations to converge to an epsilon accurate solution, and we further show that this rate hits the lower bound. Motivated by (Nesterov 2003, 2005), we utilized the composite structure of the objective function and devised an algorithm for the structured loss which converges to an epsilon accurate solution in O(1/sqrt{epsilon}) iterations