Automatic figure ranking and user interfacing for intelligent figure search

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Yu, Hong ^a,b   Liu, Feifan ^b   Ramesh, Balaji Polepalli ^a,b  

^a UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

^b University of Wisconsin Milwaukee   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; CONTROLLED STUDY; EVALUATION; HUMAN; HYPOTHESIS; INFORMATION PROCESSING; NATURAL LANGUAGE PROCESSING; NONHUMAN; ONLINE SYSTEM; PREDICTION; PUBLISHING; RESEARCH; SCIENTIST; SEARCH ENGINE; AUTOMATION; THEORETICAL MODEL;

AUTOMATION; MODELS, THEORETICAL; USER-COMPUTER INTERFACE;

EID: 78049274221     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012983     Document Type: Article

References (52)

1. Yu H, Lee M (2006) Accessing bioscience images from abstract sentences. Bioinformatics 22: e547-e556.
2. Murphy RF, Velliste M, Yao J, Porreca G (2001) Searching online journals for fluorescence microscope images depicting protein subcellular location patterns. In: IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE). pp 119-128.
3. Kou Z, Cohen WW, Murphy RF (2007) A stacked graphical model for associating sub-images with sub-captions. Pac Symp Biocomput. pp 257-268.
4. Yu H, Lee M (2006) BioEx: a novel user-interface that accesses images from abstract sentences. In: HLT-NAACL. New York, USA.
5. Demner-Fushman D, Antani S, Simpson M, Thoma GR (2009) Annotation and retrieval of clinically relevant images. International Journal of Medical Informatics.
6. Shatkay H, Chen N, Blostein D (2006) Integrating image data into biomedical text categorization. Bioinformatics 22: e446-e453.
7. Hearst MA, Divoli A, Guturu H, Ksikes A, Nakov P, et al. (2007) BioText search engine: beyond abstract search. Bioinformatics 23: 2196-7.
8. Xu S, McCusker J, Krauthammer M (2008) Yale image finder (YIF): a new search engine for retrieving biomedical images. Bioinformatics 24: 1968-1970.
9. Rafkind B, Lee M, Chang S, Yu H (2006) Exploring text and image features to classify images in bioscience literature. In: HLT-NAACL BioNLP. New York, USA.
10. Kahn CE, Thao C (2007) GoldMiner: a radiology image search engine. AJR American Journal of Roentgenology 188: 1475-1478.
11. Yu H (2006) Towards answering biological questions with experimental evidence: Automatically identifying text that summarize image content in Full- Text articles. AMIA Annu Symp Proc. pp 834-8.
12. Yu H, Agarwal S, Johnston M, Cohen A (2009) Are figure legends sufficient? evaluating the contribution of associated text to biomedical figure comprehension. J Biomed Discov Collab 4: 1.
13. Agarwal S, Yu H (2009) Automatically generating structured text summaries for figures in biomedical literature. In: AMIA Annu Symp Proc.
14. Agarwal S, Yu H (2009) Automatically classifying sentences in Full-Text biomedical arti-cles into introduction, methods, results and discussion. Bioinformatics.
15. Lane AL, Nyadong L, Galhena AS, Shearer TL, Stout EP, et al. (2009) Desorption electrospray ionization mass spectrometry reveals surface-mediated antifungal chemical defense of a tropical seaweed. Proceedings of the National Academy of Sciences 106: 7314-7319.
16. Papanayotou C, Mey A, Birot A, Saka Y, Boast S, et al. (2008) A mechanism regulating the onset of sox2 expression in the embryonic neural plate. PLoS Biol 6: e2.
17. Erkan G, Radev DR (2004) LexRank: graph-based lexical centrality as salience in text summarization. Journal of Artificial Intelligence Research 22: 457C479.
18. Salton G, Wong A, Yang CS (1975) A vector space model for automatic indexing. Commun ACM 18: 613-620.
19. Rosset S, Perlich C, Zadrozny B (2007) Ranking-based evaluation of regression models. Knowl Inf Syst 12: 331-353.
20. Yan D, Mäyränpää MI, Wong J, Perttilä J, Lehto M, et al. (2008) OSBP-related protein 8 (ORP8) suppresses ABCA1 expression and cholesterol efflux from macrophages. Journal of Biological Chemistry 283: 332-340.
21. Zhou J, Su P, Wang L, Chen J, Zimmermann M, et al. (2009) mTOR supports long-term self-renewal and suppresses mesoderm and endoderm activities of human embryonic stem cells. Proceedings of the National Academy of Sciences 106: 7840-7845.
22. Lane MC, O'Toole PW, Moore SA (2006) Molecular basis of the interaction between the flagellar export proteins FliI and FliH from helicobacter pylori. Journal of Biological Chemistry 281: 508-517.
23. Bengoechea TG, Chen Z, O'Leary DA, Masliah E, Lee K (2009) p75 reduces  -amyloid-induced sympathetic innervation deficits in an alzheimer's disease mouse model. Proceedings of the National Academy of Sciences 106: 7870-7875.
