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%A N. Kamiyama
%T The envy-free matching problem with pairwise preferences
%J IPL
%V 172
%P ?-?
%M DEC
%D 2021
%K jrnl, IPL, c2021, c202x, c20xx, zz0721, match, envy free matching, EFM,
   problem, preference, 106148
%X "... consider the situation where each agent has a pref. over a subset of
   items & exactly one item is matched to each agent. The envy-freeness of a
   matching guarantees that no one has envy for the others. We consider an
   envy-free matching in the sit'n where each agent has a pref. that is defined
   based on comparisons of any two acceptable items. We prove that in this sit'n
   the problem of checking the existence of an EFM is generally hard."
   -- [doi:10.1016/j.ipl.2021.106158]['21].
   [Also search for: matching preference].

%A C. Brosse
%A V. Limouzy
%A A. Mary
%T Polynomial delay algorithm for minimal chordal completions
%J arXiv
%M JUL
%D 2021
%K TR, c2021, c202x, c20xx, zz0721, maths, graph, tree, decomposition, minimal,
   chordal completion, Carmeli
%X "... the problem of listing all the minimal chordal completions of a g..
   ... Carmeli et al proved that all minimal c.completions or equiv. all proper
   tree decompositions of a g. can be listed in incremental polynomial time ...
   [we] provid[e] a polynomial delay alg. to solve this problem which, moreover,
   uses polynomial space. Our alg. relies on Proximity Search ... we introduce a
   new general method called canonical path reconstruction to design polynomial
   delay & polynomial space algs. based on proximity search."
   -- 2107.05972@[arXiv]['21].

%A N. K. Schaefer
%A B. Shapiro
%A R. E. Green
%T An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
%J Sci. Adv.
%V 16
%V 7
%N 29
%P eabc0776
%M JUL
%D 2021
%K MolBio, eJrnl, c2021, c202x, c20xx, zz0721, SARGE, ARG, DNA, human, homo,
   hominin, hominid, evolution, Neanderthal, Denisovan, ancient DNA,
   incomplete lineage sorting, ILS
%X "... We describe a new ancestral recombination graph inference alg. that
   scales to large genome-wide datasets & demo. its accuracy on real & simulated
   data. ... generate a g.-wide ancestral recomb. g. incl. human & archaic
   hominin genomes. From this, we generate a map within human genomes of archaic
   ancestry & of genomic regions not shared with archaic hominins either by
   admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the
   modern h. genome is uniquely h.. We also find evidence of multiple bursts of
   adaptive changes specific to modern hs. within the past 600,000 years
   involving genes related to brain development & function."
   -- [doi:10.1126/sciadv.abc0776]['21].

%A J. Jumper
%A et al ...
%A D. Hassabis
%T Highly accurate protein structure prediction with AlphaFold
%J Nature
%V 596
%P 583-589
%M JUL
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0721, protein structure prediction,
   AlphaFold, ANN, NN, alphafold2, tertiary, 3D, CASP 14, CASP14
%X "... We validated an entirely redesigned version of our NN-based model,
   AlphaFold, in the challenging 14th Critical Assessment of protein Structure
   Prediction (CASP14), demonstrating accuracy competitive with experimental
   structures in a majority of cases & greatly outperforming other methods. ..."
   -- [doi:10.1038/s41586-021-03819-2]['21].
   (Also see next paper in this vol. & a video talk about alphafold 1 and 2
   -- [www]['22].)
   [Also search for: 3D protein structure prediction ANN].

%A K. Tunyasuvunakool
%A et al ...
%A D. Hassabis
%T Highly accurate protein structure prediction for the human proteome
%J Nature
%V 596
%P 590-596
%M JUL
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0721, protein structure prediction,
   AlphaFold, alphafold2, human
%X "... we dramatically expand structural coverage by applying the
   state-of-the-art machine learning method, AlphaFold, at scale to almost the
   entire human proteome (98.5% of h. proteins). The resulting dataset covers
   58% of residues with a confident pred'n, of which a subset (36% of all r.)
   have very high confidence. We introduce several metrics developed by building
   on the AlphaFold model, & use them to interpret the dataset, identifying
   strong multi-domain pred'ns as well as regions likely to be disordered.
   Finally, we provide some case studies illustrating how high-quality pred'ns
   may be used to generate biol.hypotheses. ... we are making our pred'ns freely
   available to the community via a public DB (hosted by EBI at [www]). ..."
   -- [doi:10.1038/s41586-021-03828-1]['21].
   (Also see prev. paper in this vol. & the [bbc][23/7/2021].)

