Home        Affiliations: Senior Software Researcher (2011- ) Pingar Research, Pingar Postdoctoral Scholar (2007-2011) Andrey Rzhetsky's Group, Department of Medicine and Institute for Genomics and Systems Biology, The University of Chicago Postdoctoral Scholar (2006-2007) Marti Hearst's BioText Group, School of Information, University of California, Berkeley PhD Student (2002-2006) Teresa Attwood's Protein Sequence Analysis Group, The University of Manchester Contact Information: Email: annadivoli@gmail.com Skype/LinkedIn/Twitter: annadivoli Research Interests My research is in the area of text mining. I have mostly worked in the biomedical domain. The biomedical literature contains a deluge of information and in an attempt to keep up with the latest findings as presented in scientific publications, researchers in biomedicine almost daily search for papers related to their work, specific information within the papers and often are trying to make connections among information contained in different papers. A lot of my research has been focused on developing and evaluating text mining systems (both algorithms and user interfaces), identifying information for database annotation, as well as document clustering based on both syntactic and semantic content. All aim at making the information hunt in the literature faster and more efficient. I have also combined knowledge acquisition with text mining to compose a better understanding of a specific domain in relation to the beliefs of experts. I am also interested in knowledge representation and ontology design, the use of crowdsourcing for biomedical and linguistic studies, and studying the behavior of experts (in particular biomedical scientists), such as the language and media they use to communicate their ideas and findings. Publications Papers: Medelyan, O., Manion, S., Broekstra, J., Divoli, A., Huang A.L., and Witten, I. (2013) Constructing a Focused Taxonomy from a Document Collection, ESWC 2013, Montpellier, France (Conference Paper - to appear) Divoli, A., Nakov, P. and Hearst, M.A. (2012) Do Peers See More in a Paper than its Authors? Advances in Bioinformatics (special issue on Literature Mining Solutions for Life Science Research), 2012:750214 [PubMed] Pike, M., Wilson, M.L., Divoli, A. and Medelyan, A. (2012) CUES: Cognitive Usability Evaluation System, EuroHCIR 2012, Nijmegen, Netherlands (Workshop Paper) Divoli, A. and Medelyan, A. (2011) Search interface feature evaluation in biosciences, HCIR 2011, Google, Mountain View, CA, USA (Workshop Paper) Divoli, A., Mendonca, E. A., Evans, J. and Rzhetsky, A. (2011) Conflicting biomedical assumptions for mathematical modeling: The case of cancer metastasis, PLoS Computational Biology 7(10): e1002132 [PubMed] Yao, L., Divoli, A., Mayzus, I., Evans, J.A. and Rzhetsky, A. (2011) Benchmarking Ontologies, Bigger vs Better, PLoS Computational Biology 7(1): e1001055 [PubMed] Divoli, A., Wooldridge, M.A. and Hearst, M.A. (2010) Full Text and Figure Display Improves Bioscience Literature Search, PLoS ONE 5(4): e9619 [PubMed] Divoli, A., Hearst, M.A. and Wooldridge, M.A. (2008) Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search, PSB 2008, The Big Island of Hawaii, HI, USA (Conference Paper) [PubMed] Morgan, A.A., Lu, Z., Wang, X., Cohen, A.M., Fluck, J., Ruch, P., Divoli, A., Fundel, A., Leaman, R., Hakenberg, J., Sun, C., Liu, H., Torres, R., Krauthammer, M., Lau, W.W., Liu, H., Hsu, C-N., Schuemie, M., Cohen, K.B., Hirschman, L. (2008) Overview of BioCreative II gene normalization, Genome Biology, 9(Suppl 2):S3 [PubMed] Smith, L., Tanabe, L.K., Johnson nee Ando, R., Kuo, C-J., Chung, I-F., Hsu, C-N., Lin, Y-S., Klinger, R., Friedrich, C.M., Ganchev, K., Torii, M., Liu, H., Haddow, B., Struble, C.A., Povinelli, R.J., Vlachos, A., Baumgartner, W.A., Hunter, L., Carpenter, B., Tsai, R.T-H., Dai, H-J., Liu, F., Chen, Y., Sun, C., Katrenko, S., Adriaans, P., Blaschke, C., Torres, R., Neves, M., Nakov, P., Divoli, A., Mana-Lopez, M., Mata, J., Wilbur, J.W. (2008) Overview