Physical Sciences and Mathematics Commons^™

Minimum Description Length Measures Of Evidence For Enrichment, Zhenyu Yang, David R. Bickel

COBRA Preprint Series

In order to functionally interpret differentially expressed genes or other discovered features, researchers seek to detect enrichment in the form of overrepresentation of discovered features associated with a biological process. Most enrichment methods treat the p-value as the measure of evidence using a statistical test such as the binomial test, Fisher's exact test or the hypergeometric test. However, the p-value is not interpretable as a measure of evidence apart from adjustments in light of the sample size. As a measure of evidence supporting one hypothesis over the other, the Bayes factor (BF) overcomes this drawback of the p-value but lacks …

Reconstructability Analysis Of Epistasis, Martin Zwick

Systems Science Faculty Publications and Presentations

The literature on epistasis describes various methods to detect epistatic interactions and to classify different types of epistasis. Reconstructability analysis (RA) has recently been used to detect epistasis in genomic data. This paper shows that RA offers a classification of types of epistasis at three levels of resolution (variable-based models without loops, variable-based models with loops, state-based models). These types can be defined by the simplest RA structures that model the data without information loss; a more detailed classification can be defined by the information content of multiple candidate structures. The RA classification can be augmented with structures from related …

Spatial Semantics For Better Interoperability And Analysis: Challenges And Experiences In Building Semantically Rich Applications In Web 3.0, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

A Microrna Target Prediction Algorithm, Rupinder Singh

Master's Projects

MicroRNA target prediction using the experimental methods is a challenging task. To accelerate the process of miRNA target validation, many computational methods are used. Computational methods yield many potential candidates for experimental validation. This project is about developing a new computational method using dynamic programming to predict miRNA targets with more accuracy. The project discusses the currently available computational methods and develops a new algorithm using the currently available knowledge about miRNA interactions.

Closing The Gap Between The Industry And Higher Education Institutions- Case Examples From East African Region, Deogratias Harorimana Mr

Dr Deogratias Harorimana

Much complained about is the quality of graduates Universities put on the labour market. Less talked about however is why knowledge institutions seems to be bad knowledge managers. In this presentation I argue that DIRECT collaborative relationship between Industry,Governments and Higher Education Institutions is a per-requisite.Good relationship is key to building such a successful knowledge transfer strategies between Industries and Educational and Research Institutions. This paper explores what makes a good Knowledge Transfer Partnership Strategy and highlights some key lessons for businesses, Universities and Government bodies. This paper was a Key note presentation to the Annual International Conference on Building …

Flexible Bootstrapping-Based Ontology Alignment, Prateek Jain, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

BLOOMS (Jain et al, ISWC2010) is an ontology alignment system which, in its core, utilizes the Wikipedia category hierarchy for establishing alignments. In this paper, we present a Plug-and-Play extension to BLOOMS, which allows to flexibly replace or complement the use of Wikipedia by other online or offline resources, including domain-specific ontologies or taxonomies. By making use of automated translation services and of Wikipedia in languages other than English, it makes it possible to apply BLOOMS to alignment tasks where the input ontologies are written in different languages.

Ontology Alignment For Linked Open Data, Prateek Jain, Pascal Hitzler, Amit P. Sheth, Kunal Verma, Peter Z. Yeh

Kno.e.sis Publications

The Web of Data currently coming into existence through the Linked Open Data (LOD) effort is a major milestone in realizing the Semantic Web vision. However, the development of applications based on LOD faces difficulties due to the fact that the different LOD datasets are rather loosely connected pieces of information. In particular, links between LOD datasets are almost exclusively on the level of instances, and schema-level information is being ignored. In this paper, we therefore present a system for finding schema-level links between LOD datasets in the sense of ontology alignment. Our system, called BLOOMS, is based on the …

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam Rath, Suresh Das

Chemistry & Biochemistry Faculty Works

The title compound, C18H18O2, which exhibits blue emission in the solid state, is an inter­mediate in the preparation of liquid crystals and polymers. The mol­ecule is located on an inversion centre. In the crystal, mol­ecules are arranged in a herringbone motif.

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam P. Rath, Suresh Das

Nigam Rath

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam Rath, Alicia Beatty

Chemistry & Biochemistry Faculty Works

In the crystal structure of the title compound, C12H8Cl4N2, mol­ecules lie on crystallographic twofold axes at the centre of the C-C bonds linking the benzene rings, such that the asymmetric unit consists of a half-mol­ecule. The individual mol­ecules participate in inter­molecular N-H...N, N-H...Cl, C-H...Cl and Cl...Cl [3.4503 (3) Å] inter­actions.

