Mathematical symbols and computing methods in high dimensional biomimetic informatics and their applications

High dimensional biomimetic informatics (HDBI) is a novel theory of informatics developed in recent years. Its primary object of research is points in high dimensional Euclidean space, and its exploratory and resolving procedures are based on simple geometric computations. However, the mathematical descriptions and computing of geometric objects are inconvenient because of the characters of geometry. With the increase of the dimension and the multiformity of geometric objects, these descriptions are more complicated and prolix especially in high dimensional space. In this paper, we give some definitions and mathematical symbols, and discuss some symbolic computing methods in high dimensional space systematically from the viewpoint of HDBI. With these methods, some multi-variables problems in high dimensional space can be solved easily. Three detailed algorithms are presented as examples to show the efficiency of our symbolic computing methods: the algorithm for judging the center of a circle given three points on this circle, the algorithm for judging whether two points are on the same side of a hyperplane, and the algorithm for judging whether a point is in a simplex constructed by points in high dimensional space. Two experiments in blurred image restoration and uneven lighting image correction are presented for all these algorithms to show their good behaviors.

High-Dimensional Space Geometrical Informatics and its applications to image restoration

With a view to solve the problems in modern information science, we put forward a new subject named High-Dimensional Space Geometrical Informatics (HDSGI). It builds a bridge between information science and point distribution analysis in high-dimensional space. A good many experimental results certified the correctness and availability of the theory of HDSGI. The proposed method for image restoration is an instance of its application in signal processing. Using an iterative "further blurring-debluring-further blurring" algorithm, the deblured image could be obtained.

High-Dimensional Space Geometrical Informatics and its applications to image restoration

With a view to solve the problems in modern information science, we put forward a new subject named High-Dimensional Space Geometrical Informatics (HDSGI). It builds a bridge between information science and point distribution analysis in high-dimensional space. A good many experimental results certified the correctness and availability of the theory of HDSGI. The proposed method for image restoration is an instance of its application in signal processing. Using an iterative "further blurring-debluring-further blurring" algorithm, the deblured image could be obtained.

Simulated pathogenic conformational switch regions matched well with the biochemical findings

Pathogenic conformational conversion is a general causation of many disease, such as transmissible spon- giform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabi- lizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.

Prediction and elucidation of the population dynamics of Microcystis spp. in Lake Dianchi (China) by means of artificial neural networks

Lake Dianchi is a shallow and turbid lake, located in Southwest China. Since 1985, Lake Dianchi has experienced severe cyanabacterial blooms (dominated by Microcystis spp.). In extreme cases, the algal cell densities have exceeded three billion cells per liter. To predict and elucidate the population dynamics ofMicrocystis spp. in Lake Dianchi, a neural network based model was developed. The correlation coefficient (R 2) between the predicted algal concentrations by the model and the observed values was 0.911. Sensitivity analysis was performed to clarify the algal dynamics to the changes of environmental factors. The results of a sensitivity analysis of the neural network model suggested that small increases in pH could cause significantly reduced algal abundance. Further investigations on raw data showed that the response of Microcystis spp. concentration to pH increase was dependent on algal biomass and pH level. When Microcystis spp. population and pH were moderate or low, the response of Microcystis spp. population would be more likely to be positive in Lake Dianchi; contrarily, Microcystis spp. population in Lake Dianchi would be more likely to show negative response to pH increase when Microcystis spp. population and pH were high. The paper concluded that the extremely high concentration of algal population and high pH could explain the distinctive response of Microcystis spp. population to +1 SD (standard deviation) pH increase in Lake Dianchi. And the paper also elucidated the algal dynamics to changes of other environmental factors. One SD increase of water temperature (WT) had strongest positive relationship with Microcystis spp. biomass. Chemical oxygen demand (COD) and total phosphorus (TP) had strong positive effect on Microcystis spp. abundance while total nitrogen (TN), biological oxygen demand in five days (BOD5), and dissolved oxygen had only weak relationship with Microcystis spp. concentration. And transparency (Tr) had moderate positive relationship with Microcystis spp. concentration.

