Showing papers by "Stanford University published in 1999"

Foundations of Statistical Natural Language Processing

Abstract: Statistical approaches to processing natural language text have become dominant in recent years This foundational text is the first comprehensive introduction to statistical natural language processing (NLP) to appear The book contains all the theory and algorithms needed for building NLP tools It provides broad but rigorous coverage of mathematical and linguistic foundations, as well as detailed discussion of statistical methods, allowing students and researchers to construct their own implementations The book covers collocation finding, word sense disambiguation, probabilistic parsing, information retrieval, and other applications

Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2.

Abstract: Rett syndrome (RTT, MIM 312750) is a progressive neurodevelopmental disorder and one of the most common causes of mental retardation in females, with an incidence of 1 in 10,000-15,000 (ref. 2). Patients with classic RTT appear to develop normally until 6-18 months of age, then gradually lose speech and purposeful hand use, and develop microcephaly, seizures, autism, ataxia, intermittent hyperventilation and stereotypic hand movements. After initial regression, the condition stabilizes and patients usually survive into adulthood. As RTT occurs almost exclusively in females, it has been proposed that RTT is caused by an X-linked dominant mutation with lethality in hemizygous males. Previous exclusion mapping studies using RTT families mapped the locus to Xq28 (refs 6,9,10,11). Using a systematic gene screening approach, we have identified mutations in the gene (MECP2 ) encoding X-linked methyl-CpG-binding protein 2 (MeCP2) as the cause of some cases of RTT. MeCP2 selectively binds CpG dinucleotides in the mammalian genome and mediates transcriptional repression through interaction with histone deacetylase and the corepressor SIN3A (refs 12,13). In 5 of 21 sporadic patients, we found 3 de novo missense mutations in the region encoding the highly conserved methyl-binding domain (MBD) as well as a de novo frameshift and a de novo nonsense mutation, both of which disrupt the transcription repression domain (TRD). In two affected half-sisters of a RTT family, we found segregation of an additional missense mutation not detected in their obligate carrier mother. This suggests that the mother is a germline mosaic for this mutation. Our study reports the first disease-causing mutations in RTT and points to abnormal epigenetic regulation as the mechanism underlying the pathogenesis of RTT.

Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis

Abstract: The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome). Of the deleted ORFs, 17 percent were essential for viability in rich medium. The phenotypes of more than 500 deletion strains were assayed in parallel. Of the deletion strains, 40 percent showed quantitative growth defects in either rich or minimal medium.

Taking Time Seriously. A Theory of Socioemotional Selectivity

Abstract: Socioemotional selectivity theory claims that the perception of time plays a fundamental role in the selection and pursuit of social goals. According to the theory, social motives fall into 1 of 2 general categories--those related to the acquisition of knowledge and those related to the regulation of emotion. When time is perceived as open-ended, knowledge-related goals are prioritized. In contrast, when time is perceived as limited, emotional goals assume primacy. The inextricable association between time left in life and chronological age ensures age-related differences in social goals. Nonetheless, the authors show that the perception of time is malleable, and social goals change in both younger and older people when time constraints are imposed. The authors argue that time perception is integral to human motivation and suggest potential implications for multiple subdisciplines and research interests in social, developmental, cultural, cognitive, and clinical psychology.

