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There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines.
The hugo gene nomenclature committee (hgnc)
Sue Povey, Ruth Lovering, Elspeth Bruford, Mathew Wright, Michael Lush, and Hester Wain · 2001
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Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, and Michiel J. L. de Hoon · 2009
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The mammalian phenotype ontology: enabling robust annotation and comparative analysis
Cynthia L Smith and Janan T Eppig · 2009
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Molecular signatures database (msigdb) 3.0
Arthur Liberzon, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, and Jill P Mesirov · 2011
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Omim. org: Online mendelian inheritance in man (omim®), an online catalog of human genes and genetic disorders
Joanna S Amberger, Carol A Bocchini, François Schiettecatte, Alan F Scott, and Ada Hamosh · 2015
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann, et al · 2016
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Clinvar: public archive of interpretations of clinically relevant variants
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover, et al · 2016
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Disgenet: a comprehensive platform integrating information on human disease-associated genes and variants
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, and Laura I Furlong · 2016
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Gtrd: a database of transcription factor binding sites identified by chip-seq experiments
Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, and Fedor Kolpakov · 2016
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A structure-informed atlas of human-virus interactions
Gorka Lasso, Sandra V Mayer, Evandro R Winkelmann, Tim Chu, Oliver Elliot, Juan Angel Patino-Galindo, Kernyu Park, Raul Rabadan, Barry Honig, and Sagi D Shapira · 2019
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mirdb: an online database for prediction of functional microrna targets
Yuhao Chen and Xiaowei Wang · 2020
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Measuring massive multitask language understanding, 2021
Dan Hendrycks, Collin Burns, Steven Basart, Andy Zou, Mantas Mazeika, Dawn Song, and Jacob Steinhardt · 2021
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Highly accurate protein structure prediction with AlphaFold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A A Kohl, Andrew J Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W Senior, Koray Kavukcuoglu, Pushmeet Kohli, and Demis Hassabis · 2021
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scite: A smart citation index that displays the context of citations and classifies their intent using deep learning
Josh M. Nicholson, Milo Mordaunt, Patrice Lopez, Ashish Uppala, Domenic Rosati, Neves P. Rodrigues, Peter Grabitz, and Sean C. Rife · 2021
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Ape, a plasmid editor: A freely available dna manipulation and visualization program
M. Wayne Davis and Erik M. Jorgensen · 2022
Earlier work this paper cites.
Holistic evaluation of language models
Percy Liang, Rishi Bommasani, Tony Lee, Dimitris Tsipras, Dilara Soylu, Michihiro Yasunaga, Yian Zhang, Deepak Narayanan, Yuhuai Wu, Ananya Kumar, Benjamin Newman, Binhang Yuan, Bobby Yan, Ce Zhang, Christian Cosgrove, Christopher D Manning, Christopher Ré, Diana Acosta-Navas, Drew A Hudson, Eric Zelikman, Esin Durmus, Faisal Ladhak, Frieda Rong, Hongyu Ren, Huaxiu Yao, Jue Wang, Keshav Santhanam, Laurel Orr, Lucia Zheng, Mert Yuksekgonul, Mirac Suzgun, Nathan Kim, Neel Guha, Niladri Chatterji, Omar Khattab, Peter Henderson, Qian Huang, Ryan Chi, Sang Michael Xie, Shibani Santurkar, Surya Ganguli, Tatsunori Hashimoto, Thomas Icard, Tianyi Zhang, Vishrav Chaudhary, William Wang, Xuechen Li, Yifan Mai, Yuhui Zhang, and Yuta Koreeda · 2022
Earlier work this paper cites.
Galactica: A large language model for science
Ross Taylor, Marcin Kardas, Guillem Cucurull, Thomas Scialom, Anthony Hartshorn, Elvis Saravia, Andrew Poulton, Viktor Kerkez, and Robert Stojnic · 2022
Earlier work this paper cites.
Autonomous chemical research with large language models
Daniil A. Boiko, Robert MacKnight, Ben Kline, and Gabe Gomes · 2023
Earlier work this paper cites.
Sparks of artificial general intelligence: Early experiments with gpt-4, 2023
Sébastien Bubeck, Varun Chandrasekaran, Ronen Eldan, Johannes Gehrke, Eric Horvitz, Ece Kamar, Peter Lee, Yin Tat Lee, Yuanzhi Li, Scott Lundberg, Harsha Nori, Hamid Palangi, Marco Tulio Ribeiro, and Yi Zhang · 2023
Cited alongside, same era.
What’s going on with the open llm leaderboard?
Clémentine Fourrier, Najoung Habib, Julien Launay, and Thomas Wolf · 2023
Cited alongside, same era.
Geneturing tests gpt models in genomics
Wenpin Hou and Zhicheng Ji · 2023
Cited alongside, same era.
GPT-4 passes the bar exam
Daniel Martin Katz, Michael James Bommarito, Shang Gao, and Pablo Arredondo · 2023
Cited alongside, same era.
BioASQ-QA: A manually curated corpus for biomedical question answering
Anastasia Krithara, Anastasios Nentidis, Konstantinos Bougiatiotis, and Georgios Paliouras · 2023
Cited alongside, same era.
Performance of ChatGPT on USMLE: Potential for AI-assisted medical education using large language models
Lessons from the trenches on reproducible evaluation of language models
Stella Biderman, Hailey Schoelkopf, Lintang Sutawika, Leo Gao, Jonathan Tow, Baber Abbasi, Alham Fikri Aji, Pawan Sasanka Ammanamanchi, Sidney Black, Jordan Clive, et al · 2024
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Introducing gemini 1.5, google’s next-generation ai model, February 2024
Google · 2024
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Ensembl 2024
Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, et al · 2024
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Machine learning with a reject option: A survey
Kilian Hendrickx, Lorenzo Perini, Dries Van der Plas, Wannes Meert, and Jesse Davis · 2024
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Leveraging large language models for predictive chemistry
Kevin Maik Jablonka, Philippe Schwaller, Andres Ortega-Guerrero, and Berend Smit · 2024
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alphaXiv searches the wider corpus for related work and actual follow-ups.