%T Dynamics of Climate: Proc. Held October 26-28, 1955
%E R. L. Pfeffer
%I Sponsored jointly by Inst. for Adv. Study, Princeton, &
   Geophys. Res. Directorate
%D 1955
%K proc, conf, c1955, c195x, c19xx, zz0721, weather, climate, prediction,
   simulation, model, modelling, CO2, greenhouse gas, global warming,
   von Neumann, vonNeumann, history, computing, computers
%X Cat. entry [nla.gov.au]['21].
   "For example, only about 1/100,000 of all water on earth occurs in vapor form
   in the atmosphere, yet the presence of water vapour makes a difference of
   40 deg. C in the avg. temp. of the earth. This is more than twice the diff.
   between the temp. at the time of max. glaciation and that at the time of
   total deglaciation of the earth" -- John von Neumann,
   quoted by G.Dyson on p.171 of "Turing's Cathedral" 2012.
   Attendees also discussed rising CO2 and climate effects.
   [Also search for: global warming].

%A C. Wagner
%A et al
%T Measuring algorithmically infused societies
%J Nature
%V 595
%P 197-204
%M JUL
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0721, human, behaviour, society, social, data,
   collection, bigdata, privacy, fairness, openess, openness, justice, internet,
   www, tracking
%X "... The emergence of 'algorithmically infused societies' - societies whose
   very fabric is co-shaped by algorithmic & human behaviour - raises three key
   challenges: the insufficient quality of measurements, the complex
   consequences of (mis)measurements, & the limits of existing social theories.
   Here we argue that tackling these challenges requires new social theories
   that account for the impact of alg.systems on social realities. ... the
   development of measurements should be transparent & participatory, & include
   mechanisms to ensure measurement quality & identify possible harms. ..."
   -- [doi:10.1038/s41586-021-03666-1]['21] (153 refs).

%A J. de Vrieze
%T Large survey finds questionable research practices are common
%J Science
%V 373
%N 6552
%P 265
%M JUL
%D 2021
%K news, views, deVrieze, c2021, c202x, c20xx, zz0721, scientific, research,
   academia, ethics, fraud, academic, misconduct, Holland, Netherlands, Europe
%X "More than half of Dutch scientists regularly engage in questionable research
   practices, according to new study results that are likely to apply to other
   countries. And one in 12 admitted to committing a more serious form of res.
   misconduct within the past 3 years: fabrication or falsification of res.
   results. At 8%, that is more than double the rate reported in prev. studies.
   The Dutch National Survey on Research Integrity, the largest of its kind to
   date, took special precautions to guarantee the anonymity of respondents, so
   its organizers believe the results are more accurate than previous surveys."
   -- [doi:10.1126/science.373.6552.265]['21].
   [Also search for: scientific research misconduct].

%A S. Kean Little
%T The Icepick Surgeon: Murder, Fraud, Sabotage, Piracy, and Other Dastardly
   Deeds Perpetrated in the Name of Science
%I BrownPubl.
%P 368
%M JUL
%D 2021
%K book, c2021, c202x, c20xx, zz0721, science, scientific research, crime,
   ethics, misconduct
%X 1st ed 2021; hb us$20; uk us isbn:0316496502; isbn13:978-0316496506.
   "... beginning with Cleopatra's dark deeds in ancient Egypt. ... reveals the
   origins of much of modern sci. in the transatlantic slave trade of the 1700s,
   as well as Thomas Edison's mercenary support of the electric chair & the
   warped logic of the spies who infiltrated the Manhattan Project. But the sins
   of sci. aren't all safely buried in the past. Many of them, Kean reminds us,
   still affect us today. ..."
   [Also search for: scientific research ethics].