Similarity Search in High Dimensions via Hashing

Abstract: The nearestor near-neighbor query problems arise in a large variety of database applications, usually in the context of similarity searching. Of late, there has been increasing interest in building search/index structures for performing similarity search over high-dimensional data, e.g., image databases, document collections, time-series databases, and genome databases. Unfortunately, all known techniques for solving this problem fall prey to the \curse of dimensionality." That is, the data structures scale poorly with data dimensionality; in fact, if the number of dimensions exceeds 10 to 20, searching in k-d trees and related structures involves the inspection of a large fraction of the database, thereby doing no better than brute-force linear search. It has been suggested that since the selection of features and the choice of a distance metric in typical applications is rather heuristic, determining an approximate nearest neighbor should su ce for most practical purposes. In this paper, we examine a novel scheme for approximate similarity search based on hashing. The basic idea is to hash the points Supported by NAVY N00014-96-1-1221 grant and NSF Grant IIS-9811904. Supported by Stanford Graduate Fellowship and NSF NYI Award CCR-9357849. Supported by ARO MURI Grant DAAH04-96-1-0007, NSF Grant IIS-9811904, and NSF Young Investigator Award CCR9357849, with matching funds from IBM, Mitsubishi, Schlumberger Foundation, Shell Foundation, and Xerox Corporation. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Very Large Data Base Endowment. To copy otherwise, or to republish, requires a fee and/or special permission from the Endowment. Proceedings of the 25th VLDB Conference, Edinburgh, Scotland, 1999. from the database so as to ensure that the probability of collision is much higher for objects that are close to each other than for those that are far apart. We provide experimental evidence that our method gives signi cant improvement in running time over other methods for searching in highdimensional spaces based on hierarchical tree decomposition. Experimental results also indicate that our scheme scales well even for a relatively large number of dimensions (more than 50).

Report of an International Workshop to Standardize Response Criteria for Non-Hodgkin's Lymphomas

Abstract: Standardized guidelines for response assessment are needed to ensure comparability among clinical trials in non-Hodgkin's lymphomas (NHL). To achieve this, two meetings were convened among United States and international lymphoma experts representing medical hematology/oncology, radiology, radiation oncology, and pathology to review currently used response definitions and to develop a uniform set of criteria for assessing response in clinical trials. The criteria that were developed include anatomic definitions of response, with normal lymph node size after treatment of 1.5 cm in the longest transverse diameter by computer-assisted tomography scan. A designation of complete response/unconfirmed was adopted to include patients with a greater than 75% reduction in tumor size after therapy but with a residual mass, to include patients-especially those with large-cell NHL-who may not have residual disease. Single-photon emission computed tomography gallium scans are encouraged as a valuable adjunct to assessment of patients with large-cell NHL, but such scans require appropriate expertise. Flow cytometric, cytogenetic, and molecular studies are not currently included in response definitions. Response rates may be the most important objective in phase II trials where the activity of a new agent is important and may provide support for approval by regulatory agencies. However, the goals of most phase III trials are to identify therapies that will prolong the progression-free survival, if not the overall survival, of the treated patients. We hope that these guidelines will serve to improve communication among investigators and comparability among clinical trials until clinically relevant laboratory and imaging studies are identified and become more widely available.

Snort - Lightweight Intrusion Detection for Networks

Abstract: Network intrusion detection systems (NIDS) are an important part of any network security architecture. They provide a layer of defense which monitors network traffic for predefined suspicious activity or patterns, and alert system administrators when potential hostile traffic is detected. Commercial NIDS have many differences, but Information Systems departments must face the commonalities that they share such as significant system footprint, complex deployment and high monetary cost. Snort was designed to address these issues.

Light speed reduction to 17 metres per second in an ultracold atomic gas

Abstract: Techniques that use quantum interference effects are being actively investigated to manipulate the optical properties of quantum systems1. One such example is electromagnetically induced transparency, a quantum effect that permits the propagation of light pulses through an otherwise opaque medium2,3,4,5. Here we report an experimental demonstration of electromagnetically induced transparency in an ultracold gas of sodium atoms, in which the optical pulses propagate at twenty million times slower than the speed of light in a vacuum. The gas is cooled to nanokelvin temperatures by laser and evaporative cooling6,7,8,9,10. The quantum interference controlling the optical properties of the medium is set up by a ‘coupling’ laser beam propagating at a right angle to the pulsed ‘probe’ beam. At nanokelvin temperatures, the variation of refractive index with probe frequency can be made very steep. In conjunction with the high atomic density, this results in the exceptionally low light speeds observed. By cooling the cloud below the transition temperature for Bose–Einstein condensation11,12,13 (causing a macroscopic population of alkali atoms in the quantum ground state of the confining potential), we observe even lower pulse propagation velocities (17?m?s−1) owing to the increased atom density. We report an inferred nonlinear refractive index of 0.18?cm2?W−1 and find that the system shows exceptionally large optical nonlinearities, which are of potential fundamental and technological interest for quantum optics.

