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%A H. L. Morgan
%T The generation of a unique machine description for chemical structures - a
technique developed at chemical abstracts service
%J J. Chem. Doc.
%K jrnl, c1965, c196x, c19xx, zz1220, maths, graph, color refinement algorithm,
CRP, problem, isomorphism, colour, colouring, naive vertex classification,
chemical compound, molecule
%X -- [doi:10.1021/c160017a018]['20].
("begins with a uniform coloring of the Vs of 2 graphs G & H and refines the
V-coloring step by step ... if two Vs have identical colors but differently
colored n'hoods (with the multiplicities of colors counted), then these Vs
get new different colors [etc] ... [but color-ref.] sometime fails to
distinguish non-isomorphics graphs. ..." -- Arvind et al 2O15.
"The Color Refinement alg. can be viewed as the 1-D version of ... the
Weisfeiler-Leman alg." -- Grohe&Neuen 2020.)
[Also search for: Weisfeiler Leman algorithm].
%A R. C. Hillyard
%A Y. Liaozheng
%A K. R. Sai Vineeth
%K TR, c2020, c202x, c20xx, zz1220, sort, sorting, algorithm, access, accesses,
%X "... a more appropriate yardstick for the performance of sorting algs. is
based on the total # of array accesses that are required (the 'work'). For a
sort that is based on divide-&-conquer (inc. iterative variations on that
theme), we can divide the work into linear, i.e. O(N), work & linearithmic,
i.e. O(N log N), work. ... may be able to reduce the total # of array
accesses ... This paper describes an approach to sorting which reduces the #
of expensive comparisons in the linearithmic phase as much as possible by
substituting inexpensive comparisons. In Java, the two system sorts are
dual-pivot quicksort (for primitives) & Timsort for objects. We demonstrate
that a combination of these two algs. can run sig. faster than either alg.
alone for the types of objects which are expensive to compare. We call this
improved sorting alg. Huskysort."
[Also search for: sort algorithm].
%A D. Neuen
%T Isomorphism testing for graphs excluding small topological subgraphs
%K TR, c2020, c202x, c20xx, zz1220, maths, graph, isomorphism
%X "We give an isomorphism test that runs in time 'n^polylog(h)' on all n-vertex
graphs excluding some h-vertex vertex graph as a topological subg.. Previous
results state that isomorphism for such graphs can be tested in time
'n^polylog(n)' (Babai, STOC 2016) & 'n^f(h)' for some fn f (Grohe & Marx,
SIAM J. Comp., 2015). Our result also unifies & extends prev. isomorphism
tests for graphs of maximum degree d running in time 'n^polylog(d)'
(FOCS 2018) & for graphs of Hadwiger # h running in time 'n^polylog(h)'
[Also search for: graph isomorphism].
%A D. Lemire
%A C. Bartlett
%A O. Kaser
%A Z. Merali
%T Integer division by constants: optimal bounds
%K TR, c2020, c202x, c20xx, zz1220, fast, integer, division, divide, arithmetic,
div, constant, algorithm
%X "... Optimizing compilers accelerate software by replacing the division of n
by d with the div'n of c*n (or c*n+c) by m for convenient integers c & m
chosen so that they approx. the reciprocal: c/m ~= 1/d. Such techniques are
esp. advantageous when m is chosen to be a power of two & when d is a const.
so that c & m can be precomputed. The literature contains many bounds on the
distance between c/m & the divisor d. Some of these bounds are optimally
tight, while others are not. Using accessible mathematics, we present opt.
tight bounds for quotient & remainder computations."
[Also search for: integer arithmetic].
%A P. G. Breen
%A C. N. Foley
%A T. Boekholt
%A S. Portegies Zwart
%T Newton vs the machine: solving the chaotic three-body problem using
deep neural networks
%K TR, c2019, c201x, c20xx, zz1220, deep, ANN, NN, three body problem, gravity
%X "... We show that an ensemble of solns obtained using an arbitrarily precise
numerical integrator can be used to train a deep ANN that, over a bounded
time interval, provides accurate solns at fixed computational cost & up to
100 million times faster than a state-of-the-art solver. ... provide evidence
that, for computationally challenging regions of phase-space, a trained ANN
can replace existing numerical solvers ..."
%A F. Jacob
%T Evolution and tinkering
%K essay, MolBio, c1977, c197x, c19xx, zz1220, protein, structure, evolution,
%X -- 1744610@[Jstor]['20],
[Also search for: MolBio bricolage].
%A D. Duboule
%A A. S. Wilkins
%T The evolution of 'bricolage'
%J Trends in Genetics
%K jrnl, MolBio, c1998, c199x, c19xx, zz1220, protein, function, evolution,
%X "... have revealed that most of our genes are shared by other species
throughout the animal kingdom. Consequently, animal diversity might largely
rely on the differential use of the same components, either at the individual
level through divergent functional recruitment, or at a more integrated
level, through their participation in various genetic networks. Here, we
argue that this inevitably leads to an increase in the interdependency
between fns that, in turn, influences the degree to which novel variations
can be tolerated. In this 'transitionist' scheme, evolution is neither
inherently gradualist nor punctuated but, instead, progresses from one
extreme to the other, together with the increased complexity of organisms."
[Also search for: MolBio bricolage].
%A V. Alva
%A J. Soding
%A A. N. Lupas
%T A vocabulary of ancient peptides at the origin of folded proteins
%K jrnl, MolBio, c2015, c201x, c20xx, zz1220, protein structure, fold, motif,
pattern, ancient, peptide, origin, RNA, fragment
%X "... only a few thousand domain prototypes, but the origin of these
themselves has remained unclear. We are pursuing the hypothesis that they
arose by fusion & accretion from an ancestral set of peptides active as
co-factors in RNA-dep't replication & catalysis. Should this be true,
contemporary domains may still contain vestiges of such peptides, which could
be reconstructed by a comparative approach in the same way in which ancient
vocabularies have been reconstructed by the comparative study of modern
languages. To test this, we compared domains representative of known folds &
identified 40 fragments whose similarity is indicative of common descent ...
We propose that they represent the observable remnants of a primordial
%A Xing-Yi Ge
%A et al
%A Zheng-Li Shi
%T Coexistence of multiple coronaviruses in several bat colonies in an
%J Virologica Sinica
%K jrnl, MolBio, c2016, c201x, c20xx, zz1220, coronavirus, virus, SARS, origin,
origins, Wuhan, WIV, lab, Tongguan, Yunnan, China, bat, bats, RdRp, RaTG13,
Rhinolophus affinis, Shi Zhengli, SARS1
%X "Since the 2002-2003 severe acute respiratory syndrome (SARS) outbreak ... We
conducted a surveillance of coronaviruses in bats in an abandoned mineshaft
in Mojiang County, Yunnan Province, China, from 2012-2013. Six bat species
were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus
affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus
fuliginosus, & Miniopterus fuscus. By sequencing PCR products of the
coronavirus RNA-dependent RNA polymerase gene (RdRp), we found a high freq.
of infection by a diverse group of coronaviruses in different bat species in
the mineshaft. Sequenced partial RdRp fragments had 80%-99% nucleic acid
sequence identity with well-characterized Alphacoronavirus species, inc.
BtCoV HKU2, BtCoV HKU8, & BtCoV1, and unassigned species BtCoV HKU7 & BtCoV
Also see [bbc][22/12/2020].
[Also search for: MolBio SARS origin].
%A A. Verma
%A B. E. Engelhardt
%T A robust nonlinear low-dimensional manifold for single cell RNA-seq data
%O BMC Bioinformatics vol.21, #324, 2020
%K TR, MolBio, c2018, c201x, c20xx, zz1220, scRNAseq, nonlinear, manifold,
%X "... Analysis of these [scRNA-seq] sparse, high-dimensional experimental
results requires dimension reduction. Several methods have been developed to
est. low-dimensional embeddings for filtered & normalized single cell data.
However, methods have yet to be developed for unfiltered & unnormalized count
data. We present a nonlinear latent variable model with robust, heavy-tailed
error & adaptive kernel learning to estimate low-dimensional nonlinear
structure in scRNA-seq data. Gene expression in a single cell is modeled as a
noisy draw from a Gaussian process in high dimensions from low-dim. latent
positions. This model is called the Gaussian process latent variable model
(GPLVM). We model residual errors with a heavy-tailed Student's t-distn ..."
-- [bioRxiv]['18] or
[Also search for: scRNAseq manifold].
