Research

Healthcare 3.0

Open Innovation and Health Commons: Therapy Development in the Networked Age

(Presentation: Tenenbaum, J.M., Special Interest Group on Open Innovation, October 7, 2008) PDF

Abstract: Imagine a virtual marketplace or ecosystem where participants share data, knowledge, materials, and services to accelerate research. This Health Commons is a bold vision whose aim is no less than to change the processes, economics, and culture of translating basic research into drugs.

25+ million patients and their families suffer from over 6,000 orphan diseases that are currently uneconomical to address. The time is ripe for a radically different approach that leverages collaboration and the Internet to enable small teams of researchers to develop new therapies in a cost-effective manner and get them to patients quickly.

Virtual biotechs, using innovative research and clinical and business strategies, will exploit the Commons to slash the time and costs associated with drug development. As a result, a small group of patients with a rare disease can fund the development of new therapy in time to save their own lives. In the age of genomic sub-typing and personalized medicine–where every disease is potentially an orphan disease–the implications are far-reaching.

Health Commons: Therapy Development in a Networked World

(Paper: Tenenbaum, J. M. and Wilbanks, J., Science Commons, May 2008) PDF

Abstract: We have a rare moment in time where we can change the entire system in one motion by establishing a collaborative ecosystem of knowledge and research services that can be rapidly assembled to develop new therapies with unprecedented efficiencies and economies of scale. We can create the same radical increase in efficiency for scientific research that commerce saw in the 1990s, as secure Internet transactions transformed many vertically integrated industries into horizontally integrated ecosystems of service providers and consumers. The explosion of contract vendors in biotechnology, covering the spectrum from gene to protein to drug discovery, development and trials, is one factor. The emergence of the Semantic Web for science is part of the story, as is the existence proof that common use licensing can create explosive value in software and culture. And the power of the network to bring these elements together into a unified system, a Health Commons, is the final piece of the puzzle.

Visual Programming in BioBike, a Web-Based Biocomputing Environment

(Manuscript: Shrager, J., Massar, J. P., et al., 2008) PDF

Abstract: Within BioBike, a Web-based biocomputing environment, the BBL language enables biologists to program novel genomic algorithms. To engage users without prior programming experience, we have implemented a visual programming environment that allows users to create BBL code through a dynamic, direct-manipulation interface. The environment provides those new to programming with the ability to make use of a full-featured programming language, even to the point of easily building new functionality into BioBike.

Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment

(Paper: Waldinger, J., Shrager, J., AAAI Spring Symposium: Semantic Scientific Knowledge Integration, Stanford, CA, 2008) PDF

Abstract: An approach to question answering through automated deduction is advocated. Answers to questions are extracted from proofs of associated conjectures over an axiomatic theory of the subject domain. External knowledge resources, including data and software, are consulted through a mechanism known as procedural attachment. A researcher ignorant of the subject domain theory or its logical language can formulate questions via a query elicitation facility. A similar device allows an expert to extend the theory. An English explanation for each answer, and a justification for its correctness, is constructed automatically from the proof by which it was extracted. A deductive approach has been applied in planetary astronomy, geography, intelligence analysis, and, most recently, molecular biology and medical research applications. It is argued that the constructs in the Semantic Web languages, including OWL with SWRL, are insufficiently expressive for this kind of application.

Healthcare 3.0: Transforming Medicine through Collective Intelligence

(Video Presentation: Tenenbaum, J. M., Stanford University, May 24, 2007) Video

Abstract: All of healthcare is an experiment, but we measure only a small portion of the outcomes, i.e., in clinical trials. We’re also not very good at collaboratively analyzing the data, interpreting the results, and disseminating them in a timely and meaningful manner. In this talk, CommerceNet Chairman and Founder Marty Tenenbaum presents a vision and technological approach for addressing these problems by using the Web to tap the collective intelligence of patients, physicians, and medical researchers, ultimately bringing the world’s knowledge and resources to bear on curing diseases one patient at a time.

