5743908
A Probabilistic Model for Clustering Text Documents with Multiple Fields
We address the problem of clustering documents with multiple fields, such as scientific literature with the distinct fields: title, abstract, keywords, main text and references. By taking into consideration of the distinct word distributions of each field, we propose a new probabilistic model, Field Independent Clustering Model (FICM), for clustering documents with multiple fields. The benefits of FICM come not only from integrating the discrimination abilities of each field but also from the power of selecting the most suitable component probabilistic model for each field. We examined the performance of FICM on the problem of clustering biomedical documents with three fields (title, abstract and MeSH). From the genomics track data of TREC 2004 and TREC 2005, we randomly generated 60 datasets where the number of classes in each dataset ranged from 3 to 12. By applying the appropriate configuration of generative models for each field, FICM outperformed a classical multinomial model in 59 out of the total 60 datasets, of which 47 were statistically significant at the 95% level, and FICM also outperformed a multivariate Bernoulli model in 52 out of the total 60 datasets, of which 36 were statistically significant at the 95% level.
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.
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.
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.
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.
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.
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.
61692411
Visual learning by integrating descriptive and generative methods
This paper presents a mathematical framework for visual learning that integrates two popular statistical learning paradigms in the literature: (I). Descriptive learning, such as Markov random fields and minimax entropy learning, and (II). Generative learning, such as PCA, ICA, TCA, image coding and HMM. We apply this integrated learning framework to texton modeling, and we assume that an observed texture image is generated by multiple layers of hidden stochastic "texton processes" with each texton being a window function, like a mini-template or a wavelet, under affine transformations. The spatial arrangements of the textons are characterized by minimax entropy models. The texton processes generate images by occlusion or linear addition. Thus given a raw input image, the learning framework achieves four goals: (i). Computing the appearance of the textons. (ii) Inferring the hidden stochastic texton processes. (iii). Learning Gibbs models for each texton process and (iv). Verifying the learnt textons and Gibbs models through random sampling and texture synthesis. The integrated framework subsumes the minimax entropy learning paradigm and creates a richer class of probability models for visual patterns, which are suited for middle level vision representations. Furthermore we show that the integration of description and generative methods yields a natural and general framework of visual learning. We demonstrate the proposed framework and algorithms on many real images.
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.
6046438
A high resolution grammatical model for face representation and sketching
In this paper we present a generative, high resolution face representation which extends the well-known active appearance model (AAM) with two additional layers. (i) One layer refines the global AAM (PCA) model with a dictionary of learned face components to account for the shape and intensity variabilities of eyes, eyebrows, nose and mouth, (ii) the other layer divides the face skin into 9 zones with a learned dictionary of sketch primitives to represent skin marks and wrinkles. This model is no longer of fixed dimensions and is flexible for it can select the diverse representations in the dictionaries of face components and skin features depending on the complexity of the face. The selection is modulated by the grammatical rules through hidden "switch " variables. Our comparison experiments demonstrate that this model can achieve nearly lossless coding of face at high resolution (256 /spl times/ 256 pixels) with low bits. We also show that the generative model can easily generate cartoon sketches by changing the rendering dictionary. Our face model is aimed at a number of applications including cartoon sketch in non-photorealistic rendering, super-resolution in image processing, and low bit face communication in wireless platforms.
11176389
Incorporating visual knowledge representation in stereo reconstruction
In this paper, we present a two-layer generative model that incorporates generic middle-level visual knowledge for dense stereo reconstruction. The visual knowledge is represented by a dictionary of surface primitives including various categories of boundary discontinuities and junctions in parametric form. Given a stereo pair, we first compute a primal sketch representation which decomposes the image into a structural part for object boundaries and high intensity contrast represented by a 2D sketch graph, and a structure less part represented by Markov random field on pixels. Then we label the sketch graph and compute the 3D sketch (like a wire-frame) by fitting the primitive dictionary to the sketch graph. The surfaces between the 3D sketches are filled in by computing the depth of the MRP model on the structureless part. These two levels interact closely since the MRF is used to propagate information between the primitives, and at the same time, the primitives act as boundary conditions for the MRF. The two processes maximize a Bayesian posterior probability jointly. We propose an MCMC algorithm that simultaneously infers the 3D primitive types and parameters and estimates the depth of the scene. Our experiments show that this representation can infer the depth map with sharp boundaries and junctions for textureless images, curve objects and free-form shapes.