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%A J. Wassenberg
%A M. Blacher
%A J. Giesen
%A P. Sanders
%T Vectorized and performance-portable quicksort
%J SPE
%V ?
%m AUG
%d 2022
%K jrnl, SPE, c2022, c202x, c20xx, zz0922, sort, sorting, quicksort, algorithm,
   GPU, parallel, vectorized, vectorised, fast, vqsort, ips4o, SVE, RISCV
%X "Recent works showed that implementations of quicksort using vector CPU
   inst'ns can outperform the non-vectorized algs. ... [But] these impl'ns are
   typically single-threaded, implemented for a particular inst'n set, &
   restricted to a small set of key types. We lift these three restrictions: our
   proposed vqsort alg. integrates into the state-of-the-art parallel sorter
   ips^4o, with a geometric mean speedup of 1.59. ... works on 7 inst'n sets
   (inc. SVE & RISC-V V) across 4 platforms. It also supports floating-pt &
   16-128 bit integer keys. To the best of our knowledge, this is the fastest
   sort for large arrays of non-tuple keys on CPUs, up to 20 times as fast as
   the sorting algs. implemented in std libraries. ... focuses on the practical
   engineering aspects enabling the speed & portability ... [&] we introduce
   compact & transpose-free sorting nwks for in-register sorting of small arrays
   & a vector-friendly pivot sampling strategy that is robust against
   adversarial input."
   -- [doi:10.1002/spe.3142]['22], online Aug 2022.
   [Also search for: sorting parallel].

%A Fei Wang
%A et al ...
%A T. Rompf
%T Demystifying differentiable programming: Shift/reset the penultimate
   backpropagator
%J arXiv
%M MAR
%D 2018
%O Proc. of the ACM on Prog. Langs., vol.3, #96, pp.1-31, Aug. 2019
%K TR, c2018, c201x, c20xx, zz0922, NN, ANN, backprop, backpropagation,
   automatic differentiation, forward, reverse, training, tensorFlow
%X "... [DL] rests in crucial ways on gradient-descent opt'n & the ability to
   learn params. of a NN by backprop'ng observed errors. [but] NN architectures
   are growing increasingly sophisticated & diverse, which motivates an emerging
   quest for even more general forms of differentiable programming, where arb.
   parameterized computations can be trained by gradient descent. ... we take a
   fresh look at auto.differentiation (AD) techniques, & especially aim to
   demystify the reverse-mode form of AD that generalizes backprop. in NNs. We
   uncover a tight connection between reverse-mode AD & delimited continuations,
   which permits implementing reverse-mode AD purely via operator overloading &
   without any auxiliary data structs.. [&] show how this formulation of AD can
   be fruitfully combined with multi-stage programming (staging), leading to a
   highly efficient impl'n that combines the performance benefits of deep
   learning frameworks based on explicit reified computation graphs (e.g.,
   TensorFlow) with the expressiveness of pure library approaches (e.g.,
   PyTorch)."
   -- 1803.10228@[arXiv]['22],
   or [doi:10.1145/3341700]['22].
   (Also see AD@[wikip]['22].)
   [Also search for: automatic differentiation].

%A Xueqiu Lin
%A et al
%T Nested epistasis enhancer networks for robust genome regulation
%J Science
%V 377
%N 6610
%P 1077-1085
%K AUG
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0922, epistasis, biological network,
   regulation, enhancer, promoter, interaction, gene expression, BRD4
%X "Mammalian genomes have multiple enhancers spanning an ultralong distance
   (> megabases) to modulate important genes ... CRISPRi screening with m/c
   learning to define quantitative enhancer-enhancer interactions. We find that
   the ultralong distance enhancer n/wk has a nested multilayer architecture
   that confers functional robustness of gene expression. ..."
   -- [doi:10.1126/science.abk3512]['22].
   [Also search for: MolBio interaction network].

%A J. M. Perkel
%T Smart software untangles gene regulation in cells
%J Nature
%V 609
%P 428-431
%M SEP
%D 2022
%K news, views, survey, MolBio, c2022, c202x, c20xx, zz0922, gene regulatory,
   network, interaction, promoter, transcription factor, Inferelator, ATACseq,
   RNAseq, SCENIC+, single-cell, CellOracle, SINGE, BEELINE, Quackenbush,
   maxATAC, scRNAseq
%X "Working out how a cell is wired lets researchers find key regulators of
   behaviour ..."
   -- [doi:10.1038/d41586-022-02826-1]['22].
   [Also search for: MolBio interaction network] & [also search for: scRNAseq].

