By Topic

Information Theory, IEEE Transactions on

Issue 2 • Date Feb. 2010

Filter Results

Displaying Results 1 - 25 of 27
  • Table of contents

    Publication Year: 2010 , Page(s): C1 - C4
    Save to Project icon | Request Permissions | PDF file iconPDF (45 KB)  
    Freely Available from IEEE
  • IEEE Transactions on Information Theory publication information

    Publication Year: 2010 , Page(s): C2
    Save to Project icon | Request Permissions | PDF file iconPDF (41 KB)  
    Freely Available from IEEE
  • Introduction to the Special Issue on Information Theory in Molecular Biology and Neuroscience

    Publication Year: 2010 , Page(s): 649 - 652
    Cited by:  Papers (4)
    Save to Project icon | Request Permissions | PDF file iconPDF (811 KB) |  | HTML iconHTML  
    Freely Available from IEEE
  • Information Theory and Neural Information Processing

    Publication Year: 2010 , Page(s): 653 - 666
    Cited by:  Papers (9)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (290 KB) |  | HTML iconHTML  

    Neuroscientists want to quantify how well neurons, individually and collectively, process information and encode the result in their outputs. We demonstrate that while classic information theory demarcates optimal performance boundaries, it does not provide results that would be useful in analyzing an existing system about which little is known (such as the brain). In the classical vein, non-Poiss... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Biological Information as Set-Based Complexity

    Publication Year: 2010 , Page(s): 667 - 677
    Cited by:  Papers (8)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (420 KB) |  | HTML iconHTML  

    The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically sign... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Heredity as an Encoded Communication Process

    Publication Year: 2010 , Page(s): 678 - 687
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (161 KB) |  | HTML iconHTML  

    Heredity is relevant to information theory as a communication process. The conservation of genomes over intervals at the geological timescale and the existence of mutations at shorter intervals can be conciliated assuming that genomes possess intrinsic error-correction codes. The better conservation of old parts of genomes leads to assume that these codes are organized as a nested system set up du... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Limits of Performance of Quantitative Polymerase Chain Reaction Systems

    Publication Year: 2010 , Page(s): 688 - 695
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (402 KB) |  | HTML iconHTML  

    Estimation of the DNA copy number in a given biological sample is an important problem in genomics. Quantitative polymerase chain reaction (qPCR) systems detect the target DNA molecules by amplifying their number through a series of thermal cycles and measuring the amount of created amplicons in each cycle. Ideally, the number of target molecules doubles at the end of each cycle. However, in pract... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Compression of Whole Genome Alignments

    Publication Year: 2010 , Page(s): 696 - 705
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (409 KB) |  | HTML iconHTML  

    Recent advances in DNA sequencing technology have caused an exponential growth of publicly available genomic sequence data. A particularly voluminous, frequently used static data set are whole genome alignments. The first lossless compression algorithm for such data sets based on well-established statistical evolutionary models and prediction techniques from lossless binary image compression is in... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Compressed Genotyping

    Publication Year: 2010 , Page(s): 706 - 723
    Cited by:  Papers (9)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (684 KB) |  | HTML iconHTML  

    Over the past three decades we have steadily increased our knowledge on the genetic basis of many severe disorders. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, mainly due to the relatively tedious and expensive process of genotyping. Since the genetic variations that underlie the disorders are relatively rare in the population, they can be tho... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Joint Base-Calling of Two DNA Sequences With Factor Graphs

    Publication Year: 2010 , Page(s): 724 - 733
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (248 KB) |  | HTML iconHTML  

    Automated estimation of DNA base-sequences is an important step in genomics and in many other emerging fields in biological and medical sciences. Current automated sequencers process single strands only. To improve the utility of existing technologies, we propose to mix two independent strands prior to electrophoresis, and base-call jointly by applying the sum-product algorithm on factor graphs. W... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Computational Detection of Transcription Factor Binding Sites Through Differential Rényi Entropy

    Publication Year: 2010 , Page(s): 734 - 741
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (799 KB) |  | HTML iconHTML  

    Regulatory sequence detection is a critical facet for understanding the cell mechanisms in order to coordinate the response to stimuli. Protein synthesis involves the binding of a transcription factor to specific sequences in a process related to the gene expression initiation. A characteristic of this binding process is that the same factor binds with different sequences placed along all genome. ... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Belief Propagation Estimation of Protein and Domain Interactions Using the Sum–Product Algorithm

    Publication Year: 2010 , Page(s): 742 - 755
    Cited by:  Papers (4)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1391 KB) |  | HTML iconHTML  

    In this paper, a novel framework is presented to estimate protein-protein interactions (PPIs) and domain-domain interactions (DDIs) based on a belief propagation estimation method that efficiently computes interaction probabilities. Experimental interactions, domain architecture, and gene ontology (GO) annotations are used to create a factor graph representation of the joint probability distributi... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Rapid Sequence Homology Assessment by Subsampling the Genome Space Using Difference Sets

    Publication Year: 2010 , Page(s): 756 - 770
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (426 KB) |  | HTML iconHTML  

    Availability of DNA data is growing roughly at the rate specified by Moore's law. In many molecular biology applications this data must be compared with a reference sequence, either to establish similarity of genomes or to identify functionally homologous subsequences. Current approaches based on pair-wise sequence alignments are computationally expensive and often data dependent. To ameliorate th... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • The Minimum Entropy Mapping Spectrum of a DNA Sequence

    Publication Year: 2010 , Page(s): 771 - 783
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (973 KB) |  | HTML iconHTML  

