Above are papers related to the following paper: [Paper_ID] Paper #1135746. 	[Title] Learning Markov chains with variable memory length from noisy output [Abstract] The problem of modeling complicated data sequences, such as DNA or speech, often arises in practice. Most of the algorithms select a hypothesis from within a model class assuming that the observed sequence is the direct output of the underlying generation process. In this paper we consider the case when the output passes through a memoryless noisy channel before observation. In particular, we show that in the class of Markov chains with variable memory length, learning is affected by factors, which, despite being super-polynomial, are still small in some practical cases. Markov models with variable memory length, or probabilistic finite suffix automata, were introduced in learning theory by Ron, Singer and Tishby who also described a polynomial time learning algorithm [11, 12]. We present a modification of the algorithm which uses a noise-corrupted sample and has knowledge of the noise structure. The same algorithm is still viable if the noise is not known exactly but a good estimation is available. Finally, some experimental results are presented for removing noise from corrupted English text, and to measure how the performance of the learning algorithm is affected by the size of the noisy sample and the noise rate. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1129608. 	[Title] A New Look at Tree Models for Multiple Sequence Alignment [Abstract] Evolutionary trees are frequently used as the underlying model in the design of algorithms, optimization criteria and software packages for multiple sequence alignment (MSA). In this paper, we reexamine the suitability of trees as a universal model for MSA in light of the broad range of biological questions that MSA's are used to address. A tree model consists of a tree topology and a model of accepted mutations along the branches. After surveying the major applications of MSA, examples from the molecular biology literature are used to illustrate situations in which this tree model fails. This occurs when the relationship between residues in a column cannot be described by a tree; for example, in some structural and functional applications of MSA. It also occurs in situations, such as lateral gene transfer, where an entire gene cannot be modeled by a unique tree. In cases of nonparsimonous data or convergent evolution, it may be difficult to find a consistent mutational model. We hope that this survey will promote dialogue between biologists and computer scientists, leading to more biologically realistic research on MSA. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1152904. 	[Title] GIBBS-MARKOV MODELS [Abstract] In this paper we present a framework for building probabilistic automata parameterized by context-dependent probabilities. Gibbs distributions are used to model state transitions and output generation, and parameter estimation is carried out using an EM algorithm where the M-step uses a generalized iterative scaling procedure. We discuss relations with certain classes of stochastic feedforward neural networks, a geometric interpretation for parameter estimation, and a simple example of a statistical language model constructed using this methodology. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1152272. 	[Title] GIBBS-MARKOV MODELS [Abstract] In this paper we present a framework for building probabilistic automata parameterized by context-dependent probabilities. Gibbs distributions are used to model state transitions and output generation, and parameter estimation is carried out using an EM algorithm where the M-step uses a generalized iterative scaling procedure. We discuss relations with certain classes of stochastic feedforward neural networks, a geometric interpretation for parameter estimation, and a simple example of a statistical language model constructed using this methodology. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1152162. 	[Title] GIBBS-MARKOV MODELS [Abstract] In this paper we present a framework for building probabilistic automata parameterized by context-dependent probabilities. Gibbs distributions are used to model state transitions and output generation, and parameter estimation is carried out using an EM algorithm where the M-step uses a generalized iterative scaling procedure. We discuss relations with certain classes of stochastic feedforward neural networks, a geometric interpretation for parameter estimation, and a simple example of a statistical language model constructed using this methodology. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #10531. 	[Title] Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families [Abstract] A Bayesian method for estimating the amino acid distributions in the states of a hidden Markov model (HMM) for a protein family or the columns of a multiple alignment of that family is introduced. This method uses Dirichlet mixture densities as priors over amino acid distributions. These mixture densities are determined from examination of previously constructed HMMs or multiple alignments. It is shown that this Bayesian method can improve the quality of HMMs produced from small training sets. Specific experiments on the EF-hand motif are reported, for which these priors are shown to produce HMMs with higher likelihood on unseen data, and fewer false positives and false negatives in a database search task. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #164. 	[Title] Learning polynomials with queries: The highly noisy case  task for the case when F [Abstract] Given a function f mapping n-variate inputs from a finite field F into F , we consider the task of reconstructing a list of all n-variate degree d polynomials which agree with f on a tiny but non-negligible fraction, ffi, of the input space. We give a randomized algorithm for solving this task which accesses f as a black box and runs in time polynomial in 1 d=jF j). For the special case when d = 1, we solve this problem for all * def jF j &gt; 0. In this case the running time of our algorithm is bounded by a polynomial in 1 * ; n and exponential in d. Our algorithm generalizes a previously known algorithm, due to Goldreich and Levin, that solves this Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #12195. 	[Title] Efficient Learning of Typical Finite Automata from Random Walks (Extended Abstract) [Abstract] This paper describes new and efficient algorithms for learning deterministic finite automata. Our approach is primarily distinguished by two features: (1) the adoption of an average-case setting to model the "typical" labeling of a finite automaton, while retaining a worst-case model for the underlying graph of the automaton, along with (2) a learning model in which the learner is not provided with the means to experiment with the machine, but rather must learn solely by observing the automaton's output behavior on a random input sequence. The main contribution of this paper is in presenting the first efficient algorithms for learning non-trivial classes of automata in an entirely passive learning model. We adopt an on-line learning model in which the learner is asked to predict the output of the next state, given the next symbol of the random input sequence; the goal of the learner is to make as few prediction mistakes as possible. Assuming the learner has a means of resetting the target machine to a fixed start state, we first present an efficient algorithm that makes an expected polynomial number of mistakes in this model. Next, we show how this first algorithm can be used as a subroutine by a second algorithm that also makes a polynomial number of mistakes even in the absence of a reset. Along the way, we prove a number of combinatorial results for randomly labeled automata. We also show that the labeling of the states and the bits of the input sequence need not be truly random, but merely semi-random. Finally, we discuss an extension of our results to a model in which automata are used to represent distributions over binary strings. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #5038. 	[Title] Using and combining predictors that specialize [Abstract] We study online learning algorithms that predict by combining the predictions of several subordinate prediction algorithms, sometimes called experts. These simple algorithms belong to the multiplicative weights family of algorithms. The performance of these algorithms degrades only logarithmically with the number of experts, making them particularly useful in applications where the number of experts is very large. However, in applications such as text categorization, it is often natural for some of the experts to abstain from making predictions on some of the instances. We show how to transform algorithms that assume that all experts are always awake to algorithms that do not require this assumption. We also show how to derive corresponding loss bounds. Our method is very general, and can be applied to a large family of online learning algorithms. We also give applications to various prediction models including decision graphs and switching experts. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #43698. 	[Title] Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology [Abstract] UCSC Technical Report UCSC-CRL-96-09 Abstract This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a protein family or domain are known. We present a method for condensing the information in a protein database into a mixture of Dirichlet densities. These mixtures are designed to be combined with observed amino acid frequencies, to form estimates of expected amino acid probabilities at each position in a profile, hidden Markov model, or other statistical model. These estimates give a statistical model greater generalization capacity, such that remotely related family members can be more reliably recognized by the model. Dirichlet mixtures have been shown to outperform substitution matrices and other methods for computing these expected amino acid distributions in database search, resulting in fewer false positives and false negatives for the families tested. This paper corrects a previously published formula for estimating these expected probabilities, and contains complete derivations of the Dirichlet mixture formulas, methods for optimizing the mixtures to match particular databases, and suggestions for efficient implementation. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #171954. 	