Search engine run on: http://users.monash.edu.au/
Glookbib search for: zz0820
%A C. Finn
%A P. Abbeel
%A S. Levine
%T Model-agnostic meta-learning for fast adaptation of deep networks
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0820, ANN, model agnostic, meta learning
%X "We propose an alg. for meta-learning that is model-agnostic, in the sense
that it is compatible with any model trained with gradient descent &
applicable to a variety of different learning problems, inc. class'n,
regres'n, & reinf.learning. The goal of meta-l. is to train a model on a
variety of ... such that a small # of gradient steps with a small amount of
training data from a new task will produce good generalization performance
on that task. ... demonstrate that this approach leads to state-of-the-art
performance on two few-shot image class'n benchmarks, produces good results
on few-shot reg'n, & accelerates fine-tuning for policy gradient reinf.
learning with n.n/wk policies."
-- [arXiv]['20].
%A L. P. Kaelbling
%T The foundation of efficient robot learning
%J Science
%V 369
%N 6506
%P 915-916
%M AUG
%D 2020
%K news, views, c2020, c202x, c20xx, zz0820, AI, machine learning, intro,
robotic, robotics, robots, realWorld
%X "The past 10 y. have seen enormous breakthroughs[*] in mach.l., resulting
in game-changing applications in comp.vision & lang.proc.. The field of
intell. robotics ... has not yet been revolutionized by these breakthroughs.
A critical difficulty is that the nec. learning depends on data that can only
come from acting in a variety of real-world environments. Such data are
costly to acquire because there is enormous variability in the situations a
general-purpose robot must cope with. It will take a combination of new
alg.techniques, inspiration from natural syss, & multiple levels of
m.learning to revolutionize robotics with general-purpose intell.. ..."
-- [doi:10.1126/science.aaz7597]['20].
[*][Also search for: progress AI 6494].
%A J. W. Cooley
%A J. W. Tukey
%T An algorithm for the machine calculation of complex Fourier series
%J Math. Comp.
%V 19
%P 297-301
%D 1965
%K jrnl, maths, c1965, c196x, c19xx, zz0820, Fast Fourier Transform, FFT, DFT,
series, algorithm, Yates, Good, history
%X "An efficient method for the calculation of the interactions of a 2^m
factorial experiment was introduced by Yates & is widely known by his name.
The generalization to 3^m was given by Box et al.[1]. Good[2] generalized
these methods & gave elegant algs. for which one class of applications is the
calculation of Fourier series. ..."
-- [doi:10.1090/S0025-5718-1965-0178586-1]['20].
(Also see FFT@[wikip]['20] and
DFT@[wikip]['20].)
%A J. Cooley
%A P. Lewis
%A P. Welch
%T The finite Fourier transform
%J IEEE Trans. on Audio and Electroacoustics
%V 17
%N 2
%P 77-85
%M JUN
%D 1969
%K jrnl, c1969, c196x, c19xx, zz0820, finite Fourier transform, fast, FFT,
discrete, DFT, algorithm
%X "... The convolution & term-by-term product op'ns are defined & their equiv.
ops. in transform space are given. A discussion of the transforms of
stretched & sampled fns leads to a sampling theorem for finite seqs.. Finally
these results are used to give a simple derivation of the fast Fourier
transform algorithm."
-- [doi:10.1109/TAU.1969.1162036]['20].
(Also see DFT@[wikip]['20].)
[Also search for: FFT algorithm].
%A Bing Jian
%A B. C. Vamuri
%T Robust point set registration using Gaussian mixture models
%J IEEE Trans. Patt. Analysis and Mach. Intell.
%V 33
%N 8
%P 1633-1645
%M AUG
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0820, point set registration, defn, sets,
point cloud, alignment, match, matching, transformation, Wahba problem, pose,
RANSAC
%X "... present a unified framework for the rigid and nonrigid point set
registration problem in the presence of sig. amounts of noise ... represent
the input point sets using GMMs ..."
-- [doi:10.1109/TPAMI.2010.223]['20],
& code@[gith'b]['20].
[*Also see PSR@[wikip]['20].*]
[Also search for: point set].
%A E. Karstadt
%A O. Schwartz
%T Matrix multiplication, a little faster
%J Proc. 29th ACM Symp. on Parallelism in Algs. and Arch.
%P 101-110
%M JUL
%D 2017
%K conf, SPAA17, c2017, c201x, c20xx, zz0820, fast, matrix multiplication,
algorithm
%X "... The leading coeff. of Strassen-Winograd's alg. was believed to be
optimal for m.mult. algs. with 2x2 base case, due to a [lwb] of Probert
(1976). Surprisingly, we obtain a faster m.m.alg., with the same base case
size & asymptotic complexity as S.-W.'s alg., but with the coeff. reduced
from 6 to 5. To this end, we extend Bodrato's (2010) method for m.squaring,
& transform matrices to an alternative basis. ... apply our technique to
other S.-like algs., improving their arithmetic & communication costs by
sig. const. factors."
-- [doi:3087556.3087579]['20].
[Also search for: fast matrix miltiplication].
%A G. Beniamini
%A N. Cheng
%A O. Holtz
%A E. Karstadt
%A O. Schwartz
%T Sparsifying the operators of fast matrix multiplication algorithms
%J arXiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, matrix multiplication algorithm
%X "... Many sub-cubic algs. have large leading coeffs., rendering them
impractical. Karstadt & Schwartz (SPAA17, JACM20) demonstrated how to reduce
these coeffs. by sparsifying an alg's bilinear operator. Unfortunately, the
... finding optimal spars. is NP-Hard. We obtain three new methods to this
end ... These methods have an exponential worst case running time, but run
fast in practice & improve the performance of many fast m.mult. algs.. Two of
[them] are guaranteed to produce leading coeffs. that, under some assumptions
are optimal."
-- 2008.03759@[arXiv]['20].
[Also search for: fast matrix multiplication algorithm].
%A R. Anderson
%A R. May
%T The logic of vaccination
%J New Sci.
%V 96
%N 1332
%P 410-415
%M NOV
%D 1982
%K MolBio, c1982, c198x, c19xx, zz0820, BobMay, vaccine, vaccination, infection,
disease, epidemic, pandemic, measles, smallpox, polio, herd immunity
%X -- ref@[ncbi]['20].
[Also search for: vaccination].
%A R. Anderson
%A R. May
%T Vaccination and herd immunity to infectious diseases
%J Nature
%V 318
%P 323-329
%M NOV
%D 1985
%K jrnl, c1985, c198x, c19xx, zz0820, BobMay, vaccination, vaccine, infection,
disease, epidemic, pandemic, measles, smallpox, polio, herd immunity,
human health, medicine, spread, Robert Bob May
%X "An understanding of the relationship between the transmission dynamics of
infectious agents & herd immunity provides a template for the design of
effective control programmes based on mass immunization. Math. models of the
spread & persistence of infection provide important insights into the problem
of how best to protect the community against disease."
