Presentation is loading. Please wait.

Presentation is loading. Please wait.

George Paliouras, May 2014 www.bioasq.org National Center for Scientific Research ‘Demokritos’ George Paliouras BioASQ Intelligent Information Management.

Similar presentations


Presentation on theme: "George Paliouras, May 2014 www.bioasq.org National Center for Scientific Research ‘Demokritos’ George Paliouras BioASQ Intelligent Information Management."— Presentation transcript:

1 George Paliouras, May 2014 www.bioasq.org National Center for Scientific Research ‘Demokritos’ George Paliouras BioASQ Intelligent Information Management Targeted Competition Framework ICT-2011.4.4(d) George Paliouras, May 2014 A challenge on large-scale biomedical semantic indexing and question answering www.bioasq.org

2 George Paliouras, May 2014 www.bioasq.org Biomedical articles per year 2/43

3 George Paliouras, May 2014 www.bioasq.org Questions of biomedical experts “Are there any DNMT3 proteins present in plants?” “Yes” “Yes. The plant DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) is a homolog of the mammalian de novo methyltransferase DNMT3. DRM2 contains a novel arrangement of the motifs required for DNA methyltransferase catalytic activity.” Yes/No question Exact Answer Ideal Answer 3/43

4 George Paliouras, May 2014 www.bioasq.org Questions of biomedical experts “What is the methyl donor of DNA (cytosine-5)-methyltransferases?” “S-adenosyl-L-methionine” “S-adenosyl-L-methionine (AdoMet, SAM) is the methyl donor of DNA (cytosine-5)- methyltransferases. DNA (cytosine-5)-methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to the C-5 position of cytosine residues in DNA.” Factoid question Exact Answer Ideal Answer 4/43

5 George Paliouras, May 2014 www.bioasq.org Questions of biomedical experts (III) List question “In 1955, the production of itaconic acid was firstly described for Ustilago maydis. Some Aspergillus species, like A. itaconicus and A. terreus, show the ability to synthesize this organic acid and A. terreus can secrete significant amounts to the media. Itaconic acid is mainly supplied by biotechnological processes with the fungus Aspergillus terreus. Cloning of the cadA gene into the citric acid producing fungus A. niger showed that it is possible to produce itaconic acid also in a different host organism.” “Aspergillus terreus”, “Aspergillus niger”, “Ustilago maydis” Exact Answer Ideal Answer “Which species may be used for the biotechnological production of itaconic acid?” 5/43

6 George Paliouras, May 2014 www.bioasq.org Questions of biomedical experts (III) Summary question “Histone methyltransferases (HMTs) are responsible for the site-specific addition of covalent modifications on the histone tails, which serve as markers for the recruitment of chromatin organization complexes. There are two major types of HMTs: histone-lysine N- Methyltransferases and histone-arginine N-methyltransferases. The former methylate specific lysine (K) residues such as 4, 9, 27, 36, and 79 on histone H3 and residue 20 on histone H4. The latter methylate arginine (R) residues such as 2, 8, 17, and 26 on histone H3 and residue 3 on histone H4. Depending on what residue is modified and the degree of methylation (mono-, di- and tri-methylation), lysine methylation of histones is linked to either transcriptionally active or silent chromatin.” - Exact Answer Ideal Answer “How do histone methyltransferases cause histone modification?” 6/43

7 George Paliouras, May 2014 www.bioasq.org 7/43

8 George Paliouras, May 2014 www.bioasq.org Finding relevant snippets 8/43

9 George Paliouras, May 2014 www.bioasq.org Not only texts: ontologies, linked data, … 9/43

10 George Paliouras, May 2014 www.bioasq.org 10/43

11 George Paliouras, May 2014 www.bioasq.org Information from structured data List question http://www.disease-ontology.org/api/metadata/DOID:162 (cancer) http://www.uniprot.org/uniprot/M3K8_RAT (TPL2 synonym) Subject: http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/3003 (lung cancer) Predicate: http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/associatedGene Object: http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/TPL2" Related RDF triple Related concepts “Which forms of cancer is the Tpl2 gene associated with?” 11/43

12 George Paliouras, May 2014 www.bioasq.org 12/43

13 George Paliouras, May 2014 www.bioasq.org BioASQ Vision Make sure this knowledge is used to the benefit of patients Need to make it accessible to biomedical experts Search is not effective enough Push research in automated answering of questions A challenge for such systems can achieve a multiplying effect 13/43

14 George Paliouras, May 2014 www.bioasq.org What is BioASQ? A challenge funded by the European Union (FP7). Task a: Hierarchical text classification Organizers distribute new unclassified PubMed articles. Participants assign MeSH terms to the articles. Evaluation based on annotations of PubMed curators. Task b: IR, QA, summarization, … Organizers distribute English biomedical questions. Participants provide: relevant articles, snippets, concepts, triples, “exact” answers, “ideal” answers. Evaluation: both automatic (GMAP, MRR, ROUGE etc.) and manual (by biomedical experts). 14/43

15 George Paliouras, May 2014 www.bioasq.org Task b The challenge 15/43 Task a

16 George Paliouras, May 2014 www.bioasq.org 16/43

17 George Paliouras, May 2014 www.bioasq.org Behind the scenes 17/43

18 George Paliouras, May 2014 www.bioasq.org BioASQ Platform 18/43

19 George Paliouras, May 2014 www.bioasq.org Datasets Task b data contain gold articles, snippets, concepts, triples, “exact” and “ideal” answers prepared by biomedical experts from around Europe. Task a 1 st challenge2 nd challenge Training10,876,00412,628,968 Test8349071950 Task b 1 st challenge2 nd challenge Training29310 Test281500 19/43

