MetaCAM: Ensemble-Based Class Activation Map

The need for clear, trustworthy explanations of deep learning model predictions is essential for high-criticality fields, such as medicine and biometric identification. Class Activation Maps (CAMs) are an increasingly popular category of visual explanation methods for Convolutional Neural Networks (CNNs). However, the performance of individual CAMs depends largely on experimental parameters such as the selected image, target class, and model. Here, we propose MetaCAM, an ensemble-based method for combining multiple existing CAM methods based on the consensus of the top-k% most highly activated pixels across component CAMs. We perform experiments to quantifiably determine the optimal combination of 11 CAMs for a given MetaCAM experiment. A new method denoted Cumulative Residual Effect (CRE) is proposed to summarize large-scale ensemble-based experiments. We also present adaptive thresholding and demonstrate how it can be applied to individual CAMs to improve their performance, measured using pixel perturbation method Remove and Debias (ROAD). Lastly, we show that MetaCAM outperforms existing CAMs and refines the most salient regions of images used for model predictions. In a specific example, MetaCAM improved ROAD performance to 0.393 compared to 11 individual CAMs with ranges from -0.101-0.172, demonstrating the importance of combining CAMs through an ensembling method and adaptive thresholding.Comment: 9 page

Space assets and technology for bushfire management

The financial, emotional, and ecological impacts of bushfires can be devastating. This report was prepared by the participants of the Southern Hemisphere Space Studies Program 2021 in response to the topic: “How space assets and technologies can be applied to better predict and mitigate bushfires and their impacts.” To effectively reach the diverse set of stakeholders impacted by bushfires, Communication was identified as a key enabler central to any examination of the topic. The three pillars “predict”, “mitigate” and “communicate” were identified to frame the task at hand. Combining the diverse skills and experience of the class participants with the interdisciplinary knowledge gained from the seminars, distinguished lectures, and workshops during the SHSSP21 program, conducted a literature review With specific reference to the 2019-20 Australian fire season, we looked at the current state of the art, key challenges, and how bushfires can be better predicted and mitigated in the future. Comparing this to the future desired state, we identified gaps for each of the three domains, and worked across teams to reach consensus on a list of recommendations. Several of these recommendations were derived independently by two or more of the three groups, highlighting the importance of a holistic and collaborative approach. The report details a number of recommendations arising from this Where applicable, we also aligned our discussion with the experience and lessons from other countries and agencies to consider,learn from and respond to the international context, as others develop systems using space technology to tackle similar wildfire issues

Evaluation of polygenic risk scores for breast and ovarian cancer risk prediction in BRCA1 and BRCA2 mutation carriers

Background: Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes BRCA1 or BRCA2. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. Methods: We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through population-based GWAS: for BC (overall, estrogen receptor [ER]-positive, and ER-negative) and for OC. Using data from 15 252 female BRCA1 and 8211 BRCA2 carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. Results: The PRS for ER-negative BC displayed the strongest association with BC risk in BRCA1 carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, P = 8.2 x 10(53)). In BRCA2 carriers, the strongest association with BC risk was seen for the overall BC PRS (HR = 1.22, 95% CI = 1.17 to 1.28, P = 7.2 x 10(-20)). The OC PRS was strongly associated with OC risk for both BRCA1 and BRCA2 carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for BRCA2 carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. Conclusions: BC and OC PRS are predictive of cancer risk in BRCA1 and BRCA2 carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management

Timing of eating across ten European countries - results from the European Prospective Investigation into Cancer and Nutrition (EPIC) calibration study

Objective To examine timing of eating across ten European countries. Design Cross-sectional analysis of the European Prospective Investigation into Cancer and Nutrition (EPIC) calibration study using standardized 24 h diet recalls collected during 1995-2000. Eleven predefined food consumption occasions were assessed during the recall interview. We present time of consumption of meals and snacks as well as the later:earlier energy intake ratio, with earlier and later intakes defined as 06.00-14.00 and 15.00-24.00 hours, respectively. Type III tests were used to examine associations of sociodemographic, lifestyle and health variables with timing of energy intake. Setting Ten Western European countries. Subjects In total, 22 985 women and 13 035 men aged 35-74 years (n 36 020). Results A south-north gradient was observed for timing of eating, with later consumption of meals and snacks in Mediterranean countries compared with Central and Northern European countries. However, the energy load was reversed, with the later:earlier energy intake ratio ranging from 0 center dot 68 (France) to 1 center dot 39 (Norway) among women, and from 0 center dot 71 (Greece) to 1 center dot 35 (the Netherlands) among men. Among women, country, age, education, marital status, smoking, day of recall and season were all independently associated with timing of energy intake (all PPeer reviewe

A fast radio burst localized at detection to a galactic disk using very long baseline interferometry

