David Goldberg

Using collaborative filtering to weave an information tapestry

The Tapestry experimental mail system developed at the Xerox Palo Alto Research Center is predicated on the belief that information filtering can be more effective when humans are involved in the filtering process. Tapestry was designed to support both content-based filtering and collaborative filtering, which entails people collaborating to help each other perform filtering by recording their reactions to documents they read. The reactions are called annotations; they can be accessed by other people’s filters. Tapestry is intended to handle any incoming stream of electronic documents and serves both as a mail filter and repository; its components are the indexer, document store, annotation store, filterer, little box, remailer, appraiser and reader/browser. Tapestry’s client/server architecture, its various components, and the Tapestry query language are described.

What every computer scientist should know about floating-point arithmetic

Floating-point arithmetic is considered as esoteric subject by many people. This is rather surprising, because floating-point is ubiquitous in computer systems: Almost every language has a floating-point datatype; computers from PCs to supercomputers have floating-point accelerators; most compilers will be called upon to compile floating-point algorithms from time to time; and virtually every operating system must respond to floating-point exceptions such as overflow. This paper presents a tutorial on the aspects of floating-point that have a direct impact on designers of computer systems. It begins with background on floating-point representation and rounding error, continues with a discussion of the IEEE floating point standard, and concludes with examples of how computer system builders can better support floating point.

Continuous queries over append-only databases

In a database to which data is continually added, users may wish to issue a permanent query and be notified whenever data matches the query. If such continuous queries examine only single records, this can be implemented by examining each record as it arrives. This is very efficient because only the incoming record needs to be scanned. This simple approach does not work for queries involving joins or time. The Tapestry system allows users to issue such queries over a database of mail and bulletin board messages. The user issues a static query, such as “show me all messages that have been replied to by Jones,” as though the database were fixed and unchanging. Tapestry converts the query into an incremental query that efficiently finds new matches to the original query as new messages are added to the database. This paper describes the techniques used in Tapestry, which do not depend on triggers and thus be implemented on any commercial database that supports SQL. Although Tapestry is designed for filtering mail and news messages, its techniques are applicable to any append-only database.

Liveboard: a large interactive display supporting group meetings, presentations, and remote collaboration

This paper describes the Liveboard, a large interactive display system. With nearly one million pixels and an accurate, multi-state, cordless pen, the Liveboard provides a basis for research on user interfaces for group meetings, presentations and remote collaboration. We describe the underlying hardware and software of the Liveboard, along with several software applications that have been developed. In describing the system, we point out the design rationale that was used to make various choices. We present the results of an informal survey of Liveboard users, and describe some of the improvements that have been made in response to user feedback. We conclude with several general observations about the use of large public interactive displays.

An overview of the PARCTAB ubiquitous computing experiment

The PARCTAB system integrates a palm-sized mobile computer into an office network. The PARCTAB project serves as a preliminary testbed for ubiquitous computing, a philosophy originating at Xerox PARC that aims to enrich our computing environment by emphasizing context sensitivity, casual interaction and the spatial arrangement of computers. This article describes the ubiquitous computing philosophy, the PARCTAB system, user interface issues for small devices, and our experience in developing and testing a variety of mobile applications.

Touch-typing with a stylus

One of the attractive features of keyboards is that they support novice as well as expert users. Novice users enter text using “hunt-and-peck,” experts use touch-typing. Although it takes time to learn touch-typing, there is a large payoff in faster operation. In contrast to keyboarda, pen-based computers have only a novice mode for text entry in which users print text to a character recognize. An electronic pen (or stylus) would be more attractive as an input device if it supported expert users with some analogue of touch-typing. We present the design and preliminary analysis of an approach to stylus touch-typing using an alphabet of unistrokes, which are letters specially designed to be used with a stylus. Unistrokes have the following advantages over ordinary printing they are faster to write, less prone to recognition error, and can be entered in an “eyes-free” manner that requires very little screen real estate.

The Parctab Ubiquitous Computing Experiment

The ParcTab system integrates a palm-sized mobile computer into an office network. This project serves as a preliminary testbed for Ubiquitous Computing, a philosophy originating at Xerox PARC that aims to enrich our computing environment by emphasizing context sensitivity, casual interaction and the spatial arrangement of computers. This paper describes the Ubiquitous Computing philosophy, the ParcTab system, user-interface issues for small devices, and our experience developing and testing a variety of mobile applications.

Automatic Quality Assessment of Peptide Tandem Mass Spectra

MOTIVATION A powerful proteomics methodology couples high-performance liquid chromatography (HPLC) with tandem mass spectrometry and database-search software, such as SEQUEST. Such a set-up, however, produces a large number of spectra, many of which are of too poor quality to be useful. Hence a filter that eliminates poor spectra before the database search can significantly improve throughput and robustness. Moreover, spectra judged to be of high quality, but that cannot be identified by database search, are prime candidates for still more computationally intensive methods, such as de novo sequencing or wider database searches including post-translational modifications. RESULTS We report on two different approaches to assessing spectral quality prior to identification: binary classification, which predicts whether or not SEQUEST will be able to make an identification, and statistical regression, which predicts a more universal quality metric involving the number of b- and y-ion peaks. The best of our binary classifiers can eliminate over 75% of the unidentifiable spectra while losing only 10% of the identifiable spectra. Statistical regression can pick out spectra of modified peptides that can be identified by a de novo program but not by SEQUEST. In a section of independent interest, we discuss intensity normalization of mass spectra.

Activation of Murine CD4+ and CD8+ T Lymphocytes Leads to Dramatic Remodeling of N-Linked Glycans

Differentiation and activation of lymphocytes are documented to result in changes in glycosylation associated with biologically important consequences. In this report, we have systematically examined global changes in N-linked glycosylation following activation of murine CD4 T cells, CD8 T cells, and B cells by MALDI-TOF mass spectrometry profiling, and investigated the molecular basis for those changes by assessing alterations in the expression of glycan transferase genes. Surprisingly, the major change observed in activated CD4 and CD8 T cells was a dramatic reduction of sialylated biantennary N-glycans carrying the terminal NeuGcα2-6Gal sequence, and a corresponding increase in glycans carrying the Galα1-3Gal sequence. This change was accounted for by a decrease in the expression of the sialyltransferase ST6Gal I, and an increase in the expression of the galactosyltransferase, α1-3GalT. Conversely, in B cells no change in terminal sialylation of N-linked glycans was evident, and the expression of the same two glycosyltransferases was increased and decreased, respectively. The results have implications for differential recognition of activated and unactivated T cells by dendritic cells and B cells expressing glycan-binding proteins that recognize terminal sequences of N-linked glycans.

Stylus user interfaces for manipulating text

Abstract This paper is concerned with pen-based (also called stylus-based) computers. Two of the key questions for such computers are how to interface to handwriting recognition algorithms, and whether there are interfaces that can effectively exploit the differences between a stylus and a keyboard/mouse. We describe prototypes that explore each of these questions. Our text entry tool is designed around the idea that handwriting recognition algorithms will always be error prone, and has a different flavor from existing systems. Our prototype editor goes beyond the usual gesture editors used with styli and is based on the idea of leaving the markups visible.