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%A R. S. Bird
%T How to find a fake coin
%J JFP
%V 29
%P c8
%M APR
%D 2019
%K programming pearl, JFP, FP, c2019, c201x, c20xx, zz0519, fake coin, coins,
   weigh, heavy, light, puzzle, problem
%X "... There are n coins, all identical in appearance, one of which *may* be
   fake. The fake coin, if it exists, is either lighter or heavier than the
   fair coin ..."
   -- [doi:10.1017/S0956796819000030]['19].

%A H. A. Helfgott
%T An improved sieve of Eratosthenes
%J Math. Comp.
%V ?
%P ?-?
%M APR
%D 2019
%K jrnl, AMS, c2019, c201x, c20xx, zz0519, Eratosthenes, sieve, algorithm,
   prime, primes, Galway
%X "We show how to carry out a sieve of E. up to N in space
   (N^{1/3} (log N)^{2/3}) and time O(N log N). ... the usual versions of the
   sieve take space about O(sqrt N) and time at least linear on N. We can also
   apply our sieve to any subinterval of [1,N] of length Omega(N^{1/3}) in time
   close to linear on the length of the interval. Before, such a thing was
   possible only for subintervals of [1,N] of length Omega(sqrt N).
   Just as in (Galway, 2000), the approach here is related to Diophantine
   approximation, & also has close ties to Voronoi's work on the Dirichlet
   divisor problem. The advantage of the method here resides in the fact that,
   because the method we will give is based on the sieve of E., we will also be
   able to use it to factor ints, & not just to produce lists of consec.primes."
   -- [doi:10.1090/mcom/3438]['19],
   &  1712.09130@[arXiv]['17].
   [Also search for: sieve Eratosthenes].

%A A. S. Konagurthu
%A R. Subramanian
%A L. Allison
%A D. Abramson
%A M. Garcia de la Banda
%A P. J. Stuckey
%A A. M. Lesk
%T Information-theoretic inference of an optimal dictionary of protein
   supersecondary structures
%B Protein Supersecondary Structures
%I Springer
%P 123-131
%M APR
%D 2019
%K chapter, c2019, c201x, c20xx, zz0519, LAllison, ArunK, AMLesk,
   bioinformatics, protein, structure, proteins, supersecondary, fold, tableau,
   dictionary, library, MML, minimum message length, mdl, AI, inference
%X "We recently developed an unsupervised Bayesian inference methodology to
   automatically infer a dictionary of protein supersecondary structures
   (Subramanian et al., IEEE data compression conference proceedings (DCC),
   340-349, 2017). Specifically, this methodology uses the information-theoretic
   framework of minimum message length (MML) criterion for hypothesis selection
   (Wallace, Statistical and inductive inference by minimum message length,
   Springer Science & Business Media, New York, 2005). The best dictionary of
   supersecondary structures is the one that yields the most (lossless)
   compression on the source collection of folding patterns represented as
   tableaux (matrix representations that capture the essence of protein folding
   patterns (Lesk, J Mol Graph. 13:159–164, 1995). This book chapter outlines
   our MML methodology for inferring the supersecondary structure dictionary.
   The inferred dictionary is available at [www(click)][/4/2019]."
   -- [doi:10.1007/978-1-4939-9161-7_6]['19].
   (Also see [protein].)

%T Sydney Brenner (1927-2019)
%J Science
%V 364
%N 6441
%P 638
%M MAY
%D 2019
%K Brenner, Sir Sydney, obit, obituary, c2019, c201x, c20xx, zz0519, biol,
   genetic code, MolBio, 2002 Nobel prize, NobelPrize, C.elegans,
   Caenorhabditis elegans, roundworm, worm, nematode
%X "Sydney Brenner, an icon of science, died on 5 April at age 92. Sydney
   helped decipher the genetic code, he pioneered the use of Caenorhabditis
   elegans for genetic analysis, he made us think, and he made us laugh."
   -- [doi:10.1126/science.aax8563]['19].
   Also see, "... One of the key methods for identifying important function
      genes was the screen for roundworms that had some functional defect, such
      as being uncoordinated, leading to the identification of new sets of
      proteins, such as the set of UNC proteins. For this work, he shared the
      2002 Nobel Prize in Physiology or Medicine with H. Robert Horvitz and
      John Sulston. …"
   -- SB@[wikip]['20].
   [Also search for: Sydney Brenner].

