Search engine run on: http://users.monash.edu.au/
Glookbib search for: zz1219
%A M. Groff
%T The polynomial transform
%J arXiv
%M DEC
%D 2019
%K TR, c2019, c201x, c20xx, zz1219, polynomial transform, discrete, DFT,
algorithm, finite field
%T "We explore a new form of DFT, which we call the Polynomial Transform. It
functions over finite fields,or DFTs, of size m3 for m prime and of the form
3l+1 for some natural l. It uses only O(m3) arithmetic operations on numbers
of size log m, and takes total time N K log N, for N = Theta(m3 log m)."
-- 1912.01155@[arXiv]['19].
%T Cyrus Chothia (19/2/1942-26/11/2019)
%M NOV
%D 2019
%K Chothia, Cyrus, news, c2019, c201x, c20xx, zz1219, obit, obituary,
LMB, MolBio, bioinformatics, protein structure, domains
%X "... Cyrus pioneered the use of computational methods to study the structure
and function of proteins, and the evolution of genomes, which led to the
birth of structural bioinformatics and computational genomics. ...
[he] mentored over 21 scientists (19 PhD students and 2 postdocs) during his
career, several of whom have gone on to become leaders in the field of
bioinformatics. ..."
-- mrc-lmb[www][27/1//2019]. ---------------
And,
"Cyrus Chothia obituary. Biochemist whose work was at the cutting edge
of the understanding of protein structures, their function & evolution ...
Like most LMB staff he ran a small group, with no more than one research
student per year. He was scrupulously fair in his dealings with his
colleagues, giving students full credit for their published papers, and was
notably supportive of female researchers at a time when it was far
from the norm. ..."
-- The G [www][13/12/2019].
%T Clive James obituary: 'A man of substance'
%I BBC
%M NOV
%D 2019
%K James, Clive, Vivian, obit, obituary, news, c2019, c201x, c20xx, zz1219,
short, quote, quotable, brevity, MML, MDL, Australian, Australia, poet,
writer
%X 7/10/1939 - 24/11/2019.
'He was sanguine about his own end, maintaining a short biography on
his website, which he hoped would be used as the basis for any
appreciation of his life that might be written.
Journalists writing an obituary should "keep in mind that
shorter is better, and that a single line is best", it said.'
-- [bbc][27/11/2019]. -----------------------
(Also see,
"... He also famously once said: 'Stop worrying, nobody gets out of this
world alive.' ..."
-- [abc][28/11/2019].)
%A A. W. Senior
%A R. Evans
%A J. Jumper
%A et al ...
%A D. Hassibis
%T Protein structure prediction using multiple deep neural networks in the
13th Critical Assessment of Protein Structure Prediction (CASP13)
%J Proteins: Structure, Function, and Bioinformatics
%V 87
%N 12
%P 1141-1148
%M OCT
%D 2019
%K jrnl, MolBio, CASP, CASP13, c2019, c201x, c20xx, zz1219, AlphaFold, ANN, NN,
alphafold1, A7D, DeepMind, tertiary, 3D, protein structure prediction,
MSA, pairwise distance, Zscores, GDT_TS, GDTTS, GDTnet, google
%X "We describe AlphaFold, the protein structure prediction system that was
entered by the group A7D in CASP13. Submissions were made by three
free-modeling (FM) methods which combine the predictions of three neural
networks. All three systems were guided by predictions of distances between
pairs of residues produced by a NN. Two systems assembled fragments produced
by a generative NN, one using scores from a n/wk trained to regress GDT_TS.
The third system shows that simple gradient descent on a properly constructed
potential is able to perform on par with more expensive traditional search
techniques & without requiring domain segmentation. In the CASP13 FM
assessors' ranking by summed z-scores, this system scored highest with 68.3
vs 48.2 for the next closest group (an average GDT_TS of 61.4). The system
produced high-accuracy structures (with GDT_TS scores of 70 or higher) for
11 out of 43 FM domains. Despite not explicitly using template information,
the results in the template category were comparable to the best performing
template-based methods." [36 refs.]
-- [doi:10.1002/prot.25834]['19].
"... NN trained to predict the dists. d_ij between the beta-carbon atoms of
pairs of residues. ... predict distances between two 64-residue fragments of
a chain ... 220 2D residual blocks with 128 channels & dilated 3x3 convol'ns,
elu nonlinearity with dropout & batch normalization. [uh?] ..."
-- sec 2.1
[Also search for: AlphaFold MolBio].
