node2vec is an algorithm to generate vector representations of nodes on a graph. The node2vec framework learns low-dimensional representations for nodes in a graph through the use of random walks through a graph starting at a target node. It is useful for a variety of machine learning applications. node2vec follows the intuition that random walks through a graph can be treated like sentences in a corpus. Each node in a graph is treated like an individual word, and a random walk is treated as a sentence. By feeding these "sentences" into a skip-gram, or by using the continuous bag of words model, paths found by random walks can be treated as sentences, and traditional data-mining techniques for documents can be used. The algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and argues that the added flexibility in exploring neighborhoods is the key to learning richer representations of nodes in graphs. The algorithm is considered one of the best graph classifiers.
Spike-and-slab regression
Spike-and-slab regression is a type of Bayesian linear regression in which a particular hierarchical prior distribution for the regression coefficients is chosen such that only a subset of the possible regressors is retained. The technique is particularly useful when the number of possible predictors is larger than the number of observations. The idea of the spike-and-slab model was originally proposed by Mitchell & Beauchamp (1988). The approach was further significantly developed by Madigan & Raftery (1994) and George & McCulloch (1997). A recent and important contribution to this literature is Ishwaran & Rao (2005). == Model description == Suppose we have P possible predictors in some model. Vector γ has a length equal to P and consists of zeros and ones. This vector indicates whether a particular variable is included in the regression or not. If no specific prior information on initial inclusion probabilities of particular variables is available, a Bernoulli prior distribution is a common default choice. Conditional on a predictor being in the regression, we identify a prior distribution for the model coefficient, which corresponds to that variable (β). A common choice on that step is to use a normal prior with a mean equal to zero and a large variance calculated based on ( X T X ) − 1 {\displaystyle (X^{T}X)^{-1}} (where X {\displaystyle X} is a design matrix of explanatory variables of the model). A draw of γ from its prior distribution is a list of the variables included in the regression. Conditional on this set of selected variables, we take a draw from the prior distribution of the regression coefficients (if γi = 1 then βi ≠ 0 and if γi = 0 then βi = 0). βγ denotes the subset of β for which γi = 1. In the next step, we calculate a posterior probability for both inclusion and coefficients by applying a standard statistical procedure. All steps of the described algorithm are repeated thousands of times using the Markov chain Monte Carlo (MCMC) technique. As a result, we obtain a posterior distribution of γ (variable inclusion in the model), β (regression coefficient values) and the corresponding prediction of y. The model got its name (spike-and-slab) due to the shape of the two prior distributions. The "spike" is the probability of a particular coefficient in the model to be zero. The "slab" is the prior distribution for the regression coefficient values. An advantage of Bayesian variable selection techniques is that they are able to make use of prior knowledge about the model. In the absence of such knowledge, some reasonable default values can be used; to quote Scott and Varian (2013): "For the analyst who prefers simplicity at the cost of some reasonable assumptions, useful prior information can be reduced to an expected model size, an expected R2, and a sample size ν determining the weight given to the guess at R2." Some researchers suggest the following default values: R2 = 0.5, ν = 0.01, and π = 0.5 (parameter of a prior Bernoulli distribution).