-- [doi:10.1038/318323a0]['20].
%A V. R. Iyer
%A C. E. Horak
%A C. S. Scafe
%A D. Botstein
%A M. Snyder
%A P. O. Brown
%T Genomic binding sites of the yeast cell-cycle transcription factors SBF and
MBF
%J Nature
%M JAN
%D 2001
%V 409
%N 6819
%P 533-538
%K jrnl, MolBio, c2001, c200x, c20xx, zz0820, Chiponchip, Chipchip, defn, chip,
seq, yeast, cell cycle, Swi4, Swi6, Mbp1, mitotic, binding site
%X "Proteins interact with genomic DNA ... SBF & MBF are seq.-specific
transcription factors that activate gene expression during the G1/S
transition of the cell cycle in yeast. ... we define the genomic binding
sites of the SBF & MBF transc.factors in vivo, by using DNA microarrays. ..."
-- [doi:10.1038/35054095]['20].
[*Also see ChIP-on-chip@[wikip]['20].*]
%A D. S.Latchman
%T Transcription factors: An overview
%J Int. J. Biochem. and Cell Biol.
%V 29
%N 12
%P 1305-1312
%M DEC
%D 1997
%K MolBio, c1997, c199x, c19xx, zz0820, Transcription factor, defn, TF, TFs,
intro, survey, transcriptionFactor, gene expression, regulation
%X -- [doi:10.1016/S1357-2725(97)00085-X]['20].
[*Also see, "a transcription factor (TF) (or seq.-specific DNA-binding
factor) is a protein that controls the rate of transcription of genetic
info. from DNA to mRNA, by binding to a specific DNA seq."
-- TFs@[wikip]['20].*]
%A S. E. Boyd
%A M. Garcia de la Banda
%A R. N. Pike
%A J. C. Whisstock
%A G. B. Rudy
%T PoPS: A computational tool for modeling and predicting protease specificity
%J Proc. IEEE Comput. Syst. Bioinf. Conf.
%P 372-381
%D 2004
%K Boyd, MonashUni, conf, MolBio, c2004, c200x, c20xx, zz0820, PoPS, protease,
proteinase, peptidase, substrate, specificity, cleave
%X "... we present PoPS, a publicly accessible bio'nf. tool
[pops.csse.monash.edu.au] which provides a novel method for building
comp. models of protease specificity that, while still being based on these
amino acid seqs., can be built from any experimental data or expert knowledge
available to the user ..."
-- [doi:10.1109/csb.2004.1332450]['20].
(Also see [JBCB_'05]['20].)
%T The Cancer Genome Atlas
%D 2005
%K TCGA, NCI, MolBio, c2005, c200x, c20xx, zz0820, cancer, cell, cells, data,
stats, genomic, epigenomic, transcriptomic, proteomic, dataBase
%X [TCGA]['20],
TCGA@[wikip]['20].
%A C. B. Do
%A M. S. P. Mahabhashyam
%A M. Brudno
%A S. Batzoglou
%T ProbCons: Probabilistic consistency-based multiple sequence alignment
%J Gen. Res.
%V 15
%P 330-340
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0820, protein alignment, gap, gaps,
indel, costs
%X "... alignments, however, is a difficult comp. problem because of not only
the high computational cost but also the lack of proper objective fns for
measuring alignment quality. ... we introduce probabilistic consistency, a
novel scoring fn for multiple seq. comparisons. We present ProbCons, a
practical tool for progressive protein multiple seq. al. based on prob.
consistency, & evaluate its performance on several std al.benchmark
d.sets. ..."
-- [doi:10.1101/gr.2821705]['20].
[Also search for: MolBio protein alignment].
%A M. A. Apostol
%A et al ...
%A D. Eisenberg
%T Atomic structures of amyloid cross-beta spines reveal varied steric zippers
%J Nature
%V 447
%P 454-457
%M APR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, zz0820, amyloid fibril, prion, disease,
2OL9, GNNQQNY, protein, prions, alpha, beta spine, tau, Sup35, folded,
misfolded, Alzheimer's, Alzheimers
%X "Amyloid fibrils formed from different proteins, each assoc. with a
particular disease, contain a common cross-beta spine. ... the fibril-forming
segment GNNQQNY of the yeast prion protein Sup35, was recently revealed ...
... It is a pair of beta-sheets, with the facing side chains of the two
sheets interdigitated in a dry 'steric zipper'. ... report some 30 other
segments from fibril-forming proteins ... include segs from the Alzheimer's
amyloid-beta & tau proteins, the PrP prion protein, insulin, islet amyloid
polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein & beta-microglobulin
suggesting that common structural features are shared by amyloid diseases ...
13 of these microcrystals all reveal steric zippers, but with variations ..."
-- [doi:10.1038/nature05695]['20] (online 29/4/2007).
Also see 2OL9@[PDB]['20].
[Also search for: prion disease].
%A J. J. W. Wiltzius
%A et al ...
%A D. Eisenberg
%T Molecular mechanisms for protein-encoded inheritance
%J Nat. Struct. & Molec. Biol.
%V 16
%P 973-978
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0820, protein, fibril, folded,
elk prion, disease, prions, beta sheet, mechanism, misfolded, 3FVA, NNQNTF
%X "... phenotypic variants encoded by protein 'conformations'. However, it is
unclear how a protein conformation can be stable enough to endure
transmission between cells or organisms. ... describe new polymorphic crystal
structures of segments of prion & other amyloid proteins, which offer two
structural mechanisms for the encoding of prion strains. ... prion strains
are encoded by alternative packing arrangements (polymorphs) of beta-sheets
formed by the same segment of a protein; in segmental polymorphism, prion
strains are encoded by distinct beta-sheets built from different segments of
a protein. ..."
-- [doi:10.1038/nsmb.1643]['20].
Also see 3FVA@[PDB]['20].
[Also search for: prion disease].
%A C. Trapnell
%A L. Pachter
%A S. L. Salzberg
%T TopHat: Discovering splice junctions with RNA-Seq
%J Bioinformatics
%V 25
%N 9
%N 1
%P 1105-1111
%M MAY
%D 2009
%K MolBio, cjrnl, c2009, c200x, c20xx, zz0820, TopHat, mRNA, RNAseq, RNAseq,
splice junction, splicing, isoForm
%X "... millions of short seq. fragments ... We mapped the RNA-Seq reads from a
recent mammalian RNA-Seq experiment & recovered more than 72% of the splice
junctions reported by the annotation-based s/w from that study, along with
nearly 20,000 prev. unreported junctions. The TopHat pipeline is much faster
than prev. systems, mapping nearly 2.2 million reads per CPU hour ..."
