no code implementations • 16 Jan 2017 • Manuel Le Gallo, Abu Sebastian, Roland Mathis, Matteo Manica, Heiner Giefers, Tomas Tuma, Costas Bekas, Alessandro Curioni, Evangelos Eleftheriou
As CMOS scaling reaches its technological limits, a radical departure from traditional von Neumann systems, which involve separate processing and memory units, is needed in order to significantly extend the performance of today's computers.
Emerging Technologies
no code implementations • 29 Mar 2018 • Matteo Manica, Joris Cadow, Roland Mathis, María Rodríguez Martínez
Reliable identification of molecular biomarkers is essential for accurate patient stratification.
no code implementations • 18 Aug 2018 • Ali Oskooei, Matteo Manica, Roland Mathis, Maria Rodriguez Martinez
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data.
1 code implementation • 16 Nov 2018 • Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value.
no code implementations • 17 Jan 2019 • Atin Sood, Benjamin Elder, Benjamin Herta, Chao Xue, Costas Bekas, A. Cristiano I. Malossi, Debashish Saha, Florian Scheidegger, Ganesh Venkataraman, Gegi Thomas, Giovanni Mariani, Hendrik Strobelt, Horst Samulowitz, Martin Wistuba, Matteo Manica, Mihir Choudhury, Rong Yan, Roxana Istrate, Ruchir Puri, Tejaswini Pedapati
Application of neural networks to a vast variety of practical applications is transforming the way AI is applied in practice.
1 code implementation • 25 Apr 2019 • Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder.
no code implementations • 19 Jul 2019 • Matteo Manica, Christoph Auer, Valery Weber, Federico Zipoli, Michele Dolfi, Peter Staar, Teodoro Laino, Costas Bekas, Akihiro Fujita, Hiroki Toda, Shuichi Hirose, Yasumitsu Orii
Information extraction and data mining in biochemical literature is a daunting task that demands resource-intensive computation and appropriate means to scale knowledge ingestion.
no code implementations • 29 Aug 2019 • Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, Karsten Borgwardt, María Rodríguez Martínez
The generative process is optimized through PaccMann, a previously developed drug sensitivity prediction model to obtain effective anticancer compounds for the given context (i. e., transcriptomic profile).
1 code implementation • 20 Feb 2020 • Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloe Clavel
The task of predicting dialog acts (DA) based on conversational dialog is a key component in the development of conversational agents.
Ranked #1 on Dialogue Act Classification on Switchboard corpus
no code implementations • 21 Feb 2020 • Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloe Clavel
The task of predicting dialog acts (DA) based on conversational dialog is a key component in the development of conversational agents.
no code implementations • NeurIPS 2020 • Vijil Chenthamarakshan, Payel Das, Samuel C. Hoffman, Hendrik Strobelt, Inkit Padhi, Kar Wai Lim, Benjamin Hoover, Matteo Manica, Jannis Born, Teodoro Laino, Aleksandra Mojsilovic
CogMol also includes insilico screening for assessing toxicity of parent molecules and their metabolites with a multi-task toxicity classifier, synthetic feasibility with a chemical retrosynthesis predictor, and target structure binding with docking simulations.
1 code implementation • 27 May 2020 • Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, María Rodríguez Martínez
With the fast development of COVID-19 into a global pandemic, scientists around the globe are desperately searching for effective antiviral therapeutic agents.
no code implementations • Findings of the Association for Computational Linguistics 2020 • Emile Chapuis, Pierre Colombo, Matteo Manica, Matthieu Labeau, Chloe Clavel
We obtain our representations with a hierarchical encoder based on transformer architectures, for which we extend two well-known pre-training objectives.
Ranked #1 on Text Classification on SILICONE Benchmark
Dialogue Act Classification Emotion Recognition in Conversation +1
1 code implementation • 5 Dec 2020 • Modestas Filipavicius, Matteo Manica, Joris Cadow, Maria Rodriguez Martinez
Less than 1% of protein sequences are structurally and functionally annotated.
