Difference between revisions of "BioNLP 2023"
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==BIONLP 2016 Workshop Schedule== | ==BIONLP 2016 Workshop Schedule== | ||
| − | <table cellspacing="0" cellpadding="5" border="0"><tr><td colspan=2 style="padding-top: 14px;">< | + | <table cellspacing="0" cellpadding="5" border="0"><tr><td colspan=2 style="padding-top: 14px;"><b>Friday August 12, 2016</b></td></tr> |
<tr><td valign=top style="padding-top: 14px;"><b>8:30–8:40</b></td><td valign=top style="padding-top: 14px;"><b>Opening remarks</b></td></tr> | <tr><td valign=top style="padding-top: 14px;"><b>8:30–8:40</b></td><td valign=top style="padding-top: 14px;"><b>Opening remarks</b></td></tr> | ||
<tr><td valign=top style="padding-top: 14px;"><b>8:40–10:30</b></td><td valign=top style="padding-top: 14px;"><b>Session 1: Entity extraction and representation</b></td></tr> | <tr><td valign=top style="padding-top: 14px;"><b>8:40–10:30</b></td><td valign=top style="padding-top: 14px;"><b>Session 1: Entity extraction and representation</b></td></tr> | ||
| Line 86: | Line 86: | ||
<tr><td valign=top width=100> </td><td valign=top align=left><i>Relation extraction from clinical texts using domain invariant convolutional neural network</i><br> | <tr><td valign=top width=100> </td><td valign=top align=left><i>Relation extraction from clinical texts using domain invariant convolutional neural network</i><br> | ||
Sunil Sahu, Ashish Anand, Krishnadev Oruganty and Mahanandeeshwar Gattu</td></tr> | Sunil Sahu, Ashish Anand, Krishnadev Oruganty and Mahanandeeshwar Gattu</td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100> </td><td valign=top align=left><i>Results of the 4th edition of BioASQ Challenge</i><br>Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras and Ioannis Kakadiaris</td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100> </td> <td><b>All August 13 talks are also presented as posters on August 12 and August 13</b></td></tr> | ||
| + | |||
</table> | </table> | ||
| − | ===WORKSHOP OVERVIEW AND SCOPE | + | ==BioASQ / BioNLP-ST Workshop Program, August 13== |
| + | |||
| + | <table> | ||
| + | <tr><td valign=top width=100>'''9:00-9:15'''</td> <td><b>Welcome</b></td></tr> | ||
| + | <tr><td valign=top width=100>'''9:15-10:15'''</td> <td>'''Invited speaker: Sherri Matis-Mitchell''' <br>Solving Problems and Supporting Decisions in Pharma R&D using Text Analytics: A Recent History</td></tr> | ||
| + | <tr><td valign=top width=100>10:15-10:30</td> <td>'''Overview of BioASQ'''</td></tr> | ||
| + | <tr><td valign=top width=100>10:30-11:00</td> <td><b>Coffee break</b></td></tr> | ||
| + | <tr><td valign=top width=100>11:00-12:30</td> <td><b>BioASQ participant session</b></td></tr> | ||
| + | <tr><td valign=top width=100>11:00-11:15</td> <td>Using Learning-To-Rank to Enhance NLM Medical Text Indexer Results<br>Ilya Zavorin, James Mork and Dina Demner-Fushman</td></tr> | ||
| + | <tr><td valign=top width=100>11:15-11:30</td> <td>LABDA at the 2016 BioASQ challenge task 4a: Semantic Indexing by using ElasticSearch <br>Isabel Segura-Bedmar, Adrián Carruana and Paloma Martínez</td></tr> | ||
| + | <tr><td valign=top width=100>11:30-11:45</td> <td>Learning to Answer Biomedical Questions: OAQA at BioASQ 4B<br>Zi Yang, Yue Zhou and Eric Nyberg</td></tr> | ||
| + | <tr><td valign=top width=100>11:45-12:00</td> <td>HPI Question Answering System in BioASQ 2016 <br>Frederik Schulze, Ricarda Schuler, Tim Draeger, Daniel Dummer, Alexander Ernst, Pedro Flemming, Cindy Perscheid, Mariana Neves</td></tr> | ||
| + | <tr><td valign=top width=100>12:00-12:15</td> <td>KSAnswer: Question-answering System of Kangwon National University and Sogang University in the 2016 BioASQ Challenge<br>Hyeon-gu Lee, Minkyoung Kim, Harksoo Kim, Juae Kim, Sunjae Kwon, Jungyun Seo, Yi-Reun Kim and Jung-Kyu Choi</td></tr> | ||
