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%A L. Gourves
%A A. Harutyunyan
%A M. Lampis
%A N. Melissinos
%T Filling crosswords is very hard
%J arXiv
%M SEP
%D 2021
%K TR, c2021, c202x, c20xx, zz0921, crossword, puzzle, filling, algorithm
%X "We revisit a classical crossword filling puzzle which already appeared in
   Garey & Jonhson's book. ... given a grid with n vertical & horizontal slots
   & a dictionary with m words & are asked to place words from the d. in the
   slots so that shared cells are consistent. We attempt to pinpoint the source
   of intractability of this problem by taking into account the structure of the
   grid graph, which contains a vertex for each slot & an edge if two slots
   intersect. Our main approach is to consider the case where this graph has a
   tree-like structure. Unfortunately, if we impose the common rule that words
   cannot be reused, we show that the problem remains NP-hard even under very
   severe structural restrictions. The problem becomes slightly more tractable
   if word reuse is allowed, as we obtain an m^{tw} alg. in this case, where tw
   is the treewidth of the grid graph. However, even in this case, we show that
   our alg. cannot be improved. ..."
   -- 2109.11203@[arXiv]['21].
   [Also search for: crossword].

%A R. L. Townshend
%A et al ...
%A R. O. Dror
%T Geometric deep learning of RNA structure
%J Science
%V 373
%N 6558
%P 1047-1051
%M AUG
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0921, RNA structure, prediction,
   ARES, geometric, geometry, NN, ANN
%X "... introduce a m/c learning approach that enables identification of
   accurate structural models without assumptions about their defining
   characteristics, despite being trained with only 18 known RNA struct.. The
   resulting scoring fn, the Atomic Rotationally Equivariant Scorer (ARES),
   substantially outperforms previous methods ... By learning effectively even
   from a small amount of data, our approach overcomes a major limitation of
   std deep NNs. Because it uses only atomic coordinates as inputs &
   incorporates no RNA-specific information ..."
   -- [doi:10.1126/science.abe5650]['21].
   [Also search for: MolBio RNA structure prediction].

%A J. Hippisley-Cox
%A et al
%T Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and
   SARS-CoV-2 positive testing: self-controlled case series study
%J BMJ
%V 374
%M AUG
%D 2021
%K jrnl, MolBio, BMJ, c2021, c202x, c20xx, zz0921, medicine, SARS-CoV-2, SARS2,
   virus, covid-19, vaccine, vaccination, risk, risks, Oxford-AstraZeneca, AZ,
   covid19, ChAdOx1-S, Pfizer-BioNTech, BNT162b2, complications, blood clot,
   clots
%X "... Participants 29,121,633 people were vaccinated with first doses
   (19,608,008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) & 9,513,625 with
   Pfizer-BioNTech (BNT162b2 mRNA)) & 1,758,095 people had a +ve SARS-CoV-2
   test. People aged >=16 years who had first doses of the ChAdOx1 nCoV-19 or
   BNT162b2 mRNA vaccines & any outcome of interest were included in the study.
   ... The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19
   vaccination (incidence rate ratio 1.33, 95% c.i. 1.19 to 1.47 at 8-14 days)
   & after a +ve SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days) ... The risks
   of most of these events were substantially higher & more prolonged after
   SARS-CoV-2 infection than after vaccination in the same population."
   -- [doi:10.1136/bmj.n1931]['21].
   (Also see "Covid: Vaccine complications dwarfed by virus risks"
   -- [bbc][27/8/2021].)

%A S. Gazit
%A et al
%T Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity:
   reinfections versus breakthrough infections
%J medRxiv
%M AUG
%D 2021
%K TR, c2021, c202x, c20xx, zz0921, SARS-CoV-2, SARS2, virus, covid-19, covid19,
   infection, Pfizer BNT162b2, vaccine, immunity
%X "... vaccinees had a 13.06-fold (95% CI, 8.08 to 21.11) increased risk for
   breakthrough infection with the Delta variant [v] those previously infected,
   when the 1st event (infection or vaccination) occurred during Jan - Feb of
   2021. ... evidence of waning natural immunity was demonstrated, though ...
   vaccinees had a 5.96-fold ... increased risk for b.infection & a 7.13-fold
   ... increased risk for symptomatic disease. ... vaccinees were also at a
   greater risk for COVID-19-related-hospitalizations compared [v] those that
   were previously infected. ..."
   -- [doi:10.1101/2021.08.24.21262415]['21].
   [NB. a preprint.]

