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%A M. E. Lesk
%T Automatic sense disambiguation using machine readable dictionaries:
   how to tell a pine cone from an ice cream cone
%J Proc. of the 5th annual int. conf. on Systems documentation
%W New York
%I ACM
%P 24-26
%D 1986
%K conf, SIGDOC, c1986, c198x, c19xx, zz0518, MLesk, MELesk, algorithm,
   word sense, wordSense, NLP, context, ambiguity
%X pdf@[doi:10.1145/318723.318728]['18].
   Also see,  "... based on the assumption that words in a given
   'neighborhood' (section of text) will tend to share a common topic.
   A simplified version of the Lesk algorithm is to compare the dictionary
   defn of an ambiguous word with the terms contained in its neighborhood. ..."
   -- [wikip]['18].

%A L. Breiman
%T Random forests
%J Mach. Learning
%V 45
%N 1
%P 5-32
%M OCT
%D 2001
%K jrnl, c2001, c200x, c20xx, zz0518, decision tree, Dtree, AI, II,
   random forest, forests, randomForest, ensemble, Adaboost
%X "Random forests are a combination of tree predictors such that each tree
   depends on the values of a random vector sampled indep. & with the same
   distn for all trees in the forest. The generalization error for forests
   converges a.s. to a limit as the # of trees in the forest becomes large. ...
   depends on the strength of the individual trees in the forest & the
   correlation between them. Using a random selection of features to split each
   node yields error rates that compare favorably to Adaboost (Y. Freund & R.
   Schapire, Machine Learning: Proc. 13th Int. conf., 148–156), but are more
   robust with respect to noise. Internal estimates monitor error, strength, &
   correlation & these are used to show the response to increasing the # of
   features used in the splitting. Internal estimates are also used to measure
   variable importance. These ideas are also applicable to regression."
   -- [doi:10.1023/A:1010933404324]['18].
   [Also search for: II random forest].
   (Also see RF@[wikip]['18].)

%A C. Chothia
%A A. M. Lesk
%A A. Tramontano
%A M. Levitt
%A et al ...
%A R. J. Poljak
%T Conformations of immunoglobulin hypervariable regions
%J Nature
%V 342
%P 877-883
%M DEC
%D 1989
%K biol, jrnl, c1989, c198x, c19xx, zz0518, AMLesk, antibody, antibodies,
   structure
%X "On the basis of comparative studies of known antibody structures and
   seqs. it has been argued that there is a small repertoire of main-chain
   conformations for at least five of the six hypervariable regions of
   antibodies, and that the particular conformation adopted is determined by a
   few key conserved residues. These hypotheses are now supported by reasonably
   successful predictions of the structures of most hypervariable regions of
   various antibodies, as revealed by comparison with their subsequently
   determined structures."
   -- [doi:10.1038/342877a0]['18].

%A C. Chothia
%A A. M.Lesk
%T Canonical structures for the hypervariable regions of immunoglobulins
%J J. Molec. Biol.
%V 196
%N 4
%P 901-917
%M AUG
%D 1987
%K biol, JMB, jrnl, MolBio, c1989, c198x, c19xx, zz0518, AMLesk, antibody,
   antibodies, structure, Fab, VL, immunoglobulin
%X "... Examination of the seqs. of immunoglobulins of unknown structure shows
   that many have hypervariable regions that are similar in size to one of the
   known structures and contain identical residues at the sites responsible for
   the observed conformation. This implies that these hypervariable regions have
   conformations close to those in the known structures. For five of the
   hypervariable regions, the repertoire of conformations appears to be limited
   to a relatively small number of discrete structural classes. We call the
   commonly occurring main-chain conformations of the hypervariable regions
   'canonical structures'. ..."
   -- [doi:10.1016/0022-2836(87)90412-8]['18].

