Nicolo Fusi

VP & Distinguished Scientist

Publications

Afficher par:

- Matching Features, Not Tokens: Energy-Based Fine-Tuning of Language Models
  
  Samy Jelassi, Mujin Kwun, Rosie Zhao, Yuanzhi Li, Nicolo Fusi, Yilun Du, Sham Kakade, Carles Domingo-Enrich
  
  March 2026
  
  Publication
- scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
  
  Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
  
  NeurIPS 2025 | October 2025
  
  Publication
- Consequences of training data composition for deep learning models in single-cell biology
  
  Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2025
  
  Publication DOI Projet
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
  
  Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | December 2024
  
  Preprint Projet
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Accès
- Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
  
  Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
  
  July 2024
  
  Publication
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  
  Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2024
  
  Preprint Projet
- Tag-LLM: Repurposing General-Purpose LLMs for Specialized Domains
  
  Junhong Shen, Neil Tenenholtz, James Hall, David Alvarez-Melis, Nicolo Fusi
  
  ICML 2024 | February 2024
  
  DOI Publication Publication
- Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
  
  Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
  
  November 2023
  
  Publication
- Virchow: A Million-Slide Digital Pathology Foundation Model
  
  Eugene Vorontsov, A. Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Kristen Severson, Eric Zimmermann, James Hall, Neil Tenenholtz, Nicolo Fusi, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kun, Matthew C. H. Le, Jan H Bernhard, R. Godrich, Gerard Oakley, Ewan Millar, Matthew G Hanna, J. Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, D. Klimstra, B. Rothrock, Thomas J. Fuchs
  
  September 2023
  
  DOI Publication Publication Publication
- Dataset Dynamics via Gradient Flows in Probability Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  ICML 2021 | July 2021
  
  Publication
- Hant: Hardware-Aware Network Transformation
  
  Pavlo Molchanov, Jimmy Hall, Hongxu Yin, Jan Kautz, Nicolo Fusi, Arash Vahdat
  
  July 2021
  
  Publication Projet Projet
- Initialization and Regularization of Factorized Neural Layers
  
  Mikhail Khodak, Neil Tenenholtz, Lester Mackey, Nicolo Fusi
  
  2021 International Conference on Learning Representations | May 2021
  
  Publication Publication Github Projet Projet
- Gradient Flows in Dataset Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  October 2020
  
  Publication Projet
- Differentiable Feature Selection by Discrete Relaxation
  
  Rishit Sheth, Nicolo Fusi
  
  AISTATS | April 2020
  
  Publication Projet
- Weighted Meta-Learning
  
  Diana Cai, Rishit Sheth, Lester Mackey, Nicolo Fusi
  
  March 2020
  
  Publication PDF Projet
- Geometric Dataset Distances via Optimal Transport
  
  David Alvarez-Melis, Nicolo Fusi
  
  NeurIPS 2020 | February 2020
  
  PDF Projet
- Probabilistic Neural Architecture Search
  
  Francesco Paolo Casale, Jonathan Gordon, Nicolo Fusi
  
  February 2019
  
  Publication Publication Projet
- Probabilistic Matrix Factorization for Automated Machine Learning
  
  Nicolo Fusi, Rishit Sheth, Melih Huseyn Elibol
  
  NIPS 2018 | December 2018
  
  Preprint posted to Cornell University Library
  
  Publication Publication Projet
- Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens
  
  Nicolo Fusi, et al
  
  nature biotechnology | October 2017, Vol 36: pp. 179-189
  
  Publication
- Predicting off-target effects for end-to-end CRISPR guide design
  
  Nicolo Fusi, Jennifer Listgarten, Melih Elibol, John Doench, Michael Weinstein, Luong Hoang
  
  October 2016
  
  Publication
- Flexible Modelling of Genetic Effects on Function-Valued Traits
  
  Nicolo Fusi, Jennifer Listgarten
  
  International Conference on Research in Computational Molecular Biology (RECOMB 2016) | October 2016
  