%A J. M. perkel
%T Single-cell proteomics takes centre stage
%J Nature
%V 597
%P 580-582
%M SEP
%D 2021
%K news, views, MolBio, c2021, c202x, c20xx, zz0921, single cell proteomics,
   proteoCHIP, inanoPOTS, SCoPE-MS, SCoPEMS, proteins
%X "Deducing the full protein complement of individual cells has long played
   second fiddle to transcriptomics. That's about to change. ..."
   -- [doi:10.1038/d41586-021-02530-6]['21].

%A P. Rovelli
%A C. Curnis
%T The perks of narcissism: Behaving like a star speeds up career advancement
   to the CEO position
%J The Leadership Quarterly
%V 32
%N 3
%P #101489
%M JUN
%D 2021
%K c2021, c202x, c0xx, zz0921, leadership, leader, boss, CEO, dean, management,
   narcissism, narcissistic, personality, psychology, business, power, discord
%X "It is widely acknowledged that narcissism is a peculiar characteristic of
   leaders, such as CEOs. ... Estimates on a sample of 172 individuals partially
   confirm the hypotheses. Highly n. individuals become CEOs quicker, regardless
   of whether the firm is a family business or not. ..."
   -- [doi:10.1016/j.leaqua.2020.101489]['21].
   Also see [bbc][8/2021].
   [Also search for: narcissism].

%A C. Watson
%T Preprint ban in grant applications deemed 'plain ludicrous'
%J Nature
%V ?
%P ?-?
%M AUG
%D 2021
%K news, views, c2021, c202x, c20xx, zz0921, Australia, scientifc research,
   academia, career, preprints, applications, management, ARC, grants, funding
%X "The Australian Research Council's decision to reject early-career funding
   applications that mention preprints is hopelessly outdated, say scientists.
   ... At least 23 researchers - 7 of whom Nature contacted for comment - have
   been deemed ineligible because they ref. to preprints in applications ..."
   -- [doi:10.1038/d41586-021-02318-8]['21].

%A A. Nies
%A K. Tent 
%T Describing finite groups by short first-order sentences
%J Israel J. of Math.
%V 221
%P 85-115
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0921, maths, finite group, sentence,
   straight line program, straightLineProgram
%X "We say that a class of finite structures for a finite 1st-order signature is
   r-compressible for an unbounded fn r: N->N^+ if each struct. G in the class
   has a 1st-order desc'n of size at most O(r(|G|)). We show that the class of
   finite simple groups is log-compressible, & the class of all finite gs. is
   log^3-compressible. ... we obtain that the class of all finite transitive
   perm'n gs. is log^3-comp.. The results rely on the classification of finite
   simple groups, the bi-interpretability of the twisted Ree groups with finite
   difference fields, the existence of profinite presentations with few relators
   for finite groups, & group cohomology. We also indicate why the results are
   close to optimal."
   -- [doi:10.1007/s11856-017-1563-2]['21].
   (Also see SLP@[wikip]['21].)

%A W. Drabent
%T A note on occur-check
%J arXiv
%M SEP
%D 2021
%K TR, c2021, c202x, c20xx, zz0921, logic programming, LP, Prolog, unification,
   occurs, occur, check
%X "Most known results on avoiding the occur-check are based on the notion of
   'not subject to occur-check' (NSTO). It means that unification is performed
   only on such pairs of atoms for which the occur-check never succeeds in any
   run of a nondet. unification alg.. Here we show that this requirement is too
   strong. We show how to weaken it, & present some related sufficient condns
   under which the occur-check may be safely omitted. We show examples for which
   the proposed approach provides more general results than the approaches based
   on well-moded & nicely moded programs (this inc. cases to which the latter
   approaches are inapplicable).
   -- 2109.08278@[arXiv]['21].

%A M. P. Deisenroth
%T Mathematics for Machine Learning
%I CUP
%P 398
%M APR
%D 2020
%K CUP, book, text, c2020, c202x, c20xx, zz0921, AI, maths, algebra, stats
%X 1st ed 2020; pb us$46; uk us isbn:110845514X; uk us isbn13:978-1108455145.
   "... linear algebra, analytic geometry, matrix decompositions, vector
   calculus, optimization, probability and statistics. ..."
   [Also search for: machine learning book].