Self-Oriented Regular Arrays of Carbon Nanotubes and Their Field Emission Properties

Abstract: The synthesis of massive arrays of monodispersed carbon nanotubes that are self-oriented on patterned porous silicon and plain silicon substrates is reported. The approach involves chemical vapor deposition, catalytic particle size control by substrate design, nanotube positioning by patterning, and nanotube self-assembly for orientation. The mechanisms of nanotube growth and self-orientation are elucidated. The well-ordered nanotubes can be used as electron field emission arrays. Scaling up of the synthesis process should be entirely compatible with the existing semiconductor processes, and should allow the development of nanotube devices integrated into silicon technology.

TRUST AND DISTRUST IN ORGANIZATIONS: Emerging Perspectives, Enduring Questions

Abstract: Scholarly interest in the study of trust and distrust in organizations has grown dramatically over the past five years. This interest has been fueled, at least in part, by accumulating evidence that trust has a number of important benefits for organizations and their members. A primary aim of this review is to assess the state of this rapidly growing literature. The review examines recent progress in conceptualizing trust and distrust in organizational theory, and also summarizes evidence regarding the myriad benefits of trust within organizational systems. The review also describes different forms of trust found in organizations, and the antecedent conditions that produce them. Although the benefits of trust are well-documented, creating and sustaining trust is often difficult. Accordingly, the chapter concludes by examining some of the psychological, social, and institutional barriers to the production of trust. CONTENTS

The Immunological Synapse: A Molecular Machine Controlling T Cell Activation

Abstract: The specialized junction between a T lymphocyte and an antigen-presenting cell, the immunological synapse, consists of a central cluster of T cell receptors surrounded by a ring of adhesion molecules. Immunological synapse formation is now shown to be an active and dynamic mechanism that allows T cells to distinguish potential antigenic ligands. Initially, T cell receptor ligands were engaged in an outermost ring of the nascent synapse. Transport of these complexes into the central cluster was dependent on T cell receptor—ligand interaction kinetics. Finally, formation of a stable central cluster at the heart of the synapse was a determinative event for T cell proliferation. A critical event in the initiation of the adaptive

A Unified Theory of Underreaction, Momentum Trading, and Overreaction in Asset Markets

Abstract: We model a market populated by two groups of boundedly rational agents: “newswatchers” and “momentum traders.” Each newswatcher observes some private information, but fails to extract other newswatchers' information from prices. If information diffuses gradually across the population, prices underreact in the short run. The underreaction means that the momentum traders can profit by trend-chasing. However, if they can only implement simple (i.e., univariate) strategies, their attempts at arbitrage must inevitably lead to overreaction at long horizons. In addition to providing a unified account of under- and overreactions, the model generates several other distinctive implications.

Why Differences Make a Difference: A Field Study of Diversity, Conflict and Performance in Workgroups:

Abstract: A multimethod field study of 92 workgroups explored the influence of three types of workgroup diversity (social category diversity, value diversity, and informational diversity) and two moderators ...

Moral Disengagement in the Perpetration of Inhumanities

Abstract: Moral agency is manifested in both the power to refrain from behaving inhumanely and the proactive power to behave humanely. Moral agency is embedded in a broader sociocognitive self theory encompassing self-organizing, proactive, self-reflective, and self-regulatory mechanisms rooted in personal standards linked to self-sanctions. The self-regulatory mechanisms governing moral conduct do not come into play unless they are activated, and there are many psychosocial maneuvers by which moral self-sanctions are selectively disengaged from inhumane conduct. The moral disengagement may center on the cognitive restructuring of inhumane conduct into a benign or worthy one by moral justification, sanitizing language, and advantageous comparison; disavowal of a sense of personal agency by diffusion or displacement of responsibility; disregarding or minimizing the injurious effects of one's actions; and attribution of blame to, and dehumanization of, those who are victimized. Many inhumanities operate through a supportive network of legitimate enterprises run by otherwise considerate people who contribute to destructive activities by disconnected subdivision of functions and diffusion of responsibility. Given the many mechanisms for disengaging moral control, civilized life requires, in addition to humane personal standards, safeguards built into social systems that uphold compassionate behavior and renounce cruelty.

