Above are papers related to the following paper: [Paper_ID] Paper #31932. 	[Title] A Decision Tree System for Finding Genes in DNA [Abstract] MORGAN is an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier. The decision tree system is combined with new methods for identifying start codons, donor sites, and acceptor sites, and these are brought together in a frame-sensitive dynamic programming algorithm that finds the optimal segmentation of a DNA sequence into coding and noncoding regions (exons and introns). The optimal segmentation is dependent on a separate scoring function that takes a subsequence and assigns to it a score reflecting the probability that the sequence is an exon. The scoring functions in MORGAN are sets of decision trees that are combined to give a probability estimate. Experimental results on a database of 570 vertebrate DNA sequences show that MORGAN has excellent performance by many different measures. On a separate test set, it achieves an overall accuracy of 95%, with a correlation coefficient of 0.78 and a sensitivity and specificity for coding bases of 83% and 79%. In addition, MORGAN identifies 58% of coding exons exactly; i.e., both the beginning and end of the coding regions are predicted correctly. This paper describes the MORGAN system, including its decision tree routines and the algorithms for site recognition, and its performance on a benchmark database of vertebrate DNA. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #307336. 	[Title] A Support Vector Machine Approach to Decision Trees [Abstract] Key ideas from statistical learning theory and support vector machines are generalized to decision trees. A support vector machine is used for each decision in the tree. The "optimal" decision tree is characterized, and both a primal and dual space formulation for constructing the tree are proposed. The result is a method for generating logically simple decision trees with multivariate linear or nonlinear decisions. The preliminary results indicate that the method produces simple trees that generalize well with respect to other decision tree algorithms and single support vector machines. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1113739. 	[Title] Decision Tree Function Approximation in Reinforcement Learning [Abstract] We present a decision tree based approach to function approximation in reinforcement learning. We compare our approach with table lookup and a neural network function approximator on three problems: the well known mountain car and pole balance problems as well as a simulated automobile race car. We find that the decision tree can provide better learning performance than the neural network function approximation and can solve large problems that are infeasible using table lookup. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #350362. 	[Title] Improving Regressors using Boosting Techniques [Abstract] In the regression context, boosting and bagging are techniques to build a committee of regressors that may be superior to a single regressor. We use regression trees as fundamental building blocks in bagging committee machines and boosting committee machines. Performance is analyzed on three non-linear functions and the Boston housing database. In all cases, boosting is at least equivalent, and in most cases better than bagging in terms of prediction error. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #563613. 	[Title] Gene Structure Prediction by Linguistic Methods [Abstract] The higher-order structure of genes and other features of biological sequences can be described by means of formal grammars. These grammars can then be used by general-purpose parsers to detect and assemble such structures by means of syntactic pattern recognition. We describe a grammar and parser for eukaryotic protein-encoding genes, which by some measures is as effective as current connectionist and combinatorial algorithms in predicting gene structures for sequence database entries. Parameters on the grammar rules are optimized for several different species, and mixing experiments performed to determine the degree of species specificity and the relative importance of compositional, signal-based, and syntactic components in gene prediction. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #854434. 	[Title] Predicting Lifetimes in Dynamically Allocated Memory [Abstract] Predictions of lifetimes of dynamically allocated objects can be used to improve time and space efficiency of dynamic memory management in computer programs. Barrett and Zorn [1993] used a simple lifetime predictor and demonstrated this improvement on a variety of computer programs. In this paper, we use decision trees to do lifetime prediction on the same programs and show significantly better prediction. Our method also has the advantage that during training we can use a large number of features and let the decision tree automatically choose the relevant subset. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1110947. 	[Title] Lazy Induction Triggered by CBR [Abstract] In recent years, case-based reasoning has been demonstrated to be highly useful for problem solving in complex domains. Also, mixed paradigm approaches emerged for combining CBR and induction techniques aiming at verifying the knowledge and/or building an efficient case memory. However, in complex domains induction over the whole problem space is often not possible or too time consuming. In this paper, an approach is presented which (owing to a close interaction with the CBR part) attempts to induce rules only for a particular context, i.e. for a problem just being solved by a CBR-oriented system. These rules may then be used for indexing purposes or similarity assessment in order to support the CBR process in the future. 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 #3243. 	[Title] A System for Induction of Oblique Decision Trees [Abstract] This article describes a new system for induction of oblique decision trees. This system, OC1, combines deterministic hill-climbing with two forms of randomization to find a good oblique split (in the form of a hyperplane) at each node of a decision tree. Oblique decision tree methods are tuned especially for domains in which the attributes are numeric, although they can be adapted to symbolic or mixed symbolic/numeric attributes. We present extensive empirical studies, using both real and artificial data, that analyze OC1's ability to construct oblique trees that are smaller and more accurate than their axis-parallel counterparts. We also examine the benefits of randomization for the construction of oblique decision trees. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #30895. 	[Title] Induction of Oblique Decision Trees [Abstract] This paper introduces a randomized technique for partitioning examples using oblique hyperplanes. Standard decision tree techniques, such as ID3 and its descendants, partition a set of points with axis-parallel hyper-planes. Our method, by contrast, attempts to find hyperplanes at any orientation. The purpose of this more general technique is to find smaller but equally accurate decision trees than those created by other methods. We have tested our algorithm on both real and simulated data, and found that in some cases it produces surprisingly small trees without losing predictive accuracy. Small trees allow us, in turn, to obtain simple qualitative descriptions of each problem domain. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #368431. 	[Title] Decision Tree Induction: How Effective is the Greedy Heuristic? [Abstract] Most existing decision tree systems use a greedy approach to induce trees | locally optimal splits are induced at every node of the tree. Although the greedy approach is suboptimal, it is believed to produce reasonably good trees. In the current work, we attempt to verify this belief. We quantify the goodness of greedy tree induction empirically, using the popular decision tree algorithms, C4.5 and CART. We induce decision trees on thousands of synthetic data sets and compare them to the corresponding optimal trees, which in turn are found using a novel map coloring idea. We measure the effect on greedy induction of variables such as the underlying concept complexity, training set size, noise and dimensionality. Our experiments show, among other things, that the expected classification cost of a greedily induced tree is consistently very close to that of the optimal tree. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #194609. 	[Title] Prediction of human mRNA donor and acceptor sites from the DNA sequence [Abstract] Artificial neural networks have been applied to the prediction of splice site location in human pre-mRNA. A joint prediction scheme where prediction of transition regions between introns and exons regulates a cutoff level for splice site assignment was able to predict splice site locations with confidence levels far better than previously reported in the literature. The problem of predicting donor and acceptor sites in human genes is hampered by the presence of numerous amounts of false positives | in the paper the distribution of these false splice sites is examined and linked to a possible scenario for the splicing mechanism in vivo. When the presented method detects 95% of the true donor and acceptor sites it makes less than 0.1% false donor site assignments and less than 0.4% false acceptor site assignments. For the large data set used in this study this means that on the average there are one and a half false donor sites per true donor site and six false acceptor sites per true acceptor site. With the joint assignment method more than a fifth of the true donor sites and around one fourth of the true acceptor sites could be detected without accompaniment of any false positive predictions. Highly confident splice sites could not be isolated with a widely used weight matrix method or by separate splice site networks. A complementary relation between the confidence levels of the coding/non-coding and the separate splice site networks was observed, with many weak splice sites having sharp transitions in the coding/non-coding signal and many stronger splice sites having more ill-defined transitions between coding and non-coding. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #30901. 	[Title] Lookahead and Pathology in Decision Tree Induction [Abstract] The standard approach to decision tree induction is a top-down, greedy algorithm that makes locally optimal, irrevocable decisions at each node of a tree. In this paper, we empirically study an alternative approach, in which the algorithms use one-level lookahead to decide what test to use at a node. We systematically compare, using a very large number of real and artificial data sets, the quality of decision trees induced by the greedy approach to that of trees induced using lookahead. The main observations from our experiments are: (i) the greedy approach consistently produced trees that were just as accurate as trees produced with the much more expensive lookahead step; and (ii) we observed many instances of pathology, i.e., lookahead produced trees that were both larger and less accurate than trees produced without it. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1104055. 	[Title] LEARNING BY USING DYNAMIC FEATURE COMBINATION AND SELECTION [Abstract]  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 #96335. 	[Title] Geometry in Learning [Abstract] One of the fundamental problems in learning is identifying members of two different classes. For example, to diagnose cancer, one must learn to discriminate between benign and malignant tumors. Through examination of tumors with previously determined diagnosis, one learns some function for distinguishing the benign and malignant tumors. Then the acquired knowledge is used to diagnose new tumors. The perceptron is a simple biologically inspired model for this two-class learning problem. The perceptron is trained or constructed using examples from the two classes. Then the perceptron is used to classify new examples. We describe geometrically what a perceptron is capable of learning. Using duality, we develop a framework for investigating different methods of training a perceptron. Depending on how we define the "best" perceptron, different minimization problems are developed for training the perceptron. The effectiveness of these methods is evaluated empirically on four practical applications: breast cancer diagnosis, detection of heart disease, political voting habits, and sonar recognition. This paper does not assume prior knowledge of machine learning or pattern recognition. Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #1129572. 	[Title] Non-Deterministic, Constraint-Based Parsing of Human Genes [Abstract]  Please summarise all the given information.