of BioCreative II gene mention recognition, Genome Biology, 9(Suppl 2):S2 [PubMed] Hearst, M.A., Divoli, A., Guturu, H., Ksikes, A., Nakov, P., Wooldridge, M.A. and Ye, J. (2007) BioText Search Engine: beyond abstract search, Bioinformatics, 23: 2196-2197 [PubMed] Schwartz, A., Divoli, A. and Hearst, M.A. (2007) Multiple alignment of citation sentences with conditional random fields and posterior decoding, EMNLP-CoNLL 2007, Prague, Czech Republic (Conference Paper) Hearst, M.A., Divoli, A., Wooldridge, M.A. and Ye, J. (2007) Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces, BioNLP Workshop at ACL 2007, Prague, Czech Republic (Workshop Paper) Nakov, P. and Divoli, A. (2007) BioText Report for the Second BioCreAtIvE Challenge, Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain (Participation Report Paper) Divoli, A., Hearst, M.A., Nakov, P.I., Schwartz, A. and Ksikes, A. (2006) BioText Team Report for the TREC 2006 Genomics Track, The Fifteenth Text REtrieval Conference Proceedings, Gaithersburg, MD, USA (Participation Report Paper) Mitchell, A.L.,Divoli, A., Kim, J.-H., Hilario, M., Selimas, I. and Attwood, T.K. (2005) METIS: Multiple Extraction Techniques for Informative Sentences, Bioinformatics, 21: 4196-4197 [PubMed] Divoli, A. and Attwood, T.K. (2005) Protein Family Databases: Text-Mining and Annotation, ISMB BioLINK SIG Workshop, Detroit, USA (Workshop Paper) Divoli, A. and Attwood, T.K. (2005) BioIE: Extracting Informative Sentences from the Biomedical Literature, Bioinformatics, 21: 2138-2139 [PubMed] Short Papers, Abstracts, Posters, etc: Yao, L., Divoli, A., Mayzus, I., Evans, J., and Rzhetsky, A. (2011) Benchmarking Ontologies, Bigger vs Better, Highlights Track, ISMB/ECCB 2011, Vienna, Austria (accepted) Divoli, A., Mendonca, E. A. and Rzhetsky, A. (2010) The meaning behind the choice of words: a case in cancer metastasis, ECCB 2010, Ghent, Belgium (accepted for Poster Presentation) Divoli, A., Mendonca, E. A. and Rzhetsky, A. (2010) Considering alternative views when modeling cancer metastasis, ISMB 2010, Boston, MA, USA (Poster Presentation) Hearst, M.A., Wooldridge, M.A., Ye, J. and Divoli, A. (2007) Showing Figures and Captions in the Biotext Journal Search Engine, ISMB/ECCB 2007, Vienna, Austria (Poster Presentation) Divoli, A., Winter, R., Pettifer, S. and Attwood, T.K. (2005) BioQSpace: An interactive visualisation tool for clustering MEDLINE abstracts, ECCB ISCB SC Symposium, Madrid, Spain (Short Talk & Poster Presentation) Divoli, A. and Attwood, T.K. (2005) Text-mining challenges for protein family database annotation, ISMB, Detroit, USA (Short Talk & Poster Presentation) Divoli, A., Mitchell, A.L., Bradley, P. and Attwood, T.K. (2004) METIS: Multiple Extraction Techniques for Informative Sentences, ISMB/ECCB, Glasgow, UK (Poster Presentation) Mitchell, A.L., Bradley, P., Divoli, A. and Attwood, T.K. (2004) Sequence Analysis Workshop, MIPNETS training meeting, Liverpool, UK (Workshop Organised) Other Selected Talks (not listed above): Divoli, A. (2012) How taxonomies and facets bring end-users closer to big data, Text Analytics and Taxonomy Session, Text Analytics World, Boston, MA, USA Medelyan, A. and Divoli, A. (2012) Mining Unstructured Data: Practical Applications, Data Science Session, O'Reilly's Strata Conference, Santa Clara, CA, USA Divoli, A. (2011) Expert Opinions in Cancer Metastasis: Harvesting Knowledge from Uncertainty and Discrepancies (work with Mendonca, E. A., Evans, J., and Rzhetsky, A.), CoHeB (Workshop on Collaboration Technologies and Systems in Healthcare and Biomedical Fields) at CTS 2011, Philadelphia, USA (Invited Talk) Divoli, A. (2009) Knowledge Acquisition for Knowledge Discovery in Cancer Metastasis (work with Mendonca, E. A. and Rzhetsky, A.), Rocky 2009, Snowmass Aspen, USA (Keynote Talk) Divoli, A. (2008) Usability, Interfaces and Text Mining (work with Wooldridge, M.A. and Hearst, M.A.), Dagstuhl seminar "Ontologies and text mining for Life