%A C. Woolston
%T Impact factor abandoned by Dutch university in hiring and promotion decisions
%J Nature
%V 595
%P 462-462
%M JUL
%D 2021
%K news, views, c2021, c202x, c20xx, zz0721, university, academia, impact, JIF,
   research, publications, citations, Hindex, DORA, KPIs, KPI, Netherlands,
   Holland, Dutch, Europe, Utrecht University, hire, hiring, promoting, policy,
   promotion, tenure, scientific research, open science, sci, management
%X "... By early 2022, every department at Utrecht U. in the Netherlands will
   judge its scholars by other standards, including their commitment to teamwork
   & their efforts to promote open science  ..."
   -- [doi:10.1038/d41586-021-01759-5]['21].
     Also see, 'Indicator frameworks for fostering open knowledge practices in
     science and scholarship'
     -- [EU]['21].
   [Also search for: University management].

%A N. Subbaraman
%T Gun violence is surging - researchers finally have the money to ask why
%J Nature
%V 595
%P 486-488
%M JUL
%D 2021
%K news, views, c2021, c202x, c20xx, zz0721, USA, NRA, politics, gun control,
   research, violence, death
%X "With historically high levels of new funding, US gun-violence research is
   starting to find its footing. ..."
   -- [doi:10.1038/d41586-021-01966-0]['21].

%T Emmanuel Macron identified in leaked Pegasus project data
%J TheGuardian
%M JUL
%D 2021
%K news, c2021, c202x, c20xx, zz0721, spy, spying, spyware, abuse, Pegasus,
   NSO, Israel, NSOgroup, privacy, human rights, journalist, politician,
   politics, iPhone, iOS, Safari, iMessage, AndroidPhone, Chrysaor, smartPhone,
   mobile phone, hack, hacking, security, democracy, Guardian, grauniad
%X "The leaked database at the heart of the Pegasus project includes the mobile
   phone numbers of the French president, Emmanuel Macron, and 13 other heads
   of state and heads of government, the Guardian can reveal. ..."
   -- The G [www][21/7/2021].
   Also see [abc][22/7/2021], and
   Pegasus@[wikip]['21].

%A A. Moessner
%T Eine Bemerkung uber die Potenzen der naturlichen Zahlen
%D 1952
%S Sitzungsberichte
%D 1951,3
%K jrnl, maths, c1952, c195x, c19xx, zz0721, number, numbers, powers, Moessner,
   theorem, magic, integer, sequences, triangles, Perron, Kozen, Silva
%X -- [www]['21].
   Also see MM@[wikip]['21] and
   "On Moessner's Theorem", D. Kozen & A. Silva,
   The Amer. Math. Monthly, 120(2), 131-139, 2013
   -- [doi:10.4169/amer.math.monthly.120.02.131]['21].  (via AK)

% H. Whitegouse
%A et al...
%A P. Turchin
%T [7/7/'21, RETRACTED ARTICLE:] Complex societies precede moralizing gods
   throughout world history
%J Nature
%V 568
%P 226-229
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0721, human behaviour, society, God, Gods,
   cooperation, religious belief, religion, retracted, retraction,
   missing data, stats
%X "The origins of religion and of complex societies represent evolutionary
   puzzles. The 'moralizing gods' hypothesis offers a soln to both puzzles by
   proposing that belief in morally concerned supernatural agents culturally
   evolved to facilitate coop'n among strangers in large-scale societies. ...
   Our analyses not only confirm the assoc. between moralizing gods & social
   complexity, but also reveal that moralizing gods follow - rather than
   precede - large increases in social complexity. ..."
   -- [doi:10.1038/s41586-019-1043-4]['21], but ...
   *** 'Treatment of missing data determined conclusions regarding moralizing
   gods', B.Beheim et al, Nature, 595, E29-E34, 2021
   -- [doi:10.1038/s41586-021-03655-4]['21].
   [Also search for: moralizing gods].

