Operationalizing anthropological theory: four techniques to simplify networks of co-occurring ethnographic codes

The use of data and algorithms in the social sciences allows for exciting progress, but also poses epistemological challenges. Operations that appear innocent and purely technical may profoundly influence final results. Researchers working with data can make their process less arbitrary and more accountable by making theoretically grounded methodological choices. We apply this approach to the problem of simplifying networks representing ethnographic corpora, in the interest of visual interpretation. Network nodes represent ethnographic codes, and their edges the co-occurrence of codes in a corpus. We introduce and discuss four techniques to simplify such networks and facilitate visual analysis. We show how the mathematical characteristics of each one are aligned with an identifiable approach in sociology or anthropology: structuralism and post-structuralism; identifying the central concepts in a discourse; and discovering hegemonic and counter-hegemonic clusters of meaning. We then provide an example of how the four techniques complement each other in ethnographic analysis

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

<p>Abstract</p> <p>Background</p> <p>In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user.</p> <p>Results</p> <p>We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects.</p> <p>Conclusion</p> <p>Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.</p

PORGY: Strategy-Driven Interactive Transformation of Graphs

This paper investigates the use of graph rewriting systems as a modelling tool, and advocates the embedding of such systems in an interactive environment. One important application domain is the modelling of biochemical systems, where states are represented by port graphs and the dynamics is driven by rules and strategies. A graph rewriting tool's capability to interactively explore the features of the rewriting system provides useful insights into possible behaviours of the model and its properties. We describe PORGY, a visual and interactive tool we have developed to model complex systems using port graphs and port graph rewrite rules guided by strategies, and to navigate in the derivation history. We demonstrate via examples some functionalities provided by PORGY.Comment: In Proceedings TERMGRAPH 2011, arXiv:1102.226

FactSage thermochemical software and databases, 2010–2016

The FactSage computer package consists of a series of information, calculation and manipulation modules that enable one to access and manipulate compound and solution databases. With the various modules running under Microsoft Windows® one can perform a wide variety of thermochemical calculations and generate tables, graphs and figures of interest to chemical and physical metallurgists, chemical engineers, corrosion engineers, inorganic chemists, geochemists, ceramists, electrochemists, environmentalists, etc. This paper presents a summary of the developments in the FactSage thermochemical software and databases during the last six years. Particular emphasis is placed on the new databases and developments in calculating and manipulating phase diagrams

Beyond associations:Sensitivity to structure in pre-schoolers' linguistic predictions

One influential view of language acquisition is that children master structural generalizations by making and learning from structure-informed predictions. Previous work has shown that from 3 years of age children can use semantic associations to generate predictions. However, it is unknown whether they can generate predictions by combining these associations with knowledge of linguistic structure. We recorded the eye movements of pre-schoolers while they listened to sentences such as Pingu will ride the horse. Upon hearing ride, children predictively looked at a horse (a strongly associated and plausible patient of ride), and mostly ignored a cowboy (equally strongly associated, but an implausible patient). In a separate experiment, children did not rapidly look at the horse when they heard You can show Pingu … “riding”, showing that they do not quickly activate strongly associated patients when there are no structural constraints. Our findings demonstrate that young children’s predictions are sensitive to structure, providing support for predictive-learning models of language acquisition