Research data archiving
Research data archiving is the long-term storage of scholarly research data, including the natural sciences, social sciences, and life sciences. The various academic journals have differing policies regarding how much of their data and methods researchers are required to store in a public archive, and what is actually archived varies widely between different disciplines. Similarly, the major grant-giving institutions have varying attitudes towards public archiving of data. In general, the tradition of science has been for publications to contain sufficient information to allow fellow researchers to replicate and therefore test the research. In recent years this approach has become increasingly strained as research in some areas depends on large datasets which cannot easily be replicated independently. Data archiving is more important in some fields than others. In a few fields, all of the data necessary to replicate the work is already available in the journal article. In drug development, a great deal of data is generated and must be archived so researchers can verify that the reports the drug companies publish accurately reflect the data. Often used interchangeably, Data preservation and data archiving are both about protecting data for the long term, but they serve different purposes. Data preservation focuses on preventing data from being lost, damaged, or destroyed by creating backups, storing data in secure locations, and ensuring it remains accessible when needed. Data archiving, on the other hand, involves moving data that is no longer actively used to a separate storage location for long-term keeping. Archived data is often combined and compressed, and while it can still be accessed, it is not intended for regular use or frequent updates. The requirement of data archiving is a recent development in the history of science. It was made possible by advances in information technology allowing large amounts of data to be stored and accessed from central locations. For example, the American Geophysical Union (AGU) adopted their first policy on data archiving in 1993, about three years after the beginning of the WWW. This policy mandates that datasets cited in AGU papers must be archived by a recognised data center; it permits the creation of "data papers"; and it establishes AGU's role in maintaining data archives. But it makes no requirements on paper authors to archive their data. Prior to organized data archiving, researchers wanting to evaluate or replicate a paper would have to request data and methods information from the author. The academic community expects authors to share supplemental data. This process was recognized as wasteful of time and energy and obtained mixed results. Information could become lost or corrupted over the years. In some cases, authors simply refuse to provide the information. The need for data archiving and due diligence is greatly increased when the research deals with health issues or public policy formation. == Selected policies by journals == === Biotropica === Biotropica requires, as a condition for publication, that the data supporting the results in the paper and metadata describing them must be archived in an appropriate public archive such as Dryad, Figshare, GenBank, TreeBASE, or NCBI. Authors may elect to make the data publicly available as soon as the article is published or, if the technology of the archive allows, embargo access to the data up to three years after article publication. A statement describing Data Availability will be included in the manuscript as described in the instructions to authors. Exceptions to the required archiving of data may be granted at the discretion of the Editor-in-Chief for studies that include sensitive information (e.g., the location of endangered species). Our Editorial explaining the motivation for this policy can be found here. A more comprehensive list of data repositories is available here. Promoting a culture of collaboration with researchers who collect and archive data: The data collected by tropical biologists are often long-term, complex, and expensive to collect. The Board of Editors of Biotropica strongly encourages authors who re-use data archives archived data sets to include as fully engaged collaborators the scientists who originally collected them. We feel this will greatly enhance the quality and impact of the resulting research by drawing on the data collector’s profound insights into the natural history of the study system, reducing the risk of errors in novel analyses, and stimulating the cross-disciplinary and cross-cultural collaboration and training for which the ATBC and Biotropica are widely recognized. NB: Biotropica is one of only two journals that pays the fees for authors depositing data at Dryad. === The American Naturalist === The American Naturalist requires authors to deposit the data associated with accepted papers in a public archive. For gene sequence data and phylogenetic trees, deposition in GenBank or TreeBASE, respectively, is required. There are many possible archives that may suit a particular data set, including the Dryad repository for ecological and evolutionary biology data. All accession numbers for GenBank, TreeBASE, and Dryad must be included in accepted manuscripts before they go to Production. If the data is deposited somewhere else, please provide a link. If the data is culled from published literature, please deposit the collated data in Dryad for the convenience of your