Sciences-Current Status and Future Perspectives", Germany (Invited Session) Software BioText Search Engine: Journal Search Engine Showing Figures and Captions The BioText Search Engine provides biologists with new ways to access information from any Open Access article available at PubMedCentral. BioIE: Extracting Informative Sentences from the Biomedical Literature A rule-based system for extracting informative sentences referring to either structure, function, diseases and therapeutic compounds, localisation or familial relationships of biological entities, particularly proteins. METIS: Multiple Extraction Techniques for Informative Sentences METIS accepts Swiss-Prot identifiers or FASTA-format sequences, performs BLAST to find related sequences, and then retrieves textual information from Swiss-Prot as well as related sentences from PubMed abstracts. BioQSpace: An interactive visualisation tool for clustering PubMed abstracts BioQSpace clusters abstracts based on similarity measures calculated on user-specified weighting of certain attributes and allows for visualisation and navigation in 3D space. Bio 2007-2011: postdoc at the Institute for Genomics and Systems Biology and the Department of Medicine in The University of Chicago with the Rzhetsky Group, PI: Prof Andrey Rzhetsky 2006-2007: postdoc at the School of Information in the University of California, Berkeley with the BioText Group, PI: Prof Marti Hearst 2002-2006: PhD at The University of Manchester with the Protein Sequence Analysis Group, PI: Prof Teresa Attwood Thesis: "Biomedical Text Mining Approaches: Applications in Protein Family Annotation" 2000-2001: MSc in Biosystems and Informatics at The University of Liverpool Thesis: "Applications of Computational Linguistics for the Investigation of the Functional Genomics of Eukaryotic Transcription Factors" Dissertation (mini thesis): "Applications of Ideas from Linguistics to Functional Genomics: Formal Grammars for Biological Sequences" 1996-1999: BSc in Biomedical Sciences at The Manchester Metropolitan University News March 2013 Constructing a Focused Taxonomy from a Document Collection Our paper was recently accepted in ESWC Olena Medelyan, Steve Manion, Jeen Broekstra, Anna Divoli, Anna Lan Huang and Ian Witten Constructing a Focused Taxonomy from a Document Collection In this paper, we describe a new method for constructing custom taxonomies from document collections. We do this by identifying relevant concepts and entities in text; linking them to knowledge sources like Wikipedia, DBpedia, Freebase, and any supplied taxonomies from related domains; disambiguating conflicting concept mappings; and selecting semantic relations that best group them hierarchically. A generated taxonomy from 2000 news articles is also described in the paper as example and basis for evaluation. 08-10 February 2013 Kiwi Foo Camp I was very happy to be invited back at Kiwi Foo Camp. Much like last year, I had a great time meeting and conversing with several amazing people! Here is the best picture I could find posted from this year's unconference. 03-05 October 2012 TAW & HCIR I attended the Text Analytics World and HCIR in Boston. My TAW talk in the Text Analytics and Taxonomy session was entitled "How taxonomies and facets bring end-users closer to big data". I presented results from 4 user studies exploring end-user preferences for taxonomies and facets - both in terms of content and appearance. Taxonomies and facets can be generated automatically but user preferences and needs can (and should) be taken into account. Here are my slides: You can read more about the conferences in my Pingar Research blog post. 24-25 August 2012 CUES at EuroHCIR Over the past few months, Matthew Pike, Max Wilson, Alyona Medelyan and I have been working on a system for evaluating user interfaces of websites and desktop applications. We presented this work: CUES: Cognitive Usability Evaluation System at EuroHCIR 2012 in Nijmegen, Netherlands, as a paper and a