Saber A. Akhondi

Publication Activity (10 Years)

Years Active: 2012-2024
Publications (10 Years): 27

Top Topics

Named Entity Recognition

Chemical Reaction

Information Extraction

Anaphora Resolution

Top Venues

CLEF (Working Notes)

J. Cheminformatics

Publications

Jiayuan He, Yuan Li, Zenan Zhai, Biaoyan Fang, Camilo Thorne, Christian Druckenbrodt, Saber A. Akhondi, Karin Verspoor
Focused Contrastive Loss for Classification With Pre-Trained Language Models. IEEE Trans. Knowl. Data Eng. 36 (7) (2024)
Thomas Jurriaans, Kinga Szarkowska, Eric Nalisnick, Markus Schwörer, Camilo Thorne, Saber A. Akhondi
One Strike, You're Out: Detecting Markush Structures in Low Signal-to-Noise Ratio Images. CoRR (2023)
Chieling Yueh, Evangelos Kanoulas, Bruno Martins, Camilo Thorne, Saber A. Akhondi
Stress Testing BERT Anaphora Resolution Models for Reaction Extraction in Chemical Patents. CoRR (2023)
Maziar Moradi Fard, Paula Sorrolla Bayod, Kiomars Motarjem, Mohammad Alian Nejadi, Saber A. Akhondi, Camilo Thorne
Learning Section Weights for Multi-Label Document Classification. CoRR (2023)
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
Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. CLEF (Working Notes) (2022)
Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor
Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. CLEF (2022)
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
The ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. ECIR (2) (2022)
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
ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents. Frontiers Res. Metrics Anal. 6 (2021)
Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor
Extended Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents. CLEF (Working Notes) (2021)
Biaoyan Fang, Christian Druckenbrodt, Saber A. Akhondi, Jiayuan He, Timothy Baldwin, Karin Verspoor
ChEMU-Ref: A Corpus for Modeling Anaphora Resolution in the Chemical Domain. EACL (2021)
Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor
Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents. CLEF (2021)
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
ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents. ECIR (2) (2021)
Zenan Zhai, Christian Druckenbrodt, Camilo Thorne, Saber A. Akhondi, Dat Quoc Nguyen, Trevor Cohn, Karin Verspoor
ChemTables: a dataset for semantic classification on tables in chemical patents. J. Cheminformatics 13 (1) (2021)
Camilo Thorne, Saber A. Akhondi
Word Embeddings for Chemical Patent Natural Language Processing. CoRR (2020)
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
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) (2020)
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
Overview of ChEMU 2020: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents. CLEF (2020)
Dat Quoc Nguyen, Zenan Zhai, Hiyori Yoshikawa, Biaoyan Fang, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Saber A. Akhondi, Trevor Cohn, Timothy Baldwin, Karin Verspoor
ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents. ECIR (2) (2020)
Zubair Afzal, Vikrant Yadav, Olga Fedorova, Vaishnavi Kandala, Janneke van de Loo, Saber A. Akhondi, Pascal Coupet, George Tsatsaronis
CORA: A Deep Active Learning Covid-19 Relevancy Algorithm to Identify Core Scientific Articles. NLP4COVID@EMNLP (2020)
Zenan Zhai, Dat Quoc Nguyen, Saber A. Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, Karin Verspoor
Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings. BioNLP@ACL (2019)
Zenan Zhai, Dat Quoc Nguyen, Saber A. Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, Karin Verspoor
Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings. CoRR (2019)
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
Automatic identification of relevant chemical compounds from patents. Database J. Biol. Databases Curation 2019 (2019)
Hiyori Yoshikawa, Dat Quoc Nguyen, Zenan Zhai, Christian Druckenbrodt, Camilo Thorne, Saber A. Akhondi, Timothy Baldwin, Karin Verspoor
Detecting Chemical Reactions in Patents. ALTA (2019)
Zhemin Zhu, Saber A. Akhondi, Umesh Nandal, Marius A. Doornenbal, Michelle Gregory
Selecting Documents Relevant for Chemistry as a Classification Problem. EKAW (Satellite Events) (2016)
Zubair Afzal, Saber A. Akhondi, Herman H. H. B. M. van Haagen, Erik M. van Mulligen, Jan A. Kors
Concept Recognition in French Biomedical Text Using Automatic Translation. CLEF (2016)
Erik M. van Mulligen, Zubair Afzal, Saber A. Akhondi, Dang Vo, Jan A. Kors
Erasmus MC at CLEF eHealth 2016: Concept Recognition and Coding in French Texts. CLEF (Working Notes) (2016)
Saber A. Akhondi, Ewoud Pons, Zubair Afzal, Herman van Haagen, Benedikt F. H. Becker, Kristina M. Hettne, Erik M. van Mulligen, Jan A. Kors
Chemical entity recognition in patents by combining dictionary-based and statistical approaches. Database J. Biol. Databases Curation 2016 (2016)
Ewoud Pons, Benedikt F. H. Becker, Saber A. Akhondi, Zubair Afzal, Erik M. van Mulligen, Jan A. Kors
Extraction of chemical-induced diseases using prior knowledge and textual information. Database J. Biol. Databases Curation 2016 (2016)
Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann
A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC. J. Am. Medical Informatics Assoc. 22 (5) (2015)
Saber A. Akhondi, Kristina M. Hettne, Eelke van der Horst, Erik M. van Mulligen, Jan A. Kors
Recognition of chemical entities: combining dictionary-based and grammar-based approaches. J. Cheminformatics 7 (S-1) (2015)
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
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7 (S-1) (2015)
Saber A. Akhondi, Sorel Muresan, Antony J. Williams, Jan A. Kors
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases. J. Cheminformatics 7 (2015)
Zubair Afzal, Saber A. Akhondi, Herman van Haagen, Erik M. van Mulligen, Jan A. Kors
Biomedical Concept Recognition in French Text Using Automatic Translation of English Terms. CLEF (Working Notes) (2015)
Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann
Creating Multilingual Gold Standard Corpora for Biomedical Concept Recognition. CLEF (Working Notes) (2013)
Saber A. Akhondi, Jan A. Kors, Sorel Muresan
Consistency of systematic chemical identifiers within and between small-molecule databases. J. Cheminformatics 4 (2012)