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Ensuring Access to Safe and Nutritious Food for All Through the Transformation of Food Systems
ADS_UNet: A Nested UNet for Histopathology Image Segmentation
The UNet model consists of fully convolutional network (FCN) layers arranged
as contracting encoder and upsampling decoder maps. Nested arrangements of
these encoder and decoder maps give rise to extensions of the UNet model, such
as UNete and UNet++. Other refinements include constraining the outputs of the
convolutional layers to discriminate between segment labels when trained end to
end, a property called deep supervision. This reduces feature diversity in
these nested UNet models despite their large parameter space. Furthermore, for
texture segmentation, pixel correlations at multiple scales contribute to the
classification task; hence, explicit deep supervision of shallower layers is
likely to enhance performance. In this paper, we propose ADS UNet, a stage-wise
additive training algorithm that incorporates resource-efficient deep
supervision in shallower layers and takes performance-weighted combinations of
the sub-UNets to create the segmentation model. We provide empirical evidence
on three histopathology datasets to support the claim that the proposed ADS
UNet reduces correlations between constituent features and improves performance
while being more resource efficient. We demonstrate that ADS_UNet outperforms
state-of-the-art Transformer-based models by 1.08 and 0.6 points on CRAG and
BCSS datasets, and yet requires only 37% of GPU consumption and 34% of training
time as that required by Transformers.Comment: To be published in Expert Systems With Application
Changes in soil fertility and microbial communities following cultivation of native grassland in Horqin Sandy Land, China: a 60-year chronosequence
Background: Grassland conversion to cropland is a prevailing change of land use in traditionally nomadic areas, especially in the Mongolian Plateau. We investigated the effects of grassland conversion followed by continuous cultivation on soil properties and microbial community characteristics in Horqin Sandy Land, a typical agro-pastoral transition zone of Northern China. Soil samples were collected from the topsoil (upper 20 cm) across a 60-year cultivation chronosequence (5, 15, 25, 35 and 60 years) and unconverted native grassland. Soil physico-chemical properties were determined and high-throughput sequencing was used to assess microbial community diversity and composition. Results: Grassland cultivation resulted in changes to soil properties in both the short and longer term. Initially, it significantly increased soil bulk density (BD), electrical conductivity (EC), soil total nitrogen (TN), available phosphorus (AP) and available potassium (AK) concentrations, while reducing soil water content (SWC) and soil organic carbon content (SOC). Over the next 35–55 years of continuous cultivation, the trend for most of these characteristics was of reversion towards values nearer to those of native grassland, except for SOC which remained highly depleted. Cultivation of grassland substantially altered soil microbial communities at phylum level but there was no significant difference in microbial α-diversity between native grassland and any cropland. However, soil bacterial and fungal community structures at phylum level in the croplands of all cultivation years were different from those in the native grasslands. Heatmaps further revealed that bacterial and fungal structures in cropland tended to become more similar to native grassland after 15 and 25 years of cultivation, respectively. Redundancy analysis indicated that SOC, EC and BD were primary determinants of microbial community composition and diversity. Conclusions: These findings suggest that agricultural cultivation of grassland has considerable effects on soil fertility and microbial characteristics of Horqin Sandy Land. Intensive high-yield forage grass production is proposed as an alternative to avoid further native grassland reclamation, while meeting the grazing development needs in the ethnic minority settlements of eco-fragile regions
Reinforcing optimization enabled interactive approach for liver tumor extraction in computed tomography images
Detecting liver abnormalities is a difficult task in radiation planning and treatment. The modern development integrates medical imaging into computer techniques. This advancement has monumental effect on how medical images are interpreted and analyzed. In many circumstances, manual segmentation of liver from computerized tomography (CT) imaging is imperative, and cannot provide satisfactory results. However, there are some difficulties in segmenting the liver due to its uneven shape, fuzzy boundary and complicated structure. This leads to necessity of enabling optimization in interactive segmentation approach. The main objective of reinforcing optimization is to search the optimal threshold and reduce the chance of falling into local optimum with survival of the fittest (SOF) technique. The proposed methodology makes use of pre-processing stage and reinforcing meta heuristics optimization based fuzzy c-means (FCM) for obtaining detailed information about the image. This information gives the optimal threshold value that is used for segmenting the region of interest with minimum user input. Suspicious areas are recognized from the segmented output. Both public and simulated dataset have been taken for experimental purposes. To validate the effectiveness of the proposed strategy, performance criteria such as dice coefficient, mode and user interaction level are taken and compared with state-of-the-art algorithms
OpenContrails: Benchmarking Contrail Detection on GOES-16 ABI
Contrails (condensation trails) are line-shaped ice clouds caused by aircraft
and are likely the largest contributor of aviation-induced climate change.
