Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Here we use phylogenetic Gaussian process regression to model the evolution of simulated function-valued traits. Given function-valued data only from the tips of an evolutionary tree and utilising independent principal component analysis (IPCA) as a method for dimension reduction, we construct distributional estimates of ancestral function-valued traits, and estimate parameters describing their evolutionary dynamics.

We generalize stochastic subgradient descent methods to situations in which we do not receive independent samples from the distribution over which we optimize, but instead receive samples that are coupled over time. We show that as long as the source of randomness is suitably ergodic---it converges quickly enough to a stationary distribution---the method enjoys strong convergence guarantees, both in expectation and with high probability. This result has implications for stochastic optimization in high-dimensional spaces, peer-to-peer distributed optimization schemes, decision problems with dependent data, and stochastic optimization problems over combinatorial spaces.

The Distributed Ontology Language (DOL) is currently being standardized within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies formalized in heterogeneous logics, (2) modular ontologies, (3) links between ontologies, and (4) annotation of ontologies. This paper presents the current state of DOL's standardization. It focuses on use cases where distributed ontologies enable interoperability and reusability. We demonstrate relevant features of the DOL syntax and semantics and explain how these integrate into existing knowledge engineering environments.

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

Planning is concerned with the automated solution of action sequencing problems described in declarative languages giving the action preconditions and effects. One important application area for such technology is the creation of new processes in Business Process Management (BPM), which is essential in an ever more dynamic business environment. A major obstacle for the application of Planning in this area lies in the modeling. Obtaining a suitable model to plan with -- ideally a description in PDDL, the most commonly used planning language -- is often prohibitively complicated and/or costly. Our core observation in this work is that this problem can be ameliorated by leveraging synergies with model-based software development. Our application at SAP, one of the leading vendors of enterprise software, demonstrates that even one-to-one model re-use is possible. The model in question is called Status and Action Management (SAM). It describes the behavior of Business Objects (BO), i.e., large-scale data structures, at a level of abstraction corresponding to the language of business experts. SAM covers more than 400 kinds of BOs, each of which is described in terms of a set of status variables and how their values are required for, and affected by, processing steps (actions) that are atomic from a business perspective. SAM was developed by SAP as part of a major model-based software engineering effort. We show herein that one can use this same model for planning, thus obtaining a BPM planning application that incurs no modeling overhead at all. We compile SAM into a variant of PDDL, and adapt an off-the-shelf planner to solve this kind of problem. Thanks to the resulting technology, business experts may create new processes simply by specifying the desired behavior in terms of status variable value changes: effectively, by describing the process in their own language.

We present a set of high-probability inequalities that control the concentration of weighted averages of multiple (possibly uncountably many) simultaneously evolving and interdependent martingales. Our results extend the PAC-Bayesian analysis in learning theory from the i.i.d. setting to martingales opening the way for its application to importance weighted sampling, reinforcement learning, and other interactive learning domains, as well as many other domains in probability theory and statistics, where martingales are encountered. We also present a comparison inequality that bounds the expectation of a convex function of a martingale difference sequence shifted to the [0,1] interval by the expectation of the same function of independent Bernoulli variables. This inequality is applied to derive a tighter analog of Hoeffding-Azuma's inequality.

Distributions over rankings are used to model data in a multitude of real world settings such as preference analysis and political elections. Modeling such distributions presents several computational challenges, however, due to the factorial size of the set of rankings over an item set. Some of these challenges are quite familiar to the artificial intelligence community, such as how to compactly represent a distribution over a combinatorially large space, and how to efficiently perform probabilistic inference with these representations. With respect to ranking, however, there is the additional challenge of what we refer to as human task complexity -- users are rarely willing to provide a full ranking over a long list of candidates, instead often preferring to provide partial ranking information. Simultaneously addressing all of these challenges -- i.e., designing a compactly representable model which is amenable to efficient inference and can be learned using partial ranking data -- is a difficult task, but is necessary if we would like to scale to problems with nontrivial size. In this paper, we show that the recently proposed riffled independence assumptions cleanly and efficiently address each of the above challenges. In particular, we establish a tight mathematical connection between the concepts of riffled independence and of partial rankings. This correspondence not only allows us to then develop efficient and exact algorithms for performing inference tasks using riffled independence based representations with partial rankings, but somewhat surprisingly, also shows that efficient inference is not possible for riffle independent models (in a certain sense) with observations which do not take the form of partial rankings. Finally, using our inference algorithm, we introduce the first method for learning riffled independence based models from partially ranked data.

The minimisation problem of a sum of unary and pairwise functions of discrete variables is a general NP-hard problem with wide applications such as computing MAP configurations in Markov Random Fields (MRF), minimising Gibbs energy, or solving binary Valued Constraint Satisfaction Problems (VCSPs). We study the computational complexity of classes of discrete optimisation problems given by allowing only certain types of costs in every triangle of variable-value assignments to three distinct variables. We show that for several computational problems, the only non- trivial tractable classes are the well known maximum matching problem and the recently discovered joint-winner property. Our results, apart from giving complete classifications in the studied cases, provide guidance in the search for hybrid tractable classes; that is, classes of problems that are not captured by restrictions on the functions (such as submodularity) or the structure of the problem graph (such as bounded treewidth). Furthermore, we introduce a class of problems with convex cardinality functions on cross-free sets of assignments. We prove that while imposing only one of the two conditions renders the problem NP-hard, the conjunction of the two gives rise to a novel tractable class satisfying the cross-free convexity property, which generalises the joint-winner property to problems of unbounded arity.

In a minimal binary constraint network, every tuple of a constraint relation can be extended to a solution. The tractability or intractability of computing a solution to such a minimal network was a long standing open question. Dechter conjectured this computation problem to be NP-hard. We prove this conjecture. We also prove a conjecture by Dechter and Pearl stating that for k\geq2 it is NP-hard to decide whether a single constraint can be decomposed into an equivalent k-ary constraint network. We show that this holds even in case of bi-valued constraints where k\geq3, which proves another conjecture of Dechter and Pearl. Finally, we establish the tractability frontier for this problem with respect to the domain cardinality and the parameter k.

The rules of Sudoku are often specified using twenty seven \texttt{all\_different} constraints, referred to as the {\em big} \mrules. Using graphical proofs and exploratory logic programming, the following main and new result is obtained: many subsets of six of these big \mrules are redundant (i.e., they are entailed by the remaining twenty one \mrules), and six is maximal (i.e., removing more than six \mrules is not possible while maintaining equivalence). The corresponding result for binary inequality constraints, referred to as the {\em small} \mrules, is stated as a conjecture.