learning gene regulatory networks from only positive and unlabeled data

... each gene from the α data set, the CDC28 data set, and the integrated data sets The increase of the lower bound, when the integrated data sets were used, supports the advantages of Bayesian data ... time-series data from a single experiment, we aim at uncovering the underlying gene regulatory networks This is equivalent to learning the structure of the DBNs In specific, if we can determine that genes ... that genes and are the parents of gene in the DBNs, there will be directed links going from gene and to gene in the uncovered GRNs Second, we are also concerned with integrating two data sets...

Ngày tải lên: 22/06/2014, 19:20

Ngày tải lên: 14/08/2014, 16:21

... restrictions and 2) the same meaning can be expressed using a number of different verbs In contrast and alike (Friedman et al., 2001), we instead set out to handle only one specific biological problem and, ... relevant for the gene transcription domain, e.g [nxgene The GAL4 gene ] Relation chunking Relations between entities are recognized, e.g The expression of the cytochrome genes CYC1 and CYC7 is controlled ... Output and visualization Information is gathered from the recognised patterns and transformed into pre-defined records From the example in L4 we extract that HAP1 regulates the expression of CYC1 and...

Ngày tải lên: 31/03/2014, 03:20

Ngày tải lên: 13/08/2014, 16:20

Ngày tải lên: 04/10/2015, 16:03

... learning starting with positive and unlabeled examples Proposed Algorithm At the beginning of our algorithm, the system is provided with positive examples and unlabeled examples The positive examples ... select several example data sets from Japanese blog data crawled from Web Table shows the ambiguous words and each ambiguous senses Positive sense product name (TV) Percentage of positive sense 31.1% ... human and added to the positive dataset P or the negative dataset N according to the sense of d The above steps are repeated until dataset reaches the predefined desirable size number of initial positive...

Ngày tải lên: 23/03/2014, 17:20

... geometry, and statistics for the reverse engineering of the dynamics, as well as the gene dependencies, in biochemical regulatory networks from experimental data The algorithm can handle large regulatory ... multistate gene regulatory networks from limited and noisy data The novelty of our approach is two-fold First, the stochastic model we construct is based on all minimal models in the model space and ... switch-on data is lower than that of TSNI, it is still well above 0.40 and thus it is better than random Conclusion Gene regulatory networks are structured as inter-connected entities and their...

Ngày tải lên: 21/06/2014, 03:20

... 100 and κ = 4, and even then the needed time was still less than second per gene 3.1.2 Canalizing Networks Next, we impose the canalizing restriction and generate κ networks from C20 The general ... probabilistic gene regulatory networks, ” Bioinformatics, vol 20, no 17, pp 2918–2927, 2004 [10] W Zhao, E Serpedin, and E R Dougherty, “Inferring gene regulatory networks from time series data using ... Boolean networks, we consider sample sizes ranging from 20 to 100, θ ∈ {0.1, 0.2, 0.3}, and κ ∈ {1, 2, 3, 4} We test each of the (n, θ, κ) combinations on 30 randomly generated networks κ from Gκ and...

Ngày tải lên: 21/06/2014, 22:20

... the required data for our performance tests Quackenbush [19] pointed out, that the use of artificially generated data can help to provide an understanding of how data are handled and interpreted ... inhibition of gene j on gene i depending on its sign Data For the comparative study of reverse engineering methods we generated a large amount of expression profiles from various GRNs and different datasets ... different networks with four different sizes and six different noise levels, that is, in total of 120 datasets In case of cv and network size, values were averaged over results from 100 and 150 datasets,...

Ngày tải lên: 22/06/2014, 00:20

... represents a broad family of networks and a simpler model that represents a smaller class of networks Given a reference network from the complex model and a sampled trajectory from it, we want to estimate ... (t) and g(t), where the only information available consists of two samples, {a1 , , am } and {b1 , , br }, for f and g, respectively, both cumulative distributions F(x) and G(x) need only ... called a (discrete) transcriptional regulatory system (tRS) We generate networks using this model and a fixed set θ of parameters We call these networks reference networks A reference network is identified...

