Word Embeddings for Entity-annotated Texts

Learned vector representations of words are useful tools for many information retrieval and natural language processing tasks due to their ability to capture lexical semantics. However, while many such tasks involve or even rely on named entities as central components, popular word embedding models have so far failed to include entities as first-class citizens. While it seems intuitive that annotating named entities in the training corpus should result in more intelligent word features for downstream tasks, performance issues arise when popular embedding approaches are naively applied to entity annotated corpora. Not only are the resulting entity embeddings less useful than expected, but one also finds that the performance of the non-entity word embeddings degrades in comparison to those trained on the raw, unannotated corpus. In this paper, we investigate approaches to jointly train word and entity embeddings on a large corpus with automatically annotated and linked entities. We discuss two distinct approaches to the generation of such embeddings, namely the training of state-of-the-art embeddings on raw-text and annotated versions of the corpus, as well as node embeddings of a co-occurrence graph representation of the annotated corpus. We compare the performance of annotated embeddings and classical word embeddings on a variety of word similarity, analogy, and clustering evaluation tasks, and investigate their performance in entity-specific tasks. Our findings show that it takes more than training popular word embedding models on an annotated corpus to create entity embeddings with acceptable performance on common test cases. Based on these results, we discuss how and when node embeddings of the co-occurrence graph representation of the text can restore the performance.Comment: This paper is accepted in 41st European Conference on Information Retrieva

Advancing the Use of Games as a Model for Scientific Practice

Science is similar to a game, as both involve rules-based participation in search of optimal outcomes. Supported by key texts in history and philosophy of science, the authors propose a game-based model for understanding scientific inquiry and practice, particularly through computational resources. They conclude that this model creates space for more speculative and reflective approaches to scientific practice and can contribute to the design and development of better scientific software, simulation and visualization

Pilot Study of CYP2B6 Genetic Variation to Explore the Contribution of Nitrosamine Activation to Lung Carcinogenesis

We explored the contribution of nitrosamine metabolism to lung cancer in a pilot investigation of genetic variation in CYP2B6, a high-affinity enzymatic activator of tobacco-specific nitrosamines with a negligible role in nicotine metabolism. Previously we found that variation in CYP2A6 and CHRNA5-CHRNA3-CHRNB4 combined to increase lung cancer risk in a case-control study in European American ever-smokers (n = 860). However, these genes are involved in the pharmacology of both nicotine, through which they alter smoking behaviours, and carcinogenic nitrosamines. Herein, we separated participants by CYP2B6 genotype into a high- vs. low-risk group (*1/*1 + *1/*6 vs. *6/*6). Odds ratios estimated through logistic regression modeling were 1.25 (95% CI 0.68-2.30), 1.27 (95% CI 0.89-1.79) and 1.56 (95% CI 1.04-2.31) for CYP2B6, CYP2A6 and CHRNA5-CHRNA3-CHRNB4, respectively, with negligible differences when all genes were evaluated concurrently. Modeling the combined impact of high-risk genotypes yielded odds ratios that rose from 2.05 (95% CI 0.39-10.9) to 2.43 (95% CI 0.47-12.7) to 3.94 (95% CI 0.72-21.5) for those with 1, 2 and 3 vs. 0 high-risk genotypes, respectively. Findings from this pilot point to genetic variation in CYP2B6 as a lung cancer risk factor supporting a role for nitrosamine metabolic activation in the molecular mechanism of lung carcinogenesis

Position Paper: Collaborative Gamification Design for Scientific Software

Gamification, a design trend that is extensively applied to education and citizen science, is regarded as a means to improve scientific software usability. However, development and use of scientific software have special needs and characteristics that might present design challenges. Our position is that gamifi-cation and usability design for scientific software should be facilitated by an open, collaborative design process supported by conversational media. We believe this approach is compatible with qualities often attributed to computational science community re-garding openness and collaboration between members of varied professional backgrounds. Through an illustrative scenario, we ex-emplify the use of conversational media for collaborative design. We expect the synergy between collaborators to result in better us-ability, greater user acceptance, and adequacy to requirements, obtaining optimal design solutions in a sustainable way

The Lens of the Lab: Design Challenges in Scientific Software

Playful and gameful design could improve the quality of scientific software. However, literature about gamification methods for that particular type of software is presently scarce. As an effort to fill that gap, this paper introduces a set of design challenges and opportunities that should be informative to professionals approaching the area. This research is based on literature review on scientific software development, also contemplating material on the gamification of science, software, and work. From the gathered information, we identify, map, and discuss key aspects of development and use of professional scientific software. Those findings are, then, formatted as a Design Lens—a set of questions designers should ask themselves to gain insight, from a particular perspective, on their work. We propose the Lens of the Lab as a design lens to support designers working in collaboration with scientists and software engineers in professional scientific software initiatives

