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Article
| Open AccessReduction in mobility and COVID-19 transmission
Social distancing policies aiming to reduce COVID-19 transmission have been reflected in reductions in human mobility. Here, the authors show that reduced mobility is correlated with decreased transmission, but that this relationship weakened over time as social distancing measures were relaxed.
- Pierre Nouvellet
- , Sangeeta Bhatia
- & Christl A. Donnelly
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Article
| Open AccessBiological and therapeutic implications of a unique subtype of NPM1 mutated AML
Molecular heterogeneity of acute myeloid leukaemia (AML) across patients is a major challenge for prognosis and therapy. Here, the authors show that NPM1 mutated AML is a heterogeneous class, consisting of two subtypes which exhibit distinct molecular characteristics, differentiation state, patient survival and drug response.
- Arvind Singh Mer
- , Emily M. Heath
- & Benjamin Haibe-Kains
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Article
| Open AccessLoop competition and extrusion model predicts CTCF interaction specificity
Boundaries of topologically associated domains in genomes are marked by CTCF and cohesin binding. Here the authors predict CTCF interaction specificity by building a simple mathematical model with features including loop competition and extrusion.
- Wang Xi
- & Michael A. Beer
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Article
| Open AccessA scalable physician-level deep learning algorithm detects universal trauma on pelvic radiographs
Pelvic radiographs (PXRs) are essential for detecting proximal femur and pelvis injuries in trauma patients, but none of the currently available algorithms can detect all kinds of trauma-related radiographic findings. Here, the authors develop a multiscale deep learning algorithm trained with weakly supervised point annotation.
- Chi-Tung Cheng
- , Yirui Wang
- & Le Lu
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Article
| Open AccessPhenotypic covariance across the entire spectrum of relatedness for 86 billion pairs of individuals
Assigning inter-individual similarities to genetic and non-genetic factors is central to quantitative genetics. Here, the authors look at phenotypic covariance among pairs of individuals for 32 traits across the UK Biobank, from nominally unrelated pairs through to monozygotic twins.
- Kathryn E. Kemper
- , Loic Yengo
- & Peter M. Visscher
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Article
| Open AccessPredicting mammalian hosts in which novel coronaviruses can be generated
Homologous recombination between co-infecting coronaviruses can produce novel pathogens. Here, Wardeh et al. develop a machine learning approach to predict associations between mammals and multiple coronaviruses and hence estimate the potential for generation of novel coronaviruses by recombination.
- Maya Wardeh
- , Matthew Baylis
- & Marcus S. C. Blagrove
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Article
| Open AccessModelling safe protocols for reopening schools during the COVID-19 pandemic in France
The role of children in the spread of COVID-19 is not fully understood, and the circumstances under which schools should be opened are therefore debated. Here, the authors demonstrate protocols by which schools in France can be safely opened without overwhelming the healthcare system.
- Laura Di Domenico
- , Giulia Pullano
- & Vittoria Colizza
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Article
| Open AccessAnalysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features
Here, the authors analyze 4907 Circular Metagenome Assembled Genomes from human microbiomes and identify and characterize nearly 600 diverse genomes of crAss-like phages, finding two putative families with unusual genomic features, including high density of self-splicing introns and inteins.
- Natalya Yutin
- , Sean Benler
- & Eugene V. Koonin
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Article
| Open AccessCausal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing
Given the severity of the SARS-CoV-2 pandemic, a major challenge is to rapidly repurpose existing approved drugs for clinical interventions. Here, the authors identify robust druggable protein targets within a principled causal framework that makes use of multiple data modalities and integrates aging signatures.
- Anastasiya Belyaeva
- , Louis Cammarata
- & Caroline Uhler
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Article
| Open AccessFast and precise single-cell data analysis using a hierarchical autoencoder
Accurate analysis of single-cell RNA sequencing (scRNA-seq) data is affected by issues including technical noise and high dropout rate. Here, the authors develop a hierarchical autoencoder, scDHA, which outperforms existing methods in scRNA-seq analyses such as cell segregation and classification.