(*Also see alphafold@[deepmind]['19].*)
[Also search for: 3D protein structure prediction ANN].
%A B. Mayne
%A O. Berry
%A C. Davies
%A J. Farley
%A S. Jarman
%T A genomic predictor of lifespan in vertebrates
%J Sci. Reports
%V 121
%N #17866
%M DEC
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz1219, MolBio, DNA, age, lifespan, animal,
species, vertebrate, mammal, extinct, methylation, CpG sites, gene promoters,
DNAm, longevity, stats, AnAge
%X "... Ageing involves the decline of diverse biological functions and places a
limit on a species' max. lifespan. Ageing is assoc. with epigenetic changes
involving DNA methylation. [&] an analysis of mammals showed that the density
of CpG sites in gene promoters, which are targets for DNA methylation, is
corr. with lifespan. Using 252 whole genomes & DBs of animal age & promotor
seqs., we show a pattern across vertebrates. ... The lifespan clock
accurately predicts max. lifespan in vertebrates (R2=0.76) from the density
of CpG sites within only 42 selected promoters. ..."
-- [doi:10.1038/s41598-019-54447-w]['19].
%A T. Z. T. Jensen
%A et al ...
%A H. Schroeder
%T A 5700 year-old human genome and oral microbiome from chewed birch pitch
%J NatureComms
%V ?
%M DEC
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz1219, human, ancient DNA, genome,
stone age, Denmark, Scandinavia, Europe
%X "... complete ancient human genome & oral microbiome sequenced from a 5700
year-old piece of chewed birch pitch from Denmark. We sequence the human
genome to an average depth of 2.3x & find that the individual who chewed the
pitch was female & that she was genetically more closely related to western
hunter-gatherers from mainland Europe than hunter-gatherers from central
Scandinavia. We also find that she likely had dark skin, dark brown hair &
blue eyes. In addition, we identify DNA fragments from several bacterial &
viral taxa, inc. Epstein-Barr virus, as well as animal & plant DNA, which may
have derived from a recent meal. ..."
-- [doi:10.1038/s41467-019-13549-9]['19].
[Also search for: MolBio ancient DNA].
%T How a cake company pioneered the first office computer
%I BBC
%M NOV
%D 2019
%K computer history, LEO, Leo, c2019, c201x, c20xx, c195x, zz1219, computing,
business, Lyons Electronic Office, Mary Coombs, programmer, woman, women,
UK, cakes
%X "... [memory on] Leo1 was 2K ..." (video 3:45)
-- [bbc][27/11/2019].
Also see Leo@[wikip]['19] and
the Science Museum [www]['19].
[Also search for: LEO Lyons] and [also search for: computer history].
%A S. B. Seymore
%T How does my work become our work? Dilution of authorship in
scientific papers, and the need for the academy to obey copyright law
%J Richmond J. of Law and Tech.
%V 12
%N 3
%D 2006
%K TR, c2006, c200x, c20xx, zz1219, university, research, ethics, publication,
paper, scientific, publish, perish, author, guest, gift, authorship, faculty,
student, copyright, law, ICMJE, intellectual property, IP
%X "Professors enjoy a world of extensive institutional autonomy & individual
academic freedom. Universities & courts defer to a prof's judgment for
'genuinely academic decisions' unless they depart from academic norms.
Unis., courts, & professional societies should intervene, however, when
academic norms & custom do not comport with the law. The need to 'publish or
perish,' both in academic science & increasingly in industry, has led
professors to publish papers whose authorship is suspect. ..."
-- [www]['19].
[Also search for: publish perish].
%A L. Pachter
%T To some a citation is worth $3 per year
%M OCT
%D 2014
%K blog, c2014, c201x, c20xx, zz1219, university, ranking, rankings, impact,
USNWR, rating, research, gaming, scamming, buying, adjunct, management,
quality, KPI, KPIs, KAU, King Abdulaziz University, Saudi Arabia, grudging
%X "Earlier this week US News and World Report (USNWR) released, for the first
time, a global ranking of universities including rankings by subject area.
In mathematics, the top ten unis. are:
1. Berkeley; 2. Stanford; 3. Princeton; 4. UCLA; 5. U. of Oxford;
6. Harvard; 7. King Abdulaziz University [KAU](*);
8. Pierre and Marie Curie - Paris 6; 9. U. of Hong Kong;
10. U. of Cambridge; ... Even more surprising is the entry at #7
that I have boldfaced: the math department at King Abdulaziz U. (KAU)
in Jeddah, Saudi Arabia. ... KAU employs (as adjunct faculty) more than a
quarter of the highly cited mathematicians at Thomson Reuters. ...
profs. are hired as adjunct pros. at KAU for $72,000 per year in return for
agreeing (apparently by contract) to add KAU as a secondary affiliation..."
