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- James C Liao, Riccardo Boscolo, Young-Lyeol Yang, Linh My Tran, Chiara Sabatti, Vwani P Roychowdhury
- Proceedings of the National Academy of Sciences…
- 2003

High-dimensional data sets generated by high-throughput technologies, such as DNA microarray, are often the outputs of complex networked systems driven by hidden regulatory signals. Traditional statistical methods for computing low-dimensional or hidden representations of these data sets, such as principal component analysis and independent component… (More)

- Riccardo Boscolo, Hong Pan, Vwani P. Roychowdhury
- IEEE Transactions on Neural Networks
- 2004

In this paper, we introduce a novel independent component analysis (ICA) algorithm, which is truly blind to the particular underlying distribution of the mixed signals. Using a nonparametric kernel density estimation technique, the algorithm performs simultaneously the estimation of the unknown probability density functions of the source signals and the… (More)

- Katy C Kao, Young-Lyeol Yang, Riccardo Boscolo, Chiara Sabatti, Vwani Roychowdhury, James C Liao
- Proceedings of the National Academy of Sciences…
- 2004

Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators bind to or dissociate from DNA, respectively, and modulate transcriptional activities on particular promoters. Traditionally, individual reporter genes have… (More)

- Riccardo Boscolo, Chiara Sabatti, James C. Liao, Vwani P. Roychowdhury
- IEEE/ACM Transactions on Computational Biology…
- 2005

The authors recently introduced a framework, named Network Component Analysis (NCA), for the reconstruction of the dynamics of transcriptional regulators' activities from gene expression assays. The original formulation had certain shortcomings that limited NCA's application to a wide class of network dynamics reconstruction problems, either because of… (More)

We introduce a novel approach to the blind signal separation (BSS) problem that is capable of jointly estimating the probability density function (pdf) of the source signals and the unmixing matrix. We demonstrate that, using a kernel density estimation based Projection Pursuit (PP) algorithm , it is possible to extract, from instantaneous mixtures ,… (More)

- Riccardo Boscolo, Hong Pan, Vwani P. Roychowdhury
- ICANN
- 2002

A large number of Independent Component Analysis (ICA) algorithms are based on the minimization of the statistical mutual information between the reconstructed signals, in order to achieve the source separation. While it has been demonstrated that a global minimum of such cost function will result in the separation of the statistically independent sources,… (More)

- Riccardo Boscolo, James C. Liao, Vwani P. Roychowdhury
- IEEE/ACM Transactions on Computational Biology…
- 2008

In this article, we introduce an exploratory framework for learning patterns of conditional co-expression in gene expression data. The main idea behind the proposed approach consists of estimating how the information content shared by a set of M nodes in a network (where each node is associated to an expression profile) varies upon conditioning on a set of… (More)

The authors recently introduced a framework, named Network Component Analysis (NCA), for the reconstruction of the dynamics of transcriptional regulators activities from gene expression assays. In this paper, our goal is to characterize NCA as a general purpose network and signal reconstruction technique: given only the noisy output signals of a… (More)

- Qian Zhong, Riccardo Boscolo, Timothy S. Gardner, Vwani P. Roychowdhury
- 2007 IEEE Symposium on Computational Intelligence…
- 2007

Determining transcriptional regulatory networks has been one of the most important goals in the field of functional genomics. Despite the recent advances in experimental techniques, complementary computational techniques have lagged behind. We introduce a novel computational methodology that uses DNA microarray data and known regulatory interactions to… (More)