Am working on providing pointers and discussion on AI in Medicine (AIM).
The general place to check first is the main Artificial Intelligence in Medicine resource page. You’ll find some useful ideas about Hetnets in biomedicine. These are heterogeneous networks with multiple node or relationship types. Useful for data integration, translation, and biomedical knowledge mining. You’ll also find out aboutProject Rephetio (Drug Repurposing) developed to predict new uses for existing compounds. In addition, you’ll find links to OBI – the Ontology for Biomedical Investigations.
Referenes and links associated with IBM Watson / WatsonPaths medical applications are located here.
For convenience and robustness, I am including the initial references below. Enjoy.
AI in Medicine (AIM) approaches and applications have assisted in both trivial and profound ways, and they hold great promise. We argue that there are even larger systemic benefits when AI enabled medicine is considered at a national level.
This page aims to present relevant information and links to resources useful in furthering AIM objectives. Some links point to reports,preprints, papers, and books, other point to active and inactive databases, still others point software repositories and AIM specific software and platforms. While some of the links point to completed and/or terminated projects, we believe there’s much to be learned from the linked resources, and we hope these are used to spark curiosity and further ideas and progress in the spirit of “on the shoulders of Giants”.
AIM Related Projects
IBM WATSON / WatsonPaths: IBM’s Watson architecture was and is being employed in Medical applications.
WatsonPaths: Scenario-Based Question Answering and Inference over Unstructured Information is a key paper available here. As an illustration, the paper discusses a Patient with Erythropoietin Deficiency. Via the query “A 32-year-old woman with type 1 diabetes mellitus has had progressive renal failure… Her hemoglobin concentration is 9 g/dL… A blood smear shows normochromic, normocytic cells. What is the problem?
The table below provides links to some of the key patents in IBM’s Watson Intellectual Property portfolio- SCROLL to the right within the table to see immediate links to the patent PDFs.
|id||title||inventor/author||priority date||grant date||result link|
|US-10216804-B2||Providing answers to questions using hypothesis pruning||Jennifer Chu-Carroll, David A. Ferrucci, David C. Gondek, Adam P. Lally, James C. Murdock, IV||9/28/10||2/26/19||https://patents.google.com/patent/US10216804B2/en|
|US-10133808-B2||Providing answers to questions using logical synthesis of candidate answers||Eric W. Brown, Jennifer Chu-Carroll, David A. Ferrucci, Adam P. Lally, James W. Murdock, John M. Prager||9/28/10||11/20/18||https://patents.google.com/patent/US10133808B2/en|
|US-9805613-B2||System and method for domain adaptation in question answering||Sugato Bagchi, David A. Ferrucci, David C. Gondek, Anthony T. Levas, Wlodek W. Zadrozny||5/14/08||10/31/17||https://patents.google.com/patent/US9805613B2/en|
|US-9798800-B2||Providing question and answers with deferred type evaluation using text with limited structure||Pablo A. Duboue, James J. Fan, David A. Ferrucci, James W. Murdock, IV, Christopher A. Welty, Wlodek W. Zadrozny||9/24/10||10/24/17||https://patents.google.com/patent/US9798800B2/en|
|US-9690861-B2||Deep semantic search of electronic medical records||Keerthana Boloor, Eric W. Brown, Murthy V. Devarakonda, David Ferrucci, John M. Prager||7/17/14||6/27/17||https://patents.google.com/patent/US9690861B2/en|
|US-9529845-B2||Candidate generation in a question answering system||Jennifer Chu-Carroll, James J. Fan, David A. Ferrucci||8/13/08||12/27/16||https://patents.google.com/patent/US9529845B2/en|
|US-9508038-B2||Using ontological information in open domain type coercion||David A. Ferrucci, Aditya Kalyanpur, James W. Murdock, IV, Christopher A. Welty, Wlodek W. Zadrozny||9/24/10||11/29/16||https://patents.google.com/patent/US9508038B2/en|
|US-9454603-B2||Semantically aware, dynamic, multi-modal concordance for unstructured information analysis||Branimir K. Boguraev, Youssef Drissi, David A. Ferrucci, Paul T. Keyser, Anthony T. Levas||8/6/10||9/27/16||https://patents.google.com/patent/US9454603B2/en|
