3,342 research outputs found
On-line diagnosis of unrestricted faults
A formal model for the study of on-line diagnosis is introduced and used to investigate the diagnosis of unrestricted faults. A fault of a system S is considered to be a transformation of S into another system S' at some time tau. The resulting faulty system is taken to be the system which looks like S up to time tau, and like S' thereafter. Notions of fault tolerance error are defined in terms of the resulting system being able to mimic some desired behavior as specified by a system similar to S. A notion of on-line diagnosis is formulated which involves an external detector and a maximum time delay within which every error caused by a fault in a prescribed set must be detected. It is shown that if a system is on-line diagnosable for the unrestricted set of faults then the detector is at least as complex, in terms of state set size, as the specification. The use of inverse systems for the diagnosis of unrestricted faults is considered. A partial characterization of those inverses which can be used for unrestricted fault diagnosis is obtained
Approximations of Algorithmic and Structural Complexity Validate Cognitive-behavioural Experimental Results
We apply methods for estimating the algorithmic complexity of sequences to
behavioural sequences of three landmark studies of animal behavior each of
increasing sophistication, including foraging communication by ants, flight
patterns of fruit flies, and tactical deception and competition strategies in
rodents. In each case, we demonstrate that approximations of Logical Depth and
Kolmogorv-Chaitin complexity capture and validate previously reported results,
in contrast to other measures such as Shannon Entropy, compression or ad hoc.
Our method is practically useful when dealing with short sequences, such as
those often encountered in cognitive-behavioural research. Our analysis
supports and reveals non-random behavior (LD and K complexity) in flies even in
the absence of external stimuli, and confirms the "stochastic" behaviour of
transgenic rats when faced that they cannot defeat by counter prediction. The
method constitutes a formal approach for testing hypotheses about the
mechanisms underlying animal behaviour.Comment: 28 pages, 7 figures and 2 table
Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences
We introduce and study a set of training-free methods of
information-theoretic and algorithmic complexity nature applied to DNA
sequences to identify their potential capabilities to determine nucleosomal
binding sites. We test our measures on well-studied genomic sequences of
different sizes drawn from different sources. The measures reveal the known in
vivo versus in vitro predictive discrepancies and uncover their potential to
pinpoint (high) nucleosome occupancy. We explore different possible signals
within and beyond the nucleosome length and find that complexity indices are
informative of nucleosome occupancy. We compare against the gold standard
(Kaplan model) and find similar and complementary results with the main
difference that our sequence complexity approach. For example, for high
occupancy, complexity-based scores outperform the Kaplan model for predicting
binding representing a significant advancement in predicting the highest
nucleosome occupancy following a training-free approach.Comment: 8 pages main text (4 figures), 12 total with Supplementary (1 figure
Scanning and Sequential Decision Making for Multi-Dimensional Data - Part I: the Noiseless Case
We investigate the problem of scanning and prediction ("scandiction", for
short) of multidimensional data arrays. This problem arises in several aspects
of image and video processing, such as predictive coding, for example, where an
image is compressed by coding the error sequence resulting from scandicting it.
Thus, it is natural to ask what is the optimal method to scan and predict a
given image, what is the resulting minimum prediction loss, and whether there
exist specific scandiction schemes which are universal in some sense.
Specifically, we investigate the following problems: First, modeling the data
array as a random field, we wish to examine whether there exists a scandiction
scheme which is independent of the field's distribution, yet asymptotically
achieves the same performance as if this distribution was known. This question
is answered in the affirmative for the set of all spatially stationary random
fields and under mild conditions on the loss function. We then discuss the
scenario where a non-optimal scanning order is used, yet accompanied by an
optimal predictor, and derive bounds on the excess loss compared to optimal
scanning and prediction.
This paper is the first part of a two-part paper on sequential decision
making for multi-dimensional data. It deals with clean, noiseless data arrays.
