Vladimir Gligorijevic

29 papers A* 4B 1Misc 1Journal 21Unranked 1
YearRankTypeTitle / Venue / Authors
2025 A* conf
Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks.
ICML
Angelica Chen, Samuel Don Stanton, Frances Ding, Robert G. Alberstein, Andrew Martin Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2025 J jnl
Tokenized and continuous embedding compressions of protein sequence and structure.
Patterns
Amy X. Lu, Wilson Yan, Kevin K. Yang, Vladimir Gligorijevic, Kyunghyun Cho, Pieter Abbeel, Richard Bonneau, Nathan C. Frey
2025 J jnl
Unified all-atom molecule generation with neural fields.
CoRR
Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi
2025 J jnl
deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning.
Bioinform.
Homa Mohammadi Peyhani, Edith Lee, Richard Bonneau, Vladimir Gligorijevic, Jae Hyeon Lee
2024 A* conf
Implicitly Guided Design with PropEn: Match your Data to Follow the Gradient.
NeurIPS
Natasa Tagasovska, Vladimir Gligorijevic, Kyunghyun Cho, Andreas Loukas
2024 J jnl
Implicitly Guided Design with PropEn: Match your Data to Follow the Gradient.
CoRR
Natasa Tagasovska, Vladimir Gligorijevic, Kyunghyun Cho, Andreas Loukas
2024 J jnl
LLMs are Highly-Constrained Biophysical Sequence Optimizers.
CoRR
Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2024 A* conf
Protein Discovery with Discrete Walk-Jump Sampling.
ICLR
Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
2023 J jnl
AbDiffuser: Full-Atom Generation of In-Vitro Functioning Antibodies.
CoRR
Karolis Martinkus, Jan Ludwiczak, Kyunghyun Cho, Wei-Ching Liang, Julien Lafrance-Vanasse, Isidro Hötzel, Arvind Rajpal, Yan Wu, Richard Bonneau, Vladimir Gligorijevic, Andreas Loukas
2023 A* conf
AbDiffuser: full-atom generation of in-vitro functioning antibodies.
NeurIPS
Karolis Martinkus, Jan Ludwiczak, Wei-Ching Liang, Julien Lafrance-Vanasse, Isidro Hötzel, Arvind Rajpal, Yan Wu, Kyunghyun Cho, Richard Bonneau, Vladimir Gligorijevic, Andreas Loukas
2023 J jnl
Protein Discovery with Discrete Walk-Jump Sampling.
CoRR
Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
2023 J jnl
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs.
Bioinform.
Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijevic, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki
2022 J jnl
A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences.
CoRR
Natasa Tagasovska, Nathan C. Frey, Andreas Loukas, Isidro Hötzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Richard Bonneau, Kyunghyun Cho, Stephen Ra, Vladimir Gligorijevic
2022 J jnl
Multi-segment preserving sampling for deep manifold sampler.
CoRR
Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
2022 J jnl
PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design.
CoRR
Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew M. Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
2021 J jnl
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity.
Bioinform.
Meet Barot, Vladimir Gligorijevic, Kyunghyun Cho, Richard Bonneau
2019 J jnl
Non-Negative Matrix Factorizations for Multiplex Network Analysis.
IEEE Trans. Pattern Anal. Mach. Intell.
Vladimir Gligorijevic, Yannis Panagakis, Stefanos Zafeiriou
2018 J jnl
deepNF: deep network fusion for protein function prediction.
Bioinform.
Vladimir Gligorijevic, Meet Barot, Richard Bonneau
2017 — —
Methods for analysis and integration of heterogeneous network data.
Vladimir Gligorijevic
2016 J jnl
Fuse: multiple network alignment via data fusion.
Bioinform.
Vladimir Gligorijevic, Noël Malod-Dognin, Natasa Przulj
2016 B conf
Fusion and community detection in multi-layer graphs.
ICPR
Vladimir Gligorijevic, Yannis Panagakis, Stefanos Zafeiriou
2016 J jnl
Non-Negative Matrix Factorizations for Multiplex Network Analysis.
CoRR
Vladimir Gligorijevic, Yannis Panagakis, Stefanos Zafeiriou
2016 Misc conf
Patient-Specific Data Fusion for Cancer Stratification and Personalised Treatment.
PSB
Vladimir Gligorijevic, Noël Malod-Dognin, Natasa Przulj
2014 J jnl
Integration of molecular network data reconstructs Gene Ontology.
Bioinform.
Vladimir Gligorijevic, Vuk Janjic, Natasa Przulj
2014 J jnl
The Dynamics of Emotional Chats with Bots: Experiment and Agent-Based Simulations.
CoRR
Bosiljka Tadic, Vladimir Gligorijevic, Marcin Skowron, Milovan Suvakov
2013 J jnl
Co-Evolutionary Mechanisms of Emotional Bursts in Online Social Dynamics and Networks.
Entropy
Bosiljka Tadic, Vladimir Gligorijevic, Marija Mitrovic, Milovan Suvakov
2012 — conf
Directed Networks of Online Chats: Content-Based Linking and Social Structure.
SITIS
Vladimir Gligorijevic, Marcin Skowron, Bosiljka Tadic
2012 J jnl
How the online social networks are used: Dialogs-based structure of MySpace
CoRR
Milovan Suvakov, Marija Mitrovic, Vladimir Gligorijevic, Bosiljka Tadic
2012 J jnl
Structure and stability of online chat networks built on emotion-carrying links
CoRR
Vladimir Gligorijevic, Marcin Skowron, Bosiljka Tadic