%A A. Pinson
%A et al
%T Human TKTL1 implies greater neurogenesis in frontal neocortex of modern
   humans than Neanderthals
%J Science
%V 377
%N 6611
%P ?-?
%M SEP
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0922, gene, TKTL1, modern human,
   Neanderthal, brain, development, neurons, neuron, neurogenesis
%X "... In light of our finding that TKTL1 expression in fetal human neocortex
   is particularly high in the developing frontal lobe, our study implies that
   because of the single amino acid-based activity of hTKTL1, neocortical
   neurogenesis in modern humans was and is greater than it was in Neanderthals,
   in particular in the frontal lobe."
   -- [doi:10.1126/science.abl6422]['22].
   [Also search for: MolBio Neanderthal].

%A J. T. Kristensen
%A R. Kaarsgaard
%A M. K. Thomsen
%T Jeopardy: An invertible functional programming language
%J arXiv
%M SEP
%D 2022
%O 34th Symp. on Impl. & Appl. of Func. Lang., 31 Aug - 2 Sep, 2022
%K TR, c2022, c202x, c20xx, zz0922, FP, Jeopardy, reversible, invertible,
   inverse, algorithm, program, computing, uninvertible
%X "... we introduce Jeopardy, a functional prog. lang. that guarantees program
   invertibility without imposing local reversibility. In particular, Jeopardy
   allows the limited use of uninvertible -- & even nondeterministic! --
   operations, provided that they are used in a way that can be statically
   determined to be invertible. However, guaranteeing invertibility is not
   obvious. Thus, we furthermore outline three approaches that can give a
   partial static guarantee."
   -- 2209.02422@[arXiv]['22].

%A B. Ahrens
%A K. Wullaert
%T Category theory for programming
%J arXiv
%M SEP
%D 2022
%K TR, intro, notes, c2022, c202x, c20xx, zz0922, category theory, FP, type,
   types, datatype, monad, maths, algebra
%X "... a brief intro. to some elts of category theory. The choice of topics is
   guided by applications to [FP]. Firstly, we study initial algebras, which
   provide a math. characterization of datatypes & recursive fns on them.
   Secondly, we study monads, which give a math. framework for effects in
   F.langs.. The notes include many problems & solutions."
   -- 2209.01259@[arXiv]['22].
   [Also search for: category theory].

%A A. R. Bendixen
%A B. B. Bojesen
%A H. Huttel
%A S. Lybech
%T A generic type system for higher-order psi-calculi
%J arXiv
%M SEP
%D 2022
%O pp.43-59, Proc. Combined 29th Int. Workshop on Expressiveness in Concurrency
   & 19th Workshop on Structural Operational Semantics (EXPRESS/SOS) 2022
   [www]['22]
%K TR, c2022, c202x, c20xx, zz0922, FP, PFP, pi, psi calculus, HOpsi, CHOCS,
   piCalculus, psiCalculus, type, types
%X "The Higher-Order psi-calculus framework (HOpsi) is a generalisation of many
   first- & higher-order extensions of the pi-calculus. It was proposed by
   Parrow et al. who showed that higher-order calculi such as HOpi & CHOCS can
   be expressed as HOpsi-calculi. In this paper we present a generic type system
   for HOpsi-calculi ..."
   -- 2209.02354@[arXiv]['22].
   [Also search for: piCalculus] and [also search for: psiCalculus].

%A Junhui Wu
%A et al
%T Honesty and dishonesty in gossip strategies: a fitness interdependence
   analysis
%J Phil. Trans. of the Royal Soc. B
%M OCT
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0922, gossip, gossiping, lie, lying,
   truth, 2022, c2022, igNobel
%X "... We build formal models to provide the theor. foundation for individuals'
   gossip strategies, taking into account the gossiper's fitness interdependence
   with the receiver & the target. Our models across four different games
   suggest a very simple rule: when there is a perfect match (mismatch) between
   fitness interdependence & the effect of honest gossip, the gossiper should
   always be honest (dishonest); however, in the case of a partial match, the
   gossiper should make a choice based on their fitness interdependence with the
   receiver & the target & the marginal cost/benefit in terms of pay-off
   differences caused by possible choices of the receiver & the target in the
   game. Moreover, gossipers can use this simple rule to make optimal decisions
   even under noise. We discuss empirical examples that support the predictions
   of our model & potential extensions."
   -- [doi:10.1098/rstb.2020.0300]['22].
   (Also see *2022* IgNobel winners [www]['22].)