| + | <tr><td valign=top width=100>12:15-12:30</td> <td>Large-Scale Semantic Indexing and Question Answering in Biomedicine <br>Eirini Papagiannopoulou, Yiannis Papanikolaou, Dimitris Dimitriadis, Sakis Lagopoulos, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos and Ioannis Vlahavas</td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100>'''12:30-14:00'''</td> <td><b>Lunch break</b></td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100>'''14:00-14:15'''</td> <td><b>Overview of BioNLP-ST</b></td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100>'''14:15-15:30'''</td> <td>'''BioNLP-ST participant session 1'''</td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100>14:15-14:30</td> <td>LitWay, discriminative extraction for different bio-events<br>Chen Li, Zhiqiang Rao and Xiangrong Zhang</td></tr> | ||
| + | <tr><td valign=top width=100>14:30-14:45</td> <td>VERSE: Event and relation extraction in the BioNLP 2016 Shared Task<br>Jake Lever and Steven JM Jones</td></tr> | ||
| + | <tr><td valign=top width=100>14:45-15:00</td> <td>A dictionary- and rule-based system for identification of bacteria and habitats in text<br>Helen Cook, Evangelos Pafilis and Lars Juhl Jensen</td></tr> | ||
| + | <tr><td valign=top width=100>15:00-15:15</td> <td>Extraction of Regulatory Events Using Kernel-based Classifiers and Distant Supervision<br>Andre Lamurias, Miguel J. Rodrigues, Luka A. Clarke and Francisco M Couto</td></tr> | ||
| + | <tr><td valign=top width=100>15:15-15:30</td> <td>Deep Learning With Minimal Training Data: TurkuNLP Entry in The BioNLP Shared Task 2016<br>Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski and Filip Ginter</td></tr> | ||
| + | <tr><td valign=top width=100>'''15:30-16:00'''</td> <td>'''Coffee break'''</td></tr> | ||
| + | <tr><td valign=top width=100>16:00-17:00</td> <td>'''BioNLP-ST participant session 2'''</td></tr> | ||
| + | <tr><td valign=top width=100>16:00-16:15</td><td>Identification of mentions and relations between bacteria and biotope from PubMed abstracts<br>Cyril Grouin</td></tr> | ||
| + | <tr><td valign=top width=100>16:15-16:30</td> <td>SeeDev Binary Event Extraction Using SVMs and a Rich Feature set<br>Nagesh Panyam Chandrasekarasastry, Gitansh Khirbat, Karin Verspoor, Trevor Cohn and Kotagiri Ramamohanarao</td></tr> | ||
| + | <tr><td valign=top width=100>16:30-16:45</td> <td>Ontology Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques<br>Mert Tiftikci, Hakan Şahin, Berfu Büyüköz, Alper Yayıkçı and Arzucan Özgür</td></tr> | ||
| + | <tr><td valign=top width=100>16:45-17:00</td> <td>DUTIR in BioNLP-ST 2016: Utilizing convolutional network and distributed representation to extract complicate relations<br>Honglei Li, Jianhai Zhang, Jian Wang, Hongfei Lin and Zhihao Yang</td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100>'''17:00-17:30'''</td> <td><b>Closing session</b></td></tr> | ||
| + | |||
| + | </table> | ||
| + | <!-- | ||
| + | ==WORKSHOP OVERVIEW AND SCOPE== | ||
Over the course of the past fourteen years, the ACL BioNLP workshop associated with the SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. The workshop serves as both a venue for bringing together researchers in bio- and clinical NLP and exposing these researchers to the mainstream ACL research, and a venue for informing the mainstream ACL researchers about the fast growing and important domain. | Over the course of the past fourteen years, the ACL BioNLP workshop associated with the SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. The workshop serves as both a venue for bringing together researchers in bio- and clinical NLP and exposing these researchers to the mainstream ACL research, and a venue for informing the mainstream ACL researchers about the fast growing and important domain. | ||
| Line 110: | Line 152: | ||
* Translating NLP research to practice | * Translating NLP research to practice | ||
* Theoretical underpinnings of biomedical language processing | * Theoretical underpinnings of biomedical language processing | ||
| + | --> | ||
| + | |||
| + | |||
| − | <h5>SUBMISSION INSTRUCTIONS</h5> | + | <!-- <h5>SUBMISSION INSTRUCTIONS</h5> |