readers. Any impediments to data sharing should be brought to the attention of the editors at the time of submission so that appropriate arrangements can be worked out. === Journal of Heredity === The primary data underlying the conclusions of an article are critical to the verifiability and transparency of the scientific enterprise, and should be preserved in usable form for decades in the future. For this reason, Journal of Heredity requires that newly reported nucleotide or amino acid sequences, and structural coordinates, be submitted to appropriate public databases (e.g., GenBank; the EMBL Nucleotide Sequence Database; DNA Database of Japan; the Protein Data Bank; and Swiss-Prot). Accession numbers must be included in the final version of the manuscript. For other forms of data (e.g., microsatellite genotypes, linkage maps, images), the Journal endorses the principles of the Joint Data Archiving Policy (JDAP) in encouraging all authors to archive primary datasets in an appropriate public archive, such as Dryad, TreeBASE, or the Knowledge Network for Biocomplexity. Authors are encouraged to make data publicly available at time of publication or, if the technology of the archive allows, opt to embargo access to the data for a period up to a year after publication. The American Genetic Association also recognizes the vast investment of individual researchers in generating and curating large datasets. Consequently, we recommend that this investment be respected in secondary analyses or meta-analyses in a gracious collaborative spirit. === Molecular Ecology === Molecular Ecology expects that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, Gene Expression Omnibus, TreeBASE, Dryad, the Knowledge Network for Biocomplexity, your own institutional or funder repository, or as Supporting Information on the Molecular Ecology web site. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species. === Nature === Such material must be hosted on an accredited independent site (URL and accession numbers to be provided by the author), or sent to the Nature journal at submission, either uploaded via the journal's online submission service, or if the files are too large or in an unsuitable format for this purpose, on CD/DVD (five copies). Such material cannot solely be hosted on an author's personal or institutional web site. Nature requires the reviewer to determine if all of the supplementary data and methods have been archived. The policy advises reviewers to consider several questions, including: "Should the authors be asked to provide supplementary methods or data to accompany the paper online? (Such data might include source code for modelling studies, detailed experimental protocols or mathematical derivations.) === Science === Science supports the efforts of databases that aggregate published data for the use of the scientific community. Therefore, before publication, large data sets (including microarray data, protein or DNA sequences, and atomic c
FAIR data
FAIR data is data which meets the 2016 FAIR principles of findability, accessibility, interoperability, and reusability (FAIR). The FAIR principles emphasize machine-actionability (i.e., the capacity of computational systems to find, access, interoperate, and reuse data with none or minimal human intervention) because humans increasingly rely on computational support to deal with data as a result of the increase in the volume, complexity, and rate of production of data. The abbreviation FAIR/O data is sometimes used to indicate that the dataset or database in question complies with the FAIR principles and also carries an explicit data‑capable open license. == FAIR principles published by GO FAIR == Findable The first step in (re)using data is to find them. Metadata and data should be easy to find for both humans and computers. Machine-readable metadata are essential for automatic discovery of datasets and services, so this is an essential component of the FAIRification process. F1. (Meta)data are assigned a globally unique and persistent identifier F2. Data are described with rich metadata (defined by R1 below) F3. Metadata clearly and explicitly include the identifier of the data they describe F4. (Meta)data are registered or indexed in a searchable resource Accessible Once the user finds the required data, they need to know how they can be accessed, possibly including authentication and authorisation. A1. (Meta)data are retrievable by their identifier using a standardised communications protocol A1.1 The protocol is open, free, and universally implementable A1.2 The protocol allows for an authentication and authorisation procedure, where necessary A2. Metadata are accessible, even when the data are no longer available Interoperable The data usually need to be integrated with other data. In addition, the data need to interoperate with applications or workflows for analysis, storage, and processing. I1. (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation I2. (Meta)data use vocabularies that follow FAIR principles I3. (Meta)data include qualified references to other (meta)data Reusable The ultimate goal of FAIR is to optimise the reuse of data. To achieve this, metadata and data should be well-described so that they can be replicated and/or combined in different settings. R1. (Meta)data are richly described with a plurality of accurate and relevant attributes R1.1. (Meta)data are released with a clear and accessible data usage license R1.2. (Meta)data are associated with detailed