    Periodicities in a DNA sequence contain information about its function and structure. Frequency analysis can be used to reveal such periodicities. A definition of spectrum for DNA sequences is proposed, based on an entropy minimization criterion. It is shown that the properties of the proposed spectrum are those expected from the spectrum of a symbolic sequence. Applications to simulated and exper... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Joint Sampling Distribution Between Actual and Estimated Classification Errors for Linear Discriminant Analysis

    Publication Year: 2010 , Page(s): 784 - 804
    Cited by:  Papers (19)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1769 KB) |  | HTML iconHTML  

    Error estimation must be used to find the accuracy of a designed classifier, an issue that is critical in biomarker discovery for disease diagnosis and prognosis in genomics and proteomics. This paper presents, for what is believed to be the first time, the analytical formulation for the joint sampling distribution of the actual and estimated errors of a classification rule. The analysis presented... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Periodic Orbits and Equilibria in Glass Models for Gene Regulatory Networks

    Publication Year: 2010 , Page(s): 805 - 820
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (672 KB) |  | HTML iconHTML  

    Glass models are frequently used to model gene regulatory networks. A distinct feature of the Glass model is that its dynamics can be formalized as paths through multi-dimensional binary hypercubes. In this paper, we report a broad range of results about Glass models that have been obtained by computing the binary codes that correspond to the hypercube paths. Specifically, we propose algorithmic m... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Population Encoding With Hodgkin–Huxley Neurons

    Publication Year: 2010 , Page(s): 821 - 837
    Cited by:  Papers (5)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (495 KB) |  | HTML iconHTML  

    The recovery of (weak) stimuli encoded with a population of Hodgkin-Huxley neurons is investigated. In the absence of a stimulus, the Hodgkin-Huxley neurons are assumed to be tonically spiking. The methodology employed calls for 1) finding an input-output (I/O) equivalent description of the Hodgkin-Huxley neuron and 2) devising a recovery algorithm for stimuli encoded with the I/O equivalent neuro... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Capacity Analysis for Integrate-and-Fire Neurons With Descending Action Potential Thresholds

    Publication Year: 2010 , Page(s): 838 - 851
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (941 KB) |  | HTML iconHTML  

    Understanding how a biological neuron works has been a major goal in neuroscience. Under the Poisson-excitation assumption, results from earlier study by Suksompong and Berger on the timing jitter in the leaky integrate-and-fire (LIF) model of neurons are used to determine families of neural thresholding functions that are appropriate in certain interesting senses. Next, the neuron is treated as a... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • A Mathematical Theory of Energy Efficient Neural Computation and Communication

    Publication Year: 2010 , Page(s): 852 - 874
    Cited by:  Papers (7)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (680 KB) |  | HTML iconHTML  

    A neuroscience-based mathematical model of how a neuron stochastically processes data and communicates information is introduced and analyzed. Call the neuron in question 'neuron j", or just "j". The information j transmits approximately describes the time-varying intensity of the excitation j is continuously experiencing from neural spike trains delivered to its synapses by thousands of other neu... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Synergistic Coding by Cortical Neural Ensembles

    Publication Year: 2010 , Page(s): 875 - 889
    Cited by:  Papers (4)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1578 KB) |  | HTML iconHTML  

    An essential step towards understanding how the brain orchestrates information processing at the cellular and population levels is to simultaneously observe the spiking activity of cortical neurons that mediate perception, learning, and motor processing. In this paper, we formulate an information theoretic approach to determine whether cooperation among neurons may constitute a governing mechanism... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Anthropic Correction of Information Estimates and Its Application to Neural Coding

    Publication Year: 2010 , Page(s): 890 - 900
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (566 KB) |  | HTML iconHTML  

    Information theory has been used as an organizing principle in neuroscience for several decades. Estimates of the mutual information (MI) between signals acquired in neurophysiological experiments are believed to yield insights into the structure of the underlying information processing architectures. With the pervasive availability of recordings from many neurons, several information and redundan... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Symmetry Breaking in Soft Clustering Decoding of Neural Codes

    Publication Year: 2010 , Page(s): 901 - 927
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1407 KB) |  | HTML iconHTML  

    Information-based distortion methods have been used successfully in the analysis of neural coding problems. These approaches allow the discovery of neural symbols and the corresponding stimulus space of a neuron or neural ensemble quantitatively, while making few assumptions about the nature of either the code or of relevant stimulus features. The neural codebook is derived by quantizing sensory s... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • A Channel Model for Inferring the Optimal Number of Electrodes for Future Cochlear Implants

    Publication Year: 2010 , Page(s): 928 - 940
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (584 KB) |  | HTML iconHTML  

    Cochlear implants, also known as bionic ears, are surgically implanted biomedical devices that can provide hearing to some deaf people by direct electrical stimulation of the auditory nerve. A crucial question for the design of future cochlear implants is that of how many electrodes might achieve optimal hearing performance in patients. It is efficient to avoid using more electrodes if this does n... View full abstract»

    Full text access may be available. Click article title to sign in or learn about subscription options.
  • Special issue of the IEEE Transactions on Information Theory Facets of Coding Theory: From Algorithms to Networks Tribute to the Work of Ralf Koetter

    Publication Year: 2010 , Page(s): 941
    Save to Project icon | Request Permissions | PDF file iconPDF (132 KB)  
    Freely Available from IEEE
  • Special issue of the IEEE Transactions on Information Theory on Interference Networks

    Publication Year: 2010 , Page(s): 942
    Save to Project icon | Request Permissions | PDF file iconPDF (528 KB)  
    Freely Available from IEEE

Aims & Scope

IEEE Transactions on Information Theory publishes papers concerned with the transmission, processing, and utilization of information.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief
Frank R. Kschischang

Department of Electrical and Computer Engineering