[Title] Efficient Algorithms for Inverting Evolution [Abstract] Evolution is a stochastic process which operates on the DNA of species. The evolutionary process leaves tell-tale signs in the DNA which can be used to construct phylogenies, or evolutionary trees, for a set of species. Maximum Likelihood Estimations (MLE) methods seek the evolutionary tree which is most likely to have produced the DNA under consideration. While these methods are widely accepted and intellectually satisfying, they have been computationally intractable. In this paper, we address the intractability of MLE methods as follows. We introduce a metric on stochastic process models of evolution. We show that this metric is meaningful by proving that in order for any algorithm to distinguish between two stochatic models that are close according to this metric, it needs to be given a lot of observations. We complement this result with a simple and efficient algorithm for inverting the stochastic process of evolution, that is, for building the tree from observations on the DNA of the species. Our result can be viewed as a result on the PAC-learnability of the class of distributions produced by tree-like processes. Though there have been many heuristics suggested for this problem, our algorithm is the first one with a guaranteed convergence rate, and further, this rate is within a polynomial of the lower-bound rate we establish. Ours is also the the first polynomial-time algorithm which is guaranteed to converge at all to the correct tree. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #12210. 	[Title] Efficient Distribution-free Learning of Probabilistic Concepts [Abstract] In this paper we investigate a new formal model of machine learning in which the concept (boolean function) to be learned may exhibit uncertain or probabilistic behavior|thus, the same input may sometimes be classified as a positive example and sometimes as a negative example. Such probabilistic concepts (or p-concepts) may arise in situations such as weather prediction, where the measured variables and their accuracy are insufficient to determine the outcome with certainty. We adopt from the Valiant model of learning [27] the demands that learning algorithms be efficient and general in the sense that they perform well for a wide class of p-concepts and for any distribution over the domain. In addition to giving many efficient algorithms for learning natural classes of p-concepts, we study and develop in detail an underlying theory of learning p-concepts. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #31927. 	[Title] A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA [Abstract] We present a statistical model of genes in DNA. A Generalized Hidden Markov Model (GHMM) provides the framework for describing the grammar of a legal parse of a DNA sequence (Stormo & Haussler 1994). Probabilities are assigned to transitions between states in the GHMM and to the generation of each nucleotide base given a particular state. Machine learning techniques are applied to optimize these probabilities using a standardized training set. Given a new candidate sequence, the best parse is deduced from the model using a dynamic programming algorithm to identify the path through the model with maximum probability. The GHMM is flexible and modular, so new sensors and additional states can be inserted easily. In addition, it provides simple solutions for integrating cardinality constraints, reading frame constraints, "indels", and homology searching. The description and results of an implementation of such a gene-finding model, called Genie, is presented. The exon sensor is a codon frequency model conditioned on windowed nucleotide frequency and the preceding codon. Two neural networks are used, as in (Brunak, Engelbrecht, & Knudsen 1991), for splice site prediction. We show that this simple model performs quite well. For a cross-validated standard test set of 304 genes [ftp://www-hgc.lbl.gov/pub/genesets] in human DNA, our gene-finding system identified up to 85% of protein-coding bases correctly with a specificity of 80%. 58% of exons were exactly identified with a specificity of 51%. Genie is shown to perform favorably compared with several other gene-finding systems. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #194617. 	[Title] Finding Genes in DNA with a Hidden Markov Model [Abstract] This study describes a new Hidden Markov Model (HMM) system for segmenting uncharacterized genomic DNA sequences into exons, introns, and intergenic regions. Separate HMM modules were designed and trained for specific regions of DNA: exons, introns, intergenic regions, and splice sites. The models were then tied together to form a biologically feasible topology. The integrated HMM was trained further on a set of eukaryotic DNA sequences, and tested by using it to segment a separate set of sequences. The resulting HMM system, which is called VEIL (Viterbi Exon-Intron Locator), obtains an overall accuracy on test data of 92% of total bases correctly labelled, with a correlation coefficient of 0.73. Using the more stringent test of exact exon prediction, VEIL correctly located both ends of 53% of the coding exons, and 49% of the exons it predicts are exactly correct. These results compare favorably to the best previous results for gene structure prediction, and demonstrate the benefits of using HMMs for this problem. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #12350. 	