nils-herrmann/clean_scirepeval huggingface dataset:
Context Effects in Category Learning: An Investigation of Four Probabilistic Models

Categorization is a central activity of human cognition. When an individual is asked to categorize a sequence of items, context effects arise: categorization of one item influences category decisions for subsequent items. Specifically, when experimental subjects are shown an exemplar of some target category, the category prototype appears to be pulled toward the exemplar, and the prototypes of all nontarget categories appear to be pushed away. These push and pull effects diminish with experience, and likely reflect long-term learning of category boundaries. We propose and evaluate four principled probabilistic (Bayesian) accounts of context effects in categorization. In all four accounts, the probability of an exemplar given a category is encoded as a Gaussian density in feature space, and categorization involves computing category posteriors given an exemplar. The models differ in how the uncertainty distribution of category prototypes is represented (localist or distributed), and how it is updated following each experience (using a maximum likelihood gradient ascent, or a Kalman filter update). We find that the distributed maximum-likelihood model can explain the key experimental phenomena. Further, the model predicts other phenomena that were confirmed via reanalysis of the experimental data.
Learning from Multiple Sources

We consider the problem of learning accurate models from multiple sources of "nearby" data. Given distinct samples from multiple data sources and estimates of the dissimilarities between these sources, we provide a general theory of which samples should be used to learn models for each source. This theory is applicable in a broad decision-theoretic learning framework, and yields results for classification and regression generally, and for density estimation within the exponential family. A key component of our approach is the development of approximate triangle inequalities for expected loss, which may be of independent interest.
Conditional mean field

Despite all the attention paid to variational methods based on sum-product message passing (loopy belief propagation, tree-reweighted sum-product), these methods are still bound to inference on a small set of probabilistic models. Mean field approximations have been applied to a broader set of problems, but the solutions are often poor. We propose a new class of conditionally-specified variational approximations based on mean field theory. While not usable on their own, combined with sequential Monte Carlo they produce guaranteed improvements over conventional mean field. Moreover, experiments on a well-studied problem— inferring the stable configurations of the Ising spin glass—show that the solutions can be significantly better than those obtained using sum-product-based methods.
Relational Learning with Gaussian Processes

Correlation between instances is often modelled via a kernel function using input attributes of the instances. Relational knowledge can further reveal additional pairwise correlations between variables of interest. In this paper, we develop a class of models which incorporates both reciprocal relational information and input attributes using Gaussian process techniques. This approach provides a novel non-parametric Bayesian framework with a data-dependent covariance function for supervised learning tasks. We also apply this framework to semi-supervised learning. Experimental results on several real world data sets verify the usefulness of this algorithm.
Chained Boosting

We describe a method to learn to make sequential stopping decisions, such as those made along a processing pipeline. We envision a scenario in which a series of decisions must be made as to whether to continue to process. Further processing costs time and resources, but may add value. Our goal is to create, based on historic data, a series of decision rules (one at each stage in the pipeline) that decide, based on information gathered up to that point, whether to continue processing the part. We demonstrate how our framework encompasses problems from manufacturing to vision processing. We derive a quadratic (in the number of decisions) bound on testing performance and provide empirical results on object detection.
Fast Iterative Kernel PCA

We introduce two methods to improve convergence of the Kernel Hebbian Algorithm (KHA) for iterative kernel PCA. KHA has a scalar gain parameter which is either held constant or decreased as 1/t, leading to slow convergence. Our KHA/et algorithm accelerates KHA by incorporating the reciprocal of the current estimated eigenvalues as a gain vector. We then derive and apply Stochastic Meta-Descent (SMD) to KHA/et; this further speeds convergence by performing gain adaptation in RKHS. Experimental results for kernel PCA and spectral clustering of USPS digits as well as motion capture and image de-noising problems confirm that our methods converge substantially faster than conventional KHA.
Comparative Gene Prediction using Conditional Random Fields

Computational gene prediction using generative models has reached a plateau, with several groups converging to a generalized hidden Markov model (GHMM) incorporating phylogenetic models of nucleotide sequence evolution. Further improvements in gene calling accuracy are likely to come through new methods that incorporate additional data, both comparative and species specific. Conditional Random Fields (CRFs), which directly model the conditional probability P(y|x) of a vector of hidden states conditioned on a set of observations, provide a unified framework for combining probabilistic and non-probabilistic information and have been shown to outperform HMMs on sequence labeling tasks in natural language processing. 
 
