Large-scale entity representation learning for biomedical relationship extraction

Motivation The automatic extraction of published relationships between molecular entities has important applications in many biomedical fields, ranging from Systems Biology to Personalized Medicine. Existing works focused on extracting relationships described in single articles or in single sentences. However, a single record is rarely sufficient to judge upon the biological correctness of a relation, as experimental evidence might be weak or only valid in a certain context. Furthermore, statements may be more speculative than confirmative, and different articles often contradict each other. Experts therefore always take the complete literature into account to take a reliable decision upon a relationship. It is an open research question how to do this effectively in an automatic manner. Results We propose two novel relation extraction approaches which use recent representation learning techniques to create comprehensive models of biomedical entities or entity-pairs, respectively. These representations are learned by considering all publications from PubMed mentioning an entity or a pair. They are used as input for a neural network for classifying relations globally, i.e. the derived predictions are corpus-based, not sentence- or article based as in prior art. Experiments on the extraction of mutation–disease, drug–disease and drug–drug relationships show that the learned embeddings indeed capture semantic information of the entities under study and outperform traditional methods by 4–29% regarding F1 score. Availability and implementation Source codes are available at: https://github.com/mariosaenger/bio-re-with-entity-embeddings. Supplementary information Supplementary data are available at Bioinformatics online.

Tropical Darwin on Screen: Critiquing national values using urban frontier tropes in Charlie’s Country and Last Cab to Darwin.

Australia’s northern-most tropical city of Darwin has a strong presence in the domestic and international touristic imagination as a tropical escape destination – a small city poised on the edge of outstanding natural beauty – yet in national cinematic representations Darwin is often presented as a frontier zone, whether these tropes are pivoted around culture or nature. I would like to take up this idea of the city of Darwin as special and distinctive in the national imaginary that is discernible in recent Australian cinema, an idea that I show extends to the city’s representation in theatre and literature. This paper performs a close textual reading of the city’s recent representation in two high profile Australian feature films, Charlie’s Country (Rolf de Heer, 2013) and Last Cab to Darwin (Jeremy Sims, 2015). These are films that employ compassionate, humanistic themes, each maintaining a strong focus on main characters who find themselves both marginalized and neglected within the broader mechanisms of Australian society: hence each film is simultaneously performing the secondary work of critiquing Australian culture. In both films, I show how the tropical city of Darwin operates as a space of difference, but unlike the contemporary tourism marketing that simplistically brands the region as a “site of desire”, here we find two unique critiques of Australian law and society that work to show the ethical frontiers of legislation and of human sovereignty.

Can Civil Society Organizations Solve the Crisis of Partisan Representation in Latin America?

This article takes up the question of whether civil society organizations (CSOs) can and do act as mechanisms of representation in times of party crisis. It looks at recent representation practices in Argentina, Bolivia, and Brazil, three countries where political parties have experienced sharp crises after several decades of mixed reviews for their party systems. At such moments, any replacement of parties by CSOs should be especially apparent. This study concludes that the degree of crisis determines the extent that CSOs' representative functions replace partisan representation, at least in the short term. Where systems show signs of re-equilibration, CSOs offer alternative mechanisms through which citizens can influence political outcomes without seeking to replace parties. Where crisis is profound, CSOs claim some of the basic party functions but do not necessarily solve the problems of partisan representation.

The South American Military and (Re)Democratization: Professional Thought and Self-Perception

If a medal were to be struck in commemoration of Latin America's successful survival of the 20th century, la cava might bear a representation of democracy and el sello that of authoritarianism. These alternatives have characterized all attempts to arrive at political consensus for the past hundred years and more.The current version of the region's perpetual dichotomous nature has been called (re)democratization. In South America it has replaced professional militarism, the most recent representation of authoritarianism, and threatens to affect traditional democratic practices in countries spared the military incursions of the 1964-1989 quarter-century. To the north, (re)democratization challenges both traditional authoritarianism and Marxism-Leninism.(Re)democratization is a transitional process in which the polity shifts from one with minimal partisan and popular participation back to one based on (ever more maximized) pluralistic participation, usually characterized by meaningful elections, separation of state powers, constitutional order, rule of law, respect for human rights, and civilian regulation of armed force.

A New Plea for the Separation of Ireland

The most recent representation of “British” economic development over the century from 1855, as given in Kuznets’ Modern Economic Growth, does not suggest much vitality in this important economy. This representation is not new. Since it became fashionable to villify the “Britain” of the 1950's and 1960's as the laggard country of Europe, attempts have been made to justify or rationalize recent British performance by claiming that recent slow growth rates have been long established. The justification is based merely on the fable of the tortoise and the hare: slow but steady growth in Britain versus the erratic path of foreigners. Kuznets’ picture of Britain over the past century would, however, suggest a country in which population growth competed only with France for lowest place among developed countries; omitting Netherlands from his list because of its limited period, Kuznets showed that the decade average rate of increase of British gross product, at 21.1 percent, was third lowest and only slightly above that of France with its special population experience; and British increase in product per head, at 14.1 percent decade average, ranked only above that of Australia, with its very low rate of growth at 8 percent. No race was being won here; rather the judgment on the recent past, from the perspective of a century of growth, is that Britain has always had it so bad. The question is whether this perspective is open to reasonable doubt.