provenance R1.3. (Meta)data meet domain-relevant community standards The principles refer to three types of entities: data (or any digital object), metadata (information about that digital object), and infrastructure. For instance, principle F4 defines that both metadata and data are registered or indexed in a searchable resource (the infrastructure component). === Acceptance and implementation === Before FAIR, a 2007 OECD report was the most influential paper discussing similar ideas related to data accessibility. In January 2014, the Lorentz Centre at Leiden University hosted a workshop entitled "Jointly designing a data FAIRPORT" where the participants first formulated the FAIR principles. After further discussions, they were published in the March 2016 issue of Scientific Data. At the 2016 G20 Hangzhou summit, the G20 leaders issued a statement endorsing the application of FAIR principles to research. Also in 2016, a group of Australian organisations developed a Statement on FAIR Access to Australia's Research Outputs, which aimed to extend the principles to research outputs more generally. In 2017, Germany, Netherlands and France agreed to establish an international office to support the FAIR initiative, the GO FAIR International Support and Coordination Office. Other international organisations active in the research data ecosystem, such as CODATA or Research Data Alliance (RDA) also support FAIR implementations by their communities. FAIR principles implementation assessment is being explored by FAIR Data Maturity Model Working Group of RDA, CODATA's strategic Decadal Programme "Data for Planet: Making data work for cross-domain challenges" mentions FAIR data principles as a fundamental enabler of data driven science. The Association of European Research Libraries recommends the use of FAIR principles. A 2017 paper by advocates of FAIR data reported that awareness of the FAIR concept was increasing among various researchers and institutes, but also, understanding of the concept was becoming confused as different people apply their own differing perspectives to it. Guides on implementing FAIR data practices state that the cost of a data management plan in compliance with FAIR data practices should be 5% of the total research budget. In 2019 the Global Indigenous Data Alliance (GIDA) released the CARE Principles for Indigenous Data Governance as a complementary guide. The CARE principles extend principles outlined in FAIR data to include Collective benefit, Authority to control, Responsibility, and Ethics to ensure data guidelines address historical contexts and power differentials. The CARE Principles for Indigenous Data Governance were drafted at the International Data Week and Research Data Alliance Plenary co-hosted event, "Indigenous Data Sovereignty Principles for the Governance of Indigenous Data Workshop", held 8 November 2018, in Gaborone, Botswana. The lack of information on how to implement the guidelines have led to inconsistent interpretations of them. In January 2020, representatives of nine groups of universities around the world produced the Sorbonne declaration on research data rights, which included a commitment to FAIR data, and called on governments to provide support to enable it. In 2021, researchers identified the FAIR principles as a conceptual component of data catalog software tools, with the other components being metadata management, business context and data responsibility roles. In April 2022, Matthias Scheffler and colleagues argued in Nature that FAIR principles are "a must" so that data mining and artificial intelligence can extract useful scientific information from the data. There have been moves in the geosciences to establish FAIR data by use of decimal georeferencing However, making data (and research outcomes) FAIR is a challenging task, and it is challenging to assess the FAIRness. In 2020, the FAIR Data Maturity Model Working Group published a set of guidelines for assessing "FAIRness".
StoredIQ
StoredIQ was a company founded for information lifecycle management (ILM) of unstructured data. Founded in 2001 as Deepfile in Austin, Texas by Jeff Erramouspe, Jeff Bone, Russell Turpin, Rudy Rouhana, Laura Arbilla and Brett Funderburg, the company changed its name in 2005 to StoredIQ. It continued to operate successfully for over a decade until it was acquired in 2012 by IBM. It now serves as a platform for IBM's information life cycle governance, big data governance and enterprise content management technologies. StoredIQ was awarded five patents by the USPTO. The first, originally filed in 2003, enabled unstructured data in file systems to be manipulated in a similar way to information stored in databases. Subsequent patents built upon the patented actionable file system with further enhancements specific to Enterprise Policy Management and expanding the reach of StoredIQ's management capability all the way to individual desktops. In 2008 StoredIQ was recognized as "Best in Compliance" by Network Products Guide. At the same time, StoredIQ was being recognized as a "Top 5 Provider" by the prestigious Socha-Gelbmann eDiscovery survey. There were takeover negotiations with EMC Corporation, initially a strategic investor in StoredIQ, however, the company rejected the approach, leaving EMC to acquire a competitor. The company published a whitepaper titled The Truth About Big Data. This promotion combined with StoredIQ's patented technology led to IBM selecting StoredIQ as the basis for some products.