Deductive Biocomputing

(Shrager, J., Waldinger, R., Stickel, M., Massar, J., PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339, April 4, 2007) HTML

Abstract:

Background
As biologists increasingly rely upon computational tools, it is imperative that they be able to appropriately apply these tools and clearly understand the methods the tools employ. Such tools must have access to all the relevant data and knowledge and, in some sense, “understand” biology so that they can serve biologists’ goals appropriately and “explain” in biological terms how results are computed.

Methodology/Principal Findings
We describe a deduction-based approach to biocomputation that semi-automatically combines knowledge, software, and data to satisfy goals expressed in a high-level biological language. The approach is implemented in an open source Web-based biocomputing platform called BioDeducta, which combines SRI’s SNARK theorem prover with the BioBike interactive integrated knowledge base. The biologist/user expresses a high-level conjecture, representing a biocomputational goal query, without indicating how this goal is to be achieved. A subject domain theory, represented in SNARK’s logical language, transforms the terms in the conjecture into capabilities of the available resources and the background knowledge necessary to link them together. If the subject domain theory enables SNARK to prove the conjecture—that is, to find paths between the goal and BioBike resources—then the resulting proofs represent solutions to the conjecture/query. Such proofs provide provenance for each result, indicating in detail how they were computed. We demonstrate BioDeducta by showing how it can approximately replicate a previously published analysis of genes involved in the adaptation of cyanobacteria to different light niches.

The Evolution of BioBike: Community Adaptation of a Biocomputing Platform

(Article: Shrager, J., Studies in History and Philosophy of Science, 38, 642 – 656, 2007) PDF

Abstract: Programming languages are, at the same time, instruments and communicative artifacts that evolve rapidly through use. This paper describes an online computing platform called BioBike. BioBike is a trading zone where biologists and programmers collaborate in the development of an extended vocabulary and functionality for computational genomics. In the course of this work, they develop interactional expertise with one another’s domains. The extended BioBike vocabulary operates on two planes: as a working programming language, and as a pidgin in the conversation between the biologists and engineers. The flexibility that permits this community to dynamically extend BioBike’s working vocabulary—to form new pidgins—makes BioBike unique among computational tools, which usually are not themselves adapted through the collaborations that they facilitate. Thus BioBike is itself a crucial

BioBike and the KnowOS Vision of Intelligent Community Biocomputing

(Presentation: Shrager, J., UC Santa Cruz Genomics Technology Group, 2007) PDF

How Science Thinks: The Science and Engineering of Science and Engineering

(Presentation: Shrager, J., Stanford Symbolic Systems Forum, 2007) PDF

Smart Health: A Flexible, Open Path to Community Health Interoperability

(Report: Tenenbaum, J. M. , Schiffman, A. M., Brandman, D., and Blocker, A., February 2005) PDF

Abstract: This paper explores the application of e-commerce technologies to healthcare and concludes that there is indeed a substantial opportunity to leverage both experience and technology from industry. We begin by discussing the major integration challenges encountered in e-business, and how they are being addressed through e-marketplaces and business service networks (BSNs). We then outline the design for a healthcare BSN for the Silicon Valley, and discuss implementation and adoption issues. We conclude by speculating about the implications of this approach for other Regional Health Information Organizations (RHIOs), the National Health Information Infrastructure (NHII), and the future of healthcare.

User-Centric Security

The Seven Flaws of Identity Management: Usability and Security Challenges

(Paper: Dhamija, R., Dusseault, L., IEEE Security and Privacy, Volume 6, Issue 2, March – April 2008) PDF

Abstract: Web identity management systems are complex systems with powerful features—and many potential vulnerabilities. They aim to facilitate the management of identifiers, credentials, personal information, and the presentation of this information to other parties. In many schemes, an identity provider (IdP) issues identities or credentials to users, while a relying party (RP) depends on the IdP to check the user credentials before it allows users access to website services. By separating the role of and IdP from the RP, identity management systems let users leverage one identifier across multiple Web services.