  Publication DOI
- Impact of pre-adapted HIV transmission
  
  Jonathan M. Carlson, Victor Y Du, Nicolo Fusi, Paul A. Goepfert
  
  Nature Medicine | May 2016, Vol 22: pp. 606-613
  
  Publication
- Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
  
  John G. Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W. Vaimberg, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W. Virgin, Jennifer Listgarten, David E. Root
  
  nature biotechnology | January 2016, pp. 184-191
  
  Publication
- In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency
  
  Nicolo Fusi, Ian Smith, John Doench, Jennifer Listgarten
  
  MSR-TR-2015-54 | June 2015
  
  Publication Publication
- Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
  
  Christian Widmer, Christoph Lippert, Omer Weissbrod, Nicolo Fusi, Carl Kadie, Robert Davidson, Jennifer Listgarten, David Heckerman
  
  October 2014
  
  Publication Publication
- Warped linear mixed models for the genetic analysis of transformed phenotypes
  
  Nicolo Fusi, Christoph Lippert
  
  Nature communications | September 2014, Vol 5
  
  Publication Publication
- Genetic Analysis of Transformed Phenotypes
  
  Nicolo Fusi, Christoph Lippert, Neil D. Lawrence, Oliver Stegle
  
  February 2014
  
  Publication
- Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis
  
  Giovanni Nardo, Raffaele lennaco, Nicolo Fusi, Paul R. Heath, Marianna Marino, Maria C. Trolese, Laura Ferraiuolo, Neil Lawrence, Pamela J. Shaw, Caterina Bendotti
  
  Brain | November 2013, Vol 136(11): pp. 3305-3332
  
  Publication DOI
- A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
  
  Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson
  
  eLife | October 2013
  
  Publication
- Gaussian Processes for Big Data
  
  James Hensman, Nicolo Fusi, Neil D. Lawrence
  
  UAI-P-2013-PG-282-290 | September 2013
  
  Publié par Twenty-Ninth Conference on Uncertainty in Artificial Intelligence (UAI2013)
  
  Publication
- Detecting regulatory gene–environment interactions with unmeasured environmental factors
  
  Nicolo Fusi, Christoph Lippert, Karsten Borgwardt, Neil D. Lawrence, Oliver Stegle
  
  Bioinformatics | June 2013, Vol 29(11): pp. 1382-1389
  
  Publication
- Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity
  
  Alice Brockington, Ke Ning, Paul R. Heath, Elizabeth Wood, Janine Kirby, Nicolo Fusi, Neil Lawrence, Stephen B. Wharton, Paul G. Ince, Pamela J. Shaw
  
  Acta Neuropathologica | January 2013, Vol 125(1): pp. 95-109
  
  Publication DOI
- Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies
  
  Nicolo Fusi, Oliver Stegle, Neil D. Lawrence
  
  PLOS Computational Biology | January 2012
  
  Publication Publication
- 156 Motor neurones subtypes resistant to degeneration in amyotrophic lateral sclerosis show distinct synaptic characteristics across species
  
  Nicolo Fusi
  
  Journal of Neurology, Neurosurgery & Psychiatry | January 2012, Vol 83(3)
  
  DOI
- Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
  
  Nicolo Fusi
  
  Nature Precedings | June 2011
  
  Publication
- Intrusion Detection via Artificial Immune System: a Performance-based Approach
  
  Andrea Visconti, Nicolo Fusi, Hooman Tahayori
  
  IFIP International Conference on Biologically Inspired Collaborative Computing | October 2008
  
  Publication

- Matching Features, Not Tokens: Energy-Based Fine-Tuning of Language Models
  
  Samy Jelassi, Mujin Kwun, Rosie Zhao, Yuanzhi Li, Nicolo Fusi, Yilun Du, Sham Kakade, Carles Domingo-Enrich
  
  March 2026
  
  Publication
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Accès
- Tag-LLM: Repurposing General-Purpose LLMs for Specialized Domains
  
