nils-herrmann/clean_scirepeval huggingface dataset:
A Markovian Lattice Model for the Acquisition of Morphological Structure

First and second co-located axially extending RF coils are displaced spatially with respect to one another by 90 degrees so as to produce a pair of RF signals from the enclosed volume which are in phase quadrature. The same coils or one of them may also be utilized for transmitting NMR RF signals into the same volume. The coils have a common open-end through which objects to be imaged may be inserted and a common "closed" end for convenient location of RF coupling and feeding structures. Each of the coils has an RF feedline structure which extends across a diameter of common closed end and the two feedline structures are disposed substantially perpendicular with respect to one another so as to minimize cross coupling. The feedlines are also spatially configured to facilitate mounting of associated tuning and coupling capacitors. A fixed coupling "paddle" provides cancellation coupling between the coils and a movably mounted coupling paddle is arranged to provide variable amounts of cancellation coupling between the orthogonal feedline structures. The phase quadrature RF signals emanating from the pair of coils are preferably amplified before being combined in a 90 DEG RF hybrid circuit.
A Family of Additive Online Algorithms for Category Ranking

We describe a new family of topic-ranking algorithms for multi-labeled documents. The motivation for the algorithms stem from recent advances in online learning algorithms. The algorithms are simple to implement and are also time and memory efficient. We provide a unified analysis of the family of algorithms in the mistake bound model. We then discuss experiments with the proposed family of topic-ranking algorithms on the Reuters-21578 corpus and the new corpus released by Reuters in 2000. On both corpora, the algorithms we present achieve state-of-the-art results and outperforms topic-ranking adaptations of Rocchio's algorithm and of the Perceptron algorithm.
A Markov model for the acquisition of morphological structure

We describe a new formalism for word morphology. Our model views word generation as a random walk on a trellis of units where each unit is a set of (short) strings. The model naturally incorporates segmentation of words into morphemes. We capture the statistics of unit generation using a probabilistic suffix tree (PST) which is a variant of variable length Markov models. We present an efficient algorithm that learns a PST over the units whose output is a compact stochastic representation of morphological structure. We demonstrate the applicability of our approach by using the model in an allomorphy decision problem.
Online Classification on a Budget

Online algorithms for classification often require vast amounts of memory and computation time when employed in conjunction with kernel functions. In this paper we describe and analyze a simple approach for an on-the-fly reduction of the number of past examples used for prediction. Experiments performed with real datasets show that using the proposed algorithmic approach with a single epoch is competitive with the support vector machine (SVM) although the latter, being a batch algorithm, accesses each training example multiple times.
Smooth ε-insensitive regression by loss symmetrization

We describe a framework for solving regression problems by reduction to classification. Our reduction is based on symmetrization of margin-based loss functions commonly used in boosting algorithms, namely, the logistic loss and the exponential loss. Our construction yields a smooth version of the e-insensitive hinge loss that is used in support vector regression. A byproduct of this construction is a new simple form of regularization for boosting-based classification and regression algorithms. We present two parametric families of batch learning algorithms for minimizing these losses. The first family employs a log-additive update and is based on recent boosting algorithms while the second family uses a new form of additive update. We also describe and analyze online gradient descent (GD) and exponentiated gradient (EG) algorithms for the e-insensitive logistic loss. Our regression framework also has implications on classification algorithms, namely, a new additive batch algorithm for the log-loss and exp-loss used in boosting.
Protein Family Classification Using Sparse Markov Transducers

We present a method for classifying proteins into families based on short subsequences of amino acids using a new probabilistic model called sparse Markov transducers (SMT). We classify a protein by estimating probability distributions over subsequences of amino acids from the protein. Sparse Markov transducers, similar to probabilistic suffix trees, estimate a probability distribution conditioned on an input sequence. SMTs generalize probabilistic suffix trees by allowing for wild-cards in the conditioning sequences. Since substitutions of amino acids are common in protein families, incorporating wild-cards into the model significantly improves classification performance. We present two models for building protein family classifiers using SMTs. As protein databases become larger, data driven learning algorithms for probabilistic models such as SMTs will require vast amounts of memory. We therefore describe and use efficient data structures to improve the memory usage of SMTs. We evaluate SMTs by building protein family classifiers using the Pfam and SCOP databases and compare our results to previously published results and state-of-the-art protein homology detection methods. SMTs outperform previous probabilistic suffix tree methods and under certain conditions perform comparably to state-of-the-art protein homology methods.
Ultraconservative online algorithms for multiclass problems