%A I. Chanda
%A A. Pan
%A C. Dutta
%T Proteome composition in Plasmodium falciparum: Higher usage of GC-rich
   nonsynonymous codons in highly expressed genes
%J JME
%V 61
%N 4
%P 513-523
%M OCT
%D 2005
%K jrnl, JMW, MolBio, c2005, c200x, c20xx, zz0518, malaria parasite,
   Plasmodium falciparum, 3D7, amino acid, composition, bias
%X "... extremely AT-rich genomes ... study analyzes the amino acid usage
   pattern in 5038 annotated protein-coding seqs. in P.falciparum clone 3D7. The
   AA composition of individual proteins, though dominated by the directional
   mutational pressure, exhibits wide variation across the proteome. ...
   frequencies of residues encoded by GC-rich codons such as Gly, Ala, Arg, &
   Pro increase significantly in the products of the highly expressed genes. ...
   Negative correlation of the expression level of proteins with respective
   molecular weights supports the notion that P.falciparum, in spite of its
   intracellular parasitic lifestyle, follows the principle of cost
   minimization."  [online 7/2005.]
   -- [doi:10.1007/s00239-005-0023-5]['18].

%A T. D. Otta
%A et al ...
%A F. Prugnolle
%T Genomes of all known members of a Plasmodium subgenus reveal paths to
   virulent human malaria
%J Nature Microbiology
%V ?
%M MAY
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0518, malaria, plasmodium falciparum,
   praefalciparum, Laverania, stevor, human, parasite, genome, genomes
%X "Plasmodium falciparum, the most virulent agent of human malaria, shares a
   recent common ancestor with the gorilla parasite Plasmodium praefalciparum.
   ... generated multiple genomes from all known Laverania species. ... The
   complete genome sequence of the closest ancestor of P. falciparum enables us
   to estimate the timing of the beginning of speciation to be 40,000-60,000
   years ago followed by a population bottleneck around 4,000-6,000 years ago.
   Our data allow us also to search in detail for the features of P.falciparum
   that made it the only member of the Laverania able to infect and spread in
   humans."
   -- [doi:10.1038/s41564-018-0162-2]['18].
   (Also see the bbc[22/5/2018]].)
   [Also search for: plasmodium falciparum].

%A T. R. Simoes
%A et al ...
%A R. L. Nydam
%T The origin of squamates revealed by a Middle Triassic lizard from the
   Italian Alps
%J Nature
%V 557
%P 706-709
%M MAY
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0518, animal, tetrapod, squamate,
   lizard, lizards, reptile, dinosaur, extinction, evolution, Middle Triassic,
   Jurassic, Megachirella wachtler, fossil
%X "Modern squamates (lizards, snakes and amphisbaenians) are the world's most
   diverse group of tetrapods along with birds ... oldest known fossils dating
   from the Middle Jurassic period - 168 m.y. ago. The evolutionary origin of
   squamates is contentious because of several issues: (1) a fossil gap of
   ~70 million years exists between the oldest known fossils and their estimated
   origin ... we shed light on these problems ... articulated fossil reptile
   Megachirella wachtleri (Middle Triassic period, Italian Alps). We also
   present a phylogenetic dataset, combining fossils and extant taxa, and
   morphological and molecular data. ... present evidence that M.wachtleri is
   the oldest known stem squamate. Megachirella is 75 million years older than
   the previously known oldest squamate fossils ..."
   -- [doi:10.1038/s41586-018-0093-3]['18].

%A J. Lu Li
%T Revisiting the trolley problem on the ethics of animal model organisms
%J The Ethical Endeavor
%V 1
%N 1
%P 1
%M AUG
%D 2016
%K c2016, c201x, c20xx, zz0518, trolley problem, tram, railway, tracks,
   ethics, morality, philosophy, mouse, mice, Philippa Foot
%X "Despite the fervor with which researchers have tackled the issue in the past
   few decades, the ethical dilemma Philippa Foot famously put forth in 1967 has
   yet to be resolved. The 'Trolley Problem,' as it is often referred to,
   consists of a dilemma in which five innocent workers in the path of a
   'runaway tram' are destined to be killed; however, there also exists a fork
   in the tracks that leads to a stemming track with an equally innocent single
   person on it ..."
   -- [www]['18]
      ( theethicalendeavor.weebly.com/ ).