%A M. S. A. Graziano
%T We are machines that claim to be conscious
%J J. of Consciousness Studies
%V 26
%N 10
%P 94-104
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0721, human, brain, mind, consciousness,
   awareness, attention schema theory, materialist
%X "The attention schema theory explains how a biological, info.processing
   machine can claim to have consciousness, & how, by introspection (by
   assessing its internal data), it cannot determine that it is a machine whose
   claims are based on computations. The theory directly addresses Chalmers'
   meta-problem of c., the problem of why we think we have a
   difficult-to-explain c. in the first place."
   -- [www]['21] --$.
   Also see AST@[wikip]['21] and
   G@[pr'ncet'n]['21].
   Also search for: consciousness mind]  and  [also search for: mind Graziano].

%A J. A. Olson
%A ...
%A M. E. Webb
%T Naming unrelated words predicts creativity
%J PNAS
%V 118
%N 25
%P #e2022340118;
%M JUN
%D 2021
%K jrnl, PNAS, c2021, c202x, c20xx, zz0721, divergent association task, DAT,
   human, creative, creativity, imagination, test, naming unrelated words,
   UniMelb
%X "Several theories posit that creative people are able to generate more
   divergent ideas. If this is correct, simply naming unrelated words & then
   measuring the semantic dist. between them could serve as an objective measure
   of divergent thinking. ... we asked 8,914 participants to name 10 words that
   are as different from each other as possible. A computational alg. then est.
   the avg. semantic dist. between the words ..."
   -- [doi:10.1073/pnas.2022340118]['21].
      ("... Scores peaked in young adulthood, & females showed slightly
      higher overall scores than males. ..." :-)
   (Also see the test @[www]['21].)

%A E. Distante
%A et al ...
%A S. Welte
%T Detecting an itinerant optical photon twice without destroying it
%J Phys. Rev. Lett.
%V 126
%N #253603
%M JUN
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0721, physics, quantum, photon, detect, track,
   detector, state
%X "Nondestructive quantum measurements are central for quantum physics applns
   ... Employing the toolbox of cavity quantum electrodynamics, we here
   concatenate two identical nondestructive photon detectors to repeatedly
   detect & track a single photon propagating through a 60m long optical fiber.
   By demonstrating that the combined signal-to-noise ratio of the two detectors
   surpasses each single one by about 2 orders of magnitude, we experimentally
   verify a key practical benefit of cascaded nondemolition detectors compared
   to conventional absorbing devices."
   -- [doi:10.1103/PhysRevLett.126.253603]['21].

%A F. R. Kschischang
%A B. J. Frey
%A H.-A. Loeliger
%T Factor graphs and the sum-product algorithm
%J IEEE Trans. on Info. Theory
%V 47
%N 2
%P 498-519
%M JUL
%D 2001
%K jrnl, intro, survey, c1998, c199x, c19xx, zz0721, factor graph, factorGraph,
   dynamic programming, DPA, marginal
%X "A factor graph is a bipartite g. that expresses how a 'global' fn of many
   variables factors into a product of 'local' fns. FGs subsume many other
   graphical models inc. B.n/wks, Markov random fields, & Tanner gs..
   ... the sum-product alg. operates in FGs to compute either exactly or approx.
   various marginal fns by distributed message-passing in the g.. ...
   [Many algs] can be derived as specic instances of the sum-product alg., inc.
   the fwd/bwd alg., the Viterbi alg., the iterative 'turbo' decoding alg.,
   Pearl's belief propagation alg. for BNs, the Kalman filter, & certain fast
   F.transform algs."
   -- [doi:10.1109/18.910572]['21].
   ***NB. Longer version (76p, 1998) at [utoronto][2O21].
   (Also see FG@[wikip].)

%A D. Chakraborty
%A D. Das
%T Approximating edit distance within constant factor in truly sub-quadratic
   time
%J JACM
%V 67
%N 6
%P 1-22
%M NOV
%D 2020
%K jrnl, JACM, c2020, c202x, c20xx, zz0721, approximate, edit distance,
   approximation algorithm, strings
%X "... Andoni, Krauthgamer, & Onak (2010) gave a nearly linear time alg. that
   approx. ED within approx. factor poly(log n). ... we provide an alg. with
   running time O~(n^{2-2/7}) that approx. the ED within a const. factor."
   -- [doi:10.1145/3422823]['21].
   [Also search for: strings approximation algorithm].