-- [doi:10.1093/bioinformatics/btp120]['20] (online March 2009).
(Also see TopHat2@[doi:10.1186/gb-2013-14-4-r36][25/4/2013].)
[Also search for: MolBio RNAseq].
%A M. D. Robinson
%A A. Oshlack
%T A scaling normalization method for differential expression analysis of
RNA-seq data
%J Geno. Biol.
%V 11
%N R25
%M MAR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0820, RNA-seq, RNAseq, normalization,
normalisation, stats
%X "... we show that normalization continues to be an essential step in the
analysis. We outline a simple and effective method for performing n. & show
dramatically improved results for inferring differential expression in
simulated & publicly available data sets."
-- [doi:10.1186/gb-2010-11-3-r25]['20].
[Also search for: RNAseq normalization].
%A C. Trapnell
%A et al ...
%A L. Pachter
%T Transcript assembly and quantification by RNA-Seq reveals unannotated
transcripts and isoform switching during cell differentiation
%J Nature Biotech.
%V 28
%P 511-515
%M MAY
%D 2010
%K MolBio, jrnl, c2010, c201x, c20xx, zz0820, Cufflinks, mRNA, RNAseq, RNA seq,
isoform, gene expression
%X "... we intro. such algs. in an open-source s/w program called Cufflinks. To
test Cufflinks, we sequenced & analyzed > 430 million paired 75-bp RNA-Seq
reads from a mouse myoblast cell line over a differentiation time series. We
detected 13,692 known transcripts & 3,724 prev. unannotated ones ... Over the
time series, 330 genes showed complete switches in the dominant transcription
start site (TSS) or splice isoform, and we observed more subtle shifts in
1,304 other genes. ..."
-- [doi:10.1038/nbt.1621]['20].
%A D. T. Barken
%A et al
%T Prediction of protease substrates using sequence and structure features
%J Bioinformatics
%V 26
%N 14
%P 1714-1722
%M JUL
%D 2010
%K MolBio, c2010, c201x, c20xx, zz0820, salilab, protease, proteinase, cleave,
substrate, specificity, Granzyme B, GranzymeB, GrB, caspases, GrBah
%X "... we present a BioI. method based on support vector machine (SVM)
learning that identifies seq. & structural features important for protease
recognition of substrate peptides & then uses these features to predict
novel substrates. ..."
-- [doi:/10.1093/bioinformatics/btq267]['20].
%A Yuan-Ping Pang
%A S. Brimijoin
%A D. W Ragsdale
%A Kun Yan Zhu
%A R. Suranyi
%T Novel and viable acetylcholinesterase target site for developing effective
and environmentally safe insecticides
%J Curr. Drug Targets
%A. 2012 Apr;
%V 13
%N 4
%P 471-482
%M APR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0820, pest, insect, aphid, insecticide,
acetylcholinesterase, AChE, anticholinesterase, cysteine, cys, Cys289, 2AZG,
inhibitor, AMTS13, anti-malaria, mosquito
%X "... This review summarizes the lit. data that support the hypothesis that an
insect-specific cysteine residue located at the opening of the
acetylcholinesterase active site is a promising target site for developing
new insecticides with reduced off-target toxicity & low propensity for insect
resistance. ... discuss the differences between targeting the insect-specific
cysteine residue & targeting the ubiquitous catalytic serine residue of
acet... ... Also discussed is the prospect of developing cysteine-targeting
antichol... as effective & environmentally safe insecticides for control of
disease vectors, crop damage, & residential insect pests within the financial
confines of the present insecticide market."
-- [doi:10.2174/138945012799499703]['20].
[Also search for: MolBio insecticide].
%A P. Doherty
%T Pandemics: What Everyone Needs to Know
%I OUP
%P 272
%M AUG
%D 2013
%K book, text, c2013, c201x, c20xx, zz0820, PCDoherty, infection, disease,
epidemic, pandemic, vaccine, vaccination, spread, resistance, pathogen,
virus, viruses, Spanish flu, influenza, SARS, Wuhan, human, public health
%X 1st ed 2013; hb us$82; uk us isbn:0199898103; uk us isbn13:978-0199898107.
"... an essential guide to one of the truly life-or-death issues of our age.
In concise, question-and-answer format, he explains the causes of pandemics,
how they can be counteracted with vaccines and drugs, and how we can better
prepare for them in the future. ..."
%A A. Dobin
%A et al ...
%A T. R. Gingeras
%T STAR: ultrafast universal RNA-seq aligner
%J Bioinformatics
%V 29
%N 1
%P 15-21
%M OCT
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0820, RNA seq, RNAseq, mapping,
reference, reads, splice junction, splicing
%X "... align our large (> 80 billon reads) ENCODE Transcriptome RNA-seq dataset
we developed the Spliced Transcripts Alignment to a Reference (STAR) s/w ...
550 million 2x76bp paired-end reads per hour on a modest 12-core server ...
can discover non-canonical splices and chimeric (fusion) transcripts ..."
-- [doi:10.1093/bioinformatics/bts635]['20].
[Also search for: MolBio RNAseq].
%A M. A. Lancaster
%A J. A. Knoblich
%T Organogenesis in a dish: Modeling development and disease using
organoid technologies
%J ScienceMag
%V 345
%N 6194
%P ?-?
%M JUL
%D 2014
%K jrnl, Biol, MolBio, c2014, c201x, c20xx, zz0820, organoid, organelle, organs,
tissue types
%X "... Organoids are derived from pluripotent stem cells or isolated organ
progenitors that differentiate to form an organlike tissue exhibiting
multiple cell types that self-organize to form a structure not unlike the
organ in vivo ..."
-- [doi:10.1126/science.1247125]['20].
[Also search for: organelle].
%A S. Verma
%A R. Dixit
%A K. C. Pandey
%T Cysteine proteases: Modes of activation and future prospects as
Pharmacological targets
%J Front. Pharmacol.
%M APR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0820, MolBio, cysteine, protease, Cys, cystine,
target, drug design, proteinase
%X "... Proteases are classified according to their catalytic site, &
distributed into four major classes: cysteine p., serine p., aspartic p., &
metalloproteases. ... involved in multiple fns such as extracellular matrix
turnover, antigen presentation, processing events, digestion, immune
invasion, hemoglobin hydrolysis, parasite invasion, parasite egress, &
processing surface proteins. ..."
-- 1604.03587@[doi:10.3389/fphar.2016.00107]['20].
[Also search for: cysteine protease].
%A N. L Bray
%A H. Pimentel
%A P. Melsted
%A L. Pachter
%T Near-optimal probabilistic RNA-seq quantification
%J Nat. Biotech.