%A J. Smyth
%T The Toxic University: Zombie Leadership, Academic Rock Stars and
   Neoliberal Ideology
%I PalgraveMacmillan
%P 235
%D 2017
%K book, c2017, c201x, c20xx, zz0518, University, tertiary, higher education,
   academic, management, politics, teaching, research, faculty, dean, deanitis,
   jargon, impact, KPI, KPIs, superstars, Federation Uni, Monash, Gippsland,
   Australia, ranking, rating, performance manage, workload, league table,
   tables, neoliberal, neoliberalism, Reaganomics, zombie, leader, leadership
%X 1st ed 2017; hb us$64; uk us isbn:1137549769; uk us isbn13:978-1137549761.
   "This book considers the detrimental changes that have occurred to the
   institution of the university, as a result of the withdrawal of state funding
   and the imposition of neoliberal market reforms on higher education. It
   argues that universities have lost their way, and are currently drowning in
   an impenetrable mush of economic babble, spurious spin-offs of zombie
   economics, management-speak and militaristic-corporate jargon. ...
   meaningless marketing hype ..."
   (Also see, "John Smyth has a call to arms for academics frustrated by trends
   in higher education in the United States, Britain, Australia and
   elsewhere. ..."
   -- [www][11/12/17].)
   [Also search for: toxic university].

%A M. K. McNutt
%A et al ...
%A I. M. Verma
%T Transparency in authors' contributions and responsibilities to promote
   integrity in scientific publication
%J PNAS
%M FEB
%D 2018
%K views, c2018, c201x, c20xx, zz0518, scientific research, university, paper,
   papers, publications, author, authors, authorship, role, roles, CRediT, TACS,
   impact, publish, perish
%X "... propose changes to journal authorship policies & procedures to provide
   insight into which author is responsible for which contributions, better
   assurance that the list is complete, & clearly articulated standards to
   justify earning authorship credit. ... Contributor Roles Taxonomy (CRediT)
   (docs.casrai.org/CRediT) ... ecommend that universities & research
   institutions articulate expectations about author roles & responsibilities
   to provide a point of common understanding for discussion of authorship
   across research teams. ..."
   -- [doi:10.1073/pnas.1715374115]['18].
   [Also search for: publish perish].
   (And sadly, also see [doi:10.1126/science.aau0036][26/4/2018].)

%A C. Beeri
%A R. Fagin
%A D. Maier
%A M. Yannakakis
%T On the desirability of acyclic database schemes
%J JACM
%V 30
%N 3
%P 479-513
%M JUL
%D 1983
%K jrnl, JACM, c1983, c198x, c19xx, zz0518, maths, graph, acyclic, DB, DBMS,
   chordal, triangulation, hypergraph, dependency, dependencies, acyclicity,
   simplicial, join, properties
%X "A class of database schemes, called acyclic, was recently introduced. ...
   shown that this class has a # of desirable properties. In particular, several
   desirable properties that have been studied by other researchers in very
   different terms are all shown to be eqmvalent to acylicity.  [&] several
   equiv. characterisations of the class in terms of graphs & hypergraphs are
   given, & a simple alg. for determining acyclicity is presented.  Also given
   are several equivalent characterizations of those sets M of multivalued
   dependencies s.t. M is the set of multivalued dependencies that are the
   consequences of a given join dependency.  Several characterizations for a
   conflict-free (in the sense of Lien) set of multivalued dependencies are
   provided."
   -- pdf@[c'teseer]['18].

%A P. Bartlett
%T Undirected graphical models: Chordal graphs, decomposable graphs,
   junction trees, and factorizations
%I Berkeley
%M OCT
%D 2003
%K notes, c2003, c200x, c20xx, zz0518, maths, graph, chordal,
   recursively simplicial, junction tree, decomposable, model
%X "... G = < V, E > an undirected graph ...
   The following are equivalent
   1. G is chordal.                 2. G is decomposable.
   3. G is recursively simplicial.  4. G has a junction tree. ...
   ... the classic paper on the graph-theoretic equivalences
   presented here is C. Beeri et al, JACM 1983 ..."
   -- pdf@[berk'ley]['25/5/18].
   [Also search for: decomposition defn], [also search for: factorization defn],
   [Also search for: Beeri graph c1983].