|US-9262938-B2||Combining different type coercion components for deferred type evaluation||Sugato Bagchi, James J. Fan, David A. Ferrucci, Aditya A. Kalyanpur, James W. Murdock, IV, Christopher A. Welty||3/15/13||2/16/16||https://patents.google.com/patent/US9262938B2/en|
|US-9189541-B2||Evidence profiling||Eric W. Brown, Jennifer Chu-Carroll, James J. Fan, David A. Ferrucci, David C. Gondek, Anthony T. Levas, James W. Murdock, IV||9/24/10||11/17/15||https://patents.google.com/patent/US9189541B2/en|
|US-9165252-B2||Utilizing failures in question and answer system responses to enhance the accuracy of question and answer systems||Michael A. Barborak, Jennifer Chu-Carroll, David A. Ferrucci, James W. Murdock, IV, Wlodek W. Zadrozny||7/15/11||10/20/15||https://patents.google.com/patent/US9165252B2/en|
|US-9153142-B2||User interface for an evidence-based, hypothesis-generating decision support system||Sugato Bagchi, Michael A. Barborak, Steven D. Daniels, David A. Ferrucci, Anthony T. Levas||5/26/11||10/6/15||https://patents.google.com/patent/US9153142B2/en|
|US-9146917-B2||Validating that a user is human||Michael A. Barborak, David A. Ferrucci, James W. Murdock, IV, Wlodek W. Zadrozny||7/15/11||9/29/15||https://patents.google.com/patent/US9146917B2/en|
|US-9031832-B2||Context-based disambiguation of acronyms and abbreviations||Branimir K. Boguraev, Jennifer Chu-Carroll, David A. Ferrucci, Anthony T. Levas, John M. Prager||9/29/10||5/12/15||https://patents.google.com/patent/US9031832B2/en|
|US-8972321-B2||Fact checking using and aiding probabilistic question answering||David A. Ferrucci, David C. Gondek, Aditya A. Kalyanpur, Adam P. Lally, Siddharth Patwardham||9/29/10||3/3/15||https://patents.google.com/patent/US8972321B2/en|
|US-8943051-B2||Lexical answer type confidence estimation and application||James J. Fan, David A. Ferrucci, David C. Gondek, Aditya A. Kalyanpur, Adam P. Lally, James W. Murdock, Wlodek W. Zadrozny||9/24/10||1/27/15||https://patents.google.com/patent/US8943051B2/en|
|US-8880388-B2||Predicting lexical answer types in open domain question and answering (QA) systems||David A. Ferrucci, Alfio M. Gliozzo, Aditya A. Kalyanpur||8/4/11||11/4/14||https://patents.google.com/patent/US8880388B2/en|
|US-2014164303-A1||Method of answering questions and scoring answers using structured knowledge mined from a corpus of data||Sugato Bagchi, David A. Ferrucci, Anthony T. Levas, Erik T. Mueller||12/11/12||https://patents.google.com/patent/US20140164303A1/en|
|US-8738362-B2||Evidence diffusion among candidate answers during question answering||David A. Ferrucci, David C. Gondek, Aditya A. Kalyanpur, Adam P. Lally||9/28/10||5/27/14||https://patents.google.com/patent/US8738362B2/en|
|US-8738617-B2||Providing answers to questions using multiple models to score candidate answers||Eric W. Brown, David A. Ferrucci, James W. Murdock, IV||9/28/10||5/27/14||https://patents.google.com/patent/US8738617B2/en|
|US-2014108322-A1||Text-based inference chaining||David W. Buchanan, David A. Ferrucci, Adam P. Lally||10/12/12||https://patents.google.com/patent/US20140108322A1/en|
|US-2014072948-A1||Generating secondary questions in an introspective question answering system||Branimir K. Boguraev, David W. Buchanan, Jennifer Chu-Carroll, David A. Ferrucci, Aditya A. Kalyanpur, James W. Murdock, IV, Siddharth A. Patwardhan||9/11/12||https://patents.google.com/patent/US20140072948A1/en|
|US-8560300-B2||Error correction using fact repositories||David A. Ferrucci, David C. Gondek, Wlodek W. Zadrozny||9/9/09||10/15/13||https://patents.google.com/patent/US8560300B2/en|
|US-8510327-B2||Method and process for semantic or faceted search over unstructured and annotated data||Branimir Konstantinov Boguraev, Eric William Brown, Youssef Drissi, David Angelo Ferrucci, Paul Turquand Keyser, Anthony Tom Levas, Dafna Sheinwald||9/24/10||8/13/13||https://patents.google.com/patent/US8510327B2/en|
|US-8332394-B2||System and method for providing question and answers with deferred type evaluation||James Fan, David Ferrucci, David C. Gondek, Wlodek W. Zadrozny||5/23/08||12/11/12||https://patents.google.com/patent/US8332394B2/en|
|US-8301438-B2||Method for processing natural language questions and apparatus thereof||David Angelo Ferrucci, Li Ma, Yue Pan, Zhao Ming Qiu, Chen Wang, Christopher Welty, Lei Zhang||4/23/09||10/30/12||https://patents.google.com/patent/US8301438B2/en|