%A A. Severin
%A et al
%T Journal impact factor and peer review thoroughness and helpfulness:
   A supervised machine learning study
%J arXix
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0922, peer review, reviewing, refereeing,
   journal, JIF, scientific papers
%X "... We examined the assoc. between the content of peer review & JIF by
   analysing 10,000 peer review reports submitted to 1,644 medical & life sci.
   journals. ... examined the assoc. between ten groups of journals defined by
   JIF deciles & the content of peer reviews using linear mixed-effects models
   ... peer review in journals with higher JIF tends to be more thorough in
   discussing the methods used but less helpful in terms of suggesting solns &
   providing examples. Differences were modest & variability high, indicating
   that the JIF is a bad predictor for the quality of peer review of an
   individual manuscript."
   -- [arXiv]['22].

%A J. Tollefson
%A R. Van Noorden
%T US government reveals big changes to open-access policy
%J Nature
%M AUG
%D 2022
%K news, views, c2022, c202x, c20xx, zz0922, scientific research, publishing,
   open access, equity, paywall, publishers, papers
%X "US research agencies should make the results of federally funded research
   free to read as soon as they are published, the administration of President
   Joe Biden has announced ..."
   -- [doi:10.1038/d41586-022-02351-1]['22].
   Also, J. Brainard, J. Kaiser, Sci., 26 Aug. 2022,
   "White House requires immediate public access to all U.S.-funded
   research papers by 2025 ..."
   -- [doi:10.1126/science.ade6076]['22].
   [Also search for: research open access].

%A S. Crafa
%T From legal contracts to legal calculi: the code-driven normativity
%J arXiv
%M SEP
%D 2022
%K TR, c2022, c202x, c20xx, zz0922, law, legal, contract, automation, automatic,
   formal, programming, logic, LP, permission, prohibition, obligation
%X "... we focus on software-based legal contracts; we illustrate the design of
   a legal calculus whose primitives allow a direct formalisation of contracts'
   normative elts (i.e., permissions, prohibitions, obligations, asset transfer,
   judicial enforcement & openness to the external context). We show that
   interpreting legal contracts as interaction protocols between (untrusted)
   parties enables the generalisation of formal methods & tools for concurrent
   systems to the legal setting."
   -- 2209.02353@[arXiv]['22].
   [Also search for: automatic contract programming].

%A M. Le Conte
%T Escape: How a generation shaped, destroyed and survived the internet
%I BlinkPubl
%P 304
%M SEP
%D 2022
%K book, c2022, c202x, c20xx, LeConte, zz0922, internet, www, mail groups,
   social media, web, internet, blog, MSN, Tumblr, myspace, facebook, twitter,
   chat rooms, forums
%X "... [auth] was born in 1991, the same year the WWW was invented. She had
   her first blog at twelve ... MSN, Tumblr and MySpace, to chat rooms, forums
   and blogs; Marie is part of the millennial generation that grew up while the
   internet was growing up with them. Where did it go all wrong? How did the
   internet go from a place where you went to escape real life to where real
   life is shaped? ..."
   1st ed 2022; hb stg5; uk us isbn:1788705157; uk us isbn13:978-1788705158.
   [Also search for: social media].

%A J. V.Koski
%A J. P.Pekola
%T Maxwell's demons realized in electronic circuits,
   Demons de Maxwell realises avec des circuits electroniques
%J Comptes Rendus Physique
%V 17
%N 10
%P 1130-1138
%M DEC
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz0922, Maxwell, demon, thermodynamics,
   entropy, energy, information, Szilard engine, quantum
%X "We review recent progress in making the former gedanken experiments of
   Maxwell's demon into real experiments in a lab. ... focus on realizations
   based on single-electron tunneling in electronic circuits. We first present
   how stochastic thermodynamics can be investigated in these circuits. Next we
   review recent experiments on an electron-based Szilard engine. Finally, we
   report on experiments on single-electron tunneling-based cooling, overviewing
   the recent realization of a Coulomb gap refrigerator, as well as an
   autonomous Maxwell's demon."
   -- [doi:10.1016/j.crhy.2016.08.011]['22].
   Also see MD@[wikip]['22].
   [Also search for: thermodynamics information].

%A F. Krawiec
%A et al ...
%A A. Fitzgibbon
%T Provably correct, asymptotically efficient, higher-order reverse-mode
   automatic differentiation
%J POPL
%V 6
%P #48, 1-30
%M JAN
%D 2022
%K conf, c2022, c202x, c20xx, zz0922, FP, automatic differentiation, forward,
   reverse
%X "... give a simple & efficient impl'n of reverse-mode auto.diff., which both
   extends easily to higher-order fns, & has run time & memory consumption
   linear in the run time of the original program. [&] to a formal description
   of the translation, we also describe an implementation of this alg., & prove
   its correctness by means of a logical relations argument."
   -- [doi:10.1145/3498710]['22].
   (Also see AD@[wikip]'22].)
   [Also search for: automatic differentiation].