Study of GaN epilayers growth on freestanding Si cantilevers

Five-micron thick freestanding Si cantilevers were fabricated on bulk Si (1 1 1) substrates with surface/bulk micromachining (SBM) process. Then 1-mu m thick GaN layers were deposited on the Si cantilevers by metal-organic chemical vapor deposition (MOCVD). Epilayers on cantilever areas were obtained crack-free, and the photoluminescence (PL) spectra verified the stress reduction and better material quality in these suspended parts of GaN. Back sides of the cantilevers were also covered with GaN layers, which prevented the composite beams from bending dramatically. This paper had proved the feasibility of integrating high-quality GaN epilayers with Si micromechanical structures to realize GaN-based micro electro-mechanical system (MEMS). (C) 2009 Elsevier Ltd. All rights reserved.

A Novel Geometric Algorithm for Blind Image Restoration Based on High-Dimensional Space

A novel geometric algorithm for blind image restoration is proposed in this paper, based on High-Dimensional Space Geometrical Informatics (HDSGI) theory. In this algorithm every image is considered as a point, and the location relationship of the points in high-dimensional space, i.e. the intrinsic relationship of images is analyzed. Then geometric technique of "blurring-blurring-deblurring" is adopted to get the deblurring images. Comparing with other existing algorithms like Wiener filter, super resolution image restoration etc., the experimental results show that the proposed algorithm could not only obtain better details of images but also reduces the computational complexity with less computing time. The novel algorithm probably shows a new direction for blind image restoration with promising perspective of applications.

Silicon: the promising material for phontonic integrated circuits platform

The development of optical network demands integrated arid multiple functionality modules to lowing cost and acquire highly reliability. Among the various contender materials to be photonic integrated circuits platform, silicon exhibits dominant characteristics and is the most promising platform materials. The paper compares the characteristics of some candidate materials with silicon and reviews recent progress in silicon based photonic integration technology. Tile challenges to silicon for optical integration for optical networking application arc also indicated.

Study on the forecast effects of PI method to the north and southwest China

In this paper, the codes of Pattern Informatics (PI) method put forward by Rundle et al. have been worked out according to their algorithm published, and the retrospective forecast of PI method to North China (28.0 degrees-42.0 degrees N, 108.0 degrees-125.0 degrees E) and to Southwest China (22.0 degrees-28.3 degrees N, 98.0 degrees-106.0 degrees E) has been tested. The results show that the hit rates in different regions show a great difference. In Southwest China, 32 earthquakes with M(L)5.0 or larger have occurred during the predicted time period 2000-2007, and 26 out of the 32 earthquakes occurred in or near the hot spots. In North China, the total number of M(L)5.0 or larger was 12 during the predicted time period 2000-2007, and only 3 out of the 12 earthquakes occurred in or near the hot spots. From our results, we hold that if the PI method could be applied to all kinds of regions, the parameters associated with time points and time windows should be chosen carefully to obtain the higher hit rate. We also found that the aftershocks in a strong earthquake sequence affect the PI results obviously. Copyright (c) 2009 John Wiley & Sons, Ltd.

Study on the forecast effects of PI method to the north and southwest China

In this paper, the codes of Pattern Informatics (PI) method put forward by Rundle et al. have been worked out according to their algorithm published, and the retrospective forecast of PI method to North China (28.0 degrees-42.0 degrees N, 108.0 degrees-125.0 degrees E) and to Southwest China (22.0 degrees-28.3 degrees N, 98.0 degrees-106.0 degrees E) has been tested. The results show that the hit rates in different regions show a great difference. In Southwest China, 32 earthquakes with M(L)5.0 or larger have occurred during the predicted time period 2000-2007, and 26 out of the 32 earthquakes occurred in or near the hot spots. In North China, the total number of M(L)5.0 or larger was 12 during the predicted time period 2000-2007, and only 3 out of the 12 earthquakes occurred in or near the hot spots. From our results, we hold that if the PI method could be applied to all kinds of regions, the parameters associated with time points and time windows should be chosen carefully to obtain the higher hit rate. We also found that the aftershocks in a strong earthquake sequence affect the PI results obviously. Copyright (c) 2009 John Wiley & Sons, Ltd.

incremental learning of triadic plsa for collaborative filtering

Beijing University of Technology (BJUT); Beijing Municipal Lab of Brain Informatics; Chinese Society of Radiology; National Natural Science Foundation of China (NSFC); State Administration of Foreign Experts Affairs

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.