|US-8280838-B2||Evidence evaluation system and method based on question answering||David A. Ferrucci, Wlodek W. Zadrozny||9/17/09||10/2/12||https://patents.google.com/patent/US8280838B2/en|
|US-8275803-B2||System and method for providing answers to questions||Eric W. Brown, David Ferrucci, Adam Lally, Wlodek W. Zadrozny||5/14/08||9/25/12||https://patents.google.com/patent/US8275803B2/en|
|CA-2843405-A1||A decision-support application and system for problem solving using a question-answering system||Sugato Bagchi, David A. Ferrucci, Anthony T. Levas, Erik T. Mueller||3/8/11||https://patents.google.com/patent/CA2843405A1/en|
|US-8200656-B2||Inference-driven multi-source semantic search||Eric W. Brown, Jennifer Chu-Carroll, James J. Fan, David A. Ferrucci, David C. Gondek, Anthony T. Levas, James William Murdock, IV||11/17/09||6/12/12||https://patents.google.com/patent/US8200656B2/en|
|US-2011125734-A1||Questions and answers generation||Pablo A. Duboue, David A. Ferrucci, David C. Gondek, James W. Murdock, IV, Wlodek W. Zadrozny||11/23/09||https://patents.google.com/patent/US20110125734A1/en|
|US-7757163-B2||Method and system for characterizing unknown annotator and its type system with respect to reference annotation types and associated reference taxonomy nodes||Yurdaer N. Doganata, Youssef Drissi, David A. Ferrucci, Tong-haing Fin, Genady Grabarnik, Lev Kozakov||1/5/07||7/13/10||https://patents.google.com/patent/US7757163B2/en|
|US-7333967-B1||Method and system for automatic computation creativity and specifically for story generation||Selmer Conrad Bringsjord, David Angelo Ferrucci||12/23/99||2/19/08||https://patents.google.com/patent/US7333967B1/en|
|US-7178105-B1||Method and system for document component importation and reconciliation||David Angelo Ferrucci, Steinar Flatland, Adam Patrick Lally||2/4/00||2/13/07||https://patents.google.com/patent/US7178105B1/en|
|US-7139752-B2||System, method and computer program product for performing unstructured information management and automatic text analysis, and providing multiple document views derived from different document tokenizations||Andrei Z Broder, David Carmel, Arthur C Ciccolo, David Ferrucci, Yoelle Maarek, Yosi Mass, Aya Soffer, Wlodek W Zadrozny||5/30/03||11/21/06||https://patents.google.com/patent/US7139752B2/en|
|US-7131057-B1||Method and system for loose coupling of document and domain knowledge in interactive document configuration||David Angelo Ferrucci, Steinar Flatland, Adam Patrick Lally||2/4/00||10/31/06||https://patents.google.com/patent/US7131057B1/en|
|US-2004243554-A1||System, method and computer program product for performing unstructured information management and automatic text analysis||Andrei Broder, Arthur Ciccolo, David Ferrucci, Alan Marwick, Wlodek Zadrozny||5/30/03||https://patents.google.com/patent/US20040243554A1/en|
|US-2004243556-A1||System, method and computer program product for performing unstructured information management and automatic text analysis, and including a document common analysis system (CAS)||David Ferrucci, Thilo Goetz, Thomas Hampp, Alan Marwick, Oliver Suhre, Wlodek Zadrozny||5/30/03||https://patents.google.com/patent/US20040243556A1/en|
|US-2004243560-A1||System, method and computer program product for performing unstructured information management and automatic text analysis, including an annotation inverted file system facilitating indexing and searching||Andrei Broder, David Ferrucci, Alan Marwick, Yosi Mass, Wlodek Zadrozny||5/30/03||https://patents.google.com/patent/US20040243560A1/en|
SOME BOOKS ON IBM WATSON
(unless otherwise specified, these are of general domain applicability)
- Rob High and Tanmay Bakshi, (2019) Cognitive Computing with IBM Watson: Build smart applications using artificial intelligence as a service
- IBM Redbooks, IBM Watson Content Analytics: Discovering Actionable Insight from Your Content. 3rd Edition
- Steven Baker, (2011), Final Jeopardy: Man vs. Machine and the Quest to Know Everything
RELEVANT SOURCES INCLUDING THOSE CITED IN PATENTS:
- IBM’s DeepQA Research Team Publications
- Ferrucci et al., “Towards the Open Advancement of Question Answering Systems,” IBM Technical Report RC24789, Computer Science, Apr. 22, 2009.