%A L. Chindelevitch
%A J. Paulo Pereira Zanetti
%A J. Meidanis
%T On the rank-distance median of 3 permutations
%J BMC Bioinformatics
%V 19
%N supp.6
%M MAY
%D 2018
%O RECOMB Comparative Genomics Satellite Workshop: bioinformatics
%K wkShop, c2018, c201x, c20xx, zz0518, rank distance, permutation, algorithm,
   double cut join, DCJ, genomes, sorting, reversals, reversal, inversion,
   transposition, median, rearrangement distance, comparison
%X "... provides the first proof that, wrt the rank distance, the problem of
   finding the median of 3 genomes, as well as the median of 3 permutations, is
   exactly solvable in polynomial time, a result which should be contrasted with
   its NP-hardness for the DCJ (double cut-and-join) distance and most other
   families of genome rearrangement operations. This result, backed by our
   experimental tests, indicates that the rank distance is a viable alternative
   to the DCJ distance widely used in genome comparisons."
   -- [doi:10.1186/s12859-018-2131-4]['18].
   [Also search for: permutation rank distance].

%A N. Chater
%A P. M. B. Vitanyi
%T The generalized universal law of generalization
%J J. Math. Psych.
%V 47
%P 346-369
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0518, animal, behaviour, psychology,
   generalization, generalise, generalize, efficient coding,
   compression, information
%X "... We show that, nonetheless, the Universal Law of Generalization can be
   derived in the more complex setting of arbitrary stimuli, using a much more
   universal measure of dist.. This universal dist. is defined as the
   length of the shortest program that transforms the representations of the two
   items of interest into one another: The algorithmic information dist.. It
   is universal in the sense that it minorizes every computable dist.: It is
   the smallest computable dist.. We show that the Universal Law of
   Generalization holds with probability going to one-provided the probabilities
   concerned are computable. We also give a mathematically more appealing form
   of the Universal Law."
   -- [doi:10.1016/S0022-2496(03)00013-0]['18].
   [Also search for: MML] and [also search for: universal law generalization].

%A C. R. Sims
%T Efficient coding explains the universal law of generalization in
   human perception
%J Science
%V 360
%N 6389
%P 652-656
%M MAY
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0518, animal behaviour, generalization,
   generalise, generalize, efficient coding, compression, information
%X "... will learn to avoid preying on that species again by generalizing its
   past experience to new perceptual stimuli. ... Here, I challenge existing
   theoretical explanations for the universal law and offer an alternative
   account based on the principle of efficient coding. I show that the universal
   law emerges inevitably from any information processing system (whether
   biological or artificial) that minimizes the cost of perceptual error subject
   to constraints on the ability to process or transmit information."
   -- [doi:10.1126/science.aaq1118]['18].
   [Also search for: MML] and [also search for: universal law generalization].

%A C. K. Wong
%A E. Makalic
%A D. F. Schmidt
%T A minimum message length criterion for robust linear regression
%J arXiv
%M FEB
%D 2018
%K TR, c2018, c201x, c20xx, zz0518, MML, mdl, robust linear regression, DEnes,
   Student-t distribution, StudentT, scale mixture, scaleMixture
%X "... inference of linear regression models with Student-t errors. A new
   criterion for var. selection & parameter estimation in Student-t regression
   is proposed. By exploiting properties of the regression model, we derive a
   suitable non-informative proper uniform prior distn for the regression
   coefficients that leads to a simple & easy-to-apply criterion.  ... does not
   require spec. of hyperparameters & is invariant under both full rank
   transformations of the design matrix & linear transformations of the
   outcomes. We comp are the proposed criterion with several ..."
   -- 1802.03141@[arXiv]['18].
   [Also search for: scaleMixture].

%A S. Aaronson
%T Quantum Computing since Democritus
%I CUP
%P 398
%M APR
%D 2013
%K book, text, CUP, c2013, c201x, c20xx, zz0518, quantum computing, computer
%X 1st ed 2013; pb us$32; uk us isbn:0521199565; uk us isbn13:978-0521199568.
   "... Beginning in antiquity with Democritus, it progresses through logic and
   set theory, computability and complexity theory, quantum computing,
   cryptography, the information content of quantum states and the
   interpretation of quantum mechanics. ..."
   (Also see SA@[www]['18].)
   [Also search for: Aaronson quantum].