[Title] Cryptographic Limitations on Learning Boolean Formulae and Finite Automata [Abstract] In this paper we prove the intractability of learning several classes of Boolean functions in the distribution-free model (also called the Probably Approximately Correct or PAC model) of learning from examples. These results are representation independent, in that they hold regardless of the syntactic form in which the learner chooses to represent its hypotheses. Our methods reduce the problems of cracking a number of well-known public-key cryptosys- tems to the learning problems. We prove that a polynomial-time learning algorithm for Boolean formulae, deterministic finite automata or constant-depth threshold circuits would have dramatic consequences for cryptography and number theory: in particular, such an algorithm could be used to break the RSA cryptosystem, factor Blum integers (composite numbers equivalent to 3 modulo 4), and detect quadratic residues. The results hold even if the learning algorithm is only required to obtain a slight advantage in prediction over random guessing. The techniques used demonstrate an interesting duality between learning and cryptography. We also apply our results to obtain strong intractability results for approximating a gener - alization of graph coloring. fl This research was conducted while the author was at Harvard University and supported by an A.T.& T. Bell Laboratories scholarship. y Supported by grants ONR-N00014-85-K-0445, NSF-DCR-8606366 and NSF-CCR-89-02500, DAAL03-86-K-0171, DARPA AFOSR 89-0506, and by SERC. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #10177. 	[Title] Learning in the Presence of Malicious Errors [Abstract] In this paper we study an extension of the distribution-free model of learning introduced by Valiant [23] (also known as the probably approximately correct or PAC model) that allows the presence of malicious errors in the examples given to a learning algorithm. Such errors are generated by an adversary with unbounded computational power and access to the entire history of the learning algorithm's computation. Thus, we study a worst-case model of errors. Our results include general methods for bounding the rate of error tolerable by any learning algorithm, efficient algorithms tolerating nontrivial rates of malicious errors, and equivalences between problems of learning with errors and standard combinatorial optimization problems. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #38722. 	[Title] Learning Probabilistic Automata with Variable Memory Length [Abstract] We propose and analyze a distribution learning algorithm for variable memory length Markov processes. These processes can be described by a subclass of probabilistic finite automata which we name Probabilistic Finite Suffix Automata. The learning algorithm is motivated by real applications in man-machine interaction such as handwriting and speech recognition. Conventionally used fixed memory Markov and hidden Markov models have either severe practical or theoretical drawbacks. Though general hardness results are known for learning distributions generated by sources with similar structure, we prove that our algorithm can indeed efficiently learn distributions generated by our more restricted sources. In Particular, we show that the KL-divergence between the distribution generated by the target source and the distribution generated by our hypothesis can be made small with high confidence in polynomial time and sample complexity. We demonstrate the applicability of our algorithm by learning the structure of natural English text and using our hy pothesis for the correction of corrupted text. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #686532. 	[Title] Homology Detection via Family Pairwise Search a straightforward generalization of pairwise sequence comparison algorithms to [Abstract] The function of an unknown biological sequence can often be accurately inferred by identifying sequences homologous to the original sequence. Given a query set of known homologs, there exist at least three general classes of techniques for finding additional homologs: pairwise sequence comparisons, motif analysis, and hidden Markov modeling. Pairwise sequence comparisons are typically employed when only a single query sequence is known. Hidden Markov models (HMMs), on the other hand, are usually trained with sets of more than 100 sequences. Motif-based methods fall in between these two extremes. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #81350. 	[Title] Learning to Use Selective Attention and Short-Term Memory in Sequential Tasks [Abstract] This paper presents U-Tree, a reinforcement learning algorithm that uses selective attention and short-term memory to simultaneously address the intertwined problems of large perceptual state spaces and hidden state. By combining the advantages of work in instance-based (or memory-based) learning and work with robust statistical tests for separating noise from task structure, the method learns quickly, creates only task-relevant state distinctions, and handles noise well. U-Tree uses a tree-structured representation, and is related to work on Prediction Suffix Trees [ Ron et al., 1994 ] , Parti-game [ Moore, 1993 ] , G-algorithm [ Chap-man and Kaelbling, 1991 ] , and Variable Resolution Dynamic Programming [ Moore, 1991 ] . It builds on Utile Suffix Memory [ McCallum, 1995c ] , which only used short-term memory, not selective perception. The algorithm is demonstrated solving a highway driving task in which the agent weaves around slower and faster traffic. The agent uses active perception with simulated eye movements. The environment has hidden state, time pressure, stochasticity, over 21,000 world states and over 2,500 percepts. From this environment and sensory system, the agent uses a utile distinction test to build a tree that represents depth-three memory where necessary, and has just 143 internal statesfar fewer than the 2500 3 states that would have resulted from a fixed-sized history-window ap proach. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #67415. 	[Title] On the Learnability of Discrete Distributions (extended abstract) [Abstract]  Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1063773. 	[Title] A Gentle Guide to Multiple Alignment Version Please send comments, critique, flames and praise Instructions [Abstract] Prerequisites. An understanding of the dynamic programming (edit distance) approach to pairwise sequence alignment is useful for parts 1.3, 1.4, and 2. Also, familiarity with the use of Internet resources would be helpful for part 3. For the former, see Chapters 1.1 - 1.3, and for the latter, see Chapter 2 of the Hypertext Book of the GNA-VSNS Biocomputing Course at http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html. General Rationale. You will understand why Multiple Alignment is considered a challenging problem, you will study approaches that try to reduce the number of steps needed to calculate the optimal solution, and you will study fast heuristics. In a case study involving immunoglobulin sequences, you will study multiple alignments obtained from WWW servers, recapitulating results from an original paper. Revision History. Version 1.01 on 17 Sep 1995. Expanded Ex.9. Updated Ex.46. Revised Solution Sheet -re- Ex.3+12. Marked more Exercises by "A" (to be submitted to the Instructor). Various minor clarifications in content Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #686559. 	[Title] Parameterization studies for the SAM and HMMER methods of hidden Markov model generation [Abstract] Multiple sequence alignment of distantly related viral proteins remains a challenge to all currently available alignment methods. The hidden Markov model approach offers a new, flexible method for the generation of multiple sequence alignments. The results of studies attempting to infer appropriate parameter constraints for the generation of de novo HMMs for globin, kinase, aspartic acid protease, and ribonuclease H sequences by both the SAM and HMMER methods are described. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1129442. 	[Title] Minimum-Risk Profiles of Protein Families Based on Statistical Decision Theory [Abstract] Statistical decision theory provides a principled way to estimate amino acid frequencies in conserved positions of a protein family. The goal is to minimize the risk function, or the expected squared-error distance between the estimates and the true population frequencies. The minimum-risk estimates are obtained by adding an optimal number of pseudocounts to the observed data. Two formulas are presented, one for pseudocounts based on marginal amino acid frequencies and one for pseudocounts based on the observed data. Experimental results show that profiles constructed using minimal-risk estimates are more discriminating than those constructed using existing methods. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #286562. 	[Title] Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and their Homologs [Abstract]  Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #31336. 	[Title] The megaprior heuristic for discovering protein sequence patterns [Abstract] Several computer algorithms for discovering patterns in groups of protein sequences are in use that are based on fitting the parameters of a statistical model to a group of related sequences. These include hidden Markov model (HMM) algorithms for multiple sequence alignment, and the MEME and Gibbs sampler algorithms for discovering motifs. These algorithms are sometimes prone to producing models that are incorrect because two or more patterns have been combined. The statistical model produced in this situation is a convex combination (weighted average) of two or more different models. This paper presents a solution to the problem of convex combinations in the form of a heuristic based on using extremely low variance Dirichlet mixture priors as part of the statistical model. This heuristic, which we call the megaprior heuristic, increases the strength (i.e., decreases the variance) of the prior in proportion to the size of the sequence dataset. This causes each column in the final model to strongly resemble the mean of a single component of the prior, regardless of the size of the dataset. We describe the cause of the convex combination problem, analyze it mathematically, motivate and describe the implementation of the megaprior heuristic, and show how it can effectively eliminate the problem of convex combinations in protein sequence pattern discovery. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #51180. 	