%A C. Kosiol
%A N. Goldman
%T Different versions of the Dayhoff rate matrix
%J Mol. Biol. Evol.
%V 22
%N 2
%P 193-199
%M FEB
%D 2005
%K jrnl, MBE, MolBio, c2005, c200x, c20xx, zz0519, protein, PAM, rate, matrix,
   evolution, substitution
%X "Many phylogenetic inference methods are based on Markov models of seq.
   evolution. ... usually expressed in terms of a matrix (Q) of instantaneous
   rates of change but some models of AA replacement, most notably the PAM model
   of Dayhoff & c., were originally published only in terms of time-dependent
   prob.matrices (P(t)). Prev. published methods for deriving Q have used
   eigen-decomposition of an approximation to P(t). We show that the commonly
   used value of t is too large to ensure convergence of the ests. of elts of Q.
   We describe two simpler alternative methods for deriving Q from information
   such as that published by D. & c.. Neither of these methods requires
   approximation or e.-decomp.. We identify the methods used to derive various
   different versions of the D.model in current s/w, perform a comparison of
   existing & new implementations, &, to facilitate agreement among scientists
   using supposedly identical models, recommend that one of the new methods be
   used as a standard."
   -- [doi:10.1093/molbev/msi005]['19].
   [Also search for: MolBio substitution matrix].

%A A. G. Allegrini
%A S. Selzam
%A K. Rimfeld
%A S. von Stumm
%A J. B. Pingault
%A R. Plomin
%T Genomic prediction of cognitive traits in childhood and adolescence
%J Molec. Psychiatry
%V 24
%P 819-827
%M FEB
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0519, human behaviour, personality,
   nature, nurture, children, parents, education, predict, prediction, genes,
   genetic, cognition
%X "...  build prediction models of general cognitive ability & educational
   achievement. ... compared the performances of multi-trait genomic & polygenic
   scoring methods. In a representative UK sample of 7,026 children at ages 12 &
   16, we show that we can now predict up to 11% of the variance in intelligence
   & 16% in educational achievement. We also show that predictive power
   increases from age 12 to age 16 & genomic predictions do not differ for girls
   & boys. We found that multi-trait genomic methods were effective in boosting
   predictive power. Prediction accuracy varied across polygenic score
   approaches, however results were similar for different multi-trait &
   polygenic score methods. We discuss general caveats of multi-trait methods &
   polygenic score prediction, & conclude that polygenic scores for educational
   attainment & intelligence are currently the most powerful predictors in the
   behavioural sciences."
   -- [doi:10.1038/s41380-019-0394-4]['19].

%A E. R. Gamazon
%A A. H. Zwinderman
%A N. J. Cox
%A D. Denys
%A E. M. Derks
%T Multi-tissue transcriptome analyses identify genetic mechanisms underlying
   neuropsychiatric traits
%J Nature Genetics
%V ?
%P ?-?
%M MAY
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0519, MolBio, genes, gene, human,
   mental illness, health, psychiatric disorder, schizophrenia, bipolar, ADHD,
   depression, PrediXcan, GWAS, brain
%X "... provide comprehensive analyses using transcriptome data from an
   unprecedented collection of tissues to gain pathophysiological insights into
   the role of the brain, neuroendocrine factors (adrenal gland) &
   gastrointestinal systems (colon) in psychiatric disorders. In each tissue, we
   perform PrediXcan analysis & identify trait-assoc. genes for schizophrenia
   (n associations=499; n unique genes=275), bipolar disorder (n assoc.=17;
   n unique genes=13), attention deficit hyperactivity disorder (n assoc.=19;
   n unique genes=12) & broad depression (n assoc.=41; n unique genes=31).
   Importantly, both PrediXcan & summary-data-based Mendelian
   randomization/heterogeneity in dependent instruments analyses suggest
   potentially causal genes in non-brain tissues, showing the utility of these
   tissues for mapping psychiatric disease genetic predisposition. Our analyses
   further highlight the importance of joint tissue approaches as 76% of the
   genes were detected only in difficult-to-acquire tissues."
   -- [doi:10.1038/s41588-019-0409-8]['19].