In this paper we study a paradigm to generalize online classification algorithms for binary classification problems to multiclass problems. The particular hypotheses we investigate maintain one prototype vector per class. Given an input instance, a multiclass hypothesis computes a similarity-score between each prototype and the input instance and sets the predicted label to be the index of the prototype achieving the highest similarity. To design and analyze the learning algorithms in this paper we introduce the notion of ultraconservativeness. Ultraconservative algorithms are algorithms that update only the prototypes attaining similarity-scores which are higher than the score of the correct label's prototype. We start by describing a family of additive ultraconservative algorithms where each algorithm in the family updates its prototypes by finding a feasible solution for a set of linear constraints that depend on the instantaneous similarity-scores. We then discuss a specific online algorithm that seeks a set of prototypes which have a small norm. The resulting algorithm, which we term MIRA (for Margin Infused Relaxed Algorithm) is ultraconservative as well. We derive mistake bounds for all the algorithms and provide further analysis of MIRA using a generalized notion of the margin for multiclass problems. We discuss the form the algorithms take in the binary case and show that all the algorithms from the first family reduce to the Perceptron algorithm while MIRA provides a new Perceptron-like algorithm with a margin-dependent learning rate. We then return to multiclass problems and describe an analogous multiplicative family of algorithms with corresponding mistake bounds. We end the formal part by deriving and analyzing a multiclass version of Li and Long's ROMMA algorithm. We conclude with a discussion of experimental results that demonstrate the merits of our algorithms.
Feature-Rich Part-of-Speech Tagging with a Cyclic Dependency Network

We present a new part-of-speech tagger that demonstrates the following ideas: (i) explicit use of both preceding and following tag contexts via a dependency network representation, (ii) broad use of lexical features, including jointly conditioning on multiple consecutive words, (iii) effective use of priors in conditional loglinear models, and (iv) fine-grained modeling of unknown word features. Using these ideas together, the resulting tagger gives a 97.24% accuracy on the Penn Treebank WSJ, an error reduction of 4.4% on the best previous single automatically learned tagging result.
Log-Linear Models for Label Ranking

Label ranking is the task of inferring a total order over a predefined set of labels for each given instance. We present a general framework for batch learning of label ranking functions from supervised data. We assume that each instance in the training data is associated with a list of preferences over the label-set, however we do not assume that this list is either complete or consistent. This enables us to accommodate a variety of ranking problems. In contrast to the general form of the supervision, our goal is to learn a ranking function that induces a total order over the entire set of labels. Special cases of our setting are multilabel categorization and hierarchical classification. We present a general boosting-based learning algorithm for the label ranking problem and prove a lower bound on the progress of each boosting iteration. The applicability of our approach is demonstrated with a set of experiments on a large-scale text corpus.
Kernel Design Using Boosting

The focus of the paper is the problem of learning kernel operators from empirical data. We cast the kernel design problem as the construction of an accurate kernel from simple (and less accurate) base kernels. We use the boosting paradigm to perform the kernel construction process. To do so, we modify the booster so as to accommodate kernel operators. We also devise an efficient weak-learner for simple kernels that is based on generalized eigen vector decomposition. We demonstrate the effectiveness of our approach on synthetic data and on the USPS dataset. On the USPS dataset, the performance of the Perceptron algorithm with learned kernels is systematically better than a fixed RBF kernel.
Robust temporal and spectral modeling for query By melody

Query by melody is the problem of retrieving musical performances from melodies. Retrieval of real performances is complicated due to the large number of variations in performing a melody and the presence of colored accompaniment noise. We describe a simple yet effective probabilistic model for this task. We describe a generative model that is rich enough to capture the spectral and temporal variations of musical performances and allows for tractable melody retrieval. While most of previous studies on music retrieval from melodies were performed with either symbolic (e.g. MIDI) data or with monophonic (single instrument) performances, we performed experiments in retrieving live and studio recordings of operas that contain a leading vocalist and rich instrumental accompaniment. Our results show that the probabilistic approach we propose is effective and can be scaled to massive datasets.
Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences

Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically-motivated method for estimating probability distributions over discrete alphabets from observations using a mixture model of common ancestors. The method is an extension of substitution matrix-based probability estimation methods. In contrast to previous such methods, our method has a simple Bayesian interpretation and has the advantage over Dirichlet mixtures that it is both effective and simple to compute for large alphabets. The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods. The method is also applied to estimate probability distributions over protein families and improves protein classification accuracy.
A new family of online algorithms for category ranking

We describe a new family of topic-ranking algorithms for multi-labeled documents. The motivation for the algorithms stems from recent advances in online learning algorithms. The algorithms we present are simple to implement and are time and memory efficient. We evaluate the algorithms on the Reuters-21578 corpus and the new corpus released by Reuters in 2000. On both corpora the algorithms we present outperform adaptations to topic-ranking of Rocchio's algorithm and the Perceptron algorithm. We also outline the formal analysis of the algorithm in the mistake bound model. To our knowledge, this work is the first to report performance results with the entire new Reuters corpus.
Multiclass Learning by Probabilistic Embeddings

We describe a new algorithmic framework for learning multiclass categorization problems. In this framework a multiclass predictor is composed of a pair of embeddings that map both instances and labels into a common space. In this space each instance is assigned the label it is nearest to. We outline and analyze an algorithm, termed Bunching, for learning the pair of embeddings from labeled data. A key construction in the analysis of the algorithm is the notion of probabilistic output codes, a generalization of error correcting output codes (ECOC). Furthermore, the method of multiclass categorization using ECOC is shown to be an instance of Bunching. We demonstrate the advantage of Bunching over ECOC by comparing their performance on numerous categorization problems.
Spikernels: Embedding Spiking Neurons in Inner-Product Spaces

Inner-product operators, often referred to as kernels in statistical learning, define a mapping from some input space into a feature space. The focus of this paper is the construction of biologically-motivated kernels for cortical activities. The kernels we derive, termed Spikernels, map spike count sequences into an abstract vector space in which we can perform various prediction tasks. We discuss in detail the derivation of Spikernels and describe an efficient algorithm for computing their value on any two sequences of neural population spike counts. We demonstrate the merits of our modeling approach using the Spikernel and various standard kernels for the task of predicting hand movement velocities from cortical recordings. In all of our experiments all the kernels we tested outperform the standard scalar product used in regression with the Spikernel consistently achieving the best performance.
Discriminative Binaural Sound Localization

Time difference of arrival (TDOA) is commonly used to estimate the azimuth of a source in a microphone array. The most common methods to estimate TDOA are based on finding extrema in generalized cross-correlation waveforms. In this paper we apply microphone array techniques to a manikin head. By considering the entire cross-correlation waveform we achieve azimuth prediction accuracy that exceeds extrema locating methods. We do so by quantizing the azimuthal angle and treating the prediction problem as a multiclass categorization task. We demonstrate the merits of our approach by evaluating the various approaches on Sony's AIBO robot.
An Efficient PAC Algorithm for Reconstructing a Mixture of Lines

In this paper we study the learnability of a mixture of lines model which is of great importance in machine vision, computer graphics, and computer aided design applications. The mixture of lines is a partially-probabilistic model for an image composed of line-segments. Observations are generated by choosing one of the lines at random and picking a point at random from the chosen line. Each point is contaminated with some noise whose distribution is unknown, but which is bounded in magnitude. Our goal is to discover efficiently and rather accurately the line-segments that generated the noisy observations. We describe and analyze an efficient probably approximately correct (PAC) algorithm for solving the problem. Our algorithm combines techniques from planar geometry with simple large deviation tools and is simple to implement.
Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences

Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically-motivated method for estimating probability distributions over discrete alphabets from observations using a mixture model of common ancestors. The method is an extension of substitution matrix-based probability estimation methods. In contrast to previous such methods, our method has a simple Bayesian interpretation and has the advantage over Dirichlet mixtures that it is both effective and simple to compute for large alphabets. The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods. The method is also applied to estimate probability distributions over protein families and improves protein classification accuracy.
On the Algorithmic Implementation of Multiclass Kernel-based Vector Machines

In this paper we describe the algorithmic implementation of multiclass kernel-based vector machines. Our starting point is a generalized notion of the margin to multiclass problems. Using this notion we cast multiclass categorization problems as a constrained optimization problem with a quadratic objective function. Unlike most of previous approaches which typically decompose a multiclass problem into multiple independent binary classification tasks, our notion of margin yields a direct method for training multiclass predictors. By using the dual of the optimization problem we are able to incorporate kernels with a compact set of constraints and decompose the dual problem into multiple optimization problems of reduced size. We describe an efficient fixed-point algorithm for solving the reduced optimization problems and prove its convergence. We then discuss technical details that yield significant running time improvements for large datasets. Finally, we describe various experiments with our approach comparing it to previously studied kernel-based methods. Our experiments indicate that for multiclass problems we attain state-of-the-art accuracy.
Pranking with Ranking

