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- Hlozek, R., et al.
(författare)
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Results of the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC)
- 2023
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Ingår i: Astrophysical Journal Supplement Series. - 0067-0049 .- 1538-4365. ; 267:2
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Tidskriftsartikel (refereegranskat)abstract
- Next-generation surveys like the Legacy Survey of Space and Time (LSST) on the Vera C. Rubin Observatory (Rubin) will generate orders of magnitude more discoveries of transients and variable stars than previous surveys. To prepare for this data deluge, we developed the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC), a competition that aimed to catalyze the development of robust classifiers under LSST-like conditions of a nonrepresentative training set for a large photometric test set of imbalanced classes. Over 1000 teams participated in PLAsTiCC, which was hosted in the Kaggle data science competition platform between 2018 September 28 and 2018 December 17, ultimately identifying three winners in 2019 February. Participants produced classifiers employing a diverse set of machine-learning techniques including hybrid combinations and ensemble averages of a range of approaches, among them boosted decision trees, neural networks, and multilayer perceptrons. The strong performance of the top three classifiers on Type Ia supernovae and kilonovae represent a major improvement over the current state of the art within astronomy. This paper summarizes the most promising methods and evaluates their results in detail, highlighting future directions both for classifier development and simulation needs for a next-generation PLAsTiCC data set.
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- Kessler, R., et al.
(författare)
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Models and Simulations for the Photometric LSST Astronomical Time Series Classification Challenge (PLAsTiCC)
- 2019
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Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 131:1003
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Tidskriftsartikel (refereegranskat)abstract
- We describe the simulated data sample for the Photometric Large Synoptic Survey Telescope (LSST) Astronomical Time Series Classification Challenge (PLAsTiCC), a publicly available challenge to classify transient and variable events that will be observed by the LSST, a new facility expected to start in the early 2020s. The challenge was hosted by Kaggle, ran from 2018 September 28 to December 17, and included 1094 teams competing for prizes. Here we provide details of the 18 transient and variable source models, which were not revealed until after the challenge, and release the model libraries at https://doi.org/10.5281/zenodo.2612896. We describe the LSST Operations Simulator used to predict realistic observing conditions, and we describe the publicly available SNANA simulation code used to transform the models into observed fluxes and uncertainties in the LSST passbands (ugrizy). Although PLAsTiCC has finished, the publicly available models and simulation tools are being used within the astronomy community to further improve classification, and to study contamination in photometrically identified samples of SN Ia used to measure properties of dark energy. Our simulation framework will continue serving as a platform to improve the PLAsTiCC models, and to develop new models.
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| 9. |
- Garcia-Closas, Montserrat, et al.
(författare)
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Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics
- 2008
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 4:4, s. e1000054-
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Tidskriftsartikel (refereegranskat)abstract
- A three-stage genome-wide association study recently identified single nucleotide polymorphisms (SNPs) in five loci (fibroblast growth receptor 2 (FGFR2), trinucleotide repeat containing 9 (TNRC9), mitogen-activated protein kinase 3 K1 (MAP3K1), 8q24, and lymphocyte-specific protein 1 (LSP1)) associated with breast cancer risk. We investigated whether the associations between these SNPs and breast cancer risk varied by clinically important tumor characteristics in up to 23,039 invasive breast cancer cases and 26,273 controls from 20 studies. We also evaluated their influence on overall survival in 13,527 cases from 13 studies. All participants were of European or Asian origin. rs2981582 in FGFR2 was more strongly related to ER-positive (per-allele OR (95%CI) = 1.31 (1.27-1.36)) than ER-negative (1.08 (1.03-1.14)) disease (P for heterogeneity = 10(-13)). This SNP was also more strongly related to PR-positive, low grade and node positive tumors (P = 10(-5), 10(-8), 0.013, respectively). The association for rs13281615 in 8q24 was stronger for ER-positive, PR-positive, and low grade tumors (P = 0.001, 0.011 and 10(-4), respectively). The differences in the associations between SNPs in FGFR2 and 8q24 and risk by ER and grade remained significant after permutation adjustment for multiple comparisons and after adjustment for other tumor characteristics. Three SNPs (rs2981582, rs3803662, and rs889312) showed weak but significant associations with ER-negative disease, the strongest association being for rs3803662 in TNRC9 (1.14 (1.09-1.21)). rs13281615 in 8q24 was associated with an improvement in survival after diagnosis (per-allele HR = 0.90 (0.83-0.97). The association was attenuated and non-significant after adjusting for known prognostic factors. Our findings show that common genetic variants influence the pathological subtype of breast cancer and provide further support for the hypothesis that ER-positive and ER-negative disease are biologically distinct. Understanding the etiologic heterogeneity of breast cancer may ultimately result in improvements in prevention, early detection, and treatment.
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| 10. |
- Taubenberger, S., et al.
