14172606
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature
MOTIVATION
The importance of chemical compounds has been emphasized more in molecular biology, and 'chemical genomics' has attracted a great deal of attention in recent years. Thus an important issue in current molecular biology is to identify biological-related chemical compounds (more specifically, drugs) and genes. Co-occurrence of biological entities in the literature is a simple, comprehensive and popular technique to find the association of these entities. Our focus is to mine implicit 'chemical compound and gene' relations from the co-occurrence in the literature.


RESULTS
We propose a probabilistic model, called the mixture aspect model (MAM), and an algorithm for estimating its parameters to efficiently handle different types of co-occurrence datasets at once. We examined the performance of our approach not only by a cross-validation using the data generated from the MEDLINE records but also by a test using an independent human-curated dataset of the relationships between chemical compounds and genes in the ChEBI database. We performed experimentation on three different types of co-occurrence datasets (i.e. compound-gene, gene-gene and compound-compound co-occurrences) in both cases. Experimental results have shown that MAM trained by all datasets outperformed any simple model trained by other combinations of datasets with the difference being statistically significant in all cases. In particular, we found that incorporating compound-compound co-occurrences is the most effective in improving the predictive performance. We finally computed the likelihoods of all unknown compound-gene (more specifically, drug-gene) pairs using our approach and selected the top 20 pairs according to the likelihoods. We validated them from biological, medical and pharmaceutical viewpoints.
6739132
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
MOTIVATION
Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that MHC molecules can be classified into supertypes in terms of peptide-binding specificities. Therefore, we first give a method for reducing the redundancy in a given dataset based on information entropy, then present a novel approach for prediction by learning a predictive model from a dataset of binders for not only the molecule of interest but also for other MHC molecules.


RESULTS
We experimented on the HLA-A family with the binding nonamers of A1 supertype (HLA-A*0101, A*2601, A*2902, A*3002), A2 supertype (A*0201, A*0202, A*0203, A*0206, A*6802), A3 supertype (A*0301, A*1101, A*3101, A*3301, A*6801) and A24 supertype (A*2301 and A*2402), whose data were collected from six publicly available peptide databases and two private sources. The results show that our approach significantly improves the prediction accuracy of peptides that bind a specific HLA molecule when we combine binding data of HLA molecules in the same supertype. Our approach can thus be used to help find new binders for MHC molecules.
36453049
Parallel Models and Job Characterization for System Scheduling
In this work, we study job characterization in multi-programmed multiprocessor system by taking into consideration the parallel job models. We first introduce an example to illustrate the issues involved. Then we focus on two popular system scheduling policies: round-robin for single processor systems, and equi-partition for multiprocessor systems. We analytically study effect of job parallelization on the overall performance of the system, and also present simulation results. Through these studies, we discuss scheduling policies of parallel jobs in relation to the ratio of number of jobs and the number of processors in the multiprocessor system, and propose new paradigm for parallel algorithm designs.
15408418
CatRelate: A New Hierarchical Document Category Integration Algorithm by Learning Category Relationships
We address the problem of integrating documents from a source catalog into a master catalog. Current technologies for solving the problem deem it as a flat category integration problem without considering the useful hierarchy information in the catalog, or deal with it hierarchically but without a rigorous model. In contrast, our method is based on correctly identifying relationships among categories, such as Match, Disjoint, SubConcept, SuperConcept, and Overlap, which come from the relations of sets in Set theory. Compared with traditional Match/NotMatch relationship in literature, our approach is more expressive in defining the relationship. The relationships among categories are first learned in a probabilistic way, and then refined by considering the hierarchy context. Our preliminary experiments show that it can help to correctly identify category relationships, and thus increase the accuracy of document integration.
2853127
Using Online Relevance Feedback to Build Effective Personalized Metasearch Engine
Metasearch Engine is popular fo r facilitating users’ queries over multiple search engines and increasing the coverage of the WWW. How to rank the merged results becomes crucial f o r the success of metasearch engines. Many current metasearch engines have poor precision, f o r one or more of selected source search engine returns irrelevant results. On the other hand, users with different interests may prefer distinct ranking order even for the same query. In this work, we try to use online relevance feedback to improve precision of the search results. At the same time, Users’ preferences are recorded during the process of feedback f o r future ranking. Our elementary experiment shows that it is effective in improving precision of the metasearch engine.