Fast radio bursts (FRBs) are millisecond-duration, luminous radio transients of extragalactic origin. These events have been used to trace the baryonic structure of the Universe using their dispersion measure (DM) assuming that the contribution from host galaxies can be reliably estimated. However, contributions from the immediate environment of an FRB may dominate the observed DM, thus making redshift estimates challenging without a robust host galaxy association. Furthermore, while at least one Galactic burst has been associated with a magnetar, other localized FRBs argue against magnetars as the sole progenitor model. Precise localization within the host galaxy can discriminate between progenitor models, a major goal of the field. Until now, localizations on this spatial scale have only been carried out in follow-up observations of repeating sources. Here we demonstrate the localization of FRB 20210603A with very long baseline interferometry (VLBI) on two baselines, using data collected only at the time of detection. We localize the burst to SDSS J004105.82+211331.9, an edge-on galaxy at $z\approx 0.177$, and detect recent star formation in the kiloparsec-scale vicinity of the burst. The edge-on inclination of the host galaxy allows for a unique comparison between the line of sight towards the FRB and lines of sight towards known Galactic pulsars. The DM, Faraday rotation measure (RM), and scattering suggest a progenitor coincident with the host galactic plane, strengthening the link between the environment of FRB 20210603A and the disk of its host galaxy. Single-pulse VLBI localizations of FRBs to within their host galaxies, following the one presented here, will further constrain the origins and host environments of one-off FRBs.Comment: 40 pages, 13 figures, submitted. Fixed typo in abstrac

CHIME/FRB Discovery of 25 Repeating Fast Radio Burst Sources

We present the discovery of 25 new repeating fast radio burst (FRB) sources found among CHIME/FRB events detected between 2019 September 30 and 2021 May 1. The sources were found using a new clustering algorithm that looks for multiple events co-located on the sky having similar dispersion measures (DMs). The new repeaters have DMs ranging from $\sim$220 pc cm$^{-3}$ to $\sim$1700 pc cm$^{-3}$, and include sources having exhibited as few as two bursts to as many as twelve. We report a statistically significant difference in both the DM and extragalactic DM (eDM) distributions between repeating and apparently nonrepeating sources, with repeaters having lower mean DM and eDM, and we discuss the implications. We find no clear bimodality between the repetition rates of repeaters and upper limits on repetition from apparently nonrepeating sources after correcting for sensitivity and exposure effects, although some active repeating sources stand out as anomalous. We measure the repeater fraction and find that it tends to an equilibrium of $2.6_{-2.6}^{+2.9}$% over our exposure thus far. We also report on 14 more sources which are promising repeating FRB candidates and which merit follow-up observations for confirmation.Comment: Submitted to ApJ. Comments are welcome and follow-up observations are encouraged

Sub-second periodicity in a fast radio burst

Fast radio bursts (FRBs) are millisecond-duration flashes of radio waves that are visible at distances of billions of light-years. The nature of their progenitors and their emission mechanism remain open astrophysical questions. Here we report the detection of the multi-component FRB 20191221A and the identification of a periodic separation of 216.8(1) ms between its components with a significance of 6.5 sigmas. The long (~3 s) duration and nine or more components forming the pulse profile make this source an outlier in the FRB population. Such short periodicity provides strong evidence for a neutron-star origin of the event. Moreover, our detection favours emission arising from the neutron-star magnetosphere, as opposed to emission regions located further away from the star, as predicted by some models.Comment: Updated to conform to the accepted versio

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

<p>Abstract</p> <p>Background</p> <p>Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, <it>Arabidopsis thaliana</it>, provides means to explore their genomic complexity.</p> <p>Results</p> <p>A genome-wide physical map of a rapid-cycling strain of <it>B. oleracea </it>was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of <it>B. oleracea </it>and <it>Arabidopsis thaliana</it>, a relatively high level of genomic change since their divergence. Comparison of the <it>B. oleracea </it>physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity.</p> <p>Conclusions</p> <p>A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes.</p> <p>All the physical mapping data is freely shared at a WebFPC site (<url>http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/</url>; Temporarily password-protected: account: pgml; password: 123qwe123.</p

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures

Background Accurate cancer classification is essential for correct treatment selection and better prognostication. microRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression, and their dyresgulation is a common disease mechanism in many cancers. Through a clearer understanding of miRNA dysregulation in cancer, improved mechanistic knowledge and better treatments can be sought. Results We present a topology-preserving deep learning framework to study miRNA dysregulation in cancer. Our study comprises miRNA expression profiles from 3685 cancer and non-cancer tissue samples and hierarchical annotations on organ and neoplasticity status. Using unsupervised learning, a two-dimensional topological map is trained to cluster similar tissue samples. Labelled samples are used after training to identify clustering accuracy in terms of tissue-of-origin and neoplasticity status. In addition, an approach using activation gradients is developed to determine the attention of the networks to miRNAs that drive the clustering. Using this deep learning framework, we classify the neoplasticity status of held-out test samples with an accuracy of 91.07%, the tissue-of-origin with 86.36%, and combined neoplasticity status and tissue-of-origin with an accuracy of 84.28%. The topological maps display the ability of miRNAs to recognize tissue types and neoplasticity status. Importantly, when our approach identifies samples that do not cluster well with their respective classes, activation gradients provide further insight in cancer subtypes or grades. Conclusions An unsupervised deep learning approach is developed for cancer classification and interpretation. This work provides an intuitive approach for understanding molecular properties of cancer and has significant potential for cancer classification and treatment selection.Applied Science, Faculty ofNon UBCElectrical and Computer Engineering, Department ofReviewedFacultyResearche