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam P. Rath, Alicia M. Beatty

Nigam Rath

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam P. Rath, Alicia M. Beatty

Alicia Beatty

Sample Size And Statistical Power Considerations In High-Dimensionality Data Settings: A Comparative Study Of Classification Algorithms, Yu Guo, Armin Garber, Raji Balasubramanian

Raji Balasubramanian

Background: Data generated using ‘omics’ technologies are characterized by high dimensionality, where the number of features measured per subject vastly exceeds the number of subjects in the study. In this paper, we consider issues relevant in the design of biomedical studies in which the goal is the discovery of a subset of features and an associated algorithm that can predict a binary outcome, such as disease status. We compare the performance of four commonly used classifiers (K-Nearest Neighbors, Prediction Analysis for Microarrays, Random Forests and Support Vector Machines) in high-dimensionality data settings. We evaluate the effects of varying levels of …

Bioinformatics Across The Sciences, Nigel Yarlett

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

A Taxonomy-Based Model For Expertise Extrapolation, Delroy H. Cameron, Boanerges Aleman-Meza, Ismailcem Budak Arpinar, Sheron L. Decker, Amit P. Sheth

Kno.e.sis Publications

While many ExpertFinder applications succeed in finding experts, their techniques are not always designed to capture the various levels at which expertise can be expressed. Indeed, expertise can be inferred from relationships between topics and subtopics in a taxonomy. The conventional wisdom is that expertise in subtopics is also indicative of expertise in higher level topics as well. The enrichment of Expertise Profiles for finding experts can therefore be facilitated by taking domain hierarchies into account. We present a novel semantics-based model for finding experts, expertise levels and collaboration levels in a peer review context, such as composing a Program …

Ranking Documents Semantically Using Ontological Relationships, Boanerges Aleman-Meza, I. Budak Arpinar, Mustafa V. Nural, Amit P. Sheth

Kno.e.sis Publications

Although arguable success of today’s keyword based search engines in certain information retrieval tasks, ranking search results in a meaningful way remains an open problem. In this work, the goal is to use of semantic relationships for ranking documents without relying on the existence of any specific structure in a document or links between documents. Instead, real-world entities are identified and the relevance of documents is determined using relationships that are known to exist between the entities in a populated ontology. We introduce a measure of relevance that is based on traversal and the semantics of relationships that link entities …

G-Lattices For An Unrooted Perfect Phylogeny, Monica Grigg

Mathematical Sciences Technical Reports (MSTR)

We look at the Pure Parsimony problem and the Perfect Phylogeny Haplotyping problem. From the Pure Parsimony problem we consider structures of genotypes called g-lattices. These structures either provide solutions or give bounds to the pure parsimony problem. In particular, we investigate which of these structures supports an unrooted perfect phylogeny, a condition that adds biological interpretation. By understanding which g-lattices support an unrooted perfect phylogeny, we connect two of the standard biological inference rules used to recreate how genetic diversity propagates across generations.

A Perturbation Method For Inference On Regularized Regression Estimates, Jessica Minnier, Lu Tian, Tianxi Cai

Harvard University Biostatistics Working Paper Series

No abstract provided.

Distribution Of Health Care Expenditures For Hiv-Infected Patients, Ray Y. Chen, Neil A. Accortt, Andrew O. Westfall, Michael J. Mugavero, James L. Raper, Gretchen A. Cloud, Beth K. Stone, Jerome Carter, Stephanie Call, Maria Pisu, Jeroan J. Allison, Michael S. Saag

Jeroan J. Allison

BACKGROUND: Health care expenditures for persons infected with human immunodeficiency virus (HIV) in the United State determined on the basis of actual health care use have not been reported in the era of highly active antiretroviral therapy.

