Incorporating domain knowledge into neural-guided search

Many AutoML problems involve optimizing discrete objects under a black-box reward. Neural-guided search provides a flexible means of searching these combinatorial spaces using an autoregressive recurrent neural network. A major benefit of this approach is that builds up objects sequentially--this provides an opportunity to incorporate domain knowledge into the search by directly modifying the logits emitted during sampling. In this work, we formalize a framework for incorporating such in situ priors and constraints into neural-guided search, and provide sufficient conditions for enforcing constraints. We integrate several priors and constraints from existing works into this framework, propose several new ones, and demonstrate their efficacy in informing the task of symbolic regression

Deep symbolic regression: Recovering mathematical expressions from data via risk-seeking policy gradients

Discovering the underlying mathematical expressions describing a dataset is a core challenge for artificial intelligence. This is the problem of $\textit{symbolic regression}$. Despite recent advances in training neural networks to solve complex tasks, deep learning approaches to symbolic regression are underexplored. We propose a framework that leverages deep learning for symbolic regression via a simple idea: use a large model to search the space of small models. Specifically, we use a recurrent neural network to emit a distribution over tractable mathematical expressions and employ a novel risk-seeking policy gradient to train the network to generate better-fitting expressions. Our algorithm outperforms several baseline methods (including Eureqa, the gold standard for symbolic regression) in its ability to exactly recover symbolic expressions on a series of benchmark problems, both with and without added noise. More broadly, our contributions include a framework that can be applied to optimize hierarchical, variable-length objects under a black-box performance metric, with the ability to incorporate constraints in situ, and a risk-seeking policy gradient formulation that optimizes for best-case performance instead of expected performance.Comment: Published at International Conference on Learning Representations, 202

Improving exploration in policy gradient search: Application to symbolic optimization

Many machine learning strategies designed to automate mathematical tasks leverage neural networks to search large combinatorial spaces of mathematical symbols. In contrast to traditional evolutionary approaches, using a neural network at the core of the search allows learning higher-level symbolic patterns, providing an informed direction to guide the search. When no labeled data is available, such networks can still be trained using reinforcement learning. However, we demonstrate that this approach can suffer from an early commitment phenomenon and from initialization bias, both of which limit exploration. We present two exploration methods to tackle these issues, building upon ideas of entropy regularization and distribution initialization. We show that these techniques can improve the performance, increase sample efficiency, and lower the complexity of solutions for the task of symbolic regression.Comment: Published in 1st Mathematical Reasoning in General Artificial Intelligence Workshop, ICLR 202

ALMA observations of Elias 2–24: a protoplanetary disk with multiple gaps in the Ophiuchus molecular cloud

We present ALMA 1.3 mm continuum observations at 0. 2 (25 au) resolution of Elias 2–24, one of the largest and brightest protoplanetary disks in the Ophiuchus Molecular Cloud, and we report the presence of three partially resolved concentric gaps located at ∼20, 52, and 87 au from the star. We perform radiative transfer modeling of the disk to constrain its surface density and temperature radial profile and place the disk structure in the context of mechanisms capable of forming narrow gaps such as condensation fronts and dynamical clearing by actively forming planets. In particular, we estimate the disk temperature at the locations of the gaps to be 23, 15, and 12 K (at 20, 52, and 87 au, respectively), very close to the expected snowlines of CO (23–28 K) and N2 (12–15 K). Similarly, by assuming that the widths of the gaps correspond to 4–8× the Hill radii of forming planets (as suggested by numerical simulations), we estimate planet masses in the range of 0.2 1.5 – MJup, 1.0 8.0 – MJup, and 0.02 0.15 – MJup for the inner, middle, and outer gap, respectively. Given the surface density profile of the disk, the amount of “missing mass” at the location of each one of these gaps (between 4 and 20 MJup) is more than sufficient to account for the formation of such planets.Fil: Cieza, Lucas A.. Universidad Diego Portales; ChileFil: Casassus, Simon. Universidad de Chile; ChileFil: Pérez, Sebastian. Universidad de Chile; ChileFil: Hales, Antonio. Alma Observatory; ChileFil: Cárcamo, Miguel. Universidad de Chile; ChileFil: Ansdell, Megan. University of California at Berkeley; Estados UnidosFil: Avenhaus, Henning. Universitat Zurich; SuizaFil: Bayo, Amelia. Universidad de Valparaiso; ChileFil: Bertrang, Gesa H.-M.. Universidad Diego Portales; ChileFil: Cánovas, Hector. Agencia Espacial Europea; EspañaFil: Christiaens, Valentin. Universidad de Chile; ChileFil: Dent, William. Alma Observatory; ChileFil: Ferrero, Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Gamen, Roberto Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Olofsson, Johan. Universidad de Valparaiso; ChileFil: Orcajo, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Osses, Axel. Universidad de Chile; ChileFil: Peña Ramirez, Karla. Universidad de Antofagasta; ChileFil: Principe, David. Massachusetts Institute of Technology; Estados UnidosFil: Ruíz Rodríguez, Dary. Rochester Institute Of Technology; Estados UnidosFil: Schreiber, Matthias R.. Universidad de Valparaiso; ChileFil: Plas, Gerrit van der. Univ. Grenoble Alpes; SuizaFil: Williams, Jonathan P.. Institute For Astronomy, University Of Hawaii; Estados UnidosFil: Zurlo, Alice. Universidad Diego Portales; Chil