  Junhong Shen, Neil Tenenholtz, James Hall, David Alvarez-Melis, Nicolo Fusi
  
  ICML 2024 | February 2024
  
  DOI Publication Publication
- Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
  
  Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
  
  November 2023
  
  Publication
- Virchow: A Million-Slide Digital Pathology Foundation Model
  
  Eugene Vorontsov, A. Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Kristen Severson, Eric Zimmermann, James Hall, Neil Tenenholtz, Nicolo Fusi, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kun, Matthew C. H. Le, Jan H Bernhard, R. Godrich, Gerard Oakley, Ewan Millar, Matthew G Hanna, J. Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, D. Klimstra, B. Rothrock, Thomas J. Fuchs
  
  September 2023
  
  DOI Publication Publication Publication
- Dataset Dynamics via Gradient Flows in Probability Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  ICML 2021 | July 2021
  
  Publication
- Hant: Hardware-Aware Network Transformation
  
  Pavlo Molchanov, Jimmy Hall, Hongxu Yin, Jan Kautz, Nicolo Fusi, Arash Vahdat
  
  July 2021
  
  Publication Projet Projet
- Initialization and Regularization of Factorized Neural Layers
  
  Mikhail Khodak, Neil Tenenholtz, Lester Mackey, Nicolo Fusi
  
  2021 International Conference on Learning Representations | May 2021
  
  Publication Publication Github Projet Projet
- Gradient Flows in Dataset Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  October 2020
  
  Publication Projet
- Differentiable Feature Selection by Discrete Relaxation
  
  Rishit Sheth, Nicolo Fusi
  
  AISTATS | April 2020
  
  Publication Projet
- Weighted Meta-Learning
  
  Diana Cai, Rishit Sheth, Lester Mackey, Nicolo Fusi
  
  March 2020
  
  Publication PDF Projet
- Geometric Dataset Distances via Optimal Transport
  
  David Alvarez-Melis, Nicolo Fusi
  
  NeurIPS 2020 | February 2020
  
  PDF Projet
- Probabilistic Neural Architecture Search
  
  Francesco Paolo Casale, Jonathan Gordon, Nicolo Fusi
  
  February 2019
  
  Publication Publication Projet
- Probabilistic Matrix Factorization for Automated Machine Learning
  
  Nicolo Fusi, Rishit Sheth, Melih Huseyn Elibol
  
  NIPS 2018 | December 2018
  
  Preprint posted to Cornell University Library
  
  Publication Publication Projet
- In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency
  
  Nicolo Fusi, Ian Smith, John Doench, Jennifer Listgarten
  
  MSR-TR-2015-54 | June 2015
  
  Publication Publication
- Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
  
  Christian Widmer, Christoph Lippert, Omer Weissbrod, Nicolo Fusi, Carl Kadie, Robert Davidson, Jennifer Listgarten, David Heckerman
  
  October 2014
  
  Publication Publication
- Gaussian Processes for Big Data
  
  James Hensman, Nicolo Fusi, Neil D. Lawrence
  
  UAI-P-2013-PG-282-290 | September 2013
  
  Publié par Twenty-Ninth Conference on Uncertainty in Artificial Intelligence (UAI2013)
  
  Publication
- 156 Motor neurones subtypes resistant to degeneration in amyotrophic lateral sclerosis show distinct synaptic characteristics across species
  
  Nicolo Fusi
  
  Journal of Neurology, Neurosurgery & Psychiatry | January 2012, Vol 83(3)
  
  DOI
- scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
  
  Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
  
  NeurIPS 2025 | October 2025
  
  Publication
- Consequences of training data composition for deep learning models in single-cell biology
  
  Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2025
  
  Publication DOI Projet
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
  
  Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | December 2024
  
  Preprint Projet
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Accès
- Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
  
  Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
  
  July 2024
  
  Publication
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  
  Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2024
  
