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Glookbib search for: zz0121

%A B. Dudek
%A P. Gawrychowski
%A K. Pokorski
%T Strictly in-place algorithms for permuting and inverting permutations
%J arXiv
%M JAN
%D 2021
%K TR, c2021, c202x, c20xx, zz0121, permutation, algorithm, in situ, inSitu,
   inPlace, space, storage, Fich, Guspiel
%X "... problem of permuting an array of length n according to a given perm'n
   in place, that is, using only a small # of bits of extra storage ... Our
   first contribution is a strictly in-place generalisation of the method of
   Fich et al. that works in O_e(n^{1+e}) time, for any e>0. Then, we build on
   this generalisation to obtain a strictly in-place alg. for inverting a given
   perm. on n elts working in the same complexity. ..."
   -- 2101.03978@[arXiv]['21].

%A A. S Konagurthu
%A R. Subramanian
%A L. Allison
%A D. Abramson
%A P. J. Stuckey
%A M. Garcia de la Banda
%A A. M. Lesk
%T Universal architectural concepts underlying protein folding patterns
%J Front. Mol. Biosci.,
   A Journey Through 50 Years of Structural Bioinformatics in
   Memoriam of Cyrus Chothia
%P ?-?
%M APR
%D 2021
%K jrnl, FMB, MolBio, bioinformatics, c2021, c202x, c20xx, zz0121,
   procodic, prosodic, 3D protein structure, fold, folds, tableau, motif,
   motifs, pattern, model, concept, structural, terms, fragment, supersecondary,
   local, dictionary, recurring, library, MML, II, ArunK, LAllison, AMLesk
%X "What is the architectural 'basis set' of the observed universe of protein
   structures? Using information-theoretic inference, we answer this Q. with a
   comprehensive dictionary of 1,493 substructures - called concepts - at a
   sub-domain level, based on an unbiased subset of known protein structs. ...
   An interactive site, PROCODIC, at ...[prosodic] provides access to
   & navigation of the entire dictionary of concepts, & all assoc. info.."
   -- [doi: 10.3389/fmolb.2020.612920]['21],
      [more].

%A R. C. Gentleman
%A et al ...
%A J. Zhang
%T Bioconductor: open software development for computational biology and
   bioinformatics
%J Gen. Biol.
%V 5
%P #R80
%M SEP
%D 2004
%K jrnl, eJrnl, MolBio, c2004, c200x, c20xx, zz0121, Bioconductor, software
%X "... an initiative for the collaborative creation of extensible software for
   computational biology and bioinformatics. ..."
   -- [doi:10.1186/gb-2004-5-10-r80]['21].
   Also see BC@[wikip]['21].

%A S. C. Potter
%A A. Luciani
%A S. R. Eddy
%A Y. Park
%A R. Lopez
%A R. D. Finn
%T HMMER web server: 2018 update
%J NAR
%V 46
%N W1
%P W200-W204
%M JUL
%D 2018
%K MolBio, c2018, c201x, c20xx, zz0121, profile, alignment, HMM, HMMER,
   JackHMMER
%X "... provides fast searches against widely used seq. DBs & profile hidden
   Markov model (HMM) libraries ... The jackhmmer search alg. allows iterative
   searches against a seq. DB, where subsequent queries are profile HMMs built
   from the aligned hit sequences of a preceding search. ..."
   -- [doi:10.1093/nar/gky448]['21].
   [Also search for: MolBio HMMER].

%A B. Nikolay
%A et al
%J NEJM
%T Transmission of Nipah virus - 14 years of investigations in Bangladesh
%M MAY
%D 2019
%K MolBio, jrnl, NEJM, c2019, c201x, c20xx, zz0121, nipah, virus, NiV, RNAvirus,
   henipavirus, fruit bats, fruitBat, bat, pig, pigs
%X "... Of 248 Nipah virus cases identified, 82 were caused by person-to-person
   transmission, corr. to a reproduction number (i.e., the avg # of secondary
   cases per case patient) of 0.33 (95% [CI], 0.19 to 0.59) ..."
   -- [doi:10.1056/NEJMoa1805376]['21].
   Also see, "... ~50 to 75% risk of death ..."
   -- nipah@[wikip]['21].