%V 34
%P 525-527
%M APR
%D 2016
%K MolBio, jrnl, c2016, c201x, c20xx, zz0820, kallisto, RNAseq, PseudoAlignment,
pseudo, mRNA, mapping, reference
%X "... kallisto, an RNA-seq quantification program that is two orders of
magnitude faster than prev. approaches & achieves similar accuracy. Kallisto
pseudoaligns reads to a reference, producing a list of transcripts that are
compatible with each read while avoiding alignment of individual bases. We
use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in
< 10 min on a standard laptop computer. This removes a major computational
bottleneck in RNA-seq analysis."
-- [doi:10.1038/nbt.3519]['20].
[Also search for: PseudoAlignment].
%A D. van Dijk
%A et al ...
%A D. Pe'er
%T MAGIC: A diffusion-based imputation method reveals gene-gene interactions in
single-cell RNA-sequencing data
%J bioRxiv
%M FEB
%D 2017
%O Cell 174(3), pp.716-729, 26/7/2018 [doi:10.1016/j.cell.2018.05.061]['20].
%K MAGIC, MolBio, c2017, c201x, c20xx, zz0820, Dana Peer, scRNAseq, scRNA seq,
impute, imputation, abundance, zero, dropout, colinearity, manifold,
nearest neighbour, trajectory, diffusion, graph, cell, cells, gene expression
%X "... scRNA-seq technologies suffer from many sources of sig. technical noise,
the most prominent of which is 'dropout' due to inefficient mRNA capture. ...
MAGIC (Mark'v Affinity-based Graph Imputation of Cells), a method for
imputing missing values, & restoring the structure of the data. After MAGIC,
we find that two- & three-D gene interactions are restored & that MAGIC is
able to impute complex & non-linear shapes of interactions ..."
-- [doi:10.1101/111591]['20].
(A seminar@[ubend]['20].)
[Also search for: scRNAseq].
%A R. Patro
%A et al ...
%A C. Kingsford
%T Salmon: Fast and bias-aware quantification of transcript expression using
dual-phase inference
%J Nat. Methods
%V 14
%P 417-419
%M MAR
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0820, scRNAseq, scRNA seq, RNAseq,
Salmon, pseudo, PseudoAlignment, map mRNA reference, gene expression profile
%X "... Salmon, a lightweight method for quantifying transcript abundance from
RNA-seq reads. Salmon combines a new dual-phase parallel inference alg. &
feature-rich bias models with an ultra-fast read mapping procedure. ... the
1st transcriptome-wide quantifier to correct for fragment GC-content bias,
which, as we demo. here, substantially improves the accuracy of abundance
estimates & the sensitivity of subsequent differential expression analysis."
-- [doi:10.1038/nmeth.4197]['20].
[Also search for: PseudoAlignment].
%A E. Qi
%A D. Wang
%A B. Gao
%A Y. Li
%A G. Li
%T Block-based characterization of protease specificity from substrate sequence
profile
%J BMC Bioinformatics
%V 18
%N #438
%M OCT
%D 2017
%K MolBio, jrnl, c2017, c201x, c20xx, zz0820, protease, distance, cleave, pops,
cleaves, cleaving, cleavage, site, profile, sites, substrate, specificity,
octopeptide, prosper, MEROPS
%X "... propose a novel block-based approach to reveal the potential combns of
[AAs] which may regulate the action of proteases. Using the entropies of
eight blocks centered at a cleavage bond, we created a distance matrix for
61 proteases to compare their specificities. After quantitative analysis, we
discovered a # of prominent blocks, each of which consists of successive
[AAs] near a cleavage bond, intuitively characterizing the site cooperation
of the substrate sequences. ..."
-- [doi:10.1186/s12859-017-1851-1]['20].
[Also search for: protease specificity].
(Also see [MEROPS]['20].)
%A J. D. Welch
%A A. J. Hartemink
%A J. F. Prins
%T MATCHER: Manifold alignment reveals correspondence between single cell
transcriptome and epigenome dynamics
%J Genome Biol
%V 18
%N 138
%M JUL
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0820, manifold alignment, scRNA-seq,
scRNAseq, matcher, gene expression, epigenetic, scM&T-seq, scMTseq,
sc-GEM, scGEM, ATACseq, cell types, pseudoTime
%X "... an approach for integrating multiple types of single cell measurements.
MATCHER uses manifold alignment [Ham03] to infer single cell multiomic
profiles from transcriptomic & epigenetic measurements performed on different
cells of the same type. Using scM&T-seq & sc-GEM data ... predicts true
s.cell correlations between DNA methylation & gene expression ..."
["... [assume] variation among cells can be explained mainly by a single
latent variable ('pseudotime') ... cells in each experiment are sampled
from the same population, process, and cell type ..."]
-- [doi:10.1186/s13059-017-1269-0]['20].
Also see MA@[wikip]['20].
[Also search for: MolBio scRNAseq].
%A N. D. Rawlings
%A et al ...
%A R. D Finn
%T The MEROPS database of proteolytic enzymes, their substrates and inhibitors
in 2017 and a comparison with peptidases in the PANTHER database
%J NAR
%V 46
%N D1
%P D624-D632
%M JAN
%D 2018
%K NRA, jrnl, MolBio, c2018, c201x, c20xx, zz0820, MEROPS, protease, proteinase,
peptidase, enzyme, inhibitor, substrate, cleave, cleavage, specificity, pops,
database, collection, DB,
%X "... an integrated source of info. about peptidases, their substrates
& inhibitors. The hier.class'n is: protein-species, family, clan,
with an id. at each level. ..."
-- [doi:10.1093/nar/gkx1134]['20].
Also see MEROPS@[www]['20].
%A T. Nawy
%T Spatial transcriptomics
%J Nat. Methods
%V 15
%M JAN
%D 2018
%K news, views, MolBio, c2018, c201x, c20xx, zz0820, spatial, transcriptome,
RNA, mRNA, cells, gene expression levels, tissue
%X -- [doi:10.1038/nmeth.4542]['20].
%A S. Lamarre
%A et al ...
%A E. Maza
%T Optimization of an RNA-Seq differential gene expression analysis depending
on biological replicate number and library size
%J Front. Plant Sci.
%V ?
%P ?-?
%M FEB
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0820, gene expression levels, RNAseq,
stats, RNA-seq, replicate number, library size, DESeq, DESeq2, edgeR,
normalization, normalisation
%X "... we conducted both an analysis of a two-condition experiment (with eight
biol. replicates per condition) to compare the results with prev. benchmark
studies, & a meta-analysis of 17 experiments with up to 18 biol. conditions
eight biological replicates & 100 million (M) reads per sample. ..."
-- [doi:10.3389/fpls.2018.00108]['20].
[Also search for: RNAseq MolBio].