METHODS: Patients receiving primary care at the University of Alabama at Birmingham HIV clinic were included in the study. All encounters (except emergency room visits) that occurred within the University of Alabama at Birmingham Hospital System from 1 March 2000 to 1 March 2001 were analyzed. Medication expenditures were determined on the basis of 2001 average wholesale price. Hospitalization expenditures were determined on …

Trends In Aids-Defining And Non-Aids-Defining Malignancies Among Hiv-Infected Patients: 1989-2002, Roger Bedimo, Ray Y. Chen, Neil A. Accortt, James L. Raper, Carol Linn, Jeroan J. Allison, John Dubay, Michael S. Saag, Craig J. Hoesley

Jeroan J. Allison

In a comparison of rates of acquired immunodeficiency syndrome (AIDS)-defining malignancies (ADMs) for 1989-1996 versus 1997-2002, we found a decrease in ADMs (rate ratio, 0.31; P<.0001) and a significant increase in non-AIDS-defining malignancies (non-ADMs; rate ratio, 10.87; P<.0002). The mean CD4 cell count was lower among patients with ADMs than among those with non-ADMs. A longer duration of survival during highly active antiretroviral therapy might explain the increasing incidence of non-ADMs.

A Spectral Approach To Protein Structure Alignment, Yosi Shibberu, Allen Holder

Mathematical Sciences Technical Reports (MSTR)

We present two algorithms that use spectral methods to align protein folds. One of the algorithms is suitable for database searches, the other for difficult alignments. We present computational results for 780 pairwise alignments used to classify 40 proteins as well as results for a separate set of 36 protein alignments used for comparison to four other alignment algorithms. We also provide a mathematically rigorous development of the intrinsic geometry underlying our spectral approach.

Bilinear Programming And Protein Structure Alignment, J. Cain, D. Kamenetsky, N. Lavine

Mathematical Sciences Technical Reports (MSTR)

Proteins are a primary functional component of organic life, and understanding their function is integral to many areas of research in biochemistry. The three-dimensional structure of a protein largely determines this function. Protein structure alignment compares the structure of a protein with known function to that of a protein with unknown function. A protein’s three-dimensional structure can be transformed through a smooth piecewise-linear sigmoid function to a real symmetric contact matrix that represents the functional significance of certain parts of the protein. We address the protein alignment problem as a minimization of the 2-norm difference of two proteins’ contact matrices. …

The Maximum Clique Problem: Algorithms, Applications, And Implementations, John David Eblen

Doctoral Dissertations

Computationally hard problems are routinely encountered during the course of solving practical problems. This is commonly dealt with by settling for less than optimal solutions, through the use of heuristics or approximation algorithms. This dissertation examines the alternate possibility of solving such problems exactly, through a detailed study of one particular problem, the maximum clique problem. It discusses algorithms, implementations, and the application of maximum clique results to real-world problems. First, the theoretical roots of the algorithmic method employed are discussed. Then a practical approach is described, which separates out important algorithmic decisions so that the algorithm can be easily …

Cross-Market Model Adaptation With Pairwise Preference Data For Web Search Ranking, Jing Bai, Fernando Diaz, Yi Chang, Zhaohui Zheng, Keke Chen

Kno.e.sis Publications

Machine-learned ranking techniques automatically learn a complex document ranking function given training data. These techniques have demonstrated the effectiveness and flexibility required of a commercial web search. However, manually labeled training data (with multiple absolute grades) has become the bottleneck for training a quality ranking function, particularly for a new domain. In this paper, we explore the adaptation of machine-learned ranking models across a set of geographically diverse markets with the market-specific pairwise preference data, which can be easily obtained from clickthrough logs. We propose a novel adaptation algorithm, Pairwise-Trada, which is able to adapt ranking models that are trained …

Pattern Space Maintenance For Data Updates And Interactive Mining, Mengling Feng, Guozhu Dong, Jinyan Li, Yap-Peng Tan, Limsoon Wong

Kno.e.sis Publications

This article addresses the incremental and decremental maintenance of the frequent pattern space. We conduct an in-depth investigation on how the frequent pattern space evolves under both incremental and decremental updates. Based on the evolution analysis, a new data structure, Generator-Enumeration Tree (GE-tree), is developed to facilitate the maintenance of the frequent pattern space. With the concept of GE-tree, we propose two novel algorithms, Pattern Space Maintainer+ (PSM+) and Pattern Space Maintainer− (PSM−), for the incremental and decremental maintenance of frequent patterns. Experimental results demonstrate that the proposed algorithms, on average, outperform the representative state-of-the-art …

Body Mass Index, Treatment Practices, And Mortality In Patients With Acute Heart Failure, Timothy Fitzgibbons, Olga Hardy, Darleen Lessard, Joel Gore, Jorge Yarzebski, Robert Goldberg