We describe the use of CRFs for comparative gene prediction. We implement a model that encapsulates both a phylogenetic-GHMM (our baseline comparative model) and additional non-probabilistic features. We tested our model on the genome sequence of the fungal human pathogen Cryptococcus neoformans. Our baseline comparative model displays accuracy comparable to the the best available gene prediction tool for this organism. Moreover, we show that discriminative training and the incorporation of non-probabilistic evidence significantly improve performance. 
 
Our software implementation, Conrad, is freely available with an open source license at http://www.broad.mit.edu/annotation/conrad/.
Scalable Discriminative Learning for Natural Language Parsing and Translation

Parsing and translating natural languages can be viewed as problems of predicting tree structures. For machine learning approaches to these predictions, the diversity and high dimensionality of the structures involved mandate very large training sets. This paper presents a purely discriminative learning method that scales up well to problems of this size. Its accuracy was at least as good as other comparable methods on a standard parsing task. To our knowledge, it is the first purely discriminative learning algorithm for translation with tree-structured models. Unlike other popular methods, this method does not require a great deal of feature engineering a priori, because it performs feature selection over a compound feature space as it learns. Experiments demonstrate the method's versatility, accuracy, and efficiency. Relevant software is freely available at http://nlp.cs.nyu.edu/parser and http://nlp.cs.nyu.edu/GenPar.
Fundamental Limitations of Spectral Clustering

Spectral clustering methods are common graph-based approaches to clustering of data. Spectral clustering algorithms typically start from local information encoded in a weighted graph on the data and cluster according to the global eigenvectors of the corresponding (normalized) similarity matrix. One contribution of this paper is to present fundamental limitations of this general local to global approach. We show that based only on local information, the normalized cut functional is not a suitable measure for the quality of clustering. Further, even with a suitable similarity measure, we show that the first few eigenvectors of such adjacency matrices cannot successfully cluster datasets that contain structures at different scales of size and density. Based on these findings, a second contribution of this paper is a novel diffusion based measure to evaluate the coherence of individual clusters. Our measure can be used in conjunction with any bottom-up graph-based clustering method, it is scale-free and can determine coherent clusters at all scales. We present both synthetic examples and real image segmentation problems where various spectral clustering algorithms fail. In contrast, using this coherence measure finds the expected clusters at all scales.
Using Combinatorial Optimization within Max-Product Belief Propagation

In general, the problem of computing a maximum a posteriori (MAP) assignment in a Markov random field (MRF) is computationally intractable. However, in certain subclasses of MRF, an optimal or close-to-optimal assignment can be found very efficiently using combinatorial optimization algorithms: certain MRFs with mutual exclusion constraints can be solved using bipartite matching, and MRFs with regular potentials can be solved using minimum cut methods. However, these solutions do not apply to the many MRFs that contain such tractable components as sub-networks, but also other non-complying potentials. In this paper, we present a new method, called COMPOSE, for exploiting combinatorial optimization for sub-networks within the context of a max-product belief propagation algorithm. COMPOSE uses combinatorial optimization for computing exact max-marginals for an entire sub-network; these can then be used for inference in the context of the network as a whole. We describe highly efficient methods for computing max-marginals for subnetworks corresponding both to bipartite matchings and to regular networks. We present results on both synthetic and real networks encoding correspondence problems between images, which involve both matching constraints and pairwise geometric constraints. We compare to a range of current methods, showing that the ability of COMPOSE to transmit information globally across the network leads to improved convergence, decreased running time, and higher-scoring assignments.
Clustering appearance and shape by learning jigsaws

Patch-based appearance models are used in a wide range of computer vision applications. To learn such models it has previously been necessary to specify a suitable set of patch sizes and shapes by hand. In the jigsaw model presented here, the shape, size and appearance of patches are learned automatically from the repeated structures in a set of training images. By learning such irregularly shaped 'jigsaw pieces', we are able to discover both the shape and the appearance of object parts without supervision. When applied to face images, for example, the learned jigsaw pieces are surprisingly strongly associated with face parts of different shapes and scales such as eyes, noses, eyebrows and cheeks, to name a few. We conclude that learning the shape of the patch not only improves the accuracy of appearance-based part detection but also allows for shape-based part detection. This enables parts of similar appearance but different shapes to be distinguished; for example, while foreheads and cheeks are both skin colored, they have markedly different shapes.
Correcting Sample Selection Bias by Unlabeled Data

We consider the scenario where training and test data are drawn from different distributions, commonly referred to as sample selection bias. Most algorithms for this setting try to first recover sampling distributions and then make appropriate corrections based on the distribution estimate. We present a nonparametric method which directly produces resampling weights without distribution estimation. Our method works by matching distributions between training and testing sets in feature space. Experimental results demonstrate that our method works well in practice.
Large-Margin Gaussian Mixture Modeling for Automatic Speech Recognition

Discriminative training for acoustic models has been widely studied to improve the performance of automatic speech recognition systems. To enhance the generalization ability of discriminatively trained models, a large-margin training framework has recently been proposed. This work investigates large-margin training in detail, integrates the training with more flexible classifier structures such as hierarchical classifiers and committee-based classifiers, and compares the performance of the proposed modeling scheme with existing discriminative methods such as minimum classification error (MCE) training. Experiments are performed on a standard phonetic classification task and a large vocabulary speech recognition (LVCSR) task. In the phonetic classification experiments, the proposed modeling scheme yields about 1.5% absolute error reduction over the current state of the art. In the LVCSR experiments on the MIT lecture corpus, the large-margin model has about 6.0% absolute word error rate reduction over the baseline model and about 0.6% absolute error rate reduction over the MCE model.  James R. Glass Title: Principal Research Scientist
Hyperparameter Learning for Graph Based Semi-supervised Learning Algorithms

Semi-supervised learning algorithms have been successfully applied in many applications with scarce labeled data, by utilizing the unlabeled data. One important category is graph based semi-supervised learning algorithms, for which the performance depends considerably on the quality of the graph, or its hyperparameters. In this paper, we deal with the less explored problem of learning the graphs. We propose a graph learning method for the harmonic energy minimization method; this is done by minimizing the leave-one-out prediction error on labeled data points. We use a gradient based method and designed an efficient algorithm which significantly accelerates the calculation of the gradient by applying the matrix inversion lemma and using careful pre-computation. Experimental results show that the graph learning method is effective in improving the performance of the classification algorithm.
Adaptor Grammars: A Framework for Specifying Compositional Nonparametric Bayesian Models

This paper introduces adaptor grammars, a class of probabilistic models of language that generalize probabilistic context-free grammars (PCFGs). Adaptor grammars augment the probabilistic rules of PCFGs with "adaptors" that can induce dependencies among successive uses. With a particular choice of adaptor, based on the Pitman-Yor process, nonparametric Bayesian models of language using Dirichlet processes and hierarchical Dirichlet processes can be written as simple grammars. We present a general-purpose inference algorithm for adaptor grammars, making it easy to define and use such models, and illustrate how several existing nonparametric Bayesian models can be expressed within this framework.
An Oracle Inequality for Clipped Regularized Risk Minimizers

We establish a general oracle inequality for clipped approximate minimizers of regularized empirical risks and apply this inequality to support vector machine (SVM) type algorithms. We then show that for SVMs using Gaussian RBF kernels for classification this oracle inequality leads to learning rates that are faster than the ones established in . Finally, we use our oracle inequality to show that a simple parameter selection approach based on a validation set can yield the same fast learning rates without knowing the noise exponents which were required to be known a-priori in .
Data Integration for Classification Problems Employing Gaussian Process Priors

By adopting Gaussian process priors a fully Bayesian solution to the problem of integrating possibly heterogeneous data sets within a classification setting is presented. Approximate inference schemes employing Variational & Expectation Propagation based methods are developed and rigorously assessed. We demonstrate our approach to integrating multiple data sets on a large scale protein fold prediction problem where we infer the optimal combinations of covariance functions and achieve state-of-the-art performance without resorting to any ad hoc parameter tuning and classifier combination.
MLLE: Modified Locally Linear Embedding Using Multiple Weights

The locally linear embedding (LLE) is improved by introducing multiple linearly independent local weight vectors for each neighborhood. We characterize the reconstruction weights and show the existence of the linearly independent weight vectors at each neighborhood. The modified locally linear embedding (MLLE) proposed in this paper is much stable. It can retrieve the ideal embedding if MLLE is applied on data points sampled from an isometric manifold. MLLE is also compared with the local tangent space alignment (LTSA). Numerical examples are given that show the improvement and efficiency of MLLE.
Accelerated Variational Dirichlet Process Mixtures

Dirichlet Process (DP) mixture models are promising candidates for clustering applications where the number of clusters is unknown a priori. Due to computational considerations these models are unfortunately unsuitable for large scale data-mining applications. We propose a class of deterministic accelerated DP mixture models that can routinely handle millions of data-cases. The speedup is achieved by incorporating kd-trees into a variational Bayesian algorithm for DP mixtures in the stick-breaking representation, similar to that of Blei and Jordan (2005). Our algorithm differs in the use of kd-trees and in the way we handle truncation: we only assume that the variational distributions are fixed at their priors after a certain level. Experiments show that speedups relative to the standard variational algorithm can be significant.
Multi-Task Feature Learning