Ngày tải lên: 22/06/2014, 19:20

Ngày tải lên: 11/08/2014, 12:20

Ngày tải lên: 14/09/2015, 09:05

Ngày tải lên: 10/09/2015, 14:05

... alignment as a case study 5.1 Data We have two kinds of training data from general domain: Labeled Data (LD) and Unlabeled Data (UD) The Chinese sentences in the data are automatically segmented ... labeled data and the unlabeled data With the labeled data, we train a supervised model by directly estimating the parameters in the IBM model as described in section With the unlabeled data, we ... set RT for the training data; The reference sets RL and RU ( R L , R U ⊆ RT ) for the labeled data S L and the unlabeled data S U respectively, where S T = S U ∪ S L and S U ∩ S L = NULL ; A...

Ngày tải lên: 08/03/2014, 02:21

Ngày tải lên: 12/08/2014, 17:20

... [14–17] So far, only three Fe -only nitrogenases have been genetically (as anf systems) as well as biochemically identified and characterized These are the enzymes of Azotobacter vinelandii [5,6], ... isolated and purified as intact and catalytically active proteins, and (b) that the FeFe protein definitely does not contain an iron–molybdenum cofactor (FeMoco), but a clearly wellfunctioning Fe -only ... following approach: the FeFe and the MoFe proteins were isolated from the same organism, samples were prepared according to the same procedures and subsequently characterized and compared by EPR spectroscopy,...

Ngày tải lên: 18/03/2014, 01:20

... were expressed in and purified from E coli preparations, and each of the proteins was bound to Affigel 10 TFIIH and holoRNAPII were purified from Sc pombe whole-cell extracts and bound to IgG-Sepharose ... strand of the )35 to +6 region of Ad-MLP (B) EMSAs used 32P-labelled single-stranded DNA from the coding strand of the )35 to +6 region of Ad-MLP as the probe The double- (dsDNA) and single-stranded ... to enhance MyoD-dependent activation of transcription from muscle gene promoters [17] and binding of the proto-oncogene and transcriptional regulatory protein p53 to DNA [18] Furthermore, human...

Ngày tải lên: 23/03/2014, 07:20

... transcription and its interaction with positive regulatory factor (RLjunRP) in normal rat liver The positive regulatory factor interacting with this region was purified to homogeneity and the cDNA ... understanding of regulation of c-jun expression in quiescent rat liver We have identified a positive regulatory factor from normal rat liver that binds to the region )148 to )124 of c-jun and stimulates ... Transient transfection and reporter gene assay Promoter constructs Green fluorescent protein (GFP) does not require any exogenous substrate and cofactors for its fluorescence and its expression can...

Ngày tải lên: 23/03/2014, 20:22

... of Short-Term and Long-Term Memories 2.3.3 Content-Addressable and Associative Memory Human Learning and Adaptation 2.4.1 Types of Human Learning 2.4.2 Supervised and Unsupervised Learning Mechanisms ... Static and Dynamic Neural Networks This page intentionally left blank Static and Dynamic Neural Networks From Fundamentals to Advanced Theory Madan M Gupta, Liang Jin, and Noriyasu Homma ... Backpropagation Learning Concluding Remarks Problems ix 85 88 94 95 STATIC NEURAL NETWORKS Multilayered Feedforward Neural Networks (MFNNs) and Backpropagation Learning Algorithms 4.1 Two-Layered Neural Networks...

Ngày tải lên: 03/06/2014, 02:13

... immunobiology and role in immunomodulation and tissue regeneration Cytotherapy 2009, 11:377-391 doi:10.1186/1479-5876-8-31 Cite this article as: Stroncek and Puri: Cell and gene therapies: moving from ... and hypothesis We welcome contributions from all those participating in this field; clinicians, scientists, and engineers from academia, industry and the regulatory community Author details Department ... Cell and Gene Therapy Section is to advance this field by reporting the results of translational medicine studies and by being a forum for the exchange and discussion of new information, ideas and...

Ngày tải lên: 18/06/2014, 16:20