Multi-Task Deep Learning for Legal Document Translation, Summarization and Multi-Label Classification. - Ahmed Elnaggar; Christoph Gebendorfer; Ingo Glaser; Florian Matthes (AICCC, 2018)

Deep Learning for Named-Entity Linking with Transfer Learning for Legal Documents. - Ahmed Elnaggar; Robin Otto; Florian Matthes (AICCC, 2018)

Stop Illegal Comments: A Multi-Task Deep Learning Approach. - Ahmed Elnaggar; Bernhard Waltl; Ingo Glaser; Jörg Landthaler; Elena Scepankova; Florian Matthes (AICCC, 2018)

A Machine Learning Based Approach to Application Landscape Documentation. - Jörg Landthaler; Ömer Uludag; Gloria Bondel; Ahmed Elnaggar; Saasha Nair; Florian Matthes (PoEM, 2018)

Named-Entity Linking Using Deep Learning For Legal Documents: A Transfer Learning Approach. - Ahmed Elnaggar; Robin Otto; Florian Matthes (CoRR, 2018)

Modeling aspects of the language of life through transfer-learning protein sequences. - Michael Heinzinger; Ahmed Elnaggar; Yu Wang; Christian Dallago; Dmitrii Nechaev; Florian Matthes; Burkhard Rost (BMC Bioinform., 2019)

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (CoRR, 2020)

Automated Employee Objective Matching Using Pre-trained Word Embeddings. - Mohab Ghanem; Ahmed Elnaggar; Adam Mckinnon; Christian Debes; Olivier Boisard; Florian Matthes (EDOC, 2021)

CodeTrans: Towards Cracking the Language of Silicone's Code Through Self-Supervised Deep Learning and High Performance Computing. - Ahmed Elnaggar; Wei Ding; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Silvia Severini; Florian Matthes; Burkhard Rost (CoRR, 2021)

ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (IEEE Trans. Pattern Anal. Mach. Intell., 2022)

A journey into the Generative AI and large language models: From NLP to BioInformatics. - Ahmed Elnaggar (ICGI, 2023)

Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling. - Ahmed Elnaggar; Hazem Essam; Wafaa Salah-Eldin; Walid Moustafa; Mohamed Elkerdawy; Charlotte Rochereau; Burkhard Rost (CoRR, 2023)

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction. - Hazem Alsamkary; Mohamed Elshaffei; Mohamed Soudy; Sara Ossman; Abdallah Amr; Nehal Adel Abdelsalam; Mohamed Elkerdawy; Ahmed Elnaggar (CoRR, 2025)

Ankh3: Multi-Task Pretraining with Sequence Denoising and Completion Enhances Protein Representations. - Hazem Alsamkary; Mohamed Elshaffei; Mohamed Elkerdawy; Ahmed Elnaggar (CoRR, 2025)