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Mario Sänger

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Large Language Models to the Rescue: Reducing the Complexity in Scientific Workflow Development Using ChatGPT

Nov 06, 2023
Mario Sänger, Ninon De Mecquenem, Katarzyna Ewa Lewińska, Vasilis Bountris, Fabian Lehmann, Ulf Leser, Thomas Kosch

Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages. To address these challenges, we investigate the efficiency of Large Language Models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed three user studies in two scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.

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BLOOM: A 176B-Parameter Open-Access Multilingual Language Model

Nov 09, 2022
Teven Le Scao, Angela Fan, Christopher Akiki, Ellie Pavlick, Suzana Ilić, Daniel Hesslow, Roman Castagné, Alexandra Sasha Luccioni, François Yvon, Matthias Gallé, Jonathan Tow, Alexander M. Rush, Stella Biderman, Albert Webson, Pawan Sasanka Ammanamanchi, Thomas Wang, Benoît Sagot, Niklas Muennighoff, Albert Villanova del Moral, Olatunji Ruwase, Rachel Bawden, Stas Bekman, Angelina McMillan-Major, Iz Beltagy, Huu Nguyen, Lucile Saulnier, Samson Tan, Pedro Ortiz Suarez, Victor Sanh, Hugo Laurençon, Yacine Jernite, Julien Launay, Margaret Mitchell, Colin Raffel, Aaron Gokaslan, Adi Simhi, Aitor Soroa, Alham Fikri Aji, Amit Alfassy, Anna Rogers, Ariel Kreisberg Nitzav, Canwen Xu, Chenghao Mou, Chris Emezue, Christopher Klamm, Colin Leong, Daniel van Strien, David Ifeoluwa Adelani, Dragomir Radev, Eduardo González Ponferrada, Efrat Levkovizh, Ethan Kim, Eyal Bar Natan, Francesco De Toni, Gérard Dupont, Germán Kruszewski, Giada Pistilli, Hady Elsahar, Hamza Benyamina, Hieu Tran, Ian Yu, Idris Abdulmumin, Isaac Johnson, Itziar Gonzalez-Dios, Javier de la Rosa, Jenny Chim, Jesse Dodge, Jian Zhu, Jonathan Chang, Jörg Frohberg, Joseph Tobing, Joydeep Bhattacharjee, Khalid Almubarak, Kimbo Chen, Kyle Lo, Leandro Von Werra, Leon Weber, Long Phan, Loubna Ben allal, Ludovic Tanguy, Manan Dey, Manuel Romero Muñoz, Maraim Masoud, María Grandury, Mario Šaško, Max Huang, Maximin Coavoux, Mayank Singh, Mike Tian-Jian Jiang, Minh Chien Vu, Mohammad A. Jauhar, Mustafa Ghaleb, Nishant Subramani, Nora Kassner, Nurulaqilla Khamis, Olivier Nguyen, Omar Espejel, Ona de Gibert, Paulo Villegas, Peter Henderson, Pierre Colombo, Priscilla Amuok, Quentin Lhoest, Rheza Harliman, Rishi Bommasani, Roberto Luis López, Rui Ribeiro, Salomey Osei, Sampo Pyysalo, Sebastian Nagel, Shamik Bose, Shamsuddeen Hassan Muhammad, Shanya Sharma, Shayne Longpre, Somaieh Nikpoor, Stanislav Silberberg, Suhas Pai, Sydney Zink, Tiago Timponi Torrent, Timo Schick, Tristan Thrush, Valentin Danchev, Vassilina Nikoulina, Veronika Laippala, Violette Lepercq, Vrinda Prabhu, Zaid Alyafeai, Zeerak Talat, Arun Raja, Benjamin Heinzerling, Chenglei Si, Elizabeth Salesky, Sabrina J. Mielke, Wilson Y. Lee, Abheesht Sharma, Andrea Santilli, Antoine Chaffin, Arnaud Stiegler, Debajyoti Datta, Eliza Szczechla, Gunjan Chhablani, Han Wang, Harshit Pandey, Hendrik Strobelt, Jason Alan Fries, Jos Rozen, Leo Gao, Lintang Sutawika, M Saiful Bari, Maged S. Al-shaibani, Matteo Manica, Nihal Nayak, Ryan Teehan, Samuel Albanie, Sheng Shen, Srulik Ben-David, Stephen H. Bach, Taewoon Kim, Tali Bers, Thibault Fevry, Trishala Neeraj, Urmish Thakker, Vikas Raunak, Xiangru Tang, Zheng-Xin Yong, Zhiqing Sun, Shaked Brody, Yallow Uri, Hadar Tojarieh, Adam