Douglas Parkhill
Douglas F. Parkhill is a Canadian technologist and former research minister, best known for his pioneering work on what is now called cloud computing, and his work on Canada's Telidon videotex project. He started working at the Canadian ministry of Communications (now part of the Department of Trade and Industry) in 1969, having previously worked at the Mitre Corporation. He was responsible for many activities in communications satellites, computer communications, command and control systems and telecommunications. He was winner of the Treasury Board of Canada Secretariat's Outstanding Achievement award in 1982, the Conestoga shield for services to government and industry in computer communications research and development, the Touche Ross award for Telidon development. He was an author of several publications including the 1966 book, The Challenge of the Computer Utility. In the book, Parkhill thoroughly explored many of the modern-day characteristics of cloud computing (elastic provisioning through a utility service) as well as the comparison to the electricity industry and the use of public, private, government and community forms. The book won the McKinsey Foundation award for distinguished contributions to management literature. He worked with Dave Godfrey, the Canadian writer and novelist on a later book Gutenberg two about the social and political meaning of computer technology. He was in charge of research at the Federal Department of Communications at the time when the department was funding development of the Telidon videotext system, was heavily involved in promoting the system, and had overall control of the program. In a radio broadcast in 1980, he outlined some of the potential of the system, from financial information, to theatre reservations, with the ability to pay and print out tickets from the system. He later documented the history of the Telidon project, and the history of videotext in general. == Publications == The Challenge of the Computer Utility, Addison-Wesley, 1966, ISBN 0-201-05720-4 edited with Dave Godfrey, Gutenberg Two: The New Electronics and Social Change, Press Porcepic, 1979, ISBN 0-88878-191-1 The Beginning of a Beginning. Ottawa; Department of Communications, 1987. A history of the Telidon project.
Subject (documents)
In library and information science documents (such as books, articles and pictures) are classified and searched by subject – as well as by other attributes such as author, genre and document type. This makes "subject" a fundamental term in this field. Library and information specialists assign subject labels to documents to make them findable. There are many ways to do this and in general there is not always consensus about which subject should be assigned to a given document. To optimize subject indexing and searching, we need to have a deeper understanding of what a subject is. The question: "what is to be understood by the statement 'document A belongs to subject category X'?" has been debated in the field for more than 100 years (see below) == Theoretical view == === Charles Ammi Cutter (1837–1903) === For Cutter the stability of subjects depends on a social process in which their meaning is stabilized in a name or a designation. A subject "referred [...] to those intellections [...] that had received a name that itself represented a distinct consensus in usage" (Miksa, 1983a, p. 60) and: the "systematic structure of established subjects" is "resident in the public realm" (Miksa, 1983a, p. 69); "[s]ubjects are by their very nature locations in a classificatory structure of publicly accumulated knowledge (Miksa, 1983a, p. 61). Bernd Frohmann adds: "The stability of the public realm in turn relies upon natural and objective mental structures which, with proper education, govern a natural progression from particular to general concepts. Since for Cutter, mind, society, and SKO [Systems of Knowledge Organization] stand one behind the other, each supporting each, all manifesting the same structure, his discursive construction of subjects invites connections with discourses of mind, education, and society. The Dewey Decimal Classification (DDC), by contrast, severs those connections. Melvil Dewey emphasized more than once that his system maps no structure beyond its own; there is neither a "transcendental deduction" of its categories nor any reference to Cutter's objective structure of social consensus. It is content-free: Dewey disdained any philosophical excogitation of the meaning of his class symbols, leaving the job of finding verbal equivalents to others. His innovation and the essence of the system lay in the notation. The DDC is a poorly semiotic system of expanding nests of ten digits, lacking any referent beyond itself. In it, a subject is wholly constituted in terms of its position in the system. The essential characteristic of a subject is a class symbol which refers only to other symbols. Its verbal equivalent is accidental, a merely pragmatic characteristic... .... The conflict of interpretations over "subjects" became explicit in the battles between "bibliography" (an approach to subjects having much in common with Cutter's) and Dewey's "close classification". William Fletcher spoke for the scholarly bibliographer.... Fletcher's "subjects", like Cutter's, referred to the categories of a fantasized, stable social order, whereas Dewey's subjects were elements of a semiological system of standardized, techno-bureaucratic administrative software for the library in its corporate, rather than high culture, incarnation". (Frohmann, 1994, 112–113). Cutter's early view on what