We address the problem of robust, computationally-efficient design of biological experiments. Classical optimal experiment design methods have not been widely adopted in biological practice, in part because the resulting designs can be very brittle if the nominal parameter estimates for the model are poor, and in part because of computational constraints. We present a method for robust experiment design based on a semidefinite programming relaxation. We present an application of this method to the design of experiments for a complex calcium signal transduction pathway, where we have found that the parameter estimates obtained from the robust design are better than those obtained from an "optimal" design.

Kernel methods make it relatively easy to define complex highdimensional feature spaces. This raises the question of how we can identify the relevant subspaces for a particular learning task. When two views of the same phenomenon are available kernel Canonical Correlation Analysis (KCCA) has been shown to be an effective preprocessing step that can improve the performance of classification algorithms such as the Support Vector Machine (SVM). This paper takes this observation to its logical conclusion and proposes a method that combines this two stage learning (KCCA followed by SVM) into a single optimisation termed SVM-2K. We present both experimental and theoretical analysis of the approach showing encouraging results and insights.

The Octopus arm is a highly versatile and complex limb. How the Octopus controls such a hyper-redundant arm (not to mention eight of them!) is as yet unknown. Robotic arms based on the same mechanical principles may render present day robotic arms obsolete. In this paper, we tackle this control problem using an online reinforcement learning algorithm, based on a Bayesian approach to policy evaluation known as Gaussian process temporal difference (GPTD) learning. Our substitute for the real arm is a computer simulation of a 2-dimensional model of an Octopus arm. Even with the simplifications inherent to this model, the state space we face is a high-dimensional one. We apply a GPTDbased algorithm to this domain, and demonstrate its operation on several learning tasks of varying degrees of difficulty.

We introduce a method to automatically improve character models for a handwritten script without the use of transcriptions and using a minimum of document specific training data. We show that we can use searches for the words in a dictionary to identify portions of the document whose transcriptions are unambiguous. Using templates extracted from those regions, we retrain our character prediction model to drastically improve our search retrieval performance for words in the document.

Brain-Computer Interface (BCI) systems create a novel communication channel from the brain to an output device by bypassing conventional motor output pathways of nerves and muscles. Therefore they could provide a new communication and control option for paralyzed patients. Modern BCI technology is essentially based on techniques for the classification of single-trial brain signals. Here we present a novel technique that allows the simultaneous optimization of a spatial and a spectral filter enhancing discriminability of multi-channel EEG single-trials. The evaluation of 60 experiments involving 22 different subjects demonstrates the superiority of the proposed algorithm. Apart from the enhanced classification, the spatial and/or the spectral filter that are determined by the algorithm can also be used for further analysis of the data, e.g., for source localization of the respective brain rhythms.

This paper describes a highly successful application of MRFs to the problem of generating high-resolution range images. A new generation of range sensors combines the capture of low-resolution range images with the acquisition of registered high-resolution camera images. The MRF in this paper exploits the fact that discontinuities in range and coloring tend to co-align. This enables it to generate high-resolution, low-noise range images by integrating regular camera images into the range data. We show that by using such an MRF, we can substantially improve over existing range imaging technology.

Nonnegative matrix approximation (NNMA) is a recent technique for dimensionality reduction and data analysis that yields a parts based, sparse nonnegative representation for nonnegative input data. NNMA has found a wide variety of applications, including text analysis, document clustering, face/image recognition, language modeling, speech processing and many others. Despite these numerous applications, the algorithmic development for computing the NNMA factors has been relatively deficient. This paper makes algorithmic progress by modeling and solving (using multiplicative updates) new generalized NNMA problems that minimize Bregman divergences between the input matrix and its lowrank approximation. The multiplicative update formulae in the pioneering work by Lee and Seung [11] arise as a special case of our algorithms. In addition, the paper shows how to use penalty functions for incorporating constraints other than nonnegativity into the problem. Further, some interesting extensions to the use of "link" functions for modeling nonlinear relationships are also discussed.

This paper addresses the issue of numerical computation in machine learning domains based on similarity metrics, such as kernel methods, spectral techniques and Gaussian processes. It presents a general solution strategy based on Krylov subspace iteration and fast N-body learning methods. The experiments show significant gains in computation and storage on datasets arising in image segmentation, object detection and dimensionality reduction. The paper also presents theoretical bounds on the stability of these methods.

Experimental data indicate that norepinephrine is critically involved in aspects of vigilance and attention. Previously, we considered the function of this neuromodulatory system on a time scale of minutes and longer, and suggested that it signals global uncertainty arising from gross changes in environmental contingencies. However, norepinephrine is also known to be activated phasically by familiar stimuli in welllearned tasks. Here, we extend our uncertainty-based treatment of norepinephrine to this phasic mode, proposing that it is involved in the detection and reaction to state uncertainty within a task. This role of norepinephrine can be understood through the metaphor of neural interrupts.

Neurons can have rapidly changing spike train statistics dictated by the underlying network excitability or behavioural state of an animal. To estimate the time course of such state dynamics from single-or multiple neuron recordings, we have developed an algorithm that maximizes the likelihood of observed spike trains by optimizing the state lifetimes and the state-conditional interspike-interval (ISI) distributions. Our nonparametric algorithm is free of time-binning and spike-counting problems and has the computational complexity of a Mixed-state Markov Model operating on a state sequence of length equal to the total number of recorded spikes. As an example, we fit a two-state model to paired recordings of premotor neurons in the sleeping songbird. We find that the two state-conditional ISI functions are highly similar to the ones measured during waking and singing, respectively.