  Preprint Projet
- Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
  
  Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
  
  November 2023
  
  Publication
- Virchow: A Million-Slide Digital Pathology Foundation Model
  
  Eugene Vorontsov, A. Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Kristen Severson, Eric Zimmermann, James Hall, Neil Tenenholtz, Nicolo Fusi, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kun, Matthew C. H. Le, Jan H Bernhard, R. Godrich, Gerard Oakley, Ewan Millar, Matthew G Hanna, J. Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, D. Klimstra, B. Rothrock, Thomas J. Fuchs
  
  September 2023
  
  DOI Publication Publication Publication
- Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens
  
  Nicolo Fusi, et al
  
  nature biotechnology | October 2017, Vol 36: pp. 179-189
  
  Publication
- Predicting off-target effects for end-to-end CRISPR guide design
  
  Nicolo Fusi, Jennifer Listgarten, Melih Elibol, John Doench, Michael Weinstein, Luong Hoang
  
  October 2016
  
  Publication
- Flexible Modelling of Genetic Effects on Function-Valued Traits
  
  Nicolo Fusi, Jennifer Listgarten
  
  International Conference on Research in Computational Molecular Biology (RECOMB 2016) | October 2016
  
  Publication DOI
- Impact of pre-adapted HIV transmission
  
  Jonathan M. Carlson, Victor Y Du, Nicolo Fusi, Paul A. Goepfert
  
  Nature Medicine | May 2016, Vol 22: pp. 606-613
  
  Publication
- Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
  
  John G. Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W. Vaimberg, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W. Virgin, Jennifer Listgarten, David E. Root
  
  nature biotechnology | January 2016, pp. 184-191
  
  Publication
- In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency
  
  Nicolo Fusi, Ian Smith, John Doench, Jennifer Listgarten
  
  MSR-TR-2015-54 | June 2015
  
  Publication Publication
- Warped linear mixed models for the genetic analysis of transformed phenotypes
  
  Nicolo Fusi, Christoph Lippert
  
  Nature communications | September 2014, Vol 5
  
  Publication Publication
- Genetic Analysis of Transformed Phenotypes
  
  Nicolo Fusi, Christoph Lippert, Neil D. Lawrence, Oliver Stegle
  
  February 2014
  
  Publication
- Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis
  
  Giovanni Nardo, Raffaele lennaco, Nicolo Fusi, Paul R. Heath, Marianna Marino, Maria C. Trolese, Laura Ferraiuolo, Neil Lawrence, Pamela J. Shaw, Caterina Bendotti
  
  Brain | November 2013, Vol 136(11): pp. 3305-3332
  
  Publication DOI
- A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
  
  Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson
  
  eLife | October 2013
  
  Publication
- Detecting regulatory gene–environment interactions with unmeasured environmental factors
  
  Nicolo Fusi, Christoph Lippert, Karsten Borgwardt, Neil D. Lawrence, Oliver Stegle
  
  Bioinformatics | June 2013, Vol 29(11): pp. 1382-1389
  
  Publication
- Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity
  
  Alice Brockington, Ke Ning, Paul R. Heath, Elizabeth Wood, Janine Kirby, Nicolo Fusi, Neil Lawrence, Stephen B. Wharton, Paul G. Ince, Pamela J. Shaw
  
  Acta Neuropathologica | January 2013, Vol 125(1): pp. 95-109
  
  Publication DOI
- Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies
  
  Nicolo Fusi, Oliver Stegle, Neil D. Lawrence
  
  PLOS Computational Biology | January 2012
  
  Publication Publication
- Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
  
  Nicolo Fusi
  
  Nature Precedings | June 2011
  
  Publication
- Intrusion Detection via Artificial Immune System: a Performance-based Approach
  
  Andrea Visconti, Nicolo Fusi, Hooman Tahayori
  
  IFIP International Conference on Biologically Inspired Collaborative Computing | October 2008
  
  Publication
- Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
  
  Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
  
  July 2024
  
  Publication
- Hant: Hardware-Aware Network Transformation
  
  Pavlo Molchanov, Jimmy Hall, Hongxu Yin, Jan Kautz, Nicolo Fusi, Arash Vahdat
  
  July 2021
  
  Publication Projet Projet
- Initialization and Regularization of Factorized Neural Layers
  
