title: Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions.
abstract: The Drosophila gene expression pattern images document the spatial and temporal dynamics of gene expression and they are valuable tools for explicating the gene functions, interaction, and networks during Drosophila embryogenesis. To provide text-based pattern searching, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with ontology terms manually by human curators. We present a systematic approach for automating this task, because the number of images needing text descriptions is now rapidly increasing. We consider both improved feature representation and novel learning formulation to boost the annotation performance. For feature representation, we adapt the bag-of-words scheme commonly used in visual recognition problems so that the image group information in the BDGP study is retained. Moreover, images from multiple views can be integrated naturally in this representation. To reduce the quantization error caused by the bag-of-words representation, we propose an improved feature representation scheme based on the sparse learning technique. In the design of learning formulation, we propose a local regularization framework that can incorporate the correlations among terms explicitly. We further show that the resulting optimization problem admits an analytical solution. Experimental results show that the representation based on sparse learning outperforms the bag-of-words representation significantly. Results also show that incorporation of the term-term correlations improves the annotation performance consistently.
authors: Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287.
authors: Shuiwang
authors: S
authors: Ji
authors: Lei
authors: L
authors: Yuan
authors: Ying-Xin
authors: YX
authors: Li
authors: Zhi-Hua
authors: ZH
authors: Zhou
authors: Sudhir
authors: S
authors: Kumar
authors: Jieping
authors: J
authors: Ye
references: IEEE Trans Pattern Anal Mach Intell. 2008 Sep;30(9):1632-46
references: 18617720
references: BMC Bioinformatics. 2004 Dec 16;5:202
references: 15603586
references: BMC Bioinformatics. 2009 Apr 21;10:119
references: 19383139
references: Cell. 2007 Oct 5;131(1):174-87
references: 17923096
references: IEEE Trans Pattern Anal Mach Intell. 2005 Oct;27(10):1615-30
references: 16237996
references: Genome Biol. 2007;8(7):R145
references: 17645804
references: Bioinformatics. 2008 Sep 1;24(17):1881-8
references: 18632750
references: Comput Syst Bioinformatics Conf. 2006;:293-8
references: 17369647
references: Genetics. 2002 Dec;162(4):2037-47
references: 12524369
references: IJCAI (U S). 2009 Jan 1;2009:1445-1450
references: 20824158
references: Genome Biol. 2002;3(12):RESEARCH0088
references: 12537577
references: Cell. 2008 Apr 18;133(2):364-74
references: 18423206
references: ACM Trans Knowl Discov Data. 2008 Mar;2(1):
references: 18769656