Steering Committee Meeting

Transcription

1 Steering Committee Meeting To hear the meeting, you must call in Toll-free phone number: Access Code: For international call in numbers, please visit:

2 Agenda Pilot Project Data Recommendation using Machine Learning and Crowdsourcing biocaddie All-Hands Meeting BD2K All-Hands Meeting Core Development Team Updates and Demo

3 Pilot Project 2.1 Data Recommendation using Machine Learning and Crowdsourcing Xiaoqian Jiang, PhD

4 Motivation v Datasets w Health-science datasets are being created and collected at an increasing speed v Data repositories w NIH organized biomedical datasets into 50+ repositories (e.g., GEO, dbgap, GenBank) v Retrieval w Researchers often need lots of background knowledge to find datasets of interest v We need the PubMed for integrated data indexing and searching

5 Goal v Develop biomedical data recommendation system to meet researcher s need Network of Authors Network of Papers Datasets used citations paper. references

6 Our outputs v v v v Two accepted paper (KDD, TBC) w w Oh J, Han W-S, Yu H, Jiang X, Fast and Robust Parallel SGD Matrix Factorization, ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 15), Sydney, Australia, 2015 Iranmehr A, Wang H, Chen H, Jiang X, DataRank: A Framework for Ranking Biomedical Datasets, Translational Bioinformatics Conference (TBC 15), Tokyo, Japan, 2015 One submission (AMIA CRI) w Garcia-Ulloa D, Xiong L, Luo Y, Ohno-Machado L, Jiang X, Recommendation system for biomedical datasets using Bayesian networks and tensor factorization, AMIA CRI (submitted), 2015 A demo webservice w Extraction of paper-data bipartite graphs

7 Outline v Datarank: Personalized dataset recommendation service v Alternative methods v Integration progress

8 DataRank related work v User-based recommendation, like Netflix w A user likes certain genre of movies v Item-based recommendation, like Amazon w Similar items are frequently purchased together v DataRank? w Researchers can switch topics over time w Researchers might be interested in different datasets under different context

9 DataRank MetaData Enrichment 26,685 articles 35,497 datasets 401,153 mentions

10 DataRank: Feature Representation v v v A MeSH is a tag from a controlled vocabulary that was assigned to all articles in the corpus. w MeSH (Medical Subject Headings) is the NLM controlled vocabulary thesaurus used for indexing articles for PubMed. Each document can be represented via (binary) BoW of MeSH. Document features are aggregated to dataset features using "OR". Query = {genetics, Female} DNA, Feature = [0,..., 0, 1, 0,..., 1, 0,..., 1, 0,..., 0] T Sparse Feature = {1023:1, 9861:1, 22397:1}

11 DataRank: Modeling v We take a Bayesian approach to model the posterior probability over datasets given a query and support re-ranking

12 DataRank system

13 DataRank: Evaluation w Regret: w Average disagreement:

14 Outline v Datarank: Personalized dataset recommendation service v Alternative methods v Integration progress

15 Alternative methods v Can be represented with a sparse tensor Authors Datasets Mesh Terms

16 Alternative methods v The question is, given an author and mesh terms, what is the best dataset to recommend? These are not independent

17 Alternative methods Bayesian Network Tensor factorization db 1 db 2 db nd a 1,m 1 p 11 p 12 p 1nd a 1,m 2 p 21 p 22 p 2nd a na,m nm p q1 p q2 p qnd

18 Alternative methods Based on 2,398 JAMIA ar.cles ci.ng 2,735 GEO datasets, which involve 16,363 different authors and 5,345 MeSH terms

19 Alternative methods Based on 2,398 JAMIA ar.cles ci.ng 2,735 GEO datasets, which involve 16,363 different authors and 5,345 MeSH terms

20 Outline v Datarank: Personalized dataset recommendation service v Alternative methods v Integration progress

21 Integration progress v Attended weekly biocaddie core development meetings v Presented detailed DataRank algorithm to the team v Uploaded DataRank code to the biocaddie github v Shared with the core team the paper citation data

