Restoration of riverine ecosystems is often stated as a management objective for regulated rivers, and floods are one of the most effective tools for accomplishing restoration. The National Re- search Council (NRC 1992) argued that ecological restoration means re- turning "an ecosystem to a close approximation of its condition prior to disturbance" and that "restoring altered, damaged, O f destroyed lakes, rivers, and wetlands is a high-priority task." Effective restoration must be based on a clear definition of the value of riverine resources to society; on scientific studies that document ecosystem status and provide an understanding of ecosystem processes and resource interactions; on scientific studies that predict, mea- sure, and monitor the effectiveness of restoration techniques; and on engineering and economic studies that evaluate societal costs and benefits of restoration.

In the case of some large rivers, restoration is not a self-evident goal. Indeed, restoration may be impossible; a more feasible goal may be rehabilitation of some ecosystem components and processes in parts of the river (Gore and Shields 1995, Kondolfand Wilcock 1996, Stanford et al. 1996). In other cases, the appropriate decision may be to do nothing. The decision to manipulate ecosystem processes and components involves not only a scientific judgment that a restored or rehabilitated condition is achievable, but also a value judgment that this condition is more desirable than the status quo. These judgments involve prioritizing different river resources, and they should be based on extensive and continuing public debate.

In this article, we examine the appropriate role of science in determining whether or not to restore or rehabilitate the Colorado River in the Grand Canyon by summarizing studies carried out by numerous agencies, universities, and consulting firms since 1983. This reach of the Colorado extends 425 km between Glen Canyon Dam and Lake Mead reservoir (Figure 1). Efforts to manipulate ecosystem processes and components in the Grand Canyon have received widespread public attention, such as the 1996 controlled flood released from Glen Canyon Dam and the proposal to drain Lake Powell reservoir.

Background:
Drosophila gene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for studying the regulatory networks governing development. To facilitate pattern comparison and searching, groups of images in the Berkeley Drosophila Genome Project (BDGP) high-throughput study were annotated with a variable number of anatomical terms manually using a controlled vocabulary. Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task.

Results:
We present a computational method to annotate gene expression pattern images automatically. The proposed method uses the bag-of-words scheme to utilize the existing information on pattern annotation and annotates images using a model that exploits correlations among terms. The proposed method can annotate images individually or in groups (e.g., according to the developmental stage). In addition, the proposed method can integrate information from different two-dimensional views of embryos. Results on embryonic patterns from BDGP data demonstrate that our method significantly outperforms other methods.

Conclusion:
The proposed bag-of-words scheme is effective in representing a set of annotations assigned to a group of images, and the model employed to annotate images successfully captures the correlations among different controlled vocabulary terms. The integration of existing annotation information from multiple embryonic views improves annotation performance.