Biologie et écologie du Lérot Eliomys quercinus L. dans les Hautes-Alpes

Dans la région de Rriançon (Hautes-Alpes), le Lérot Eliomys quercinus est un des principaux constituants de la faune de Ron geurs de tous les types de forêts. La sortie d’hibernation se produit à la tin de la première quinzaine de mai. Les individus sont aussitôt sexuellement actifs, les mises bas ont lieu de la mi-juin à la tin juillet. L’entrée en hibernation débute à la mi-septembre et intéresse d’abord les adultes. Du fait de la faible durée de la vie active, il ne semble pas y avoir d’estivation. La saison de reproduction étant bien loca lisée dans le temps, il est facile d’estimer l’âge des individus et de tracer leur courbe de croissance. Il est à remarquer que la croissance n’est pas terminée lors de l’entrée en hibernation, et qu’elle se poursuit au printemps suivant. Les types de forêts les plus fréquentées sont les boisements mixtes, Pin sylvestre - Mélèze et Feuillus - Mélèze de l’étage mon tagnard (1 400 à 1 700 m d’altitude). Les facteurs du milieu les plus favorables sont la présence de substrat rocheux et d’une végétation herbacée claire accompagnée d’arbrisseaux nains. Le régime alimentaire est en grande partie composé d’insec tes, surtout de larves de Lépidoptères.Around Briançon, Hautes-Alpes, France, the Garden dormouse Eliomys quercinus is one of the most common rodents in all types of forests. When they arouse from hibernation these animals are immediately active sexually. Parturition takes place from mid-June to the end of July. Dormice enter hibernation in mid- September, first the adult animals and then the younger ones. Owing to the short lenght of their active life, there is apparently no estivation in this part of France. The breeding season is temporally well defined. It is therefore easy to estimate the age of the animals and to establish their growth curve. Sexual maturity is not achieved when young of the year enter hibernation ; they do not become mature before the next spring. Garden dormice live usually in mixed forests of Pine (Pinus sylvestris) and Larch, and of Larch and deciduous trees, at an altitude of 1 400-1 700 m above sea-level. The most important parameters of their environment are the presence of a rocky substrate and of a sparse grass layer with dwarf shrubs. Garden dormice are mostly insectivorous and are particularly fond of caterpillars and pupae

A propos de l’étude des micromammifères par l’analyse des pelotes de rapaces. intérêt et limites de la méthode

Les auteurs exposent les divers problèmes concernant les micromammifères qui sont susceptibles d’être étudiés par analyse des pelotes de rapaces, en particulier de la Chouette Effraie ( Tyto alba). C’est d’abord la répartition géographique qui peut être étu diée de façon précise à partir du moment où l’on dispose de lots suffisamments bien répartis et suffisamment nombreux ; en outre il est possible de déterminer la position relative de l’espèce étudiée dans chaque région en la rapportant au groupe des espèces homo logues ; on montre ici l’exemple de Microtus arvalis étudié au sein d’un groupe d’espèces homologues comprenant M. arvalis, M. agrestis et Clethrionomys glareolus. Il apparaît que la portée des résultats doit être soigneusement délimitée : ainsi par les pelotes de l’Effraye on ne peut espérer définir que la microfaune des zones découvertes d’altitude peu élevée où elle chasse, et, pour une espèce donnée, la répartition en région forestière ou en haute montagne doit être étudiée d’une autre façon. Les espèces très rares dans les pelotes ne le sont pas forcément dans la nature, et l’on doit s’en assurer par d’autres méthodes de recherches. Si l’on possède pour une région donnée un certain nombre de gros échantillons de proies correspondants à des biotopes de chasse bien distincts de l’Effraye, il est possible d’en tirer des enseigne ments sur Y habitat des micromammifères ; mais les renseigne ments obtenus ainsi ne sont pas aussi précis que par piégeage puisqu’on ne peut définir que le « paysage de chasse » du rapace et non le microbiotope du mammifère ; néanmoins on peut arriver à définir les communautés de micromammifères correspondant à divers paysages végétaux (naturels ou agricoles) ce qui n’est pas négligeable. Des exemples sont donnés pour la région camar- guaise entre autres. La densité des populations ne peut être déterminée de façon absolue par l’étude des pelotes, mais dans certains cas il est pos sible de suivre l’évolution des populations d’une ou plusieurs espèces ; cela impose au préalable d’avoir rassemblé par d’autres moyens quelques renseignements sur le cycle annuel d’abondance des espèces étudiées ; en outre il ne doit pas y avoir une espèce constamment très abondante relativement aux autres car dans ce cas on constate que son abondance relative dans les pelotes reste à peu près constante. Enfin l’examen détaillé des éléments osseux trouvés permet dans certains cas de déterminer le sexe et l’âge des mammifères présents ; la structure de population ainsi trouvée peut alors être comparée à la structure réelle établie par piégeage et l’on obtient ainsi une idée de la façon dont s’exerce la prédation sur une population. Le travail sur ces divers problèmes ne fait que commencer et l’accent doit être mis en priorité sur l’étude de la répartition géo graphique encore très insuffisamment connue pour les Mammi fères de France.The authors deal with various problems concerning small mammals which can be investigated by analysis of the pellets of predators, particularly the Barn Owl ( Tyto alba). First, accurate information can be obtained on geographical distribution provided that sufficient material from a wide area is available ; it is further possible to determine the relevant impor tance of a particular species in each region of the country in relation to other homologous species of a group. The example chosen is that of Microtus arvalis considered within the group comprising itself, M. agrestis and Clethrionomys glareolus. The scope of results is however strictly limited. Thus Barn Owls only hunt in open country at low or medium altitudes, and other methods would have to be used to determine the distribution in forests and high mountains of their prey species. Moreover, species seldom found in pellets are not necessarily rare, and here again the real situation can only be verified by other means. Secondly, granted a large sample of pellets from the various distinct biotopes hunted over by the Barn Owl, it is possible to draw some conclusions on habitat preferences of small mammals