Feature Markov Decision Processes (PhiMDPs) are well-suited for learning agents in general environments. Nevertheless, unstructured (Phi)MDPs are limited to relatively simple environments. Structured MDPs like Dynamic Bayesian Networks (DBNs) are used for large-scale real-world problems. In this article I extend PhiMDP to PhiDBN. The primary contribution is to derive a cost criterion that allows to automatically extract the most relevant features from the environment, leading to the "best" DBN representation. I discuss all building blocks required for a complete general learning algorithm.

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 posteri-ori (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.

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.

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 nontrivial 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.

Given i.i.d. observations of a random vector $X \in \mathbb{R}^p$, we study the problem of estimating both its covariance matrix $\Sigma^*$, and its inverse covariance or concentration matrix {$\Theta^* = (\Sigma^*)^{-1}$.} We estimate $\Theta^*$ by minimizing an $\ell_1$-penalized log-determinant Bregman divergence; in the multivariate Gaussian case, this approach corresponds to $\ell_1$-penalized maximum likelihood, and the structure of $\Theta^*$ is specified by the graph of an associated Gaussian Markov random field. We analyze the performance of this estimator under high-dimensional scaling, in which the number of nodes in the graph $p$, the number of edges $s$ and the maximum node degree $d$, are allowed to grow as a function of the sample size $n$. In addition to the parameters $(p,s,d)$, our analysis identifies other key quantities covariance matrix $\Sigma^*$; and (b) the $\ell_\infty$ operator norm of the sub-matrix $\Gamma^*_{S S}$, where $S$ indexes the graph edges, and $\Gamma^* = (\Theta^*)^{-1} \otimes (\Theta^*)^{-1}$; and (c) a mutual incoherence or irrepresentability measure on the matrix $\Gamma^*$ and (d) the rate of decay $1/f(n,\delta)$ on the probabilities $ \{|\hat{\Sigma}^n_{ij}- \Sigma^*_{ij}| > \delta \}$, where $\hat{\Sigma}^n$ is the sample covariance based on $n$ samples. Our first result establishes consistency of our estimate $\hat{\Theta}$ in the elementwise maximum-norm. This in turn allows us to derive convergence rates in Frobenius and spectral norms, with improvements upon existing results for graphs with maximum node degrees $d = o(\sqrt{s})$. In our second result, we show that with probability converging to one, the estimate $\hat{\Theta}$ correctly specifies the zero pattern of the concentration matrix $\Theta^*$.

Regression is a very important method in engineering and science for the estimation of the dependencies between two or more variables on the basis of some given sample points. The best known regression method is certainly the parametric regression technique after Legendre and Gauss, which minimizes the squared error between a model - often a polynom - and the samples. The least squares method is fast and well suitable for strongly linearly correlated data, but seldom appropriate for high-dimensional problems with difficult, unknown, and nonlinear dependencies. For these problems, nonparametric regression techniques - like kernel or Nadaraya-Watson regression methods - are more suitable (Nadaraya [1964], Watson [1964]).

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.

We study Bayesian discriminative inference given a model family $p(c,\x, \theta)$ that is assumed to contain all our prior information but still known to be incorrect. This falls in between "standard" Bayesian generative modeling and Bayesian regression, where the margin $p(\x,\theta)$ is known to be uninformative about $p(c|\x,\theta)$. We give an axiomatic proof that discriminative posterior is consistent for conditional inference; using the discriminative posterior is standard practice in classical Bayesian regression, but we show that it is theoretically justified for model families of joint densities as well. A practical benefit compared to Bayesian regression is that the standard methods of handling missing values in generative modeling can be extended into discriminative inference, which is useful if the amount of data is small. Compared to standard generative modeling, discriminative posterior results in better conditional inference if the model family is incorrect. If the model family contains also the true model, the discriminative posterior gives the same result as standard Bayesian generative modeling. Practical computation is done with Markov chain Monte Carlo.

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.