Matteo Manica

48 papers A* 5B 1Journal 37Unranked 4
YearRankTypeTitle / Venue / Authors
2025 — conf
Aligning Foundation Models on Encoded Synthetic Omic Data for Patient Stratification.
ICDH
Nikita Janakarajan, Antonio Foncubierta-Rodríguez, Matteo Manica
2025 J jnl
Integrating genetic algorithms and language models for enhanced enzyme design.
Briefings Bioinform.
Yves Gaetan Nana Teukam, Federico Zipoli, Teodoro Laino, Emanuele Criscuolo, Francesca Grisoni, Matteo Manica
2025 J jnl
Multiscale Byte Language Models - A Hierarchical Architecture for Causal Million-Length Sequence Modeling.
CoRR
Eric Egli, Matteo Manica, Jannis Born
2025 J jnl
Unified lookup tables: training foundation models on encoded data.
Mach. Learn. Sci. Technol.
Nikita Janakarajan, Irina Espejo Morales, Marvin Alberts, Andrea Giovannini, Matteo Manica, Antonio Foncubierta-Rodríguez
2025 J jnl
We Need Improved Data Curation and Attribution in AI for Scientific Discovery.
CoRR
Mara Graziani, Antonio Foncubierta, Dimitrios Christofidellis, Irina Espejo Morales, Malina Molnar, Marvin Alberts, Matteo Manica, Jannis Born
2024 J jnl
Transforming the Hybrid Cloud for Emerging AI Workloads.
CoRR
Deming Chen, Alaa Youssef, Ruchi Pendse, André Schleife, Bryan K. Clark, Hendrik F. Hamann, Jingrui He, Teodoro Laino, Lav R. Varshney, Yuxiong Wang, Avirup Sil, Reyhaneh Jabbarvand, Tianyin Xu, Volodymyr V. Kindratenko, Carlos H. A. Costa, Sarita V. Adve, Charith Mendis, Minjia Zhang, Santiago Núñez-Corrales, Raghu K. Ganti, Mudhakar Srivatsa, Nam Sung Kim, Josep Torrellas, Jian Huang, Seetharami R. Seelam, Klara Nahrstedt, Tarek F. Abdelzaher, Tamar Eilam, Huimin Zhao, Matteo Manica, Ravishankar K. Iyer, Martin Hirzel, Vikram S. Adve, Darko Marinov, Hubertus Franke, Hanghang Tong, Elizabeth A. Ainsworth, Han Zhao, Deepak Vasisht, Minh Do, Fábio Oliveira, Giovanni Pacifici, Ruchir Puri, Priya Nagpurkar
2023 J jnl
Domain-agnostic and Multi-level Evaluation of Generative Models.
CoRR
Girmaw Abebe Tadesse, Jannis Born, Celia Cintas, William Ogallo, Dmitry Zubarev, Matteo Manica, Komminist Weldemariam
2023 J jnl
Regression Transformer enables concurrent sequence regression and generation for molecular language modelling.
Nat. Mac. Intell.
Jannis Born, Matteo Manica
2023 A* conf
Unifying Molecular and Textual Representations via Multi-task Language Modelling.
ICML
Dimitrios Christofidellis, Giorgio Giannone, Jannis Born, Ole Winther, Teodoro Laino, Matteo Manica
2023 J jnl
Unifying Molecular and Textual Representations via Multi-task Language Modelling.
CoRR
Dimitrios Christofidellis, Giorgio Giannone, Jannis Born, Ole Winther, Teodoro Laino, Matteo Manica
2023 — conf
Zero-Shot-BERT-Adapters: a Zero-Shot Pipeline for Unknown Intent Detection.
EMNLP (Findings)
Daniele Comi, Dimitrios Christofidellis, Pier Francesco Piazza, Matteo Manica
2022 A* conf
A Fully Differentiable Set Autoencoder.
