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4,693
Reveal, A General Reverse Engineering Algorithm For Inference Of Genetic Network Architectures
, 1998
"... c biological data sets. The ability to adequately solve the inverse problem may enable indepth analysis of complex dynamic systems in biology and other fields. Binary models of genetic networks Virtually all molecular and cellular signaling processes involve several inputs and outputs, forming ..."
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Cited by 234 (5 self)
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c biological data sets. The ability to adequately solve the inverse problem may enable indepth analysis of complex dynamic systems in biology and other fields. Binary models of genetic networks Virtually all molecular and cellular signaling processes involve several inputs and outputs, forming a complex feedback network. The information for the construction and maintenance of this signaling system is stored in the genome. The DNA sequence codes for the structure and molecular dynamics of RNA and proteins, in turn determining biochemical recognition or signaling processes. The regulatory molecules that control the expression of genes are themselves the products of other genes. Effectively, genes turn each other on and off within a proximal genetic network of transcriptional regulators (Somogyi and Sniegoski, 1996). Furthermore, complex webs involving various intra and extracellular signaling systems on the one hand depend on the expression of the genes that encode them, and on the
Evaluating Probabilistic Queries over Imprecise Data
 In SIGMOD
, 2003
"... Sensors are often employed to monitor continuously changing entities like locations of moving objects and temperature. The sensor readings are reported to a database system, and are subsequently used to answer queries. Due to continuous changes in these values and limited resources (e.g., network ..."
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Cited by 219 (41 self)
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Sensors are often employed to monitor continuously changing entities like locations of moving objects and temperature. The sensor readings are reported to a database system, and are subsequently used to answer queries. Due to continuous changes in these values and limited resources (e.g., network bandwidth and battery power), the database may not be able to keep track of the actual values of the entities. Queries that use these old values may produce incorrect answers. However, if the degree of uncertainty between the actual data value and the database value is limited, one can place more confidence in the answers to the queries. More generally, query answers can be augmented with probabilistic guarantees of the validity of the answers. In this paper, we study probabilistic query evaluation based on uncertain data. A classification of queries is made based upon the nature of the result set. For each class, we develop algorithms for computing probabilistic answers, and provide efficient indexing and numeric solutions. We address the important issue of measuring the quality of the answers to these queries, and provide algorithms for efficiently pulling data from relevant sensors or moving objects in order to improve the quality of the executing queries. Extensive experiments
Sampling signals with finite rate of innovation
 IEEE Transactions on Signal Processing
, 2002
"... Abstract—Consider classes of signals that have a finite number of degrees of freedom per unit of time and call this number the rate of innovation. Examples of signals with a finite rate of innovation include streams of Diracs (e.g., the Poisson process), nonuniform splines, and piecewise polynomials ..."
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Cited by 218 (51 self)
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Abstract—Consider classes of signals that have a finite number of degrees of freedom per unit of time and call this number the rate of innovation. Examples of signals with a finite rate of innovation include streams of Diracs (e.g., the Poisson process), nonuniform splines, and piecewise polynomials. Even though these signals are not bandlimited, we show that they can be sampled uniformly at (or above) the rate of innovation using an appropriate kernel and then be perfectly reconstructed. Thus, we prove sampling theorems for classes of signals and kernels that generalize the classic “bandlimited and sinc kernel ” case. In particular, we show how to sample and reconstruct periodic and finitelength streams of Diracs, nonuniform splines, and piecewise polynomials using sinc and Gaussian kernels. For infinitelength signals with finite local rate of innovation, we show local sampling and reconstruction based on spline kernels. The key in all constructions is to identify the innovative part of a signal (e.g., time instants and weights of Diracs) using an annihilating or locator filter: a device well known in spectral analysis and errorcorrection coding. This leads to standard computational procedures for solving the sampling problem, which we show through experimental results. Applications of these new sampling results can be found in signal processing, communications systems, and biological systems. Index Terms—Analogtodigital conversion, annihilating filters, generalized sampling, nonbandlimited signals, nonuniform splines, piecewise polynomials, poisson processes, sampling. I.
Using mutual information for selecting features in supervised neural net learning
 IEEE Transactions on Neural Networks
, 1994
"... AbstractThis paper investigates the application of the mutual infor “ criterion to evaluate a set of candidate features and to select an informative subset to be used as input data for a neural network classifier. Because the mutual information measures arbitrary dependencies between random variabl ..."
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Cited by 198 (1 self)
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AbstractThis paper investigates the application of the mutual infor “ criterion to evaluate a set of candidate features and to select an informative subset to be used as input data for a neural network classifier. Because the mutual information measures arbitrary dependencies between random variables, it is suitable for assessing the “information content ” of features in complex classification tasks, where methods bases on linear relations (like the correlation) are prone to mistakes. The fact that the mutual information is independent of the coordinates chosen permits a robust estimation. Nonetheless, the use of the mutual information for tasks characterized by high input dimensionality requires suitable approximations because of the prohibitive demands on computation and samples. An algorithm is proposed that is based on a “greedy ” selection of the features and that takes both the mutual information with respect to the output class and with respect to the alreadyselected features into account. Finally the results of a series of experiments are discussed. Index TermsFeature extraction, neural network pruning, dimensionality reduction, mutual information, supervised learning,
An InformationTheoretic Model for Steganography
, 1998
"... An informationtheoretic model for steganography with passive adversaries is proposed. The adversary's task of distinguishing between an innocentcover message C and a modified message S containing a secret part is interpreted as a hypothesis testing problem. The security of a steganographic system i ..."