-- [www]['19].
(I must confess to feeling a little grudging admiration of KAU
for exploiting such a weak measure.)
Also see Y.Bhattacharjee in Science, Dec 2011,
[www]['19].
[Also search for: university rankings].
%A C. Smith
%T The hidden stories of Australia's first women working in computing
%I ABC
%D DEC
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, history, computer, computing, STEM,
women, www, HREF, Australia, Australian, Astrographic Catalogue, CSIRAC,
SILLIAC, Pearcey, Semkiw, Kay Thorne, Harcourt, Vorrath, www, HREF
%X -- abc[1/12/2019].
[Also search for: women computing].
%T Quality over quantity: How the Dutch Research Council is giving
researchers the opportunity to showcase diverse types of talent
%I DORA
%M NOV
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, scientific, university, research,
CV, CVs, management, DORA, NWO Veni, quality, diversity, publish, perish,
citations, unreliable, KPI, KPIs, ban, Hindex, topN, top10
%X "The Dutch Research Council (NWO) is piloting a narrative CV format in the
Veni scheme, its major funding instrument for early career researchers. The
format advances showcasing diverse types of talent and encourages assessment
of quality rather than quantity. ... The Key output section allows a maximum
of ten output items. ... banned what we consider unreliable metrics. We
exclude the use of journal impact factors and any kind of metric that refers
to journal, publisher, or publication platform, and also ban (H-)indexes,
citation avgs, totals, & sums, as these measures are sensitive to bias. ..."
-- [www][14/11/2019].
[Also search for: publish perish].
%A J. Mervis
%T Universities move to stop passing the harasser
%J Science
%M NOV
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, MeToo, #metoo, meto, harassment,
abuse, bullying, bully, sexual, university, academic, conduct, misconduct,
research, management, work, job, jobs, study, staff, faculty
%X "... major research universities are taking steps to penetrate the veil of
silence that abets the practice of 'passing the harasser.' The Davis and
San Diego campuses of the U. of Cal. system are conducting pilot programs
that ask certain faculty candidates to waive some privacy protections ..."
-- [doi:10.1126/science.366.6469.1057]['19].
[Also search for: MeToo].
%A A. Hatch
%T To fix research assessment, swap slogans for definitions
%J Nature
%V 576
%N 9
%M DEC
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, publish, perish, DORA, university,
scientific, research, impact, rating, rankings, KPI, KPIs, quality
%X "... My view is that most assessment guidelines permit sliding standards:
instead of clearly defined terms, they give us feel-good slogans that lack
any fixed meaning. Facing the problem will get us much of the way towards a
solution. ...":
-- [doi:10.1038/d41586-019-03696-w]['19].
[Also search for: publish perish].
%T China due to introduce face scans for mobile users
%I BBC
%D Dec
%D 2019
%K news, bbc, c2019, c201x, c20xx, zz1219, China, mobile phone, phones, face,
scan, facial recognition, privacy, state, surveillance, identity, Chinese,
social credit
%X "People in China are now required to have their faces scanned when
registering new mobile phone services, as the authorities seek to verify the
identities of the country's hundreds of millions of internet users. ..."
-- [bbc][1/12/2019].
%A C. S. Meijer
%A Uber Whittakersche bzw. Besselsche Funktionen und deren Produkte
%J Nieuw Archief voor Wiskunde (2)
%V 2
%V 18
%N 4
%P 10-39
%D 1936
%K jrnl, c1936, c193x, c19xx, zz1219, Meijer, G function, Gfunction, Gfunctions,
general, functions, hypergeometric
%X Also see MGF@[wikip]['19].
[Also search for: Meijer Gfunction].
%A R. Beals
%A J. Szmigielski
%T Meijer G-Functions: A Gentle Introduction
%J Notices of the Amer. Math. Soc..
%V 60
%N 7
%P 866-872
%M AUG
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1219, AMS, Meijer, G function, functions,
Gfunction, Gfunctions, general, hypergeometric, GHGE, Meijer
%X "The Meijer G-functions are a remarkable family of fns of one variable, each
of them determined by finitely many indices. ... Most special fns, & many
products of special fns, are G-fns or are expressible as products of
G-fns with elementary fns. ..."
-- pdf@[doi:10.1090/noti1016]['19].