%A S. W. Hawking
%A T. J. Hertog
%T A smooth exit from eternal inflation?
%J J. of High Energy Physics
%V 147
%M APR
%D 2018
%K jrnl, physics, c2018, c201x, c20xx, zz0518, cosmology, universe, inflation,
   big bang, bigBang, string theory, multiverse, quantum gravity
%X "The usual theory of inflation breaks down in eternal inflation. We derive a
   dual description of eternal inflation in terms of a deformed Euclidean CFT
   located at the threshold of eternal inflation. The partition function gives
   the amplitude of different geometries of the threshold surface in the
   no-boundary state. Its local and global behavior in dual toy models shows
   that the amplitude is low for surfaces which are not nearly conformal to the
   round three-sphere and essentially zero for surfaces with negative curvature.
   Based on this we conjecture that the exit from eternal inflation does not
   produce an infinite fractal-like multiverse, but is finite and reasonably
   smooth."
   -- [doi:10.1007/JHEP04(2018)147]['18],
      1707.07702@[arXiv]['18].
   (Also see [www][2/5/2018.)

%T Challenging local realism with human choices
%Q The BIG Bell Test Collaboration
%J Nature
%V 557
%P 212-216
%M MAY
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0518, quantum theory, mechanics, physics,
   Bell test, local realism, freedom of choice, loophole
%X "... We recruited about 100,000 human participants to play an online video
   game that incentivizes fast, sustained input of unpredictable selections and
   illustrates Bell-test methodology ... The observed correlations strongly
   contradict local realism and other realistic positions in bipartite and
   tripartite scenarios. Project outcomes include closing the
   ‘freedom-of-choice loophole’ (the possibility that the setting choices are
   influenced by ‘hidden variables’ to correlate with the particle
   properties) ..."
   -- [doi:10.1038/s41586-018-0085-3]['18].

%A J. MacQueen
%T Some methods for classification and analysis of multivariate observations
%J Proc. 5th Berkeley Symp. on Math. Statist. and Prob.
%I Univ. of Calif. Press
%V 1
%P 281-297
%D 1967
%K c1967, c1968, c19xx, zz0518, k means, kmeans, clustering, classification
%X -- 1200512992@[projecteuclid]['18].
   Also see kmeans@[wikip]['18].

%A S. Lloyd
%T Least squares quantization in PCM
%J IEEE Trans. on Inf. Th.
%V 28
%N 2
%P 129-137
%M MAR
%D 1982
%K jrnl, stats, c1957, c195x, c1982, c198x, c19xx, zz0518,
   least squares, PCM, Lloyd max, k means, kmeans, EM algorithm, clustering
%X "... In this paper the corresponding result for any finite number # quanta is
   derived; that is, necessary conditions are found that the quanta & associated
   quantization intervals of an optimum finite quantization scheme must satisfy.
   The optimization criterion used is that the avg. quantization noise power be
   a minimum. It is shown that the result obtained here goes over into the
   Panter & Dite result as the # of quanta become large. The optimum
   quantization schemes for2^{b}quanta,b=1,2, \cdots, 7, are given numerically
   for Gaussian & for Laplacian distribution of signal amplitudes."
   -- [doi:10.1109/TIT.1982.1056489]['18].
   ("... The std alg. was first proposed by Stuart Lloyd in 1957 as
   a technique for pulse-code modulation, though it wasn't
   published outside of Bell Labs until 1982. ..."
   -- kmeans@[wikip]['18].)

%A M. West
%T On scale mixtures of normal distributions
%J Biometrika
%V 74
%N 3
%P 646-648
%M SEP
%D 1987
%K jrnl, c1987, c198x, c19xx, zz0518, scale mixture, scaleMixture, normal,
   stable
%X "The exponential power family of distns of Box & Tiao (1973) is shown to be a
   subset of the class of scale mixtures of normals. The corr. mixing distn. are
   explicitly obtained, identifying a close relationship between the exponential
   power family & a further class of normal scale mixtures, namely the stable
   distributions."
   -- [doi:10.1093/biomet/74.3.646]['18].
   [Also search for: scaleMixture].
   (Also see locn-test@[wikip]['18].)