%A G. Davis
%T The Republic of Learning: Higher Education Transforms Australia
%I ABCbooks, HarperCollins
%P 127
%M NOV
%D 2010
%K book, text, c2010, c201x, c20xx, zz0519, university, management,
   faculty, teaching, research, administration, Melbourne, Australia,
   BoyerLectures
%X pb; uk us isbn:0733328741; uk us isbn13:978-0733328749.
   (as of 2019, auth is the ex VC of Melbourne University.)
   (Also see the abc[14/11/2010]['19].)
   [Also search for: university management].

%A J. Belluz
%A B. Plumer
%A B. Resnick
%T The 7 biggest problems facing science, according to 270 scientists
%J Vox
%M SEP
%D 2016
%K news, views, c2019, c201x, c20xx, zz0519, scientific research, science,
   misuse, KPI, KPIs, university management, jobs, work, Hindex, grants, JIF,
   impact, ethics, ERA, ARC, pHacking, p hacking, peer review,
   perverse incentives
%X "... we sent scientists a survey asking this simple question: If you could
   change one thing about how science works today, what would it be and why?
   We heard back from 270 scientists all over the world, including graduate
   students, senior professors, laboratory heads, and Fields Medalists. They
   told us that, in a variety of ways, their careers are being hijacked by
   perverse incentives. The result is bad science. ..."
   -- [www]['19].
   [Also search for: university management].

%A R. Connell
%T The Good University. What universities actually do and why it's time for
   radical change
%I MonashUP
%P 240
%M FEB
%D 2019
%K book, text, c2019, c201x, c20xx, zz0519, university, management, KPI, KPIs,
   rankings, league tables, ERA, quality, higher education, neoliberal,
   Reaganomics, faculty, teaching, research, ethics, administration,
   Monash, MUP, Australia
%X 1st ed 2019; hb us uk isbn:1786995417; uk us isbn13:978-1786995414;
                pb au$30; isbn13:978-1925835038.
   "The higher ed. industry might seem like it's booming, with over 200 million
   students in universities & colleges worldwide & funds flowing in like never
   before. But the truth is that these institutions have never been unhappier
   places to work. Corporate-style management, cost-cutting governments,
   mobilisations by angry students & strikes by disgruntled staff have all taken
   their toll - in almost every country around the world. It's no wonder that
   there is talk of 'universities in crisis.' ... outlines a practical vision
   for how our unis. can become both more engaging & more productive places,
   driven by social good rather than profit, & helping to build fairer
   societies."
   [Also search for: university management].

%T Heath Robinson: WW2 codebreaking machine reconstructed
%I BBC
%M APR
%D 2019
%K news, c2019, c201x, c20xx, zz0519, Heath Robinson, WW2, WWII, gadget,
   code breaker, breaking, cracking, automation, history, computing, computers,
   Bletchley Park, Colossus, 1943
%X "A World War Two codebreaking machine has been reconstructed after a
   seven-year project so it can run in public for the first time.  The Heath
   Robinson has been restored at The National Museum of Computing in Milton
   Keynes by a team of six.  The machine was an early attempt to automate
   code-cracking and, due to its complexity, was named after the illustrator
   W Heath Robinson. ... The machine, which went into operation at Bletchley
   Park in June 1943, is acknowledged as the inspiration for Colossus, the
   world's first programmable computer. ..."
   -- bbc[6/4/2019].
   (Also see [B.Park].)
   [Also search for: Bletchley Park].

