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.

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.

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.

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.

This paper examines from an experimental perspective random forests, the increasingly used statistical method for classification and regression problems introduced by Leo Breiman in 2001. It first aims at confirming, known but sparse, advice for using random forests and at proposing some complementary remarks for both standard problems as well as high dimensional ones for which the number of variables hugely exceeds the sample size. But the main contribution of this paper is twofold: to provide some insights about the behavior of the variable importance index based on random forests and in addition, to propose to investigate two classical issues of variable selection. The first one is to find important variables for interpretation and the second one is more restrictive and try to design a good prediction model. The strategy involves a ranking of explanatory variables using the random forests score of importance and a stepwise ascending variable introduction strategy.

We present exact algorithms for identifying deterministic-actions' effects and preconditions in dynamic partially observable domains. They apply when one does not know the action model(the way actions affect the world) of a domain and must learn it from partial observations over time. Such scenarios are common in real world applications. They are challenging for AI tasks because traditional domain structures that underly tractability (e.g., conditional independence) fail there (e.g., world features become correlated). Our work departs from traditional assumptions about partial observations and action models. In particular, it focuses on problems in which actions are deterministic of simple logical structure and observation models have all features observed with some frequency. We yield tractable algorithms for the modified problem for such domains. Our algorithms take sequences of partial observations over time as input, and output deterministic action models that could have lead to those observations. The algorithms output all or one of those models (depending on our choice), and are exact in that no model is misclassified given the observations. Our algorithms take polynomial time in the number of time steps and state features for some traditional action classes examined in the AI-planning literature, e.g., STRIPS actions. In contrast, traditional approaches for HMMs and Reinforcement Learning are inexact and exponentially intractable for such domains. Our experiments verify the theoretical tractability guarantees, and show that we identify action models exactly. Several applications in planning, autonomous exploration, and adventure-game playing already use these results. They are also promising for probabilistic settings, partially observable reinforcement learning, and diagnosis.

EVOC (for EVOlution of Culture) is a computer model of culture that enables us to investigate how various factors such as barriers to cultural diffusion, the presence and choice of leaders, or changes in the ratio of innovation to imitation affect the diversity and effectiveness of ideas. It consists of neural network based agents that invent ideas for actions, and imitate neighbors' actions. The model is based on a theory of culture according to which what evolves through culture is not memes or artifacts, but the internal models of the world that give rise to them, and they evolve not through a Darwinian process of competitive exclusion but a Lamarckian process involving exchange of innovation protocols. EVOC shows an increase in mean fitness of actions over time, and an increase and then decrease in the diversity of actions. Diversity of actions is positively correlated with population size and density, and with barriers between populations. Slowly eroding borders increase fitness without sacrificing diversity by fostering specialization followed by sharing of fit actions. Introducing a leader that broadcasts its actions throughout the population increases the fitness of actions but reduces diversity of actions. Increasing the number of leaders reduces this effect. Efforts are underway to simulate the conditions under which an agent immigrating from one culture to another contributes new ideas while still'fitting in'.

Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called graph-guided fused lasso (GFlasso) to address this issue in a principled way. Our approach explicitly represents the dependency structure among the quantitative traits as a network, and leverages this trait network to encode structured regularizations in a multivariate regression model over the genotypes and traits, so that the genetic markers that jointly influence subgroups of highly correlated traits can be detected with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently and combined the results afterwards, our approach analyzes all of the traits jointly in a single statistical method, and borrow information across correlated phenotypes to discover the genetic markers that perturbe a subset of correlated triats jointly rather than a single trait. Using simulated datasets based on the HapMap consortium data and an asthma dataset, we compare the performance of our method with the single-marker analysis, and other sparse regression methods such as the ridge regression and the lasso that do not use any structural information in the traits. Our results show that there is a significant advantage in detecting the true causal SNPs when we incorporate the correlation pattern in traits using our proposed methods.

This paper investigates the use of different Artificial Intelligence methods to predict the values of several continuous variables from a Steam Generator. The objective was to determine how the different artificial intelligence methods performed in making predictions on the given dataset. The artificial intelligence methods evaluated were Neural Networks, Support Vector Machines, and Adaptive Neuro-Fuzzy Inference Systems. The types of neural networks investigated were Multi-Layer Perceptions, and Radial Basis Function. Bayesian and committee techniques were applied to these neural networks. Each of the AI methods considered was simulated in Matlab. The results of the simulations showed that all the AI methods were capable of predicting the Steam Generator data reasonably accurately. However, the Adaptive Neuro-Fuzzy Inference system out performed the other methods in terms of accuracy and ease of implementation, while still achieving a fast execution time as well as a reasonable training time.

This paper presents the computational logic foundations of a model of agency called the KGP (Knowledge, Goals and Plan model. This model allows the specification of heterogeneous agents that can interact with each other, and can exhibit both proactive and reactive behaviour allowing them to function in dynamic environments by adjusting their goals and plans when changes happen in such environments. KGP provides a highly modular agent architecture that integrates a collection of reasoning and physical capabilities, synthesised within transitions that update the agent's state in response to reasoning, sensing and acting. Transitions are orchestrated by cycle theories that specify the order in which transitions are executed while taking into account the dynamic context and agent preferences, as well as selection operators for providing inputs to transitions.