Contrail avoidance is potentially an inexpensive way to significantly reduce
the climate impact of aviation. An automated contrail detection system is an
essential tool to develop and evaluate contrail avoidance systems. In this
paper, we present a human-labeled dataset named OpenContrails to train and
evaluate contrail detection models based on GOES-16 Advanced Baseline Imager
(ABI) data. We propose and evaluate a contrail detection model that
incorporates temporal context for improved detection accuracy. The human
labeled dataset and the contrail detection outputs are publicly available on
Google Cloud Storage at gs://goes_contrails_dataset
Path integrals and stochastic calculus
Path integrals are a ubiquitous tool in theoretical physics. However, their
use is sometimes hindered by the lack of control on various manipulations --
such as performing a change of the integration path -- one would like to carry
out in the light-hearted fashion that physicists enjoy. Similar issues arise in
the field of stochastic calculus, which we review to prepare the ground for a
proper construction of path integrals. At the level of path integration, and in
arbitrary space dimension, we not only report on existing Riemannian
geometry-based approaches that render path integrals amenable to the standard
rules of calculus, but also bring forth new routes, based on a fully
time-discretized approach, that achieve the same goal. We illustrate these
various definitions of path integration on simple examples such as the
diffusion of a particle on a sphere.Comment: 96 pages, 4 figures. New title, expanded introduction and additional
references. Version accepted in Advandes in Physic
Floquet Weyl semimetal phases in light-irradiated higher-order topological Dirac semimetals
Floquet engineering, the concept of tailoring a system by a periodic drive,
is increasingly exploited to design and manipulate topological phases of
matter. In this work, we study periodically driven higher-order topological
Dirac semimetals associated with a -dependent quantized quadrupole moment by
applying circularly polarized light. The undriven Dirac semimetals feature
gapless higher-order hinge Fermi arc states which are the consequence of the
higher-order topology of the Dirac nodes. Floquet Weyl semimetal phases with
hybrid-order topology, characterized by both a -dependent quantized
quadrupole moment and a -dependent Chern number, emerge when illumining
circularly polarized light. Such Floquet Weyl semimetals support both hinge
Fermi arc states and topological surface Fermi arc states. In addition, Floquet
Weyl semimetals with tilted Weyl cones in higher-order topological Dirac
semimetals are also discussed. Considering numerous higher-order topological
Dirac semimetal materials were recently proposed, our findings can be testable
soon.Comment: Accepted for publication as a Letter in Phys. Rev.
Model Diagnostics meets Forecast Evaluation: Goodness-of-Fit, Calibration, and Related Topics
Principled forecast evaluation and model diagnostics are vital in fitting probabilistic models and forecasting outcomes of interest. A common principle is that fitted or predicted distributions ought to be calibrated, ideally in the sense that the outcome is indistinguishable from a random draw from the posited distribution. Much of this thesis is centered on calibration properties of various types of forecasts.
In the first part of the thesis, a simple algorithm for exact multinomial goodness-of-fit tests is proposed. The algorithm computes exact -values based on various test statistics, such as the log-likelihood ratio and Pearson\u27s chi-square. A thorough analysis shows improvement on extant methods. However, the runtime of the algorithm grows exponentially in the number of categories and hence its use is limited.
In the second part, a framework rooted in probability theory is developed, which gives rise to hierarchies of calibration, and applies to both predictive distributions and stand-alone point forecasts. Based on a general notion of conditional T-calibration, the thesis introduces population versions of T-reliability diagrams and revisits a score decomposition into measures of miscalibration, discrimination, and uncertainty. Stable and efficient estimators of T-reliability diagrams and score components arise via nonparametric isotonic regression and the pool-adjacent-violators algorithm. For in-sample model diagnostics, a universal coefficient of determination is introduced that nests and reinterprets the classical in least squares regression.
In the third part, probabilistic top lists are proposed as a novel type of prediction in classification, which bridges the gap between single-class predictions and predictive distributions. The probabilistic top list functional is elicited by strictly consistent evaluation metrics, based on symmetric proper scoring rules, which admit comparison of various types of predictions
The MeerKAT Galaxy Cluster Legacy Survey: Survey overview and highlights
MeerKAT’s large number (64) of 13.5 m diameter antennas, spanning 8 km with a densely packed 1 km core, create a powerful instrument for wide-area surveys, with high sensitivity over a wide range of angular scales. The MeerKAT Galaxy Cluster Legacy Survey (MGCLS) is a programme of long-track MeerKAT L-band (900−1670 MHz) observations of 115 galaxy clusters, observed for ∼6−10 h each in full polarisation. The first legacy product data release (DR1), made available with this paper, includes the MeerKAT visibilities, basic image cubes at ∼8″ resolution, and enhanced spectral and polarisation image cubes at ∼8″ and 15″ resolutions. Typical sensitivities for the full-resolution MGCLS image products range from ∼3−5 μJy beam−1. The basic cubes are full-field and span 2° × 2°. The enhanced products consist of the inner 1.2° × 1.2° field of view, corrected for the primary beam. The survey is fully sensitive to structures up to ∼10′ scales, and the wide bandwidth allows spectral and Faraday rotation mapping. Relatively narrow frequency channels (209 kHz) are also used to provide H I mapping in windows of 0 < z < 0.09 and 0.19 < z < 0.48. In this paper, we provide an overview of the survey and the DR1 products, including caveats for usage. We present some initial results from the survey, both for their intrinsic scientific value and to highlight the capabilities for further exploration with these data. These include a primary-beam-corrected compact source catalogue of ∼626 000 sources for the full survey and an optical and infrared cross-matched catalogue for compact sources in the primary-beam-corrected areas of Abell 209 and Abell S295. We examine dust unbiased star-formation rates as a function of cluster-centric radius in Abell 209, extending out to 3.5 R 200. We find no dependence of the star-formation rate on distance from the cluster centre, and we observe a small excess of the radio-to-100 μm flux ratio towards the centre of Abell 209 that may reflect a ram pressure enhancement in the denser environment. We detect diffuse cluster radio emission in 62 of the surveyed systems and present a catalogue of the 99 diffuse cluster emission structures, of which 56 are new. These include mini-halos, halos, relics, and other diffuse structures for which no suitable characterisation currently exists. We highlight some of the radio galaxies that challenge current paradigms, such as trident-shaped structures, jets that remain well collimated far beyond their bending radius, and filamentary features linked to radio galaxies that likely illuminate magnetic flux tubes in the intracluster medium. We also present early results from the H I analysis of four clusters, which show a wide variety of H I mass distributions that reflect both sensitivity and intrinsic cluster effects, and the serendipitous discovery of a group in the foreground of Abell 3365
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