(författare)
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SN2012dn from early to late times : 09dc-like supernovae reassessed
- 2019
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 488:4, s. 5473-5488
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Tidskriftsartikel (refereegranskat)abstract
- As a candidate super-Chandrasekhar' or 09dc-like TypeIa supernova (SNIa), SN 2012dn shares many characteristics with other members of this remarkable class of objects but lacks their extraordinary luminosity. Here, we present and discuss the most comprehensive optical data set of this SN to date, comprised of a densely sampled series of early-time spectra obtained within the Nearby Supernova Factory project, plus photometry and spectroscopy obtained at the Very Large Telescope about 1yr after the explosion. The light curves, colour curves, spectral time series, and ejecta velocities of SN 2012dn are compared with those of other 09dc-like and normal SNeIa, the overall variety within the class of 09dc-like SNeIa is discussed, and new criteria for 09dc-likeness are proposed. Particular attention is directed to additional insight that the late-phase data provide. The nebular spectra show forbidden lines of oxygen and calcium, elements that are usually not seen in late-time spectra of SNeIa, while the ionization state of the emitting iron plasma is low, pointing to low ejecta temperatures and high densities. The optical light curves are characterized by an enhanced fading starting similar to 60d after maximum and very low luminosities in the nebular phase, which is most readily explained by unusually early formation of clumpy dust in the ejecta. Taken together, these effects suggest a strongly perturbed ejecta density profile, which might lend support to the idea that 09dc-like characteristics arise from a brief episode of interaction with a hydrogen-deficient envelope during the first hours or days after the explosion.
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| 11. |
- Léget, P-F, et al.
(författare)
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SUGAR : An improved empirical model of Type Ia supernovae based on spectral features
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 636
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Tidskriftsartikel (refereegranskat)abstract
- Context. Type Ia supernovae (SNe Ia) are widely used to measure the expansion of the Universe. Improving distance measurements of SNe Ia is one technique to better constrain the acceleration of expansion and determine its physical nature.Aims. This document develops a new SNe Ia spectral energy distribution (SED) model, called the SUpernova Generator And Reconstructor (SUGAR), which improves the spectral description of SNe Ia, and consequently could improve the distance measurements.Methods. This model was constructed from SNe Ia spectral properties and spectrophotometric data from the Nearby Supernova Factory collaboration. In a first step, a principal component analysis-like method was used on spectral features measured at maximum light, which allowed us to extract the intrinsic properties of SNe Ia. Next, the intrinsic properties were used to extract the average extinction curve. Third, an interpolation using Gaussian processes facilitated using data taken at different epochs during the lifetime of an SN Ia and then projecting the data on a fixed time grid. Finally, the three steps were combined to build the SED model as a function of time and wavelength. This is the SUGAR model.Results. The main advancement in SUGAR is the addition of two additional parameters to characterize SNe Ia variability. The first is tied to the properties of SNe Ia ejecta velocity and the second correlates with their calcium lines. The addition of these parameters, as well as the high quality of the Nearby Supernova Factory data, makes SUGAR an accurate and efficient model for describing the spectra of normal SNe Ia as they brighten and fade.Conclusions. The performance of this model makes it an excellent SED model for experiments like the Zwicky Transient Facility, the Large Synoptic Survey Telescope, or the Wide Field Infrared Survey Telescope.
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| 12. |
- Malz, A., et al.
(författare)
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The Photometric LSST Astronomical Time-series Classification Challenge PLAsTiCC : Selection of a Performance Metric for Classification Probabilities Balancing Diverse Science Goals
- 2019
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 158:5
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Tidskriftsartikel (refereegranskat)abstract
- Classification of transient and variable light curves is an essential step in using astronomical observations to develop an understanding of the underlying physical processes from which they arise. However, upcoming deep photometric surveys, including the Large Synoptic Survey Telescope (LSST), will produce a deluge of low signal-to-noise data for which traditional type estimation procedures are inappropriate. Probabilistic classification is more appropriate for such data but is incompatible with the traditional metrics used on deterministic classifications. Furthermore, large survey collaborations like LSST intend to use the resulting classification probabilities for diverse science objectives, indicating a need for a metric that balances a variety of goals. We describe the process used to develop an optimal performance metric for an open classification challenge that seeks to identify probabilistic classifiers that can serve many scientific interests. The Photometric LSST Astronomical Time-series Classification Challenge (PLASTICC) aims to identify promising techniques for obtaining classification probabilities of transient and variable objects by engaging a broader community beyond astronomy. Using mock classification probability submissions emulating realistically complex archetypes of those anticipated of PLASTICC, we compare the sensitivity of two metrics of classification probabilities under various weighting schemes, finding that both yield results that are qualitatively consistent with intuitive notions of classification performance. We thus choose as a metric for PLASTICC a weighted modification of the cross-entropy because it can be meaningfully interpreted in terms of information content. Finally, we propose extensions of our methodology to ever more complex challenge goals and suggest some guiding principles for approaching the choice of a metric of probabilistic data products.
