Text Mining for Systems Biology and MetNet

The rapidly expanding volume of biological and biomedical literature motivates demand for more friendly access. Better automated mining of this literature can help find useful and desired citations and can extract new knowledge from the massive biological literaturome. The research objectives presented here, when met, will provide comprehensive text mining utilities within the MetNet (Metabolic Network Exchange) (Wurtele et al., 2007), platform to help biologists visualize, explore, and analyze the biological literaturome. The overarching research question to be addressed is how to automatically extract biomolecular interactions from numerous biomedical texts. Here are the specific aims of this work. 1. Research on the text empirics of interaction-indicating terms to find more clues to improve the current algorithm applied in PathBinder to more precisely judge whether biomolecular interaction descriptions are present in sentences from the biological literature. 2. Based on these research results, extract interacting biomolecule pairs from literature and use those pairs to construct a biomolecule interaction database and network. 3. Integrate biomolecular interaction-indicating term extraction into MetNet\u27s existing metabolomic network database. 4. Apply all of the above results in PathBinder software. 5. Quantitatively evaluate the success of algorithms developed based on the text empirics results. This work is expected to advance systems biology by answering scientific questions about biological text empirics, by contributing to the engineering task of building MetNet and key constituent subsystems of MetNet, and by supporting the MetNet project through selected maintenance tasks

The Capacity Region of the Source-Type Model for Secret Key and Private Key Generation

The problem of simultaneously generating a secret key (SK) and private key (PK) pair among three terminals via public discussion is investigated, in which each terminal observes a component of correlated sources. All three terminals are required to generate a common secret key concealed from an eavesdropper that has access to public discussion, while two designated terminals are required to generate an extra private key concealed from both the eavesdropper and the remaining terminal. An outer bound on the SK-PK capacity region was established in [1], and was shown to be achievable for one case. In this paper, achievable schemes are designed to achieve the outer bound for the remaining two cases, and hence the SK-PK capacity region is established in general. The main technique lies in the novel design of a random binning-joint decoding scheme that achieves the existing outer bound.Comment: 20 pages, 4 figure

Precise Phase Transition of Total Variation Minimization

Characterizing the phase transitions of convex optimizations in recovering structured signals or data is of central importance in compressed sensing, machine learning and statistics. The phase transitions of many convex optimization signal recovery methods such as $\ell_1$ minimization and nuclear norm minimization are well understood through recent years' research. However, rigorously characterizing the phase transition of total variation (TV) minimization in recovering sparse-gradient signal is still open. In this paper, we fully characterize the phase transition curve of the TV minimization. Our proof builds on Donoho, Johnstone and Montanari's conjectured phase transition curve for the TV approximate message passing algorithm (AMP), together with the linkage between the minmax Mean Square Error of a denoising problem and the high-dimensional convex geometry for TV minimization.Comment: 6 page

Development of Finger Touch Position Detection System Methods Using Single Camera

We propose a new image processing-based finger touch position detection sensing method using a reflected image reflected on the screen. Using single camera by image processing to detect touch position has several significant advantages: (1) Installation of camera becomes easily (2) This system can reduce the failure rate to realize maintenance free operation. (2) This approach enables easy attachment and low-cost touch sensing. The problem when using single camera is impossible to detect the depth of the finger from capture image. In order to solve this problem, we use the reflected image of the finger appears on the screen. Detecting the fingertip and the reflected image on the screen effectively, we enable to detect touch position only using single camera. In this paper, we provide concrete method to extract fingertip and reflected image, implementation details, results of evaluation experiment, and outline future works.The 2nd International Conference on Intelligent Systems and Image Processing 2014, Nishinippon Institute of Technology, Kitakyushu, Japan, September 26-29, 201

Image reconstruction method along electrical field centre lines using a modified mixed normalization model for electrical capacitance tomography

During the process of image reconstruction for electrical capacitance tomography (ECT), normalization of measured capacitance values is carried out with the low and high permittvity. The parallel normalization model (PM) and series normalization model (SM) are most commonly used. In recent years, using different combination methods such as electrical field centre line (EFCL) for PM and SM, several mixed normalization models (MM) obtained better description of the permittivity distribution of the two-phase media in pipe. In this paper, a new method of determining the weight factors of the PM and SM sensitivity matrix to form the MM sensitivity matrix is proposed. This weight factors are determined according to the minimum distance between the element and EFCL. Simulation and experimental test were carried out and the results show that both the accuracy and the shape fidelity can be improved obviously

Development of Finger Touch Position Detection System Methods Using Single Camera

The 2nd International Conference on Intelligent Systems and Image Processing 2014, Nishinippon Institute of Technology, Kitakyushu, Japan, September 26-29, 2014We propose a new image processing-based finger touch position detection sensing method using a reflected image reflected on the screen. Using single camera by image processing to detect touch position has several significant advantages: (1) Installation of camera becomes easily (2) This system can reduce the failure rate to realize maintenance free operation. (2) This approach enables easy attachment and low-cost touch sensing. The problem when using single camera is impossible to detect the depth of the finger from capture image. In order to solve this problem, we use the reflected image of the finger appears on the screen. Detecting the fingertip and the reflected image on the screen effectively, we enable to detect touch position only using single camera. In this paper, we provide concrete method to extract fingertip and reflected image, implementation details, results of evaluation experiment, and outline future works