Chemical reaction networks by which individual cells gather and process information abouttheir chemical environments have been dubbed "signal transduction" networks. Despite this suggestive terminology, there have been few attempts to analyze chemical signaling systems with the quantitative tools of information theory. Gradientsensing in the social amoeba Dictyostelium discoideum is a well characterized signal transduction system in which a cell estimates the direction of a source of diffusing chemoattractant molecules based on the spatiotemporal sequence of ligand-receptor binding events at the cell membrane. Using Monte Carlo techniques (MCell) we construct a simulation in which a collection of individual ligandparticles undergoing Brownian diffusion in a three-dimensional volume interact with receptors on the surface of a static amoeboid cell. Adapting a method for estimation of spike train entropies described by Victor (originally due to Kozachenko and Leonenko), we estimate lower bounds on the mutual information betweenthe transmitted signal (direction of ligand source) and the received signal (spatiotemporal pattern of receptor binding/unbinding events). Hence we provide a quantitative framework for addressing the question: how much could the cell know, and when could it know it? We show that the time course of the mutual informationbetween the cell's surface receptors and the (unknown) gradient direction is consistent with experimentally measured cellular response times. We find that the acquisition of directional information depends strongly on the time constant at which the intracellular response is filtered.

This paper introduces adaptor grammars, a class of probabilistic models of language thatgeneralize probabilistic context-free grammars (PCFGs). Adaptor grammars augment the probabilistic rules of PCFGs with "adaptors" that can induce dependenciesamong successive uses. With a particular choice of adaptor, based on the Pitman-Yor process, nonparametric Bayesian models of language using Dirichlet processes and hierarchical Dirichlet processes can be written as simple grammars. We present a general-purpose inference algorithm for adaptor grammars, making it easy to define and use such models, and illustrate how several existing nonparametric Bayesian models can be expressed within this framework.

The study of point cloud data sampled from a stratification, a collection of manifolds withpossible different dimensions, is pursued in this paper. We present a technique for simultaneously soft clustering and estimating the mixed dimensionality anddensity of such structures. The framework is based on a maximum likelihood estimationof a Poisson mixture model. The presentation of the approach is completed with artificial and real examples demonstrating the importance of extending manifold learning to stratification learning.

Sequence labeling, the task of assigning labels y: yl, ..., yL to an input sequence x: 1:1, ...,:cL, is

Policy gradient methods are reinforcement learning algorithms that adapt a parameterized policyby following a performance gradient estimate. Conventional policy gradient methods use Monte-Carlo techniques to estimate this gradient. Since Monte Carlo methods tend to have high variance, a large number of samples is required, resulting in slow convergence. In this paper, we propose a Bayesian framework that models the policy gradient as a Gaussian process. This reduces the number of samples needed to obtain accurate gradient estimates. Moreover, estimates of the natural gradient as well as a measure of the uncertainty in the gradient estimates are provided at little extra cost.

Many computer aided diagnosis (CAD) problems can be best modelled as a multiple-instance learning (MIL) problem with unbalanced data: i.e., the training data typically consists of a few positive bags, and a very large number of negative instances.Existing MIL algorithms are much too computationally expensive for these datasets. We describe CH, a framework for learning a Convex Hull representation of multiple instances that is significantly faster than existing MIL algorithms. Our CH framework applies to any standard hyperplane-based learning algorithm, and for some algorithms, is guaranteed to find the global optimal solution. Experimentalstudies on two different CAD applications further demonstrate that the proposed algorithm significantly improves diagnostic accuracy when compared toboth MIL and traditional classifiers. Although not designed for standard MIL problems (which have both positive and negative bags and relatively balanced datasets),comparisons against other MIL methods on benchmark problems also indicate that the proposed method is competitive with the state-of-the-art.

Multinomial logistic regression provides the standard penalised maximum-likelihood solution to multi-Class pattern recognition problems.

Geometrically based methods for various tasks of machine learning have attracted considerable attention over the last few years. In this paper we show convergence of eigenvectors of the point cloud Laplacian to the eigenfunctions ofthe Laplace-Beltrami operator on the underlying manifold, thus establishing the first convergence results for a spectral dimensionality reduction algorithmin the manifold setting.

Another recent innovation is the use of long and rich stimuli in MRI experiments, such as a commercial movie [8], rather than the traditional controlled, repeating simple stimuli.

Bob offers a face-detection web service where clients can submit their images for analysis. Alice would very much like to use the service, but is reluctant to reveal the content of her images to Bob. Bob, for his part, is reluctant to release his face detector, as he spent a lot of time, energy and money constructing it. Secure Multi-Party computations use cryptographic tools to solve this problem without leaking any information. Unfortunately, these methods are slow to compute and we introduce acouple of machine learning techniques that allow the parties to solve the problem while leaking a controlled amount of information. The first method is an information-bottleneck variant of AdaBoost that lets Bob find a subset of features that are enough for classifying an image patch, but not enough to actually reconstruct it.The second machine learning technique is active learning that allows Alice to construct an online classifier, based on a small number of calls to Bob's face detector. She can then use her online classifier as a fast rejector before using a cryptographically secure classifier on the remaining image patches.