Long-Term Potentiation--A Decade of Progress?

Abstract: Long-term potentiation of synaptic transmission in the hippocampus is the leading experimental model for the synaptic changes that may underlie learning and memory. This review presents a current understanding of the molecular mechanisms of this long-lasting increase in synaptic strength and describes a simple model that unifies much of the data that previously were viewed as contradictory.

An Empirical Comparison of Voting Classification Algorithms: Bagging, Boosting, and Variants

Abstract: Methods for voting classification algorithms, such as Bagging and AdaBoost, have been shown to be very successful in improving the accuracy of certain classifiers for artificial and real-world datasets. We review these algorithms and describe a large empirical study comparing several variants in conjunction with a decision tree inducer (three variants) and a Naive-Bayes inducer. The purpose of the study is to improve our understanding of why and when these algorithms, which use perturbation, reweighting, and combination techniques, affect classification error. We provide a bias and variance decomposition of the error to show how different methods and variants influence these two terms. This allowed us to determine that Bagging reduced variance of unstable methods, while boosting methods (AdaBoost and Arc-x4) reduced both the bias and variance of unstable methods but increased the variance for Naive-Bayes, which was very stable. We observed that Arc-x4 behaves differently than AdaBoost if reweighting is used instead of resampling, indicating a fundamental difference. Voting variants, some of which are introduced in this paper, include: pruning versus no pruning, use of probabilistic estimates, weight perturbations (Wagging), and backfitting of data. We found that Bagging improves when probabilistic estimates in conjunction with no-pruning are used, as well as when the data was backfit. We measure tree sizes and show an interesting positive correlation between the increase in the average tree size in AdaBoost trials and its success in reducing the error. We compare the mean-squared error of voting methods to non-voting methods and show that the voting methods lead to large and significant reductions in the mean-squared errors. Practical problems that arise in implementing boosting algorithms are explored, including numerical instabilities and underflows. We use scatterplots that graphically show how AdaBoost reweights instances, emphasizing not only “hard” areas but also outliers and noise.

Putting Time in perspective : A valid, reliable individual-differences metric

Abstract: Time perspective (TP), a fundamental dimension in the construction of psychological time, emerges from cognitive processes partitioning human experience into past, present, and future temporal frames. The authors’ research program proposes that TP is a pervasive and powerful yet largely unrecognized influence on much human behavior. Although TP variations are learned and modified by a variety of personal, social, and institutional influences, TP also functions as an individual-differences variable. Reported is a new measure assessing personal variations in TP profiles and specific TP biases. The five factors of the Zimbardo Time Perspective Inventory were established through exploratory and confirmatory factor analyses and demonstrate acceptable internal and test–retest reliability. Convergent, divergent, discriminant, and predictive validity are shown by correlational and experimental research supplemented by case studies.

Modeling Term Structures of Defaultable Bonds

Abstract: This article presents convenient reduced-form models of the valuation of contingent claims subject to default risk, focusing on applications to the term structure of interest rates for corporate or sovereign bonds. Examples include the valuation of a credit-spread option. This article presents a new approach to modeling term structures of bonds and other contingent claims that are subject to default risk. As in previous “reduced-form” models, we treat default as an unpredictable event governed by a hazard-rate process. 1 Our approach is distinguished by the parameterization of losses at default in terms of the fractional reduction in market value that occurs at default. Specifically, we fix some contingent claim that, in the event of no default, pays X at time T . We take as given an arbitrage-free setting in which all securities are priced in terms of some short-rate process r and equivalent martingale measure Q [see Harrison and Kreps (1979) and Harrison and Pliska (1981)]. Under this “risk-neutral” probability measure, we letht denote the hazard rate for default at time t and let Lt denote the expected fractional loss in market value if default were to occur at time t , conditional

