We consider the problem of inferring the structure of a network from cooccurrence data: observations that indicate which nodes occur in a signaling pathway but do not directly reveal node order within the pathway. This problem is motivated by network inference problems arising in computational biology and communication systems, in which it is difficult or impossible to obtain precise time ordering information. Without order information, every permutation of the activated nodes leads to a different feasible solution, resulting in combinatorial explosion of the feasible set. However, physical principles underlying most networked systems suggest that not all feasible solutions are equally likely. Intuitively, nodes that cooccur more frequently are probably more closely connected. Building on this intuition, we model path co-occurrences as randomly shuffled samples of a random walk on the network. We derive a computationally efficient network inference algorithm and, via novel concentration inequalities for importance sampling estimators, prove that a polynomial complexity Monte Carlo version of the algorithm converges with high probability.

The performance of EEGbased Brain-Computer-Interfaces (BCIs) critically depends on the extraction of features from the EEG carrying information relevant for the classification of different mental states. For BCIs employing imaginary movements of different limbs, the method of Common Spatial Patterns (CSP) has been shown to achieve excellent classification results. The CSP-algorithm however suffers from a lack of robustness, requiring training data without artifacts for good performance. To overcome this lack of robustness, we propose an adaptive spatial filter that replaces the training data in the CSP approach by a-priori information. More specifically, we design an adaptive spatial filter that maximizes the ratio of the variance of the electric field originating in a predefined region of interest (ROI) and the overall variance of the measured EEG. Since it is known that the component of the EEG used for discriminating imaginary movements originates in the motor cortex, we design two adaptive spatial filters with the ROIs centered in the hand areas of the left and right motor cortex. We then use these to classify EEG data recorded during imaginary movements of the right and left hand of three subjects, and show that the adaptive spatial filters outperform the CSP-algorithm, enabling classification rates of up to 94.7 % without artifact rejection.

Modelling the dynamics of transcriptional processes in the cell requires the knowledge of a number of key biological quantities. While some of them are relatively easy to measure, such as mRNA decay rates and mRNA abundance levels, it is still very hard to measure the active concentration levels of the transcription factor proteins that drive the process and the sensitivity of target genes to these concentrations. In this paper we show how these quantities for a given transcription factor can be inferred from gene expression levels of a set of known target genes. We treat the protein concentration as a latent function with a Gaussian process prior, and include the sensitivities, mRNA decay rates and baseline expression levels as hyperparameters. We apply this procedure to a human leukemia dataset, focusing on the tumour repressor p53 and obtaining results in good accordance with recent biological studies.

Autonomous helicopter flight is widely regarded to be a highly challenging control problem. This paper presents the first successful autonomous completion on a real RC helicopter of the following four aerobatic maneuvers: forward flip and sideways roll at low speed, tail-in funnel, and nose-in funnel. Our experimental results significantly extend the state of the art in autonomous helicopter flight. We used the following approach: First we had a pilot fly the helicopter to help us find a helicopter dynamics model and a reward (cost) function. Then we used a reinforcement learning (optimal control) algorithm to find a controller that is optimized for the resulting model and reward function. More specifically, we used differential dynamic programming (DDP), an extension of the linear quadratic regulator (LQR).

We have developed a novel algorithm for integrating source localization and noise suppression based on a probabilistic graphical model of stimulus-evoked MEG/EEG data. Our algorithm localizes multiple dipoles while suppressing noise sources with the computational complexity equivalent to a single dipole scan, and is therefore more efficient than traditional multidipole fitting procedures. In simulation, the algorithm can accurately localize and estimate the time course of several simultaneously-active dipoles, with rotating or fixed orientation, at noise levels typical for averaged MEG data. Furthermore, the algorithm is superior to beamforming techniques, which we show to be an approximation to our graphical model, in estimation of temporally correlated sources. Success of this algorithm for localizing auditory cortex in a tumor patient and for localizing an epileptic spike source are also demonstrated.

In this paper we focus on the issue of normalization of the affinity matrix in spectral clustering.

Survival in a non-stationary, potentially adversarial environment requires animals to detect sensory changes rapidly yet accurately, two oft competing desiderata. Neurons subserving such detections are faced with the corresponding challenge to discern "real" changes in inputs as quickly as possible, while ignoring noisy fluctuations. Mathematically, this is an example of a change-detection problem that is actively researched in the controlled stochastic processes community. In this paper, we utilize sophisticated tools developed in that community to formalize an instantiation of the problem faced by the nervous system, and characterize the Bayes-optimal decision policy under certain assumptions. We will derive from this optimal strategy an information accumulation and decision process that remarkably resembles the dynamics of a leaky integrate-and-fire neuron. This correspondence suggests that neurons are optimized for tracking input changes, and sheds new light on the computational import of intracellular properties such as resting membrane potential, voltage-dependent conductance, and post-spike reset voltage. We also explore the influence that factors such as timing, uncertainty, neuromodulation, and reward should and do have on neuronal dynamics and sensitivity, as the optimal decision strategy depends critically on these factors.

We present a local learning approach for clustering. The basic idea is that a good clustering result should have the property that the cluster label of each data point can be well predicted based on its neighboring data and their cluster labels, using current supervised learning methods. An optimization problem is formulated such that its solution has the above property. Relaxation and eigen-decomposition are applied to solve this optimization problem. We also briefly investigate the parameter selection issue and provide a simple parameter selection method for the proposed algorithm. Experimental results are provided to validate the effectiveness of the proposed approach.

Go is an ancient board game that poses unique opportunities and challenges for AI and machine learning. Here we develop a machine learning approach to Go, and related board games, focusing primarily on the problem of learning a good evaluation function in a scalable way. Scalability is essential at multiple levels, from the library of local tactical patterns, to the integration of patterns across the board, to the size of the board itself. The system we propose is capable of automatically learning the propensity of local patterns from a library of games. Propensity and other local tactical information are fed into a recursive neural network, derived from a Bayesian network architecture.

The ill-posed nature of the MEG/EEG source localization problem requires the incorporation of prior assumptions when choosing an appropriate solution out of an infinite set of candidates. Bayesian methods are useful in this capacity because they allow these assumptions to be explicitly quantified. Recently, a number of empirical Bayesian approaches have been proposed that attempt a form of model selection by using the data to guide the search for an appropriate prior. While seemingly quite different in many respects, we apply a unifying framework based on automatic relevance determination (ARD) that elucidates various attributes of these methods and suggests directions for improvement. We also derive theoretical properties of this methodology related to convergence, local minima, and localization bias and explore connections with established algorithms.