  Mikhail Khodak, Neil Tenenholtz, Lester Mackey, Nicolo Fusi
  
  2021 International Conference on Learning Representations | May 2021
  
  Publication Publication Github Projet Projet
- Gradient Flows in Dataset Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  October 2020
  
  Publication Projet
- Geometric Dataset Distances via Optimal Transport
  
  David Alvarez-Melis, Nicolo Fusi
  
  NeurIPS 2020 | February 2020
  
  PDF Projet
- Warped linear mixed models for the genetic analysis of transformed phenotypes
  
  Nicolo Fusi, Christoph Lippert
  
  Nature communications | September 2014, Vol 5
  
  Publication Publication
- Gradient Flows in Dataset Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  October 2020
  
  Publication Projet
- In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency
  
  Nicolo Fusi, Ian Smith, John Doench, Jennifer Listgarten
  
  MSR-TR-2015-54 | June 2015
  
  Publication Publication
- Warped linear mixed models for the genetic analysis of transformed phenotypes
  
  Nicolo Fusi, Christoph Lippert
  
  Nature communications | September 2014, Vol 5
  
  Publication Publication

- Matching Features, Not Tokens: Energy-Based Fine-Tuning of Language Models
  
  Samy Jelassi, Mujin Kwun, Rosie Zhao, Yuanzhi Li, Nicolo Fusi, Yilun Du, Sham Kakade, Carles Domingo-Enrich
  
  March 2026
  
  Publication
- Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
  
  Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
  
  July 2024
  
  Publication
- Virchow: A Million-Slide Digital Pathology Foundation Model
  
  Eugene Vorontsov, A. Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Kristen Severson, Eric Zimmermann, James Hall, Neil Tenenholtz, Nicolo Fusi, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kun, Matthew C. H. Le, Jan H Bernhard, R. Godrich, Gerard Oakley, Ewan Millar, Matthew G Hanna, J. Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, D. Klimstra, B. Rothrock, Thomas J. Fuchs
  
  September 2023
  
  DOI Publication Publication Publication
- Hant: Hardware-Aware Network Transformation
  
  Pavlo Molchanov, Jimmy Hall, Hongxu Yin, Jan Kautz, Nicolo Fusi, Arash Vahdat
  
  July 2021
  
  Publication Projet Projet
- Gradient Flows in Dataset Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  October 2020
  
  Publication Projet
- Weighted Meta-Learning
  
  Diana Cai, Rishit Sheth, Lester Mackey, Nicolo Fusi
  
  March 2020
  
  Publication PDF Projet
- Probabilistic Neural Architecture Search
  
  Francesco Paolo Casale, Jonathan Gordon, Nicolo Fusi
  
  February 2019
  
  Publication Publication Projet
- scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
  
  Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
  
  NeurIPS 2025 | October 2025
  
  Publication
- Tag-LLM: Repurposing General-Purpose LLMs for Specialized Domains
  
  Junhong Shen, Neil Tenenholtz, James Hall, David Alvarez-Melis, Nicolo Fusi
  
  ICML 2024 | February 2024
  
  DOI Publication Publication
- Dataset Dynamics via Gradient Flows in Probability Space
  
  David Alvarez-Melis, Nicolo Fusi
  
  ICML 2021 | July 2021
  
  Publication
- Initialization and Regularization of Factorized Neural Layers
  
  Mikhail Khodak, Neil Tenenholtz, Lester Mackey, Nicolo Fusi
  
  2021 International Conference on Learning Representations | May 2021
  
  Publication Publication Github Projet Projet
- Differentiable Feature Selection by Discrete Relaxation
  
