MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

title: Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
abstract: 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: MEGA2: molecular evolutionary genetics analysis software
abstract: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.


AVAILABILITY
http://www.megasoftware.net.

title: Toward A Formalism for Conversation Protocols Using Joint Intention Theory
abstract: Conversation protocols are meant to achieve certain tasks or to bring about certain state of affairs in the world. Therefore, one may identify the landmarks or the state of affairs that must be brought about during the execution of a protocol in order to achieve its goal. Accordingly, the most important aspect of protocols is these landmarks rather than the communicative actions needed to achieve the landmarks. We show that families of conversation protocols can be expressed formally as partially ordered landmarks where each landmark is characterized by propositions that are true in the state represented by that landmark. Dialogue in natural languages is regarded as joint activity. Conversation protocols in multi-agent systems are treated as dialogue templates and are composed using speech acts from natural language dialogues. As such, we treat conversation protocols as joint action expressions and gainfully apply existing formal theories of dialogue, specifically the Joint Intention Theory, to protocols and their compositions. Conversation protocols may require agents to communicate with groups as well as individuals. However, most contemporary agent communication languages, notably FIPA and KQML, have either no provision or no well-defined semantics for group communication. Furthermore, the research on protocols so far does not correctlymore » incorporate groups into the protocols. We give a formal semantics to group communicative acts and use it to handle group communication in a formal treatment of protocols.« less

title: Wavelet directional histograms for classification of human gestures represented by spatio-temporal templates
abstract: This paper evaluates the efficacy of directional information of wavelet multi-resolution decomposition for histogram-based classification of human gestures represented by spatio-temporal templates. This template collapses temporal component into gesture representation in a way that no explicit sequence matching or temporal analysis is needed, and characterizes the motion from a very high dimensional space to a low dimensional space. These templates are modified to be invariant to translation, rotation and scale. Two dimensional, 3 level dyadic wavelet transform applied on these templates results in one low pass subimage and nine highpass directional subimages. Histograms of wavelet coefficients at different scales are compared to establish significance of available information for classification. The preliminary experiments show that while the statistical properties of the template provide high level of classification accuracy, the available information in high pass or low pass decompositions by itself is not sufficient to provide significant efficiency of accuracy.

title: Hybrid transactional memory
abstract: High performance parallel programs are currently difficult to write and debug. One major source of difficulty is protecting concurrent accesses to shared data with an appropriate synchronization mechanism. Locks are the most common mechanism but they have a number of disadvantages, including possibly unnecessary serialization, and possible deadlock. Transactional memory is an alternative mechanism that makes parallel programming easier. With transactional memory, a transaction provides atomic and serializable operations on an arbitrary set of memory locations. When a transaction commits, all operations within the transaction become visible to other threads. When it aborts, all operations in the transaction are rolled back.Transactional memory can be implemented in either hardware or software. A straightforward hardware approach can have high performance, but imposes strict limits on the amount of data updated in each transaction. A software approach removes these limits, but incurs high overhead. We propose a novel hybrid hardware-software transactional memory scheme that approaches the performance of a hardware scheme when resources are not exhausted and gracefully falls back to a software scheme otherwise.

title: An observation-constrained generative approach for probabilistic classification of image regions
abstract: In this paper, we propose a probabilistic region classification scheme for natural scene images. In conventional generative methods, a generative model is learnt for each class using all the available training data belonging to that class. However, if an input image has been generated from only a subset of the model support, use of the full model to assign generative probabilities can produce serious artifacts in the probability assignments. This problem arises mainly when the different classes have multimodal distributions with considerable overlap in the feature space. We propose an approach to constrain the class generative probability of a set of newly observed data by exploiting the distribution of the new data itself and using linear weighted mixing. A Kullback–Leibler Divergence-based fast model selection procedure is also proposed for learning mixture models in a low dimensional feature space. The preliminary results on the natural scene images support the effectiveness of the proposed approach.

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.