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 #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 #1135750. 	[Title] TREE CONTRACTIONS AND EVOLUTIONARY TREES [Abstract] An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of species. An agreement subtree of two evolutionary trees is an evolutionary tree which is also a topological subtree of the two given trees. We give an algorithm to determine the largest possible number of leaves in any agreement subtree of two trees T 1 and T 2 with n leaves each. If the maximum degree d of these trees is bounded by a constant, the time complexity is O(n log 2 n) and is within a log n factor of optimal. For general d, this algorithm runs in O(nd 2 log d log 2 n) time or alternately in O(nd p d log 3 n) time. 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 #1138970. 	[Title] The Disk-Covering Method for Tree Reconstruction [Abstract] Evolutionary tree reconstruction is a very important step in many biological research problems, and yet is extremely difficult for a variety of computational, statistical, and scientific reasons. In particular, the reconstruction of very large trees containing significant amounts of divergence is especially challenging. We present in this paper a new tree reconstruction method, which we call the Disk-Covering Method, which can be used to recover accurate estimations of the evolutionary tree for otherwise intractable datasets. DCM obtains a decomposition of the input dataset into small overlapping sets of closely related taxa, reconstructs trees on these subsets (using a "base" phylogenetic method of choice), and then combines the subtrees into one tree on the entire set of taxa. Because the subproblems analyzed by DCM are smaller, com-putationally expensive methods such as maximum likelihood estimation can be used without incurring too much cost. At the same time, because the taxa within each subset are closely related, even very simple methods (such as neighbor-joining) are much more likely to be highly accurate. The result is that DCM-boosted methods are typically faster and more accurate as compared to "naive" use of the same method. In this paper we describe the basic ideas and techniques in DCM, and demonstrate the advantages of DCM experimentally by simulating sequence evolution on a variety of trees. 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 #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 #33325. 	[Title] Applying Winnow to Context-Sensitive Spelling Correction [Abstract] Multiplicative weight-updating algorithms such as Winnow have been studied extensively in the COLT literature, but only recently have people started to use them in applications. In this paper, we apply a Winnow-based algorithm to a task in natural language: context-sensitive spelling correction. This is the task of fixing spelling errors that happen to result in valid words, such as substituting to for too, casual for causal, and so on. Previous approaches to this problem have been statistics-based; we compare Winnow to one of the more successful such approaches, which uses Bayesian classifiers. We find that: (1) When the standard (heavily-pruned) set of features is used to describe problem instances, Winnow performs comparably to the Bayesian method; (2) When the full (unpruned) set of features is used, Winnow is able to exploit the new features and convincingly outperform Bayes; and (3) When a test set is encountered that is dissimilar to the training set, Winnow is better than Bayes at adapting to the unfamiliar test set, using a strategy we will present for combining learning on the training set with unsupervised learning on the (noisy) test set. This work may not be copied or reproduced in whole or in part for any commercial purpose. Permission to copy in whole or in part without payment of fee is granted for nonprofit educational and research purposes provided that all such whole or partial copies include the following: a notice that such copying is by permission of Mitsubishi Electric Information Technology Center America; an acknowledgment of the authors and individual contributions to the work; and all applicable portions of the copyright notice. Copying, reproduction, or republishing for any other purpose shall require a license with payment of fee to Mitsubishi Electric Information Technology Center America. All rights reserved. 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 #820662. 	[Title] Constructing Big Trees from Short Sequences [Abstract] The construction of evolutionary trees is a fundamental problem in biology, and yet methods for reconstructing evolutionary trees are not reliable when it comes to inferring accurate topologies of large divergent evolutionary trees from realistic length sequences. We address this problem and present a new polynomial time algorithm for reconstructing evolutionary trees called the Short Quartets Method which is consistent and which has greater statistical power than other polynomial time methods, such as Neighbor-Joining and the 3-approximation algorithm by Agarwala et al. (and the "Double Pivot" variant of the Agarwala et al. algorithm by Cohen and Farach) for the L 1 -nearest tree problem. Our study indicates that our method will produce the correct topology from shorter sequences than can be guaranteed using these other methods. 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 #66751. 	[Title] A Faster Algorithm for the Perfect Phylogeny Problem when the number of Characters is Fixed TR94-05 [Abstract]  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 #1138755. 	[Title] Design of Optimization Criteria for Multiple Sequence Alignment [Abstract] DIMACS Technical Report 96-53 January 1997 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 #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 #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 #573553. 	[Title] On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics) [Abstract] We consider the problem of fitting an n fi n distance matrix D by a tree metric T . Let " be the distance to the closest tree metric, that is, " = min T fk T; D k 1 g. First we present an O(n 2 ) algorithm for finding an additive tree T such that k T; D k 1 3", giving the first algorithm for this problem with a performance guarantee. Second we show that it is N P-hard to find a tree T such that k T; D k 1 &lt; 9 Please summarise all the given information.

Paper #171954 has the title `Efficient Algorithms for Inverting Evolution  
` and the 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. 
`.
Question: Which category should Paper #171954 be classified as ?
You can select one from ['Neural_Networks', 'Case_Based', 'Theory', 'Reinforcement_Learning', 'Probabilistic_Methods', 'Rule_Learning', 'Genetic_Algorithms'].


Paper #171954 has the title `Efficient Algorithms for Inverting Evolution  
` and the 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. 
`.
Question: Which category should Paper #171954 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