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Jason Yosinski

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RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods

Jan 13, 2023
Maciej Sypetkowski, Morteza Rezanejad, Saber Saberian, Oren Kraus, John Urbanik, James Taylor, Ben Mabey, Mason Victors, Jason Yosinski, Alborz Rezazadeh Sereshkeh, Imran Haque, Berton Earnshaw

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High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

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Beyond the Imitation Game: Quantifying and extrapolating the capabilities of language models

Jun 10, 2022
Aarohi Srivastava, Abhinav Rastogi, Abhishek Rao, Abu Awal Md Shoeb, Abubakar Abid, Adam Fisch, Adam R. Brown, Adam Santoro, Aditya Gupta, Adrià Garriga-Alonso, Agnieszka Kluska, Aitor Lewkowycz, Akshat Agarwal, Alethea Power, Alex Ray, Alex Warstadt, Alexander W. Kocurek, Ali Safaya, Ali Tazarv, Alice Xiang, Alicia Parrish, Allen Nie, Aman Hussain, Amanda Askell, Amanda Dsouza, Ambrose Slone, Ameet Rahane, Anantharaman S. Iyer, Anders Andreassen, Andrea Madotto, Andrea Santilli, Andreas Stuhlmüller, Andrew Dai, Andrew La, Andrew Lampinen, Andy Zou, Angela Jiang, Angelica Chen, Anh Vuong, Animesh Gupta, Anna Gottardi, Antonio Norelli, Anu Venkatesh, Arash Gholamidavoodi, Arfa Tabassum, Arul Menezes, Arun Kirubarajan, Asher Mullokandov, Ashish Sabharwal, Austin Herrick, Avia Efrat, Aykut Erdem, Ayla Karakaş, B. Ryan Roberts, Bao Sheng Loe, Barret Zoph, Bartłomiej Bojanowski, Batuhan Özyurt, Behnam Hedayatnia, Behnam Neyshabur, Benjamin Inden, Benno Stein, Berk Ekmekci, Bill Yuchen Lin, Blake Howald, Cameron Diao, Cameron Dour, Catherine Stinson, Cedrick Argueta, César Ferri Ramírez, Chandan Singh, Charles Rathkopf, Chenlin Meng, Chitta Baral, Chiyu Wu, Chris Callison-Burch, Chris Waites, Christian Voigt, Christopher D. Manning, Christopher Potts, Cindy Ramirez, Clara E. Rivera, Clemencia Siro, Colin Raffel, Courtney Ashcraft, Cristina Garbacea, Damien Sileo, Dan Garrette, Dan Hendrycks, Dan Kilman, Dan Roth, Daniel Freeman, Daniel Khashabi, Daniel Levy, Daniel Moseguí González, Danielle Perszyk, Danny Hernandez, Danqi Chen, Daphne Ippolito, Dar Gilboa, David Dohan, David Drakard, David Jurgens, Debajyoti Datta, Deep Ganguli, Denis Emelin, Denis Kleyko, Deniz Yuret, Derek Chen, Derek Tam, Dieuwke Hupkes, Diganta Misra, Dilyar Buzan, Dimitri Coelho Mollo, Diyi Yang, Dong-Ho Lee, Ekaterina Shutova, Ekin Dogus Cubuk, Elad Segal, Eleanor Hagerman, Elizabeth Barnes, Elizabeth Donoway, Ellie Pavlick, Emanuele Rodola, Emma Lam, Eric Chu, Eric Tang, Erkut Erdem, Ernie Chang, Ethan A. Chi, Ethan Dyer, Ethan Jerzak, Ethan Kim, Eunice Engefu Manyasi, Evgenii Zheltonozhskii, Fanyue Xia, Fatemeh Siar, Fernando Martínez-Plumed, Francesca Happé, Francois Chollet, Frieda Rong, Gaurav Mishra, Genta Indra Winata, Gerard de Melo, Germán Kruszewski, Giambattista Parascandolo, Giorgio Mariani, Gloria Wang, Gonzalo Jaimovitch-López, Gregor Betz, Guy Gur-Ari, Hana Galijasevic, Hannah Kim, Hannah Rashkin, Hannaneh Hajishirzi, Harsh Mehta, Hayden Bogar, Henry Shevlin, Hinrich Schütze, Hiromu Yakura, Hongming Zhang, Hugh Mee Wong, Ian Ng, Isaac Noble, Jaap Jumelet, Jack Geissinger, Jackson Kernion, Jacob Hilton, Jaehoon Lee, Jaime Fernández Fisac, James B. Simon, James Koppel, James Zheng, James Zou, Jan Kocoń, Jana Thompson, Jared Kaplan, Jarema Radom, Jascha Sohl-Dickstein, Jason Phang, Jason Wei, Jason Yosinski, Jekaterina Novikova, Jelle Bosscher, Jennifer Marsh, Jeremy Kim, Jeroen Taal, Jesse Engel, Jesujoba Alabi, Jiacheng Xu, Jiaming Song, Jillian Tang, Joan Waweru, John Burden, John Miller, John U. Balis, Jonathan Berant, Jörg Frohberg, Jos Rozen, Jose Hernandez-Orallo, Joseph