%A M. Amodio
%A S. Krishnaswamy
%T MAGAN: Aligning biological manifolds
%J arXiv
%M FEB
%D 2018
%O 35th ICML
%K Conf, ICML, MolBio, c2018, c201x, c20xx, zz0820, MAGAN, scRNAseq,
mass cytometry, manifold alignment
%X "... many types of natural and physical systems ... different types of
measurements ... important to align the manifolds arising from each
measurement in order to integrate such data and gain an improved picture of
the system. We tackle this problem using generative adversarial networks
(GANs). ... present a new GAN called the Manifold-Aligning GAN (MAGAN) that
aligns two manifolds s.t. related points in each measurement space are
aligned together. ... [e.g.] single-cell biology ... scRNAseq and proteomic
(mass cytometry) ..."
-- 1803.00385@[arXiv]['20],
[mlrPress]['20].
Also see MA@[wikip]['20].
[Also search for: scRNAseq] and [also search for: Ham03].
%A M. Gehringer
%A S. A. Laufer
%T Emerging and re-emerging warheads for targeted covalent inhibitors:
Applications in Medicinal Chemistry and Chemical Biology
%J J. Med. Chem.
%V 62
%N 12
%P 5673-5724
%M DEC
%D 2018
%K MolBio, jrnl, c2018, c201x, c20xx, zz0820, drug design, warhead, ligand,
inhibitor, Cys, TCI, TCIs, reactivity, anions
%X "... Currently, targeting noncatalytic cysteine residues with acrylamides &
other alpha,beta-unsaturated carbonyl compounds is the predominant strategy
in TCI development. ... provides an overview of warheads - beyond
a,b-unsaturated amides - recently used in the design of targeted covalent
ligands. Promising reactive groups that have not yet demonstrated their
utility in TCI development are also highlighted. ..."
-- [doi:10.1021/acs.jmedchem.8b01153]['20],
[www]['20].
%A R. Molania
%T Identification and removal of unwanted variation in large gene expression
data
%I Uni. Melb.
%D 2018
%K PhD thesis, MolBio, stats, c2018, c201x, c20xx, zz0820, RNAseq, RNA-seq,
mRNA, Nanostring, nCounter, gene expression levels, microarray, purity,
batch effects, normalisation, normalization, screening,
The Cancer Genome Atlas, TCGA
%X "Gene expression experiments ... include: identifying & classifying disease
types, assessing the transcriptional differences between the state of a
disease & normal cells, & identifying biomarkers to predict clinical outcome
of diseases such as cancer, ..."
-- [www]['20].
[WEHIseminar 4/8/'20].
[Also search for: MolBio RNAseq].
%A R. Salomon
%A et al
%T Droplet-based single cell RNAseq tools: a practical guide
%J Lab. Chip
%V 19
%N 10
%P 1706-1727
%M MAY
%D 2019
%K MolBio, c2019, c201x, c20xx, zz0820, droplet, flow cell, flowCell, intro,
survey, guide, scRNA seq, scRNAseq, RNAseq, DropSeq, inDrop, 10X
%X "Droplet based scRNA-seq sys. such as Drop-seq, inDrop & Chromium 10X ...
scRNA-seq technologies in the res.lab.. ... we provide a practical guide
through all the steps involved in a typical scRNA-seq experiment. ..."
-- [doi:10.1039/c8lc01239c]['20],
abs@[p'bmed]['20].
[Also search for: scRNAseq] and [also search for: MolBio flowCell].
%A R. Molania
%A J. A. Gagnon-Bartsch
%A A. Dobrovic
%A T. P. Speed
%T A new normalization for Nanostring nCounter gene expression data
%J NAR
%V 47
%N 12
%P 6073-6083
%M JUL
%D 2019
%K jrnl, NAR, MolBio, c2019, c201x, c20xx, zz0820, stats, normalisation,
amount, batch effects, RUV-III, RUVIII, RUV3, technical replicate,
pseudoreplicate, expression levels, RNA-seq, RNAseq
%X "The Nanostring nCounter gene expression assay uses molecular barcodes &
single molecule imaging to detect & count hundreds of unique transcripts in a
single reaction. These counts need to be normalized to adjust for the amount
of sample, variations in assay efficiency & other factors. ... we present a
new n.method, Removing Unwanted Variation-III (RUV-III), which makes vital
use of technical replicates & suitable control genes. We also propose an
approach using pseudo-replicates when tech.replicates are not available. ..."
-- [doi:10.1093/nar/gkz433]['20].
%A V. Kiselev
%A et al ...
%A M. Hemberg
%T Analysis of single cell RNA-seq data
%I Sanger Inst.
%M JUL
%D 2019
%K intro, course, MolBio, c2019, c20x, c20xx, zz0820, scRNA-seq, scRNAseq,
Sanger, uk, cells, transcriptome data, mRNA, RNA, gene expression
%X "Today it is possible to obtain genome-wide transcriptome data from single
cells using high-throughput sequencing (scRNA-seq). ..."
-- [www]['20].
[Also search for: scRNAseq].
%A D. Kim
%A et al ...
%A S. L. Salzberg
%T Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
%J Nat. Biotechnology
%V 37
%P 907-915
%M AUG
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0820, HISAT, HISAT2, DNA, RNA, mRNA,
mapping, reference, scRNAseq, scRNA seq, BWT, FMindex, GFM
%X "... HISAT2 (hierarchical indexing for spliced alignment of transcripts 2)
that can align both DNA & RNA seqs. using a graph Ferragina Manzini index. We
use HISAT2 to represent & search an expanded model of the human reference
genome in which over 14.5 million genomic variants in combination with
haplotypes ... outperforms other computational methods & matches or exceeds
the performance of laboratory-based assays."
-- [doi:10.1038/s41587-019-0201-4]['20],
& s/w@[gith'b]['20].
[Also search for: scRNAseq].
%A S. R. Hackett
%A et al
%A R. S. McIsaac
%A Learning causal networks using inducible transcription factors and
transcriptome-wide time series
%J Mol. Syst. Biol.
%N 16
%P e9174
%M MAR
%D 2020
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0820, IDEA, Bnet, network,
model, transcription factor, TF, TFs, gene expression, budding yeast, Aft1
%X "... IDEA (the Induction Dynamics gene Expression Atlas), a dataset
constructed by indep. inducing hundreds of transcription factors (TFs) &
measuring time-courses of the resulting gene exp'n responses in budding
yeast. Each experiment captures a regulatory cascade connecting a single
induced regulator to the genes it causally regulates. ... IDEA contains
>200 TF induction experiments with 20 million individual observations &
100,000 signal-containing dynamic responses. As an application of IDEA, we
integrate all timecourses into a whole-cell transcriptional model ..."
-- [doi:10.15252/msb.20199174]['20].
(some auths @Calico Life Sci.)
%A I. Astuti
%A Ysrafil
%T Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of
viral structure and host response
%J Diabetes Metab. Syndr.
