Explaining deep neural networks: A survey on the global interpretation methods

A substantial amount of research has been carried out in Explainable Artificial Intelligence (XAI) models, especially in those which explain the deep architectures of neural networks. A number of XAI approaches have been proposed to achieve trust in Artificial Intelligence (AI) models as well as provide explainability of specific decisions made within these models. Among these approaches, global interpretation methods have emerged as the prominent methods of explainability because they have the strength to explain every feature and the structure of the model. This survey attempts to provide a comprehensive review of global interpretation methods that completely explain the behaviour of the AI models. We present a taxonomy of the available global interpretations models and systematically highlight the critical features and algorithms that differentiate them from local as well as hybrid models of explainability. Through examples and case studies from the literature, we evaluate the strengths and weaknesses of the global interpretation models and assess challenges when these methods are put into practice. We conclude the paper by providing the future directions of research in how the existing challenges in global interpretation methods could be addressed and what values and opportunities could be realized by the resolution of these challenges

Addition of the lewis acid Zn(C6 F5 )2 enables organic transistors with a maximum hole mobility in excess of 20 cm2 V-1 s-1

Incorporating the molecular organic Lewis acid tris(pentafluorophenyl)borane [B(C6 F5 )3 ] into organic semiconductors has shown remarkable promise in recent years for controlling the operating characteristics and performance of various opto/electronic devices, including, light-emitting diodes, solar cells, and organic thin-film transistors (OTFTs). Despite the demonstrated potential, however, to date most of the work has been limited to B(C6 F5 )3 with the latter serving as the prototypical air-stable molecular Lewis acid system. Herein, the use of bis(pentafluorophenyl)zinc [Zn(C6 F5 )2 ] is reported as an alternative Lewis acid additive in high-hole-mobility OTFTs based on small-molecule:polymer blends comprising 2,7-dioctyl[1]benzothieno [3,2-b][1]benzothiophene and indacenodithiophene-benzothiadiazole. Systematic analysis of the materials and device characteristics supports the hypothesis that Zn(C6 F5 )2 acts simultaneously as a p-dopant and a microstructure modifier. It is proposed that it is the combination of these synergistic effects that leads to OTFTs with a maximum hole mobility value of 21.5 cm2 V-1 s-1 . The work not only highlights Zn(C6 F5 )2 as a promising new additive for next-generation optoelectronic devices, but also opens up new avenues in the search for high-mobility organic semiconductors

A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage

Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four genera of the order Enterobacterales, primarily Escherichia coli, were purified from livestock (cattle, pigs and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long- and short-read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although E. coli isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep isolates, with cattle isolates being intermediates. Approximately 28 % of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90 % of sequenced isolates harboured diverse plasmids, only 11 % of plasmids (n=58 out of 522) identified contained AMR genes, with 91 % of AMR plasmids being from pig, 9 % from cattle and none from sheep isolates; these results indicated that pigs were a principle reservoir of AMR genes harboured by plasmids and likely to be involved in their horizontal transfer. Significant associations were observed between AMU (mg kg−1) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than those from other livestock species. Therefore, our results indicate that AMR prevalence in livestock is not only influenced by recent AMU on-farm but also livestock-related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmission

Genomic network analysis of environmental and livestock F-type 1 plasmid populations

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation

Effect of early vasopressin vs norepinephrine on kidney failure in patients with septic shock. The VANISH Randomized Clinical Trial

IMPORTANCE: Norepinephrine is currently recommended as the first-line vasopressor in septic shock; however, early vasopressin use has been proposed as an alternative. OBJECTIVE: To compare the effect of early vasopressin vs norepinephrine on kidney failure in patients with septic shock. DESIGN, SETTING, AND PARTICIPANTS: A factorial (2×2), double-blind, randomized clinical trial conducted in 18 general adult intensive care units in the United Kingdom between February 2013 and May 2015, enrolling adult patients who had septic shock requiring vasopressors despite fluid resuscitation within a maximum of 6 hours after the onset of shock. INTERVENTIONS: Patients were randomly allocated to vasopressin (titrated up to 0.06 U/min) and hydrocortisone (n = 101), vasopressin and placebo (n = 104), norepinephrine and hydrocortisone (n = 101), or norepinephrine and placebo (n = 103). MAIN OUTCOMES AND MEASURES: The primary outcome was kidney failure-free days during the 28-day period after randomization, measured as (1) the proportion of patients who never developed kidney failure and (2) median number of days alive and free of kidney failure for patients who did not survive, who experienced kidney failure, or both. Rates of renal replacement therapy, mortality, and serious adverse events were secondary outcomes. RESULTS: A total of 409 patients (median age, 66 years; men, 58.2%) were included in the study, with a median time to study drug administration of 3.5 hours after diagnosis of shock. The number of survivors who never developed kidney failure was 94 of 165 patients (57.0%) in the vasopressin group and 93 of 157 patients (59.2%) in the norepinephrine group (difference, -2.3% [95% CI, -13.0% to 8.5%]). The median number of kidney failure-free days for patients who did not survive, who experienced kidney failure, or both was 9 days (interquartile range [IQR], 1 to -24) in the vasopressin group and 13 days (IQR, 1 to -25) in the norepinephrine group (difference, -4 days [95% CI, -11 to 5]). There was less use of renal replacement therapy in the vasopressin group than in the norepinephrine group (25.4% for vasopressin vs 35.3% for norepinephrine; difference, -9.9% [95% CI, -19.3% to -0.6%]). There was no significant difference in mortality rates between groups. In total, 22 of 205 patients (10.7%) had a serious adverse event in the vasopressin group vs 17 of 204 patients (8.3%) in the norepinephrine group (difference, 2.5% [95% CI, -3.3% to 8.2%]). CONCLUSIONS AND RELEVANCE: Among adults with septic shock, the early use of vasopressin compared with norepinephrine did not improve the number of kidney failure-free days. Although these findings do not support the use of vasopressin to replace norepinephrine as initial treatment in this situation, the confidence interval included a potential clinically important benefit for vasopressin, and larger trials may be warranted to assess this further. TRIAL REGISTRATION: clinicaltrials.gov Identifier: ISRCTN 20769191