The Emperor’s New Security Indicators

(Paper: Schechter, S. E., Dhamija, R., Ozment, A., Fischer, I., The 2007 IEEE Symposium on Security and Privacy, May 2007) PDF

Abstract: We evaluate website authentication measures that are designed to protect users from man-in-the-middle, ‘phishing,’ and other site forgery attacks. We asked 67 bank customers to conduct common online banking tasks. Each time they logged in, we presented increasingly alarming clues that their connection was insecure. First, we removed HTTPS indicators. Next, we removed the participant’s site-authentication image—the customer-selected image that many websites now expect their users to verify before entering their passwords. Finally, we replaced the bank’s password-entry page with a warning page. After each clue, we determined whether participants entered their passwords or withheld them. We also investigate how a study’s design affects participant behavior: we asked some participants to play a role and others to use their own accounts and passwords. We also presented some participants with security-focused instructions. We confirm prior findings that users ignore HTTPS indicators: no participants withheld their passwords when these indicators were removed. We present the first empirical investigation of site-authentication images, and we find them to be ineffective: even when we removed them, 23 of the 25 (92%) participants who used their own accounts entered their passwords. We also contribute the first empirical evidence that role playing affects participants’ security behavior: role-playing participants behaved significantly less securely than those using their own passwords.

Emerging Internet Technologies / Standards

Agoric Architectural Styles for Decentralized Space Exploration

(Presentation: Khare, R. and Taylor, R.N., IEEE, Space Mission Challenges in Information Technology Workshop on Deep Space Communications, July 17 – 18, 2006) PDF

Abstract: A survey of how market-based approaches can affect space-mission planning, ranging from Information Markets to prioritize science goals at planning-time to Agoric Computing to trade computing resources during a mission. We also briefly introduce the challenges of Mechanism Design to outline the limits of market institutions, and its implications for new Architectural Styles that guide software development and integration based on these principles.

Hierarchy in Web Page Similarity Link Analysis

(Technical Report: Schiffman, Allan M., May 2006) PDF

Abstract: Rather than using traditional text analysis to discover Web pages similar to a given page, we investigate applying link analysis. Since web pages exist in a link-rich environment, that has the potential to relate pages by any property imaginable — since links are not restricted to intrinsic properties of the page text or metadata. In particular, while Web page similarity link analysis has been explored, prior work has deliberately ignored the explicitly hierarchical host & pathname structure within URLs. To exploit this property, we generalize Kleinberg’s well-known “hubs and authorities” HITS algorithm; adapt this algorithm to accommodate hierarchical link structure; test some sample web queries; and argue that the results are potentially superior and that the algorithm itself is better motivated.

Zocalo and Prediction Market Design

(Presentation: Hibbert, Chris, Prediction Market Summit, February 4, 2006) PDF, PPT

Abstract: This presentation recaps the status of the Zocalo project, presents a proposal that existing prediction markets would benefit from increasing their search engine visibility and providing price feeds, and shows how most of the existing prediction markets are missing an easy chance to offer more liquidity in their multi-outcome claims. The Zocalo Prediction Market toolkit is available as open source at SourceForge, and is being used in laboratory experiments at George Mason University. Those experiment are characterizing the effects of manipulators on Prediction Markets. We show a web-based replay of one session of those experiments. There are quite a few topics covered by the existing publicly visible prediction markets that are of widespread interest. The companies operating those markets could increase their visibility substantially by making their markets more searchable. If the descriptions of the claims were posted with stable web addresses, people interested in the topics could refer to them more easily, and the search engines would be more likely to notice them when crawling the web, and more able to show them as results when they are relevant to a query. When prediction markets are based on claims with multiple exclusive outcomes, most of the current markets are not presenting traders with the best available prices. These markets maintain a separate double auction for each outcome, segmenting the available order volume into non-interacting submarkets. When outcomes are exclusive, bids on each outcome are bets against each of the others, and could add to the liquidity of all positions. Since most traders are price takers, this results in fewer trades taking place. Arbitrageurs are not a substitute for the market in offering these trading opportunities,

Microformats: The Next (Small) Thing on the Semantic Web?

(Article: Khare, R., IEEE Internet Computing, Vol. 10, No. 1, pp. 68 – 75, January/February 2006)
HTML

Abstract: Clever application of existing XHTML elements and class attributes can make it easier to describe people, places, events, and other semistructured information in human-readable form.