Also see MGF@[wikip]['19].
[Also search for: Meijer Gfunction].
%A P. Hudak
%A D. Quick
%T The Haskell School of Music: From Signals to Symphonies
%I CUP
%P 398
%M OCT
%D 2018
%K book, text, c2018, c201x, c20xx, zz1219, computer, FP, Haskell, music,
generation, synthesis, euterpea
%X "... explores the fundamentals of computer music & functional programming
through the Haskell programming language ... learn how to use the Euterpea
library for Haskell (www.euterpea.com) to represent & create their own
music with code ... Other topics covered include the basics of signal-based
systems in Haskell, sound synthesis, & virtual instrument design."
1st ed 2018; hb $49; uk us isbn:1108416756; uk us isbn13:978-1108416757.
%A D. S. Wilson
%T Human groups as adaptive units: toward a permanent consensus
%E P. Carruthers et al
%B The Innate Mind: Culture and Cognition
%I OUP
%D 2006
%K chapter, OUP, c2006, c200x, c20xx, zz1219, group selection, cooperation,
altruism, kin, PD, IPD, human, animal, behaviour
%X "... The founding fathers of the human social sciences spoke about groups as
organisms as if it were common sense (Wegner 1986). ... groups can evolve
into adaptive units that are designed to maximize their contribution to the
total gene pool to the extent that selection among groups prevails against
selection within groups. ..." (In uk us isbn13:978-0195310146.)
Also see groupSel@[wikip]['19].
[Also search for: cooperation behaviour].
%A C. Fields
%T Effective dark energy from decoherence
%J arXiv
%M FEB
%D 2015
%K TR, c2015, c201x, c20xx, zz1219, physics, cosmology, dark energy, universe,
bit, bits, energy, information, cosmological constant, decoherence, Landauer,
controversial
%X "... observers obtain pointer-state information about quantum systems by
interacting with a local sample of the surrounding environment, e.g. a local
sample of the ambient photon field. Because the environment encodes such
pointer state information uniformly & hence redundantly throughout its entire
volume, the information is equally available to all observers regardless of
their location. This framework is applied to the observation of stellar
center-of-mass positions, which are assumed to be encoded by the ambient
photon field in a way that is uniformly accessible to all possible observers.
Assuming Landauer's Principle, constructing such environmental encodings
requires (ln2)kT per encoded bit. For the observed 1024 stars & a uniform
binary encoding of center-of-mass positions into voxels with a linear
dimension of 5km, the free energy required at the current CMB temperature
T = 2.7K is ~2.5 10^{â27} kg m^{â3}, strikingly close to the observed value
of Omega_{Dealta rho_c}. Decreasing the voxel size to (lP)^3 results in a
free energy requirement 10^{117} times larger."
-- 1502.03424@[arXiv]['19].
(Also see [www][18/2/'15].)
%A O. Manzyuk
%A B. A. Pearlmutter
%A A. A. Radul
%A D. R. Rush
%T Perturbation confusion in forward automatic differentiation of
higher-order functions
%J JFP
%V 29
%P e12
%M SEP
%D 2019
%K jrnl, JFP, FP, c2019, c201x, c20xx, zz1219, automatic differentiation, bug,
error, implementation, maths, high order function, tags, curried
%X "... a technique for augmenting computer programs to compute derivatives. The
essence of AD in its forward accumulation mode is to attach perturbations to
each number, & propagate these through the computation by overloading the
arithmetic operators. ... The essence of the bug is as follows: a unique
tag is needed for each derivative calculation, but in existing
implementations unique tags are created when taking the derivative of a fn at
a point. When taking derivatives of higher-order fns, these need not corr.!
We exhibit a simple example: a higher-order fn f whose derivative at a pt x,
namely fâ˛(x), is itself a fn which calculates a derivative. This situation
arises naturally when taking derivatives of curried fns. Two potential solns
are presented, & their deficiencies discussed. ..."
-- [doi:10.1017/S095679681900008X]['19].
Also see [AD@wikip]['08].
[Also search for: automatic differentiation].
%A F. Dahlqvist
%A R. Salvia
%A G. A. Constantinides
%T A probabilistic approach to floating point arithmetic
%J arXiv
%M DEC
%D 2019
%K TR, c2019, c201x, c20xx, zz1219, floating point arithmetic, precision,
accuracy, distribution, rounding error, Kozen
%X "Finite-precision floating point arithmetic unavoidably introduces rounding
errors .., worst-case analysis might be overly conservative because
worst-case errors can be extremely rare events in practice. Here we develop a
probabilistic model of rounding errors with which it becomes possible to
estimate the likelihood that the rounding error of an alg. lies within a
given interval. ... show how to compute the distribution of rounding errors.
