For natural and artificial systems with some symmetry structure, computational understanding and manipulation can be achieved without learning by exploiting the algebraic structure. Here we describe this algebraic coordinatization method and apply it to permutation puzzles. Coordinatization yields a structural understanding, not just solutions for the puzzles.

Nearly invariably, phenotypes are reported in the scientific literature in meticulous detail, utilizing the full expressivity of natural language. Often it is particularly these detailed observations (facts) that are of interest, and thus specific to the research questions that motivated observing and reporting them. However, research aiming to synthesize or integrate phenotype data across many studies or even fields is often faced with the need to abstract from detailed observations so as to construct phenotypic concepts that are common across many datasets rather than specific to a few. Yet, observations or facts that would fall under such abstracted concepts are typically not directly asserted by the original authors, usually because they are "obvious" according to common domain knowledge, and thus asserting them would be deemed redundant by anyone with sufficient domain knowledge. For example, a phenotype describing the length of a manual digit for an organism implicitly means that the organism must have had a hand, and thus a forelimb; the presence or absence of a forelimb may have supporting data across a far wider range of taxa than the length of a particular manual digit. Here we describe how within the Phenoscape project we use a pipeline of OWL axiom generation and reasoning steps to infer taxon-specific presence/absence of anatomical entities from anatomical phenotypes. Although presence/absence is all but one, and a seemingly simple way to abstract phenotypes across data sources, it can nonetheless be powerful for linking genotype to phenotype, and it is particularly relevant for constructing synthetic morphological supermatrices for comparative analysis; in fact presence/absence is one of the prevailing character observation types in published character matrices.

One of the biggest challenges in real world decision making process is to cope with uncertainty, complexity, volatility and ambiguity. How do we deal with this growing confusion in our world? In scene understanding, an important and yet difficult image understanding problem due to their variability, ambiguity, wide range of illumination and scale conditions falls into this category. The conventional goal of the works is to assign an unknown scene image to one of the several possible classes. For example, Figure 1(a) is a Coast class scene while Figure 1(c) is a Mountain class scene. Intentionally, most state-of-the-art approaches in scene understanding domain [1]-[4] are exemplar-based and assume that scene images are mutually exclusive, P (A B) 0. This simplifies the complex problem of scene understanding (uncertainty, complexity, volatility, and ambiguity) to a simple binary classification task. Such approaches learn patterns from a training set and subsequently, search for the images similar to it. As a result of this, classification errors often occur when the scene classes overlap in the selected feature space.

Artifact systems are a novel paradigm for specifying and implementing business processes described in terms of interacting modules called artifacts. Artifacts consist of data and lifecycles, accounting respectively for the relational structure of the artifacts states and their possible evolutions over time. In this paper we put forward artifact-centric multi-agent systems, a novel formalisation of artifact systems in the context of multi-agent systems operating on them. Differently from the usual process-based models of services, we give a semantics that explicitly accounts for the data structures on which artifact systems are defined. We study the model checking problem for artifact-centric multi-agent systems against specifications expressed in a quantified version of temporal-epistemic logic expressing the knowledge of the agents in the exchange. We begin by noting that the problem is undecidable in general. We identify a noteworthy class of systems that admit bisimilar, finite abstractions. It follows that we can verify these systems by investigating their finite abstractions; we also show that the corresponding model checking problem is EXPSPACE-complete. We then introduce artifact-centric programs, compact and declarative representations of the programs governing both the artifact system and the agents. We show that, while these in principle generate infinite-state systems, under natural conditions their verification problem can be solved on finite abstractions that can be effectively computed from the programs. We exemplify the theoretical results here pursued through a mainstream procurement scenario from the artifact systems literature.

The increasing importance of renewable energy, especially solar and wind power, has led to new forces in the formation of electricity prices. Hence, this paper introduces an econometric model for the hourly time series of electricity prices of the European Power Exchange (EPEX) which incorporates specific features like renewable energy. The model consists of several sophisticated and established approaches and can be regarded as a periodic VAR-TARCH with wind power, solar power, and load as influences on the time series. It is able to map the distinct and well-known features of electricity prices in Germany. An efficient iteratively reweighted lasso approach is used for the estimation. Moreover, it is shown that several existing models are outperformed by the procedure developed in this paper.