Boudeman, Joseph Jones, Joshua B. Tenenbaum, Joshua S. Rule, Joyce Chua, Kamil Kanclerz, Karen Livescu, Karl Krauth, Karthik Gopalakrishnan, Katerina Ignatyeva, Katja Markert, Kaustubh D. Dhole, Kevin Gimpel, Kevin Omondi, Kory Mathewson, Kristen Chiafullo, Ksenia Shkaruta, Kumar Shridhar, Kyle McDonell, Kyle Richardson, Laria Reynolds, Leo Gao, Li Zhang, Liam Dugan, Lianhui Qin, Lidia Contreras-Ochando, Louis-Philippe Morency, Luca Moschella, Lucas Lam, Lucy Noble, Ludwig Schmidt, Luheng He, Luis Oliveros Colón, Luke Metz, Lütfi Kerem Şenel, Maarten Bosma, Maarten Sap, Maartje ter Hoeve, Maheen Farooqi, Manaal Faruqui, Mantas Mazeika, Marco Baturan, Marco Marelli, Marco Maru, Maria Jose Ramírez Quintana, Marie Tolkiehn, Mario Giulianelli, Martha Lewis, Martin Potthast, Matthew L. Leavitt, Matthias Hagen, Mátyás Schubert, Medina Orduna Baitemirova, Melody Arnaud, Melvin McElrath, Michael A. Yee, Michael Cohen, Michael Gu, Michael Ivanitskiy, Michael Starritt, Michael Strube, Michał Swędrowski, Michele Bevilacqua, Michihiro Yasunaga, Mihir Kale, Mike Cain, Mimee Xu, Mirac Suzgun, Mo Tiwari, Mohit Bansal, Moin Aminnaseri, Mor Geva, Mozhdeh Gheini, Mukund Varma T, Nanyun Peng, Nathan Chi, Nayeon Lee, Neta Gur-Ari Krakover, Nicholas Cameron, Nicholas Roberts, Nick Doiron, Nikita Nangia, Niklas Deckers, Niklas Muennighoff, Nitish Shirish Keskar, Niveditha S. Iyer, Noah Constant, Noah Fiedel, Nuan Wen, Oliver Zhang, Omar Agha, Omar Elbaghdadi, Omer Levy, Owain Evans, Pablo Antonio Moreno Casares, Parth Doshi, Pascale Fung, Paul Pu Liang, Paul Vicol, Pegah Alipoormolabashi, Peiyuan Liao, Percy Liang, Peter Chang, Peter Eckersley, Phu Mon Htut, Pinyu Hwang, Piotr Miłkowski, Piyush Patil, Pouya Pezeshkpour, Priti Oli, Qiaozhu Mei, Qing Lyu, Qinlang Chen, Rabin Banjade, Rachel Etta Rudolph, Raefer Gabriel, Rahel Habacker, Ramón Risco Delgado, Raphaël Millière, Rhythm Garg, Richard Barnes, Rif A. Saurous, Riku Arakawa, Robbe Raymaekers, Robert Frank, Rohan Sikand, Roman Novak, Roman Sitelew, Ronan LeBras, Rosanne Liu, Rowan Jacobs, Rui Zhang, Ruslan Salakhutdinov, Ryan Chi, Ryan Lee, Ryan Stovall, Ryan Teehan, Rylan Yang, Sahib Singh, Saif M. Mohammad, Sajant Anand, Sam Dillavou, Sam Shleifer, Sam Wiseman, Samuel Gruetter, Samuel R. Bowman, Samuel S. Schoenholz, Sanghyun Han, Sanjeev Kwatra, Sarah A. Rous, Sarik Ghazarian, Sayan Ghosh, Sean Casey, Sebastian Bischoff, Sebastian Gehrmann, Sebastian Schuster, Sepideh Sadeghi, Shadi Hamdan, Sharon Zhou, Shashank Srivastava, Sherry Shi, Shikhar Singh, Shima Asaadi, Shixiang Shane Gu, Shubh Pachchigar, Shubham Toshniwal, Shyam Upadhyay, Shyamolima, Debnath, Siamak Shakeri, Simon Thormeyer, Simone Melzi, Siva Reddy, Sneha Priscilla Makini, Soo-Hwan Lee, Spencer Torene, Sriharsha Hatwar, Stanislas Dehaene, Stefan Divic, Stefano Ermon, Stella Biderman, Stephanie Lin, Stephen Prasad, Steven T. Piantadosi, Stuart M. Shieber, Summer Misherghi, Svetlana Kiritchenko, Swaroop Mishra, Tal Linzen, Tal Schuster, Tao Li, Tao Yu, Tariq Ali, Tatsu Hashimoto, Te-Lin Wu, Théo Desbordes, Theodore Rothschild, Thomas Phan, Tianle Wang, Tiberius Nkinyili, Timo Schick, Timofei Kornev, Timothy Telleen-Lawton, Titus Tunduny, Tobias Gerstenberg, Trenton Chang, Trishala Neeraj, Tushar Khot, Tyler Shultz, Uri Shaham, Vedant Misra, Vera Demberg, Victoria Nyamai, Vikas Raunak, Vinay Ramasesh, Vinay Uday Prabhu, Vishakh Padmakumar, Vivek Srikumar, William Fedus, William Saunders, William Zhang, Wout Vossen, Xiang Ren, Xiaoyu Tong, Xinran Zhao, Xinyi Wu, Xudong Shen, Yadollah Yaghoobzadeh, Yair Lakretz, Yangqiu Song, Yasaman Bahri, Yejin Choi, Yichi Yang, Yiding Hao, Yifu Chen, Yonatan Belinkov, Yu Hou, Yufang Hou, Yuntao Bai, Zachary Seid, Zhuoye Zhao, Zijian Wang, Zijie J. Wang, Zirui Wang, Ziyi Wu