- Duc Tran
- , Hung Nguyen
- & Tin Nguyen
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Article
| Open AccessPrimeDesign software for rapid and simplified design of prime editing guide RNAs
Prime editing guide RNA design is more complex than for standard CRISPR-based nucleases or base editors. Here the authors present PrimeDesign and PrimeVar for the rapid and simplified design of pegRNA and ngRNA combinations.
- Jonathan Y. Hsu
- , Julian Grünewald
- & Luca Pinello
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Article
| Open AccessMachine learning identifies candidates for drug repurposing in Alzheimer’s disease
Clinical trials of novel therapeutics for Alzheimer’s Disease (AD) have provided largely negative results, so far. Here, the authors present a machine learning framework that quantifies potential associations between the pathology of AD severity and gene-based molecular mechanisms to enable drug repurposing.
- Steve Rodriguez
- , Clemens Hug
- & Artem Sokolov
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Article
| Open AccessRare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism
Metabolites are indicators of health and disease; genetic studies can reveal variants influencing their levels. Here, the authors investigate the contribution of rare, exonic variants on the levels of urine metabolites and generate predictions on metabolic consequences underlying metabolic disease.
- Yurong Cheng
- , Pascal Schlosser
- & Anna Köttgen
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Article
| Open AccessRNA secondary structure prediction using deep learning with thermodynamic integration
Accurately predicting the secondary structure of non-coding RNAs can help unravel their function. Here the authors propose a method integrating thermodynamic information and deep learning to improve the robustness of RNA secondary structure prediction compared to several existing algorithms.
- Kengo Sato
- , Manato Akiyama
- & Yasubumi Sakakibara
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Article
| Open AccessAutomatic deep learning-driven label-free image-guided patch clamp system
Patch clamp recording of neurons is slow and labor-intensive. Here the authors present a method for automated deep learning driven label-free image guided patch clamp physiology to perform measurements on hundreds of human and rodent neurons.
- Krisztian Koos
- , Gáspár Oláh
- & Peter Horvath
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Article
| Open AccessLETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C
Long noncoding RNAs regulate tissue-specific gene expression. Here the authors profile lineage-specific lncRNAs in human dermal lymphatic and blood vascular endothelial cells (LECs and BECs) and show a role of LEC-specific lncRNA, LETR1, in cell proliferation and migration.
- Luca Ducoli
- , Saumya Agrawal
- & Michael Detmar
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Article
| Open AccessReplication dynamics of recombination-dependent replication forks
Replication forks that are stalled at obstacles on the DNA template can be restarted by homologous recombination. Here, the authors show replication dynamics during homologous recombination-dependent replication fork restart by combining polymerase usage sequencing and a Monte Carlo mathematical model.
- Karel Naiman
- , Eduard Campillo-Funollet
- & Antony M. Carr
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Article
| Open AccessForecasting influenza activity using machine-learned mobility map
Human mobility plays a central role in the spread of infectious diseases and can help in forecasting incidence. Here the authors show a comparison of multiple mobility benchmarks in forecasting influenza, and demonstrate the value of a machine-learned mobility map with global coverage at multiple spatial scales.
- Srinivasan Venkatramanan
- , Adam Sadilek
- & Madhav Marathe
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Article
| Open AccessGenetic predictors of participation in optional components of UK Biobank
Large BioBank studies are commonly used in GWAS, but may be biased by factors affecting participation and dropout. Here the authors show that some of the factors affecting participation may have underlying genetic components.
- Jessica Tyrrell
- , Jie Zheng
- & Kate Tilling
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Article
| Open AccessQuantifying population contact patterns in the United States during the COVID-19 pandemic
Physical distancing measures have been widely adopted to reduce the spread of COVID-19. This study quantifies changes in interpersonal contact patterns in the US and finds an 82% reduction in contacts during early lockdowns in March and steady increases thereafter.