%V 14
%N 4
%P 407-412
%M JUL-AUG
%D 2020
%K MolBio, survey, intro, review, c2020, c202x, c20xx, zz0820, SARSCoV2,
SARS-CoV-2, virus, covd-19, covid19, ACE2, nsp, nsp3, nsp5, Wuhan, China,
protein, immune response, system
%X "... provide a complete review related to structure, origin, & how the body
responds to this virus infection & explain the possibility of an immune
system over-reaction or cytokine storm. We also inc. an explanation of how
this virus creates modes of avoidance to evade immune system attacks. ..."
-- [doi:10.1016/j.dsx.2020.04.020]['20] (online 18/4/2020) (45 refs),
PMC7165108@[ncbi]['20].
[Also search for: MolBio SARSCoV2], maybe add Intro.
%A Peng He
%A et al ...
%A B. J. Wold
%T The changing mouse embryo transcriptome at whole tissue and
single-cell resolution
%J Nature
%V 583
%P 760-767
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0820, scRNAseq, scRNA-seq, mouse,
embryo, development, cell, tissue, type, embryogenesis, gene expression,
animal, mammal
%X "During mammalian embryogenesis, differential gene expression gradually
builds the identity & complexity of each tissue & organ system. Here we
systematically quantified mouse polyA-RNA from day 10.5 of embryonic
development to birth, sampling 17 tissues & organs. The resulting
developmental transcriptome ... Focusing on the developing limb, single-cell
RNA data identified 25 candidate cell types ..."
-- [doi:10.1038/s41586-020-2536-x]['20].
[Also search for: scRNAseq].
%A Jingyun Yang
%A et al ...
%A Xiawei Wei
%T A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces
protective immunity
%J Nature
%V ?
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0820, SARS-CoV-2, SARSCoV2, vaccine,
SARS2, S-RBD, SRBD, spike protein
%X "... Here we showed that a recombinant vaccine comprising residues 319-545
of the S-RBD could induce a potent functional antibody response in the
immunized mice, rabbits & non-human primates (Macaca mulatta) as early as
7 or 14 days after a single dose injection ..."
-- [doi:10.1038/s41586-020-2599-8]['20] (online 29/7/2020).
(Apparently over 100 *potential* vacs. are in the works.)
[Also search for: SARSCoV2 vaccine].
%A M. Minguez-Toral
%A B. Cuevas-Zuviria
%A M. Garrido-Arandia
%A L. F. Pacios
%T A computational structural study on the DNA-protecting role of the
tardigrade-unique Dsup protein
%J Sci. Reports
%V 10
%N #13424
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0820, MolBio, biol, tardigrade, invertebrate,
animal, DNA, damage suppression, protection, Dsup, disordered protein
%X "The remarkable ability of t. to withstand a wide range of physical & chem.
extremes ... By means of molec. mod., calculations of electrostatic
potentials & electric fields, & all-atom molec. dynamics sim'ns, we obtained
a dynamic picture of the Dsup-DNA interaction. ... suggest that the protein
is intrinsically disordered, which enables Dsup to adjust its structure to
fit DNA shape. Strong electrostatic attractions & high protein flexibility
drive the formation of a molecular aggregate in which Dsup shields DNA. While
the precise mechanism of DNA protection conferred by Dsup remains to be
elucidated, our study provides some molec. clues of their assoc. that could
be of interest for further investigation in this line."
-- [doi:10.1038/s41598-020-70431-1]['20].
%A J. D. Stone
%T Algorithms for Functional Programming
%I Springer
%P 265
%M FEB
%D 2020
%K book, text, c2020, c20x, c20xx, zz0820, algorithm, FP, Scheme, L2Ref, L3Ref
%X 1st ed 2018; hb us$55; uk us isbn:0387955704; uk us isbn13:978-0387955704.
[Also search for: book FP algorithm].
%A C. M. Case
%T Scholarship in Sociology
%J Sociology and Social Res.
%V 12
%P 323-340
%D 1928
%K c1928, c192x, c19xx, zz0820, publish or perish, quote, quotable, aphorism,
academic, academia, university, scientific, research, management, journals,
pressure, KPI, KPIs
%X "Publish or perish" attributed:
"... The earliest known use of the term [P or P] in an
academic context was in a 1928 journal article. ..."
-- PorP@[wikip]['20].
%A M. V. Malin
%T The Science Citation Index: A new concept in indexing
%J Library Trends
%P 374-387
%M JAN
%D 1968
%K c1968, c196x, c19xx, zz0820, bibliometrics, citation index, source index,
corporate index, SCI, history, scientific research, literature, papers,
bibliometrics, publications, citations, references
%X -- [www]['20].
[Also search for: science citation index history].
%A H. E. Chandler
%A V. de P. Roper
%T Citation indexing: Uses and limitations
%J The Indexer
%V 17
%N 4
%M OCT
%D 1991
%K c1991, c199x, c19xx, zz0820, science citation index, history, SCI,
scientific literature, source, citation index, corporate, permuterm,
history, examples, use
%X "... Explanations, with examples, are given of the four parts of the C.I.
published by the Inst. for Sci. Inf.: the Source i., Citation I., Permuterm
I., & Corporate I.. ..."
-- [www]['20].
%A J. D. Wren
%A C. Georgescu
%T Detecting potential reference list manipulation within a citation network
%J bioRxiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, publish, perish, KPI, KPIs, Hindex, impact,
misconduct, gaming, scamming, paper, peer review, reviewing, cite, citation,
abuse, reference, manipulation, scam, coercive, coercion, RLM,
Kuo-Chen Chou, KCChou, KuoChenChou, Roukos, journals, JTB, Elsevier,
modified bibliometrics, Gini, GiniIndex
%X "... reference list manipulation (RLM) could take place during the
peer-review process (e.g., coercive citation from editors or reviewers), or
prior to it (e.g., a quid-pro-quo between authors). ... find the freq. of
non-self citations (NSC) to one author coming from one paper ~ Zipf's law.
We propose the Gini Index as a simple means of quantifying skew in this
dist'n ... We estimate between 81 (FDR < 0.05) & 231 (FDR < 0.10) authors are
outliers on the curve, suggestive of chronic, repeated RLM. Based upon the
distribution, we est. ~ 3,284 (16%) of all authors may have engaged in RLM
to some degree ..."
-- [bioRxiv]['20],
[doi:10.1101/2020.08.12.248369]['20].
(Also see: "Signs of 'citation hacking' flagged in scientific papers",
Nature 14/8/2020 [www]['20] and
"Highly cited researcher banned from journal board for citation abuse",
Nature 6/2/2020 [www]['20].)
[Also search for: Hindex manipulation] and [also search for: KuoChenChou].
