Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
BackgroundModern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatially similar and to ultimately infer potential gene interactions. However, the rapid accumulation of gene expression pattern data over the last two decades, facilitated by high-throughput techniques, has produced a need for the development of efficient approaches for direct comparison of images, rather than their textual descriptions, to identify spatially similar expression patterns.ResultsThe effectiveness of the Binary Feature Vector (BFV) and Invariant Moment Vector (IMV) based digital representations of the gene expression patterns in finding biologically meaningful patterns was compared for a small (226 images) and a large (1819 images) dataset. For each dataset, an ordered list of images, with respect to a query image, was generated to identify overlapping and similar gene expression patterns, in a manner comparable to what a developmental biologist might do. The results showed that the BFV representation consistently outperforms the IMV representation in finding biologically meaningful matches when spatial overlap of the gene expression pattern and the genes involved are considered. Furthermore, we explored the value of conducting image-content based searches in a dataset where individual expression components (or domains) of multi-domain expression patterns were also included separately. We found that this technique improves performance of both IMV and BFV based searches.ConclusionsWe conclude that the BFV representation consistently produces a more extensive and better list of biologically useful patterns than the IMV representation. The high quality of results obtained scales well as the search database becomes larger, which encourages efforts to build automated image query and retrieval systems for spatial gene expression patterns.

title: TimeTree: a public knowledge-base of divergence times among organisms
abstract: Biologists and other scientists routinely need to know times of divergence between species and to construct phylogenies calibrated to time (timetrees). Published studies reporting time estimates from molecular data have been increasing rapidly, but the data have been largely inaccessible to the greater community of scientists because of their complexity. TimeTree brings these data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility. Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature.


AVAILABILITY
TimeTree is available at http://www.timetree.net

title: Digital tapestry [automatic image synthesis]
abstract: This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov random field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with "almost" metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented.

title: Dynamic memory management for programmable devices

title: Increased watermark-to-host correlation of uniform random phase watermarks in audio signals
abstract: We analyze the watermark-to-host correlation (WHC) of random phase watermarks, in the context of additive embedding and blind correlation-detection of the watermark in audio signals. Interestingly, we find that WHC is higher when a legitimate watermark is present in the audio signal. Instead of trying to minimize the WHC, one could also attempt to harness this increased correlation in order to result in better detection performance. The analysis shows that uniformly distributed phase difference (between the host signal and the watermark) provides maximum advantage. It is also verified that, a uniformly distributed watermark phase provides the most advantage, experimented over a variety of audio signals.

title: A Hierarchical Multiclassifier System for Hyperspectral Data Analysis
abstract: Many real world classification problems involve high dimensional inputs and a large number of classes. Feature extraction and modular learning approaches can be used to simplify such problems. In this paper, we introduce a hierarchical multiclassifier paradigm in which a C- class problem is recursively decomposed into C - 1 two-class problems. A generalized modular learning framework is used to partition a set of classes into two disjoint groups called meta-classes. The coupled problem of finding a good partition and of searching for a linear feature extractor that best discriminates the resulting two meta-classes are solved simultaneously at each stage of the recursive algorithm. This results in a binary tree whose leaf nodes represent the original C classes. The proposed hierarchical multiclassifier architecture was used to classify 12 types of landcover from 183-dimensional hyperspectral data. The classification accuracy was significantly improved by 4 to 10% relative to other feature extraction and modular learning approaches. Moreover, the class hierarchy that was automatically discovered conformed very well with a human domain expert's opinion, which demonstrates the potential of such a modular learning approach for discovering domain knowledge automatically from data.

title: Hierarchical Fusion of Multiple Classifiers for Hyperspectral Data Analysis
abstract: Many classification problems involve high dimensional inputs and a large number of classes. Multiclassifier fusion approaches to such difficult problems typically centre around smart feature extraction, input resampling methods, or input space partitioning to exploit modular learning. In this paper, we investigate how partitioning of the output space (i.e. the set of class labels) can be exploited in a multiclassifier fusion framework to simplify such problems and to yield better solutions. Specifically, we introduce a hierarchical technique to recursively decompose a C-class problem into C_1 ) class problems. A generalised modular learning framework is used to partition a set of classes into two disjoint groups called meta-classes. The coupled problems of finding a good partition and of searching for a linear feature extractor that best discriminates the resulting two meta-classes are solved simultaneously at each stage of the recursive algorithm. This results in a binary tree whose leaf nodes represent the original C classes. The proposed hierarchical multiclassifier framework is particularly effective for difficult classification problems involving a moderately large number of classes. The proposed method is illustrated on a problem related to classification of landcover using hyperspectral data: a 12-class AVIRIS subset with 180 bands. For this problem, the classification accuracies obtained were superior to most other techniques developed for hyperspectral classification. Moreover, the class hierarchies that were automatically discovered conformed very well with human domain experts’ opinions, which demonstrates the potential of using such a modular learning approach for discovering domain knowledge automatically from data.