- Dennis M. Feehan
- & Ayesha S. Mahmud
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Article
| Open AccessGenome-wide fine-mapping identifies pleiotropic and functional variants that predict many traits across global cattle populations
Genomic prediction of phenotype may be improved by using DNA mutations with functional, evolutionary, and pleiotropic consequences. Here the authors describe a method for genome-wide fine-mapping of QTLs and develop a genotyping array for improved prediction of genetic values for cattle traits.
- Ruidong Xiang
- , Iona M. MacLeod
- & Michael E. Goddard
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Article
| Open AccessAssessing the influence of climate on wintertime SARS-CoV-2 outbreaks
Spread of SARS-CoV-2 in the early phase of the pandemic has been driven by high population susceptibility, but virus sensitivity to climate may play a role in future outbreaks. Here, the authors simulate SARS-CoV-2 dynamics in winter assuming climate dependence is similar to an endemic coronavirus strain.
- Rachel E. Baker
- , Wenchang Yang
- & Bryan T. Grenfell
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Article
| Open AccessIndividualized interactomes for network-based precision medicine in hypertrophic cardiomyopathy with implications for other clinical pathophenotypes
Understanding patient-specific pathobiological pathways is a critical step for advancing precision medicine. Here the authors show that individualized protein-protein interaction networks provide key insight on patient-level pathobiology and clinically relevant pathophenotypic characteristics in a complex disease.
- Bradley A. Maron
- , Rui-Sheng Wang
- & Joseph Loscalzo
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Article
| Open AccessNanoscopic subcellular imaging enabled by ion beam tomography
Secondary ion beam mass spectrometry (SIMS) is a method to obtain a chemical snapshot of biological tissue, but the spatial resolution is low. Here, the authors develop a computational and technology pipeline to localise a chemical signal in SIMS in 3D and sub-25 nm accuracy, called Ion Beam Tomography
- Ahmet F. Coskun
- , Guojun Han
- & Garry P. Nolan
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Article
| Open AccessThe molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp
Connecting genotypes to complex social behaviour is challenging. Taylor et al. use machine learning to show a strong response of caste-associated gene expression to queen loss, wherein individual wasp’s expression profiles become intermediate between queen and worker states, even in the absence of behavioural changes.
- Benjamin A. Taylor
- , Alessandro Cini
- & Seirian Sumner
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Article
| Open AccessThe natural history of symptomatic COVID-19 during the first wave in Catalonia
Establishing the natural history of COVID-19 requires longitudinal data from population-based cohorts. Here, the authors use linked primary care, testing, and hospital data to describe the disease in ~100,000 individuals with a COVID-19 diagnosis among a population of ~5.5 million in Catalonia, Spain.
- Edward Burn
- , Cristian Tebé
- & Talita Duarte-Salles
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Article
| Open AccessA fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits
Statistical colocalisation is a method to identify causal genes and shared genetic aetiology across traits. Here, the authors describe HyPrColoc, an efficient Bayesian divisive clustering algorithm which integrates summary statistics from genome-wide association studies to detect clusters of colocalised traits from large numbers of traits.
- Christopher N. Foley
- , James R. Staley
- & Joanna M. M. Howson
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Article
| Open AccessA practical solution to pseudoreplication bias in single-cell studies
Single cell genomics uses cells from the same individual, or pseudoreplicates, that can introduce biases and inflate type I error rates. Here the authors apply generalized linear mixed models with a random effect for individual, to properly account for both zero inflation and the correlation structure among cells within an individual.
- Kip D. Zimmerman
- , Mark A. Espeland
- & Carl D. Langefeld
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Article
| Open AccessPopDel identifies medium-size deletions simultaneously in tens of thousands of genomes
Identifying structural variants (SVs) from whole genome sequence data has been a significant bioinformatic challenge. Here, the authors describe PopDel, which uses a joint SV detection approach to reliably and efficiently identify 500-10,000 bp deletions across large population cohorts.