Microformats: A Pragmatic Path to the Semantic Web

(Technical Report: Khare, Rohit and Çelik, Tantek, January 2006) PDF

Abstract: Microformats are a clever adaptation of semantic XHTML that makes it easier to publish, index, and extract semi-structured information such as tags, calendar entries, contact information, and reviews on the Web. This makes it a pragmatic path towards achieving the vision set forth for the Semantic Web. Even though it sidesteps the existing “technology stack” of RDF, ontologies, and Artificial Intelligence-inspired processing tools, various microformats have emerged that parallel the goals of several well-known Semantic Web projects. This position paper introduces the ideas behind microformats and gives examples; compares to similar efforts in the Semantic Web; and compares their prospects according to Rogers’ Diffusion of Innovation model.

AI Meets Web 2.0: Building The Web of Tomorrow Today

(Technical Report: Tenenbaum, J. M., December 2005) PDF

Abstract: Imagine an Internet-scale Knowledge System where people and intelligent agents can collaborate on solving complex problems in business, engineering, science, medicine, and other endeavors. Its resources include semantically tagged Web sites, wikis, and blogs, as well as social networks, vertical search engines and a vast array of Web services from business processes to AI planners and domain models. Research prototypes of decentralized knowledge systems have been demonstrated for years, but now, thanks to the Web and Moore’s Law, they appear ready for prime time. Architectural concepts for incrementally growing an Internet-scale knowledge system are introduced, with descriptions of early commercial deployments in manufacturing and healthcare.

KudoRank: A Market Model for Mail Management

(Technical Report: Khare, R., November 2005) PDF

Abstract: This paper describes a novel approach to searching personal information archives: a market mechanism for ‘pricing’ the value of information from different authors. Traditional text indexing assumes all documents in a collection are equally important, so the ranking of search results is based on the frequency of term occurrence, age, or other endogenous properties of the result set itself. We investigated whether higher-quality results can be obtained by ranking documents based on analysis of the social network between correspondents. This approach appears particularly promising for personal information archives, where much of the data to be retrieved is private and little contextual metadata exists.

QuestionMarket: A Marketplace Mechanism for Tapping into the Value of Human Cognition

(Technical Report: Hill, B., October 2005) PDF

Abstract: A QuestionMarket enables the exchange of units of human-generated information. While many other distributed ‘grid’ systems create a marketplace for trading computational resources like processing, bandwidth, and storage, QuestionMarket deals in the acquisition and exchange of small units of human cognition. By focusing on puzzles that are difficult to solve with a computer but relatively easy for humans, so called AI-complete problems are resistant to Moore’s Law while encompassing a wide range of valuable human-only work, such as translation, tagging, and filtering.

Decentralizing Sponsored Web Advertising

(Technical Report: Khare, R. and Sittler, B., April 2005) PDF

Abstract: Today, sponsored search auctions are purely centralized. A single, trusted agency controls who can advertise; acceptable advertising messages; the mapping of ads to pages; placement within pages; and, of course, the entire bidding process. We are interested in learning more about the challenges of building a peer-to-peer alternative; and to discuss our experiments with an alternative mechanism, Ross Mayfield’s “cost-per-influence.”

Business Services Networks: Delivering the Promises of B2B

(Article and Presentation: Tenenbaum, J. M., and Khare, R., IEEE Workshop on Business Services Network, March 29, 2005, pp. 52 – 60) Article, BSN05-EEE05.slides

Abstract: The fundamental challenge of e-commerce is enabling companies to do business with one another across a network, despite different business processes and computer systems. Traditionally, these problems were overcome through custom point-to-point integration or Electronic Data Interchange (EDI) networks. These expensive, time-consuming approaches make economic sense only when companies do a lot of business together. The promise of the Internet, by contrast, is an open e-business platform where companies can do business spontaneously with anyone, anywhere, anytime. Business Services Networks fulfill that vision. This vision paper also presents CommerceNet’s role in catalyzing industrial adoption.