%T Springer Nature journals unify their policy to encourage preprint sharing
%A editor
%J Nature
%V ?
%P ?-?
%M MAY
%D 2019
%K news, views, c2019, c201x, c20xx, zz0519, scientific research,
   publishing, preprint, preprints, server, arXiv, Springer, Nature,
   journal, policy, journals, plan S planS
%X "For more than two decades, Nature and its sister journals have supported
   pre-publication sharing of manuscripts on preprint servers ... we now make it
   clear that authors may choose any licence for preprints, including Creative
   Commons licences. Licensing choice will not impede consideration at a
   Springer Nature journal, but authors should bear in mind that it could affect
   sharing, adaptation and reuse of the preprint itself."
   -- [doi:10.1038/d41586-019-01493-z]['19].
   (Also see, 'Facing Plan S, publishers may set papers free'
   -- Science [doi:10.1126/science.364.6441.620][17/5/2019].)

%A S. B. Kaufman
%A D. B. Yaden
%A E. Hyde
%A E. Tsukayama
%T The light vs. dark triad of personality: Contrasting two very different
   profiles of human nature
%J Front. Psychol.
%V ?
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0519, psychology, human beahaviour, good, evil,
   people, Kantianism, Humanism, Humanity, goodness, agreeable, HEXACO,
   honesty humility
%X "... we contrasted the nomological network of the Dark Triad (a well-studied
   cluster of socially aversive traits) with the nomological network of the
   Light Triad, measured by the 12-item Light Triad Scale (LTS). The LTS is a
   first draft measure of a loving and beneficent orientation toward others
   ('everyday saints') that consists of three facets: Kantianism (treating
   people as ends unto themselves), Humanism (valuing the dignity and worth of
   each individual), and Faith in Humanity (believing in the fundamental
   goodness of humans). ..."
   -- [doi:10.3389/fpsyg.2019.00467]['19].
   (Also see the bbc[16/5/2019].)

%A K. Bansal
%A S. M. Loos
%A M. N. Rabe
%A C. Szegedy
%A S. Wilcox
%T HOList: An environment for machine learning of higher-order theorem proving
   (extended version)
%J arXiv
%M APR
%D 2019
%K TR, c2019, c201x, c20xx, zz0519, HOList, HOL light, maths, mathematical,
   automated, theorem, proving, maths, proof, prove, prover, assistant,
   HOList, HOL light
%X "We present an environment, benchmark, and deep learning driven automated
   theorem prover for higher-order logic. Higher-order interactive theorem
   provers enable the formalization of arbitrary mathematical theories and
   thereby present an interesting, open-ended challenge for deep learning. We
   provide an open-source framework based on the HOL Light theorem prover that
   can be used as a reinforcement learning environment. HOL Light comes with a
   broad coverage of basic mathematical theorems on calculus and the formal
   proof of the Kepler conjecture, from which we derive a challenging benchmark
   for automated reasoning. We also present a deep reinforcement learning driven
   automated theorem prover, DeepHOL, with strong initial results on this
   benchmark."
   -- 1904.03241@[arXiv]['19].
   (Also see RL@[wikip]['22].)
   [Also search for: theorem proving].

%A K. Topley
%T Computationally efficient bounds for the sum of Catalan numbers
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0519, sum, cummulative, Catalan number,
   bound, Dyck paths, asymptotic, approximations
%X "Easily computable lower & upper bounds are found for the sum of Catalan #s.
   The lwb is proven to be tighter than the upb, which previously was declared
   to be only an asymptotic. The avg. of these bounds is proven to be also an
   upb, & empirically it is shown that the avg. is superior to the prev. upb by
   a factor greater than (9/2)."
   -- [arXiv]['5/19].

%A A. Arman
%A P. Gao
%A N. Wormald
%T Fast uniform generation of random graphs with given degree sequences
%J arXiv
%M MAY
%D 2019
%K TR, c2019, c201x, c20xx, zz0519, generate, sample, random, graph, maths,
   degree sequence
%X "... provide an alg. that generates a graph with given degree seq. uniformly
   at random. Provided that D^4=O(m), where D is the maximal degree & m is the
   # of edges, the alg. runs in expected time O(m). ... sig. improves the prev.
   most efficient uniform sampler, which runs in expected time O(m^2D^2) for the
   same family of degree seqs.. ...uses a novel ingredient which progressively
   relaxes restrictions on an object being generated uniformly at random, & we
   use this to give fast algs. for uniform sampling of graphs with other degree
   seqs. as well. Using the same method, we also obtain algs. with expected run
   time which is (i) linear for power-law degree seqs. in cases where the prev.
   best was O(n^{4.081}), and (ii) O(nd+d^4) for d-regular graphs when
   d=o(sqrt(n)), where the prev. best was O(nd^3)."
   -- 1905.03446@[arXiv]['19].
   [Also search for: random graph].