- Sebastian Niehus
- , Hákon Jónsson
- & Birte Kehr
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Article
| Open AccessIdentification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
The profiling of genetic variants affecting splicing can give insight into disease mechanisms. Here, the authors develop a pipeline for discovery of variants affecting splicing (sQTLs) and with application to the GTEx dataset they generate a catalog of human sQTLs.
- Diego Garrido-Martín
- , Beatrice Borsari
- & Roderic Guigó
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Article
| Open AccessArtificial intelligence in sepsis early prediction and diagnosis using unstructured data in healthcare
Early prediction and diagnosis of sepsis, which is critical in reducing mortality, is challenging as many of its signs and symptoms are similar to other less critical conditions. Here, the authors develop an artificial intelligence algorithm which uses both structured data and unstructured clinical notes to predict sepsis.
- Kim Huat Goh
- , Le Wang
- & Gamaliel Yu Heng Tan
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Article
| Open AccessSplicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition
Chromatin is known to regulate splicing by modulating recruitment of splicing factors. Using machine learning approaches, the authors have underlined a chromatin code for alternative splicing regulation that is conserved amongst cell lines.
- E. Agirre
- , A. J. Oldfield
- & R. F. Luco
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Article
| Open AccessBackbone-independent NMR resonance assignments of methyl probes in large proteins
Here, the authors present Methyl Assignments Using Satisfiability (MAUS), a method for the assignment of methyl groups using raw NOE data. They use eight proteins in the 10–45 kDa size range as test cases and show that MAUS yields 100% accurate assignments at high completeness levels.
- Santrupti Nerli
- , Viviane S. De Paula
- & Nikolaos G. Sgourakis
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Article
| Open AccessDeep convolutional neural networks to predict cardiovascular risk from computed tomography
Coronary artery calcium is an accurate predictor of cardiovascular events but this information is not routinely quantified. Here the authors show a robust and time-efficient deep learning system to automatically quantify coronary calcium on CT scans and predict cardiovascular events in a large, multicentre study.
- Roman Zeleznik
- , Borek Foldyna
- & Hugo J. W. L. Aerts
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Article
| Open AccessIntegrating deep learning CT-scan model, biological and clinical variables to predict severity of COVID-19 patients
The SARS-COV-2 pandemic has put pressure on intensive care units, so that predicting severe deterioration early is a priority. Here, the authors develop a multimodal severity score including clinical and imaging features that has significantly improved prognostic performance in two validation datasets compared to previous scores.
- Nathalie Lassau
- , Samy Ammari
- & Michael G. B. Blum
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Article
| Open AccessRUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia
The fusion gene RUNX1/RUNX1T1 is oncogenic in acute myeloid leukemia. Here, the authors show that the fusion gene alters the transcriptional landscape of the cells by changing the structure of the 5’UTR, altering isoform expression, and controlling the expression of splicing factors.
- Vasily V. Grinev
- , Farnaz Barneh
- & Olaf Heidenreich
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Article
| Open AccessDetection of aberrant splicing events in RNA-seq data using FRASER
Aberrant splicing is a major contributor to rare disease, but detection accuracy using current methods is limited. Here, the authors develop an algorithm that detects aberrant splicing and intron retention events from RNA-seq data and apply it to diagnosis in mitochondrial disease.
- Christian Mertes
- , Ines F. Scheller
- & Julien Gagneur
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Article
| Open AccessAn integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease
Some cholesterol-lowering drugs can increase the risk of type 2 diabetes, but the mechanism behind this is not fully understood. Here the authors show that there is a single genetic regulatory module that influences both cholesterol levels and glucose levels, providing a link between cholesterol levels and diabetes.
- Ariella T. Cohain
- , William T. Barrington
- & Eric E. Schadt
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Article
| Open AccessSarcoma classification by DNA methylation profiling
Sarcomas are morphologically heterogeneous tumours rendering their classification challenging. Here the authors developed a classifier using DNA methylation data from several soft tissue and bone sarcoma subtypes, which has the potential to improve classification for research and clinical purposes.