%Q Google AI Quantum and Collaborators
%T Hartree-Fock on a superconducting qubit quantum computer
%J Science
%V 369
%N 6507
%P 1084-1089
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0820, quantum computer, qubits, chemistry,
fermion, physics
%X "... We performed several quantum simulations of chemistry with up to
one dozen qubits, inc. modeling the isomerization mechanism of diazene. ..."
-- 2004.04174@[arXiv]['20],
pub49057@[go'gle]['20],
[doi:10.1126/science.abb9811]['20].
%T 'Make research fun again': UK's powerful funding chief is on a mission to
change scientific culture
%J Nature
%V 584
%P 508
%M AUG
%D 2020
%K news, views, c2020, c202x, c20xx, zz0820, Ottoline Leyser, UK, UKRI,
scientific research, university, management, impact, KPI, KPIs, grant,
grants, peer review
%X -- [doi:10.1038/d41586-020-02424-z]['20].
[Also search for: scientific research grants].
%A F. Dagnino
%A D. Ancona
%A E. Zucca
%T Flexible coinductive logic programming
%J arXiv
%M AUG
%D 2020
%K TR, conf, ICLP, ICLP2019, LP, ILP, c2020, c202x, c20xx, zz0820, coinduction,
coLP, inductive logic programming, coClause
%X "Recursive defns of predicates are usually interpreted either inductively or
coinductively. Recently, a more powerful approach has been proposed, called
flexible coinduction, to express a variety of intermediate interpretations,
nec. in some cases to get the correct meaning. We provide a detailed formal
a/c of an extension of LP supporting flexible coinduction. ... coclauses,
clauses with a special meaning used to tune the interpretation of predicates.
As usual, the declarative semantics can be expressed as a fixed pt which,
however, is not nec. the least, nor the greatest one, but is determined by
the coclauses. ... the op.semantics is a combination of std SLD resolution &
coSLD res'n. We prove that the op.semantics is sound & complete ..."
-- 2008.02140@[arXiv][5/8/2020].
(Also see coI@[wikip]['20].)
[Also search for: LP ILP] and [also search for: coinduction].
%A E. P. Wigner
%T The unreasonable effectiveness of mathematics in the natural sciences
%J Comm. on Pure and Appl. Maths
%V 13
%N 1
%P 1-14
%M FEB
%D 1960
%O Richard Courant lecture in Math. Sci., delivered at New York Univ.,
11 May 1959
%K lecture, seminar, talk, c1960, c196x, c19xx, zz0820, science, maths, model,
prediction, predict, effective, useful, mathematics, seminars,
physics, quote, quotable
%X -- [doi:10.1002/cpa.3160130102]['20],
[wikip]['20].
%A M. Naor
%T Succinct representation of general unlabeled graphs
%J Discr. Applied Math.
%V 28
%N 3
%P 303-307
%M SEP
%D 1990
%K jrnl, c1990, c199x, c19xx, zz0820, maths, graph, compress, encode, decode
%X "We show that general unlabeled graphs on n nodes can be represented by
(^n_2)-nlog2(n)+O(n) bits which is optimal up to the O(n) term. Both the
encoding & decoding require linear time."
-- [doi:10.1016/0166-218X(90)90011-Z]['20].
[Also search for: graph compress].
%A V. A. Traag
%A L. Waltman
%A N. J. van Eck
%A From Louvain to Leiden: Guaranteeing well-connected communities
%J Sci. Reps.
%V 9
%N 5233
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0820, vanEck, network, maths, graph,
Louvain algorithm, louvian, modularity, modular, Leiden,
community, detection, networks
%X "... We show that this [Lo.] alg. has a major defect that largely went
unnoticed until now: the Lo.alg. may yield arbitrarily badly connected
communities. In the worst case, communities may even be disconnected, esp.
when running [it] iteratively. ... we introduce the Leiden alg.. We prove
that the Le.alg. yields communities that are guaranteed to be connected. [&]
prove that, when the Le.alg. is applied iteratively, it converges to a
partition in which all subsets of all communities are locally optimally
assigned. ... [&] runs faster ..."
-- [doi:10.1038/s41598-019-41695-z]['20].
(Also see Louvain@[wikip]['20].)
[Also search for: community network].
%A L. Piccirillo
%T The Conway knot is not slice
%J Annals of Mathematics
%V 191
%N 2
%M MAR
%D 2020
%K maths, jrnl, c2020, c202x, c20xx, zz0820, maths, knot theory, slice,
Conway, JHConway, 4ball, 11n34, Crossings, Lisa Piccirillo, women, STEM
%X "A knot is said to be slice if it bounds a smooth properly embedded disk in
the 4-ball. We demonstrate that the Conway knot, 11n34 in the Rolfsen tables,
is not slice. This completes the class'n of slice knots under 13 crossings,
& gives the 1st example of a non-slice knot which is both topologically slice
& a positive mutant of a slice knot."
-- [doi:10.4007/annals.2020.191.2.5]['20],
[arXiv]['20], and
Auth@[wikip]['20].
%A D. Q. Huynh
%T Metrics for 3D rotations: Comparison and analysis
%J J. Math Imaging Vis.
%V 35
%P 155-164
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0820, maths, Matrix Lie group, Lie algebra,
Quaternion, SO3, 3D rotation, distance, similarity, norm, UWA
%X "3D rotations arise in many computer vision ... evaluation of the distance
between two 3D rotns is often an essential task. ... presents a detailed
analysis of six fns for measuring dist. between 3D rotns that have been
proposed in the lit.. ... we demonstrate that five of them are biinvariant
metrics on SO(3) but that only four of them are boundedly equiv. to each
other. We conclude that it is both spatially & computationally more efficient
to use q. for 3D rotns. Lastly, by treating the two rotns as a true & an est.
rotn matrix, we illustrate the geometry assoc. with iso-error measures."
-- [doi:10.1007/s10851-009-0161-2]['20] (online 18/6/2009).
%A A. Gaikwad
%A S. Maity
%A S. K. Tripathi
%T The satisfactory partition problem
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, satisfactory partition problem, SPP,
adequate, network, community, graph, vertex, vertices, modularity,
Gerber, Kobler
%X "The Satisfactory Partition problem consists in deciding if the set of
vertices of a given undirected g. can be partitioned into two nonempty parts
s.t. each vertex has at least as many neighbours in its part as in the other
part. ... its parameterized complexity remains open until now. ... It is
known that the SP problem [&] a variant where the parts are required to be
of the same cardinality, are NP-complete. ... showing that (1) the problem
is FPT when parameterized by the neighbourhood diversity of the input g.,
(2) it can be solved in O(n^{8cw})) where cw is the clique-width, (3) a
generalized version ... is W[1]-hard when parameterized by the treewidth."
-- 2007.14339@[arXiv][28/7/20].
(Also see Mod@[wikip]['20].)
[Also search for: network modularity] and [also search for: graph partition].