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Tiffany H Kung, Morgan Cheatham, Arielle Medenilla, Czarina Sillos, Lorie De Leon, Camille Elepaño, Maria Madriaga, Rimel Aggabao, Giezel Diaz-Candido, James Maningo, and Victor Tseng · 2023
Cited alongside, same era.
Paperqa: Retrieval-augmented generative agent for scientific research, 2023
Jakub Lála, Odhran O’Donoghue, Aleksandar Shtedritski, Sam Cox, Samuel G. Rodriques, and Andrew D. White · 2023
Cited alongside, same era.
Scaling deep learning for materials discovery
Amil Merchant, Simon Batzner, Samuel S Schoenholz, Muratahan Aykol, Gowoon Cheon, and Ekin Dogus Cubuk · 2023
Cited alongside, same era.
Proteingym: Large-scale benchmarks for protein fitness prediction and design
Pascal Notin, Aaron Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Han Spinner, Nathan Rollins, Ada Shaw, Rose Orenbuch, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Yarin Gal, and Debora Marks · 2023
Cited alongside, same era.
Ai-assisted coding: Experiments with gpt-4, 2023
Russell A Poldrack, Thomas Lu, and Gašper Beguš · 2023
Cited alongside, same era.
Gpqa: A graduate-level google-proof q&a benchmark, 2023
David Rein, Betty Li Hou, Asa Cooper Stickland, Jackson Petty, Richard Yuanzhe Pang, Julien Dirani, Julian Michael, and Samuel R. Bowman · 2023
Cited alongside, same era.
Biollmbench: A comprehensive benchmarking of large language models in bioinformatics
Varuni Sarwal, Viorel Munteanu, Timur Suhodolschi, Dumitru Ciorba, Eleazar Eskin, Wei Wang, and Serghei Mangul · 2023
Cited alongside, same era.
Samy Jelassi, David Brandfonbrener, Sham M. Kakade, and Eran Malach · 2024
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Swe-bench: Can language models resolve real-world github issues?, 2024
Carlos E. Jimenez, John Yang, Alexander Wettig, Shunyu Yao, Kexin Pei, Ofir Press, and Karthik Narasimhan · 2024
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GeneGPT: augmenting large language models with domain tools for improved access to biomedical information
Qiao Jin, Yifan Yang, Qingyu Chen, and Zhiyong Lu · 2024
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Augmenting large language models with chemistry tools
Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D. White, and Philippe Schwaller · 2024
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Chat: meta-llama/meta-llama-3-70b-instruct, April 2024a
Meta · 2024
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Introducing meta llama 3: The most capable openly available llm to date, April 2024b
Meta · 2024
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Are large language models superhuman chemists?, 2024
Adrian Mirza, Nawaf Alampara, Sreekanth Kunchapu, Benedict Emoekabu, Aswanth Krishnan, Mara Wilhelmi, Macjonathan Okereke, Juliane Eberhardt, Amir Mohammad Elahi, Maximilian Greiner, Caroline T. Holick, Tanya Gupta, Mehrdad Asgari, Christina Glaubitz, Lea C. Klepsch, Yannik Köster, Jakob Meyer, Santiago Miret, Tim Hoffmann, Fabian Alexander Kreth, Michael Ringleb, Nicole Roesner, Ulrich S. Schubert, Leanne M. Stafast, Dinga Wonanke, Michael Pieler, Philippe Schwaller, and Kevin Maik Jablonka · 2024
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Sequence modeling and design from molecular to genome scale with evo
Eric Nguyen, Michael Poli, Matthew G. Durrant, Armin W. Thomas, Brian Kang, Jeremy Sullivan, Madelena Y. Ng, Ashley Lewis, Aman Patel, Aaron Lou, Stefano Ermon, Stephen A. Baccus, Tina Hernandez-Boussard, Christopher Ré, Patrick D. Hsu, and Brian L. Hie · 2024
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Hello gpt-4o, May 2024a
OpenAI · 2024
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Gpt-4 and gpt-4 turbo, 2024b
OpenAI · 2024
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Can good benchmarks contain mistakes?
David Rein · 2024
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Delocalized, asynchronous, closed-loop discovery of organic laser emitters
Felix Strieth-Kalthoff, Han Hao, Vandana Rathore, Joshua Derasp, Théophile Gaudin, Nicholas H Angello, Martin Seifrid, Ekaterina Trushina, Mason Guy, Junliang Liu, Xun Tang, Masashi Mamada, Wesley Wang, Tuul Tsagaantsooj, Cyrille Lavigne, Robert Pollice, Tony C Wu, Kazuhiro Hotta, Leticia Bodo, Shangyu Li, Mohammad Haddadnia, Agnieszka Wołos, Rafał Roszak, Cher Tian Ser, Carlota Bozal-Ginesta, Riley J Hickman, Jenya Vestfrid, Andrés Aguilar-Granda, Elena L Klimareva, Ralph C Sigerson, Wenduan Hou, Daniel Gahler, Slawomir Lach, Adrian Warzybok, Oleg Borodin, Simon Rohrbach, Benjamin Sanchez-Lengeling, Chihaya Adachi, Bartosz A Grzybowski, Leroy Cronin, Jason E Hein, Martin D Burke, and Alán Aspuru-Guzik · 2024
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Benchmarking large language models for molecule prediction tasks, 2024
Zhiqiang Zhong, Kuangyu Zhou, and Davide Mottin · 2024
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