- Christian Koelsche
- , Daniel Schrimpf
- & Andreas von Deimling
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Article
| Open AccessMVP predicts the pathogenicity of missense variants by deep learning
Accurate prediction of variant pathogenicity is essential to understanding genetic risks in disease. Here, the authors present a deep neural network method for prediction of missense variant pathogenicity, MVP, and demonstrate its utility in prioritizing de novo variants contributing to developmental disorders.
- Hongjian Qi
- , Haicang Zhang
- & Yufeng Shen
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Article
| Open AccessA network-based framework for shape analysis enables accurate characterization of leaf epidermal cells
While cell shape is crucial for function and development of organisms, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Here, the authors use a network-based framework for Arabidopsis leaf epidermal cell shape characterization and classification.
- Jacqueline Nowak
- , Ryan Christopher Eng
- & Zoran Nikoloski
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Article
| Open AccessCrystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism
Steroid 5α-reductase 2 (SRD5A2), a testosterone metabolism enzyme, is implicated in human disease. Structural and biochemical analyses of PbSRD5A, a bacterial homolog, reveal SRD5A2 substrate binding pocket and provide framework for the design of new drugs targeting this enzyme.
- Yufei Han
- , Qian Zhuang
- & Ruobing Ren
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Article
| Open AccessA spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
Alternative RNA splicing varies across the brain. Its mapping at single cell resolution is unclear. Here, the authors provide a spatial and single-cell splicing atlas reporting brain region- and cell type-specific expression of different isoforms in the postnatal mouse brain.
- Anoushka Joglekar
- , Andrey Prjibelski
- & Hagen U. Tilgner
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Article
| Open AccessModelling the global burden of drug-resistant tuberculosis avertable by a post-exposure vaccine
Vaccines preventing tuberculosis disease progression have shown promising results in recent trials. Here, the authors use mathematical modelling to estimate that this type of vaccine could avert 10% of cases of rifampicin-resistant tuberculosis and 7% of deaths from 2020-2035.
- Han Fu
- , Joseph A. Lewnard
- & Nimalan Arinaminpathy
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Article
| Open AccessMathematical model of COVID-19 intervention scenarios for São Paulo—Brazil
Incidence of COVID-19 has been high in parts of South America including Brazil, and information on effective intervention strategies is needed. Here, the authors use mathematical modelling to show that reductions in social distancing should be made gradually to avoid a severe second peak of cases.
- Osmar Pinto Neto
- , Deanna M. Kennedy
- & Renato Amaro Zângaro
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Article
| Open AccessCellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression
Here, the authors introduce Cell Heterogeneity–Adjusted cLonal Methylation (CHALM) as a methylation quantification method that considers the heterogeneity of sequenced bulk cells. They apply CHALM to methylation datasets to detect differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.
- Jianfeng Xu
- , Jiejun Shi
- & Wei Li
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Article
| Open AccessHeme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.
- Gloria Gamiz-Arco
- , Luis I. Gutierrez-Rus
- & Jose M. Sanchez-Ruiz
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Article
| Open AccessTwo distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations
Family 43 glycoside hydrolases (GH43) are involved in the breakdown of hemicellulose. Functional, structural and computational characterization of a GH43 enzyme, including a snapshot of an active Michaelis complex, reveal the hydrolysis mechanism and suggest two possible reaction pathways.
- Mariana A. B. Morais
- , Joan Coines
- & Mario T. Murakami
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Article
| Open AccessDeep learning encodes robust discriminative neuroimaging representations to outperform standard machine learning
Recent critical commentaries unfavorably compare deep learning (DL) with standard machine learning (SML) for brain imaging data analysis. Here, the authors show that if trained following prevalent DL practices, DL methods substantially improve compared to SML methods by encoding robust discriminative brain representations.
- Anees Abrol
- , Zening Fu
- & Vince Calhoun
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