demo poster. CUES integrates brain derived signals and emotions with other common usability measures, such as interaction logs, screen capture, and think aloud. Matt's blog post on CUES can be found here. 9 June 2012 Do Peers See More in a Paper than its Authors? Our paper was recently accepted by Advances in Bioinformatics in a special issue on Literature Mining Solutions for Life Science Research. Anna Divoli, Preslav Nakov and Marti A. Hearst Do Peers See More in a Paper than its Authors? Citation sentences (or citances) are produced by peers and represent subjective points of interest of a paper. In this paper we focus in the area of molecular interactions and compare the content of abstracts (containing the main points of a paper as judged by the authors) and the content of citances (containing the main points of a paper as judged by peers). We use MeSH terms to annotate the content and present a detailed summary of the differences across different information types represented in abstracts and citances - we also examine the effects of other citations and time. We propose that collectively the content of these citances can be used for automatic annotation (assigning relationships among biological entities and concepts) and for a number of NLP tasks such as producing summaries. 28 February - 01 March 2012 O'Reilly Strata Conference 2012 My colleague, Alyona Medelyan, and I presented at the Data Science Session of O'Reilly's Strata Conference, a leading conference for data scientists and analysts. Here are our slides: It was a great event with interesting, busy program and fantastic speakers. You can also find the slides from our talk "Mining Unstructured Data: Practical Applications" on Strata's website. 10-12 February 2012 Kiwi Foo Camp What an honor, 3 months in New Zealand and I found myself invited at Kiwi Foo Camp, where I met so many intelligent, driven people from all kinds of fields! The meeting took place in Warkworth, the sessions were very versatile, the conversations lively and inspiring, and the werewolves vicious! Here is a photograph on flickr of the happy campers. 07 February 2012 Interview with O'Reilly Radar Alyona Medelyan and I were interviewed by the O'Reilly Radar: "Unstructured data is worth the effort when you've got the right tools". The interview was also featured in Forbes: "Unlocking Opportunities in Messy Data". 04 January 2012 HCIR 2011 on YouTube and slideshare The presentations from the HCIR 2011 Workshop are now online! Here is the video from our paper (presented by Alyona Medelyan, starting around minute 36). Here are our slides: Pingar's blog post on HCIR 2011 and a poster version of our paper can be found here. 22 September 2011 CTS 2011 special issue in Elsevier Future Generation Computer Systems I am guest editor for CTS 2011 special issue in Elsevier Future Generation Computer Systems. Here is the: CFP. Abstract Submission Deadline: October 10 & Full Manuscript Submission Deadline: December 19. I look forward to an interesting special issue! 9 September 2011 Search interface feature evaluation in biosciences Our paper was accepted for full presentation at the HCIR 2011 Workshop. The workshop will take place in October at Google's main campus in Mountain View, California. Anna Divoli and Alyona Medelyan Search interface feature evaluation in biosciences In this paper we report findings on desirable interface features for different search tasks in the biomedical domain. We conducted a user study where we asked bioscientists to evaluate the usefulness of autocomplete, query expansions, facetted refinement, related searches and results preview implementations in new pilot interfaces and publicly available systems while using baseline and their own queries. You can find a blog post on the study here. 5 September 2011 Pingar I joined Pingar as Senior Software Researcher. I look forward to working on text analytics, improving search systems and interface usability research with immediate real world applications. I am starting this exciting research post in the Silicon Valley office but I will soon head to Auckland for at least several months. 