28798884
Linear and Integer Programming Techniques for Cooperative Games
Let Γ = (N, v) be a cooperative game with the player set N and value function v : 2N → R. A solution of the game is in the core if no subset of players could gain advantage by breaking away from the grand coalition of all players. This paper surveys theoretical results on the cores for some cooperative game models. These results proved that the linear program duality characterization of the core is a very powerful tool. We will focus on linear and integer programming techniques applied in this area.
27556792
Stochastic computation of medial axis in Markov random fields
In this paper the computation of medial axis is posed as a statistical inference problem not as a mathematical transform. This method provides answers to two essential problems in computing the medial axis representation. I) Prior knowledge are adopted for axes and junctions so that the axes around junctions become well defined. II) A stochastic jump-diffusion process is proposed for estimating medial axis in a Markov random field. We argue that the stochastic algorithm for computing medial axis is compatible with existing algorithms for image segmentation, such as snake and region competition. Thus it provides a new direction for computing medial axis from real textured images. Experiments ale demonstrated on both synthetic and real shapes.
8004737
A generative model of human hair for hair sketching
Human hair is a very complex visual pattern whose representation is rarely studied in the vision literature despite its important role in human recognition. In this paper, we propose a generative model for hair representation and hair sketching, which is far more compact than the physically based models in graphics. We decompose a color hair image into three bands: a color band (a) (by Luv transform), a low frequency band (b) for lighting variations, and a high frequency band (c) for the hair pattern. Then we propose a three level generative model for the hair image (c). In this model, image (c) is generated by a vector field (d) that represents hair orientation, gradient strength, and directions; and this vector field is in turn generated by a hair sketch layer (e). We identify five types of primitives for the hair sketch each specifying the orientations of the vector field on the two sides of the sketch. With the five-layer representation (a-e) computed, we can reconstruct vivid hair images and generate hair sketches. We test our algorithm on a large data set of hairs and some results are reported in the experiments.
570616
Least privilege and privilege deprivation: towards tolerating mobile sink compromises in wireless sensor networks
Mobile sinks are needed in many sensor network applications for efficient data collection, data querying, localized sensor reprogramming, identifying and revoking compromised sensors, and other network maintenance. Employing mobile sinks however raises a new security challenge: if a mobile sink is given too many privileges, it will become very attractive for attack and compromise. Using a compromised mobile sink, an adversary may easily bring down or even take over the sensor network. Thus, security mechanisms that can tolerate mobile sink compromises are essential. In this paper, based on the principle of least privilege, we first propose several efficient schemes to restrict the privilege of a mobile sink without impeding its capability of carrying out any authorized operations for an assigned task. To further reduce the possible damages caused by a compromised mobile sink, we then propose efficient message forwarding schemes for depriving the privilege assigned to a compromised mobile sink immediately after its compromise has been detected. Through detailed analysis and simulations, we show that our schemes are secure and efficient, and are highly practical for sensor networks consisting of the current generation of sensors.
15097946
Algorithms for clustering high dimensional and distributed data
Clustering is the problem of identifying the distribution of patterns and intrinsic correlations in large data sets by partitioning the data points into similarity classes. The clustering problem has been widely studied in machine learning, databases, and statistics. This paper studies the problem of clustering high dimensional data. The paper proposes an algorithm called the CoFD algorithm, which is a non-distance based clustering algorithm for high dimensional spaces. Based on the Maximum Likelihood Principle, CoFD attempts to optimize its parameter settings to maximize the likelihood between data points and the model generated by the parameters. The distributed versions of the problem, called the D-CoFD algorithms, are also proposed. Experimental results on both synthetic and real data sets show the efficiency and effectiveness of CoFD and D-CoFD algorithms.
1511154
Association-based similarity testing and its applications
This paper proposes a new similarity measure between basket datasets based on associations. The new measure is calculated from support counts using a formula inspired by information entropy. Experiments on both real and synthetic datasets show the effectiveness of the measure. This paper then investigates the applications of the similarity measure. It first studies the problem of finding a mapping between categorical database attribute sets using similarity measures. A generic approach for identifying such a mapping is proposed. The approach is implemented based on the similarity measure proposed in the paper and its performance has been evaluated and validated. Moreover, this paper also explores the applications of using the similarity measure to mine distributed datasets.