Zocalo: An Open-Source Platform for Deploying Prediction Markets

(Technical Report: Hibbert, C., February 2005) PDF

Abstract: We propose developing an open-source toolkit for creating markets, called Zocalo, in order to catalyze broader adoption of markets in academia, industry, and throughout society. We are primarily interested in prediction markets, which allow traders to buy and sell securities that pay out based on the outcome of some future event, but Zocalo would also be useful for creating markets in other goods.

Business Services Networks: Delivering the Promises of B2B

(Technical Report: Tenenbaum, J. M. and Khare, R., January 2005) PDF

Leveraging Product Codes for Internet Commerce

(Technical Report: Stapleton-Gray, R., November 2004) PDF

Abstract: A Registry complementary to the Object Naming Service (ONS) planned for RFID – but specifically mapping the previous generation of product codes – would jump-start the use of product codes as unique identifiers in Internet commerce. In the long run, it would be subsumed by the ONS itself, but would play a valuable role now as a means to rapidly facilitate conversion of product codes to useful handles on the Internet. The white paper outlines the challenge of creating such a Registry and associated open-source product information-publishing tools, with estimates of the effort required.

Web Services After Five Years (Panel Discussion)

Technical Report: Khare, R., November 2004) PDF

Nutch: A Flexible and Scalable Open-Source Web Search Engine

(Technical Report: Khare, R., Cutting, D., Sitaker, K., and Rifkin, A., November 2004) PDF

Abstract: Nutch is an open-source Web search engine that can be used at global, local, and even personal scale. Its initial design goal was to enable a transparent alternative for global Web search in the public interest. It has also been used for intranets; by local communities with richer data models, such as the Creative Commons metadata-enabled search for licensed content; on a personal scale to index a user’s files, email, and web-surfing history. We also report on several other research projects built on Nutch and how Nutch’s architecture enables it to be more flexible and scalable than other comparable systems today.

Event-Driven Information: A Core Component of the Now Economy

(Technical Report: Stapleton-Gray, R., November 2004) PDF

Abstract: The potential for applications that make use of networked, time-driven information is huge. Today’s portals have no concept of event personalization or collaboration. Today’s applications have only the most basic concept of integrating with or subscribing to time-driven data. And there are no providers of horizontal event-based services. The hosted calendar model deserves exploration and development it can make communities stronger and more vibrant, and organizations better informed. Software and the Internet has freed online music from its proprietary data and application jails, why not do the same with events? The traditional calendar interface deserves a overhaul.

Extending the Representational State Transfer (REST) Architectural Style for Decentralized Systems

(Article: Khare, R. and Taylor, R. N., May 23 – 28, 2004) PDF

Abstract: Because it takes time and trust to establish agreement, traditional consensus-based architectural styles cannot safely accommodate resources that change faster than it takes to transmit notification of that change, nor resources that must be shared across independent agencies. The alternative is decentralization: permitting independent agencies to make their own decisions. Our definition contrasts with that of distribution, in which several agents share control of a single decision. Ultimately, the physical limits of network latency and the social limits of independent agency call for solutions that can accommodate multiple values for the same variable. Our approach to this challenge is architectural: proposing constraints on the configuration of com-ponents and connectors to induce particular desired properties of the whole application. Specifically, we present, implement, and evaluate variations of the World Wide Web’s Representational State Transfer (REST) architectural style that support distributed and decentralized systems.

Business Service Networks

(Presentation: Tenenbaum, J. M. IEEE Conference on Electronic Commerce 2004 and IEEE International Conference on Web Services 2004, July 6 – 9, 2004) PDF

An Introduction to zLab

(Technical Report: Khare, R., July 2004) PDF

Abstract: zLab is the first initiative from CommerceNet Labs, our new research initiative. This draft speech reviews the history and successes of the first decade of CommerceNet to put this strategy into perspective. zLab is an investment in our updated mission: Inspiring ideas to advance commerce in the Now Economy. In particular, we are investigating how to build software that can work the way society works, without any absolute center of power. This could lead to an entirely new generation of tools for decentralized commerce, in which individuals and firms can connect dynamically and in real-time. This is illustrated through experimental concepts such as zBay, zSearch, and zClassifieds