Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites

AAAI Conferences

Regulation of gene expression often involves proteins that bind to particular regions of DNA. Determining the binding sites for a protein and its specificity usually requires extensive biochemical and/or genetic experimentation. In this paper we illustrate the use of a neural network to obtain the desired information with much less experimental effort. It is often fairly easy to obtain a set of moderate length sequences, perhaps one or two hundred base-pairs, that each contain binding sites for the protein being studied. For example, the upstream regions of a set of genes that are all regulated by the same protein should each contain binding sites for that protein.

Sharing Clusters among Related Groups: Hierarchical Dirichlet Processes

Neural Information Processing Systems

We propose the hierarchical Dirichlet process (HDP), a nonparametric Bayesian model for clustering problems involving multiple groups of data. Each group of data is modeled with a mixture, with the number of components being open-ended and inferred automatically by the model. Further, components can be shared across groups, allowing dependencies across groups to be modeled effectively as well as conferring generalization tonew groups. Such grouped clustering problems occur often in practice, e.g. in the problem of topic discovery in document corpora. We report experimental results on three text corpora showing the effective and superior performance of the HDP over previous models.

On the Difficulty of Achieving Equilibrium in Interactive POMDPs

AAAI Conferences

We analyze the asymptotic behavior of agents engaged in an infinite horizon partially observable stochastic game as formalized by the interactive POMDP framework. We show that when agents' initial beliefs satisfy a truth compatibility condition, their behavior converges to a subjective ɛ-equilibrium in a finite time, and subjective equilibrium in the limit. This result is a generalization of a similar result in repeated games, to partially observable stochastic games. However, it turns out that the equilibrating process is difficult to demonstrate computationally because of the difficulty in coming up with initial beliefs that are both natural and satisfy the truth compatibility condition. Our results, therefore, shed some negative light on using equilibria as a solution concept for decision making in partially observable stochastic games.

Multiagent Stochastic Planning With Bayesian Policy Recognition

AAAI Conferences

When operating in stochastic, partially observable, multiagent settings, it is crucial to accurately predict the actions of other agents. In my thesis work, I propose methodologies for learning the policy of external agents from their observed behavior, in the form of finite state controllers. To perform this task, I adopt Bayesian learning algorithms based on nonparametric prior distributions, that provide the flexibility required to infer models of unknown complexity. These methods are to be embedded in decision making frameworks for autonomous planning in partially observable multiagent systems.

Parallelising MCMC via Random Forests Machine Learning

Markov chain Monte Carlo (MCMC) algorithm, a generic sampling method, is ubiquitous in modern statistics, especially in Bayesian fields. MCMC algorithms require only the evaluation of the target pointwise, up to a multiple constant, in order to sample from it. In Bayesian analysis, the object of main interest is the posterior, which is not in closed form in general, and MCMC has become a standard tool in this domain. However, MCMC is difficult to scale and its applications are limited when the observation size is very large, for it needs to sweep over the entire observations set in order to evaluate the likelihood function at each iteration. Recently, many methods have been proposed to better scale MCMC algorithms for big data sets and these can be roughly classified into two groups Bardenet et al. (2017): divide-and-conquer methods and subsampling-based methods. For divide-and-conquer methods, one splits the whole data set into subsets, runs MCMC over each subset to generate samples of parameters and combine these to produce an approximation of the true posterior. Depending on how MCMC is handled over the subsets, these methods can be further classified into two sub-categories.