An information-based sequence distance and its application to whole mitochondrial genome phylogeny

By Ming Li, Jonathan H. Badger, Xin Chen, Sam Kwong, P. Kearney, Haoyong Zhang. Bioinform., 2001

565 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6769a28d898063edc3ef6f2fea6df9e4608ebf67

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Citations in the corpus

A Machine Learning Perspective on Predictive Coding with PAQ (2011, background): “Li et al (Li et al., 2001) propose the following metric to measure the distance between the strings x and y : ) is deﬁned to be the Kolmogorov complexity of a string x .”
Towards parameter-free data mining (2004, background): “In fact, CDM depends on the choice of the specific compressor (gzip, compress, bzip2, etc.), and on the compression parameters (for example, the sliding window size in gzip).”
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions (2009, methodology): “A normalized compression distance can be formed from the Kolmogorov complexity of a, Ka, which is defined as the length of the smallest program that will produce the output a (19, 20).”
The similarity metric (2001, background): “In [31], we considered a first attempt at a normalized information distance.”
Clustering by compression (2003, methodology): “Earlier approaches resulted in the first completely automatic construction of the phylogeny tree based on whole mitochondrial genomes, [29]–[31], a completely automatic construction of a language tree for over 50”
Effective and Fast Near Duplicate Detection via Signature-Based Compression Metrics (2016, background): “NCD has been proven to be universal and can naturally be applied to a variety of domains such as genomics, languages, music, and images [5–10].”
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure (2008, methodology): “The Kolmogorov complexity K ((cid:129)) of an object o is defined by the length of the shortest program P for a Universal Turing Machine U that is needed to output o [18]. and Intuitively, K ( x ) represents the minimal amount of information required to generate × by an algorithm.”
Information Theoretic Distance Measures in Phylogenomics (2007, methodology): “The idea of using compression for phylogenetic classification of whole genomes was first introduced in 2001 [5].”
Sequence learning using the adaptive suffix trie algorithm (2012, methodology): “The first two datasets are the mitochodrial(mtDNA) genome dataset of 20 and 34 mammals with sequences of length ranging from 16,299 -17,245 nucleotides used by[24].”
Author ' s personal copy A Fast Quartet tree heuristic for hierarchical clustering (2010, methodology): “The algorithm does not address the problem of how to obtain the quartet topology weights from sequence data [25,30,32], but takes as input the weights of all quartet topologies and executes the step of how to reconstruct the hierarchical clustering from there.”
TSclust: An R Package for Time Series Clustering (2014, methodology): “Two prominent approaches to evaluate complexity diﬀerences between two time series are: (i) using algorithms based on data compression (see, e.g., Li, Badger, Chen, Kwong, Kearney, and Zhang 2001; Li et al. 2004; Keogh, Lonardi, and Ratanamahatana 2004; Cilibrasi and Vit´anyi 2005; Keogh et al.…”
Shared information and program plagiarism detection (2004, methodology): “Meanwhile, three problems [22] that plague most of the other metrics may all be viewed as special cases of d(x; y).”
DYNOTEARS: Structure Learning from Time-Series Data (2020, background): “The normalized mutual information (NMI, Li et al., 2001) between this community-induced partition and the sector-based partition is approximately 0 .”
Alignment-free sequence comparison-a review (2003, methodology): “In that report (Li et al., 2001), sequence compression is performed using the GenCompress software program (Chen et al., 1999), empirically assessing the Kolmogorov complexity, K (X), of a sequence, X by the length of its compressed representation.”