%A M. Boroujeni
%A S. Ehsani
%T Approximating edit distance in truly subquadratic time: Quantum and mapReduce
%J JACM
%V 68
%N 3
%P 1-41
%M MAY
%D 2021
%K jrnl, JACM, c2021, c202x, c20xx, zz0721, approximate, edit distance,
   quantum computing, approximation algorithm, strings
%X "... Our main result is a quantum constant approx. alg. for computing the
   ED in truly subquadratic time. More precisely, we give an q.alg. that
   approximates the ED within a factor of 3. We further extend this result to an
   q.alg. that approximates the ED within a larger constant factor. ... further
   show that this f/wk enables us to approx. ED in distributed settings. To this
   end, we provide a MapReduce alg. to approx. ED within a factor of ??, with
   sublinearly many machines & sublinear memory. Also, our alg. runs in a
   logarithmic number of rounds."
   -- [doi:10.1145/3456807]['21].
   [Also search for: strings approximation algorithm].

%A M. Khan
%A A. Miranskyy
%T String comparison on a quantum computer using Hamming distance
%J arXiv
%M JUN
%D 2021
%K TR, c2021, c202x, c20xx, zz0721, Hamming distance, quantum computing,
   algorithm, strings, QisKit
%X "... we extend an existing alg. for computing the H.dist.. ... can compare
   strings with symbols drawn from an arbitrary-long alphabet (which the
   orig. alg. could not). We implement our extended alg. using the QisKit
   f/wk to be executed by a programmer without the knowledge of a QC (the code
   is publicly available). We then provide four pedagogical examples: two from
   the field of bioinf. & two from the field of SWEng. We finish by discussing
   resource requirements & the time horizon of the QCs becoming practical for
   string comp.."
   -- 2106.16173@[arXiv]['21].
   [Also search for: quantum algorithm strings].

%A Y. Galluzzo
%A R. Giancarlo
%A M. Randazzo
%A S. E. Rombo
%T Burrows Wheeler transform on a large scale: Algorithms implemented in
   Apache Spark
%J arXiv
%M JUL
%D 2021
%K TR, c2021, c202x, c20xx, zz0721, strings, Burrows Wheeler Transform, BWT,
   parallel, cloud, distributed, Apache Spark, Hadoop
%X "With the rapid growth of Next Generation Sequencing (NGS) technologies,
   large amounts of "omics" data are daily collected & need to be processed. ...
   Here we propose algs. for the comp'n of BWT relying on Big Data tech., i.e.,
   Apache Spark & Hadoop. Our algs. are the first ones that distribute the
   index comp'n & not only the input dataset, allowing to fully benefit of the
   available cloud resources."
   -- 2107.03341@[arXiv]['21].

%A S. Stucki
%A P. G. Giarrusso
%T A theory of higher-order subtyping with type intervals
%J arXiv
%P 73
%M JUL
%D 2021
%O 26th ACM SIGPLAN Int. Conf. on Func. Prog. (ICFP) 2021
%K TR, FP, c2021, c202x, c20xx, zz0721, type, types, kind, kinds, Scala, Agda,
   high order, Dependent Object Types, subtype, subtypes, Fomega, check,
   checking, normalization
%X "... we propose F^w.., a rigorous theor. foundation for Scala's
   higher-kinded types. F^w.. extends F^w_{<:} with interval kinds, which afford
   a unified treatment of important type- & kind-level abstraction mechanisms
   found in Scala, such as bounded quantification, bounded operator
   abstractions, translucent type definitions & first-class subtyping
   constraints. The result is a flexible & general theory of higher-order
   subtyping. We prove type & kind safety of F^w.., as well as weak
   normalization of types & undecidability of subtyping. All our proofs are
   mechanized in Agda using a fully syntactic approach based on hereditary
   substitution."
  -- 2107.01883@[arXiv]['21].
  [Also search for: dependent type].