20 George Paliouras, May 2014 www.bioasq.org Data sources They include both text and structured info. ► PubMed abstracts, PubMed Central articles, MeSH. ► Gene Ontology, UniProt, Jochem, Disease Ontology. 20/43

21 George Paliouras, May 2014 www.bioasq.org Annotation: questions and queries 21/43

22 George Paliouras, May 2014 www.bioasq.org Annotation: snippets 22/43

23 George Paliouras, May 2014 www.bioasq.org Annotation: answers 23/43

24 George Paliouras, May 2014 www.bioasq.org Assessment: relevance of material 24/43

25 George Paliouras, May 2014 www.bioasq.org Assessment: information in answers 25/43

26 George Paliouras, May 2014 www.bioasq.org BioASQ social network 26/43

27 George Paliouras, May 2014 www.bioasq.org Oracle 27/43

28 George Paliouras, May 2014 www.bioasq.org Oracle 28/43

29 George Paliouras, May 2014 www.bioasq.org Two cycles March 2013 June 2013 August 2013 September 2013 2013 Schedule February 2014 March 2014 May 2014 September 2014 2014 Schedule The official challenge is over, but… ►Task a continues to run each week. ►An oracle for task b will be available soon. ►Oracles will remain available. ►Third cycle is being designed … 29/43

30 George Paliouras, May 2014 www.bioasq.org Challenge participants so far 30/43

31 George Paliouras, May 2014 www.bioasq.org Challenge participants in each cycle 31/43

32 George Paliouras, May 2014 www.bioasq.org Evaluation measures Task a: Hierarchical text classification Flat measures for multi-label classification: Accuracy, MiF, MaF, EBF Hierarchical measures: LCA-F (new), HF Task b: IR, QA, summarization, … Phase A: standard IR measures, mean precision, mean recall, mean F- measure, MAP (used for winners selection), G-MAP Phase B: ‘Exact answers’ (based on type): accuracy (yes/no), strict/lenient accuracy, MRR (factoid), mean F-measure (list) ‘Ideal answers’: manual scores from the experts {Readability, Repetition, Information Precision and Recall}, plus ROUGE 32/43

33 George Paliouras, May 2014 www.bioasq.org First year technology/results overview Task 1a –Mainly SVMs and learning-to-rank. –Mostly flat classification, ignoring class taxonomy. –Mediocre results by hierarchical methods. –One of the systems outperformed NLM’s system. Task 1b –Phase A (retrieve relevant documents, concepts, snippets, triples): low performance (compared to baselines). –Phase B (formulate ‘exact’ and ‘ideal’ answers): poor performance for ‘exact’ answers (except for yes/no questions); high performance for ‘ideal’ answers (paragraph-sized summaries), but starting with gold documents, snippets etc. Large scope for improvements, esp. in Task 1b. 33/43

34 George Paliouras, May 2014 www.bioasq.org “Exact” answer results (batch 2/3) 34/43

35 George Paliouras, May 2014 www.bioasq.org “Ideal” answer results (batch 2/3) 35/43

36 George Paliouras, May 2014 www.bioasq.org Results – task a – flat measures 36/43

37 George Paliouras, May 2014 www.bioasq.org Results – task a – hierarchical 37/43

38 George Paliouras, May 2014 www.bioasq.org First challenge prizes 38/43

39 George Paliouras, May 2014 www.bioasq.org Sustainability BioASQ Oracle Software release and installation instructions Benchmark datasets BioASQ social network Involvement of the biomedical community in the process Attracting sponsors for prizes Making the challenge viable, at very low cost, after the end of the project 39/43

40 George Paliouras, May 2014 www.bioasq.org Project Consortium 1.National Centre for Scientific Research “Demokritos” - NSCR “D” (EL) 2.Transinsight GmbH – TI (D) 3.Universite Joseph Fourier- UJF (F) 4.University Leipzig - ULEI (D) 5.Universite Pierre et Marie Curie Paris 6 – UPMC (F) 6.Athens University of Economics and Business – Research Centre – AUEB-RC (EL) 40/43

41 George Paliouras, May 2014 www.bioasq.org Project Consortium 41/43

42 George Paliouras, May 2014 www.bioasq.org Get in touch! BioASQ workshop @CLEF (Sheffield, Sept 14) Visit www.bioasq.org Follow @BioASQ 42/43

43 George Paliouras, May 2014 www.bioasq.org Useful Links BioASQ Annotation & assessment tools: –http://at.bioasq.org/http://at.bioasq.org/ –http://assess.bioasq.org/http://assess.bioasq.org/ –https://github.com/AKSW/BioASQ-AThttps://github.com/AKSW/BioASQ-AT BioASQ social network: –http://sn.bioasq.org/http://sn.bioasq.org/ –https://github.com/AKSW/BioASQ-SNhttps://github.com/AKSW/BioASQ-SN BioASQ platform: –http://bioasq.lip6.fr/http://bioasq.lip6.fr/ BioASQ Oracles: –http://bioasq.lip6.fr/oracle/http://bioasq.lip6.fr/oracle/ 43/43 A. Kosmopoulos, I. Partalas, E. Gaussier, G. Paliouras, I. Androutsopoulos, Evaluation Measures for Hierarchical Classification: a unified view and novel approaches. Data Mining and Knowledge Discovery (To appear)


Download ppt "George Paliouras, May 2014 www.bioasq.org National Center for Scientific Research ‘Demokritos’ George Paliouras BioASQ Intelligent Information Management."

Similar presentations


Ads by Google