KDD
Nikita Janakarajan, Jannis Born, Matteo Manica
2022 J jnl
Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model.
J. Chem. Inf. Model.
Jannis Born, Tien Huynh, Astrid Stroobants, Wendy D. Cornell, Matteo Manica
2022 J jnl
GT4SD: Generative Toolkit for Scientific Discovery.
CoRR
Matteo Manica, Joris Cadow, Dimitrios Christofidellis, Ashish Dave, Jannis Born, Dean Clarke, Yves Gaetan Nana Teukam, Samuel C. Hoffman, Matthew Buchan, Vijil Chenthamarakshan, Timothy Donovan, Hsiang-Han Hsu, Federico Zipoli, Oliver Schilter, Giorgio Giannone, Akihiro Kishimoto, Lisa Hamada, Inkit Padhi, Karl Wehden, Lauren McHugh, Alexy Khrabrov, Payel Das, Seiji Takeda, John R. Smith
2022 A* conf
Multitask Prompted Training Enables Zero-Shot Task Generalization.
ICLR
Victor Sanh, Albert Webson, Colin Raffel, Stephen H. Bach, Lintang Sutawika, Zaid Alyafeai, Antoine Chaffin, Arnaud Stiegler, Arun Raja, Manan Dey, M Saiful Bari, Canwen Xu, Urmish Thakker, Shanya Sharma Sharma, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal V. 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 Févry, Jason Alan Fries, Ryan Teehan, Teven Le Scao, Stella Biderman, Leo Gao, Thomas Wolf, Alexander M. Rush
2022 J jnl
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction.
J. Chem. Inf. Model.
Jannis Born, Yoel Shoshan, Tien Huynh, Wendy D. Cornell, Eric J. Martin, Matteo Manica
2022 J jnl
PCfun: a hybrid computational framework for systematic characterization of protein complex function.
Briefings Bioinform.
Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony W. Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi Aebersold, Chen Li
2022 J jnl
Regression Transformer: Concurrent Conditional Generation and Regression by Blending Numerical and Textual Tokens.
CoRR
Jannis Born, Matteo Manica
2022 J jnl
Z-BERT-A: a zero-shot Pipeline for Unknown Intent detection.
CoRR
Daniele Comi, Dimitrios Christofidellis, Pier Francesco Piazza, Matteo Manica
2021 J jnl
COSIFER: a Python package for the consensus inference of molecular interaction networks.
Bioinform.
Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A. Stolovitzky, María Rodríguez Martínez
2021 J jnl
Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2.
Mach. Learn. Sci. Technol.
Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, Nikita Janakarajan, Antonio Cardinale, Teodoro Laino, María Rodríguez Martínez
2021 J jnl
Multitask Prompted Training Enables Zero-Shot Task Generalization.
CoRR
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, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal V. 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 Févry, Jason Alan Fries, Ryan Teehan, Stella Biderman, Leo Gao, Tali Bers, Thomas Wolf, Alexander M. Rush
2021 J jnl
On the feasibility of deep learning applications using raw mass spectrometry data.
Bioinform.
Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
2021 J jnl
On the role of artificial intelligence in medical imaging of COVID-19.
Patterns
Jannis Born, David Beymer, Deepta Rajan, Adam Coy, Vandana V. Mukherjee, Matteo Manica, Prasanth Prasanna, Deddeh Ballah, Michal Guindy, Dorith Shaham, Pallav L. Shah, Emmanouil Karteris, Jan L. Robertus, Maria Gabrani, Michal Rosen-Zvi
2021 J jnl
On the role of artificial intelligence in medical imaging of COVID-19.
Patterns
Jannis Born, David Beymer, Deepta Rajan, Adam Coy, Vandana V. Mukherjee, Matteo Manica, Prasanth Prasanna, Deddeh Ballah, Michal Guindy, Dorith Shaham, Pallav L. Shah, Emmanouil Karteris, Jan L. Robertus, Maria Gabrani, Michal Rosen-Zvi
2021 — conf
Understood in Translation: Transformers for Domain Understanding.