%A M. Steinegger
%A et al ...
%A J. Soding
%T HH-suite3 for fast remote homology detection and deep protein annotation
%J BMC Bioinformatics
%V 20
%N 1
%P 473
%M SEP
%D 2019
%K jrnl, eJrnl, MolBio, c2019, c201x, c20xx, zz0121, HMM, profile, HH, HHblits,
   HHsuite, HH suite, HHsearch, HMMER, alignment
%X "... developed a single-instruction multiple-data (SIMD) vectorized
   implementation of the Vit.alg. for profile HMM alignment & introduced
   various other speed-ups. ..."
   -- [doi:10.1186/s12859-019-3019-7]['21].
   [Also search for: HHsuite]  and  [also search for: MolBio HMM].

%A Chengxin Zhang
%A Wei Zheng
%A S. M. Mortuza
%A Yang Li
%A Yang Zhang
%X "DeepMSA: constructing deep multiple sequence alignment to improve contact
   prediction and fold-recognition for distant-homology proteins
%J Bioinformatics
%V 36
%N 7
%P 2105-2112
%M APR
%D 2020
%K MolBio, c2020, c292x, c20xx, zz0121, protein, deep MSA, deepMSA,
   multiple sequence alignment
%X "... DeepMSA was utilized to generate MSAs for residue-level contact
   prediction by six coevolution & deep learning-based programs, which resulted
   in an accuracy increase in long-range contacts by up to 24.4% compared to the
   default programs. Next, multiple threading programs are performed for
   homologous structure identification, where the average TM-score of the
   template alignments has over 7.5% increases with the use of the new DeepMSA
   profiles. Finally, DeepMSA was used for secondary structure prediction ..."
   -- [doi:10.1093/bioinformatics/btz863]['21].
  [Also search for: MolBio multiple alignment protein].

%A B. Dereka
%A et al
%T Crossover from hydrogen to chemical bonding
%J Science
%V 371
%N 6525
%P 160-164
%M JAN
%D 2021
%K c2021, c202x, c20xx, zz0121, chemistry, chemical bonding, hydrogen bond, FHF
%X "Hydrogen bonds (H-bonds) can be interpreted as a classical electrostatic
   interaction or as a covalent chemical bond if the interaction is strong
   enough. [so] short strong H-bonds exist at an intersection between
   qualitatively different bonding descriptions, with few experimental methods
   to understand this dichotomy. ... demonstrate a distinct crossover in
   spectroscopic properties from conventional to short strong H-bonds, which
   identify where hydrogen bonding ends and chemical bonding begins."
   -- [doi:10.1126/science.abe1951]['21].

%T Open access takes flight
%J Science
%V 371
%N 6524
%P 16-20
%M JAN
%D 2021
%K news, views, c2021, c202x, c20xx, zz0121, publications, journal, open access,
   papers, PlanS, paywall
%X "In 2018, a group of mostly European funders sent shock waves through the
   world of sci. publishing by proposing an unprecedented rule: The scientists
   they funded would be required to make j.articles developed with their support
   immediately free to read when published. ..."
   -- [doi:10.1126/science.371.6524.16]['21].
   [Also search for: open access].

%A S. Patsantzis
%A S. H. Muggleton
%T Top program construction and reduction for polynomial time meta-interpretive
   learning
%J arXiv
%K JAN
%D 2021
%O to appear in Machine Learning J., Spec. Issue on Learning & Reasoning
%K TR, c2021, c202x, c20xx, zz0121, inductive logic programming, ILP, LP, AI,
   top program, topProgram, Louise, Metagol, MIL
%X "Meta-Interpretive Learners, like most ILP systems, learn by searching for a
   correct hypothesis in the hyp.space, the powerset of all constructible
   clauses. We show how this exponentially-growing search can be replaced by the
   construction of a Top program: the set of clauses in all correct hypotheses
   that is itself a correct hypothesis. We give an alg. for Top program
   construction & show that it constructs a correct Top program in polynomial
   time & from a finite # of examples. ...  Louise, that constructs a Top
   program & then reduces it by removing redundant clauses. ..."
   -- 2101.05050@[arXiv]['21].
   [Also search for: LP ILP].