We invite two types of submissions: full papers and short papers. | We invite two types of submissions: full papers and short papers. | ||
Submissions are due by 11:59 PM EST on Sunday May 8, 2016. | Submissions are due by 11:59 PM EST on Sunday May 8, 2016. | ||
| Line 128: | Line 173: | ||
<b>Submissions should be anonymous. </b> | <b>Submissions should be anonymous. </b> | ||
| − | Dual submission policy: papers may <b>NOT</b> be submitted to the BioNLP 2016 workshop if they are or will be concurrently submitted to another meeting or publication. | + | Dual submission policy: papers may <b>NOT</b> be submitted to the BioNLP 2016 workshop if they are or will be concurrently submitted to another meeting or publication. --> |
| − | < | + | <!-- |
| + | <b>Program Committee:</b> | ||
* Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK | * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK | ||
| Line 167: | Line 213: | ||
| − | < | + | <b>Organizers</b> |
* Kevin Bretonnel Cohen, University of Colorado School of Medicine | * Kevin Bretonnel Cohen, University of Colorado School of Medicine | ||
* Dina Demner-Fushman, US National Library of Medicine | * Dina Demner-Fushman, US National Library of Medicine | ||
| Line 174: | Line 220: | ||
| − | <h5> | + | <h5>The BioNLP Shared Task (BioNLP-ST) and the BioASQ Challenge associated with the workshop</h5> |
The <b>BioNLP Shared Task (BioNLP-ST)</b> has been organized three times so far, leading to the development of information extraction systems for molecular biology and medicine in 2009, 2011 and 2013. One of the major contributions of BioNLP-ST is the availability of resources such as high quality manually curated corpora, tools, and evaluation services. | The <b>BioNLP Shared Task (BioNLP-ST)</b> has been organized three times so far, leading to the development of information extraction systems for molecular biology and medicine in 2009, 2011 and 2013. One of the major contributions of BioNLP-ST is the availability of resources such as high quality manually curated corpora, tools, and evaluation services. | ||
| − | < | + | <b>Shared Task Organizers:</b> |
* Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan | * Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan | ||
| Line 189: | Line 235: | ||
BioASQ assesses the performance of information systems in supporting two tasks that are central in the biomedical question answering process: (a) the indexing of large volumes of unlabeled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generation of answers and supporting material. BioASQ has been making publicly available the following benchmark data and tools: more than 1300 questions and related answers, as well as online "oracle" for objective evaluation of any system throughout the year, not only during the challenge. | BioASQ assesses the performance of information systems in supporting two tasks that are central in the biomedical question answering process: (a) the indexing of large volumes of unlabeled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generation of answers and supporting material. BioASQ has been making publicly available the following benchmark data and tools: more than 1300 questions and related answers, as well as online "oracle" for objective evaluation of any system throughout the year, not only during the challenge. | ||
| − | < | + | <b>BioASQ Organizers:</b> |
* Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA | * Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA | ||
| Line 195: | Line 241: | ||
* Anastasia Krithara, NCSR "Demokritos", Greece | * Anastasia Krithara, NCSR "Demokritos", Greece | ||
| − | + | --> | |
<!-- ==BIONLP 2015 Workshop Schedule== | <!-- ==BIONLP 2015 Workshop Schedule== | ||
Revision as of 19:37, 7 August 2016
BIONLP 2016
An ACL 2016 Workshop associated with the SIGBIOMED special interest group Featuring two associated tasks: BioASQ (http://www.bioasq.org/workshop) and BioNLP-ST (http://2016.bionlp-st.org).