SDU@AAAI
Dimitrios Christofidellis, Matteo Manica, Leonidas Georgopoulos, Hans Vandierendonck
2020 A* conf
CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models.
NeurIPS
Vijil Chenthamarakshan, Payel Das, Samuel C. Hoffman, Hendrik Strobelt, Inkit Padhi, Kar Wai Lim, Benjamin Hoover, Matteo Manica, Jannis Born, Teodoro Laino, Aleksandra Mojsilovic
2020 J jnl
FPGA Accelerated Analysis of Boolean Gene Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, María Rodríguez Martínez
2020 J jnl
Guider l'attention dans les modeles de sequence a sequence pour la prediction des actes de dialogue.
CoRR
Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloé Clavel
2020 A* conf
Guiding Attention in Sequence-to-Sequence Models for Dialogue Act Prediction.
AAAI
Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloé Clavel
2020 J jnl
Guiding attention in Sequence-to-sequence models for Dialogue Act prediction.
CoRR
Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloé Clavel
2020 — conf
Hierarchical Pre-training for Sequence Labelling in Spoken Dialog.
EMNLP (Findings)
Emile Chapuis, Pierre Colombo, Matteo Manica, Matthieu Labeau, Chloé Clavel
2020 J jnl
Hierarchical Pre-training for Sequence Labelling in Spoken Dialog.
CoRR
Emile Chapuis, Pierre Colombo, Matteo Manica, Matthieu Labeau, Chloé Clavel
2020 B conf
PaccMann
RECOMB
Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez
2020 J jnl
PaccMann
CoRR
Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, María Rodríguez Martínez
2020 J jnl
PaccMann: a web service for interpretable anticancer compound sensitivity prediction.
Nucleic Acids Res.
Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
2020 J jnl
Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks.
CoRR
Modestas Filipavicius, Matteo Manica, Joris Cadow, María Rodríguez Martínez
2020 J jnl
Understood in Translation, Transformers for Domain Understanding.
CoRR
Dimitrios Christofidellis, Matteo Manica, Leonidas Georgopoulos, Hans Vandierendonck
2019 J jnl
AI Enables Explainable Drug Sensitivity Screenings.
ERCIM News
Matteo Manica, Ali Oskooei, Jannis Born
2019 J jnl
An Information Extraction and Knowledge Graph Platform for Accelerating Biochemical Discoveries.
CoRR
Matteo Manica, Christoph Auer, Valéry Weber, Federico Zipoli, Michele Dolfi, Peter W. J. Staar, Teodoro Laino, Costas Bekas, Akihiro Fujita, Hiroki Toda, Shuichi Hirose, Yasumitsu Orii
2019 J jnl
Context-specific interaction networks from vector representation of words.
Nat. Mach. Intell.
Matteo Manica, Roland Mathis, Joris Cadow, María Rodríguez Martínez
2019 J jnl
NeuNetS: An Automated Synthesis Engine for Neural Network Design.
CoRR
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 R. Choudhury, Rong Yan, Roxana Istrate, Ruchir Puri, Tejaswini Pedapati
2019 J jnl
Reinforcement learning-driven de-novo design of anticancer compounds conditioned on biomolecular profiles.
CoRR
Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
2019 J jnl
Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders.
CoRR
Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
2018 — —
Exploring Multi-Modal Learning Approaches Towards Precision Medicine.
Matteo Manica
2018 J jnl
Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer.
CoRR
Ali Oskooei, Matteo Manica, Roland Mathis, María Rodríguez Martínez
2018 J jnl
PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks.
CoRR
Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
2017 J jnl
Mixed-Precision Memcomputing.
CoRR
Manuel Le Gallo, Abu Sebastian, Roland Mathis, Matteo Manica, Tomas Tuma, Costas Bekas, Alessandro Curioni, Evangelos Eleftheriou