Laplacian Mixture Modeling for Network Analysis and Unsupervised Learning on Graphs

Laplacian mixture models identify overlapping regions of influence in unlabeled graph and network data in a scalable and computationally efficient way, yielding useful low-dimensional representations. By combining Laplacian eigenspace and finite mixture modeling methods, they provide probabilistic or fuzzy dimensionality reductions or domain decompositions for a variety of input data types, including mixture distributions, feature vectors, and graphs or networks. Provable optimal recovery using the algorithm is analytically shown for a nontrivial class of cluster graphs. Heuristic approximations for scalable high-performance implementations are described and empirically tested. Connections to PageRank and community detection in network analysis demonstrate the wide applicability of this approach. The origins of fuzzy spectral methods, beginning with generalized heat or diffusion equations in physics, are reviewed and summarized. Comparisons to other dimensionality reduction and clustering methods for challenging unsupervised machine learning problems are also discussed.Comment: 13 figures, 35 reference

Epitope profiling via mixture modeling of ranked data

We propose the use of probability models for ranked data as a useful alternative to a quantitative data analysis to investigate the outcome of bioassay experiments, when the preliminary choice of an appropriate normalization method for the raw numerical responses is difficult or subject to criticism. We review standard distance-based and multistage ranking models and in this last context we propose an original generalization of the Plackett-Luce model to account for the order of the ranking elicitation process. The usefulness of the novel model is illustrated with its maximum likelihood estimation for a real data set. Specifically, we address the heterogeneous nature of experimental units via model-based clustering and detail the necessary steps for a successful likelihood maximization through a hybrid version of the Expectation-Maximization algorithm. The performance of the mixture model using the new distribution as mixture components is compared with those relative to alternative mixture models for random rankings. A discussion on the interpretation of the identified clusters and a comparison with more standard quantitative approaches are finally provided.Comment: (revised to properly include references

Recognising, Representing and Mapping Natural Features in Unstructured Environments

This thesis addresses the problem of building statistical models for multi-sensor perception in unstructured outdoor environments. The perception problem is divided into three distinct tasks: recognition, representation and association. Recognition is cast as a statistical classification problem where inputs are images or a combination of images and ranging information. Given the complexity and variability of natural environments, this thesis investigates the use of Bayesian statistics and supervised dimensionality reduction to incorporate prior information and fuse sensory data. A compact probabilistic representation of natural objects is essential for many problems in field robotics. This thesis presents techniques for combining non-linear dimensionality reduction with parametric learning through Expectation Maximisation to build general representations of natural features. Once created these models need to be rapidly processed to account for incoming information. To this end, techniques for efficient probabilistic inference are proposed. The robustness of localisation and mapping algorithms is directly related to reliable data association. Conventional algorithms employ only geometric information which can become inconsistent for large trajectories. A new data association algorithm incorporating visual and geometric information is proposed to improve the reliability of this task. The method uses a compact probabilistic representation of objects to fuse visual and geometric information for the association decision. The main contributions of this thesis are: 1) a stochastic representation of objects through non-linear dimensionality reduction; 2) a landmark recognition system using a visual and ranging sensors; 3) a data association algorithm combining appearance and position properties; 4) a real-time algorithm for detection and segmentation of natural objects from few training images and 5) a real-time place recognition system combining dimensionality reduction and Bayesian learning. The theoretical contributions of this thesis are demonstrated with a series of experiments in unstructured environments. In particular, the combination of recognition, representation and association algorithms is applied to the Simultaneous Localisation and Mapping problem (SLAM) to close large loops in outdoor trajectories, proving the benefits of the proposed methodology

Configuring of extero- and interoceptive senses in actions on food

This paper reviews all the published evidence on the theory that the act of selecting a piece of food or drink structurally coordinates quantitative information across several sensory modalities. The existing data show that the momentary disposition to consume the item is strengthened or weakened by learnt configurations of stimuli perceived through both exteroceptive and interoceptive senses. The observed configural structure of performance shows that the multimodal stimuli are interacting perceptually, rather than merely combining quantities of information from the senses into the observed response

Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table