  Rishit Sheth, Nicolo Fusi
  
  AISTATS | April 2020
  
  Publication Projet
- Geometric Dataset Distances via Optimal Transport
  
  David Alvarez-Melis, Nicolo Fusi
  
  NeurIPS 2020 | February 2020
  
  PDF Projet
- Probabilistic Matrix Factorization for Automated Machine Learning
  
  Nicolo Fusi, Rishit Sheth, Melih Huseyn Elibol
  
  NIPS 2018 | December 2018
  
  Preprint posted to Cornell University Library
  
  Publication Publication Projet
- Flexible Modelling of Genetic Effects on Function-Valued Traits
  
  Nicolo Fusi, Jennifer Listgarten
  
  International Conference on Research in Computational Molecular Biology (RECOMB 2016) | October 2016
  
  Publication DOI
- Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
  
  Nicolo Fusi
  
  Nature Precedings | June 2011
  
  Publication
- Intrusion Detection via Artificial Immune System: a Performance-based Approach
  
  Andrea Visconti, Nicolo Fusi, Hooman Tahayori
  
  IFIP International Conference on Biologically Inspired Collaborative Computing | October 2008
  
  Publication
- Consequences of training data composition for deep learning models in single-cell biology
  
  Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2025
  
  Publication DOI Projet
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
  
  Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | December 2024
  
  Preprint Projet
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Accès
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  
  Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2024
  
  Preprint Projet
- Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens
  
  Nicolo Fusi, et al
  
  nature biotechnology | October 2017, Vol 36: pp. 179-189
  
  Publication
- Predicting off-target effects for end-to-end CRISPR guide design
  
  Nicolo Fusi, Jennifer Listgarten, Melih Elibol, John Doench, Michael Weinstein, Luong Hoang
  
  October 2016
  
  Publication
- Impact of pre-adapted HIV transmission
  
  Jonathan M. Carlson, Victor Y Du, Nicolo Fusi, Paul A. Goepfert
  
  Nature Medicine | May 2016, Vol 22: pp. 606-613
  
  Publication
- Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
  
  John G. Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W. Vaimberg, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W. Virgin, Jennifer Listgarten, David E. Root
  
  nature biotechnology | January 2016, pp. 184-191
  
  Publication
- Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
  
  Christian Widmer, Christoph Lippert, Omer Weissbrod, Nicolo Fusi, Carl Kadie, Robert Davidson, Jennifer Listgarten, David Heckerman
  
  October 2014
  
  Publication Publication
- Warped linear mixed models for the genetic analysis of transformed phenotypes
  
  Nicolo Fusi, Christoph Lippert
  
  Nature communications | September 2014, Vol 5
  
  Publication Publication
- Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis
  
  Giovanni Nardo, Raffaele lennaco, Nicolo Fusi, Paul R. Heath, Marianna Marino, Maria C. Trolese, Laura Ferraiuolo, Neil Lawrence, Pamela J. Shaw, Caterina Bendotti
  
  Brain | November 2013, Vol 136(11): pp. 3305-3332
  
  Publication DOI
- A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
  
  Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson
  
  eLife | October 2013
  
  Publication
- Detecting regulatory gene–environment interactions with unmeasured environmental factors
  
  Nicolo Fusi, Christoph Lippert, Karsten Borgwardt, Neil D. Lawrence, Oliver Stegle
  
  Bioinformatics | June 2013, Vol 29(11): pp. 1382-1389
  
  Publication
- Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity
  
  Alice Brockington, Ke Ning, Paul R. Heath, Elizabeth Wood, Janine Kirby, Nicolo Fusi, Neil Lawrence, Stephen B. Wharton, Paul G. Ince, Pamela J. Shaw
  
  Acta Neuropathologica | January 2013, Vol 125(1): pp. 95-109
  
  Publication DOI
- Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies
  
  Nicolo Fusi, Oliver Stegle, Neil D. Lawrence
  
  PLOS Computational Biology | January 2012
  
  Publication Publication
- 156 Motor neurones subtypes resistant to degeneration in amyotrophic lateral sclerosis show distinct synaptic characteristics across species
  