9 June 2011 Conflicting biomedical assumptions for mathematical modeling: The case of cancer metastasis Our paper was recently accepted by PLoS Computational Biology. Anna Divoli, Eneida Mendonca, James Evans and Andrey Rzhetsky Conflicting biomedical assumptions for mathematical modeling: The case of cancer metastasis In this paper individual viewpoints from 28 experts in clinical or molecular aspects of cancer metastasis were harvested and summarized computationally. Detailed analysis of the data reveals areas of disagreement and a range of opinions on underlying causes and processes in metastasis. 23 - 27 May 2011 CTS 2011 I attended CTS (International Conference on Collaboration Technologies and Systems) in Philadelphia. The meeting covered a large range of Collaboration Web technologies, Human Factors and HCI topics I am interested in. I was invited to give a talk at CoHeB (Workshop on Collaboration Technologies and Systems in Healthcare and Biomedical Fields) as part of CTS. My talk was entitled: "Expert Opinions in Cancer Metastasis: Harvesting Knowledge from Uncertainty and Discrepancies" 13 Apr 2011 EBI visit I visited the EBI interfaces group at the European Bioinformatics Institute in Hinxton. It was great to discuss usability and HCI issues for bioinformatics and computational biology with several scientists there. We jointly started the Biological Interfaces Group last summer and we hope to get this community growing! I also had the chance to meet a few researchers from Microsoft Research in Cambridge and caught up with several of my ex-colleagues from Inpharmatica and the Universities of Manchester and Chicago that, what do you know, are currently in EBI and Sanger. During my visit, I gave a talk on: "Human factors in computational biology - from mathematical models to user interfaces" Here are some slides from my presentation: Special thanks to my host Francis Rowland! 11 Apr 2011 Cardiff visit I visited the Cardiff School of Computer Science & Informatics, where a gave a talk on: "Expert opinions in cancer metastasis: Uncertainty, discrepancies, range and models" and had wonderful conversations with several faculty members and other researchers there that work on biodiversity informatics, ontologies, and medical informatics. Special thanks to my host Irena Spasic! 24 Nov 2010 Benchmarking Ontologies, Bigger vs Better One of our group's papers was recently accepted by PLoS Computational Biology. Lixia Yao, Anna Divoli, Ilya Mayzus, James Evans and Andrey Rzhetsky Benchmarking Ontologies, Bigger vs Better In this paper we introduce a family of ontology metrics and we test them on four medical ontologies and seven popular English thesauri. 9 Aug 2010 Bio-Interfaces Google Group Together with some of the Interfaces people at EBI (if you haven't already, check out their fantastic site: http://ebiinterfaces.wordpress.com ), I have started a Google Group "Biological Interfaces". We are hoping that this will serve as a platform for all bio-interfaces researchers around the world to discuss research matters, post CFP for pertinent meetings/conferences and advertise for related jobs. Areas covered: design, visualization, human-computer interaction, usability. The archives of the group are public. You can read and join here: Subscribe to Biological Interfaces Email: Visit this group 14 Jul 2010 ISMB 2010 I just came back from ISMB which took place in Boston, MA this year. The meeting was very interesting and stimulating and I got the chance to catch up with many wonderful colleagues as well as to meet new interesting people. There, I presented a poster entitled "Considering alternative views when modeling cancer metastasis". 14 Jul 2010 Some kind of blog... I decided to start a "News" tab on my website. I suppose this will allow me to do something in between microblogging and proper blogging...