Saber A. Akhondi

According to our database, Saber A. Akhondi authored at least 35 papers between 2012 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Focused Contrastive Loss for Classification With Pre-Trained Language Models.

Jiayuan He, Yuan Li, Zenan Zhai, Biaoyan Fang, Camilo Thorne, Christian Druckenbrodt, Saber A. Akhondi, Karin Verspoor

IEEE Trans. Knowl. Data Eng., July, 2024

Automated Synonym Discovery for Taxonomy Maintenance Using Semantic Search Techniques.

Maziar Moradi Fard, Camilo Thorne, Paula Sorrolla Bayod, Saber A. Akhondi, Wytze Vlietstra

Proceedings of the Natural Language Processing and Information Systems, 2024

Learning Section Weights for Multi-label Document Classification.

Maziar Moradi Fard, Paula Sorrolla Bayod, Kiomars Motarjem, Mohammad Alian Nejadi, Saber A. Akhondi, Camilo Thorne

Proceedings of the Natural Language Processing and Information Systems, 2024

2023

One Strike, You're Out: Detecting Markush Structures in Low Signal-to-Noise Ratio Images.

Thomas Jurriaans, Kinga Szarkowska, Eric T. Nalisnick, Markus Schwörer, Camilo Thorne, Saber A. Akhondi

CoRR, 2023

Stress Testing BERT Anaphora Resolution Models for Reaction Extraction in Chemical Patents.

Chieling Yueh, Evangelos Kanoulas, Bruno Martins, Camilo Thorne, Saber A. Akhondi

CoRR, 2023

2022

The ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.

Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zenan Zhai, Zubair Afzal, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Proceedings of the Advances in Information Retrieval, 2022

Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.

Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor

Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2022

Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.

Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Kojiro Machi, Masaharu Yoshioka, Youngrok Jang, Hosung Song, Junho Lee, Gyeonghun Kim, Yireun Kim, Stanley Jungkyu Choi, Honglak Lee, Kyunghoon Bae, Darshini Mahendran, Christina Tang, Bridget T. McInnes, Timothy Baldwin, Karin Verspoor

Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, Bologna, Italy, September 5th - to, 2022

2021

ChemTables: a dataset for semantic classification on tables in chemical patents.

Zenan Zhai, Christian Druckenbrodt, Camilo Thorne, Saber A. Akhondi, Dat Quoc Nguyen, Trevor Cohn, Karin Verspoor

J. Cheminformatics, 2021

ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents.

Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Frontiers Res. Metrics Anal., 2021

ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents.

Jiayuan He, Biaoyan Fang, Hiyori Yoshikawa, Yuan Li, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Proceedings of the Advances in Information Retrieval, 2021

ChEMU-Ref: A Corpus for Modeling Anaphora Resolution in the Chemical Domain.

Biaoyan Fang, Christian Druckenbrodt, Saber A. Akhondi, Jiayuan He, Timothy Baldwin, Karin Verspoor

Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume, 2021

Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents.

Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor

Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2021

Extended Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents.

Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor

Proceedings of the Working Notes of CLEF 2021 - Conference and Labs of the Evaluation Forum, Bucharest, Romania, September 21st - to, 2021

2020

Word Embeddings for Chemical Patent Natural Language Processing.

Camilo Thorne, Saber A. Akhondi

CoRR, 2020

CORA: A Deep Active Learning Covid-19 Relevancy Algorithm to Identify Core Scientific Articles.

Zubair Afzal, Vikrant Yadav, Olga Fedorova, Vaishnavi Kandala, Janneke van de Loo, Saber A. Akhondi, Pascal Coupet, George Tsatsaronis

Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020, 2020

ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents.

Dat Quoc Nguyen, Zenan Zhai, Hiyori Yoshikawa, Biaoyan Fang, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Saber A. Akhondi, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Proceedings of the Advances in Information Retrieval, 2020

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents.

Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M. Couto, Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro, Daniel M. Lowe, John Mayfield, Abdullatif Köksal, Hilal Dönmez, Elif Özkirimli, Arzucan Özgür, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes, C. S. Malarkodi, Pattabhi Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Proceedings of the Working Notes of CLEF 2020, 2020

Overview of ChEMU 2020: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents.

Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2020

2019

Automatic identification of relevant chemical compounds from patents.

Saber A. Akhondi, Hinnerk Rey, Markus Schwörer, Michael Maier, John P. Toomey, Heike Nau, Gabriele Ilchmann, Mark Sheehan, Matthias Irmer, Claudia Bobach, Marius A. Doornenbal, Michelle Gregory, Jan A. Kors

Database J. Biol. Databases Curation, 2019

Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings.

Zenan Zhai, Dat Quoc Nguyen, Saber A. Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, Karin Verspoor

Proceedings of the 18th BioNLP Workshop and Shared Task, 2019

Detecting Chemical Reactions in Patents.

Hiyori Yoshikawa, Dat Quoc Nguyen, Zenan Zhai, Christian Druckenbrodt, Camilo Thorne, Saber A. Akhondi, Timothy Baldwin, Karin Verspoor

Proceedings of the The 17th Annual Workshop of the Australasian Language Technology Association, 2019

2017

The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts.

Ander Intxaurrondo, Martín Pérez-Pérez, Gael Pérez Rodríguez, Jose Antonio López-Martín, Jesus Santamaría, Santiago de la Peña, Marta Villegas, Saber Ahmad Akhondi, Alfonso Valencia, Anália Lourenço, Martin Krallinger

Proceedings of the Second Workshop on Evaluation of Human Language Technologies for Iberian Languages (IberEval 2017) co-located with 33th Conference of the Spanish Society for Natural Language Processing (SEPLN 2017), 2017

2016

Extraction of chemical-induced diseases using prior knowledge and textual information.

Ewoud Pons, Benedikt F. H. Becker, Saber A. Akhondi, Zubair Afzal, Erik M. van Mulligen, Jan A. Kors

Database J. Biol. Databases Curation, 2016

Chemical entity recognition in patents by combining dictionary-based and statistical approaches.

Saber A. Akhondi, Ewoud Pons, Zubair Afzal, Herman van Haagen, Benedikt F. H. Becker, Kristina M. Hettne, Erik M. van Mulligen, Jan A. Kors

Database J. Biol. Databases Curation, 2016

Selecting Documents Relevant for Chemistry as a Classification Problem.

Zhemin Zhu, Saber A. Akhondi, Umesh Nandal, Marius A. Doornenbal, Michelle Gregory

Proceedings of the Knowledge Engineering and Knowledge Management, 2016

Erasmus MC at CLEF eHealth 2016: Concept Recognition and Coding in French Texts.

Erik M. van Mulligen, Zubair Afzal, Saber A. Akhondi, Dang Vo, Jan A. Kors

Proceedings of the Working Notes of CLEF 2016, 2016

Concept Recognition in French Biomedical Text Using Automatic Translation.

Zubair Afzal, Saber A. Akhondi, Herman H. H. B. M. van Haagen, Erik M. van Mulligen, Jan A. Kors

Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2016

2015

The CHEMDNER corpus of chemicals and drugs and its annotation principles.

Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia

J. Cheminformatics, 2015

Ambiguity of non-systematic chemical identifiers within and between small-molecule databases.

Saber A. Akhondi, Sorel Muresan, Antony J. Williams, Jan A. Kors

J. Cheminformatics, 2015

Recognition of chemical entities: combining dictionary-based and grammar-based approaches.

Saber A. Akhondi, Kristina M. Hettne, Eelke van der Horst, Erik M. van Mulligen, Jan A. Kors

J. Cheminformatics, 2015

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC.

Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann

J. Am. Medical Informatics Assoc., 2015

Biomedical Concept Recognition in French Text Using Automatic Translation of English Terms.

Zubair Afzal, Saber A. Akhondi, Herman van Haagen, Erik M. van Mulligen, Jan A. Kors

Proceedings of the Working Notes of CLEF 2015, 2015

2013

Creating Multilingual Gold Standard Corpora for Biomedical Concept Recognition.

Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann

Proceedings of the Working Notes for CLEF 2013 Conference , 2013

2012

Consistency of systematic chemical identifiers within and between small-molecule databases.

Saber A. Akhondi, Jan A. Kors, Sorel Muresan

J. Cheminformatics, 2012