Structured literature image finder: Extracting information from text and images in biomedical literature

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6004 LNBI, Issue , 2010, Pages 23-32

  Coelho, Luís Pedro ^a,b   Ahmed, Amr ^a   Arnold, Andrew ^a   Kangas, Joshua ^a,b   Sheikh, Abdul Saboor ^b   Xing, Eric P ^a,b   Cohen, William W ^a,b   Murphy, Robert F ^a,b  

^a Carnegie Mellon University   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE LEARNING; BIOMEDICAL LITERATURE; COLLECTION OF DOCUMENTS; DEVELOPED MODEL; EXTRACTING INFORMATION; FLUORESCENCE MICROSCOPY IMAGES; MULTI-MODALITY; SEARCHABLE DATABASE; SUB-CELLULAR; TEXT-MINING; TRAINING SETS;

FLUORESCENCE MICROSCOPY;

IMAGE PROCESSING;

EID: 77953756788     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-13131-8_4     Document Type: Conference Paper

References (19)

1. Murphy, R.F., Velliste, M., Yao, J., Porreca, G.: Searching online journals for fluorescence microscope images depicting protein subcellular location patterns. In: BIBE 2001: Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering, Washington, DC, USA, pp. 119-128. IEEE Computer Society, Los Alamitos (2001)
2. Cohen, W.W., Wang, R., Murphy, R.F.: Understanding captions in biomedical publications. In: KDD 2003: Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining, pp. 499-504. ACM, New York (2003)
3. Murphy, R.F., Kou, Z., Hua, J., Joffe, M., Cohen, W.W.: Extracting and structuring subcellular location information from on-line journal articles: The subcellular location image finder. In: Proceedings of IASTED International Conference on Knowledge Sharing and Collaborative Engineering, pp. 109-114 (2004)
4. Kou, Z., Cohen, W.W., Murphy, R.F.: A stacked graphical model for associating sub-images with sub-captions. In: Altman, R.B., Dunker, A.K., Hunter, L., Murray, T., Klein, T.E. (eds.) Proceedings of the Pacific Symposium on Biocomputing, pp. 257-268. World Scientific, Singapore (2007)
5. Ahmed, A., Arnold, A., Coelho, L.P., Kangas, J., Sheikh, A.S., Xing, E.P., Cohen, W.W., Murphy, R.F.: Structured literature image finder: Parsing text and figures in biomedical literature. Journal of Web Semantics (2009) (in press)
6. Gingras, D., Michaud, M., Tomasso, G.D., Bliveau, E., Nyalendo, C., Bliveau, R.: Sphingosine-1-phosphate induces the association of membrane-type 1 matrix metalloproteinase with p130cas in endothelial cells. FEBS Letters 582(3), 399-404 (2008)
7. Kou, Z., Cohen, W.W., Murphy, R.F.: High-recall protein entity recognition using a dictionary. Bioinformatics 21, i266-i273 (2005)
8. Geusebroek, J.M., Hoang, M.A., van Gernert, J., Worring, M.: Genre-based search through biomedical images. In: Proceedings of 16th International Conference on Pattern Recognition, vol.1, pp. 271-274 (2002)
9. Shatkay, H., Chen, N., Blostein, D.: Integrating image data into biomedical text categorization. Bioinformatics 22(14), 446-453 (2006)
10. Rafkind, B., Lee, M., Chang, S., Yu, H.: Exploring text and image features to classify images in bioscience literature. In: Proceedings of the BioNLPWorkshop on Linking Natural Language Processing and Biology at HLT-NAACL, Morristown, NJ, USA. Association for Computational Linguistics, pp. 73-80 (2006)
11. Roy, N., Mccallum, A.: Toward optimal active learning through sampling estimation of error reduction. In: Proc. 18th International Conf. on Machine Learning, pp. 441-448. Morgan Kaufmann, San Francisco (2001)
12. Mitchell, T.M.: Machine Learning. McGraw-Hill, New York (1997)
13. Haralick, R.M.: Statistical and structural approaches to texture. Proceedings of the IEEE 67, 786-804 (1979)
14. Boland, M.V., Murphy, R.F.: A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics 17(12), 1213-1223 (2001)
15. Jennrich, R.: Stepwise Regression & Stepwise Discriminant Analysis. In: Statistical Methods for Digital Computers, pp. 58-95. John Wiley & Sons, Inc., New York (1977)
16. Hamilton, N., Pantelic, R., Hanson, K., Teasdale, R.: Fast automated cell phenotype image classification. BMC Bioinformatics 8(1), 110 (2007)
17. Ridler, T., Calvard, S.: Picture thresholding using an iterative selection method. IEEE Trans. Systems, Man and Cybernetics 8(8), 629-632 (1978)
18. Ahmed, A., Xing, E.P., Cohen, W.W., Murphy, R.F.: Structured correspondence topic models for mining captioned figures in biological literature. In: Proceedings of The Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2009), pp. 39-47. ACM, New York (2009)
19. Ponte, J.M., Croft, W.B.: A language modeling approach to information retrieval. In: SIGIR 1998: Proceedings of the 21st annual international ACM SIGIR conference on Research and development in information retrieval, pp. 275-281. ACM, New York (1998)