%A S. M. Cooley
%A et al
%T A novel metric reveals previously unrecognized distortion in dimensionality
   reduction of scRNA-Seq data
%J bioRxiv
%M JUL
%D 2019
%K TR, MolBio, c2019, c201x, c20xx, zz0921, tSNE, t-SNU, UMAP, distortion,
   errors, dimensionality reduction, scRNA
%X "... we introduce a straightforward approach to quantifying this distortion
   by comparing the local neighborhoods of points before & after dimensionality
   red'n. We found that popular techniques like t-SNE & UMAP introduce sig.
   distortion even for relatively simple geometries such as simulated
   hyperspheres. For scRNA-Seq data, we found the distortion in local
   neighborhoods was greater than 95% in the 2- & 3-[D] space typically used for
   downstream analysis. This high level of distortion can readily introduce
   important errors into cell type identification, pseudotime ordering, & other
   analyses ..."
   -- 689851v1@[bioRxiv]['21].

%A A. Clayton
%T Bernoulli's Fallacy: Statistical Illogic and the Crisis of Modern Science
%I ColumbiaUPress
%P 368
%M AUG
%D 2021
%K book, text, c2021, c202x, c20xx, zz0921, history, foundations, stats,
   statistics, probability, frequentist, Bayesian, Bernoulli
%X "There is a logical flaw in the statistical methods used across experimental
   science. ... traces the history of how statistics went astray, beginning with
   the groundbreaking work of the 17C-century mathematician Jacob Bernoulli ...
   contends that we need to take a Bayesian approach ... B's Fallacy explains
   why something has gone wrong with how we use data - & how to fix it."
   1st ed 2021; hb us$33; uk us isbn:0231199945; uk is isbn13:978-0231199940.
   [Also search for: Bayesian stats book].

%A V. Fulber-Garcia
%A S. Luis Sardi Mergen
%T LUISA: Decoupling the frequency model from the context model in
   prediction-based compression
%J COMPJ
%V 64
%N 9
%P 1437-1450
%M SEP
%D 2021
%K jrnl, compj, c2021, c202x, c20xx, zz0921, Luisa, PPM, strings, compress,
   compression, model
%X "... methods, like prediction by partial matching, achieve a remarkable
    compression ratio ... However, they are not efficient in terms of speed.
   Part of the problem concerns the usage of dynamic entropy encoding, which is
   considerably slower than the static alternatives. ... we propose a
   predn-based comp. method that decouples the context model from the freq.
   model. ... allows static entropy encoding to be used without a sig. overhead
   in the meta-data embedded in the compressed data. The result is a reasonably
   efficient alg. that is particularly suited for small textual files, as the
   experiments show. We also show it is relatively easy to built strategies
   designed to handle specific cases, like the comp'n of files whose symbols are
   only locally frequent."
   -- [doi:10.1093/comjnl/bxaa074]['21].
   (Also see LUISA@[gith'b]['21].)
   [Also search for: compress PPM].

%A M. Kosche
%A T. Koss
%A F. Manea
%A S. Siemer
%T Absent subsequences in words
%J arXiv
%M AUG
%D 2021
%O ext. abs. in Proc. 15th Int. Conf. on Reachability Problems RP2021
%K TR, c2021, c202x, c20xx, zz0921, strings, word, absent subsequence, shortest,
   minimal, missing, substring, algorithm
%X "An absent factor of a string w is a string u which does not occur as a
   contiguous substring ... We extend this ... & define absent subsequences: a
   string u is an absent subseq. of a string w if ... Of particular interest to
   us are minimal absent subseqs., i.e., absent subseq. whose every subseq. is
   not absent, & shortest absent subseq. ... For instance: we give combinatorial
   characterisations of the sets of minimal & shortest ... as well as compact
   representations of these sets; ... we can test efficiently if a string is a
   shortest or minimal absent subseq. ... give efficient algs. computing the
   lexicographically smallest [AS] of each kind; also, we show how a data
   structure for answering [SAS]-queries for the factors of a given string can
   be efficiently computed."
   -- 2108.13968@[arXiv]['21].
   [Also search for: string absent].