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Cited by 194 (3 self)
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An informationtheoretic model for steganography with passive adversaries is proposed. The adversary's task of distinguishing between an innocentcover message C and a modified message S containing a secret part is interpreted as a hypothesis testing problem. The security of a steganographic system is quantified in terms of the relative entropy (or discrimination) between PC and PS . Several secure steganographic schemes are presented in this model; one of them is a universal information hiding scheme based on universal data compression techniques that requires no knowledge of the covertext statistics.
The complexity of finite objects and the development of the concepts of information and randomness by means of the theory of algorithms
 Russian Math. Surveys
, 1970
"... In 1964 Kolmogorov introduced the concept of the complexity of a finite object (for instance, the words in a certain alphabet). He defined complexity as the minimum number of binary signs containing all the information about a given object that are sufficient for its recovery (decoding). This defini ..."
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Cited by 189 (1 self)
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In 1964 Kolmogorov introduced the concept of the complexity of a finite object (for instance, the words in a certain alphabet). He defined complexity as the minimum number of binary signs containing all the information about a given object that are sufficient for its recovery (decoding). This definition depends essentially on the method of decoding. However, by means of the general theory of algorithms, Kolmogorov was able to give an invariant (universal) definition of complexity. Related concepts were investigated by Solotionoff (U.S.A.) and Markov. Using the concept of complexity, Kolmogorov gave definitions of the quantity of information in finite objects and of the concept of a random sequence (which was then defined more precisely by MartinLof). Afterwards, this circle of questions developed rapidly. In particular, an interesting development took place of the ideas of Markov on the application of the concept of complexity to the study of quantitative questions in the theory of algorithms. The present article is a survey of the fundamental results connected with the brief remarks above.
Expander Graphs and their Applications
, 2003
"... Contents 1 The Magical Mystery Tour 7 1.1 Some Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.1.1 Hardness results for linear transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.1.2 Error Correcting Codes . . . . . . . ..."
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Cited by 188 (5 self)
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Contents 1 The Magical Mystery Tour 7 1.1 Some Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.1.1 Hardness results for linear transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.1.2 Error Correcting Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.1.3 Derandomizing Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.2 Magical Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 1.2.1 A Super Concentrator with O(n) edges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1.2.2 Error Correcting Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1.2.3 Derandomizing Random Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 1.3 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
How to Recycle Random Bits
, 1989
"... We show that modified versions of the linear congruential generator and the shift register generator are provably good for amplifying the correctness of a probabilistic algorithm. More precisely, if r random bits are needed for a BPP algorithm to be correct with probability at least 2=3, then O(r + ..."
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Cited by 183 (12 self)
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We show that modified versions of the linear congruential generator and the shift register generator are provably good for amplifying the correctness of a probabilistic algorithm. More precisely, if r random bits are needed for a BPP algorithm to be correct with probability at least 2=3, then O(r + k 2 ) bits are needed to improve this probability to 1 \Gamma 2 \Gammak . We also present a different pseudorandom generator that is optimal, up to a constant factor, in this regard: it uses only O(r + k) bits to improve the probability to 1 \Gamma 2 \Gammak . This generator is based on random walks on expanders. Our results do not depend on any unproven assumptions. Next we show that our modified versions of the shift register and linear congruential generators can be used to sample from distributions using, in the limit, the informationtheoretic lower bound on random bits. 1. Introduction Randomness plays a vital role in almost all areas of computer science, both in theory and in...
Information Retrieval Interaction
, 1992
"... this document, text or image about?' Gradually moving from the left to the right in Figure 3.1, different understandings of this concept evolve ..."
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Cited by 181 (6 self)
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this document, text or image about?' Gradually moving from the left to the right in Figure 3.1, different understandings of this concept evolve
Computational Models of Sensorimotor Integration
 SCIENCE
, 1997
"... The sensorimotor integration system can be viewed as an observer attempting to estimate its own state and the state of the environment by integrating multiple sources of information. We describe a computational framework capturing this notion, and some specific models of integration and adaptati ..."
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Cited by 178 (10 self)
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The sensorimotor integration system can be viewed as an observer attempting to estimate its own state and the state of the environment by integrating multiple sources of information. We describe a computational framework capturing this notion, and some specific models of integration and adaptation that result from it. Psychophysical results from two sensorimotor systems, subserving the integration and adaptation of visuoauditory maps, and estimation of the state of the hand during arm movements, are presented and analyzed within this framework. These results suggest that: (1) Spatial information from visual and auditory systems is integrated so as to reduce the variance in localization. (2) The effects of a remapping in the relation between visual and auditory space can be predicted from a simple learning rule. (3) The temporal propagation of errors in estimating the hand's state is captured by a linear dynamic observer, providing evidence for the existence of an intern...