Solving different types of optimization models (including parameters fitting) for support vector machines on large-scale training data is often an expensive computational task. This paper proposes a multilevel algorithmic framework that scales efficiently to very large data sets. Instead of solving the whole training set in one optimization process, the support vectors are obtained and gradually refined at multiple levels of coarseness of the data. The proposed framework includes: (a) construction of hierarchy of large-scale data coarse representations, and (b) a local processing of updating the hyperplane throughout this hierarchy. Our multilevel framework substantially improves the computational time without loosing the quality of classifiers. The algorithms are demonstrated for both regular and weighted support vector machines. Experimental results are presented for balanced and imbalanced classification problems. Quality improvement on several imbalanced data sets has been observed.

We introduce propagation kernels, a general graph-kernel framework for efficiently measuring the similarity of structured data. Propagation kernels are based on monitoring how information spreads through a set of given graphs. They leverage early-stage distributions from propagation schemes such as random walks to capture structural information encoded in node labels, attributes, and edge information. This has two benefits. First, off-the-shelf propagation schemes can be used to naturally construct kernels for many graph types, including labeled, partially labeled, unlabeled, directed, and attributed graphs. Second, by leveraging existing efficient and informative propagation schemes, propagation kernels can be considerably faster than state-of-the-art approaches without sacrificing predictive performance. We will also show that if the graphs at hand have a regular structure, for instance when modeling image or video data, one can exploit this regularity to scale the kernel computation to large databases of graphs with thousands of nodes. We support our contributions by exhaustive experiments on a number of real-world graphs from a variety of application domains.

Mass spectrometry can involve two soft ionization techniques: matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption and ionization (SELDI). For each analyzed fluid sample, MALDI or SELDI hardwares generate a high-dimensional mass spectrum, recording between 10,000 and 20,000 "mass-to-charge (m/z) ratios" corresponding to the ionized peptides present in the fluid sample, as well as "intensities" roughly quantifying the concentrations of these peptides in the sample. Generally m/z ratios take values anywhere between 200 and 20,000 Daltons, and are acquired with a known relative accuracy ρ which depends on the acquisition modalities, and ranges from 0.1% to 0.3%. Analyzing this type of high dimensional data oftern requires specialized software tools, implementing sophisticated machine learning techniques such as SVM (support vector machines) (Li and others (2004), Yu and others (2005)), artificial neural networks (Ball and others (2002)), or random forests (Izmirlian (2004)). These techniques typically generate "black-box" classifiers, which often reach good discrimination levels between cancerous and control groups, but are difficult to interpret biologically in terms of characteristic biomarkers patterns. This often leads to unexpected performance variations on totally new data sets. To develop clinically usable software tools for analysis of mass spectra acuired by MALDI or SELDI hardwares, a key step is to implement automated discovery of explicit "signatures", i.e. short lists of proteomic biomarkers with high discriminating powers between cancer groups (Yasui and others (2003)). Some easily interpretable automatic classifiers, such as linear combinations of biomarker weights (Wang and Chang (2011)), can be found in previous studies, but these approaches do not attempt to quantify the discriminating impact of simultaneous presence for specific pairs of biomarkers.

Neural population activity often exhibits rich variability and temporal structure. This variability is thought to arise from single-neuron stochasticity, neural dynamics on short time-scales, as well as from modulations of neural firing properties on long time-scales, often referred to as "non-stationarity". To better understand the nature of co-variability in neural circuits and their impact on cortical information processing, we need statistical models that are able to capture multiple sources of variability on different time-scales. Here, we introduce a hierarchical statistical model of neural population activity which models both neural population dynamics as well as inter-trial modulations in firing rates. In addition, we extend the model to allow us to capture non-stationarities in the population dynamics itself (i.e., correlations across neurons). We develop variational inference methods for learning model parameters, and demonstrate that the method can recover non-stationarities in both average firing rates and correlation structure. Applied to neural population recordings from anesthetized macaque primary visual cortex, our models provide a better account of the structure of neural firing than stationary dynamics models.

The goal of this paper is to introduce a preliminary version of what we call multi-scale local shape analysis (MLSA), a method for extracting features of a dataset that describe the local structure, both manifold and singular, of points within the dataset. MLSA is a mixture of multi-scale local principal component analysis (MLPCA) and persistent local homology (PLH). In this paper, we will describe both of these techniques and our merger of them, and we will demonstrate the potential of MLSA on two synthetic datasets and one real one. The potential of these methods and their merger is investigated in the context of one of the typical applications for data analytics: the classification problem for multidimensional datasets. Thus the relevance of the developed techniques is assessed as the quality of the resulting classification decision rule, measured by the expected test misclassification error, its sensitivity and specificity (false positive and false negative error rates).