Results for “binary classification” — Page 21

DOE OSTI2015

GOTTCHA, Version2

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions. In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure. During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably. During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.

Freitas, Tracey↗

DOE OSTI2015

GOTTCHA, Version 1

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions. In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure. During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably. During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.

Freitas, Tracey↗

DOE OSTI2020

False metals, real insulators, and degenerate gapped metals

This paper deals with a significant family of compounds predicted by simplistic electronic structure theory to be metals but are, in fact, insulators. This false metallic state has been traditionally attributed in the literature to reflect the absence of proper treatment of electron-electron correlation (“Mott insulators”) whereas, in fact, even mean-field like density functional theory describes the insulating phase correctly if the restrictions posed on the simplistic theory are avoided. Such unwarranted restrictions included different forms of disallowing symmetry breaking described in this article. As the science and technology of conductors have transitioned from studying simple elemental metals such as Al or Cu to compound conductors such as binary or ternary oxides and pnictides, a special class of degenerate but gapped metals has been noticed. Their presumed electronic configurations show the Fermi level inside the conduction band or valence band, yet there is an “internal band gap” between the principal band edges. The significance of this electronic configuration is that it might be unstable toward the formation of states inside the internal band gap when the formation of such states costs less energy than the energy gained by transferring carriers from the conduction band to these lower energy acceptor states, changing the original (false) metal to an insulator. The analogous process also exists for degenerate but gapped metals with the Fermi level inside the valence band, where the energy gain is defined by transfer of electrons from the donor level to the unoccupied part of the valence band. We focus here on the fact that numerous electronic structure methodologies have overlooked some physical factors that could stabilize the insulating alternative, predicting instead false metals that do not really exist (note that this is in general not a physical phase transition, but a correction of a previous error in theory that led to a false prediction of a metal). Such errors include: (i) ignoring spin symmetry breaking, such as disallowing magnetic spin ordering in CuBi2O4 or disallowing the formation of polymorphous spin networks in paramagnetic LaTiO 3 and YTiO 3 ; (ii) ignoring structural symmetry breaking, e.g., not enabling energy-lowering bond disproportionation (Li-doped TiO 2 , SrBiO 3 , and rare-earth nickelates), or not exploring pseudo-Jahn–Teller-like distortions in LaMnO 3 , or disallowing spontaneous formation of ordered vacancy compounds in Ba 4 As 3 and Ag 3 Al 22 O 34 ; and (iii) ignoring spin–orbit coupling forcing false metallic states in CaIrO 3 and Sr 2 IrO 4 . The distinction between false metals vs real insulators is important because (a) predicting theoretically that a given compound is metal even though it is found to be an insulator often creates the temptation to invoke high order novel physical effects (such as correlation in d-electron Mott insulators) to explain what was in effect caused by a more mundane artifact in a lower-level mean-field band theory, (b) recent prediction of exotic physical effects such as topological semimetals were unfortunately based on the above compounds that were misconstrued by theory to be metal, but are now recognized to be stable insulators not hosting exotic effects, and (c) practical technological applications based on stable degenerate but gapped metals such as transparent conductors or electrides for catalysis must rely on the systematically correct and reliable theoretical classification of metals vs insulators.

36 MATERIALS SCIENCE↗

DOE OSTI2011

THE MASSIVE PROGENITOR OF THE POSSIBLE TYPE II-LINEAR SUPERNOVA 2009hd IN MESSIER 66

We present early- and late-time photometric and spectroscopic observations of supernova (SN) 2009hd in the nearby spiral galaxy NGC 3627 (M66). This SN is one of the closest to us in recent years and provides an uncommon opportunity to observe and study the nature of SNe. However, the object was heavily obscured by dust, rendering it unusually faint in the optical given its proximity. We find that the observed properties of SN 2009hd support its classification as a possible Type II-Linear SN (SN II-L), a relatively rare subclass of core-collapse SNe. High-precision relative astrometry has been employed to attempt to identify an SN progenitor candidate, based on a pixel-by-pixel comparison between Hubble Space Telescope (HST) F555W and F814W images of the SN site prior to explosion and at late times. A progenitor candidate is identified in the F814W images only; this object is undetected in F555W. Significant uncertainty exists in the astrometry, such that we cannot definitively identify this object as the SN progenitor. Via insertion of artificial stars into the pre-SN HST images, we are able to constrain the progenitor's properties to those of a possible supergiant, with intrinsic absolute magnitude M {sup 0}{sub F555W} {approx}> -7.6 mag and intrinsic color (V - I){sup 0} {approx}> 0.99 mag. The magnitude and color limits are consistent with a luminous red supergiant (RSG); however, they also allow for the possibility that the star could have been more yellow than red. From a comparison with theoretical massive-star evolutionary tracks which include rotation and pulsationally enhanced mass loss, we can place a conservative upper limit on the initial mass for the progenitor of M{sub ini} {approx}< 20 M{sub Sun }. If the actual mass of the progenitor is near the upper range allowed by our derived mass limit, then it would be consistent with that for the identified progenitors of the SN II-L 2009kr and the high-luminosity SN II-Plateau (II-P) 2008cn. The progenitors of these three SNe may possibly bridge the gap between lower-mass RSGs that explode as SNe II-P and luminous blue variables, or more extreme RSGs, from which the more exotic SNe II-narrow may arise. Very late time imaging of the SN 2009hd site may provide us with more clues regarding the true nature of its progenitor.

79 ASTRONOMY AND ASTROPHYSICS↗