Exact reconstruction of gene regulatory networks using compressive sensing.

BackgroundWe consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity. We assume that the network is sparse, meaning the connectivity among genes is much less than full connectivity. We develop a method for network reconstruction based on compressive sensing, which takes advantage of the network's sparseness.ResultsFor the case in which all genes are accessible for measurement, and there is no measurement noise, we show that our method can be used to exactly reconstruct the network. For the more general problem, in which hidden genes exist and all measurements are contaminated by noise, we show that our method leads to reliable reconstruction. In both cases, coherence of the model is used to assess the ability to reconstruct the network and to design new experiments. We demonstrate that it is possible to use the coherence distribution to guide biological experiment design effectively. By collecting a more informative dataset, the proposed method helps reduce the cost of experiments. For each problem, a set of numerical examples is presented.ConclusionsThe method provides a guarantee on how well the inferred graph structure represents the underlying system, reveals deficiencies in the data and model, and suggests experimental directions to remedy the deficiencies

Data based identification and prediction of nonlinear and complex dynamical systems

We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin

An agent-driven semantical identifier using radial basis neural networks and reinforcement learning

Due to the huge availability of documents in digital form, and the deception possibility raise bound to the essence of digital documents and the way they are spread, the authorship attribution problem has constantly increased its relevance. Nowadays, authorship attribution,for both information retrieval and analysis, has gained great importance in the context of security, trust and copyright preservation. This work proposes an innovative multi-agent driven machine learning technique that has been developed for authorship attribution. By means of a preprocessing for word-grouping and time-period related analysis of the common lexicon, we determine a bias reference level for the recurrence frequency of the words within analysed texts, and then train a Radial Basis Neural Networks (RBPNN)-based classifier to identify the correct author. The main advantage of the proposed approach lies in the generality of the semantic analysis, which can be applied to different contexts and lexical domains, without requiring any modification. Moreover, the proposed system is able to incorporate an external input, meant to tune the classifier, and then self-adjust by means of continuous learning reinforcement.Comment: Published on: Proceedings of the XV Workshop "Dagli Oggetti agli Agenti" (WOA 2014), Catania, Italy, Sepember. 25-26, 201

Learning to automatically detect features for mobile robots using second-order Hidden Markov Models

In this paper, we propose a new method based on Hidden Markov Models to interpret temporal sequences of sensor data from mobile robots to automatically detect features. Hidden Markov Models have been used for a long time in pattern recognition, especially in speech recognition. Their main advantages over other methods (such as neural networks) are their ability to model noisy temporal signals of variable length. We show in this paper that this approach is well suited for interpretation of temporal sequences of mobile-robot sensor data. We present two distinct experiments and results: the first one in an indoor environment where a mobile robot learns to detect features like open doors or T-intersections, the second one in an outdoor environment where a different mobile robot has to identify situations like climbing a hill or crossing a rock.Comment: 200