Erving Was a Brilliant Scholar and a Mensch

This interview with Joseph Gusfield, Professor Emeritus of Sociology at the the University of California, San Diego, was recorded over the phone on December 19, 2008. Dmitri Shalin transcribed the interview, after which Dr. Gusfield edited the transcript and gave his approval for posting the present version in the Erving Goffman Archives. Breaks in the conversation flow are indicated by ellipses. Supplementary information and additional materials inserted during the editing process appear in square brackets. Undecipherable words and unclear passages are identified in the text as “[?]”

Efficient chaining of seeds in ordered trees

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

<p>Abstract</p> <p>Background</p> <p>The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters.</p> <p>Methods</p> <p>In this work, we propose <it>e</it>-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters.</p> <p>Results</p> <p>We present results in real data showing the effectiveness of <it>e</it>-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in <it>Saccharomyces cerevisiae </it>in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series.</p> <p>Discussion</p> <p>The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to efficiently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms.</p> <p>Availability</p> <p>A prototype implementation of the algorithm coded in Java together with the dataset and examples used in the paper is available in <url>http://kdbio.inesc-id.pt/software/e-ccc-biclustering</url>.</p

The powers of problem definition: The case of government paperwork

Problem definition is a package of ideas that includes, at least implicitly, an account of the causes and consequences of undesirable circumstances and a theory about how to improve them. As such, it serves as the overture to policymaking, as an integral part of the process of policymaking, and as a policy outcome. In each of these roles it seems to exert influence on government action. Distinguishing among the roles clarifies the nature of that influence. A case study examines the transition from one problem definition to another in the domain of information collection by the federal government. The rise of the Paperwork Reduction definition illustrates the variety of ways in which problem definition has powerful consequences.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45448/1/11077_2004_Article_BF00141381.pd

Significations disputées

Que se passe-t-il quand on qualifie une condition ou une situation donnée de « problème social » ? Lui donner le nom de « problème social » revient à la cadrer comme porteuse de conduites pathologiques ou problématiques. Cela revient à minimiser le caractère « naturel » ou « normal » de ces activités et à les définir comme opposées à l’intérêt public, c’est-à-dire comme une situation qui devrait être éradiquée ou atténuée par une action publique. Les « problèmes sociaux » se distinguent du ca..

Une passerelle entre deux mondes. Contribution de Kenneth Burk l'étude de Paction sociale

The work of Kenneth Burke has a persistent even though limited impact on the social sciences. He has never been recognized as one of the major theorists of sociology yet for decades has deeply influenced anthropologists, sociologists and political scientists. Structuralism, linguistic analysis, critical theory, symbolic anthropology and cognitive sociology have all focused on Burke's specific themes from different angles: an understanding of social action as dramatic in form, language being of central importance in such a theory, the development of a rhetoric built around the complementary roles of the performer and his audience, the performative character of human action. While Burke's first readers were theorists and literary critics, his dialectical method and the theory of "dramatism" he developed in the 1930s and 1940s is now being applied in much empirical research. In this paper Joseph Gusfield considers how Burke has in effect undermined the traditional frontiers between literature and social science and succeeded in erecting a "bridge over separated lands".L'oeuvre de Kenneth Burke exerce sur les sciences sociales une influence à la fois marginale et persistante. Burke n'a jamais été reconnu comme l'un des grands théoriciens de la sociologie. Et pourtant, pendant des décennies, il a profondément influencé anthropologues, politologues et sociologues. Le structuralisme, l'analyse linguistique, la théorie critique, l'anthropologie symbolique, la sociologie cognitive, ont exploré de diverses façons les thèmes privilégiés de Burke : importance du langage pour une théorie de l'action sociale conçue en termes dramaturgiques ; constitution d'une rhétorique faisant intervenir les rôles complémentaires de l'acteur et de son public ; caractère performatif de toute action humaine. Développées dans les années 30 et 40, la méthode dialectique de Burke et sa théorie du « dramatisme » dépassent un public initial de théoriciens et de critiques littéraires, pour influencer nombre de recherches empiriques. L'auteur s'interroge ici sur les raisons d'un succès qui déplace les frontières traditionnellement établies entre littérature et sciences sociales, constituant ainsi « une passerelle entre deux mondes »