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16
Minimum Message Length and Kolmogorov Complexity
 Computer Journal
, 1999
"... this paper is to describe some of the relationships among the different streams and to try to clarify some of the important differences in their assumptions and development. Other studies mentioning the relationships appear in [1, Section IV, pp. 10381039], [2, sections 5.2, 5.5] and [3, p. 465] ..."
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Cited by 105 (25 self)
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this paper is to describe some of the relationships among the different streams and to try to clarify some of the important differences in their assumptions and development. Other studies mentioning the relationships appear in [1, Section IV, pp. 10381039], [2, sections 5.2, 5.5] and [3, p. 465]
MML clustering of multistate, Poisson, von Mises circular and Gaussian distributions
 Statistics Computing
, 2000
"... Minimum Message Length (MML) is an invariant Bayesian point estimation technique which is also statistically consistent and efficient. We provide a brief overview of MML inductive inference ..."
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Cited by 32 (10 self)
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Minimum Message Length (MML) is an invariant Bayesian point estimation technique which is also statistically consistent and efficient. We provide a brief overview of MML inductive inference
Circular Clustering Of Protein Dihedral Angles By Minimum Message Length
 In Proceedings of the 1st Pacific Symposium on Biocomputing (PSB1
, 1996
"... this paper is given in [DADH95] and is available from ftp://www.cs.monash.edu.au/www/publications/1995/TR237.ps.Z.) Section 2introduces the MML principle and how it can be used for this circular clustering problem. The remaining sections give the results of the secondary structure groups [KaSa83] th ..."
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Cited by 15 (11 self)
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this paper is given in [DADH95] and is available from ftp://www.cs.monash.edu.au/www/publications/1995/TR237.ps.Z.) Section 2introduces the MML principle and how it can be used for this circular clustering problem. The remaining sections give the results of the secondary structure groups [KaSa83] that resulted from applying Snob to cluster our dihedral angle data.
A Simple Statistical Algorithm for Biological Sequence Compression
 DATA COMPRESSION CONFERENCE
, 2007
"... This paper introduces a novel algorithm for biological sequence compression that makes use of both statistical properties and repetition within sequences. A panel of experts is maintained to estimate the probability distribution of the next symbol in the sequence to be encoded. Expert probabilities ..."
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Cited by 11 (0 self)
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This paper introduces a novel algorithm for biological sequence compression that makes use of both statistical properties and repetition within sequences. A panel of experts is maintained to estimate the probability distribution of the next symbol in the sequence to be encoded. Expert probabilities are combined to obtain the final distribution. The resulting information sequence provides insight for further study of the biological sequence. Each symbol is then encoded by arithmetic coding. Experiments show that our algorithm outperforms existing compressors on typical DNA and protein sequence datasets while maintaining a practical running time. 1.
MML mixture modelling of multistate, Poisson, von Mises circular and Gaussian distributions
 In Proc. 6th Int. Workshop on Artif. Intelligence and Statistics
, 1997
"... Minimum Message Length (MML) is an invariant Bayesian point estimation technique which is also consistent and efficient. We provide a brief overview of MML inductive inference (Wallace and Boulton (1968), Wallace and Freeman (1987)), and how it has both an informationtheoretic and a Bayesian interp ..."
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Cited by 8 (5 self)
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Minimum Message Length (MML) is an invariant Bayesian point estimation technique which is also consistent and efficient. We provide a brief overview of MML inductive inference (Wallace and Boulton (1968), Wallace and Freeman (1987)), and how it has both an informationtheoretic and a Bayesian interpretation. We then outline how MML is used for statistical parameter estimation, and how the MML mixture modelling program, Snob (Wallace and Boulton (1968), Wallace (1986), Wallace and Dowe(1994)) uses the message lengths from various parameter estimates to enable it to combine parameter estimation with selection of the number of components. The message length is (to within a constant) the logarithm of the posterior probability of the theory. So, the MML theory can also be regarded as the theory with the highest posterior probability. Snob currently assumes that variables are uncorrelated, and permits multivariate data from Gaussian, discrete multistate, Poisson and von Mises circular dist...
Sequence Complexity for Biological Sequence Analysis
, 2000
"... A new statistical model for DNA considers a sequence to be a mixture of regions with little structure and regions that are approximate repeats of other subsequences, i.e. instances of repeats do not need to match each other exactly. Both forward and reversecomplementary repeats are allowed. The mo ..."
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Cited by 8 (0 self)
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A new statistical model for DNA considers a sequence to be a mixture of regions with little structure and regions that are approximate repeats of other subsequences, i.e. instances of repeats do not need to match each other exactly. Both forward and reversecomplementary repeats are allowed. The model has a small number of parameters which are fitted to the data. In general there are many explanations for a given sequence and how to compute the total probability of the data given the model is shown. Computer algorithms are described for these tasks. The model can be used to compute the information content of a sequence, either in total or base by base. This amounts to looking at sequences from a datacompression point of view and it is argued that this is a good way to tackle intelligent sequence analysis in general.