1 code implementation • 18 Dec 2020 • Dimitrios Christofidellis, Matteo Manica, Leonidas Georgopoulos, Hans Vandierendonck
Focusing on scientific document understanding, we present a new health domain dataset based on publications extracted from PubMed and we successfully utilize our method on this.
no code implementations • 1 Jan 2021 • Nil Adell Mill, Jannis Born, Nathaniel Park, James Hedrick, María Rodríguez Martínez, Matteo Manica
We explore a spectrum of models, ranging from uniquely learning representations based on the isolated features of the nodes (focusing on Variational Autoencoders), to uniquely learning representations based on the topology (using node2vec) passing through models that integrate both node features and topological information in a hybrid fashion.
no code implementations • 1 Jan 2021 • Dimitrios Christofidellis, Matteo Manica, Leonidas Georgopoulos, Hans Vandierendonck
Initially, the structure of the domain of interest is inferred from the corpus in the form of a metagraph.
no code implementations • NeurIPS Workshop AI4Scien 2021 • Loïc Kwate Dassi, Matteo Manica, Daniel Probst, Philippe Schwaller, Yves Gaetan Nana Teukam, Teodoro Laino
Herein, we apply a Transformer architecture to a language representation of bio-catalyzed chemical reactions to learn the signal at the base of the substrate-active site atomic interactions.
7 code implementations • ICLR 2022 • Victor Sanh, Albert Webson, Colin Raffel, Stephen H. Bach, Lintang Sutawika, Zaid Alyafeai, Antoine Chaffin, Arnaud Stiegler, Teven Le Scao, Arun Raja, Manan Dey, M Saiful Bari, Canwen Xu, Urmish Thakker, Shanya Sharma Sharma, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal Nayak, Debajyoti Datta, Jonathan Chang, Mike Tian-Jian Jiang, Han Wang, Matteo Manica, Sheng Shen, Zheng Xin Yong, Harshit Pandey, Rachel Bawden, Thomas Wang, Trishala Neeraj, Jos Rozen, Abheesht Sharma, Andrea Santilli, Thibault Fevry, Jason Alan Fries, Ryan Teehan, Tali Bers, Stella Biderman, Leo Gao, Thomas Wolf, Alexander M. Rush
Large language models have recently been shown to attain reasonable zero-shot generalization on a diverse set of tasks (Brown et al., 2020).
1 code implementation • 1 Feb 2022 • Jannis Born, Matteo Manica
To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem.
1 code implementation • 8 Jul 2022 • Matteo Manica, Jannis Born, Joris Cadow, Dimitrios Christofidellis, Ashish Dave, Dean Clarke, Yves Gaetan Nana Teukam, Giorgio Giannone, Samuel C. Hoffman, Matthew Buchan, Vijil Chenthamarakshan, Timothy Donovan, Hsiang Han Hsu, Federico Zipoli, Oliver Schilter, Akihiro Kishimoto, Lisa Hamada, Inkit Padhi, Karl Wehden, Lauren McHugh, Alexy Khrabrov, Payel Das, Seiji Takeda, John R. Smith
With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery.
2 code implementations • 15 Aug 2022 • Daniele Comi, Dimitrios Christofidellis, Pier Francesco Piazza, Matteo Manica
In our evaluation, we first analyze the quality of the model after adaptive fine-tuning on known classes.
6 code implementations • 9 Nov 2022 • BigScience Workshop, :, 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, Davut Emre Taşar, 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, Shachar Mirkin, 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, Daniel McDuff, 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, 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.
no code implementations • 20 Jan 2023 • Girmaw Abebe Tadesse, Jannis Born, Celia Cintas, William Ogallo, Dmitry Zubarev, Matteo Manica, Komminist Weldemariam
To this end, we propose a framework for Multi-level Performance Evaluation of Generative mOdels (MPEGO), which could be employed across different domains.
1 code implementation • 29 Jan 2023 • Dimitrios Christofidellis, Giorgio Giannone, Jannis Born, Ole Winther, Teodoro Laino, Matteo Manica
Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains.
Ranked #3 on Molecule Captioning on ChEBI-20