- David Ferrucci, Eric Brown, Jennifer Chu-Carroll, James Fan, David Gondek, Aditya A. Kalyanpur, Adam Lally, J. William Murdock, Eric Nyberg, John Prager, Nico Schlaefer, and Chris Welty, (2010) *Building Watson: An Overview of the DeepQA Project, AI Magazine Fall, 2010.
- William Murdock (2015), Decision Making in IBM Watson Question Answering Web presentation: Ontology Summit 2015
- M. Devarakonda, Dongyang Zhang, Ching-Huei Tsou, M. Bornea, Problem-oriented patient record summary: An early report on a Watson application, e-Health Networking, Applications and Services (Healthcom), 2014 IEEE 16th International Conference on, pp. 281-286
- WatsonPaths: Scenario-based Question Answering and Inference over Unstructured Information,IBM Research Report RC25489, IBM, 2014
- Nico Schlaefer, (2011),Statistical Source Expansion for Question Answering, PHD Thesis,CMU-LTI-11-019
- Special Issue on Question Answering, AI Magazine Vol 31 No 3: Fall 2010
- Bernstein et al., Ginseng: A Guided Input Natural Language Search Engine for Querying Ontologies, 2006, Jena User Conference, pp. 1-3.
- Blitzer, Domain Adaptation of Natural Language Processing Systems, Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy, 2007.
- Bollen et al., Mining associative relations from website logs and their application to context-dependent retrieva
- l using spreading activation, 1999, ACM, pp. 1-6.
- Broekstra et al., Sesame: A Generic Architecture for Storing and Querying RDF and RDF Schema, 2002, ISWC, vol. 2342/2002, pp. 54-68.
- Chang et al., “Creating An Online Dictionary of Abbreviations from MEDLINE,” J Am Med Inform Assoc. 2002; 9:612-620. DOI 10.1197/jamia.M1139.
- Chu-Carroll et al., “In Question-Ansering, Two Heads are Better than One”, HLT-NAACL’03, May-Jun. 2003, pp. 24-31, Edmonton, Canada.
- Cucerzan et al., “Factoid Question Answering over Unstructured and Structured Web Content”, In Proceedings of the 14th Text Retrieval Conference TREC 2005, Dec. 31, 2005.
- Finin, Swoogle: a search and metadata engine for the semantic web, 2004, ACM, pp. 652-659.
- Fininet al., Information Retrieval and the Semantic Web, 2005, System Sciences, pp. 1-10.
- Kaufmann et al., How Useful Are Natural Language Interfaces to the Semantic Web for Casual End-Users?, 2007, Springer, pp. 281-294.
- Ran et al., Natrual Language Query System for RDF Repositories, 2007, SNLP, pp. 1-6.
- Tablan et al., A Natural Language Query Interface to Structured Information, 2008, Springer pp. 1-15.
- Wang et al., PANTO: A Portable Natural Language Interface to Ontologies, 2007, Springer, pp. 473-487.
- Bouzegboub et al, Search and Composition of Learning Objects in a Visual Environment, in Learning in the Synergy of Multiple Disciplines Lecture Notes in Computer Science, Springer: Berlin & Heidelberg, vol. 5794 (2009) ISSN 0302-9743 (Print) 1611-3349 (Online), ISBN 978-3-642-04635-3.
