1,720,958 research outputs found
Interpretable pairwise distillations for generative protein sequence models
Full text linkMany different types of generative models for protein sequences have been proposed in literature. Their uses include the prediction of mutational effects, protein design and the prediction of structural properties. Neural network (NN) architectures have shown great performances, commonly attributed to the capacity to extract non-trivial higher-order interactions from the data. In this work, we analyze two different NN models and assess how close they are to simple pairwise distributions, which have been used in the past for similar problems. We present an approach for extracting pairwise models from more complex ones using an energy-based modeling framework. We show that for the tested models the extracted pairwise models can replicate the energies of the original models and are also close in performance in tasks like mutational effect prediction. In addition, we show that even simpler, factorized models often come close in performance to the original models
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Entropic gradient descent algorithms and wide flat minima
Full text linkThe properties of flat minima in the empirical risk landscape of neural networks have been debated for some time. Increasing evidence suggests they possess better generalization capabilities with respect to sharp ones. In this work we first discuss the relationship between alternative measures of flatness: The local entropy, which is useful for analysis and algorithm development, and the local energy, which is easier to compute and was shown empirically in extensive tests on state-of-the-art networks to be the best predictor of generalization capabilities. We show semi-analytically in simple controlled scenarios that these two measures correlate strongly with each other and with generalization. Then, we extend the analysis to the deep learning scenario by extensive numerical validations. We study two algorithms, Entropy-SGD and Replicated-SGD, that explicitly include the local entropy in the optimization objective. We devise a training schedule by which we consistently find flatter minima (using both flatness measures), and improve the generalization error for common architectures (e.g. ResNet, EfficientNet)
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Entropic gradient descent algorithms and wide flat minima
No full textThe properties of flat minima in the empirical risk landscape of neural networks have been debated for some time. Increasing evidence suggests they possess better generalization capabilities with respect to sharp ones. In this work we first discuss the relationship between alternative measures of flatness: the local entropy, which is useful for analysis and algorithm development, and the local energy, which is easier to compute and was shown empirically in extensive tests on state-of-the-art networks to be the best predictor of generalization capabilities. We show semi-analytically in simple controlled scenarios that these two measures correlate strongly with each other and with generalization. Then, we extend the analysis to the deep learning scenario by extensive numerical validations. We study two algorithms, entropy-stochastic gradient descent and replicated-stochastic gradient descent, that explicitly include the local entropy in the optimization objective. We devise a training schedule by which we consistently find flatter minima (using both flatness measures), and improve the generalization error for common architectures (e.g. ResNet, EfficientNet)
Deep Networks on Toroids: Removing Symmetries Reveals the Structure of Flat Regions in the Landscape Geometry
Full text linkWe systematize the approach to the investigation of deep neural network landscapes by basing it on the geometry of the space of implemented functions rather than the space of parameters. Grouping classifiers into equivalence classes, we develop a standardized parameterization in which all symmetries are removed, resulting in a toroidal topology. On this space, we explore the error landscape rather than the loss. This lets us derive a meaningful notion of the flatness of minimizers and of the geodesic paths connecting them. Using different optimization algorithms that sample minimizers with different flatness we study the mode connectivity and relative distances. Testing a variety of state-of-the-art architectures and benchmark datasets, we confirm the correlation between flatness and generalization performance; we further show that in function space flatter minima are closer to each other and that the barriers along the geodesics connecting them are small. We also find that minimizers found by variants of gradient descent can be connected by zero-error paths composed of two straight lines in parameter space, i.e. polygonal chains with a single bend. We observe similar qualitative results in neural networks with binary weights and activations, providing one of the first results concerning the connectivity in this setting. Our results hinge on symmetry removal, and are in remarkable agreement with the rich phenomenology described by some recent analytical studies performed on simple shallow models
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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