Systematic determination of genetic network architecture

Abstract: Technologies to measure whole-genome mRNA abundances1,2,3 and methods to organize and display such data4,5,6,7,8,9,10 are emerging as valuable tools for systems-level exploration of transcriptional regulatory networks. For instance, it has been shown that mRNA data from 118 genes, measured at several time points in the developing hindbrain of mice, can be hierarchically clustered into various patterns (or 'waves') whose members tend to participate in common processes5. We have previously shown that hierarchical clustering can group together genes whose cis-regulatory elements are bound by the same proteins in vivo6. Hierarchical clustering has also been used to organize genes into hierarchical dendograms on the basis of their expression across multiple growth conditions7. The application of Fourier analysis to synchronized yeast mRNA expression data has identified cell-cycle periodic genes, many of which have expected cis-regulatory elements8. Here we apply a systematic set of statistical algorithms, based on whole-genome mRNA data, partitional clustering and motif discovery, to identify transcriptional regulatory sub-networks in yeast—without any a priori knowledge of their structure or any assumptions about their dynamics. This approach uncovered new regulons (sets of co-regulated genes) and their putative cis-regulatory elements. We used statistical characterization of known regulons and motifs to derive criteria by which we infer the biological significance of newly discovered regulons and motifs. Our approach holds promise for the rapid elucidation of genetic network architecture in sequenced organisms in which little biology is known.

Exploring the Black Box: An Analysis of Work Group Diversity, Conflict and Performance

Abstract: In this paper we present an integrative model of the relationships among diversity, conflict, and performance, and we test that model with a sample of 45 teams. Findings show that diversity shapes conflict and that conflict, in turn, shapes performance, but these linkages have subtleties. Functional background diversity drives task conflict, but multiple types of diversity drive emotional conflict. Race and tenure diversity are positively associated with emotional conflict, while age diversity is negatively associated with such conflict. Task routineness and group longevity moderate these relationships. Results further show that task conflict has more favorable effects on cognitive task performance than does emotional conflict. Overall, these patterns suggest a complex link between work group diversity and work group functioning.

Using the Berlin Questionnaire To Identify Patients at Risk for the Sleep Apnea Syndrome

Abstract: Although sleep apnea is common, it often goes undiagnosed in primary care encounters. The Berlin Questionnaire was found to be a means of identifying patients who are likely to have sleep apnea.

Exploring the new world of the genome with DNA microarrays

Abstract: Thousands of genes are being discovered for the first time by sequencing the genomes of model organisms, an exhilarating reminder that much of the natural world remains to be explored at the molecular level. DNA microarrays provide a natural vehicle for this exploration. The model organisms are the first for which comprehensive genome-wide surveys of gene expression patterns or function are possible. The results can be viewed as maps that reflect the order and logic of the genetic program, rather than the physical order of genes on chromosomes. Exploration of the genome using DNA microarrays and other genome-scale technologies should narrow the gap in our knowledge of gene function and molecular biology between the currently-favoured model organisms and other species.

Evidence suggesting that a chronic disease self-management program can improve health status while reducing hospitalization: a randomized trial.

Abstract: Objectives.This study evaluated the effectiveness (changes in health behaviors, health status, and health service utilization) of a self-management program for chronic disease designed for use with a heterogeneous group of chronic disease patients. It also explored the differential effectiveness of

Phenomenology, astrophysics and cosmology of theories with submillimeter dimensions and TeV scale quantum gravity