%A I. Kontoyiannis
%A Y. Heng Lim
%A K. Papakonstantinopoulou
%A W. Szpankowski
%T Compression and symmetry of small-world graphs and structures
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, graph, model, graphModel, compress
%X "... a graph can be examined at three levels. Its structure can be described
as the unlabeled version of the g.; then the labeling of its structure can be
added; & finally, given the structure & labeling, the contents of the labels
can be described ... we focus on a class of small-world gs.. These are
geometric random gs. ... establish the degree dist'n of this model ... derive
the relevant entropy & structural entropy of these random gs., in connection
with g.compression."
-- 2007.15981@[arXiv]['20].
[Also search for: graphModel].
%A R. K. Gautam
%A A. S. Kare
%A S. D. Bhavani
%T Faster heuristics for graph burning
%J arXiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, graph, burn, burning, NPH, heuristic
%X "Graph burning is a process of info. spreading through the n/wk by an agent
in discrete steps. The problem is to find an optimal seq. of nodes which have
to be given info. so that the n/wk is covered in least # of steps. G.burning
problem is NP-Hard for which two approx'n algs. & a few heuristics have been
proposed ... we propose three heuristics, namely, Backbone Based Greedy
Heuristic (BBGH), Improved Cutting Corners Heuristic (ICCH) & Component Based
Recursive Heuristic (CBRH). These are mainly based on Eigenvector centrality
measure. ..."
-- 2008.08811@[arXiv]['20].
%A Jiahao Guo
%A P. Singh
%A K. E. Bassler
%T Reduced network extremal ensemble learning (RenEEL) scheme for
community detection in complex networks
%J Sci. Rep.
%V 9
%P #14234
%M OCT
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0820, community detection, algorithm,
network
%X "... ensemble learning scheme for community detection ... found by a
conventional base alg., to find a node partition that maximizes modularity.
At each iter'n, core groups of nodes that are in the same community in every
ensemble part'n are identified & used to form a reduced n/wk. Partitions of
the reduced n/wk are then found & used to update the ensemble. ..."
-- [doi:10.1038/s41598-019-50739-3]['20].
(Also see ComStr@[wikip]['20].)
[Also search for: community network].
%A J. E. Hirsch
%T Superconductivity, what the H? The Emperor has no clothes
%J Physics and Society
%M JAN
%D 2020
%K publish, perish, JEHirsch, TR, c2020, c202x, c20xx, zz0820, news, views,
physics, superconductor, citations, publications, Hindex, misuse, abuse,
jrnl, KPI, KPIs, impact, university, scientific research, bibliometrics, wry,
quote, quotable, controversial
%X "... For better or for worse, I am most famous (or infamous) for the
invention of the Hindex. ... In a nutshell, my observation is that about half
the scientific community loves the Hindex & half hates it, & the Hindex of
the scientist itself is a great predictor of whether s/he belongs to the 1st
or the 2nd group, in addition to its other virtues. I am not completely
unhappy with the impact of my paper, which is by far my most highly cited
one. As Oscar Wilde said, 'There is only one thing in life worse than being
talked about ...'. ... But I have now come to believe that it can also fail
spectacularly & have severe unintended -ve consequences. I can understand how
the sorcerer's apprentice must have felt. ..."
-- 2001.09496@[arXiv]['20].
[Also search for: publish perish] and [also search for: Hirsch Hindex].
%A Kok-Wei Bong
%A et al ...
%A H. M. Wiseman
%T A strong no-go theorem on the Wigner's friend paradox
%J Nat. Physics
%V ?
%M AUG
%D 2020
%K jrnl, physics, c2020, c202x, c20xx, zz0820, quantum theory, Wigner, friend,
paradox, measurement, collapse, fact, facts, observation, observer,
observed, event, events, determinism, superdeterminism, locality,
objectivity, weirdness, absoluteness, inequality, theorem, Bell,
inequalities, Bells, KokWeiBong, HMWiseman, GriffithUni
%X "Does quantum theory apply at all scales, inc. that of observers? ... Here,
by building on a scenario with two separated but entangled friends introduced
by Brukner, we prove that if q.evol'n is controllable on the scale of an
observer, then one of 'No-Superdeterminism', 'Locality' or 'Absoluteness of
Observed Events' - that every observed event exists absolutely, not
relatively - must be false. We show that although the violation of Bell-type
inequalities in such scenarios is not in general suff. to demo. the
contradiction between those three assumptions, new inequalities can be
derive ..."
-- [doi:10.1038/s41567-020-0990-x][17/8/2020].
Also see, "Testing the reality of Wigner's friend's observations", 4/2020,
at 1907.05607@[arXiv]['20], and
WF@[wikip]['20].
%A J. H. Ham
%A D. D. Lee
%A L. K. Saul
%T Learning high dimensional correspondences from low dimensional manifolds
%I Dept. Elec. & Sys. Eng., U. Penn.
%M AUG
%D 2003
%O Workshop on The Continuum from Labeled to Unlabeled Data in M.Learning &
DataMining, at 20th ICML 2003
%K Ham03, wkshop, UPenn, c2003, c200x, c20xx, zz0820, manifold, alignment,
manifolds, stats, dimension, dimensionality, reduction, PCA, stats,
FactorAnalysis, match, correspond, correspondence
%X "Many different high-D data sets are characterized by the same underlying
modes of variability. When ... continuous & few in #, they can be viewed as
parameterizing a low-D manifold. ... provides a compact shared rep'n of the
data, suggesting corr. b/ween the high-D examples from different data sets.
... difficult to learn using trad. methods in supervised learning. ... we
generalize three methods in unsupervised learning - principal components
analysis, factor analysis, & locally linear embedding - to discover subspaces
& manifolds that provide common low-D repns of different high-D data sets. We
use the shared repns ... to put high-D examples from different data sets into
corr.. Finally, we show that a notion of 'self-correspondence' b/ween
examples in the same dataset can be used to improve the performance of these
algs on small data sets. ... demonstrated on images & text."
-- [UPenn]['20].
Also see MA@[wikip]['20].
[Also search for: FactorAnalysis] and [also search for: PCA stats].
%A V. R. Tabar
%A F. Elahi
%T A novel method for aggregation of Bayesian networks without considering an
ancestral ordering
%J Applied AI
%V 32
%N 2
%P 214-227
%D 2018
%K jrnl, Bnet, c2018, c201x, c20xx, zz0820, Bnets, network, aggregate, combine,
merge, Feng, II
%X "... ensures a combined BN meets three important criteria of avoiding cycles,
preserving cond.independencies ... first combine the BNs using the mods. of
the method intro. by Feng et al. We then use the sim.ann.alg. for getting an
acyclic g. in which the minimum arcs have been removed. ..."
-- [doi:10.1080/08839514.2018.1451134]['20].
[Also search for: Bayesian network].