Intrinsic Classification by MML—the Snob Program
 Proc. Seventh Australian Joint Conf. Artificial Intelligence
, 1994
"... Abstract: We provide a brief overview ofMinimum Message Length (MML) inductive inference (Wallace and Boulton (1968), Wallace and Freeman (1987)). We then outline how MML is used for statistical parameter estimation, and how the MML intrinsic classification program, Snob (Wallace and Boulton (1968), ..."
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Cited by 6 (0 self)
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Abstract: We provide a brief overview ofMinimum Message Length (MML) inductive inference (Wallace and Boulton (1968), Wallace and Freeman (1987)). We then outline how MML is used for statistical parameter estimation, and how the MML intrinsic classification program, Snob (Wallace and Boulton (1968), Wallace (1986), Wallace (1990)) uses the message lengths from various parameter estimates to enable it to combine parameter estimation with model selection in intrinsic classification. We mention here the most recent extensions to Snob, permitting Poisson and von Mises circular distributions. We also survey some applications of Snob (albeit briefly), and further provide some documentation on how the user can guide Snob’s search through various models of the given data to try to obtain that model whose message length is a minimum.
Compression and Approximate Matching
 The Computer Journal
, 1999
"... A population of sequences is called nonrandom if there is a statistical model and an associated compression algorithm that allows members of the population to be compressed, on average. Any available statistical model of a population should be incorporated into algorithms for alignment of the seque ..."
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Cited by 5 (2 self)
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A population of sequences is called nonrandom if there is a statistical model and an associated compression algorithm that allows members of the population to be compressed, on average. Any available statistical model of a population should be incorporated into algorithms for alignment of the sequences and doing so changes the rank order of possible alignments in general. The model should also be used in deciding if a resulting approximate match between two sequences is significant or not. It is shown how to do this for two plausible interpretations involving pairs of sequences that might or might not be related. Efficient alignment algorithms are described for quite general statistical models of sequences. The new alignment algorithms are more sensitive to what might be termed 'features' of the sequences. A natural significance test is shown to be rarely fooled by apparent similarities between two sequences that are merely typical of all or most members of the population, even unrelated members. The Computer Journal, Volume 42, Issue 1, pp. 110, 1999. http://www.csse.monash.edu.au/~lloyd/tildeStrings/
MML, HYBRID BAYESIAN NETWORK GRAPHICAL MODELS, STATISTICAL CONSISTENCY, INVARIANCE AND UNIQUENESS
"... The problem of statistical — or inductive — inference pervades a large number of human activities and a large number of (human and nonhuman) actions requiring ‘intelligence’. Human and other ‘intelligent ’ activity often entails making inductive inferences, remembering and recording observations fr ..."
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Cited by 4 (3 self)
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The problem of statistical — or inductive — inference pervades a large number of human activities and a large number of (human and nonhuman) actions requiring ‘intelligence’. Human and other ‘intelligent ’ activity often entails making inductive inferences, remembering and recording observations from which one can make
CIRCULAR CLUSTERING BY MINIMUM MESSAGE LENGTH OF PROTEIN DIHEDRAL ANGLES
, 1995
"... Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a highlevel classification which remains popular today. Using the Snob program for informationtheoretic Minimum Message Length (MML) intrinsic classification, we are able to take the pro ..."
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Cited by 4 (4 self)
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Early work on proteins identified the existence of helices and extended sheets in protein secondary structures, a highlevel classification which remains popular today. Using the Snob program for informationtheoretic Minimum Message Length (MML) intrinsic classification, we are able to take the protein dihedral angles as determined by Xray crystallography, and cluster sets of dihedral angles into groups. Previous work by Hunter and States had applied a similar Bayesian classification method, AutoClass, to protein data with site position represented by 3 Cartesian coordinates for each of the αCarbon, βCarbon and Nitrogen, totalling 9 coordinates. By using the von Mises circular distribution in the Snob program rather than the Normal distribution in the Hunter and States model, we are instead able to represent local site properties by the two dihedral angles, φ and ψ. Since each site can be modelled as having 2 degrees of freedom, this orientationinvariant dihedral angle representation of the data is more compact than that of nine highlycorrelated Cartesian coordinates. Using the informationtheoretic message length concepts discussed in the paper, such a more concise model is more likely to represent the underlying generating process from which the data comes. We report on the results of our classification, plotting the classes in (φ,ψ)space and introducing a symmetric informationtheoretic distance measure to build a minimum spanning tree between the classes. We also give a transition matrix between the classes and note the existence of three classes in the region φ ≈−1. 09 rad and ψ ≈−0. 75 rad which are close on the spanning tree and have high intertransition probabilities. These properties give rise to a tight, abundant, selfperpetuating, αhelical structure.