%A K. V. Mardia
%A et al
%T Mixtures of concentrated multivariate sine distributions with applications
   to bioinformatics
%J J. Appl. Stats.
%V 39
%N 11
%P 2475-2492
%M AUG
%D 2012
%K jrnl, stats, c2012, c201x, c20xx, zz0922, vonMises, direction, angle, angles,
   mixture model, directional, probability distribution, protein, MolBio, sine
%X "... study a mixture model of multivariate angular dist'ns. The distin
   treated here (multivariate sine dist'n) is a multivariate extension of the
   well-known von Mises distribution on the circle. The density of the sine
   dist'n has an intractable normalizing constant & here we propose to replace
   it in the concentrated case by a simple approx.. We study the EM alg. for
   this dist'n & apply it to a practical example from protein bioinf.."
   -- [doi:10.1080/02664763.2012.719221]['22].
   [Also search for: vonMises direction]  &  [also search for: mixture model].

%A G. Fici
%T A classification of trapezoidal words
%J arXiv
%M AUG
%D 2011
%O 8th Int. Conf. WORDS 2011, EPTCS 63, 2011, pp. 129-137,
%K TR, c2011, c201x, c20xx, zz0922, closed string, strings, defn, trapezoidal,
   word, open, Sturmian, palindrome
%X "Trapezoidal words are finite words having at most n+1 distinct factors of
   length n, for every n >= 0. They encompass finite Sturmian words. We
   distinguish t.words into two disjoint subsets: open & closed t.words. A
   t.word is closed if its longest repeated prefix has exactly two occurrences
   in the word, the second one being a suffix of the word. Otherwise it is open.
   We show that open t.words are all primitive & that closed t.words are all
   Sturmian. We then show that t.palindromes are closed (& therefore Sturmian).
   This allows us to characterize the special factors of Sturmian palindromes.
   We end with several open problems."
   -- 1108.3629v1@[arXiv]['22],
      [doi:10.4204/EPTCS.63]['22].
   [Also search for: closed string].

%A G. Badkobeh
%A A. De Luca
%A G. Fici
%A S. Puglisi
%T Maximal closed substrings
%K arXiv
%M SEP
%D 2022
%K TR, c2011, c201x, c20xx, zz0922, maximal closed substring, MCS, string,
   strings, run, repeat
%X "A string is closed if it has length 1 or has a nonempty border without
   internal occurrences. ... we introduce the defn of a maximal closed substring
   (MCS) ... an occurrence of a closed substring that cannot be extended to the
   left nor to the right into a longer ... MCSs with exponent at least 2 are
   commonly called runs; those with exponent < 2, instead, are particular cases
   of maximal gapped repeats. We show that a string of length n contains
   O(n^{1.5}) MCSs. We also provide an output-sensitive alg. that, given a
   string of length n over a constant-size alphabet, locates all m MCSs the
   string contains in O(n.log(n)+m) time."
   -- 2209.00271@[arXiv]['22].
   [Also search for: closed string].

%A K. Maillard
%A M. Lennon-Bertrand
%A N. Tabareau
%A E. Tanter
%T A reasonably gradual type theory
%J arXiv
%M SEP
%D 2022
%K TR, c2022, c202x, c20xx, zz0922, gradual type, types, datatype, theory, Coq,
   Calculus of Inductive Constructions, CIC, GCIC, CastCIC, GRIP, Agda, FP
%X "Gradualizing the Calculus of Inductive Constructions (CIC) involves dealing
   with subtle tensions between normalization, graduality, & conservativity with
   respect to CIC. ... We develop the metatheory of GRIP using a model
   formalized in Coq, & provide a prototype implementation of GRIP in Agda."
   -- 2209.00975@[arXiv]['22].
   [Also search for: gradual type].

%A Yaoda Zhou
%A Jinxu Zhao
%A C. D. S. Oliveira
%T Revisiting iso-recursive subtyping
%J TOPLAS
%V 44
%N 4
%P #24
%M DEC
%D 2022
%K jrnl, TOPLAS, c2022, c202x, c20xx, zz0922, data type types, isorecursive,
   Amber, FP, Cardelli, subtype, subtypes, unfolding
%X "... This article aims to revisit the problem of subtyping iso-recursive
   types. We start by introducing a novel declarative spec. for Amber-style
   iso-recursive subtyping. Informally, the spec. states that two recursive
   types are subtypes if all their finite unfoldings are subtypes. The Amber
   rules are shown to have equivalent expressive power to this declarative
   spec.. We then show two variants of sound, complete & decidable algorithmic
   formulations of subtyping wrt the declarative spec., which employ the idea
   of double unfoldings. ..."
   -- [doi:10.1145/3549537]['22], online Sept 2022.