Language models demonstrate both quantitative improvement and new qualitative capabilities with increasing scale. Despite their potentially transformative impact, these new capabilities are as yet poorly characterized. In order to inform future research, prepare for disruptive new model capabilities, and ameliorate socially harmful effects, it is vital that we understand the present and near-future capabilities and limitations of language models. To address this challenge, we introduce the Beyond the Imitation Game benchmark (BIG-bench). BIG-bench currently consists of 204 tasks, contributed by 442 authors across 132 institutions. Task topics are diverse, drawing problems from linguistics, childhood development, math, common-sense reasoning, biology, physics, social bias, software development, and beyond. BIG-bench focuses on tasks that are believed to be beyond the capabilities of current language models. We evaluate the behavior of OpenAI's GPT models, Google-internal dense transformer architectures, and Switch-style sparse transformers on BIG-bench, across model sizes spanning millions to hundreds of billions of parameters. In addition, a team of human expert raters performed all tasks in order to provide a strong baseline. Findings include: model performance and calibration both improve with scale, but are poor in absolute terms (and when compared with rater performance); performance is remarkably similar across model classes, though with benefits from sparsity; tasks that improve gradually and predictably commonly involve a large knowledge or memorization component, whereas tasks that exhibit "breakthrough" behavior at a critical scale often involve multiple steps or components, or brittle metrics; social bias typically increases with scale in settings with ambiguous context, but this can be improved with prompting.

* 27 pages, 17 figures + references and appendices, repo: https://github.com/google/BIG-bench 
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Language Models are Few-shot Multilingual Learners

Sep 16, 2021
Genta Indra Winata, Andrea Madotto, Zhaojiang Lin, Rosanne Liu, Jason Yosinski, Pascale Fung

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General-purpose language models have demonstrated impressive capabilities, performing on par with state-of-the-art approaches on a range of downstream natural language processing (NLP) tasks and benchmarks when inferring instructions from very few examples. Here, we evaluate the multilingual skills of the GPT and T5 models in conducting multi-class classification on non-English languages without any parameter updates. We show that, given a few English examples as context, pre-trained language models can predict not only English test samples but also non-English ones. Finally, we find the in-context few-shot cross-lingual prediction results of language models are significantly better than random prediction, and they are competitive compared to the existing state-of-the-art cross-lingual models.

