356 research outputs found
Research on knowledge representation, machine learning, and knowledge acquisition
Research in knowledge representation, machine learning, and knowledge acquisition performed at Knowledge Systems Lab. is summarized. The major goal of the research was to develop flexible, effective methods for representing the qualitative knowledge necessary for solving large problems that require symbolic reasoning as well as numerical computation. The research focused on integrating different representation methods to describe different kinds of knowledge more effectively than any one method can alone. In particular, emphasis was placed on representing and using spatial information about three dimensional objects and constraints on the arrangement of these objects in space. Another major theme is the development of robust machine learning programs that can be integrated with a variety of intelligent systems. To achieve this goal, learning methods were designed, implemented and experimented within several different problem solving environments
Automatic Annotation of Protein Motif Function with Gene Ontology terms
Background: Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist for identifying candidate protein motifs at the whole genome level. However, a much needed and important task is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results: This paper presents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifs is viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and a GO term association is found to be a very useful feature. We take advantage of the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correct association. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions: In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about the functions of newly discovered candidate protein motifs
A Spitzer IRS Spectral Atlas of Luminous 8 micron Sources in the Large Magellanic Cloud
We present an atlas of Spitzer Space Telescope Infrared Spectrograph (IRS)
spectra of highly luminous, compact mid-infrared sources in the Large
Magellanic Cloud. Sources were selected on the basis of infrared colors and 8
micron (MSX) fluxes indicative of highly evolved, intermediate- to high-mass
stars with current or recent mass loss at large rates. We determine the
chemistry of the circumstellar envelope from the mid-IR continuum and spectral
features and classify the spectral types of the stars. In the sample of 60
sources, we find 21 Red Supergiants (RSGs), 16 C-rich Asymptotic Giant Branch
(AGB) stars, 11 HII regions, 4 likely O-rich AGB stars, 4 Galactic O-rich AGB
stars, 2 OH/IR stars, and 2 B[e] supergiants with peculiar IR spectra. We find
that the overwhelming majority of the sample AGB stars (with typical IR
luminosities ~1.0E4 L_sun) have C-rich envelopes, while the O-rich objects are
predominantly luminous RSGs with L_IR ~ 1.0E5 L_sun. We determine mean
bolometric corrections to the stellar K-band flux densities and find that for
carbon stars, the bolometric corrections depend on the infrared color, whereas
for RSGs, the bolometric correction is independent of IR color. Our results
reveal that objects previously classified as PNe on the basis of IR colors are
in fact compact HII regions with very red IRS spectra that include strong
atomic recombination lines and PAH emission features. We demonstrate that the
IRS spectral classes in our sample separate clearly in infrared color-color
diagrams that use combinations of 2MASS data and synthetic IRAC/MIPS fluxes
derived from the IRS spectra. On this basis, we suggest diagnostics to identify
and classify, with high confidence levels, IR-luminous evolved stars and HII
regions in nearby galaxies using Spitzer and near-infrared photometry.Comment: 46 pages, 9 figures; accepted for publication in AJ; abstract
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On religion and cultural policy: notes on the Roman Catholic Church
This paper argues that religious institutions have largely been neglected within the study of cultural policy. This is attributed to the inherently secular tendency of most modern social sciences. Despite the predominance of the ‘secularisation paradigm’, the paper notes that religion continues to promote powerful attachments and denunciations. Arguments between the ‘new atheists’, in particular, Richard Dawkins, and their opponents are discussed, as is Habermas’s conciliatory encounter with Joseph Ratzinger (later Pope Benedict XVI). The paper then moves to a consideration of the Roman Catholic Church as an agent of cultural policy, whose overriding aim is the promotion of ‘Christian consciousness’. Discussion focuses on the contested meanings of this, with reference to (1) the deliberations of Vatican II and (2) the exercise of theological and cultural authority by the Pope and the Congregation for the Doctrine of the Faith (CDF). It is argued that these doctrinal disputes intersect with secular notions of social and cultural policy and warrant attention outside the specialist realm of theological discourse
An Assessment of the Impact of Hafting on Paleoindian Point Variability
It has long been argued that the form of North American Paleoindian points was affected by hafting. According to this hypothesis, hafting constrained point bases such that they are less variable than point blades. The results of several studies have been claimed to be consistent with this hypothesis. However, there are reasons to be skeptical of these results. None of the studies employed statistical tests, and all of them focused on points recovered from kill and camp sites, which makes it difficult to be certain that the differences in variability are the result of hafting rather than a consequence of resharpening. Here, we report a study in which we tested the predictions of the hafting hypothesis by statistically comparing the variability of different parts of Clovis points. We controlled for the potentially confounding effects of resharpening by analyzing largely unused points from caches as well as points from kill and camp sites. The results of our analyses were not consistent with the predictions of the hypothesis. We found that several blade characters and point thickness were no more variable than the base characters. Our results indicate that the hafting hypothesis does not hold for Clovis points and indicate that there is a need to test its applicability in relation to post-Clovis Paleoindian points
A Morphometric Assessment of the Intended Function of Cached Clovis Points
A number of functions have been proposed for cached Clovis points. The least complicated hypothesis is that they were intended to arm hunting weapons. It has also been argued that they were produced for use in rituals or in connection with costly signaling displays. Lastly, it has been suggested that some cached Clovis points may have been used as saws. Here we report a study in which we morphometrically compared Clovis points from caches with Clovis points recovered from kill and camp sites to test two predictions of the hypothesis that cached Clovis points were intended to arm hunting weapons: 1) cached points should be the same shape as, but generally larger than, points from kill/camp sites, and 2) cached points and points from kill/camp sites should follow the same allometric trajectory. The results of the analyses are consistent with both predictions and therefore support the hypothesis. A follow-up review of the fit between the results of the analyses and the predictions of the other hypotheses indicates that the analyses support only the hunting equipment hypothesis. We conclude from this that cached Clovis points were likely produced with the intention of using them to arm hunting weapons
The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe
The preponderance of matter over antimatter in the early Universe, the
dynamics of the supernova bursts that produced the heavy elements necessary for
life and whether protons eventually decay --- these mysteries at the forefront
of particle physics and astrophysics are key to understanding the early
evolution of our Universe, its current state and its eventual fate. The
Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed
plan for a world-class experiment dedicated to addressing these questions. LBNE
is conceived around three central components: (1) a new, high-intensity
neutrino source generated from a megawatt-class proton accelerator at Fermi
National Accelerator Laboratory, (2) a near neutrino detector just downstream
of the source, and (3) a massive liquid argon time-projection chamber deployed
as a far detector deep underground at the Sanford Underground Research
Facility. This facility, located at the site of the former Homestake Mine in
Lead, South Dakota, is approximately 1,300 km from the neutrino source at
Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino
charge-parity symmetry violation and mass ordering effects. This ambitious yet
cost-effective design incorporates scalability and flexibility and can
accommodate a variety of upgrades and contributions. With its exceptional
combination of experimental configuration, technical capabilities, and
potential for transformative discoveries, LBNE promises to be a vital facility
for the field of particle physics worldwide, providing physicists from around
the globe with opportunities to collaborate in a twenty to thirty year program
of exciting science. In this document we provide a comprehensive overview of
LBNE's scientific objectives, its place in the landscape of neutrino physics
worldwide, the technologies it will incorporate and the capabilities it will
possess.Comment: Major update of previous version. This is the reference document for
LBNE science program and current status. Chapters 1, 3, and 9 provide a
comprehensive overview of LBNE's scientific objectives, its place in the
landscape of neutrino physics worldwide, the technologies it will incorporate
and the capabilities it will possess. 288 pages, 116 figure
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