UBVRIz Light Curves of 51 Type II Supernovae

We present a compilation of UBV RIz light curves of 51 type II supernovae discovered during the course of four different surveys during 1986 to 2003: the Cerro Tololo Supernova Survey, the Calan/Tololo Supernova Program (C&T), the Supernova Optical and Infrared Survey (SOIRS), and the Carnegie Type II Supernova Survey (CATS). The photometry is based on template-subtracted images to eliminate any potential host galaxy light contamination, and calibrated from foreground stars. This work presents these photometric data, studies the color evolution using different bands, and explores the relation between the magnitude at maximum brightness and the brightness decline parameter (s) from maximum light through the end of the recombination phase. This parameter is found to be shallower for redder bands and appears to have the best correlation in the B band. In addition, it also correlates with the plateau duration, being thus shorter (longer) for larger (smaller) s values.Comment: 110 pages, 9 Figures, 6 Tables, accepted in A

Unconventional Magnetization Processes and Thermal Runaway in Spin-Ice Dy₂Ti₂O₇

We investigate the nonequilibrium behavior of the spin-ice Dy₂Ti₂O₇ by studying its magnetization as a function of the field sweep rate. Below the enigmatic ''freezing'' temperature Tequil ≈ 600 mK, we find that even the slowest sweeps fail to yield the equilibrium magnetization curve and instead give an initially much flatter curve. For higher sweep rates, the magnetization develops sharp steps accompanied by similarly sharp peaks in the temperature of the sample. We ascribe the former behavior to the energy barriers encountered in the magnetization process, which proceeds via flipping of spins on filaments traced out by the field-driven motion of the gapped, long-range interacting magnetic monopole excitations. The peaks in temperature result from the released Zeeman energy not being carried away efficiently; the resulting heating triggers a chain reaction.Facultad de Ciencias ExactasInstituto de Investigaciones Fisicoquímicas Teóricas y AplicadasInstituto de Física La PlataInstituto de Física de Líquidos y Sistemas Biológico

Volcanism and climate change as drivers in Holocene depositional dynamic of Laguna del Maule (Andes of central Chile – 36° S)

Late Quaternary volcanic basins are active landscapes from which detailed archives of past climate and seismic and volcanic activity can be obtained. A multidisciplinary study performed on a transect of sediment cores was used to reconstruct the depositional evolution of the high-elevation Laguna del Maule (LdM) (36∘ S, 2180 m a.s.l., Chilean Andes). The recovered 5 m composite sediment sequence includes two thick turbidite units (LT1 and LT2) and numerous tephra layers (23 ash and 6 lapilli). We produced an age model based on nine new 14C AMS dates, existing 210Pb and 137Cs data, and the Quizapú ash horizon (1932 CE). According to this age model, the relatively drier Early Holocene was followed by a phase of increased productivity during the mid-Holocene and higher lake levels after 4.0 ka cal BP. Major hydroclimate transitions occurred at ca. 11, 8.0, 4.0 and 0.5 ka cal BP. Decreased summer insolation and winter precipitation due to a southward shift in the southern westerly winds and a strengthened Pacific Subtropical High could explain Early Holocene lower lake levels. Increased biological productivity during the mid-Holocene (∼8.0 to 6.0 ka cal BP) is coeval with a warm–dry phase described for much of southern South America. Periods of higher lake productivity are synchronous to a higher frequency of volcanic events. During the Late Holocene, the tephra layers show compositional changes suggesting a transition from silica-rich to silica-poor magmas at around 4.0 ka cal BP. This transition was synchronous with increased variability of sedimentary facies and geochemical proxies, indicating higher lake levels and increased moisture at LdM after 4.0 ka cal BP, most likely caused by the inception of current El Niño–Southern Oscillation and Pacific Decadal Oscillation (ENSO–PDO) dynamics in central Chile.Postprin

Neutrophil extracellular traps mediate transfer of cytoplasmic neutrophil antigens to myeloid dendritic cells toward ANCA induction and associated autoimmunity.

Antineutrophil cytoplasmic antibodies (ANCAs) target proteins normally retained within neutrophils, indicating that cell death is involved in the autoimmunity process. Still, ANCA pathogenesis remains obscure. ANCAs activate neutrophils inducing their respiratory burst and a peculiar form of cell death, named NETosis, characterized by formation of neutrophil extracellular traps (NETs), decondensed chromatin threads decorated with cytoplasmic proteins endorsed with antimicrobial activity. NETs have been consistently detected in ANCA-associated small-vessel vasculitis, and this association prompted us to test whether the peculiar structure of NET favors neutrophil proteins uploading into myeloid dendritic cells and the induction of ANCAs and associated autoimmunity. Here we show that myeloid DCs uploaded with and activated by NET components induce ANCA and autoimmunity when injected into naive mice. DC uploading and autoimmunity induction are prevented by NET treatment with DNAse, indicating that NET structural integrity is needed to maintain the antigenicity of cytoplasmic proteins. We found NET intermingling with myeloid dendritic cells also positive for neutrophil myeloperoxidase in myeloperoxidase-ANCA-associated microscopic poliangiitis providing a potential correlative picture in human pathology. These data provide the first demonstration that NET structures are highly immunogenic such to trigger adaptive immune response relevant for autoimmunity

Giant tortoise genomes provide insights into longevity and age-related disease

© 2018, The Author(s), under exclusive licence to Springer Nature Limited. Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii—and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London