Berlin, Germany, August 12 -13, 2016
IMPORTANT DATES
- BioNLP workshop: Friday, August 12, 2016
- BioNLP-ST and BioASQ workshop: Saturday August 13, 2016
BIONLP 2016 Workshop Schedule
| Friday August 12, 2016 | |
| 8:30–8:40 | Opening remarks |
| 8:40–10:30 | Session 1: Entity extraction and representation |
| 8:40–9:00 | A Machine Learning Approach to Clinical Terms Normalization Jose Castano, María Laura Gambarte, Hee Joon Park, Maria del Pilar Avila Williams, David Perez, Fernando Campos, Daniel Luna, Sonia Benitez, Hernan Berinsky and Sofía Zanetti |
| 9:00–9:20 | Improved Semantic Representation for Domain-Specific Entities Mohammad Taher Pilehvar and Nigel Collier |
| 9:20–9:40 | Identification, characterization, and grounding of gradable terms in clinical text Chaitanya Shivade, Marie-Catherine de Marneffe, Eric Fosler-Lussier and Albert M. Lai |
| 9:40–10:00 | Graph-based Semi-supervised Gene Mention Tagging Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Anoop Sarkar and Inanc Birol |
| 10:00–10:30 | Invited Talk: The BioNLP-ST challenges on information extraction and knowledge acquisition in biology Speakers: Robert Bossy and Jin-Dong Kim |
| 10:30–11:00 | Coffee Break |
| 11:00–12:30 | Session 2: Event and Relation Extraction |
| 11:00–11:20 | Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses Dayne Freitag and John Niekrasz |
| 11:40–12:00 | Inferring Implicit Causal Relationships in Biomedical Literature Halil Kilicoglu |
| 12:00–12:20 | SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction Marco A. Valenzuela-Escárcega, Gus Hahn-Powell, Dane Bell and Mihai Surdeanu |
| 12:20–12:40 | Character based String Kernels for Bio-Entity Relation Detection Ritambhara Singh and Yanjun Qi |
| 12:40–14:00 | Lunch break |
| 14:00–15:40 | Session 3: Disambiguation, Classification, and more |
| 14:00–14:20 | Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge Amy Siu, Patrick Ernst and Gerhard Weikum |
| 14:20–14:40 | Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts Stephan Tulkens, Simon Suster and Walter Daelemans |
| 14:40–15:00 | Unsupervised Document Classification with Informed Topic Models Timothy Miller, Dmitriy Dligach and Guergana Savova |
| 15:00–15:20 | Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes Sumithra Velupillai, Danielle L Mowery, Mike Conway, John Hurdle and Brent Kious |
| 15:20–15:40 | Syntactic analyses and named entity recognition for PubMed and PubMed Central __ up-to-the-minute Kai Hakala, Suwisa Kaewphan, Tapio Salakoski and Filip Ginter |
| 15:40–16:00 | Coffee Break |
| 16:00–16:30 | Invited Talk: BioASQ: A challenge on large-scale biomedical semantic indexing and question answering Speaker: Anastasia Krithara |
| 16:30–17:30 | Poster Session |
| Improving Temporal Relation Extraction with Training Instance Augmentation Chen Lin, Timothy Miller, Dmitriy Dligach, Steven Bethard and Guergana Savova | |
| Using Centroids of Word Embeddings and Word Mover’s Distance for Biomedical Document Retrieval in Question Answering Georgios-Ioannis Brokos, Prodromos Malakasiotis and Ion Androutsopoulos | |
| Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway Michael Spranger, Sucheendra Palaniappan and Samik Gosh | |
| Construction of a Personal Experience Tweet Corpus for Health Surveillance Keyuan Jiang, Ricardo Calix and Matrika Gupta | |
| Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification Nut Limsopatham and Nigel Collier | |
| PubTermVariants: biomedical term variants and their use for PubMed search Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Doğan, Wanli Liu, Donald C Comeau, Zhiyong Lu and W John Wilbur | |
| This before That: Causal Precedence in the Biomedical Domain Gus Hahn-Powell, Dane Bell, Marco A. Valenzuela-Escárcega and Mihai Surdeanu | |
| Syntactic methods for negation detection in radiology reports in Spanish Viviana Cotik, Vanesa Stricker, Jorge Vivaldi and Horacio Rodriguez | |
| How to Train good Word Embeddings for Biomedical NLP Billy Chiu, Gamal Crichton, Anna Korhonen and Sampo Pyysalo | |