%A D. F. Andrews
%A C. L. Mallows
%T Scale mixtures of normal distributions
%J J. Royal Stat. Soc.. Series B (Methodological)
%V 36
%N 1
%P 99-102
%D 1974
%K jrnl, JRSS, c1974, c197x, c19xx, zz0518, scale mixture, scaleMixture, stats,
   normal, exponential, logistic
%X "This paper presents necessary & sufficient condns under which a random
   variable X may be generated as the ratio Z/V where Z & V are indep.
   & Z has a std normal distn. This representation is useful in Monte Carlo
   calculations. It is established that when 0.5*V^2 is exponential,
   X is double exponential; & that when V/2 has the asymptotic distribution
   of the Kolmogorov distance statistic, X is logistic."
   -- 2984774@[Jstor]['18].
   [Also search for: scaleMixture].
   (Also see locn-test@[wikip]['18].)

%A E. F. O. Sandes
%A G. L. M. Teodoro
%A M. Emilia
%A M. T. Walter
%A X. Martorell
%A E. Ayguade
%A A. C. M. A. Melo
%T Formalization of block pruning: Reducing the number of cells computed in
   exact biological sequence comparison algorithms
%J COMPJ
%V 61
%N 5
%P 687-713
%M MAY
%D 2018
%K Compj, jrnl, c2018, c201x, c20xx, zz0518, sequence comparison algorithm,
   alignment, dynamic programming, 2D, DPA, fast, prune, cell
%X "... The DP matrix H is calculated with a recurrence relation in which the
   value of each cell Hi,j is the result of a maximum operation on the cells’
   values Hi−1,j−1, Hi−1,j and Hi,j−1 added or subtracted by a constant value.
   ... define a generic pruning method which determines the cells that can
   pruned (i.e. no need to be computed since they will not contribute to the
   final solution), accelerating the computation but keeping the guarantee that
   the optimal result will be produced. The goal of this paper is thus to
   investigate and formalize properties of the DP matrix in order to estimate
   and increase the pruning method efficiency. We also show that the pruning
   efficiency depends mainly on three characteristics: (a) the order in which
   the cells of H are calculated, (b) the values of the parameters used in the
   recurrence relation and (c) the contents of the sequences compared."
   -- [doi:10.1093/comjnl/bxx090]['18].
   [Also search for: fast DPA].

%A J. Cockx
%A D. Devriese
%T Proof-relevant unification: Dependent pattern matching with only the
   axioms of your type theory
%J JFP
%V 20
%N e12
%M MAY
%D 2018
%K jrnl, JFP, c2018, c201x, c20xx, zz0518, functional programming language, FP,
   type, types, check, checking, axiom, proof, logic, dependent pattern,
   unification, dependencies, Agda, Coq, Idris, eta equality, record, records
%X "Dependently typed languages such as Agda, Coq, & Idris use a syntactic
   first-order unification alg. to check definitions by dependent pattern
   matching. ... proposes a proof-relevant framework for reasoning formally
   about unification in a dependently typed setting. In this framework,
   unification rules compute not just a unifier but also a corresponding
   soundness proof in the form of an equivalence between two sets of equations.
   By rephrasing the standard unification rules in a proof-relevant manner, they
   are guaranteed to preserve soundness of the theory. [&] it enables us to
   safely add new rules that can exploit the dependencies between the types of
   equns, such as rules for eta-equality of record types & higher dimensional
   unification rules for solving equns between equality proofs. ... implemented
   a complete overhaul of the unification algorithm used by Agda. ..."
   -- [doi:10.1017/S095679681800014X]['18].

%T General Data Protection Regulation (GDPR)
%I EU
%M MAY
%D 2018
%K law, regulation, c2018, c201x, c20xx, zz0518, internet, data, privacy,
   personal, protection, GDPR, Europe, European, EU, UK, www, website, HREF,
   opt in, out, optin, optout, consent, conditions of use
%X "... the official PDF of the Regulation (EU) 2016/679 (General Data
   Protection Regulation) ..."
   -- [www]['5/2018].
   (Also see the [bbc][25/5/2018].)
   [Also search for: internet privacy].


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