We do this exactly for low precision arithmetic, for high precision arith.
we derive a simple approxn. The model is then entirely compositional ..."
-- 1912.00867@[arXiv]['19].
%A E. D. Berger
%A C. Hollenbeck
%A P. Maj
%A O. Vitek
%A J. Vitek
%T On the impact of programming languages on code quality: A reproduction study
%J TOPLAS
%V 41
%N 4
%M DEC
%D 2019
%K jrnl, TOPLAS, c2019, c201x, c20xx, zz1219, programming language, languages,
Ray, Posnett, Devanbu, Filkov, c2014, github, software, errors, bugs,
defects, static, dynamic, types, checking, typing, FP, rebuttal,
language wars, controversy, controversial, fuss
%X "In a 2014 article, Ray, Posnett, Devanbu, and Filkov claimed to have
uncovered a stat. sig. assoc. between 11 programming languages & s/w defects
in 729 projects hosted on GitHub. Specifically, their work answered four
research Qs relating to s/w defects & PLs. With data & code provided by the
authors, the present article first attempts to conduct an experimental
repetition of the original study. The repetition is only partially
successful, due to missing code & issues with the class'n of languages. The
2nd part of this work focuses on their main claim, the assoc. between bugs
& languages, & performs a complete, independent reanalysis of the data & of
the statistical modeling steps undertaken by Ray et al. in 2014. ...
uncovers a # of serious flaws that reduce the # of languages with an assoc.
with defects down from 11 to only 4. Moreover, the practical effect size is
exceedingly small. ... thus undermine the conclusions of the original study.
Correcting the record is important, as many subsequent works have cited the
2014 article & have asserted, without evidence, a causal link between the
choice of PL for a given task and the # of s/w defects. Causation is not
supported by the data at hand; &, in our opinion, even after fixing the
methodological flaws we uncovered, too many unaccounted sources of bias
remain to hope for a meaningful comparison of bug rates across languages."
-- [doi:10.1145/3340571]['19].
Also see the original paper by Ray et al,
'A Large Scale Study of Programming Languages and Code Quality in Github',
FSE14, Nov. 2014 [www]['19] &
CACM 60(10), pp.91-100, Oct 2017 [doi:10.1145/3126905]['19],
Ray et al, 'Rebuttal to Berger et al., TOPLAS 2019'
[arXiv][18/11/2019],
and finally(?) Berger et al,
'FSE/CACM Rebuttal: Correcting A Large-Scale Study of
Programming Languages and Code Quality in GitHub ...',
1911.11894@[arXiv][27/11/2019].
%A C. R. Rao
%T Information and the accuracy attainable in the estimation of
statistical parameters
%J Bulletin of the Calcutta Math. Soc.
%V 37
%P 81-89
%D 1945
%K jrnl, c1945, c194x, c19xx, zz1219, stats, Cramer Rao Bound, CRB, limit,
statistics, efficient, efficiency, Calyampudi Radakrishna Rao
%X Reprinted(?),
"The earliest method of estimation of statistical parameters is the method
of least squares due to Markoff. A set of observations whose expectations
are linear functions of a number of unknown parameters being given, the
problem which Markoff posed for solution is to find out a linear function of
observations whose expectation is an assigned linear function of the unknown
parameters and whose variance is a minimum. There is no assumption about the
distribution of the observations except that each has a finite variance.",
in
'Breakthroughs in Statistics', pp.235-247, Springer, 1992
-- [doi:10.1007/978-1-4612-0919-5_16]['19].
Also see [wikip]['19].
[Also search for: Cramer Rao stats].
%A H. Cramer
%T Math. Methods of Statistics
%I PrincetonUP
%D 1946
%K book, text, stats, c1946, c194x, c19xx, zz1219, Cramer Rao Bound, CRB, limit,
CRLB, inequality, statistics, estimation, variance, Cramer, kramer,
efficient, efficiency
%X Also see, "... [CRB] expresses a lower bound on the variance of unbiased
estimators of a deterministic (fixed, though unknown) parameter. ...
In its simplest form, the bound states that the variance of any unbiased
estimator is at least as high as the inverse of the Fisher information. An
unbiased estimator which achieves this lower bound is said to be (fully)
efficient. ..."
-- [wikip]['19].
[Also search for: Cramer Rao stats].