The second part deals with noisy data arrays, namely, with the case where the
decision maker observes only a noisy version of the data, yet it is judged with
respect to the original, clean data.Comment: 46 pages, 2 figures. Revised version: title changed, section 1
revised, section 3.1 added, a few minor/technical corrections mad
GPU-Accelerated BWT Construction for Large Collection of Short Reads
Advances in DNA sequencing technology have stimulated the development of
algorithms and tools for processing very large collections of short strings
(reads). Short-read alignment and assembly are among the most well-studied
problems. Many state-of-the-art aligners, at their core, have used the
Burrows-Wheeler transform (BWT) as a main-memory index of a reference genome
(typical example, NCBI human genome). Recently, BWT has also found its use in
string-graph assembly, for indexing the reads (i.e., raw data from DNA
sequencers). In a typical data set, the volume of reads is tens of times of the
sequenced genome and can be up to 100 Gigabases. Note that a reference genome
is relatively stable and computing the index is not a frequent task. For reads,
the index has to computed from scratch for each given input. The ability of
efficient BWT construction becomes a much bigger concern than before. In this
paper, we present a practical method called CX1 for constructing the BWT of
very large string collections. CX1 is the first tool that can take advantage of
the parallelism given by a graphics processing unit (GPU, a relative cheap
device providing a thousand or more primitive cores), as well as simultaneously
the parallelism from a multi-core CPU and more interestingly, from a cluster of
GPU-enabled nodes. Using CX1, the BWT of a short-read collection of up to 100
Gigabases can be constructed in less than 2 hours using a machine equipped with
a quad-core CPU and a GPU, or in about 43 minutes using a cluster with 4 such
machines (the speedup is almost linear after excluding the first 16 minutes for
loading the reads from the hard disk). The previously fastest tool BRC is
measured to take 12 hours to process 100 Gigabases on one machine; it is
non-trivial how BRC can be parallelized to take advantage a cluster of
machines, let alone GPUs.Comment: 11 page
Universal lossless source coding with the Burrows Wheeler transform
The Burrows Wheeler transform (1994) is a reversible sequence transformation used in a variety of practical lossless source-coding algorithms. In each, the BWT is followed by a lossless source code that attempts to exploit the natural ordering of the BWT coefficients. BWT-based compression schemes are widely touted as low-complexity algorithms giving lossless coding rates better than those of the Ziv-Lempel codes (commonly known as LZ'77 and LZ'78) and almost as good as those achieved by prediction by partial matching (PPM) algorithms. To date, the coding performance claims have been made primarily on the basis of experimental results. This work gives a theoretical evaluation of BWT-based coding. The main results of this theoretical evaluation include: (1) statistical characterizations of the BWT output on both finite strings and sequences of length n → ∞, (2) a variety of very simple new techniques for BWT-based lossless source coding, and (3) proofs of the universality and bounds on the rates of convergence of both new and existing BWT-based codes for finite-memory and stationary ergodic sources. The end result is a theoretical justification and validation of the experimentally derived conclusions: BWT-based lossless source codes achieve universal lossless coding performance that converges to the optimal coding performance more quickly than the rate of convergence observed in Ziv-Lempel style codes and, for some BWT-based codes, within a constant factor of the optimal rate of convergence for finite-memory source
Early pioneers to reversible computation
Reversible computing is one of the most intensively developing research areas nowadays. We present a survey of less known or forgotten papers to show that a transfer of ideas between different disciplines is possible
Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability
Previously referred to as `miraculous' in the scientific literature because
of its powerful properties and its wide application as optimal solution to the
problem of induction/inference, (approximations to) Algorithmic Probability
(AP) and the associated Universal Distribution are (or should be) of the
greatest importance in science. Here we investigate the emergence, the rates of
emergence and convergence, and the Coding-theorem like behaviour of AP in
Turing-subuniversal models of computation. We investigate empirical
distributions of computing models in the Chomsky hierarchy. We introduce
measures of algorithmic probability and algorithmic complexity based upon
resource-bounded computation, in contrast to previously thoroughly investigated
distributions produced from the output distribution of Turing machines. This
approach allows for numerical approximations to algorithmic
(Kolmogorov-Chaitin) complexity-based estimations at each of the levels of a
computational hierarchy. We demonstrate that all these estimations are
correlated in rank and that they converge both in rank and values as a function
of computational power, despite fundamental differences between computational
models. In the context of natural processes that operate below the Turing
universal level because of finite resources and physical degradation, the
investigation of natural biases stemming from algorithmic rules may shed light
on the distribution of outcomes. We show that up to 60\% of the
simplicity/complexity bias in distributions produced even by the weakest of the
computational models can be accounted for by Algorithmic Probability in its
approximation to the Universal Distribution.Comment: 27 pages main text, 39 pages including supplement. Online complexity
calculator: http://complexitycalculator.com
On the invertibility of finite state machines
Structural properties of finite state machines invertible with delay
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