Roberts, Hyung Won Chung, Jaesung Tae, Jason Phang, Ofir Press, Conglong Li, Deepak Narayanan, Hatim Bourfoune, Jared Casper, Jeff Rasley, Max Ryabinin, Mayank Mishra, Minjia Zhang, Mohammad Shoeybi, Myriam Peyrounette, Nicolas Patry, Nouamane Tazi, Omar Sanseviero, Patrick von Platen, Pierre Cornette, Pierre François Lavallée, Rémi Lacroix, Samyam Rajbhandari, Sanchit Gandhi, Shaden Smith, Stéphane Requena, Suraj Patil, Tim Dettmers, Ahmed Baruwa, Amanpreet Singh, Anastasia Cheveleva, Anne-Laure Ligozat, Arjun Subramonian, Aurélie Névéol, Charles Lovering, Dan Garrette, Deepak Tunuguntla, Ehud Reiter, Ekaterina Taktasheva, Ekaterina Voloshina, Eli Bogdanov, Genta Indra Winata, Hailey Schoelkopf, Jan-Christoph Kalo, Jekaterina Novikova, Jessica Zosa Forde, Jordan Clive, Jungo Kasai, Ken Kawamura, Liam Hazan, Marine Carpuat, Miruna Clinciu, Najoung Kim, Newton Cheng, Oleg Serikov, Omer Antverg, Oskar van der Wal, Rui Zhang, Ruochen Zhang, Sebastian Gehrmann, Shani Pais, Tatiana Shavrina, Thomas Scialom, Tian Yun, Tomasz Limisiewicz, Verena Rieser, Vitaly Protasov, Vladislav Mikhailov, Yada Pruksachatkun, Yonatan Belinkov, Zachary Bamberger, Zdeněk Kasner, Alice Rueda, Amanda Pestana, Amir Feizpour, Ammar Khan, Amy Faranak, Ana Santos, Anthony Hevia, Antigona Unldreaj, Arash Aghagol, Arezoo Abdollahi, Aycha Tammour, Azadeh HajiHosseini, Bahareh Behroozi, Benjamin Ajibade, Bharat Saxena, Carlos Muñoz Ferrandis, Danish Contractor, David Lansky, Davis David, Douwe Kiela, Duong A. Nguyen, Edward Tan, Emi Baylor, Ezinwanne Ozoani, Fatima Mirza, Frankline Ononiwu, Habib Rezanejad, Hessie Jones, Indrani Bhattacharya, Irene Solaiman, Irina Sedenko, Isar Nejadgholi, Jesse Passmore, Josh Seltzer, Julio Bonis Sanz, Karen Fort, Livia Dutra, Mairon Samagaio, Maraim Elbadri, Margot Mieskes, Marissa Gerchick, Martha Akinlolu, Michael McKenna, Mike Qiu, Muhammed Ghauri, Mykola Burynok, Nafis Abrar, Nazneen Rajani, Nour Elkott, Nour Fahmy, Olanrewaju Samuel, Ran An, Rasmus Kromann, Ryan Hao, Samira Alizadeh, Sarmad Shubber, Silas Wang, Sourav Roy, Sylvain Viguier, Thanh Le, Tobi Oyebade, Trieu Le, Yoyo Yang, Zach Nguyen, Abhinav Ramesh Kashyap, Alfredo Palasciano, Alison Callahan, Anima Shukla, Antonio Miranda-Escalada, Ayush Singh, Benjamin Beilharz, Bo Wang, Caio Brito, Chenxi Zhou, Chirag Jain, Chuxin Xu, Clémentine Fourrier, Daniel León Periñán, Daniel Molano, Dian Yu, Enrique Manjavacas, Fabio Barth, Florian Fuhrimann, Gabriel Altay, Giyaseddin Bayrak, Gully Burns, Helena U. Vrabec, Imane Bello, Ishani Dash, Jihyun Kang, John Giorgi, Jonas Golde, Jose David Posada, Karthik Rangasai Sivaraman, Lokesh Bulchandani, Lu Liu, Luisa Shinzato, Madeleine Hahn de Bykhovetz, Maiko Takeuchi, Marc Pàmies, Maria A Castillo, Marianna Nezhurina, Mario Sänger, Matthias Samwald, Michael Cullan, Michael Weinberg, Michiel De Wolf, Mina Mihaljcic, Minna Liu, Moritz Freidank, Myungsun Kang, Natasha Seelam, Nathan Dahlberg, Nicholas Michio Broad, Nikolaus Muellner, Pascale Fung, Patrick Haller, Ramya Chandrasekhar, Renata Eisenberg, Robert Martin, Rodrigo Canalli, Rosaline Su, Ruisi Su, Samuel Cahyawijaya, Samuele Garda, Shlok S Deshmukh, Shubhanshu Mishra, Sid Kiblawi, Simon Ott, Sinee Sang-aroonsiri, Srishti Kumar, Stefan Schweter, Sushil Bharati, Tanmay Laud, Théo Gigant, Tomoya Kainuma, Wojciech Kusa, Yanis Labrak, Yash Shailesh Bajaj, Yash Venkatraman, Yifan Xu, Yingxin Xu, Yu Xu, Zhe Tan, Zhongli Xie, Zifan Ye, Mathilde Bras, Younes Belkada, Thomas Wolf