Abstract: We recently proposed a solution to the hierarchy problem not relying on low-energy supersymmetry or technicolor. Instead, the problem is nullified by bringing quantum gravity down to the TeV scale. This is accomplished by the presence of $ng~2$ new dimensions of submillimeter size, with the SM fields localized on a 3-brane in the higher dimensional space. In this paper we systematically study the experimental viability of this scenario. Constraints arise both from strong quantum gravitational effects at the TeV scale, and more importantly from the production of massless higher dimensional gravitons with TeV suppressed couplings. Theories with $ng2$ are safe due mainly to the infrared softness of higher dimensional gravity. For $n=2,$ the six dimensional Planck scale must be pushed above $\ensuremath{\sim}30\mathrm{TeV}$ to avoid cooling SN 1987A and distortions of the diffuse photon background. Nevertheless, the particular implementation of our framework within type I string theory can evade all constraints, for any $ng~2,$ with string scale ${m}_{s}\ensuremath{\sim}1\mathrm{TeV}.$ We also explore novel phenomena resulting from the existence of new states propagating in the higher dimensional space. The Peccei-Quinn solution to the strong $\mathrm{CP}$ problem is revived with a weak scale axion in the bulk. Gauge fields in the bulk can mediate repulsive forces $\ensuremath{\sim}{10}^{6}--{10}^{8}$ times stronger than gravity at submillimeter distances, as well as help stabilize the proton. Higher-dimensional gravitons produced on our brane and captured on a different ``fat'' brane can provide a natural dark matter candidate.

The transcriptional program in the response of human fibroblasts to serum.

Abstract: The temporal program of gene expression during a model physiological response of human cells, the response of fibroblasts to serum, was explored with a complementary DNA microarray representing about 8600 different human genes. Genes could be clustered into groups on the basis of their temporal patterns of expression in this program. Many features of the transcriptional program appeared to be related to the physiology of wound repair, suggesting that fibroblasts play a larger and richer role in this complex multicellular response than had previously been appreciated.

Reducing Children's Television Viewing to Prevent Obesity: A Randomized Controlled Trial

Abstract: ContextSome observational studies have found an association between television viewing and child and adolescent adiposity.ObjectiveTo assess the effects of reducing television, videotape, and video game use on changes in adiposity, physical activity, and dietary intake.DesignRandomized controlled school-based trial conducted from September 1996 to April 1997.SettingTwo sociodemographically and scholastically matched public elementary schools in San Jose, Calif.ParticipantsOf 198 third- and fourth-grade students, who were given parental consent to participate, 192 students (mean age, 8.9 years) completed the study.InterventionChildren in 1 elementary school received an 18-lesson, 6-month classroom curriculum to reduce television, videotape, and video game use.Main Outcome MeasuresChanges in measures of height, weight, triceps skinfold thickness, waist and hip circumferences, and cardiorespiratory fitness; self-reported media use, physical activity, and dietary behaviors; and parental report of child and family behaviors. The primary outcome measure was body mass index, calculated as weight in kilograms divided by the square of height in meters.ResultsCompared with controls, children in the intervention group had statistically significant relative decreases in body mass index (intervention vs control change: 18.38 to 18.67 kg/m2 vs 18.10 to 18.81 kg/m2, respectively; adjusted difference −0.45 kg/m2 [95% confidence interval {CI}, −0.73 to −0.17]; P=.002), triceps skinfold thickness (intervention vs control change: 14.55 to 15.47 mm vs 13.97 to 16.46 mm, respectively; adjusted difference, −1.47 mm [95% CI, −2.41 to −0.54]; P=.002), waist circumference (intervention vs control change: 60.48 to 63.57 cm vs 59.51 to 64.73 cm, respectively; adjusted difference, −2.30 cm [95% CI, −3.27 to −1.33]; P<.001), and waist-to-hip ratio (intervention vs control change: 0.83 to 0.83 vs 0.82 to 0.84, respectively; adjusted difference, −0.02 [95% CI, −0.03 to −0.01]; P<.001). Relative to controls, intervention group changes were accompanied by statistically significant decreases in children's reported television viewing and meals eaten in front of the television. There were no statistically significant differences between groups for changes in high-fat food intake, moderate-to-vigorous physical activity, and cardiorespiratory fitness.ConclusionsReducing television, videotape, and video game use may be a promising, population-based approach to prevent childhood obesity.