Edge stabilization in reduced-dimensional perovskites

Reduced-dimensional perovskites are attractive light-emitting materials due to their efficient luminescence, color purity, tunable bandgap, and structural diversity. A major limitation in perovskite light-emitting diodes is their limited operational stability. Here we demonstrate that rapid photodegradation arises from edge-initiated photooxidation, wherein oxidative attack is powered by photogenerated and electrically-injected carriers that diffuse to the nanoplatelet edges and produce superoxide. We report an edge-stabilization strategy wherein phosphine oxides passivate unsaturated lead sites during perovskite crystallization. With this approach, we synthesize reduced-dimensional perovskites that exhibit 97 ± 3% photoluminescence quantum yields and stabilities that exceed 300 h upon continuous illumination in an air ambient. We achieve green-emitting devices with a peak external quantum efficiency (EQE) of 14% at 1000 cd m-2; their maximum luminance is 4.5 × 104 cd m-2 (corresponding to an EQE of 5%); and, at 4000 cd m-2, they achieve an operational half-lifetime of 3.5 h.This publication is based in part on work supported by an award (KUS-11-009-21) from the King Abdullah University of Science and Technology (KAUST), by the Ontario Research Fund Research Excellence Program, by the Ontario Research Fund (ORF), by the Natural Sciences and Engineering Research Council (NSERC) of Canada, and by the US Department of Navy, Office of Naval Research (Grant Award No. N00014-17-1-2524). H.Y. acknowledges the Research Foundation-Flanders (FWO Vlaanderen) for a postdoctoral fellowship. E.B. gratefully acknowledges financial support by the Research Foundation-Flanders (FWO Vlaanderen). S.B. acknowledges financial support from European Research Council (ERC Starting Grant #815128-REALNANO). M.B.J.R. and J.H. acknowledge the Research Foundation-Flanders (FWO, Grants G.0962.13, G.0B39.15, AKUL/11/14 and G0H6316N), KU Leuven Research Fund (C14/15/053) and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No. [307523], ERC-Stg LIGHT to M.B.J.R. DFT calculations were performed on the IBM BlueGene Q supercomputer with support from the Southern Ontario Smart Computing Innovation Platform (SOSCIP). M.I.S. acknowledges the Banting Postdoctoral Fellowship program from the Natural Sciences and Engineering Research Council of Canada (NSERC). H.T. acknowledges the Netherlands Organisation for Scientific Research (NWO) for a Rubicon grant (680-50-1511)

Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma

Patients with multiple myeloma (MM) who are treated with lenalidomide rarely develop a secondary B-cell acute lymphoblastic leukemia (B-ALL). The clonal and biological relationship between these sequential malignancies is not yet clear. We identified 17 patients with MM treated with lenalidomide, who subsequently developed B-ALL. Patient samples were evaluated through sequencing, cytogenetics/fluorescence in situ hybridization (FISH), immunohistochemical (IHC) staining, and immunoglobulin heavy chain (IgH) clonality assessment. Samples were assessed for shared mutations and recurrently mutated genes. Through whole exome sequencing and cytogenetics/FISH analysis of 7 paired samples (MM vs matched B-ALL), no mutational overlap between samples was observed. Unique dominant IgH clonotypes between the tumors were observed in 5 paired MM/B-ALL samples. Across all 17 B-ALL samples, 14 (83%) had a TP53 variant detected. Three MM samples with sufficient sequencing depth (\u3e500×) revealed rare cells (average of 0.6% variant allele frequency, or 1.2% of cells) with the same TP53 variant identified in the subsequent B-ALL sample. A lack of mutational overlap between MM and B-ALL samples shows that B-ALL developed as a second malignancy arising from a founding population of cells that likely represented unrelated clonal hematopoiesis caused by a TP53 mutation. The recurrent variants in TP53 in the B-ALL samples suggest a common path for malignant transformation that may be similar to that of TP53-mutant, treatment-related acute myeloid leukemia. The presence of rare cells containing TP53 variants in bone marrow at the initiation of lenalidomide treatment suggests that cellular populations containing TP53 variants expand in the presence of lenalidomide to increase the likelihood of B-ALL development

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo