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%A A. K. Lenstra
%A H. W. Lenstra jr.
%A L. Lovasz
%T Factoring polynomials with rational coefficients
%J Mathematische Annalen
%V 261
%P 515-534
%D 1982
%K jrnl, c1982, c198x, c19xx, zz0321, LLL algorithm, polynomial, factoring,
   factors, lattice basis reduction
%X -- [doi:10.1007%2FBF01457454]['21].
   Also see, "The Lenstra-Lenstra-Lovasz (LLL) lattice basis red'n alg. ...
   calculates an LLL-reduced (short, nearly orthogonal) lattice basis in
   time O(d^5 n log^3 B) ..."
   -- LLL@[wikip]['21].

%A P. Bille
%A I. Li Gortz
%T The tree inclusion problem: In linear space and faster
%J ACM Trans. on Algorithms
%P #38
%M JUL
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0321, tree inclusion, subtree,
   problem, algorithm
%X "Given two rooted, ordered, & labeled trees P & T the tree inclusion problem
   is to determine if P can be obtained from T by deleting nodes in T. ... has
   recently been recognized as an important query primitive in XML databases.
   Kilpelainen & Mannila ['95] presented the first polynomial-time alg. using
   quadratic time & space. Since then several improved results have been
   obtained for special cases when P & T have a small # of leaves or small
   depth. However, in the worst case these algs. still use quadratic time &
   space. Let n_S, l_S, & d_S denote the # of nodes, the # of leaves, & the
   depth of a tree S in P, T. . . . show that the tree inc. problem can be
   solved in space O(n_T) & time:
   O(min(l_P n_T, l_P l_T log log n_T + n_T, (n_P n_T)/(log n_T + n_T log n_T)).
   This improves or matches the best known time complexities while using only
   linear space instead of quadratic. ... important in practical applications,
   such as XML databases, where the space is likely to be a bottleneck."
   -- [doi:10.1145/1978782.1978793]['21] and
      0608124@[arXiv]['21].

%A Yuansi Chen
%T An almost constant lower bound of the isoperimetric coefficient in the
   KLS conjecture
%M NOV
%D 2020
%K TR, c2020, c202x, c20xx, zz0321, Burgain, KLS conjecture, convex,
   high dimension, geometry
%T "We prove an almost constant lower bound of the isoperimetric coefficient in
   the KLS conjecture. The lwb has the dimension dependency d-od(1). When the
   dimension is large enough, our lwb is tighter than the prev. best bound which
   has the dimension dependency d-1/4. Improving the current best lwb of the
   isoperimetric coefficient in the KLS conjecture has many implications, inc.
   improvements of the current best bounds in Bourgain's slicing conjecture & in
   the thin-shell conjecture, better concentration inequalities for Lipschitz
   fns of log-concave measures and better mixing time bounds for MCMC sampling
   algs. on log-concave measures."
   -- 2011.13661@[arXiv]['21].
   (Also see news@[www]['21].)

%A J. Morris
%A Fang Song
%T Simple vertex coloring algorithms
%J arXiv
%M FEB
%D 2021
%K TR, c2021, c202x, c20xx, zz0321, maths, graph, vertex colouring algorithm
%X "Given a graph G with n vertices and maximum degree D, it is known that G
   admits a vertex coloring with D+1 colors s.t. no edge of G is monochromatic.
   This can be seen constructively by a simple greedy alg., which runs in time
   O(n.D). Very recently, a seq. of results ... we give a simple alg. for
   (1+eps)D-coloring. ..."
   -- 2102.07089@[arXiv]['21].

%A L. Allison
%A A. S. Konakurthu
%A D. F. Schmidt
%T On universal codes for integers: Wallace Tree, Elias Omega and beyond
%J Data Compression Conference
%I IEEE
%P 313-322
%M MAR
%D 2021
%K conf, DCC, DCC21, DCC2021, c2021, c202x, c20xx, zz0321, universal code,
   ints, integer, Elias omega, omega2, omega*, omega star, Fibonacci,
   Wallace Tree code, WTC, probability distribution, compression, entropy,
   LAllison, ArunK
%X "A universal code for the (positive) integers is a variable length code that
   can be used to store or compress a sequence of integers. It also implies a
   probability distribution on integers which can be a natural choice when the
   true distribution of a source of integers is unknown; such a code and
   distribution may be useful in statistical inference. This paper provides two
   improvements to the theory and practice of universal codes. First, it defines
   and examines a new universal code omega* (omega-star) that asymptotically
   beats the Elias omega code.  Second, it analyses the properties of a code
   proposed by Wallace based on trees, and shows it to be a universal code, to
   have desirable properties for use in inference, and to beat the Elias omega
   code on almost all integers up to the 1697-bit code-word mark. Encoding and
   decoding routines for the codes described here are implemented and available
   for interactive use[1]."
   -- [more].
   

%A Swayambhoo Jain
%A et al
%T Low rank based end-to-end deep neural network compression
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, MolBio, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN, DNN,
   compress, simplify
%X "Deep neural networks (DNNs), despite their performance on a wide variety of
   tasks, are still out of reach for many applications as they require sig.
   comp'l resources. ... we present a low-rank based end-to-end deep NN
   compression frame-work with the goal of enabling DNNs performance to
   computationally constrained devices.The proposed framework includes
   techniques for low-rank based structural approx'n, quantization & lossless
   arith.coding. Many of these techniques have been accepted in the MPEG working
   draft on compressed NN Representations. We demonstrate the efficacy of the
   proposed framework via extensive experiments on a variety of DNNs for various
   tasks considered in this standardization activity. These techniques provide
   impressive performance on DNNs used in ImageNet Large-Scale Visual
   Recognition Challenge by compressing VGG16 by 61x, ResNet50 by almost 15x, &
   MobileNetV2 by almost 7x.
   -- [doi:10.1109/DCC50243.2021.00031]['21].
   [Also search for: DCC21].

%A M. Soltani
%A et al
%T Compressing deep networks using Fisher score of feature maps
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, MolBio, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN, DNN,
   deep, neural network, compress, simplify, map
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN,
   simplification, compress
%X "... propose a new structural technique for pruning deep neural networks with
   skip-connections. ... based on measuring the importance of feature maps in
   predicting the output of the model using their Fisher scores. These scores
   subsequently used for removing the less informative layers from the graph of
   the n/w. Extensive experiments on the classification of CIFAR-10, CIFAR-100,
   & SVHN data sets demonstrate the efficacy of our compressing method both in
   the # of parameters & operations.
   -- [doi:10.1109/DCC50243.2021.00083]['21].
   [Also search for: DCC21].

%A Y. Idelbayev
%A M. A. Carreira-Perpinan
%T Neural network compression via additive combination of reshaped, low-rank
   matrices
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN,
   simplification, compress
%X "... NN compression has become an important problem due to the increasing
   necessity of running complex networks on small devices. We consider a form of
   n/wk compression that has not been explored before: an additive combination
   of reshaped low-rank matrices. That is, given the weights of a NN, we
   constrain them as a sum of differently shaped low-rank matrices to reduce the
   n/wk's size & inference demands. Computationally, this is a hard problem ...
   We formulate it as a model selection over the family of compressed models &
   give an optimization alg. that efficiently handles the inherent
   combinatorial structure. This results in a 'Learning-Compression' alg. which
   alternates between a std machine learning step & a step involving signal
   compression.  We demonstrate the effectiveness of the proposed  compression
   scheme & the corr. alg. on multiple networks and datasets."
   -- [doi:10.1109/DCC50243.2021.00032]['21].
   [Also search for: DCC21].

%A B. P. Blackburne
%A S. Whelan
%T Measuring the distance between multiple sequence alignments
%J Bioinformatics
%V 28
%N 4
%P 495-502
%M FEB
%D 2012
%K MolBio, c2012, c201x, c20xx, zz0321, distance between sequence alignments,
   difference, multiple alignment, MSA, sum pairs, total column count, score
%X "... By measuring the differences between inferred alignments, we may be able
   to develop an understanding of how these differences (i) relate to the
   objective fns & heuristics used in MSA methods, & (ii) affect downstream
   analyses. Results: We introduce four metrics to compare MSAs, which include
   the posn in a seq. where a gap occurs or the location on a phylogenetic tree
   where an insertion or deletion (indel) event occurs. ..."
   -- [doi:10.1093/bioinformatics/btr701]['21].

%A R. Singh
%A et al
%T Unsupervised manifold alignment for single-cell multi-omics data
%J bioRxiv
%M JUN
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0321, MMD-MA, MMDMA, scRNAseq, scRNA,
   manifold alignment, learning
%X "Integrating single-cell measurements that capture different properties of
   the genome is vital to extending our understanding of genome biology. This
   task is challenging due to the lack of a shared axis across datasets obtained
   from different types of single-cell experiments. ... unsupervised algs. that
   are capable of aligning single-cell experiments are critical to learning an
   in silico co-assay that can help draw corr. among the cells. Maximum mean
   discrepancy-based manifold alignment (MMD-MA) is such an unsupervised alg.
   ... we apply MMD-MA to two recent datasets that measure transcriptome &
   chromatin accessibility in ~2000 single cells ..."
   -- [doi:10.1101/2020.06.13.149195]['21],
      [bioRxiv]['21].
   Talk: [www]['20].

%A T. van der Valk
%A et al
%T Million-year-old DNA sheds light on the genomic history of mammoths
%J Nature
%M FEB
%D 2021
%K MolBio, c2021, c202x, c20xx, zz0321, ancient DNA, fossil, woolly mammoth,
   M. primigenius, mamoth, Pleistocene
%X "... report the recovery of genome-wide data from three mammoth specimens
   dating to the Early and Middle Pleistocene subepochs, two of which are more
   than one million years old. We find that two distinct mammoth lineages were
   present in eastern Siberia during the Early Pleistocene. ..."
   -- [doi:10.1038/s41586-021-03224-9]['21].
   [Also search for: MolBio ancient DNA].

%A D. Diaz-Dominguez
%A G. Navarro
%T A grammar compressor for collections of reads with applications to the
   construction of the BWT
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, MolBio, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021,
   DNA sequencing, grammar compressor, compression
%X "We describe a grammar for DNA sequencing reads from which we can compute the
   BWT directly. Our motivation is to perform in succinct space genomic analyses
   that require complex string queries not yet supported by repetition-based
   self-indexes. Our approach is to store the set of reads as a grammar, but
   when required, compute its BWT to carry out the analysis by using
   self-indexes. Our experiments in real data showed that the space red'n we
   achieve with our compressor is competitive with LZ-based methods & better
   than entropy-based approaches. Compared to other popular grammars, in this
   kind of data, we achieve, on avg., 12% extra compression & require less
   working space and time."
   -- [doi:10.1109/DCC50243.2021.00016]['21].
   [Also search for: DCC21].

%A T. Freeth
%A et al
%T A model of the cosmos in the ancient Greek Antikythera mechanism
%J Scientific Reports
%V 11
%N #5821
%M MAR
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0321, Antikythera mechanism, ancient, Greek,
   astronomy, device, cosmos, history, computing, calculator
%X "The Antikythera Mechanism, an ancient Greek astronomical calculator, has
   challenged researchers since its discovery in 1901. Now split into 82
   fragments, only a third of the original survives, including 30 corroded
   bronze gear wheels. Microfocus X-ray Computed Tomography (X-ray CT) in 2005
   decoded the structure of the rear of the machine but the front remained
   largely unresolved. X-ray CT also revealed inscriptions describing the
   motions of the Sun, Moon and all five planets known in antiquity ..."
   -- [doi:10.1038/s41598-021-84310-w].
   (Also see [bbc]['21].)
   [Also search for: Antikythera mechanism].

%A H. Else
%A R. Van Noorden
%T The fight against fake-paper factories that churn out sham science
%J Nature
%V 591
%P 516-519
%M MAR
%D 2021
%K news, c2021, c202x, c20xx, zz0321, papers, publications, paper mill, China,
   PaperMill, scam, fraud, scientific research, cheating, ghostwriter,
   academia, academic misconduct
%X "When Laura Fisher noticed striking similarities between research papers
   submitted to RSC Advances, she grew suspicious. None of the papers had
   authors or institutions in common, but their charts and titles looked
   alarmingly similar, says Fisher, the executive editor at the journal.
   'I was determined to try to get to the bottom of what was going on.' ..."
   -- [doi:10.1038/d41586-021-00733-5]['21].
   [Also search for: PaperMill].

%T Generating conjectures on fundamental constants with the Ramanujan Machine
%J Nature
%V 590
%P 67-73
%M FEB
%D 2021
%K jrnl, Ramanujan Machine, c2021, c202x, c20xx, zz0321, AI, maths, conjecture,
   equations
%X "... Our algs. find dozens of well known formulas as well as previously
   unknown ones, such as continued fraction representations of pi, e, Catalan's
   constant, and values of the Riemann zeta fn. Several conjectures found by our
   algs. were (in retrospect) simple to prove, whereas others remain as yet
   unproved. ..."
   -- [doi:10.1038/s41586-021-03229-4]['21].
   Also see [ramanujanmachine]['21].

%A M. K. Varanasi
%A B. Aazhang
%T Parametric generalized Gaussian density estimation
%J J. of the Acoustical Soc. of America
%V 86
%P 1404
%D 1989
%K jrnl, c1989, c198x, c19xx, zz0321, generalized Gaussian density, GGD, normal,
   exponential power, probability distribution, estimate, estimator, gnorm,
   shape parameter, generalised
%X "... compare the large-sample as well as the small-sample properties of
   different methods for estimating the parameters of a three-parameter
   generalized Gaussian distribution. Three estimators, namely, the moment
   method (MM), the maximum-likelihood (ML), & the moment/Newton-step (MNS)
   estimators ..."
   -- [doi:10.1121/1.398700]['21].
   Also see,
   "... is either of two families of parametric continuous prob. distn on the
   real line. Both families add a shape parameter to the normal distn ...
   (1) AKA exponential power distn, or the generalized error distn, this is a
       parametric family of symmetric distns. It includes all normal & Laplace
       distns & as limiting cases it includes all cts uniform distns on
       bounded intervals of the real line. ...
   (2) ... a family of continuous prob. distns in which the shape parameter can
       be used to introduce skew. ..."
   -- [wikip]['21].
   (And see
   gnorm@[r-project.org]['21].)

%A T. Ameen ur Rahman
%A et al ...
%T L. R. Varshney
%T The twelvefold way of non-sequential lossless compression
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, data sets, dataset,
   twelvefold, twelve, unordered, equivalence, symmetry, compress
%X "... huge amounts of data that are not simple sequences of distinguishable
   symbols, but have certain equivalence classes for patterns of symbols within
   which lossless rep'n does not require unique indices. As a simple example,
   the ordering of seqs. of scientific data records are often irrelevant & so
   only the histogram or type class must be represented. Such rep'n problems
   arise for biol. data, social graph structure, NN architecture, & elsewhere
   due to the functional process generating or using the data. These
   non-sequential info.sources may be studied implicitly via group theory & some
   may explicitly be characterized using interchange entropies. ..."
   -- [doi:10.1109/DCC50243.2021.00061]['21],
      2011.04069@[arXiv]['21].
   [Also search for: DCC21].

%A T. Gagie
%A G. Navarro
%A N. Prezza
%T Fully functional suffix trees and optimal text searching in BWT-runs bounded
   space
%J JACM
%V 67
%N 1
%P 1-54
%M JAN
%D 2020
%K Jrnl, JACM, c020, c202x, c20xx, zz0321, run length FM index, FMindex, BWT,
   RLBWT, suffix tree, repetitive strings, stringology
%X "Indexing highly repetitive text - such as genomic databases, s/w
   repositories & versioned text collections ... One of the earliest indexes for
   rep.collections, the Run-Length FM-index, used O(r) space & was able to
   efficiently count the # of occurrences of a pattern of length m in a text of
   length n (in O(m log log n) time, with current techniques). However, it was
   unable to locate the posns of those occurrences efficiently within a space
   bounded in terms of r. ... we close this long-standing problem, showing how
   to extend the Run-Length FM-index so that it can locate the occ occurrences
   efficiently (in O(occ log log n) time) within O(r) space. By raising the
   space to O(r log log n), our index counts the occurrences in optimal time,
   O(m), & locates them in optimal time as well, O(m+occ). By further raising
   the space by an O(w/log s) factor, where s is the alphabet size &
   w=Omega(log n) is the RAM machine size in bits, we support count & locate in
   O(ceil(m log (s)/w)) & O(ceil(m log (s)/w)+occ) time, which is optimal in the
   packed setting & had not been obtained before in compressed space. We also
   describe a structure using O(r log (n/r)) space that replaces the text &
   extracts any text substring of length L in the almost-optimal time
   O(log (n/r)+L log (s)/w). Within that space, we similarly provide access to
   arbitrary suffix array, inverse suffix array, & longest common prefix array
   cells in time O(log(n/r)), and extend these capabilities to full suffix tree
   functionality, typically in O(log(n/r)) time per operation. Our experiments
   show that our O(r)-space index outperforms the space-competitive alternatives
   by 1 to 2 orders of magnitude in time. Competitive implementations of the
   original FM-index are outperformed by 1 to 2 orders of magnitude in space
   &/or 2 to 3 in time.
   -- [doi:10.1145/3375890]['21].

%A S. J. Puglisi
%A B. Zhukova
%T Smaller RLZ-compressed suffix arrays
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, Snowbird, strings,
   suffix array, index, RLZ, RLZSA, SAdiff
%X "Recently it was shown (auths SPIRE, 2020) that the suffix array (SA) data
   structure can be effectively compressed with relative Lempel-Ziv (RLZ)
   dictionary comp'n in such a way that arbitrary subarrays can be rapidly
   decompressed, thus facilitating compressed indexing. ... we describe
   optimizations to RLZ-compressed SAs, including generation of more effective
   dictionaries & compact encodings of index components, both of which reduce
   index size without adversely affecting subarray access speeds relative to
   other compressed indexes. Our experimental analysis also elucidates the
   relationship between subarray size and per elt access time.
   -- [doi:0.1109/DCC50243.2021.00029]['21].
   [Also search for: DCC21].


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