The Art of Counting: Scoring and ranking co-occurrences in literature

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Lars Juhl Jensen

The Art of Counting: Scoring and ranking co-occurrences in literature

Lars Juhl Jensen
The Art of Counting
Scoring and ranking co-occurrences in
literature

score entity co-occurrences

rank entities for a query

co-occurrence scoring

named entity recognition

diseases

genes

count co-occurrences

what should we count?

within documents

within paragraphs

within sentences

weighted sum

famous diseases/genes

observed / expected

single co-occurrences

weighted combination

hard to interpret

z-score transformation

no change to ranking

diseases.jensenlab.org Frankild et al., Methods, 2015

tissue expression

tissues.jensenlab.org Santos et al., PeerJ, 2015

subcellular localization

Binder et al., Database, 2014compartments.jensenlab.org

query-based ranking

rank named entities

PubMed query

query has no position

only count documents

rank i with respect to j

simplified scoring scheme

j terms become constant

no change to ranking

implementation

PubMed query

NCBI E-utilities

PMID list

relational database

precompute NER results

precompute all Ci

single SQL query

takes only seconds

REST API

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Context. WASP-76 b has been a recurrent subject of study since the detection of a signature in high-resolution transit spectroscopy data indicating an asymmetry between the two limbs of the planet. The existence of this asymmetric signature has been confirmed by multiple studies, but its physical origin is still under debate. In addition, it contrasts with the absence of asymmetry reported in the infrared (IR) phase curve. Aims. We provide a more comprehensive dataset of WASP-76 b with the goal of drawing a complete view of the physical processes at work in this atmosphere. In particular, we attempt to reconcile visible high-resolution transit spectroscopy data and IR broadband phase curves. Methods. We gathered 3 phase curves, 20 occultations, and 6 transits for WASP-76 b in the visible with the CHEOPS space telescope. We also report the analysis of three unpublished sectors observed by the TESS space telescope (also in the visible), which represents 34 phase curves. Results. WASP-76 b displays an occultation of 260±11 and 152±10 ppm in TESS and CHEOPS bandpasses respectively. Depending on the composition assumed for the atmosphere and the data reduction used for the IR data, we derived geometric albedo estimates that range from 0.05 ± 0.023 to 0.146 ± 0.013 and from <0.13 to 0.189 ± 0.017 in the CHEOPS and TESS bandpasses, respectively. As expected from the IR phase curves, a low-order model of the phase curves does not yield any detectable asymmetry in the visible either. However, an empirical model allowing for sharper phase curve variations offers a hint of a flux excess before the occultation, with an amplitude of ∼40 ppm, an orbital offset of ∼−30◦ , and a width of ∼20◦ . We also constrained the orbital eccentricity of WASP-76 b to a value lower than 0.0067, with a 99.7% confidence level. This result contradicts earlier proposed scenarios aimed at explaining the asymmetry observed in high-resolution transit spectroscopy. Conclusions. In light of these findings, we hypothesise that WASP-76 b could have night-side clouds that extend predominantly towards its eastern limb. At this limb, the clouds would be associated with spherical droplets or spherically shaped aerosols of an unknown species, which would be responsible for a glory effect in the visible phase curves.

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The Art of Counting: Scoring and ranking co-occurrences in literature

1. Lars Juhl Jensen The Art of Counting Scoring and ranking co-occurrences in literature

4. score entity co-occurrences

5. rank entities for a query

6. co-occurrence scoring

7. named entity recognition

10. count co-occurrences

11. what should we count?

12. within documents

13. within paragraphs

14. within sentences

15. weighted sum

16.

17. famous diseases/genes

18. observed / expected

19.

20. single co-occurrences

21. weighted combination

22.

23. hard to interpret

24. z-score transformation

25. no change to ranking

26. diseases.jensenlab.org Frankild et al., Methods, 2015

27. tissue expression

28. tissues.jensenlab.org Santos et al., PeerJ, 2015

29. subcellular localization

30. Binder et al., Database, 2014compartments.jensenlab.org

31. query-based ranking

32. rank named entities

33. i

34. PubMed query

35. j

36. query has no position

37. only count documents

38.

39.

40. rank i with respect to j

41. simplified scoring scheme

42. j terms become constant

43.

44.

45. no change to ranking

46. implementation

47. PubMed query

48. NCBI E-utilities

50. relational database

51. precompute NER results

52. precompute all Ci

53. single SQL query

54. takes only seconds