24. Yoneda T, Imaizumi K, Maeda M, Yui D, Manabe T, et al. (2000) Regulatory mechanisms of TRAF2-mediated signal transduction by bcl10, a MALT lymphoma-associated protein. J Biol Chem 275: 11114-11120.
25. Ge Y, Rybakova IN, Xu Q, Moss RL (2009) Top-down high-resolution mass spectrometry of cardiac myosin binding protein c revealed that truncation alters protein phosphorylation state. Proceedings of the National Academy of Sciences 106: 12658-12663.
26. Robertson S, Zaragoza H, Taylor M (2004) Simple BM25 extension to multiple weighted fields. In: ACM CIKM.
27. Barzilay R, Elhadad M, McKeown K (1999) Information fusion in the context of multi-document summarization. In: The 37th Association for Computational Linguistics. Maryland.
28. Zhou Z, Gao J, Soong FK, Meng H (2006) A comparative study of discriminative methods for reranking LVCSR N-Best hypotheses in domain adaptation and generalization. In: Proc. ICASSP. volume 1. 141C144 p.
29. Liu Y, Liu F (2008) Unsupervised language model adaptation via topic modeling based on named entity hypotheses. In: Proceedings of ICASSP, volume 8. 4921C4924 p.
30. Collins M (2002) Ranking algorithms for named-entity extraction: Boosting and the voted perceptron. In: Proceedings of the 40th Annual Meeting on Association for Computational Linguistics, July. 07C12 p.
31. Liu F, Liu F, Liu Y (2010) A supervised framework for keyword extraction from meeting transcripts IEEE Transactions on Audio, Speech and Language Processing.
32. Yates RB, Neto BR (1999) Modern information retrieval. New York: ACM Press.
33. Xu J, Croft WB (2000) Improving the effectiveness of information retrieval with local context analysis. ACM Transactions on Information Systems (TOIS) 18: 79C112.
34. Radev D, Fan W, Qi H, Wu H, Grewal A (2002) Probabilistic question answering on the web. In: Proceedings of the 11th international conference on World Wide Web. 408C419 p.
35. Collins M, Koo T (2005) Discriminative reranking for natural language parsing. Computational Linguistics 31: 25C70.
36. Charniak E, Johnson M (2005) Coarse-to-fine n-best parsing and MaxEnt discriminative reranking. In: Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics. 180 p.
37. Huang L (2008) Forest reranking: Discriminative parsing with non-local features. In: Proc. of ACL.
38. Shen L, Joshi AK (2005) Ranking and reranking with perceptron. Machine Learning 60: 73C96.
39. Li Z, Khudanpur S (2009) Forest reranking for machine translation with the perceptron algorithm. GALE book chapter on MT From Text.
40. Liu Q, Crammer K, Pereira F, Roos D (2008) Reranking candidate gene models with cross-species comparison for improved gene prediction. BMC Bioinformatics 9: 433.
41. Braschler M, Peters C (2004) Cross-language evaluation forum: Objectives, results, achievements. Inf Retr 7: 7-31.
42. McCullagh P (1980) Regression models for ordinal data. Journal of the Royal Statistical Society Series B (Methodological) 42: 109C142.
43. Crammer K, Singer Y (2001) Pranking with ranking. In: In Proceedings of the conference on Neural Information Processing Systems (NIPS). URL.
44. Chu W, Ghahramani Z (2006) Gaussian processes for ordinal regression. Journal of Machine Learning Research 6: 1019.
45. Collobert R, Bengio S, Williamson C (2001) SVMTorch: support vector machines for Large-Scale regression problems. JOURNAL OF MACHINE LEARNING RESEARCH 1: 143-160.
46. Shashua A, Levin A (2003) Ranking with large margin principle: Two approaches. Advances in neural information processing systems. 961C968 p.
47. Chu W, Keerthi SS (2007) Support vector ordinal regression. Neural Computation 19: 792C815.
48. Rajaram S, Garg A, Zhou XS, Huang TS (2003) Classification approach towards ranking and sorting problems. In: Machine Learning: ECML 2003. pp. 301-312. URL http://www.springerlink.com/content/nyajf4xe15e0mfq7.
49. Har-peled S, Roth D, Zimak D (2003) Constraint classification for multiclass classification and ranking. Advances in Neural Information Processing Systems 15: 785-792.
50. Li L, Lin H (2007) Ordinal regression by extended binary classification. Advances in Neural Information Processing Systems 19: 865.
51. Shen L, Sarkar A, Och FJ (2004) Discriminative reranking for machine translation. In: Proceedings of the Joint HLT and NAACL Conference (HLT 04). 177C184 p.
52. Shen L, Joshi AK (2003) An SVM based voting algorithm with application to parse reranking. IN PROC OF CONLL 2003: 9-16.