2869410
UMass at TREC 2003: HARD and QA
Abstract : The Center for Intelligent Information Retrieval (CIIR) at UMass Amherst participated in two tracks for TREC 2003: High Accuracy Retrieval from Documents (HARD) and Question Answering (QA). In the HARD track, we developed document metadata to correspond to query metadata requirements; implemented clarification forms based on query expansion, passage retrieval, and clustering; and retrieved variable length passages deemed most likely to be relevant. This work is discussed at length in Section 1. In the QA track, we focused on retrieving passages that were likely to contain the answer to the question. In the QA track, we developed a dynamic passaging retrieval system to identify passages likely to contain answers. CIIR last participated in the QA task in TREC 9 (2000). At that time we fielded the Marsha system [11]. This system was based on an INQUERY document retrieval engine followed by the application of a series of heuristics rules to identify 250-byte long passages in the retrieved documents that were likely to contain the desired answers. This year's passage sub-task in the QA track has allowed us to participate once again utilizing our current approach to passage retrieval with language models. We developed a dynamic passaging system that retrieved document passages based on the simplest implementation of language models: cross-entropy between bag-of-word models for a question and a candidate passage.
7988049
Word Sense Disambiguation for Cross-Language Information Retrieval
We have developed a word sense disambiguation algorithm, following Cheng and Wilensky (1997), to disambiguate among WordNet synsets. This algorithm is to be used in a cross-language information retrieval system, CINDOR, which indexes queries and documents in a language-neutral concept representation based on WordNet synsets. Our goal is to improve retrieval precision through word sense disambiguation. An evaluation against human disambiguation judgements suggests promise for our approach.
13969434
Genre based navigation on the Web
We report on our ongoing study of using the genre of Web pages to facilitate information exploration. By genre, we mean socially recognized regularities of form and purpose in documents (e.g., a letter, a memo, a research paper). Our study had three phases. First, through a user study, we identified genres which most/least frequently meet searchers' information needs. We found that certain genres are better suited for certain types of needs. We identified five major groups of document genres that might be used in an interactive search tool that would allow genre based navigation. We tried to balance the following dual objectives: i) each group should be recognizable by a computer algorithm as easily as possible; ii) each group has a better chance of satisfying particular types of information needs. Finally, we developed a novel user interface for Web searching that allows genre based navigation through three major functionalities: 1) limiting search to specified genres, 2) visualizing the hierarchy of genres discovered in the search results and 3) accepting user feedback on the relevancy of the specified genres.
265423
Prediction of Protein Secondary Structure Based on Residue Pairs
The GOR program for predicting protein secondary structure is extended to include triple correlation. A score system for a residue pair to be at certain conformation state is derived from the conditional weight matrix describing amino acid frequencies at each position of a window flanking the pair under the condition for the pair to be at the fixed state. A program using this score system to predict protein secondary structure is established. After training the model with a learning set created from PDB_SELECT, the program is tested with two test sets. As a method using single sequence for predicting secondary structures, the approach achieves a high accuracy near 70%.
2180147
An experimental evaluation of a loop versus a reference design for two-channel microarrays
MOTIVATION
Despite theoretical arguments that so-called 'loop designs' for two-channel DNA microarray experiments are more efficient, biologists continue to use 'reference designs'. We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicolor). In each case, both a loop and a reference design were used with the same RNA preparations with the aim of studying their relative efficiency.


RESULTS
The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example, by taking log-ratios or including spot effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice.


AVAILABILITY
The data and R code are available at http://exgen.ma.umist.ac.uk


CONTACT
veronica.vinciotti@brunel.ac.uk.
792291
Variable grouping in multivariate time series via correlation
The decomposition of high-dimensional multivariate time series (MTS) into a number of low-dimensional MTS is a useful but challenging task because the number of possible dependencies between variables is likely to be huge. This paper is about a systematic study of the "variable groupings" problem in MTS. In particular, we investigate different methods of utilizing the information regarding correlations among MTS variables. This type of method does not appear to have been studied before. In all, 15 methods are suggested and applied to six datasets where there are identifiable mixed groupings of MTS variables. This paper describes the general methodology, reports extensive experimental results, and concludes with useful insights on the strength and weakness of this type of grouping method.
13088953
A polynomial algorithm for recognizing perfect graphs
We present a polynomial algorithm for recognizing whether a graph is perfect, thus settling a long standing open question. The algorithm uses a decomposition theorem of Conforti, Cornuejols and Vuskovic. Another polynomial algorithm for recognizing perfect graphs, which does not use decomposition, was obtained simultaneously by Chudnovsky and Seymour. Both algorithms need a first phase developed jointly by Chudnovsky, Cornuejols, Liu, Seymour and Vuskovic.
6032766
A Novel Volume Constrained Smoothing Method for Meshes
In general, mesh smoothing is performed by minimizing the discrete energy function for the surface. One of the major problems in mesh smoothing is to prevent the mesh from shrinking. In this paper, we propose a novel volume constraint to address the shrinking problem in mesh smoothing. Our key observation is that the mesh can be efficiently smoothed patch by patch in a signal processing manner, and then a local volume preserving constraint can be easily imposed to the energy minimization problem associated with the small patch, called the smoothing stencil, so as to effectively avoid the mesh shrinkage. In our implementation, the smoothing stencil is the 1-ring neighboring region of an edge or a triangle. And the constrained minimization problem is solved by a 2-step approximation method for efficiency. A series of examples demonstrate that the proposed smoothing method can be applied to remove noise from a mesh or remove rough detail from an original mesh to generate a smooth model in object reconstruction and geometry modeling.