%A K. R. Moon
%A J. S. Stanley
%A D. Burkhardt
%A D. van Dijk
%A G. Wolf
%A S. Krishnaswamy
%T Manifold learning-based methods for analyzing single-cell RNA-sequencing data
%J Current Opinion in Sys. Biol.
%K MolBio, jrnl, survey, intro, c2020, c202x, c20xx, zz1220, manifold alignment,
single cell RNA seq, scRNAseq
%X "... Manifold learning provides a powerful structure for alg. approaches to
process the data, extract its dynamics, & infer patterns in it. ... we cover
manifold learning-based methods for denoising the data, revealing gene
interactions, extracting pseudotime progressions with model fitting,
visualizing the cellular state space via dimensionality reduction, &
clustering the data."
%A K. G. Andersen
%A A. Rambaut
%A W. Ian Lipkin
%A E. C. Holmes
%A R. F. Garry
%T The proximal origin of SARS-CoV-2
%K news, views, MolBio, c2020, c202x, c20xx, zz1220, coronavirus, zoonotic,
virus, SARS, origin, origins, SARS1, SARS-CoV-2, SARSCoV2, SARS2, covid19,
origin, spike protein, RBD, ACE2, furin, polybasic cleavage, RaTG13,
Rhinolophus affinis, bat, pangolin
%X "... It is improbable that SARS-CoV-2 emerged through laboratory manipulation
... It is possible that a progenitor of SARS-CoV-2 jumped into humans,
acquiring the genomic features described above through adaptation during
undetected human-to-human transmission. ..."
Also see [bbc][22/12/2020].
[Also search for: MolBio SARS origin].
%A R. F. Service
%T 'The game has changed.' AI triumphs at protein folding
%K MolBio, news, views, c2020, c202x, c20xx, zz1220, CASP, CASP14,
protein, fold, folding, structure, prediction, AlphaFold, DeepMind, ANN, NN
%X "[AI] has solved one of biology's grand challenges: predicting how proteins
curl up from a linear chain of AAs into 3D shapes that allow them to carry
out life's tasks. ... the DeepMind method will have far-reaching effects,
among them helping researchers identify protein-based targets for novel
medications. Because contest rules require competitors to reveal enough of
their methods for others to make use of them, organizers say it's only a
matter of months before other groups match DeepMind's success."
[Also search for: MolBio AlphaFold].
%T Search for extraterrestrial intelligence gets a $100-million boost
Russian billionaire Yuri Milner announces most comprehensive hunt for
%K news, views, Breakthrough Listen, Milner, c2015, c201x, c20xx, zz1220, SETI,
search, radio, signal, BLC, BLC1, extraterrestrial life, intelligence, space,
%X "You could say that the silence has been deafening. Since its beginnings more
than half a century ago, the dedicated search for extraterrestrial
intelligence (SETI) has failed to detect the presence of alien civilizations.
But at London's Royal Society today (20 July), Russian billionaire Yuri
Milner announced a shot in the arm for SETI: a US$100-million decadal project
to provide the most comprehensive hunt for alien communications so far. ..."
(Also see [wikip]['20].)
[Also search for: extraterrestrial life].
%A D. Hope
%A J. Limberg
%T The economic consequences of major tax cuts for the rich
%R WorkingPaper 55
%K TR, LSE, c2020, c202x, c20xx, zz1220, Economics, tax, cut, cuts, rich, poor,
trickle down, Reaganomics, income inequality, wealth, unemployment, poverty,
%X "... uses data from 18 OECD countries over the last five decades to est. the
causal effect of major tax cuts for the rich on income inequality, economic
growth, & unemployment. First, we use a new encompassing measure of taxes on
the rich to identify instances of major red'ns in tax progressivity. ... We
find that major reforms reducing taxes on the rich lead to higher income
inequality ... The effect remains stable in the medium term. In contrast,
such reforms do not have any sig. effect on economic growth & unemployment.
%A M. Ajtai
%T Generating hard instances of lattice problems (extended abstract)
%J Proc. 28th annual ACM symp. on Theory of Computing (STOC)
%K conf, c1996, c199x, c19xx, zz1220, hard, lattice, problem, cryptography,
based, public key encryption, shortest vector problem, SVP
%X "We give a random class of lattices in Z^n s.t. if there is a probabilistic
polynomial time alg. which finds a short vector in a random lattice with a
prob. of at least 1/2 then there is also a prob. polynomial time alg. which
solves the following three lattice problems in every lattice in Z^n with a
prob. exponentially close to one. (1) Find the length of a shortest nonzero
vector in an n-dim. lattice, approximately, up to a polynomial factor.
(2) Find the shortest nonzero vector in an n-dim. lattice L where the
shortest vector v is unique in the sense that any other vector whose length
is at most n c kvk is parallel to v, where c is a sufficiently large absolute
constant. (3) Find a basis b_1,...,b_n in the n-dim. lattice L whose length,
defined as max n i=1 kb i k, is the smallest possible up to a polynomial
Also see LBC@[wikip]['20].
[Also search for lattice based cryptography].
%A I. Ullisch
%T A closed-form solution to the geometric goat problem
%J The Mathematical Intelligencer
%K c2020, c202x, c20xx, zz1220, geometric goat problem, tethered-bull,
women, STEM, maths, puzzle, Ladies Diary, Woman's Almanack
%X via DS
"The goat problem is a problem in recreational maths known since the 18th
century. It was 1st published in 1748 in England, in the yearly publ'n
The Ladies Diary: or, the Woman's Almanack ..."
Also see the LD@[wikip]['20].
%A A. Grover
%A J. Leskovec
%T node2vec: Scalable feature learning for networks
%K Conf, KDD, c2016, c201x, c20xx, zz1220, node2vec, graph, network, feature,
neighbourhood, node, embed, embedding, Gensi, word2vec, algorithm, SNAP
%X "... we propose node2vec, an algorithmic framework for learning cts feature
rep'ns for nodes in networks. In node2vec, we learn a mapping of nodes to a
low-dimensional space of features that maximizes the likelihood of preserving
n/wk neighborhoods of nodes ..."
Also see snap@[www]['20].
%A S. Klabnik
%A C. Nichols
%T The Rust Programming Language
%K book, text, c2020, c202x, c20xx, zz1220, Rust, programming language
%X 2nd ed 2019; uk us isbn:1718500440; uk us isbn13:978-1718500440.
"... Rust offers the control and performance of a low-level language with the
helpful abstractions of a high level one, and does this all without having a
garbage collector. ..."
[Also search for: Rust programming language].
%A P. Jaccard
%T Etude comparative de la distribution florale dans une portion des Alpes et
%J Bulletin de la Societe vaudoise des sciences naturelles
%K jrnl, c1901, c1902, c19xx, zz1220, Jaccard index, Tanimoto coefficient,
distance, similar, similarity, classification, plants, flowers, attributes,
features, stats, search, chemical compound
%X "... Jaccard index = Tanimoto index, but J_distance != T_distance ..."
%A W. Buntine
%A S. Perttu
%T Is multinomial PCA multi-faceted clustering or dimensionality reduction?
%J AI and Statistics
%K conf, AIS, principal components analysis, PCA, c2003, c200x, c20xx, zz1220,
discrete, documents, dimensionality reduction, stats, statistics
%X "Discrete analogues to Principal Components Analysis (PCA) are intended
to handle discrete or positive-only data, for instance sets of documents.
The class of methods is appropriately called multinomial PCA because it
replaces the Gaussian in the probabilistic formulation of PCA with a
multinomial. Experiments to date, however, have been on small data sets, for
instance, from early information retrieval collections. This paper
demonstrates the method on two large data sets and considers 2 extremes of
behaviour: (1) dimensionality reduction where the feature set (i.e. bag of
words) is considerably reduced, and (2) multi-faceted clustering (or aspect
modelling) where clustering is done but items can now belong in several
clusters at once."
[Also search for: multinomial clustering].
%A Chang Wang
%A S. Mahadevan
%T Heterogeneous domain adaptation using manifold alignment
%J 22nd Int. Joint Conf. on AI
%K conf, IJCAI, c2011, c201x, c20xx, zz1220, manifold alignment, correspondence,
%X "... construct mappings to link different feature spaces in order to transfer
knowledge across domains. ... can reuse labelled data from multiple source
domains even in the case when the input domains do not share any common
features or instances. ..."
Also see MA@[wikip]['20].
[Also search for: manifold alignment].