* 14 pages 
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When does loss-based prioritization fail?

Jul 16, 2021
Niel Teng Hu, Xinyu Hu, Rosanne Liu, Sara Hooker, Jason Yosinski

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Not all examples are created equal, but standard deep neural network training protocols treat each training point uniformly. Each example is propagated forward and backward through the network the same amount of times, independent of how much the example contributes to the learning protocol. Recent work has proposed ways to accelerate training by deviating from this uniform treatment. Popular methods entail up-weighting examples that contribute more to the loss with the intuition that examples with low loss have already been learned by the model, so their marginal value to the training procedure should be lower. This view assumes that updating the model with high loss examples will be beneficial to the model. However, this may not hold for noisy, real world data. In this paper, we theorize and then empirically demonstrate that loss-based acceleration methods degrade in scenarios with noisy and corrupted data. Our work suggests measures of example difficulty need to correctly separate out noise from other types of challenging examples.

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Supermasks in Superposition

Jun 30, 2020
Mitchell Wortsman, Vivek Ramanujan, Rosanne Liu, Aniruddha Kembhavi, Mohammad Rastegari, Jason Yosinski, Ali Farhadi

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We present the Supermasks in Superposition (SupSup) model, capable of sequentially learning thousands of tasks without catastrophic forgetting. Our approach uses a randomly initialized, fixed base network and for each task finds a subnetwork (supermask) that achieves good performance. If task identity is given at test time, the correct subnetwork can be retrieved with minimal memory usage. If not provided, SupSup can infer the task using gradient-based optimization to find a linear superposition of learned supermasks which minimizes the output entropy. In practice we find that a single gradient step is often sufficient to identify the correct mask, even among 2500 tasks. We also showcase two promising extensions. First, SupSup models can be trained entirely without task identity information, as they may detect when they are uncertain about new data and allocate an additional supermask for the new training distribution. Finally the entire, growing set of supermasks can be stored in a constant-sized reservoir by implicitly storing them as attractors in a fixed-sized Hopfield network.

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Estimating Q(s,s') with Deep Deterministic Dynamics Gradients

Feb 21, 2020
Ashley D. Edwards, Himanshu Sahni, Rosanne Liu, Jane Hung, Ankit Jain, Rui Wang, Adrien Ecoffet, Thomas Miconi, Charles Isbell, Jason Yosinski

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In this paper, we introduce a novel form of value function, $Q(s, s')$, that expresses the utility of transitioning from a state $s$ to a neighboring state $s'$ and then acting optimally thereafter. In order to derive an optimal policy, we develop a forward dynamics model that learns to make next-state predictions that maximize this value. This formulation decouples actions from values while still learning off-policy. We highlight the benefits of this approach in terms of value function transfer, learning within redundant action spaces, and learning off-policy from state observations generated by sub-optimal or completely random policies. Code and videos are available at \url{sites.google.com/view/qss-paper}.

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Plug and Play Language Models: A Simple Approach to Controlled Text Generation

Jan 08, 2020
Sumanth Dathathri, Andrea Madotto, Janice Lan, Jane Hung, Eric Frank, Piero Molino, Jason Yosinski, Rosanne Liu

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Large transformer-based language models (LMs) trained on huge text corpora have shown unparalleled generation capabilities. However, controlling attributes of the generated language (e.g. switching topic or sentiment) is difficult without modifying the model architecture or fine-tuning on attribute-specific data and entailing the significant cost of retraining. We propose a simple alternative: the Plug and Play Language Model (PPLM) for controllable language generation, which combines a pretrained LM with one or more simple attribute classifiers that guide text generation without any further training of the LM. In the canonical scenario we present, the attribute models are simple classifiers consisting of a user-specified bag of words or a single learned layer with 100,000 times fewer parameters than the LM. Sampling entails a forward and backward pass in which gradients from the attribute model push the LM's hidden activations and thus guide the generation. Model samples demonstrate control over a range of topics and sentiment styles, and extensive automated and human annotated evaluations show attribute alignment and fluency. PPLMs are flexible in that any combination of differentiable attribute models may be used to steer text generation, which will allow for diverse and creative applications beyond the examples given in this paper.

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