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 #1102850. 	[Title] Optimal Alignments in Linear Space using Automaton-derived Cost Functions (Extended Abstract) Submitted to CPM'96 [Abstract] In a previous paper [SM95], we showed how finite automata could be used to define objective functions for assessing the quality of an alignment of two (or more) sequences. In this paper, we show some results of using such cost functions. We also show how to extend Hischberg's linear space algorithm [Hir75] to this setting, thus generalizing a result of Myers and Miller [MM88b]. Please summarise all the given information.

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 #1130634. 	[Title] Protein Secondary Structure Modelling with Probabilistic Networks (Extended Abstract) [Abstract] In this paper we study the performance of probabilistic networks in the context of protein sequence analysis in molecular biology. Specifically, we report the results of our initial experiments applying this framework to the problem of protein secondary structure prediction. One of the main advantages of the probabilistic approach we describe here is our ability to perform detailed experiments where we can experiment with different models. We can easily perform local substitutions (mutations) and measure (probabilistically) their effect on the global structure. Window-based methods do not support such experimentation as readily. Our method is efficient both during training and during prediction, which is important in order to be able to perform many experiments with different networks. We believe that probabilistic methods are comparable to other methods in prediction quality. In addition, the predictions generated by our methods have precise quantitative semantics which is not shared by other classification methods. Specifically, all the causal and statistical independence assumptions are made explicit in our networks thereby allowing biologists to study and experiment with different causal models in a convenient manner. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #36620. 	[Title] Towards a Better Understanding of Memory-Based Reasoning Systems [Abstract] We quantify both experimentally and analytically the performance of memory-based reasoning (MBR) algorithms. To start gaining insight into the capabilities of MBR algorithms, we compare an MBR algorithm using a value difference metric to a popular Bayesian classifier. These two approaches are similar in that they both make certain independence assumptions about the data. However, whereas MBR uses specific cases to perform classification, Bayesian methods summarize the data probabilistically. We demonstrate that a particular MBR system called Pebls works comparatively well on a wide range of domains using both real and artificial data. With respect to the artificial data, we consider distributions where the concept classes are separated by functional discriminants, as well as time-series data generated by Markov models of varying complexity. Finally, we show formally that Pebls can learn (in the limit) natural concept classes that the Bayesian classifier cannot learn, and that it will attain perfect accuracy whenever 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 #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 #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 #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 #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 #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.

Paper #43698 has the title `Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology  
` and the 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. 
`.
Question: Which category should Paper #43698 be classified as ?
You can select one from ['Neural_Networks', 'Case_Based', 'Theory', 'Reinforcement_Learning', 'Probabilistic_Methods', 'Rule_Learning', 'Genetic_Algorithms'].


Paper #43698 has the title `Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology  
` and the 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. 
`.
Question: Which category should Paper #43698 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: Neural_Networks