  Nicolo Fusi
  
  Journal of Neurology, Neurosurgery & Psychiatry | January 2012, Vol 83(3)
  
  DOI
- Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
  
  Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
  
  November 2023
  
  Publication
- Genetic Analysis of Transformed Phenotypes
  
  Nicolo Fusi, Christoph Lippert, Neil D. Lawrence, Oliver Stegle
  
  February 2014
  
  Publication
- In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency
  
  Nicolo Fusi, Ian Smith, John Doench, Jennifer Listgarten
  
  MSR-TR-2015-54 | June 2015
  
  Publication Publication
- Gaussian Processes for Big Data
  
  James Hensman, Nicolo Fusi, Neil D. Lawrence
  
  UAI-P-2013-PG-282-290 | September 2013
  
  Publié par Twenty-Ninth Conference on Uncertainty in Artificial Intelligence (UAI2013)
  
  Publication

Nicolo Fusi

Publications

Matching Features, Not Tokens: Energy-Based Fine-Tuning of Language Models

scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling

Consequences of training data composition for deep learning models in single-cell biology

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

Protein generation with evolutionary diffusion: sequence is all you need

Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology

Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data

Tag-LLM: Repurposing General-Purpose LLMs for Specialized Domains

Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine

Virchow: A Million-Slide Digital Pathology Foundation Model

Dataset Dynamics via Gradient Flows in Probability Space

Hant: Hardware-Aware Network Transformation

Initialization and Regularization of Factorized Neural Layers

Gradient Flows in Dataset Space

Differentiable Feature Selection by Discrete Relaxation

Weighted Meta-Learning

Geometric Dataset Distances via Optimal Transport

Probabilistic Neural Architecture Search

Probabilistic Matrix Factorization for Automated Machine Learning

Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens

Predicting off-target effects for end-to-end CRISPR guide design

Flexible Modelling of Genetic Effects on Function-Valued Traits

Impact of pre-adapted HIV transmission

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency

Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

Warped linear mixed models for the genetic analysis of transformed phenotypes

Genetic Analysis of Transformed Phenotypes

Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Gaussian Processes for Big Data

Detecting regulatory gene–environment interactions with unmeasured environmental factors

Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

156 Motor neurones subtypes resistant to degeneration in amyotrophic lateral sclerosis show distinct synaptic characteristics across species

Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects

Intrusion Detection via Artificial Immune System: a Performance-based Approach

Matching Features, Not Tokens: Energy-Based Fine-Tuning of Language Models

Protein generation with evolutionary diffusion: sequence is all you need

Tag-LLM: Repurposing General-Purpose LLMs for Specialized Domains

Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine

Virchow: A Million-Slide Digital Pathology Foundation Model

Dataset Dynamics via Gradient Flows in Probability Space

Hant: Hardware-Aware Network Transformation

Initialization and Regularization of Factorized Neural Layers

Gradient Flows in Dataset Space

Differentiable Feature Selection by Discrete Relaxation

Weighted Meta-Learning

Geometric Dataset Distances via Optimal Transport

Probabilistic Neural Architecture Search

Probabilistic Matrix Factorization for Automated Machine Learning

In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency

Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

Gaussian Processes for Big Data

156 Motor neurones subtypes resistant to degeneration in amyotrophic lateral sclerosis show distinct synaptic characteristics across species

scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling

Consequences of training data composition for deep learning models in single-cell biology

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

Protein generation with evolutionary diffusion: sequence is all you need

Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology

Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data

Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine

Virchow: A Million-Slide Digital Pathology Foundation Model

Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens

Predicting off-target effects for end-to-end CRISPR guide design

Flexible Modelling of Genetic Effects on Function-Valued Traits

Impact of pre-adapted HIV transmission

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency

Warped linear mixed models for the genetic analysis of transformed phenotypes

Genetic Analysis of Transformed Phenotypes

Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Detecting regulatory gene–environment interactions with unmeasured environmental factors

Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects

Intrusion Detection via Artificial Immune System: a Performance-based Approach