[Title] On the Learnability and Usage of Acyclic Probabilistic Finite Automata [Abstract] We propose and analyze a distribution learning algorithm for a subclass of Acyclic Probabilistic Finite Automata (APFA). This subclass is characterized by a certain distinguishability property of the automata's states. Though hardness results are known for learning distributions generated by general APFAs, we prove that our algorithm can efficiently learn distributions generated by the subclass of APFAs we consider. In particular, we show that the KL-divergence between the distribution generated by the target source and the distribution generated by our hypothesis can be made arbitrarily small with high confidence in polynomial time. We present two applications of our algorithm. In the first, we show how to model cursively written letters. The resulting models are part of a complete cursive handwriting recognition system. In the second application we demonstrate how APFAs can be used to build multiple-pronunciation models for spoken words. We evaluate the APFA based pronunciation models on labeled speech data. The good performance (in terms of the log-likelihood obtained on test data) achieved by the APFAs and the little time needed for learning suggests that the learning algorithm of APFAs might be a powerful alternative to commonly used probabilistic models. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1124844. 	[Title] Stochastic Decomposition of DNA Sequences Using Hidden Markov Models [Abstract] This work presents an application of a machine learning for characterizing an important property of natural DNA sequences compositional inhomogeneity. Compositional segments often correspond to meaningful biological units. Taking into account such inhomogeneity is a prerequisite of successful recognition of functional features in DNA sequences, especially, protein-coding genes. Here we present a technique for DNA segmentation using hidden Markov models. A DNA sequence is represented by a chain of homogeneous segments, each described by one of a few statistically discriminated hidden states, whose contents form a first-order Markov chain. The technique is used to describe and compare chromosomes I and IV of the completely sequenced Saccharomyces cerevisiae (yeast) genome. Our results indicate the existence of a few well separated states, which gives support to the isochore theory. We also explore the model's likelihood landscape and analyze the dynamics of the optimization process, thus addressing the problem of reliability of the obtained optima and efficiency of the algorithms. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1107567. 	[Title] Learning Algorithms with Applications to Robot Navigation and Protein Folding [Abstract]  Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1110256. 	[Title] Learning Distributions from Random Walks [Abstract] We introduce a new model of distributions generated by random walks on graphs. This model suggests a variety of learning problems, using the definitions and models of distribution learning defined in [6]. Our framework is general enough to model previously studied distribution learning problems, as well as to suggest new applications. We describe special cases of the general problem, and investigate their relative difficulty. We present algorithms to solve the learning problem under various conditions. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #65650. 	[Title] Machine Learning 27(1):51-68, 1997. Predicting nearly as well as the best pruning of a decision tree [Abstract] Many algorithms for inferring a decision tree from data involve a two-phase process: First, a very large decision tree is grown which typically ends up "over-fitting" the data. To reduce over-fitting, in the second phase, the tree is pruned using one of a number of available methods. The final tree is then output and used for classification on test data. In this paper, we suggest an alternative approach to the pruning phase. Using a given unpruned decision tree, we present a new method of making predictions on test data, and we prove that our algorithm's performance will not be "much worse" (in a precise technical sense) than the predictions made by the best reasonably small pruning of the given decision tree. Thus, our procedure is guaranteed to be competitive (in terms of the quality of its predictions) with any pruning algorithm. We prove that our procedure is very efficient and highly robust. Our method can be viewed as a synthesis of two previously studied techniques. First, we apply Cesa-Bianchi et al.'s [4] results on predicting using "expert advice" (where we view each pruning as an "expert") to obtain an algorithm that has provably low prediction loss, but that is com-putationally infeasible. Next, we generalize and apply a method developed by Buntine [3], [2] and Willems, Shtarkov and Tjalkens [20], [21] to derive a very efficient implementation of this procedure. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #31349. 	[Title] Meta-MEME: Motif-based Hidden Markov Models of Protein Families [Abstract]  Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1123576. 	[Title] Density Networks and their Application to Protein Modelling [Abstract] I define a latent variable model in the form of a neural network for which only target outputs are specified; the inputs are unspecified. Although the inputs are missing, it is still possible to train this model by placing a simple probability distribution on the unknown inputs and maximizing the probability of the data given the parameters. The model can then discover for itself a description of the data in terms of an underlying latent variable space of lower dimensionality. I present preliminary results of the application of these models to protein data. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #31353. 	[Title] Hidden Markov Models in Computational Biology: Applications to Protein Modeling UCSC-CRL-93-32 Keywords: Hidden Markov Models, [Abstract] Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated on the globin family, the protein kinase catalytic domain, and the EF-hand calcium binding motif. In each case the parameters of an HMM are estimated from a training set of unaligned sequences. After the HMM is built, it is used to obtain a multiple alignment of all the training sequences. It is also used to search the SWISS-PROT 22 database for other sequences that are members of the given protein family, or contain the given domain. The HMM produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate three-dimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a database fit the globin, kinase and EF-hand HMMs), the HMM is able to distinguish members of these families from non-members with a high degree of accuracy. Both the HMM and PRO-FILESEARCH (a technique used to search for relationships between a protein sequence and multiply aligned sequences) perform better in these tests than PROSITE (a dictionary of sites and patterns in proteins). The HMM appears to have a slight advantage Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1106172. 	[Title] Category: Control, Navigation and Planning. Key words: Reinforcement learning, Exploration, Hidden state. Prefer oral presentation. [Abstract] This paper presents Fringe Exploration, a technique for efficient exploration in partially observable domains. The key idea, (applicable to many exploration techniques), is to keep statistics in the space of possible short-term memories, instead of in the agent's current state space. Experimental results in a partially observable maze and in a difficult driving task with visual routines show dramatic performance improvements. Please summarise all the given information.

Paper #1135746 has the title `Learning Markov chains with variable memory length from noisy output  
` and the abstract `The problem of modeling complicated data sequences, such as DNA or speech, often arises in practice. Most of the algorithms select a hypothesis from within a model class assuming that the observed sequence is the direct output of the underlying generation process. In this paper we consider the case when the output passes through a memoryless noisy channel before observation. In particular, we show that in the class of Markov chains with variable memory length, learning is affected by factors, which, despite being super-polynomial, are still small in some practical cases. Markov models with variable memory length, or probabilistic finite suffix automata, were introduced in learning theory by Ron, Singer and Tishby who also described a polynomial time learning algorithm [11, 12]. We present a modification of the algorithm which uses a noise-corrupted sample and has knowledge of the noise structure. The same algorithm is still viable if the noise is not known exactly but a good estimation is available. Finally, some experimental results are presented for removing noise from corrupted English text, and to measure how the performance of the learning algorithm is affected by the size of the noisy sample and the noise rate. 
`.
Question: Which category should Paper #1135746 be classified as ?
You can select one from ['Neural_Networks', 'Case_Based', 'Theory', 'Reinforcement_Learning', 'Probabilistic_Methods', 'Rule_Learning', 'Genetic_Algorithms'].


Paper #1135746 has the title `Learning Markov chains with variable memory length from noisy output  
` and the abstract `The problem of modeling complicated data sequences, such as DNA or speech, often arises in practice. Most of the algorithms select a hypothesis from within a model class assuming that the observed sequence is the direct output of the underlying generation process. In this paper we consider the case when the output passes through a memoryless noisy channel before observation. In particular, we show that in the class of Markov chains with variable memory length, learning is affected by factors, which, despite being super-polynomial, are still small in some practical cases. Markov models with variable memory length, or probabilistic finite suffix automata, were introduced in learning theory by Ron, Singer and Tishby who also described a polynomial time learning algorithm [11, 12]. We present a modification of the algorithm which uses a noise-corrupted sample and has knowledge of the noise structure. The same algorithm is still viable if the noise is not known exactly but a good estimation is available. Finally, some experimental results are presented for removing noise from corrupted English text, and to measure how the performance of the learning algorithm is affected by the size of the noisy sample and the noise rate. 
`.
Question: Which category should Paper #1135746 be classified as ?
You can select one from ['Neural_Networks', 'Case_Based', 'Theory', 'Reinforcement_Learning', 'Probabilistic_Methods', 'Rule_Learning', 'Genetic_Algorithms'].

This paper should be classified into: Theory