22 Thank you! Questions?

23 biocaddie All-Hands Meeting v Date: Friday, December 4, 2015 v Location: Telemedicine Building, UCSD v Draft agenda (Google Drive > All-Hands Meeting 2015) w Events: Steering Committee meeting DDI prototype overview and demo Working groups and supplement presentations v Core Development Team meetings w Date: Saturday, December 5 w CEDAR Discuss collaboration with biocaddie

24 biocaddie All-Hands Meeting Time Title Presenter(s) 8:30 9:30 AM Steering Committee Meeting Lucila Ohno-Machado 8:30 9:30 AM Breakfast and Registration 9:30 AM Welcome and Introduction to biocaddie Lucila Ohno-Machado 9:50 AM DDI Prototype Hua Xu/Jeffrey Grethe 10:50 AM Break 11:00 AM DDI Prototype/Integration with Pilot Projects Hua Xu 11:30 AM Hands-on DDI Demo All 12:00 PM Lunch 1:00 PM WG2 - Data Identifiers Recommendation Jeffrey Grethe 1:15 PM WG3 - Descriptive Metadata for Datasets Susanna Sansone 1:45 PM WG4 - Use Cases and Testing Benchmarks Hua Xu 2:00 PM WG5 - Dataset Citation Metrics Jeffrey Grethe/Susanna Sansone 2:15 PM WG6 - Criteria for Being Included in the DDI Lucila Ohno-Machado/Ian Fore 2:30 PM WG7 - Accessibility Metadata for Datasets George Alter 2:45 PM WG8 - Ranking Search Results Hua Xu 3:00 PM Break 3:10 PM Supplement: Count Everything David Haussler/Ida Sim/Isaac Kohane 3:30 PM Supplement: OmicsDI Eric Deutch/Henning Hermjakob/Peipei Ping/Susanna Sansone 3:50 PM Supplement: F11 Data Citation Pilot Maryann Martone/Tim Clark 4:10 PM Closing Session Lucila Ohno-Machado

25 BD2K - All-Hands Meeting v Date: November 12-13, 2015 v Location: Bethesda, MD v Agenda - w Prototype Demo? w Posters w Other topics

26 Core Dev. Team - Progress Task ElasticSearch Endpoint Developers have access to API keys ElasticSearch EndPoint Documentation Available at GitHub wiki ElasticSearch Endpoint Enhancements Additional storage for end-point Need to add additional clean-up routines (e.g. logs) Data Ingestion Pipeline Begun discussions with ICPSR Reconciliation of indices with WG3 metadata model Data Set Ingestion PDB/GEO: stable LINCS: In contact about APIs BioProject, ArrayExpress, GEMMA, dbgap: Currently in-process ICPSR: Will be receiving sample data files Due Operational Deployed Ongoing Ongoing Ongoing Ongoing

27 Pilot Project Integration PP Presented to CDT / / / /01 As Integrated Specialized advanced search for GWAS datasets Ranking function based on citation metrics for GEO series data a) isee similarity metric in ElasticSearch b) DELVE implementation as exploratory search and visualization option. (i) for PDB (ii) for gene expression data Ranking function based on citation metrics (dataset mentions) for PDB data Completed On 09/22 Ongoing (10/20) 9/01 Ongoing (11/10) Ongoing (10/27)

28 Core Dev. Team - Progress Task UI Development Preliminary UI (v0.1) demo UI (v0.2) deployed (new design) Pop-up dialog box for search result on homepage Global statistics Track user s search history (recent activity) Similar datasets function (PDB data only) Related publications from PubMed (dataset title) Link to collect user s feedback Error prevention Improvements/additional functions based on feedback Ontology web services: 1) Imported terminologies (6) and validate them 2) Created UI-Browser for TS 3) Integration to Scigraph API 4) Create auto complete feature 5) Integrate terminology server Due 09/01 10/09 Ongoing 08/31 09/30 Ongoing Ongoing Ongoing

29 Core Dev. Team Prototype DEMO

30 Announcements v To access private repositories in the biocaddie GitHub account, send GitHub username to Anupama.E.Gururaj@uth.tmc.edu v Stephanie (sthagstrom@ucsd.edu) to be added to working group mailing lists v Next Steering Committee meeting w November 5, 2015 at 9:00 am PST