We present a method for learning a low-dimensional representation which is shared across a set of multiple related tasks. The method builds upon the well-known 1-norm regularization problem using a new regularizer which controls the number of learned features common for all the tasks. We show that this problem is equivalent to a convex optimization problem and develop an iterative algorithm for solving it. The algorithm has a simple interpretation: it alternately performs a supervised and an unsupervised step, where in the latter step we learn commonacross-tasks representations and in the former step we learn task-specific functions using these representations. We report experiments on a simulated and a real data set which demonstrate that the proposed method dramatically improves the performance relative to learning each task independently. Our algorithm can also be used, as a special case, to simply select – not learn – a few common features across the tasks.
Doubly Stochastic Normalization for Spectral Clustering

In this paper we focus on the issue of normalization of the affinity matrix in spectral clustering. We show that the difference between N-cuts and Ratio-cuts is in the error measure being used (relative-entropy versus L1 norm) in finding the closest doubly-stochastic matrix to the input affinity matrix. We then develop a scheme for finding the optimal, under Frobenius norm, doubly-stochastic approximation using Von-Neumann's successive projections lemma. The new normalization scheme is simple and efficient and provides superior clustering performance over many of the standardized tests.
Sample Complexity of Policy Search with Known Dynamics

We consider methods that try to find a good policy for a Markov decision process by choosing one from a given class. The policy is chosen based on its empirical performance in simulations. We are interested in conditions on the complexity of the policy class that ensure the success of such simulation based policy search methods. We show that under bounds on the amount of computation involved in computing policies, transition dynamics and rewards, uniform convergence of empirical estimates to true value functions occurs. Previously, such results were derived by assuming boundedness of pseudodimension and Lipschitz continuity. These assumptions and ours are both stronger than the usual combinatorial complexity measures. We show, via minimax inequalities, that this is essential: boundedness of pseudodimension or fat-shattering dimension alone is not sufficient.
implicit Online Learning with Kernels

We present two new algorithms for online learning in reproducing kernel Hilbert spaces. Our first algorithm, ILK (implicit online learning with kernels), employs a new, implicit update technique that can be applied to a wide variety of convex loss functions. We then introduce a bounded memory version, SILK (sparse ILK), that maintains a compact representation of the predictor without compromising solution quality, even in non-stationary environments. We prove loss bounds and analyze the convergence rate of both. Experimental evidence shows that our proposed algorithms outperform current methods on synthetic and real data.
Modeling General and Specific Aspects of Documents with a Probabilistic Topic Model

Techniques such as probabilistic topic models and latent-semantic indexing have been shown to be broadly useful at automatically extracting the topical or semantic content of documents, or more generally for dimension-reduction of sparse count data. These types of models and algorithms can be viewed as generating an abstraction from the words in a document to a lower-dimensional latent variable representation that captures what the document is generally about beyond the specific words it contains. In this paper we propose a new probabilistic model that tempers this approach by representing each document as a combination of (a) a background distribution over common words, (b) a mixture distribution over general topics, and (c) a distribution over words that are treated as being specific to that document. We illustrate how this model can be used for information retrieval by matching documents both at a general topic level and at a specific word level, providing an advantage over techniques that only match documents at a general level (such as topic models or latent-sematic indexing) or that only match documents at the specific word level (such as TF-IDF).
A Hidden Markov Dirichlet Process Model for Genetic Recombination in Open Ancestral Space

We present a new statistical framework called hidden Markov Dirichlet process (HMDP) to jointly model the genetic recombinations among possibly infinite number of founders and the coalescence-with-mutation events in the resulting genealogies. The HMDP posits that a haplotype of genetic markers is generated by a sequence of recombination events that select an ancestor for each locus from an unbounded set of founders according to a 1st-order Markov transition process. Conjoining this process with a mutation model, our method accommodates both between-lineage recombination and withinlineage sequence variations, and leads to a compact and natural interpretation of the population structure and inheritance process. An efficient sampling algorithm based on a two-level nested Pólya urn scheme was also developed.
Branch and Bound for Semi-Supervised Support Vector Machines

Semi-supervised SVMs (S3VM) attempt to learn low-density separators by maximizing the margin over labeled and unlabeled examples. The associated optimization problem is non-convex. To examine the full potential of S3VMs modulo local minima problems in current implementations, we apply branch and bound techniques for obtaining exact, globally optimal solutions. Empirical evidence suggests that the globally optimal solution can return excellent generalization performance in situations where other implementations fail completely. While our current implementation is only applicable to small datasets, we discuss variants that can potentially lead to practically useful algorithms.