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| 13. |
- Galbany, L., et al.
(författare)
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PISCO: The PMAS/PPak Integral-field Supernova Hosts Compilation
- 2018
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Ingår i: Astrophysical Journal. - : IOP PUBLISHING LTD. - 0004-637X .- 1538-4357. ; 855:2
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Tidskriftsartikel (refereegranskat)abstract
- We present the PMAS/PPak Integral-field Supernova hosts COmpilation (PISCO), which comprises integral field spectroscopy (IFS) of 232 supernova (SN) host galaxies that hosted 272 SNe, observed over several semesters with the 3.5 m telescope at the Calar Alto Observatory (CAHA). PISCO is the largest collection of SN host galaxies observed with wide-field IFS, totaling 466,347 individual spectra covering a typical spatial resolution of similar to 380 pc. Focused studies regarding specific SN Ia-related topics will be published elsewhere; this paper aims to present the properties of the SN environments, using stellar population (SP) synthesis, and the gas-phase interstellar medium, providing additional results separating stripped-envelope SNe into their subtypes. With 11,270 H ii regions detected in all galaxies, we present for the first time a statistical analysis of H ii regions, which puts H ii regions that have hosted SNe in context with all other star-forming clumps within their galaxies. SNe Ic are associated with environments that are more metal-rich and have higher EW(H alpha) and higher star formation rate within their host galaxies than the mean of all H ii regions detected within each host. This in contrast to SNe IIb, which occur in environments that are very different compared to other core-collapse SNe types. We find two clear components of young and old SPs at SNe IIn locations. We find that SNe II fast decliners tend to explode at locations where the Sigma(SFR) is more intense. Finally, we outline how a future dedicated IFS survey of galaxies in parallel to an untargeted SN search would overcome the biases in current environmental studies.
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| 14. |
- Cox, Angela, et al.
(författare)
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A common coding variant in CASP8 is associated with breast cancer risk
- 2007
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 352-358
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Tidskriftsartikel (refereegranskat)abstract
- The Breast Cancer Association Consortium (BCAC) has been established to conduct combined case-control analyses with augmented statistical power to try to confirm putative genetic associations with breast cancer. We genotyped nine SNPs for which there was some prior evidence of an association with breast cancer: CASP8 D302H (rs1045485), IGFBP3 -202 C --> A (rs2854744), SOD2 V16A (rs1799725), TGFB1 L10P (rs1982073), ATM S49C (rs1800054), ADH1B 3' UTR A --> G (rs1042026), CDKN1A S31R (rs1801270), ICAM5 V301I (rs1056538) and NUMA1 A794G (rs3750913). We included data from 9-15 studies, comprising 11,391-18,290 cases and 14,753-22,670 controls. We found evidence of an association with breast cancer for CASP8 D302H (with odds ratios (OR) of 0.89 (95% confidence interval (c.i.): 0.85-0.94) and 0.74 (95% c.i.: 0.62-0.87) for heterozygotes and rare homozygotes, respectively, compared with common homozygotes; P(trend) = 1.1 x 10(-7)) and weaker evidence for TGFB1 L10P (OR = 1.07 (95% c.i.: 1.02-1.13) and 1.16 (95% c.i.: 1.08-1.25), respectively; P(trend) = 2.8 x 10(-5)). These results demonstrate that common breast cancer susceptibility alleles with small effects on risk can be identified, given sufficiently powerful studies.
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- Esteller, Manel, et al.
(författare)
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DNA methylation patterns in hereditary human cancers mimic sporadic tumorigenesis
- 2001
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 10:26, s. 3001-3007
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Tidskriftsartikel (refereegranskat)abstract
- Cancer cells have aberrant patterns of DNA methylation including hypermethylation of gene promoter CpG islands and global demethylation of the genome. Genes that cause familial cancer, as well as other genes, can be silenced by promoter hypermethylation in sporadic tumors, but the methylation of these genes in tumors from kindreds with inherited cancer syndromes has not been well characterized. Here, we examine CpG island methylation of 10 genes (hMLH1, BRCA1, APC, LKB1, CDH1, p16(INK4a), p14(ARF), MGMT, GSTP1 and RARbeta2) and 5-methylcytosine DNA content, in inherited (n = 342) and non-inherited (n = 215) breast and colorectal cancers. Our results show that singly retained alleles of germline mutated genes are never hypermethylated in inherited tumors. However, this epigenetic change is a frequent second "hit", associated with the wild-type copy of these genes in inherited tumors where both alleles are retained. Global hypomethylation was similar between sporadic and hereditary cases, but distinct differences existed in patterns of methylation at non-familial genes. This study demonstrates that hereditary cancers "mimic" the DNA methylation patterns present in the sporadic tumors.
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