- Cao, TH. et al.; A robust ontology-based method for translating natural language queries to conceptual graphs, 2008.
- Chabane Djeraba, Marinette Bouet, and Henri Briand, “Concept-Based Query in Visual Information Systems,” IEEE International Forum on Research and Technology Advances in Digital Libraries ADL’98 ,pp. 299-308.
- D. Braga, A. Campi, and S. Ceri, XQBE (XQuery by Example): A Visual Interface to the Standard XML Query Language, ACM Transactions on Database Systems 30.2 (2005) 398-443.
- G. Barzdins, E. Liepins, M. Veilande, & M. Zviedris, “Ontology Enabled Graphical Database Query Tool for End-Users,” in H.-M. Haav & A. Kalja, edd., Databases and Information Systems V (2009) 105-116.
- Gustavo O. Arocena, Alberto O. Mendelzon, and George A. Mihailal, “Applications of a Web query language,” Computer Networks and ISDN Systems ,29.8-13 (Sep. 1997) 1305-1316 = Papers from the Sixth International World Wide Web Conference.
- Irna M.R. Evangelista Filha, Altigran S. Da Silva, Alberto H.F. Laender, and David W. Embley, “Using Nested Tables for Representing and Querying Semistructured Web Data,” in Anne Banks Pidduck, John Mylopoulos, Carson C. Woo, and M. Tamer Ozsu, edd., Advanced Information Systems Engineering LNCS 2348 (2002) 719-723.
- Kudelka, M. et al.; Semantic Analysis of Web Pages Using Web Patterns, 2006 (IEEE).
- Li et al, “XGI: A Graphical Interface for XQuery Creation,” in AMIA Annu Symp Proc . (2007) 453-457.
- Moller, M. et al, RadSem: semantic annotation and retrieval for medical images,2009.
- Petropoulos et al, (Querying and Reporting Semistructured Data, QURSED, 2002.
- S. Jeromy Carriere and Rick Kazman, “WebQuery: searching and visualizing the Web through connectivity,” Computer Networks and ISDN Systems 29.8-13 (Sep. 1997) 1257-1267 = Papers from the Sixth International World Wide Web Conference.
- Sriram Raghavana and Hector Garcia-Molina, “Complex Queries over Web Repositories,” Proceedings 2003 VLDB Conference (2003) 33-44.
- Urbain, J. et al.; Probabilistic passages models for semantic search search of genomics literature, 2008.
- Wen-Syan Li and Junho Shim, “Facilitating complex Web queries through visual user interfaces and query relaxation,” in Computer Networks and ISDN Systems ,vol. 30, Issues 1-7, Apr. 1998, pp. 149-159 = Proceedings of the Seventh International World Wide Web Conference.
- Wen-Syan Li, Junho Shim and K. Selcuk Candan, “WebDB: A System for Querying Semi-structured Data on the Web,” Journal o/Visual Languages & Computing 13.1 (Feb. 2002) 3-33.
- Xian Ding et al, An ontology-based semantic expansion search model using semantic condition transform,2009.
- Apache incubator, Apache UIMA, http://incubatorapache.org/uima/.
- Berger et al., A Maximum Entropy Approach to Natural Language Processing, Association for Computational Linguistics, 1996.
- Etzioni et al.,”Open information extraction from the web” Communications of the ACM , vol. 51 Issue 12, Dec. 2008 pp. 68-74. *
- Wikipedia, UIMA, http://en.wikipedia.org/wiki/UIMA.
- “INDRI Language modeling meets inference networks,” http://www.lemurproject.org/indri/, last modified May 23, 2011; pp. 1-2.
- Question answering,” From Wikipedia, the free encyclopedia, http://en.wikipedia.org/wiki/Question-answering
- Adar, “SaRAD: a Simple and Robust Abbreviation Dictionary,” Bioinformatics, Mar. 2004, pp. 527-533, vol. 20 Issue 4.
- Aditya et al., “Leveraging Community-built Knowledge for Type Coercion in Question Answering,” Proceedings of ISWC 2011.
- Balahur, “Going Beyond Traditional QA Systems: Challenges and Keys in Opinions Question Answering,” Coling 2010: Poster Volume, pp. 27-35, Beijing, Aug. 2010.
- — more references coming 🙂