Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the origin of life. In this work we define a P system based artificial graph chemistry to understand the principles leading to the evolution of life-like structures in an AC set up and to develop a unified framework to characterize and classify symbolic artificial chemistries by devising appropriate formalism to capture semantic and organizational information. An extension of P system is considered by associating probabilities with the rules providing the topological framework for the evolution of a labeled undirected graph based molecular reaction semantics.

In bioinformatics it is often desirable to combine data from various measurement sources and thus structured feature vectors are to be analyzed that possess different intrinsic blocking characteristics (e.g., different patterns of missing values, observation noise levels, effective intrinsic dimensionalities). We propose a new machine learning tool, heterogeneous component analysis (HCA), for feature extraction in order to better understand the factors that underlie such complex structured heterogeneous data. HCA is a linear block-wise sparse Bayesian PCA based not only on a probabilistic model with block-wise residual variance terms but also on a Bayesian treatment of a block-wise sparse factor-loading matrix. We study various algorithms that implement our HCA concept extracting sparse heterogeneous structure by obtaining common components for the blocks and specific components within each block. Simulations on toy and bioinformatics data underline the usefulness of the proposed structured matrix factorization concept.

We propose a new measure of conditional dependence of random variables, based on normalized cross-covariance operators on reproducing kernel Hilbert spaces. Unlike previous kernel dependence measures, the proposed criterion does not depend on the choice of kernel in the limit of infinite data, for a wide class of kernels. At the same time, it has a straightforward empirical estimate with good convergence behaviour. We discuss the theoretical properties of the measure, and demonstrate its application in experiments.

Recent experimental studies have focused on the specialization of different neural structures for different types of instrumental behavior. Recent theoretical work has provided normative accounts for why there should be more than one control system, and how the output of different controllers can be integrated. Two particlar controllers have been identified, one associated with a forward model and the prefrontal cortex and a second associated with computationally simpler, habitual, actor-critic methods and part of the striatum. We argue here for the normative appropriateness of an additional, but so far marginalized control system, associated with episodic memory, and involving the hippocampus and medial temporal cortices. We analyze in depth a class of simple environments to show that episodic control should be useful in a range of cases characterized by complexity and inferential noise, and most particularly at the very early stages of learning, long before habitization has set in. We interpret data on the transfer of control from the hippocampus to the striatum in the light of this hypothesis.

A nonlinear dynamic system is called contracting if initial conditions are forgotten exponentially fast, so that all trajectories converge to a single trajectory. We use contraction theory to derive an upper bound for the strength of recurrent connections that guarantees contraction for complex neural networks. Specifically, we apply this theory to a special class of recurrent networks, often called Cooperative Competitive Networks (CCNs), which are an abstract representation of the cooperative-competitive connectivity observed in cortex. This specific type of network is believed to play a major role in shaping cortical responses and selecting the relevant signal among distractors and noise. In this paper, we analyze contraction of combined CCNs of linear threshold units and verify the results of our analysis in a hybrid analog/digital VLSI CCN comprising spiking neurons and dynamic synapses.

Hierarchical penalization is a generic framework for incorporating prior information in the fitting of statistical models, when the explicative variables are organized in a hierarchical structure. The penalizer is a convex functional that performs soft selection at the group level, and shrinks variables within each group. This favors solutions with few leading terms in the final combination. The framework, originally derived for taking prior knowledge into account, is shown to be useful in linear regression, when several parameters are used to model the influence of one feature, or in kernel regression, for learning multiple kernels. Keywords - Optimization: constrained and convex optimization.

Brain-Computer Interfaces can suffer from a large variance of the subject conditions within and across sessions. For example vigilance fluctuations in the individual, variable task involvement, workload etc. alter the characteristics of EEG signals and thus challenge a stable BCI operation. In the present work we aim to define features based on a variant of the common spatial patterns (CSP) algorithm that are constructed invariant with respect to such nonstationarities. We enforce invariance properties by adding terms to the denominator of a Rayleigh coefficient representation of CSP such as disturbance covariance matrices from fluctuations in visual processing. In this manner physiological prior knowledge can be used to shape the classification engine for BCI. As a proof of concept we present a BCI classifier that is robust to changes in the level of parietal α -activity. In other words, the EEG decoding still works when there are lapses in vigilance.

We present an efficient generalization of the sparse pseudo-input Gaussian process (SPGP) model developed by Snelson and Ghahramani [1], applying it to binary classification problems.

Maximum variance unfolding (MVU) is an effective heuristic for dimensionality reduction. It produces a low-dimensional representation of the data by maximizing the variance of their embeddings while preserving the local distances of the original data. We show that MVU also optimizes a statistical dependence measure which aims to retain the identity of individual observations under the distancepreserving constraints. This general view allows us to design "colored" variants of MVU, which produce low-dimensional representations for a given task, e.g.

We present a probabilistic generative model of visual attributes, together with an efficient learning algorithm. Attributes are visual qualities of objects, such as'red', 'striped', or'spotted'. The model sees attributes as patterns of image segments, repeatedly sharing some characteristic properties. These can be any combination of appearance, shape, or the layout of segments within the pattern. Moreover, attributes with general appearance are taken into account, such as the pattern of alternation of any two colors which is characteristic for stripes. To enable learning from unsegmented training images, the model is learnt discriminatively, by optimizing a likelihood ratio. As demonstrated in the experimental evaluation, our model can learn in a weakly supervised setting and encompasses a broad range of attributes. We show that attributes can be learnt starting from a text query to Google image search, and can then be used to recognize the attribute and determine its spatial extent in novel real-world images.