| An Information Foraging Approach to Determining the Number of Relevant Features Brian Connolly, Benjamin Glass and John Pestian | |
| Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians Brian E. Chapman, Danielle L Mowery, Evan Narasimhan, Neel Patel, Wendy Chapman and Marta Heilbrun | |
| Building a dictionary of lexical variants for phenotype descriptors Simon Kocbek and Tudor Groza | |
| Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections Olof Jacobson and Hercules Dalianis | |
| Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning Genevieve Gorrell, Sherifat Oduola, Angus Roberts, Tom Craig, Craig Morgan and Rob Stewart | |
| Relation extraction from clinical texts using domain invariant convolutional neural network Sunil Sahu, Ashish Anand, Krishnadev Oruganty and Mahanandeeshwar Gattu | |
| Results of the 4th edition of BioASQ Challenge Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras and Ioannis Kakadiaris | |
| All August 13 talks are also presented as posters on August 12 and August 13 | |
BioASQ / BioNLP-ST Workshop Program, August 13
| 9:00-9:15 | Welcome |
| 9:15-10:15 | Invited speaker: Sherri Matis-Mitchell Solving Problems and Supporting Decisions in Pharma R&D using Text Analytics: A Recent History |
| 10:15-10:30 | Overview of BioASQ |
| 10:30-11:00 | Coffee break |
| 11:00-12:30 | BioASQ participant session |
| 11:00-11:15 | Using Learning-To-Rank to Enhance NLM Medical Text Indexer Results Ilya Zavorin, James Mork and Dina Demner-Fushman |
| 11:15-11:30 | LABDA at the 2016 BioASQ challenge task 4a: Semantic Indexing by using ElasticSearch Isabel Segura-Bedmar, Adrián Carruana and Paloma Martínez |
| 11:30-11:45 | Learning to Answer Biomedical Questions: OAQA at BioASQ 4B Zi Yang, Yue Zhou and Eric Nyberg |
| 11:45-12:00 | HPI Question Answering System in BioASQ 2016 Frederik Schulze, Ricarda Schuler, Tim Draeger, Daniel Dummer, Alexander Ernst, Pedro Flemming, Cindy Perscheid, Mariana Neves |
| 12:00-12:15 | KSAnswer: Question-answering System of Kangwon National University and Sogang University in the 2016 BioASQ Challenge Hyeon-gu Lee, Minkyoung Kim, Harksoo Kim, Juae Kim, Sunjae Kwon, Jungyun Seo, Yi-Reun Kim and Jung-Kyu Choi |
| 12:15-12:30 | Large-Scale Semantic Indexing and Question Answering in Biomedicine Eirini Papagiannopoulou, Yiannis Papanikolaou, Dimitris Dimitriadis, Sakis Lagopoulos, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos and Ioannis Vlahavas |
| 12:30-14:00 | Lunch break |
| 14:00-14:15 | Overview of BioNLP-ST |
| 14:15-15:30 | BioNLP-ST participant session 1 |
| 14:15-14:30 | LitWay, discriminative extraction for different bio-events Chen Li, Zhiqiang Rao and Xiangrong Zhang |
| 14:30-14:45 | VERSE: Event and relation extraction in the BioNLP 2016 Shared Task Jake Lever and Steven JM Jones |
| 14:45-15:00 | A dictionary- and rule-based system for identification of bacteria and habitats in text Helen Cook, Evangelos Pafilis and Lars Juhl Jensen |
| 15:00-15:15 | Extraction of Regulatory Events Using Kernel-based Classifiers and Distant Supervision Andre Lamurias, Miguel J. Rodrigues, Luka A. Clarke and Francisco M Couto |
| 15:15-15:30 | Deep Learning With Minimal Training Data: TurkuNLP Entry in The BioNLP Shared Task 2016 Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski and Filip Ginter |
| 15:30-16:00 | Coffee break |
| 16:00-17:00 | BioNLP-ST participant session 2 |
| 16:00-16:15 | Identification of mentions and relations between bacteria and biotope from PubMed abstracts Cyril Grouin |
| 16:15-16:30 | SeeDev Binary Event Extraction Using SVMs and a Rich Feature set Nagesh Panyam Chandrasekarasastry, Gitansh Khirbat, Karin Verspoor, Trevor Cohn and Kotagiri Ramamohanarao |
| 16:30-16:45 | Ontology Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques Mert Tiftikci, Hakan Şahin, Berfu Büyüköz, Alper Yayıkçı and Arzucan Özgür |
| 16:45-17:00 | DUTIR in BioNLP-ST 2016: Utilizing convolutional network and distributed representation to extract complicate relations Honglei Li, Jianhai Zhang, Jian Wang, Hongfei Lin and Zhihao Yang |
| 17:00-17:30 | Closing session |