We discuss the problem of ranking instances. In our framework each instance is associated with a rank or a rating, which is an integer from 1 to k. Our goal is to find a rank-predict ion rule that assigns each instance a rank which is as close as possible to the instance's true rank. We describe a simple and efficient online algorithm, analyze its performance in the mistake bound model, and prove its correctness. We describe two sets of experiments, with synthetic data and with the EachMovie dataset for collaborative filtering. In the experiments we performed, our algorithm outperforms online algorithms for regression and classification applied to ranking.
Boosting for document routing

RankBoost is a recently proposed algorithm for learning ranking functions. It is simple to implement and has strong justifica tions from computational learning theory. We describe the algorithm and present experimental results on applying it to the document routing problem. The first set of results applies RankBoost t o a text representation produced using modern term weighting methods. Performance of RankBoost is somewhat inferior to that of a state-of-the-art routing algorithm which is, however, more complex and less theoretically justified than RankBoost.  oost achieves comparable performance to the state-of-the-art algorithm when combined with feature or example selection heuristics. Our second set of results examines the behavior of RankBoost when it has to learn not only a ranking function but also all aspect s of term weighting from raw data. Performance is usually, though not always, less good here, but the term weighting functions implicit in the resulting ranking functions are intriguing, and the a pproach could easily be adapted to mixtures of textual and nontextual data.
Protein Family Classification Using Sparse Markov Transducers

In this paper we present a method for classifying proteins into families using sparse Markov transducers (SMTs). Sparse Markov transducers, similar to probabilistic suffix trees, estimate a probability distribution conditioned on an input sequence. SMTs generalize probabilistic suffix trees by allowing for wild-cards in the conditioning sequences. Because substitutions of amino acids are common in protein families, incorporating wildcards into the model significantly improves classification performance. We present two models for building protein family classifiers using SMTs. We also present efficient data structures to improve the memory usage of the models. We evaluate SMTs by building protein family classifiers using the Pfam database and compare our results to previously published results.
State-based Classification of Finger Gestures from Electromyographic Signals

Electromyographic signals may provide an important new class of user interface for consumer electronics. In order to make such interfaces effective, it will be crucial to map EMG signals to user gestures in real time. The mapping from signals to gestures will vary from user to user, so it must be acquired adaptively. In this paper, we describe and compare three methods for static classification of EMG signals. We then go on to explore methods for adapting the classifiers over time and for sequential analysis of the gesture stream by combining the static classification algorithm with a hidden Markov model. We conclude with an evaluation of the combined model on an unsegmented stream of gestures.
Reducing Multiclass to Binary: A Unifying Approach for Margin Classifiers

We present a unifying framework for studying the solution of multiclass categorization problems by reducing them to multiple binary problems that are then solved using a margin-based binary learning algorithm. The proposed framework unifies some of the most popular approaches in which each class is compared against all others, or in which all pairs of classes are compared to each other, or in which output codes with error-correcting properties are used. We propose a general method for combining the classifiers generated on the binary problems, and we prove a general empirical multiclass loss bound given the empirical loss of the individual binary learning algorithms. The scheme and the corresponding bounds apply to many popular classification learning algorithms including support-vector machines, AdaBoost, regression, logistic regression and decision-tree algorithms. We also give a multiclass generalization error analysis for general output codes with AdaBoost as the binary learner. Experimental results with SVM and AdaBoost show that our scheme provides a viable alternative to the most commonly used multiclass algorithms.
Improved Output Coding for Classification Using Continuous Relaxation

Output coding is a general method for solving multiclass problems by reducing them to multiple binary classification problems. Previous research on output coding has employed, almost solely, predefined discrete codes. We describe an algorithm that improves the performance of output codes by relaxing them to continuous codes. The relaxation procedure is cast as an optimization problem and is reminiscent of the quadratic program for support vector machines. We describe experiments with the proposed algorithm, comparing it to standard discrete output codes. The experimental results indicate that continuous relaxations of output codes often improve the generalization performance, especially for short codes.