Above are papers related to the following paper: [Paper_ID] Paper #215912. 	[Title] A Method for Identifying Splice Sites and Translational Start Sites in [Abstract] This paper describes a new method for determining the consensus sequences that signal the start of translation and the boundaries between exons and introns (donor and acceptor sites) in eukaryotic mRNA. The method takes into account the dependencies between adjacent bases, in contrast to the usual technique of considering each position independently. When coupled with a dynamic program to compute the most likely sequence, new consensus sequences emerge. The consensus sequence information is summarized in conditional probability matrices which, when used to locate signals in uncharacter-ized genomic DNA, have greater sensitivity and specificity than conventional matrices. Species-specific versions of these matrices are especially effective at distinguishing true and false sites. 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 #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 #1103610. 	[Title] A hierarchical ensemble of decision trees applied to classifying data from a psychological experiment [Abstract] Classifying by hand complex data coming from psychology experiments can be a long and difficult task, because of the quantity of data to classify and the amount of training it may require. One way to alleviate this problem is to use machine learning techniques. We built a classifier based on decision trees that reproduces the classifying process used by two humans on a sample of data and that learns how to classify unseen data. The automatic classifier proved to be more accurate, more constant and much faster than classification by hand. Please summarise all the given information.

Paper #31932 has the title `A Decision Tree System for Finding Genes in DNA  
` and the abstract `MORGAN is an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier. The decision tree system is combined with new methods for identifying start codons, donor sites, and acceptor sites, and these are brought together in a frame-sensitive dynamic programming algorithm that finds the optimal segmentation of a DNA sequence into coding and noncoding regions (exons and introns). The optimal segmentation is dependent on a separate scoring function that takes a subsequence and assigns to it a score reflecting the probability that the sequence is an exon. The scoring functions in MORGAN are sets of decision trees that are combined to give a probability estimate. Experimental results on a database of 570 vertebrate DNA sequences show that MORGAN has excellent performance by many different measures. On a separate test set, it achieves an overall accuracy of 95%, with a correlation coefficient of 0.78 and a sensitivity and specificity for coding bases of 83% and 79%. In addition, MORGAN identifies 58% of coding exons exactly; i.e., both the beginning and end of the coding regions are predicted correctly. This paper describes the MORGAN system, including its decision tree routines and the algorithms for site recognition, and its performance on a benchmark database of vertebrate DNA. 
`.
Question: Which category should Paper #31932 be classified as ?
You can select one from ['Neural_Networks', 'Case_Based', 'Theory', 'Reinforcement_Learning', 'Probabilistic_Methods', 'Rule_Learning', 'Genetic_Algorithms'].


Paper #31932 has the title `A Decision Tree System for Finding Genes in DNA  
` and the abstract `MORGAN is an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier. The decision tree system is combined with new methods for identifying start codons, donor sites, and acceptor sites, and these are brought together in a frame-sensitive dynamic programming algorithm that finds the optimal segmentation of a DNA sequence into coding and noncoding regions (exons and introns). The optimal segmentation is dependent on a separate scoring function that takes a subsequence and assigns to it a score reflecting the probability that the sequence is an exon. The scoring functions in MORGAN are sets of decision trees that are combined to give a probability estimate. Experimental results on a database of 570 vertebrate DNA sequences show that MORGAN has excellent performance by many different measures. On a separate test set, it achieves an overall accuracy of 95%, with a correlation coefficient of 0.78 and a sensitivity and specificity for coding bases of 83% and 79%. In addition, MORGAN identifies 58% of coding exons exactly; i.e., both the beginning and end of the coding regions are predicted correctly. This paper describes the MORGAN system, including its decision tree routines and the algorithms for site recognition, and its performance on a benchmark database of vertebrate DNA. 
`.
Question: Which category should Paper #31932 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