%A D. G. Willis
%T Computational complexity and probability constructions
%J JACM
%V 17
%N 2
%P 241-259
%M APR
%D 1970
%K jrnl, JACM, c1970, c197x, c19xx, zz0519, information theory, code, codes,
   maths, inductive inference, II, stats, probability, UTM
%X "There exist constructive correspondences between Turing machines having
   finitely determinable behavior & computable probability measures on their
   output seqs.. These correspondences determine limits on the relative
   accuracies with which different computable probability measures predict
   events. Using any UTM as a basis, it is possible to construct an infinite
   hierarchy of increasingly accurate computable prob.measures which are indep.
   of any probability assumptions. The relationship of such measures to real
   events is considered."
   -- [doi:10.1145/321574.321578]['19].
   [Also search for: information theory].

%A P. D. Grunwald
%A P. M. B. Vitanyi
%T Kolmogorov complexity and information theory: With an interpretation in
   terms of questions and answers
%J J. of Logic, Language, and Info. (Special Issue on Connecting the
   Different Faces of Information)
%V 12
%N 4
%P 497-529
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0519, information theory, universal code, codes,
   Shannon, entropy, Kolmogorov complexity, algorithmic, intro
%X "We compare the elementary theories of Shannon information & Kolmogorov
   complexity, the extent to which they have a common purpose, & where they are
   fundamentally different. We discuss & relate the basic notions of both
   theories: Shannon entropy, Kolmogorov complexity, Shannon mutual information
   & Kolmogorov ('algorithmic') mutual information. We explain how universal
   coding may be viewed as a middle ground between the two theories. We consider
   Shannon's rate distortion theory, which quantifies useful (in a certain
   sense) information. We use the communication of information as our guiding
   motif, & we explain how it relates to sequential question-answer sessions"
   -- 40167357@[Jstor]['19].
   [Also search for: information theory inference].

%A M. Gonen
%A D. Shapira
%A J. A Storer
%T Edit distance with multiple block operations
%J COMPJ
%V 62
%N 5
%P 657-669
%M MAY
%D 2019
%K jrnl, COMPJ, c2019, c201x, c20xx, zz0519, string, strings, edit distance,
   similarity, block moves, move
%X "... consider the edit distance with block moves, block copies & block
   deletions, which is shown to be NP-hard, & employ a simple left-to-right
   greedy sliding window algorithm that achieves a constant factor approximation
   ratio of 5. This is an improvement on the constant approximation of 12
   presented by Ergun & Sahinalp (Ergün, F., Muthukrishnan, S., & Sahinalp,
   S. C. Comparing sequences with segment rearrangements. FST TCS 2003:
   Foundations of Software Technology & Theor. C. Sci.), & is achieved by a
   proof that introduces two non-trivial kinds of substrings for different
   purposes, so recursive & non-recursive ops can be treated at the same time."
   -- [doi:10.1093/comjnl/bxy066]['19].
   [Also search for: strings block moves].

%A A. Nellore
%A A. Nguyen
%A R. F. Thompson
%T A multidimensional analog to the Burrows-Wheeler transform
%J arXiv
%M MAY
%D 2019
%K TR, c2019, c201x, c20xx, zz0519, strings, BWT, search, indexing, 2D, grid,
   pattern, text
%X "We show how to perform multidimensional pattern matching over an
   n-dimensional grid of text spanning a total of s characters with nength, an
   analog to the Burrows-Wheeler transform. Nength exploits a Fourier duality
   between two kinds of grid products to map a search problem that naively takes
   O(s^2) arithmetic ops to an equivalent problem that takes O(s log s)
   arithmetic operations."
   -- 1905.03424@[arXiv]['19].
   ?where is it useful?


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