Inferring latent task structure for Multitask Learning by Multiple Kernel Learning

<p>Abstract</p> <p>Background</p> <p>The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics, many problems can be cast into the Multitask Learning scenario by incorporating data from several organisms. However, combining information from several tasks requires careful consideration of the degree of similarity between tasks. Our proposed method simultaneously learns or refines the similarity between tasks along with the Multitask Learning classifier. This is done by formulating the Multitask Learning problem as Multiple Kernel Learning, using the recently published <it>q</it>-Norm MKL algorithm.</p> <p>Results</p> <p>We demonstrate the performance of our method on two problems from Computational Biology. First, we show that our method is able to improve performance on a splice site dataset with given hierarchical task structure by refining the task relationships. Second, we consider an MHC-I dataset, for which we assume no knowledge about the degree of task relatedness. Here, we are able to learn the task similarities<it> ab initio</it> along with the Multitask classifiers. In both cases, we outperform baseline methods that we compare against.</p> <p>Conclusions</p> <p>We present a novel approach to Multitask Learning that is capable of learning task similarity along with the classifiers. The framework is very general as it allows to incorporate prior knowledge about tasks relationships if available, but is also able to identify task similarities in absence of such prior information. Both variants show promising results in applications from Computational Biology.</p

Learning Output Kernels for Multi-Task Problems

Simultaneously solving multiple related learning tasks is beneficial under a variety of circumstances, but the prior knowledge necessary to correctly model task relationships is rarely available in practice. In this paper, we develop a novel kernel-based multi-task learning technique that automatically reveals structural inter-task relationships. Building over the framework of output kernel learning (OKL), we introduce a method that jointly learns multiple functions and a low-rank multi-task kernel by solving a non-convex regularization problem. Optimization is carried out via a block coordinate descent strategy, where each subproblem is solved using suitable conjugate gradient (CG) type iterative methods for linear operator equations. The effectiveness of the proposed approach is demonstrated on pharmacological and collaborative filtering data

Discovering Valuable Items from Massive Data

Suppose there is a large collection of items, each with an associated cost and an inherent utility that is revealed only once we commit to selecting it. Given a budget on the cumulative cost of the selected items, how can we pick a subset of maximal value? This task generalizes several important problems such as multi-arm bandits, active search and the knapsack problem. We present an algorithm, GP-Select, which utilizes prior knowledge about similarity be- tween items, expressed as a kernel function. GP-Select uses Gaussian process prediction to balance exploration (estimating the unknown value of items) and exploitation (selecting items of high value). We extend GP-Select to be able to discover sets that simultaneously have high utility and are diverse. Our preference for diversity can be specified as an arbitrary monotone submodular function that quantifies the diminishing returns obtained when selecting similar items. Furthermore, we exploit the structure of the model updates to achieve an order of magnitude (up to 40X) speedup in our experiments without resorting to approximations. We provide strong guarantees on the performance of GP-Select and apply it to three real-world case studies of industrial relevance: (1) Refreshing a repository of prices in a Global Distribution System for the travel industry, (2) Identifying diverse, binding-affine peptides in a vaccine de- sign task and (3) Maximizing clicks in a web-scale recommender system by recommending items to users

Parallelizing Exploration-Exploitation Tradeoffs in Gaussian Process Bandit Optimization

How can we take advantage of opportunities for experimental parallelization in exploration-exploitation tradeoffs? In many experimental scenarios, it is often desirable to execute experiments simultaneously or in batches, rather than only performing one at a time. Additionally, observations may be both noisy and expensive. We introduce Gaussian Process Batch Upper Confidence Bound (GP-BUCB), an upper confidence bound-based algorithm, which models the reward function as a sample from a Gaussian process and which can select batches of experiments to run in parallel. We prove a general regret bound for GP-BUCB, as well as the surprising result that for some common kernels, the asymptotic average regret can be made independent of the batch size. The GP-BUCB algorithm is also applicable in the related case of a delay between initiation of an experiment and observation of its results, for which the same regret bounds hold. We also introduce Gaussian Process Adaptive Upper Confidence Bound (GP-AUCB), a variant of GP-BUCB which can exploit parallelism in an adaptive manner. We evaluate GP-BUCB and GP-AUCB on several simulated and real data sets. These experiments show that GP-BUCB and GP-AUCB are competitive with state-of-the-art heuristics