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.

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BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing

Jun 30, 2022
Jason Alan Fries, Leon Weber, Natasha Seelam, Gabriel Altay, Debajyoti Datta, Samuele Garda, Myungsun Kang, Ruisi Su, Wojciech Kusa, Samuel Cahyawijaya, Fabio Barth, Simon Ott, Matthias Samwald, Stephen Bach, Stella Biderman, Mario Sänger, Bo Wang, Alison Callahan, Daniel León Periñán, Théo Gigant, Patrick Haller, Jenny Chim, Jose David Posada, John Michael Giorgi, Karthik Rangasai Sivaraman, Marc Pàmies, Marianna Nezhurina, Robert Martin, Michael Cullan, Moritz Freidank, Nathan Dahlberg, Shubhanshu Mishra, Shamik Bose, Nicholas Michio Broad, Yanis Labrak, Shlok S Deshmukh, Sid Kiblawi, Ayush Singh, Minh Chien Vu, Trishala Neeraj, Jonas Golde, Albert Villanova del Moral, Benjamin Beilharz

Figure 1 for BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing
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Figure 4 for BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

* Submitted to NeurIPS 2022 Datasets and Benchmarks Track 
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HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition

Aug 18, 2020
Leon Weber, Mario Sänger, Jannes Münchmeyer, Maryam Habibi, Ulf Leser, Alan Akbik

Figure 1 for HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition
Figure 2 for HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition

Summary: Named Entity Recognition (NER) is an important step in biomedical information extraction pipelines. Tools for NER should be easy to use, cover multiple entity types, highly accurate, and robust towards variations in text genre and style. To this end, we propose HunFlair, an NER tagger covering multiple entity types integrated into the widely used NLP framework Flair. HunFlair outperforms other state-of-the-art standalone NER tools with an average gain of 7.26 pp over the next best tool, can be installed with a single command and is applied with only four lines of code. Availability: HunFlair is freely available through the Flair framework under an MIT license: https://github.com/flairNLP/flair and is compatible with all major operating systems. Contact:{weberple,saengema,alan.akbik}@informatik.hu-berlin.de

* - Corrected author list - Updated project link 
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