%A J. H. Conway
%A R. T. Curtis
%A S. P. Norton
%A R. A. Parker
%A R. A. Wilson
%T Atlas of Finite Groups. Maximal Subgroups and Ordinary Characters for
   Simple Groups. With computational assistance from J. G. Thackray
%I OUP
%D 1985
%K book, text, OUP, c1985, c198x, c19xx, zz0121, maths, group, simple groups,
   finite, monster, symmetry, sporadic, Lie, classification of, atlas,
   JHConway, John Horton Conway
%X 1st ed 1985; isbn:0198531990.
   Also see, "... The classification theorem states that the list of finite
   simple groups consists of 18 countably infinite families plus 26 exceptions
   that do not follow such a systematic pattern. ..."
   --  SGs@[wikip]['21].

%A S. P. Dwivedi
%T Some algorithms on exact, approximate and error-tolerant graph matching
%J arXiv
%M DEC
%D 2020
%K TR, c2020, c202x, c20xx, zz0121, maths, graph, matching,
   graph, geometric edit distance, GED, algorithm, IIT, phd thesis
%X "... present an extensive survey of various exact & inexact graph matching
   techniques. Graph matching using the concept of homeomorphism is presented.
   A category of GM-algs. is presented, which reduces the g.size by removing the
   less important nodes using some measure of relevance. We present an approach
   to error-tolerant GM using node contraction where the given g. is transformed
   into another g. by contracting smaller degree nodes. We use this scheme to
   extend the notion of graph edit distance ..."
   -- [arXiv]['21].
   Also see GED@[wikip]['21].
   (*Beware, there's another meaning to 'graph matching'.*)
   [Also search for: maths graph matching] and
   [also search for: graph edit distance GED].

%A J. Jacobs
%T Paradoxes of probabilistic programming and how to condition on events of
   measure zero with infinitesimal probabilities
%J arXiv
%M JAN
%D 2021
%O Proc. ACM Prog.Lang. 5, POPL, #58, JAN 2021
%K conf, c2021, c202x, c20xx, zz0121, probabilistic programming language, STAN,
   Anglican, observe, probability, simulation, sampling, stats
%X "... run by accumulating likelihood at each observe statement, & using the
   likelihood to steer random choices & weigh results with inference algs. such
   as importance sampling or MCMC. We argue that naive LH-accumulation does not
   give desirable semantics & leads to paradoxes when an observe statement is
   used to condition on a measure-zero event ... show that the paradoxes
   disappear if we explicitly model measure-zero events as a limit of +ve
   measure events, & that we can execute these type of prob.programs by
   accumulating infinitesimal probs. rather than prob.densities. ..."
   -- 2101.03391@[arXiv]['21].
   Also see conf@[doi:10.1145/3434339]['21].
   [Also search for: probabilistic programming language].

%A L. McInnes
%A J. Healy
%A J. Melville
%T UMAP: Uniform manifold approximation and projection for dimension reduction
%J arXiv
%M FEB
%D 2018
%K TR, c2018, c201x, c20xx, zz0121, stats, UMAP, dimension reduction,
   dimensionality, embedding, nonlinear, manifold, learning, t-SNE, tSNE
%X "UMAP (Uniform Manifold Approx. & Projection) is a novel m.learning technique
   for dim'n red'n. ... constructed from a theoretical f/wk based in Riemannian
   geometry & algebraic topology. ... is a practical scalable alg. that applies
   to real world data. The UMAP alg. is competitive with t-SNE for visualization
   quality, & arguably preserves more of the global structure with superior run
   time performance. [&] UMAP has no computational restrictions on embedding
   dimension, making it viable as a general purpose dim.red. technique for
   machine learning."
   -- [arXiv]['21].
   Also see nonLDR@[wikip]['21].
   [Also search for: UMAP].