The relation between Pearson's correlation coefficient r and Salton's cosine measure

The relation between Pearson's correlation coefficient and Salton's cosine measure is revealed based on the different possible values of the division of the L1-norm and the L2-norm of a vector. These different values yield a sheaf of increasingly straight lines which form together a cloud of points, being the investigated relation. The theoretical results are tested against the author co-citation relations among 24 informetricians for whom two matrices can be constructed, based on co-citations: the asymmetric occurrence matrix and the symmetric co-citation matrix. Both examples completely confirm the theoretical results. The results enable us to specify an algorithm which provides a threshold value for the cosine above which none of the corresponding Pearson correlations would be negative. Using this threshold value can be expected to optimize the visualization of the vector space

The potential of text mining in data integration and network biology for plant research : a case study on Arabidopsis

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies

Decoding Pure Rotational Molecular Spectra for Asymmetric Molecules

In this paper we demonstrate how asymmetric molecular rotational spectra may be introduced to students both "pictorially" and with simple formulae. It is shown that the interpretation of such spectra relies heavily upon pattern recognition. The presentation of some common spectral patterns in near-prolate asymmetric rotational spectra provides a means by which spectral assignment, and approximate rotational constant determination, may be usefully explored in the physics and chemistry classrooms. To aid in this endeavor we have created a supporting, free, web page and mobile web page.Comment: 20 pages, 11 figure

The State-of-the-Art of Set Visualization

Sets comprise a generic data model that has been used in a variety of data analysis problems. Such problems involve analysing and visualizing set relations between multiple sets defined over the same collection of elements. However, visualizing sets is a non-trivial problem due to the large number of possible relations between them. We provide a systematic overview of state-of-the-art techniques for visualizing different kinds of set relations. We classify these techniques into six main categories according to the visual representations they use and the tasks they support. We compare the categories to provide guidance for choosing an appropriate technique for a given problem. Finally, we identify challenges in this area that need further research and propose possible directions to address these challenges. Further resources on set visualization are available at http://www.setviz.net

Distributional Inclusion Vector Embedding for Unsupervised Hypernymy Detection

Modeling hypernymy, such as poodle is-a dog, is an important generalization aid to many NLP tasks, such as entailment, coreference, relation extraction, and question answering. Supervised learning from labeled hypernym sources, such as WordNet, limits the coverage of these models, which can be addressed by learning hypernyms from unlabeled text. Existing unsupervised methods either do not scale to large vocabularies or yield unacceptably poor accuracy. This paper introduces distributional inclusion vector embedding (DIVE), a simple-to-implement unsupervised method of hypernym discovery via per-word non-negative vector embeddings which preserve the inclusion property of word contexts in a low-dimensional and interpretable space. In experimental evaluations more comprehensive than any previous literature of which we are aware-evaluating on 11 datasets using multiple existing as well as newly proposed scoring functions-we find that our method provides up to double the precision of previous unsupervised embeddings, and the highest average performance, using a much more compact word representation, and yielding many new state-of-the-art results.Comment: NAACL 201