18,190 research outputs found
Multivariate Approaches to Classification in Extragalactic Astronomy
Clustering objects into synthetic groups is a natural activity of any
science. Astrophysics is not an exception and is now facing a deluge of data.
For galaxies, the one-century old Hubble classification and the Hubble tuning
fork are still largely in use, together with numerous mono-or bivariate
classifications most often made by eye. However, a classification must be
driven by the data, and sophisticated multivariate statistical tools are used
more and more often. In this paper we review these different approaches in
order to situate them in the general context of unsupervised and supervised
learning. We insist on the astrophysical outcomes of these studies to show that
multivariate analyses provide an obvious path toward a renewal of our
classification of galaxies and are invaluable tools to investigate the physics
and evolution of galaxies.Comment: Open Access paper.
http://www.frontiersin.org/milky\_way\_and\_galaxies/10.3389/fspas.2015.00003/abstract\>.
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An Algorithm For Building Language Superfamilies Using Swadesh Lists
The main contributions of this thesis are the following: i. Developing an algorithm to generate language families and superfamilies given for each input language a Swadesh list represented using the international phonetic alphabet (IPA) notation. ii. The algorithm is novel in using the Levenshtein distance metric on the IPA representation and in the way it measures overall distance between pairs of Swadesh lists. iii. Building a Swadesh list for the author\u27s native Kinyarwanda language because a Swadesh list could not be found even after an extensive search for it.
Adviser: Peter Reves
Towards a Taxonomically Intelligent Phylogenetic Database
This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
The organization and mining of malaria genomic and post-genomic data is
highly motivated by the necessity to predict and characterize new biological
targets and new drugs. Biological targets are sought in a biological space
designed from the genomic data from Plasmodium falciparum, but using also the
millions of genomic data from other species. Drug candidates are sought in a
chemical space containing the millions of small molecules stored in public and
private chemolibraries. Data management should therefore be as reliable and
versatile as possible. In this context, we examined five aspects of the
organization and mining of malaria genomic and post-genomic data: 1) the
comparison of protein sequences including compositionally atypical malaria
sequences, 2) the high throughput reconstruction of molecular phylogenies, 3)
the representation of biological processes particularly metabolic pathways, 4)
the versatile methods to integrate genomic data, biological representations and
functional profiling obtained from X-omic experiments after drug treatments and
5) the determination and prediction of protein structures and their molecular
docking with drug candidate structures. Progresses toward a grid-enabled
chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa
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Prediction of microbial communities for urban metagenomics using neural network approach.
BACKGROUND:Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious diseases and detect potentially urgent threats. To achieve this goal, the DNA sample collection and analysis have been conducted at subway stations in major cities. However, city-scale sampling with the fine-grained geo-spatial resolution is expensive and laborious. In this paper, we introduce MetaMLAnn, a neural network based approach to infer microbial communities at unsampled locations given information reflecting different factors, including subway line networks, sampling material types, and microbial composition patterns. RESULTS:We evaluate the effectiveness of MetaMLAnn based on the public metagenomics dataset collected from multiple locations in the New York and Boston subway systems. The experimental results suggest that MetaMLAnn consistently performs better than other five conventional classifiers under different taxonomic ranks. At genus level, MetaMLAnn can achieve F1 scores of 0.63 and 0.72 on the New York and the Boston datasets, respectively. CONCLUSIONS:By exploiting heterogeneous features, MetaMLAnn captures the hidden interactions between microbial compositions and the urban environment, which enables precise predictions of microbial communities at unmeasured locations
Visual and computational analysis of structure-activity relationships in high-throughput screening data
Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent work in visualisation and data mining that can be used to develop structure-activity relationships from such chemical/biological datasets
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