Jorge L. Yarzebski

OBJECTIVES: Obesity is associated with an increased risk of heart failure (HF). Among patients presenting with acute HF, however, differences in clinical characteristics, treatment regimens, and short-term prognosis of varying weights are largely unknown, particularly from a broader population-based perspective. METHODS: A total of 3722 patients admitted with acute HF to 11 greater Worcester (Massachusetts, USA) hospitals during 1995 and 2000 were categorized as being lean (n = 216), normal weight (n = 1465), overweight (n = 1007), or obese (n = 1034) at the time of hospitalization. RESULTS: Obese patients with decompensated HF were significantly younger (mean age = …

Prognosis Of Acute Myocardial Infarction Complicated By Complete Heart Block (The Worcester Heart Attack Study), Robert Goldberg, Juan Zevallos, Jorge Yarzebski, Joseph Alpert, Joel Gore, Z. Chen, James Dalen

Jorge L. Yarzebski

As part of a community-based study of patients hospitalized with acute myocardial infarction (AMI) in the Worcester, Massachusetts, metropolitan area, changes over time in the incidence rates of complete heart block (CHB) complicating AMI, and the prognostic impact of CHB on the in-hospital and long-term survival of these patients were examined. In all, 4,762 patients with validated AMI hospitalized at 16 hospitals in the Worcester metropolitan area during 1975, 1978, 1981, 1984, 1986 and 1988 constituted the study sample. The incidence rates of CHB complicating AMI remained relatively stable at 5.8% over the 13-year (1975 to 1988) period studied. The …

Changes Over Time In The Use Of Aspirin In Patients Hospitalized With Acute Myocardial Infarction (1975 To 1997): A Population-Based Perspective, Elizabeth Jackson, Ramya Sivasubramian, Frederick Spencer, Jorge Yarzebski, Darleen Lessard, Joel Gore, Robert Goldberg

Jorge L. Yarzebski

OBJECTIVE: The purpose of this study was to examine 2 decade-long trends in the use of aspirin and associated outcomes in patients hospitalized with acute myocardial infarction. BACKGROUND: Aspirin has been shown to be beneficial in the secondary prevention of AMI. However, little is known about changes over time in the use of aspirin in patients hospitalized with AMI and associated outcomes, particularly from a more generalizable population-based perspective. METHODS: We examined trends in aspirin use and hospital and long-term outcomes in 9336 metropolitan Worcester, Mass, residents hospitalized with validated AMI in all area hospitals between 1975 and 1997. RESULTS: …

Thirty-Year Trends (1975-2005) In The Magnitude, Patient Characteristics, And Hospital Outcomes Of Patients With Acute Myocardial Infarction Complicated By Ventricular Fibrillation, Robert Goldberg, Jorge Yarzebski, Frederick Spencer, Juan Zevallos, Darleen Lessard, Joel Gore

Jorge L. Yarzebski

Limited contemporary data are available describing the incidence rates, hospital prognosis, and factors associated with the occurrence of ventricular fibrillation (VF) in patients hospitalized with acute myocardial infarction (AMI). The objectives of our study were to examine 3-decade-long trends (1975 to 2005) in the magnitude, predictors, and hospital case-fatality rates associated with VF in residents of a large New England metropolitan area hospitalized at all area medical centers with an uncomplicated AMI. The study population consisted of 7,472 residents of the Worcester (Massachusetts) metropolitan area hospitalized with an uncomplicated AMI in 15 annual periods from 1975 to 2005. The overall …

Temporal Trends (1975 Through 1990) In The Incidence And Case-Fatality Rates Of Primary Ventricular Fibrillation Complicating Acute Myocardial Infarction. A Communitywide Perspective, David Chiriboga, Jorge Yarzebski, Robert Goldberg, Joel Gore, Joseph Alpert

Jorge L. Yarzebski

BACKGROUND: As part of a population-based study of acute myocardial infarction, we examined changes over time in the incidence and in-hospital case-fatality rates of primary ventricular fibrillation complicating acute myocardial infarction. METHODS AND RESULTS: Patients with validated acute myocardial infarction hospitalized at 16 hospitals in the Worcester, Mass, metropolitan area between 1975 and 1990 comprised the study sample. During the 15-year study period, 5.1% of patients developed primary ventricular fibrillation in the setting of uncomplicated acute myocardial infarction, with this rate remaining relatively constant over time. Both age- and multivariable-adjusted analyses showed no significant trend in the incidence rates of …