We give polynomial-time algorithms for the exact computation of lowest-energy (ground) states, worst margin violators, log partition functions, and marginal edge probabilities in certain binary undirected graphical models. Our approach provides an interesting alternative to the well-known graph cut paradigm in that it does not impose any submodularity constraints; instead we require planarity to establish a correspondence with perfect matchings (dimer coverings) in an expanded dual graph. We implement a unified framework while delegating complex but well-understood subproblems (planar embedding, maximum-weight perfect matching) to established algorithms for which efficient implementations are freely available. Unlike graph cut methods, we can perform penalized maximum-likelihood as well as maximum-margin parameter estimation in the associated conditional random fields (CRFs), and employ marginal posterior probabilities as well as maximum a posteriori (MAP) states for prediction. Maximum-margin CRF parameter estimation on image denoising and segmentation problems shows our approach to be efficient and effective. A C++ implementation is available from http://nic.schraudolph.org/isinf/

Motivation: Profile hidden Markov Models (pHMMs) are a popular and very useful tool in the detection of the remote homologue protein families. Unfortunately, their performance is not always satisfactory when proteins are in the 'twilight zone'. We present HMMER-STRUCT, a model construction algorithm and tool that tries to improve pHMM performance by using structural information while training pHMMs. As a first step, HMMER-STRUCT constructs a set of pHMMs. Each pHMM is constructed by weighting each residue in an aligned protein according to a specific structural property of the residue. Properties used were primary, secondary and tertiary structures, accessibility and packing. HMMER-STRUCT then prioritizes the results by voting. Results: We used the SCOP database to perform our experiments. Throughout, we apply leave-one-family-out cross-validation over protein superfamilies. First, we used the MAMMOTH-mult structural aligner to align the training set proteins. Then, we performed two sets of experiments. In a first experiment, we compared structure weighted models against standard pHMMs and against each other. In a second experiment, we compared the voting model against individual pHMMs. We compare method performance through ROC curves and through Precision/Recall curves, and assess significance through the paired two tailed t-test. Our results show significant performance improvements of all structurally weighted models over default HMMER, and a significant improvement in sensitivity of the combined models over both the original model and the structurally weighted models.

We obtain an index of the complexity of a random sequence by allowing the role of the measure in classical probability theory to be played by a function we call the generating mechanism. Typically, this generating mechanism will be a finite automata. We generate a set of biased sequences by applying a finite state automata with a specified number, $m$, of states to the set of all binary sequences. Thus we can index the complexity of our random sequence by the number of states of the automata. We detail optimal algorithms to predict sequences generated in this way.

Autoencoder neural network is implemented to estimate the missing data. Genetic algorithm is implemented for network optimization and estimating the missing data. Missing data is treated as Missing At Random mechanism by implementing maximum likelihood algorithm. The network performance is determined by calculating the mean square error of the network prediction. The network is further optimized by implementing Decision Forest. The impact of missing data is then investigated and decision forrests are found to improve the results.

Answer set programming (ASP) is a logic programming paradigm that can be used to solve complex combinatorial search problems. Aggregates are an ASP construct that plays an important role in many applications. Defining a satisfactory semantics of aggregates turned out to be a difficult problem, and in this paper we propose a new approach, based on an analogy between aggregates and propositional connectives. First, we extend the definition of an answer set/stable model to cover arbitrary propositional theories; then we define aggregates on top of them both as primitive constructs and as abbreviations for formulas. Our definition of an aggregate combines expressiveness and simplicity, and it inherits many theorems about programs with nested expressions, such as theorems about strong equivalence and splitting.

This paper proposes a novel solution to spam detection inspired by a model of the adaptive immune system known as the crossregulation model. We report on the testing of a preliminary algorithm on six e-mail corpora. We also compare our results statically and dynamically with those obtained by the Naive Bayes classifier and another binary classification method we developed previously for biomedical text-mining applications. We show that the cross-regulation model is competitive against those and thus promising as a bio-inspired algorithm for spam detection in particular, and binary classification in general.

The paper introduces the notion of off-line justification for Answer Set Programming (ASP). Justifications provide a graph-based explanation of the truth value of an atom w.r.t. a given answer set. The paper extends also this notion to provide justification of atoms during the computation of an answer set (on-line justification), and presents an integration of on-line justifications within the computation model of Smodels. Off-line and on-line justifications provide useful tools to enhance understanding of ASP, and they offer a basic data structure to support methodologies and tools for debugging answer set programs. A preliminary implementation has been developed in ASP-PROLOG. (To appear in Theory and Practice of Logic Programming (TPLP))

This paper develops a declarative language, P-log, that combines logical and probabilistic arguments in its reasoning. Answer Set Prolog is used as the logical foundation, while causal Bayes nets serve as a probabilistic foundation. We give several non-trivial examples and illustrate the use of P-log for knowledge representation and updating of knowledge. We argue that our approach to updates is more appealing than existing approaches. We give sufficiency conditions for the coherency of P-log programs and show that Bayes nets can be easily mapped to coherent P-log programs.

This philosophical paper explores the relation between modern scientific simulations and the future of the universe. We argue that a simulation of an entire universe will result from future scientific activity. This requires us to tackle the challenge of simulating open-ended evolution at all levels in a single simulation. The simulation should encompass not only biological evolution, but also physical evolution (a level below) and cultural evolution (a level above). The simulation would allow us to probe what would happen if we would "replay the tape of the universe" with the same or different laws and initial conditions. We also distinguish between real-world and artificial-world modelling. Assuming that intelligent life could indeed simulate an entire universe, this leads to two tentative hypotheses. Some authors have argued that we may already be in a simulation run by an intelligent entity. Or, if such a simulation could be made real, this would lead to the production of a new universe. This last direction is argued with a careful speculative philosophical approach, emphasizing the imperative to find a solution to the heat death problem in cosmology. The reader is invited to consult Annex 1 for an overview of the logical structure of this paper. -- Keywords: far future, future of science, ALife, simulation, realization, cosmology, heat death, fine-tuning, physical eschatology, cosmological natural selection, cosmological artificial selection, artificial cosmogenesis, selfish biocosm hypothesis, meduso-anthropic principle, developmental singularity hypothesis, role of intelligent life.

Shapley's impossibility result indicates that the two-person bargaining problem has no non-trivial ordinal solution with the traditional game-theoretic bargaining model. Although the result is no longer true for bargaining problems with more than two agents, none of the well known bargaining solutions are ordinal. Searching for meaningful ordinal solutions, especially for the bilateral bargaining problem, has been a challenging issue in bargaining theory for more than three decades. This paper proposes a logic-based ordinal solution to the bilateral bargaining problem. We argue that if a bargaining problem is modeled in terms of the logical relation of players' physical negotiation items, a meaningful bargaining solution can be constructed based on the ordinal structure of bargainers' preferences. We represent bargainers' demands in propositional logic and bargainers' preferences over their demands in total preorder. We show that the solution satisfies most desirable logical properties, such as individual rationality (logical version), consistency, collective rationality as well as a few typical game-theoretic properties, such as weak Pareto optimality and contraction invariance. In addition, if all players' demand sets are logically closed, the solution satisfies a fixed-point condition, which says that the outcome of a negotiation is the result of mutual belief revision. Finally, we define various decision problems in relation to our bargaining model and study their computational complexity.