a subject is, is probably wiser than most understandings that dominated the 20th century – and also the understanding reflected in the ISO-standard quoted below. The early statements quoted by Frohmann indicate that subjects are somehow shaped in social processes. When that is said, it should be added that they are not particularly detailed or clear. We only get a vague idea of the social nature of subjects. === S. R. Ranganathan (1892–1972) === A classification system with an explicit theoretical foundation is Ranganathan's Colon Classification. Ranganathan provided an explicit definition of the concept of "subject": Subject – an organized body of ideas, whose extension and intension are likely to fall coherently within the field of interests and comfortably within the intellectual competence and the field of inevitable specialization of a normal person. A related definition is given by one of Ranganathan's students: A subject is an organized and systematized body of ideas. It may consist of one idea or a combination of several... Ranganathan's definition of "subject" is strongly influenced by his Colon Classification system. The colon system is based on the combination of single elements from facets to subject designation. This is the reason why the combined nature of subjects are emphasized so strongly. It leads, however, to absurdities such as the claim that gold cannot be a subject (but is alternatively termed "an isolate"). This aspect of the theory has been criticized by Metcalfe (1973, p. 318). Metcalfe's skepticism regarding Ranganathan's theory is formulated in hard words (op. cit., p. 317): "This pseudo-science imposed itself on British disciples from about 1950 on...". It seems unacceptable that Ranganathan defines the word subject in a way that favors his own system. A scientific concept like "subject" should make it possible to compare different ways of establishing access to information. Whether or not subjects are combined or not should be examined once their definition has been given, it should not determined a priori, in the definition. Besides the emphasis on the combined, organizing and systematizing nature of subjects contains Ranganathan's definition of subject the pragmatic demand, that a subject should be determined in a way that suits a normal person's competency or specialization. Again we see a strange kind of wishful thinking mixing a general understanding of a concept with demands put by his own specific system. One thing is what the word subject means, quite another issue is how to provide subject descriptions that fulfill demands such as the specificity of a given information retrieval language which fulfill demands put on the system, such as precision and recall. If researchers too often define terms in ways that favor specific kinds of systems, that are such definitions not useful to provide more general theories about subjects, subject analysis and IR. Among other things are comparative studies of different kinds of systems made difficult. Based on these arguments, as well as additional arguments which have been used in the literature, we may conclude that Ranganathan's definition of the concept "subject" is not suited for scientific use. Like the definition of "subject" given by the ISO-standard for topic maps, may Ranganathan's definition be useful within his own closed system. The purpose of a scientific and scholarly field is, however, to examine the relative fruitfulness of systems such as topic maps and Colon Classification. For such purpose is another understanding of "subject" necessary. === Patrick Wilson (1927–2003) === In his book Wilson (1968) examined – in particular by thought experiments – the suitability of different methods of examining the subject of a document. The methods were: identifying the author's purpose for writing the document, weighing the relative dominance and subordination of different elements in the picture, which the reading imposes on the reader, grouping or count the document's use of concepts and references, construing a set of rules for selecting elements deemed necessary (as opposed to unnecessary) for the work as a whole. Patrick Wilson shows convincingly that each of these methods are insufficient to determine the subject of a document and is led to conclude ( p. 89): "The notion of the subject of a writing is indeterminate..." or, on p. 92 (about what users may expect to find using a particular position in a library classification system): "For nothing definite can be expected of the things found at any given position". In connection to the last quote has Wilson an interesting footnote in which he writes that authors of documents often use terms in ambiguous ways ("hostility" is used as an example). Even if the librarian could personally develop a very precise understanding of a concept, he would be unable to use it in his classification, because none of the documents use the term in the same precise way. Based on this argumentation is Wilson led to conclude: "If people write on what are for them ill-defined phenomena, a correct description of their subjects must reflect the ill-definedness". Wilson's concept of subject was discussed by Hjørland (1992) who found that it is problematic to give up the precise understanding of such a basic term in LIS. Wilson's arguments led him to an agnostic position which Hjørland found unacceptable and unnecessary. Concerning the authors' use of ambiguous terms, the role of the subject analysis is to determine which documents would be fruitful for users to identify whether or not the documents use one or another term or whether a given term i